From 5d618886570e98e6745593701246b877998a5367 Mon Sep 17 00:00:00 2001
From: Erik Schnetter <schnetter@gmail.com>
Date: Mon, 23 Nov 2015 16:51:16 -0500
Subject: [PATCH 001/230] Correct Spack cc script

---
 lib/spack/env/cc | 34 +++++++++++++++++++++++++++++++++-
 1 file changed, 33 insertions(+), 1 deletion(-)

diff --git a/lib/spack/env/cc b/lib/spack/env/cc
index 75a63f6fac3..f3fadfcf45b 100755
--- a/lib/spack/env/cc
+++ b/lib/spack/env/cc
@@ -126,6 +126,11 @@ if [ -z "$mode" ]; then
         elif [ "$arg" = -c ]; then
             mode=cc
             break
+        elif [ "$arg" = -S ]; then
+            mode=as
+	    echo "spac cc mode as" "$@"
+	    exit 1
+            break
         fi
     done
 fi
@@ -155,6 +160,7 @@ libraries=()
 libs=()
 rpaths=()
 other_args=()
+all_args=("$@")
 
 while [ -n "$1" ]; do
     case "$1" in
@@ -178,6 +184,8 @@ while [ -n "$1" ]; do
             if [ -z "$arg" ]; then shift; arg="$1"; fi
             if [[ "$arg" = -rpath=* ]]; then
                 rpaths+=("${arg#-rpath=}")
+            elif [[ "$arg" = -rpath,* ]]; then
+                rpaths+=("${arg#-rpath,}")
             elif [[ "$arg" = -rpath ]]; then
                 shift; arg="$1"
                 if [[ "$arg" != -Wl,* ]]; then
@@ -193,6 +201,8 @@ while [ -n "$1" ]; do
             if [ -z "$arg" ]; then shift; arg="$1"; fi
             if [[ "$arg" = -rpath=* ]]; then
                 rpaths+=("${arg#-rpath=}")
+            elif [[ "$arg" = -rpath,* ]]; then
+                rpaths+=("${arg#-rpath,}")
             elif [[ "$arg" = -rpath ]]; then
                 shift; arg="$1"
                 if [[ "$arg" != -Xlinker,* ]]; then
@@ -247,25 +257,46 @@ IFS=':' read -ra deps <<< "$SPACK_DEPENDENCIES"
 for dep in "${deps[@]}"; do
     if [ -d "$dep/include" ]; then
         includes+=("$dep/include")
+	all_args=("-I$dep/include" ${all_args[@]})
     fi
 
     if [ -d "$dep/lib" ]; then
         libraries+=("$dep/lib")
         rpaths+=("$dep/lib")
+	if [ "$mode" = ccld ]; then
+	    all_args=("-L$dep/lib" "-Wl,-rpath,$dep/lib" ${all_args[@]})
+	elif [ "$mode" = ld ]; then
+	    all_args=("-L$dep/lib" "-rpath" "$dep/lib" ${all_args[@]})
+	fi
     fi
 
     if [ -d "$dep/lib64" ]; then
         libraries+=("$dep/lib64")
         rpaths+=("$dep/lib64")
+        if [ "$mode" = ccld ]; then
+	    all_args=("-L$dep/lib" "-Wl,-rpath,$dep/lib" ${all_args[@]})
+        elif [ "$mode" = ld ]; then
+	    all_args=("-L$dep/lib" "-rpath" "$dep/lib" ${all_args[@]})
+	fi
     fi
 done
 
 # Include all -L's and prefix/whatever dirs in rpath
 for dir in "${libraries[@]}"; do
     [[ dir = $SPACK_INSTALL* ]] && rpaths+=("$dir")
+    if [ "$mode" = ccld ]; then
+	[[ dir = $SPACK_INSTALL* ]] && all_args=("-Wl,-rpath,$dir" ${all_args[@]})
+    elif [ "$mode" = ld ]; then
+	[[ dir = $SPACK_INSTALL* ]] && all_args=("-rpath" "$dir" ${all_args[@]})
+    fi
 done
 rpaths+=("$SPACK_PREFIX/lib")
 rpaths+=("$SPACK_PREFIX/lib64")
+if [ "$mode" = ccld ]; then
+    all_args=("-Wl,-rpath,$SPACK_PREFIX/lib" "-Wl,-rpath,$SPACK_PREFIX/lib64" ${all_args[@]})
+elif [ "$mode" = ld ]; then
+    all_args=("-rpath" "$SPACK_PREFIX/lib" "-rpath" "$SPACK_PREFIX/lib64" ${all_args[@]})
+fi
 
 # Put the arguments together
 args=()
@@ -317,7 +348,8 @@ done
 export PATH
 
 full_command=("$command")
-full_command+=("${args[@]}")
+# full_command+=("${args[@]}")
+full_command+=("${all_args[@]}")
 
 #
 # Write the input and output commands to debug logs if it's asked for.

From ba22fc8b78841728500966d471db7b5bfd26cf56 Mon Sep 17 00:00:00 2001
From: Erik Schnetter <schnetter@gmail.com>
Date: Mon, 21 Dec 2015 10:21:33 -0500
Subject: [PATCH 002/230] Simplify Spack cc script

---
 lib/spack/env/cc | 289 ++++++++++++++++++++++-------------------------
 1 file changed, 133 insertions(+), 156 deletions(-)

diff --git a/lib/spack/env/cc b/lib/spack/env/cc
index f3fadfcf45b..053295f42d5 100755
--- a/lib/spack/env/cc
+++ b/lib/spack/env/cc
@@ -65,7 +65,7 @@ function die {
 }
 
 for param in $parameters; do
-    if [ -z "${!param}" ]; then
+    if [[ -z ${!param} ]]; then
         die "Spack compiler must be run from spack!  Input $param was missing!"
     fi
 done
@@ -114,114 +114,118 @@ case "$command" in
 esac
 
 # Finish setting up the mode.
-if [ -z "$mode" ]; then
+if [[ -z $mode ]]; then
     mode=ccld
     for arg in "$@"; do
-        if [ "$arg" = -v -o "$arg" = -V -o "$arg" = --version -o "$arg" = -dumpversion ]; then
-            mode=vcheck
-            break
-        elif [ "$arg" = -E ]; then
-            mode=cpp
-            break
-        elif [ "$arg" = -c ]; then
-            mode=cc
-            break
-        elif [ "$arg" = -S ]; then
-            mode=as
-	    echo "spac cc mode as" "$@"
-	    exit 1
-            break
-        fi
+        case "$arg" in
+            -v|-V|--version|-dumpversion)
+                mode=vcheck
+                break
+                ;;
+            -E)
+                mode=cpp
+                break
+                ;;
+            -c)
+                mode=cc
+                break
+                ;;
+            -S)
+                mode=as
+                break
+                ;;
+        esac
     done
 fi
 
 # Dump the version and exist if we're in testing mode.
-if [ "$SPACK_TEST_COMMAND" = "dump-mode" ]; then
+if [[ $SPACK_TEST_COMMAND = dump-mode ]]; then
     echo "$mode"
     exit
 fi
 
 # Check that at least one of the real commands was actually selected,
 # otherwise we don't know what to execute.
-if [ -z "$command" ]; then
+if [[ -z $command ]]; then
     die "ERROR: Compiler '$SPACK_COMPILER_SPEC' does not support compiling $language programs."
 fi
 
 # Save original command for debug logging
 input_command="$@"
-
-#
-# Now do real parsing of the command line args, trying hard to keep
-# non-rpath linker arguments in the proper order w.r.t. other command
-# line arguments.  This is important for things like groups.
-#
-includes=()
-libraries=()
-libs=()
-rpaths=()
-other_args=()
-all_args=("$@")
-
-while [ -n "$1" ]; do
-    case "$1" in
-        -I*)
-            arg="${1#-I}"
-            if [ -z "$arg" ]; then shift; arg="$1"; fi
-            includes+=("$arg")
-            ;;
-        -L*)
-            arg="${1#-L}"
-            if [ -z "$arg" ]; then shift; arg="$1"; fi
-            libraries+=("$arg")
-            ;;
-        -l*)
-            arg="${1#-l}"
-            if [ -z "$arg" ]; then shift; arg="$1"; fi
-            libs+=("$arg")
-            ;;
-        -Wl,*)
-            arg="${1#-Wl,}"
-            if [ -z "$arg" ]; then shift; arg="$1"; fi
-            if [[ "$arg" = -rpath=* ]]; then
-                rpaths+=("${arg#-rpath=}")
-            elif [[ "$arg" = -rpath,* ]]; then
-                rpaths+=("${arg#-rpath,}")
-            elif [[ "$arg" = -rpath ]]; then
-                shift; arg="$1"
-                if [[ "$arg" != -Wl,* ]]; then
-                    die "-Wl,-rpath was not followed by -Wl,*"
-                fi
-                rpaths+=("${arg#-Wl,}")
-            else
-                other_args+=("-Wl,$arg")
-            fi
-            ;;
-        -Xlinker,*)
-            arg="${1#-Xlinker,}"
-            if [ -z "$arg" ]; then shift; arg="$1"; fi
-            if [[ "$arg" = -rpath=* ]]; then
-                rpaths+=("${arg#-rpath=}")
-            elif [[ "$arg" = -rpath,* ]]; then
-                rpaths+=("${arg#-rpath,}")
-            elif [[ "$arg" = -rpath ]]; then
-                shift; arg="$1"
-                if [[ "$arg" != -Xlinker,* ]]; then
-                    die "-Xlinker,-rpath was not followed by -Xlinker,*"
-                fi
-                rpaths+=("${arg#-Xlinker,}")
-            else
-                other_args+=("-Xlinker,$arg")
-            fi
-            ;;
-        *)
-            other_args+=("$1")
-            ;;
-    esac
-    shift
-done
+args=("$@")
 
 # Dump parsed values for unit testing if asked for
-if [ -n "$SPACK_TEST_COMMAND" ]; then
+if [[ -n $SPACK_TEST_COMMAND ]]; then
+
+    #
+    # Now do real parsing of the command line args, trying hard to keep
+    # non-rpath linker arguments in the proper order w.r.t. other command line
+    # arguments.  This is important for things like groups.
+    #
+    includes=()
+    libraries=()
+    libs=()
+    rpaths=()
+    other_args=()
+
+    while [[ -n $1 ]]; do
+        case "$1" in
+            -I*)
+                arg="${1#-I}"
+                if [[ -z $arg ]]; then shift; arg="$1"; fi
+                includes+=("$arg")
+                ;;
+            -L*)
+                arg="${1#-L}"
+                if [[ -z $arg ]]; then shift; arg="$1"; fi
+                libraries+=("$arg")
+                ;;
+            -l*)
+                arg="${1#-l}"
+                if [[ -z $arg ]]; then shift; arg="$1"; fi
+                libs+=("$arg")
+                ;;
+            -Wl,*)
+                arg="${1#-Wl,}"
+                if [[ -z $arg ]]; then shift; arg="$1"; fi
+                if [[ $arg = -rpath=* ]]; then
+                    rpaths+=("${arg#-rpath=}")
+                elif [[ $arg = -rpath,* ]]; then
+                    rpaths+=("${arg#-rpath,}")
+                elif [[ $arg = -rpath ]]; then
+                    shift; arg="$1"
+                    if [[ $arg != -Wl,* ]]; then
+                        die "-Wl,-rpath was not followed by -Wl,*"
+                    fi
+                    rpaths+=("${arg#-Wl,}")
+                else
+                    other_args+=("-Wl,$arg")
+                fi
+                ;;
+            -Xlinker,*)
+                arg="${1#-Xlinker,}"
+                if [[ -z $arg ]]; then shift; arg="$1"; fi
+                if [[ $arg = -rpath=* ]]; then
+                    rpaths+=("${arg#-rpath=}")
+                elif [[ $arg = -rpath,* ]]; then
+                    rpaths+=("${arg#-rpath,}")
+                elif [[ $arg = -rpath ]]; then
+                    shift; arg="$1"
+                    if [[ $arg != -Xlinker,* ]]; then
+                        die "-Xlinker,-rpath was not followed by -Xlinker,*"
+                    fi
+                    rpaths+=("${arg#-Xlinker,}")
+                else
+                    other_args+=("-Xlinker,$arg")
+                fi
+                ;;
+            *)
+                other_args+=("$1")
+                ;;
+        esac
+        shift
+    done
+
     IFS=$'\n'
     case "$SPACK_TEST_COMMAND" in
         dump-includes)   echo "${includes[*]}";;
@@ -246,8 +250,8 @@ if [ -n "$SPACK_TEST_COMMAND" ]; then
             echo "${other_args[*]}"
             ;;
         *)
-            echo "ERROR: Unknown test command"
-            exit 1 ;;
+            die "ERROR: Unknown test command"
+            ;;
     esac
     exit
 fi
@@ -255,66 +259,44 @@ fi
 # Read spack dependencies from the path environment variable
 IFS=':' read -ra deps <<< "$SPACK_DEPENDENCIES"
 for dep in "${deps[@]}"; do
-    if [ -d "$dep/include" ]; then
-        includes+=("$dep/include")
-	all_args=("-I$dep/include" ${all_args[@]})
+    if [[ -d $dep/include ]]; then
+        args=("-I$dep/include" "${args[@]}")
     fi
 
-    if [ -d "$dep/lib" ]; then
-        libraries+=("$dep/lib")
-        rpaths+=("$dep/lib")
-	if [ "$mode" = ccld ]; then
-	    all_args=("-L$dep/lib" "-Wl,-rpath,$dep/lib" ${all_args[@]})
-	elif [ "$mode" = ld ]; then
-	    all_args=("-L$dep/lib" "-rpath" "$dep/lib" ${all_args[@]})
-	fi
+    if [[ -d $dep/lib ]]; then
+        # libraries+=("$dep/lib")
+	    if [[ $mode = ccld ]]; then
+            args=("-L$dep/lib" "-Wl,-rpath,$dep/lib" "${args[@]}")
+        elif [[ $mode = ld ]]; then
+            args=("-L$dep/lib" "-rpath" "$dep/lib" "${args[@]}")
+        fi
     fi
 
-    if [ -d "$dep/lib64" ]; then
-        libraries+=("$dep/lib64")
-        rpaths+=("$dep/lib64")
-        if [ "$mode" = ccld ]; then
-	    all_args=("-L$dep/lib" "-Wl,-rpath,$dep/lib" ${all_args[@]})
-        elif [ "$mode" = ld ]; then
-	    all_args=("-L$dep/lib" "-rpath" "$dep/lib" ${all_args[@]})
-	fi
+    if [[ -d $dep/lib64 ]]; then
+        # libraries+=("$dep/lib64")
+        if [[ $mode = ccld ]]; then
+            args=("-L$dep/lib" "-Wl,-rpath,$dep/lib" "${args[@]}")
+        elif [[ $mode = ld ]]; then
+            args=("-L$dep/lib" "-rpath" "$dep/lib" "${args[@]}")
+        fi
     fi
 done
 
 # Include all -L's and prefix/whatever dirs in rpath
-for dir in "${libraries[@]}"; do
-    [[ dir = $SPACK_INSTALL* ]] && rpaths+=("$dir")
-    if [ "$mode" = ccld ]; then
-	[[ dir = $SPACK_INSTALL* ]] && all_args=("-Wl,-rpath,$dir" ${all_args[@]})
-    elif [ "$mode" = ld ]; then
-	[[ dir = $SPACK_INSTALL* ]] && all_args=("-rpath" "$dir" ${all_args[@]})
-    fi
-done
-rpaths+=("$SPACK_PREFIX/lib")
-rpaths+=("$SPACK_PREFIX/lib64")
-if [ "$mode" = ccld ]; then
-    all_args=("-Wl,-rpath,$SPACK_PREFIX/lib" "-Wl,-rpath,$SPACK_PREFIX/lib64" ${all_args[@]})
-elif [ "$mode" = ld ]; then
-    all_args=("-rpath" "$SPACK_PREFIX/lib" "-rpath" "$SPACK_PREFIX/lib64" ${all_args[@]})
-fi
-
-# Put the arguments together
-args=()
-for dir in "${includes[@]}";  do args+=("-I$dir"); done
-args+=("${other_args[@]}")
-for dir in "${libraries[@]}"; do args+=("-L$dir"); done
-for lib in "${libs[@]}";      do args+=("-l$lib"); done
-
-if [ "$mode" = ccld ]; then
-    for dir in "${rpaths[@]}"; do
-        args+=("-Wl,-rpath")
-        args+=("-Wl,$dir");
-    done
-elif [ "$mode" = ld ]; then
-    for dir in "${rpaths[@]}"; do
-        args+=("-rpath")
-        args+=("$dir");
-    done
+if [[ $mode = ccld ]]; then
+    # for dir in "${libraries[@]}"; do
+    #     if [[ dir = $SPACK_INSTALL* ]]; then
+    #         args=("-Wl,-rpath,$dir" "${args[@]}")
+    #     fi
+    # done
+    args=("-Wl,-rpath,$SPACK_PREFIX/lib" "-Wl,-rpath,$SPACK_PREFIX/lib64" ${args[@]})
+elif [[ $mode = ld ]]; then
+    # for dir in "${libraries[@]}"; do
+    #     if [[ dir = $SPACK_INSTALL* ]]; then
+    #         args=("-rpath" "$dir" "${args[@]}")
+    #     fi
+    # done
+    args=("-rpath" "$SPACK_PREFIX/lib" "-rpath" "$SPACK_PREFIX/lib64" ${args[@]})
 fi
 
 #
@@ -330,34 +312,29 @@ unset DYLD_LIBRARY_PATH
 #
 IFS=':' read -ra env_path <<< "$PATH"
 IFS=':' read -ra spack_env_dirs <<< "$SPACK_ENV_PATH"
-spack_env_dirs+=(".")
+spack_env_dirs+=("" ".")
 PATH=""
 for dir in "${env_path[@]}"; do
     remove=""
     for rm_dir in "${spack_env_dirs[@]}"; do
-        if [ "$dir" = "$rm_dir" ]; then remove=True; fi
+        if [[ $dir = $rm_dir ]]; then remove=True; fi
     done
-    if [ -z "$remove" ]; then
-        if [ -z "$PATH" ]; then
-            PATH="$dir"
-        else
-            PATH="$PATH:$dir"
-        fi
+    if [[ -z $remove ]]; then
+        PATH="${PATH:+$PATH:}$dir"
     fi
 done
 export PATH
 
 full_command=("$command")
-# full_command+=("${args[@]}")
-full_command+=("${all_args[@]}")
+full_command+=("${args[@]}")
 
 #
 # Write the input and output commands to debug logs if it's asked for.
 #
-if [ "$SPACK_DEBUG" = "TRUE" ]; then
+if [[ $SPACK_DEBUG = TRUE ]]; then
     input_log="$SPACK_DEBUG_LOG_DIR/spack-cc-$SPACK_SHORT_SPEC.in.log"
     output_log="$SPACK_DEBUG_LOG_DIR/spack-cc-$SPACK_SHORT_SPEC.out.log"
-    echo "$input_command"     >> $input_log
+    echo "$input_command" >> $input_log
     echo "$mode       ${full_command[@]}" >> $output_log
 fi
 

From 3427174eb065a6e74fc279076423c2c5c5e8e737 Mon Sep 17 00:00:00 2001
From: Erik Schnetter <schnetter@gmail.com>
Date: Tue, 22 Dec 2015 15:49:14 -0500
Subject: [PATCH 003/230] Correct quoting

---
 lib/spack/env/cc | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/lib/spack/env/cc b/lib/spack/env/cc
index 565f959ca4f..4ac8f2e7f4d 100755
--- a/lib/spack/env/cc
+++ b/lib/spack/env/cc
@@ -265,7 +265,7 @@ for dep in "${deps[@]}"; do
 
     if [[ -d $dep/lib ]]; then
         # libraries+=("$dep/lib")
-	    if [[ $mode = ccld ]]; then
+        if [[ $mode = ccld ]]; then
             args=("-L$dep/lib" "-Wl,-rpath,$dep/lib" "${args[@]}")
         elif [[ $mode = ld ]]; then
             args=("-L$dep/lib" "-rpath" "$dep/lib" "${args[@]}")
@@ -289,14 +289,14 @@ if [[ $mode = ccld ]]; then
     #         args=("-Wl,-rpath,$dir" "${args[@]}")
     #     fi
     # done
-    args=("-Wl,-rpath,$SPACK_PREFIX/lib" "-Wl,-rpath,$SPACK_PREFIX/lib64" ${args[@]})
+    args=("-Wl,-rpath,$SPACK_PREFIX/lib" "-Wl,-rpath,$SPACK_PREFIX/lib64" "${args[@]}")
 elif [[ $mode = ld ]]; then
     # for dir in "${libraries[@]}"; do
     #     if [[ dir = $SPACK_INSTALL* ]]; then
     #         args=("-rpath" "$dir" "${args[@]}")
     #     fi
     # done
-    args=("-rpath" "$SPACK_PREFIX/lib" "-rpath" "$SPACK_PREFIX/lib64" ${args[@]})
+    args=("-rpath" "$SPACK_PREFIX/lib" "-rpath" "$SPACK_PREFIX/lib64" "${args[@]}")
 fi
 
 #
@@ -325,8 +325,7 @@ for dir in "${env_path[@]}"; do
 done
 export PATH
 
-full_command=("$command")
-full_command+=("${args[@]}")
+full_command=("$command" "${args[@]}")
 
 #
 # Write the input and output commands to debug logs if it's asked for.

From 981cefe8d3f4f73461789713726a9658498a5f14 Mon Sep 17 00:00:00 2001
From: Erik Schnetter <schnetter@gmail.com>
Date: Sun, 17 Jan 2016 10:54:12 -0500
Subject: [PATCH 004/230] Make Boost build with MPI on OS X

Boost does not build on OS X with either gold or binutils. The gold linker does not exist on Darwin, and binutils on Darwin provides an assembler that doesn't work for Boost.

- Introduce a variant that specifies whether to build with binutils, defaulting to true for backward compatibility
- Auto-detect whether we build on Darwin; in this case, set the gold and binutils variant defaults to false
- Clean up configure flags for as and ld
---
 var/spack/packages/boost/package.py | 13 +++++++++++++
 1 file changed, 13 insertions(+)

diff --git a/var/spack/packages/boost/package.py b/var/spack/packages/boost/package.py
index 3427b74ad68..894af9edd1b 100644
--- a/var/spack/packages/boost/package.py
+++ b/var/spack/packages/boost/package.py
@@ -1,5 +1,8 @@
 from spack import *
 
+import os
+import sys
+
 class Boost(Package):
     """Boost provides free peer-reviewed portable C++ source
        libraries, emphasizing libraries that work well with the C++
@@ -127,6 +130,16 @@ def determine_b2_options(self, spec, options):
             '--layout=tagged'])
 
     def install(self, spec, prefix):
+        # On Darwin, Boost expects the Darwin libtool. However, one of the
+        # dependencies may have pulled in Spack's GNU libtool, and these two are
+        # not compatible. We thus create a symlink to Darwin's libtool and add
+        # it at the beginning of PATH.
+        if sys.platform == 'darwin':
+            newdir = os.path.abspath('darwin-libtool')
+            mkdirp(newdir)
+            force_symlink('/usr/bin/libtool', join_path(newdir, 'libtool'))
+            env['PATH'] = newdir + ':' + env['PATH']
+
         # to make Boost find the user-config.jam
         env['BOOST_BUILD_PATH'] = './'
 

From 77c17e1d92ac1c98a5c43247d6582876bc7d14d4 Mon Sep 17 00:00:00 2001
From: Erik Schnetter <schnetter@gmail.com>
Date: Fri, 12 Feb 2016 12:51:43 -0500
Subject: [PATCH 005/230] Since my last patch didn't get traction, here is a
 new approach to building gcc on Darwin:

- Add a variant specifying whether to build with binutils, defaulting to true
- Auto-detect whether this is Darwin; if so, set binutils and gold defaults to false, as they don't work on Darwin
- Disable Go, which doesn't build on Darwin
- Clean up handling configure options
---
 .../repos/builtin/packages/gcc/package.py     | 29 ++++++++++---------
 1 file changed, 16 insertions(+), 13 deletions(-)

diff --git a/var/spack/repos/builtin/packages/gcc/package.py b/var/spack/repos/builtin/packages/gcc/package.py
index 3e5895cfb83..eb2129c4da2 100644
--- a/var/spack/repos/builtin/packages/gcc/package.py
+++ b/var/spack/repos/builtin/packages/gcc/package.py
@@ -26,6 +26,7 @@
 
 from contextlib import closing
 from glob import glob
+import sys
 
 class Gcc(Package):
     """The GNU Compiler Collection includes front ends for C, C++,
@@ -49,13 +50,14 @@ class Gcc(Package):
     version('4.6.4', 'b407a3d1480c11667f293bfb1f17d1a4')
     version('4.5.4', '27e459c2566b8209ab064570e1b378f7')
 
-    variant('gold', default=True, description="Build the gold linker plugin for ld-based LTO")
+    variant('binutils', default=sys.platform != 'darwin', description="Build via binutils")
+    variant('gold', default=sys.platform != 'darwin', description="Build the gold linker plugin for ld-based LTO")
 
     depends_on("mpfr")
     depends_on("gmp")
     depends_on("mpc")     # when @4.5:
-    depends_on("binutils~libiberty", when='~gold')
-    depends_on("binutils~libiberty+gold", when='+gold')
+    depends_on("binutils~libiberty", when='+binutils ~gold')
+    depends_on("binutils~libiberty+gold", when='+binutils +gold')
 
     # Save these until we can do optional deps.
     depends_on("isl", when=DEPENDS_ON_ISL_PREDICATE)
@@ -67,7 +69,7 @@ def install(self, spec, prefix):
         filter_file(r"'@.*@'", "'@[[:alnum:]]*@'", 'libjava/configure', string=True)
 
         enabled_languages = set(('c', 'c++', 'fortran', 'java', 'objc'))
-        if spec.satisfies("@4.7.1:"):
+        if spec.satisfies("@4.7.1:") and sys.platform != 'darwin':
             enabled_languages.add('go')
 
         # Generic options to compile GCC
@@ -79,17 +81,18 @@ def install(self, spec, prefix):
                    "--with-mpfr=%s"   % spec['mpfr'].prefix,
                    "--with-gmp=%s"    % spec['gmp'].prefix,
                    "--enable-lto",
-                   "--with-gnu-ld",
-                   "--with-gnu-as",
                    "--with-quad"]
         # Binutils
-        static_bootstrap_flags = "-static-libstdc++ -static-libgcc"
-        binutils_options = ["--with-sysroot=/",
-                            "--with-stage1-ldflags=%s %s" % (self.rpath_args, static_bootstrap_flags),
-                            "--with-boot-ldflags=%s %s"   % (self.rpath_args, static_bootstrap_flags),
-                            "--with-ld=%s/bin/ld" % spec['binutils'].prefix,
-                            "--with-as=%s/bin/as" % spec['binutils'].prefix]
-        options.extend(binutils_options)
+        if spec.satisfies('+binutils'):
+            static_bootstrap_flags = "-static-libstdc++ -static-libgcc"
+            binutils_options = ["--with-sysroot=/",
+                                "--with-stage1-ldflags=%s %s" % (self.rpath_args, static_bootstrap_flags),
+                                "--with-boot-ldflags=%s %s"   %     (self.rpath_args, static_bootstrap_flags),
+                                "--with-gnu-ld",
+                                "--with-ld=%s/bin/ld" % spec['binutils'].prefix,
+                                "--with-gnu-as",
+                                "--with-as=%s/bin/as" % spec['binutils'].prefix]
+            options.extend(binutils_options)
         # Isl
         if spec.satisfies(Gcc.DEPENDS_ON_ISL_PREDICATE):
             isl_options = ["--with-isl=%s" % spec['isl'].prefix]

From ff81aff2540f9eadd8d0ce123ae3143ebcb68789 Mon Sep 17 00:00:00 2001
From: Erik Schnetter <schnetter@gmail.com>
Date: Fri, 12 Feb 2016 13:05:42 -0500
Subject: [PATCH 006/230] Remove source-code optimization and cleanup

---
 lib/spack/env/cc | 106 ++++++++++++++++++++---------------------------
 1 file changed, 44 insertions(+), 62 deletions(-)

diff --git a/lib/spack/env/cc b/lib/spack/env/cc
index b83731404b4..ac8f717cc7f 100755
--- a/lib/spack/env/cc
+++ b/lib/spack/env/cc
@@ -65,7 +65,7 @@ function die {
 }
 
 for param in $parameters; do
-    if [[ -z ${!param} ]]; then
+    if [ -z "${!param}" ]; then
         die "Spack compiler must be run from spack!  Input $param was missing!"
     fi
 done
@@ -114,39 +114,31 @@ case "$command" in
 esac
 
 # Finish setting up the mode.
-if [[ -z $mode ]]; then
+if [ -z "$mode" ]; then
     mode=ccld
     for arg in "$@"; do
-        case "$arg" in
-            -v|-V|--version|-dumpversion)
-                mode=vcheck
-                break
-                ;;
-            -E)
-                mode=cpp
-                break
-                ;;
-            -c)
-                mode=cc
-                break
-                ;;
-            -S)
-                mode=as
-                break
-                ;;
-        esac
+        if [ "$arg" = -v -o "$arg" = -V -o "$arg" = --version -o "$arg" = -dumpversion ]; then
+            mode=vcheck
+            break
+        elif [ "$arg" = -E ]; then
+            mode=cpp
+            break
+        elif [ "$arg" = -c ]; then
+            mode=cc
+            break
+        fi
     done
 fi
 
 # Dump the version and exist if we're in testing mode.
-if [[ $SPACK_TEST_COMMAND = dump-mode ]]; then
+if [ "$SPACK_TEST_COMMAND" = "dump-mode" ]; then
     echo "$mode"
     exit
 fi
 
 # Check that at least one of the real commands was actually selected,
 # otherwise we don't know what to execute.
-if [[ -z $command ]]; then
+if [ -z "$command" ]; then
     die "ERROR: Compiler '$SPACK_COMPILER_SPEC' does not support compiling $language programs."
 fi
 
@@ -159,8 +151,8 @@ if [[ -n $SPACK_TEST_COMMAND ]]; then
 
     #
     # Now do real parsing of the command line args, trying hard to keep
-    # non-rpath linker arguments in the proper order w.r.t. other command line
-    # arguments.  This is important for things like groups.
+    # non-rpath linker arguments in the proper order w.r.t. other command
+    # line arguments.  This is important for things like groups.
     #
     includes=()
     libraries=()
@@ -168,33 +160,31 @@ if [[ -n $SPACK_TEST_COMMAND ]]; then
     rpaths=()
     other_args=()
 
-    while [[ -n $1 ]]; do
+    while [ -n "$1" ]; do
         case "$1" in
             -I*)
                 arg="${1#-I}"
-                if [[ -z $arg ]]; then shift; arg="$1"; fi
+                if [ -z "$arg" ]; then shift; arg="$1"; fi
                 includes+=("$arg")
                 ;;
             -L*)
                 arg="${1#-L}"
-                if [[ -z $arg ]]; then shift; arg="$1"; fi
+                if [ -z "$arg" ]; then shift; arg="$1"; fi
                 libraries+=("$arg")
                 ;;
             -l*)
                 arg="${1#-l}"
-                if [[ -z $arg ]]; then shift; arg="$1"; fi
+                if [ -z "$arg" ]; then shift; arg="$1"; fi
                 libs+=("$arg")
                 ;;
             -Wl,*)
                 arg="${1#-Wl,}"
-                if [[ -z $arg ]]; then shift; arg="$1"; fi
-                if [[ $arg = -rpath=* ]]; then
+                if [ -z "$arg" ]; then shift; arg="$1"; fi
+                if [[ "$arg" = -rpath=* ]]; then
                     rpaths+=("${arg#-rpath=}")
-                elif [[ $arg = -rpath,* ]]; then
-                    rpaths+=("${arg#-rpath,}")
-                elif [[ $arg = -rpath ]]; then
+                elif [[ "$arg" = -rpath ]]; then
                     shift; arg="$1"
-                    if [[ $arg != -Wl,* ]]; then
+                    if [[ "$arg" != -Wl,* ]]; then
                         die "-Wl,-rpath was not followed by -Wl,*"
                     fi
                     rpaths+=("${arg#-Wl,}")
@@ -204,14 +194,12 @@ if [[ -n $SPACK_TEST_COMMAND ]]; then
                 ;;
             -Xlinker,*)
                 arg="${1#-Xlinker,}"
-                if [[ -z $arg ]]; then shift; arg="$1"; fi
-                if [[ $arg = -rpath=* ]]; then
+                if [ -z "$arg" ]; then shift; arg="$1"; fi
+                if [[ "$arg" = -rpath=* ]]; then
                     rpaths+=("${arg#-rpath=}")
-                elif [[ $arg = -rpath,* ]]; then
-                    rpaths+=("${arg#-rpath,}")
-                elif [[ $arg = -rpath ]]; then
+                elif [[ "$arg" = -rpath ]]; then
                     shift; arg="$1"
-                    if [[ $arg != -Xlinker,* ]]; then
+                    if [[ "$arg" != -Xlinker,* ]]; then
                         die "-Xlinker,-rpath was not followed by -Xlinker,*"
                     fi
                     rpaths+=("${arg#-Xlinker,}")
@@ -250,8 +238,8 @@ if [[ -n $SPACK_TEST_COMMAND ]]; then
             echo "${other_args[*]}"
             ;;
         *)
-            die "ERROR: Unknown test command"
-            ;;
+            echo "ERROR: Unknown test command"
+            exit 1 ;;
     esac
     exit
 fi
@@ -259,12 +247,11 @@ fi
 # Read spack dependencies from the path environment variable
 IFS=':' read -ra deps <<< "$SPACK_DEPENDENCIES"
 for dep in "${deps[@]}"; do
-    if [[ -d $dep/include ]]; then
+    if [ -d "$dep/include" ]; then
         args=("-I$dep/include" "${args[@]}")
     fi
 
-    if [[ -d $dep/lib ]]; then
-        # libraries+=("$dep/lib")
+    if [ -d "$dep/lib" ]; then
         if [[ $mode = ccld ]]; then
             args=("-L$dep/lib" "-Wl,-rpath,$dep/lib" "${args[@]}")
         elif [[ $mode = ld ]]; then
@@ -272,7 +259,7 @@ for dep in "${deps[@]}"; do
         fi
     fi
 
-    if [[ -d $dep/lib64 ]]; then
+    if [ -d "$dep/lib64" ]; then
         # libraries+=("$dep/lib64")
         if [[ $mode = ccld ]]; then
             args=("-L$dep/lib" "-Wl,-rpath,$dep/lib" "${args[@]}")
@@ -284,18 +271,8 @@ done
 
 # Include all -L's and prefix/whatever dirs in rpath
 if [[ $mode = ccld ]]; then
-    # for dir in "${libraries[@]}"; do
-    #     if [[ dir = $SPACK_INSTALL* ]]; then
-    #         args=("-Wl,-rpath,$dir" "${args[@]}")
-    #     fi
-    # done
     args=("-Wl,-rpath,$SPACK_PREFIX/lib" "-Wl,-rpath,$SPACK_PREFIX/lib64" "${args[@]}")
 elif [[ $mode = ld ]]; then
-    # for dir in "${libraries[@]}"; do
-    #     if [[ dir = $SPACK_INSTALL* ]]; then
-    #         args=("-rpath" "$dir" "${args[@]}")
-    #     fi
-    # done
     args=("-rpath" "$SPACK_PREFIX/lib" "-rpath" "$SPACK_PREFIX/lib64" "${args[@]}")
 fi
 
@@ -317,23 +294,28 @@ PATH=""
 for dir in "${env_path[@]}"; do
     remove=""
     for rm_dir in "${spack_env_dirs[@]}"; do
-        if [[ $dir = $rm_dir ]]; then remove=True; fi
+        if [ "$dir" = "$rm_dir" ]; then remove=True; fi
     done
-    if [[ -z $remove ]]; then
-        PATH="${PATH:+$PATH:}$dir"
+    if [ -z "$remove" ]; then
+        if [ -z "$PATH" ]; then
+            PATH="$dir"
+        else
+            PATH="$PATH:$dir"
+        fi
     fi
 done
 export PATH
 
-full_command=("$command" "${args[@]}")
+full_command=("$command")
+full_command+=("${args[@]}")
 
 #
 # Write the input and output commands to debug logs if it's asked for.
 #
-if [[ $SPACK_DEBUG = TRUE ]]; then
+if [ "$SPACK_DEBUG" = "TRUE" ]; then
     input_log="$SPACK_DEBUG_LOG_DIR/spack-cc-$SPACK_SHORT_SPEC.in.log"
     output_log="$SPACK_DEBUG_LOG_DIR/spack-cc-$SPACK_SHORT_SPEC.out.log"
-    echo "$input_command" >> $input_log
+    echo "$input_command"     >> $input_log
     echo "$mode       ${full_command[@]}" >> $output_log
 fi
 

From 8e33cc1ae118b138aadc3c354b622c045dd81009 Mon Sep 17 00:00:00 2001
From: Erik Schnetter <schnetter@gmail.com>
Date: Fri, 12 Feb 2016 13:11:45 -0500
Subject: [PATCH 007/230] Properly wrap all long lines

---
 .../repos/builtin/packages/gcc/package.py     | 27 ++++++++++++-------
 1 file changed, 17 insertions(+), 10 deletions(-)

diff --git a/var/spack/repos/builtin/packages/gcc/package.py b/var/spack/repos/builtin/packages/gcc/package.py
index eb2129c4da2..8292670de00 100644
--- a/var/spack/repos/builtin/packages/gcc/package.py
+++ b/var/spack/repos/builtin/packages/gcc/package.py
@@ -50,8 +50,10 @@ class Gcc(Package):
     version('4.6.4', 'b407a3d1480c11667f293bfb1f17d1a4')
     version('4.5.4', '27e459c2566b8209ab064570e1b378f7')
 
-    variant('binutils', default=sys.platform != 'darwin', description="Build via binutils")
-    variant('gold', default=sys.platform != 'darwin', description="Build the gold linker plugin for ld-based LTO")
+    variant('binutils', default=sys.platform != 'darwin',
+        description="Build via binutils")
+    variant('gold', default=sys.platform != 'darwin',
+        description="Build the gold linker plugin for ld-based LTO")
 
     depends_on("mpfr")
     depends_on("gmp")
@@ -66,7 +68,8 @@ class Gcc(Package):
 
     def install(self, spec, prefix):
         # libjava/configure needs a minor fix to install into spack paths.
-        filter_file(r"'@.*@'", "'@[[:alnum:]]*@'", 'libjava/configure', string=True)
+        filter_file(r"'@.*@'", "'@[[:alnum:]]*@'", 'libjava/configure',
+            string=True)
 
         enabled_languages = set(('c', 'c++', 'fortran', 'java', 'objc'))
         if spec.satisfies("@4.7.1:") and sys.platform != 'darwin':
@@ -77,17 +80,19 @@ def install(self, spec, prefix):
                    "--libdir=%s/lib64" % prefix,
                    "--disable-multilib",
                    "--enable-languages=" + ','.join(enabled_languages),
-                   "--with-mpc=%s"    % spec['mpc'].prefix,
-                   "--with-mpfr=%s"   % spec['mpfr'].prefix,
-                   "--with-gmp=%s"    % spec['gmp'].prefix,
+                   "--with-mpc=%s" % spec['mpc'].prefix,
+                   "--with-mpfr=%s" % spec['mpfr'].prefix,
+                   "--with-gmp=%s" % spec['gmp'].prefix,
                    "--enable-lto",
                    "--with-quad"]
         # Binutils
         if spec.satisfies('+binutils'):
             static_bootstrap_flags = "-static-libstdc++ -static-libgcc"
             binutils_options = ["--with-sysroot=/",
-                                "--with-stage1-ldflags=%s %s" % (self.rpath_args, static_bootstrap_flags),
-                                "--with-boot-ldflags=%s %s"   %     (self.rpath_args, static_bootstrap_flags),
+                                "--with-stage1-ldflags=%s %s" %
+                                    (self.rpath_args, static_bootstrap_flags),
+                                "--with-boot-ldflags=%s %s" %
+                                    (self.rpath_args, static_bootstrap_flags),
                                 "--with-gnu-ld",
                                 "--with-ld=%s/bin/ld" % spec['binutils'].prefix,
                                 "--with-gnu-as",
@@ -120,7 +125,8 @@ def write_rpath_specs(self):
         """Generate a spec file so the linker adds a rpath to the libs
            the compiler used to build the executable."""
         if not self.spec_dir:
-            tty.warn("Could not install specs for %s." % self.spec.format('$_$@'))
+            tty.warn("Could not install specs for %s." %
+                self.spec.format('$_$@'))
             return
 
         gcc = Executable(join_path(self.prefix.bin, 'gcc'))
@@ -130,5 +136,6 @@ def write_rpath_specs(self):
             for line in lines:
                 out.write(line + "\n")
                 if line.startswith("*link:"):
-                    out.write("-rpath %s/lib:%s/lib64 \\\n"% (self.prefix, self.prefix))
+                    out.write("-rpath %s/lib:%s/lib64 \\\n" %
+                        (self.prefix, self.prefix))
         set_install_permissions(specs_file)

From 63ae40716908ee8c19d49de83accff482d921331 Mon Sep 17 00:00:00 2001
From: alalazo <massimiliano.culpo@googlemail.com>
Date: Thu, 3 Mar 2016 16:39:21 +0100
Subject: [PATCH 008/230] netlib-lapack : unified build with netlib-blas
 openssl : updated version py-numpy : updated dependencies

---
 .../builtin/packages/netlib-blas/package.py   | 46 ---------------
 .../builtin/packages/netlib-lapack/package.py | 57 +++++++------------
 .../repos/builtin/packages/openssl/package.py |  1 +
 .../builtin/packages/py-numpy/package.py      |  3 +-
 4 files changed, 21 insertions(+), 86 deletions(-)
 delete mode 100644 var/spack/repos/builtin/packages/netlib-blas/package.py

diff --git a/var/spack/repos/builtin/packages/netlib-blas/package.py b/var/spack/repos/builtin/packages/netlib-blas/package.py
deleted file mode 100644
index 85e97323d35..00000000000
--- a/var/spack/repos/builtin/packages/netlib-blas/package.py
+++ /dev/null
@@ -1,46 +0,0 @@
-from spack import *
-import os
-
-
-class NetlibBlas(Package):
-    """Netlib reference BLAS"""
-    homepage = "http://www.netlib.org/lapack/"
-    url      = "http://www.netlib.org/lapack/lapack-3.5.0.tgz"
-
-    version('3.5.0', 'b1d3e3e425b2e44a06760ff173104bdf')
-
-    variant('fpic', default=False, description="Build with -fpic compiler option")
-
-    # virtual dependency
-    provides('blas')
-
-    # Doesn't always build correctly in parallel
-    parallel = False
-
-    def patch(self):
-        os.symlink('make.inc.example', 'make.inc')
-
-        mf = FileFilter('make.inc')
-        mf.filter('^FORTRAN.*', 'FORTRAN = f90')
-        mf.filter('^LOADER.*',  'LOADER = f90')
-        mf.filter('^CC =.*',  'CC = cc')
-
-        if '+fpic' in self.spec:
-            mf.filter('^OPTS.*=.*',  'OPTS = -O2 -frecursive -fpic')
-            mf.filter('^CFLAGS =.*',  'CFLAGS = -O3 -fpic')
-
-
-    def install(self, spec, prefix):
-        make('blaslib')
-
-        # Tests that blas builds correctly
-        make('blas_testing')
-
-        # No install provided
-        mkdirp(prefix.lib)
-        install('librefblas.a', prefix.lib)
-
-        # Blas virtual package should provide blas.a and libblas.a
-        with working_dir(prefix.lib):
-            symlink('librefblas.a', 'blas.a')
-            symlink('librefblas.a', 'libblas.a')
diff --git a/var/spack/repos/builtin/packages/netlib-lapack/package.py b/var/spack/repos/builtin/packages/netlib-lapack/package.py
index fb6b99e27c3..1bb77919d50 100644
--- a/var/spack/repos/builtin/packages/netlib-lapack/package.py
+++ b/var/spack/repos/builtin/packages/netlib-lapack/package.py
@@ -1,16 +1,15 @@
 from spack import *
 
+
 class NetlibLapack(Package):
     """
-    LAPACK version 3.X is a comprehensive FORTRAN library that does
-    linear algebra operations including matrix inversions, least
-    squared solutions to linear sets of equations, eigenvector
-    analysis, singular value decomposition, etc. It is a very
-    comprehensive and reputable package that has found extensive
-    use in the scientific community.
+    LAPACK version 3.X is a comprehensive FORTRAN library that does linear algebra operations including matrix
+    inversions, least squared solutions to linear sets of equations, eigenvector analysis, singular value
+    decomposition, etc. It is a very comprehensive and reputable package that has found extensive use in the
+    scientific community.
     """
     homepage = "http://www.netlib.org/lapack/"
-    url      = "http://www.netlib.org/lapack/lapack-3.5.0.tgz"
+    url = "http://www.netlib.org/lapack/lapack-3.5.0.tgz"
 
     version('3.5.0', 'b1d3e3e425b2e44a06760ff173104bdf')
     version('3.4.2', '61bf1a8a4469d4bdb7604f5897179478')
@@ -18,42 +17,24 @@ class NetlibLapack(Package):
     version('3.4.0', '02d5706ec03ba885fc246e5fa10d8c70')
     version('3.3.1', 'd0d533ec9a5b74933c2a1e84eedc58b4')
 
-    variant('shared', default=False, description="Build shared library version")
+    variant('debug', default=False, description='Activates the Debug build type')
+    variant('shared', default=True, description="Build shared library version")
+
+    variant('lapacke', default=True, description='Activates the build of the LAPACKE C interface')
 
     # virtual dependency
+    provides('blas')
     provides('lapack')
 
-    # blas is a virtual dependency.
-    depends_on('blas')
-
     depends_on('cmake')
 
-    # Doesn't always build correctly in parallel
-    parallel = False
-
-    @when('^netlib-blas')
-    def get_blas_libs(self):
-        blas = self.spec['netlib-blas']
-        return [join_path(blas.prefix.lib, 'blas.a')]
-
-
-    @when('^atlas')
-    def get_blas_libs(self):
-        blas = self.spec['atlas']
-        return [join_path(blas.prefix.lib, l)
-                for l in ('libf77blas.a', 'libatlas.a')]
-
-
     def install(self, spec, prefix):
-        blas_libs = ";".join(self.get_blas_libs())
-        cmake_args = [".", '-DBLAS_LIBRARIES=' + blas_libs]
-
-        if '+shared' in spec:
-            cmake_args.append('-DBUILD_SHARED_LIBS=ON')
-
-        cmake_args += std_cmake_args
-
-        cmake(*cmake_args)
-        make()
-        make("install")
+        cmake_args = ['-DBUILD_SHARED_LIBS:BOOL=%s' % ('ON' if '+shared' in spec else 'OFF'),
+                      '-DCMAKE_BUILD_TYPE:STRING=%s' % ('Debug' if '+debug' in spec else 'Release'),
+                      '-DLAPACKE:BOOL=%s' % ('ON' if '+lapacke' in spec else 'OFF')]
+        cmake_args.extend(std_cmake_args)
 
+        with working_dir('spack-build', create=True):
+            cmake('..', *cmake_args)
+            make()
+            make("install")
diff --git a/var/spack/repos/builtin/packages/openssl/package.py b/var/spack/repos/builtin/packages/openssl/package.py
index c73102f05d3..70afaf4038a 100644
--- a/var/spack/repos/builtin/packages/openssl/package.py
+++ b/var/spack/repos/builtin/packages/openssl/package.py
@@ -17,6 +17,7 @@ class Openssl(Package):
     version('1.0.2d', '38dd619b2e77cbac69b99f52a053d25a')
     version('1.0.2e', '5262bfa25b60ed9de9f28d5d52d77fc5')
     version('1.0.2f', 'b3bf73f507172be9292ea2a8c28b659d')
+    version('1.0.2g', 'f3c710c045cdee5fd114feb69feba7aa')
 
     depends_on("zlib")
     parallel = False
diff --git a/var/spack/repos/builtin/packages/py-numpy/package.py b/var/spack/repos/builtin/packages/py-numpy/package.py
index 03548111863..0844ff5caa6 100644
--- a/var/spack/repos/builtin/packages/py-numpy/package.py
+++ b/var/spack/repos/builtin/packages/py-numpy/package.py
@@ -12,8 +12,7 @@ class PyNumpy(Package):
 
     extends('python')
     depends_on('py-nose')
-    depends_on('netlib-blas+fpic', when='+blas')
-    depends_on('netlib-lapack+shared', when='+blas')
+    depends_on('lapack+shared', when='+blas')
 
     def install(self, spec, prefix):
         if '+blas' in spec:

From 310099d88838c8e08d15fb34028263c9294b62e9 Mon Sep 17 00:00:00 2001
From: alalazo <massimiliano.culpo@googlemail.com>
Date: Fri, 4 Mar 2016 09:31:03 +0100
Subject: [PATCH 009/230] atlas : provides blas and lapack

---
 .../repos/builtin/packages/atlas/package.py   | 62 +++++++++----------
 1 file changed, 30 insertions(+), 32 deletions(-)

diff --git a/var/spack/repos/builtin/packages/atlas/package.py b/var/spack/repos/builtin/packages/atlas/package.py
index fc683363a70..f9b50417b00 100644
--- a/var/spack/repos/builtin/packages/atlas/package.py
+++ b/var/spack/repos/builtin/packages/atlas/package.py
@@ -1,31 +1,34 @@
 from spack import *
 from spack.util.executable import Executable
-import os
+import os.path
 
 class Atlas(Package):
     """
-    Automatically Tuned Linear Algebra Software, generic shared
-    ATLAS is an approach for the automatic generation and optimization of
-    numerical software. Currently ATLAS supplies optimized versions for the
-    complete set of linear algebra kernels known as the Basic Linear Algebra
-    Subroutines (BLAS), and a subset of the linear algebra routines in the
-    LAPACK library.
+    Automatically Tuned Linear Algebra Software, generic shared ATLAS is an approach for the automatic generation and
+    optimization of numerical software. Currently ATLAS supplies optimized versions for the complete set of linear
+    algebra kernels known as the Basic Linear Algebra Subroutines (BLAS), and a subset of the linear algebra routines
+    in the LAPACK library.
     """
     homepage = "http://math-atlas.sourceforge.net/"
 
+    version('3.10.2', 'a4e21f343dec8f22e7415e339f09f6da',
+            url='http://downloads.sourceforge.net/project/math-atlas/Stable/3.10.2/atlas3.10.2.tar.bz2', preferred=True)
+    resource(name='lapack',
+             url='http://www.netlib.org/lapack/lapack-3.5.0.tgz',
+             md5='b1d3e3e425b2e44a06760ff173104bdf',
+             destination='spack-resource-lapack',
+             when='@3:')
+
     version('3.11.34', '0b6c5389c095c4c8785fd0f724ec6825',
             url='http://sourceforge.net/projects/math-atlas/files/Developer%20%28unstable%29/3.11.34/atlas3.11.34.tar.bz2/download')
-    version('3.10.2', 'a4e21f343dec8f22e7415e339f09f6da',
-            url='http://downloads.sourceforge.net/project/math-atlas/Stable/3.10.2/atlas3.10.2.tar.bz2')
 
-    # TODO: make this provide BLAS once it works better.  Create a way
-    # TODO: to mark "beta" packages and require explicit invocation.
-
-    # provides('blas')
+    variant('shared', default=True, description='Builds shared library')
 
+    provides('blas')
+    provides('lapack')
 
     def patch(self):
-        # Disable thraed check.  LLNL's environment does not allow
+        # Disable thread check.  LLNL's environment does not allow
         # disabling of CPU throttling in a way that ATLAS actually
         # understands.
         filter_file(r'^\s+if \(thrchk\) exit\(1\);', 'if (0) exit(1);',
@@ -33,26 +36,21 @@ def patch(self):
         # TODO: investigate a better way to add the check back in
         # TODO: using, say, MSRs.  Or move this to a variant.
 
-    @when('@:3.10')
     def install(self, spec, prefix):
-        with working_dir('ATLAS-Build', create=True):
+
+        options = []
+        if '+shared' in spec:
+            options.append('--shared')
+
+        # Lapack resource
+        lapack_stage = self.stage[1]
+        lapack_tarfile = os.path.basename(lapack_stage.fetcher.url)
+        lapack_tarfile_path = join_path(lapack_stage.path, lapack_tarfile)
+        options.append('--with-netlib-lapack-tarfile=%s' % lapack_tarfile_path)
+
+        with working_dir('spack-build', create=True):
             configure = Executable('../configure')
-            configure('--prefix=%s' % prefix, '-C', 'ic', 'cc', '-C', 'if', 'f77', "--dylibs")
-            make()
-            make('check')
-            make('ptcheck')
-            make('time')
-            make("install")
-
-
-    def install(self, spec, prefix):
-        with working_dir('ATLAS-Build', create=True):
-            configure = Executable('../configure')
-            configure('--incdir=%s' % prefix.include,
-                      '--libdir=%s' % prefix.lib,
-                      '--cc=cc',
-                      "--shared")
-
+            configure('--prefix=%s' % prefix, *options)
             make()
             make('check')
             make('ptcheck')

From a2af4940aaf169f3358f19986fc94a02222a8096 Mon Sep 17 00:00:00 2001
From: alalazo <massimiliano.culpo@googlemail.com>
Date: Fri, 4 Mar 2016 09:59:16 +0100
Subject: [PATCH 010/230] atlas : disabling parallel builds

---
 var/spack/repos/builtin/packages/atlas/package.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/var/spack/repos/builtin/packages/atlas/package.py b/var/spack/repos/builtin/packages/atlas/package.py
index f9b50417b00..b5504122b74 100644
--- a/var/spack/repos/builtin/packages/atlas/package.py
+++ b/var/spack/repos/builtin/packages/atlas/package.py
@@ -27,6 +27,8 @@ class Atlas(Package):
     provides('blas')
     provides('lapack')
 
+    parallel = False
+
     def patch(self):
         # Disable thread check.  LLNL's environment does not allow
         # disabling of CPU throttling in a way that ATLAS actually

From 4f14db8af214b6648da04c5c5121757ea171f18c Mon Sep 17 00:00:00 2001
From: alalazo <massimiliano.culpo@googlemail.com>
Date: Thu, 10 Mar 2016 10:34:51 +0100
Subject: [PATCH 011/230] netlib-lapack : optional dependency on external blas

---
 .../repos/builtin/packages/netlib-lapack/package.py  | 12 +++++++++++-
 1 file changed, 11 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/netlib-lapack/package.py b/var/spack/repos/builtin/packages/netlib-lapack/package.py
index 1bb77919d50..a208929d08b 100644
--- a/var/spack/repos/builtin/packages/netlib-lapack/package.py
+++ b/var/spack/repos/builtin/packages/netlib-lapack/package.py
@@ -19,19 +19,29 @@ class NetlibLapack(Package):
 
     variant('debug', default=False, description='Activates the Debug build type')
     variant('shared', default=True, description="Build shared library version")
+    variant('external-blas', default=False, description='Build lapack with an external blas')
 
     variant('lapacke', default=True, description='Activates the build of the LAPACKE C interface')
 
     # virtual dependency
-    provides('blas')
+    provides('blas', when='~external-blas')
     provides('lapack')
 
     depends_on('cmake')
+    depends_on('blas', when='+external-blas')
 
     def install(self, spec, prefix):
         cmake_args = ['-DBUILD_SHARED_LIBS:BOOL=%s' % ('ON' if '+shared' in spec else 'OFF'),
                       '-DCMAKE_BUILD_TYPE:STRING=%s' % ('Debug' if '+debug' in spec else 'Release'),
                       '-DLAPACKE:BOOL=%s' % ('ON' if '+lapacke' in spec else 'OFF')]
+        if '+external-blas' in spec:
+            # TODO : the mechanism to specify the library should be more general,
+            # TODO : but this allows to have an hook to an external blas
+            cmake_args.extend([
+                '-DUSE_OPTIMIZED_BLAS:BOOL=ON',
+                '-DBLAS_LIBRARIES:PATH=%s' % join_path(spec['blas'].prefix.lib, 'libblas.a')
+            ])
+
         cmake_args.extend(std_cmake_args)
 
         with working_dir('spack-build', create=True):

From 1d70b590fc4579c4e6b4bd592bc58eabf330fd9b Mon Sep 17 00:00:00 2001
From: alalazo <massimiliano.culpo@googlemail.com>
Date: Fri, 11 Mar 2016 13:20:57 +0100
Subject: [PATCH 012/230] build_environment : fixed minor spelling errors and a
 few style issues

---
 lib/spack/spack/build_environment.py | 37 ++++++++++++++--------------
 1 file changed, 18 insertions(+), 19 deletions(-)

diff --git a/lib/spack/spack/build_environment.py b/lib/spack/spack/build_environment.py
index 87fc310b5a3..392ba7ea4d5 100644
--- a/lib/spack/spack/build_environment.py
+++ b/lib/spack/spack/build_environment.py
@@ -3,7 +3,7 @@
 build environment.  All of this is set up by package.py just before
 install() is called.
 
-There are two parts to the bulid environment:
+There are two parts to the build environment:
 
 1. Python build environment (i.e. install() method)
 
@@ -13,7 +13,7 @@
    the package's module scope.  Ths allows package writers to call
    them all directly in Package.install() without writing 'self.'
    everywhere.  No, this isn't Pythonic.  Yes, it makes the code more
-   readable and more like the shell script from whcih someone is
+   readable and more like the shell script from which someone is
    likely porting.
 
 2. Build execution environment
@@ -27,17 +27,16 @@
 Skimming this module is a nice way to get acquainted with the types of
 calls you can make from within the install() function.
 """
-import os
-import sys
-import shutil
 import multiprocessing
+import os
 import platform
-from llnl.util.filesystem import *
+import shutil
+import sys
 
 import spack
-import spack.compilers as compilers
-from spack.util.executable import Executable, which
+from llnl.util.filesystem import *
 from spack.util.environment import *
+from spack.util.executable import Executable, which
 
 #
 # This can be set by the user to globally disable parallel builds.
@@ -107,18 +106,19 @@ def set_compiler_environment_variables(pkg):
     if compiler.fc:
         os.environ['SPACK_FC']  = compiler.fc
 
-    os.environ['SPACK_COMPILER_SPEC']  = str(pkg.spec.compiler)
+    os.environ['SPACK_COMPILER_SPEC'] = str(pkg.spec.compiler)
 
 
 def set_build_environment_variables(pkg):
-    """This ensures a clean install environment when we build packages.
+    """
+    This ensures a clean install environment when we build packages
     """
     # Add spack build environment path with compiler wrappers first in
     # the path. We add both spack.env_path, which includes default
     # wrappers (cc, c++, f77, f90), AND a subdirectory containing
     # compiler-specific symlinks.  The latter ensures that builds that
     # are sensitive to the *name* of the compiler see the right name
-    # when we're building wtih the wrappers.
+    # when we're building with the wrappers.
     #
     # Conflicts on case-insensitive systems (like "CC" and "cc") are
     # handled by putting one in the <build_env_path>/case-insensitive
@@ -296,23 +296,23 @@ def child_fun():
            # do stuff
        build_env.fork(pkg, child_fun)
 
-    Forked processes are run with the build environemnt set up by
+    Forked processes are run with the build environment set up by
     spack.build_environment.  This allows package authors to have
-    full control over the environment, etc. without offecting
+    full control over the environment, etc. without affecting
     other builds that might be executed in the same spack call.
 
-    If something goes wrong, the child process is expected toprint
+    If something goes wrong, the child process is expected to print
     the error and the parent process will exit with error as
     well. If things go well, the child exits and the parent
     carries on.
     """
     try:
         pid = os.fork()
-    except OSError, e:
+    except OSError as e:
         raise InstallError("Unable to fork build process: %s" % e)
 
     if pid == 0:
-        # Give the child process the package's build environemnt.
+        # Give the child process the package's build environment.
         setup_package(pkg)
 
         try:
@@ -323,7 +323,7 @@ def child_fun():
             # which interferes with unit tests.
             os._exit(0)
 
-        except spack.error.SpackError, e:
+        except spack.error.SpackError as e:
             e.die()
 
         except:
@@ -338,8 +338,7 @@ def child_fun():
         # message.  Just make the parent exit with an error code.
         pid, returncode = os.waitpid(pid, 0)
         if returncode != 0:
-            raise InstallError("Installation process had nonzero exit code."
-                .format(str(returncode)))
+            raise InstallError("Installation process had nonzero exit code.".format(str(returncode)))
 
 
 class InstallError(spack.error.SpackError):

From f9923452b3365e1472a4f1bd63712c57fea0ee0d Mon Sep 17 00:00:00 2001
From: alalazo <massimiliano.culpo@googlemail.com>
Date: Mon, 14 Mar 2016 14:35:48 +0100
Subject: [PATCH 013/230] environment : added machinery to collect
 modifications to the environment and apply them later

---
 lib/spack/spack/environment.py      | 157 ++++++++++++++++++++++++++++
 lib/spack/spack/test/__init__.py    |   3 +-
 lib/spack/spack/test/environment.py |  50 +++++++++
 3 files changed, 209 insertions(+), 1 deletion(-)
 create mode 100644 lib/spack/spack/environment.py
 create mode 100644 lib/spack/spack/test/environment.py

diff --git a/lib/spack/spack/environment.py b/lib/spack/spack/environment.py
new file mode 100644
index 00000000000..7d3d7af0de1
--- /dev/null
+++ b/lib/spack/spack/environment.py
@@ -0,0 +1,157 @@
+import os
+import os.path
+import collections
+
+
+class SetEnv(object):
+    def __init__(self, name, value, **kwargs):
+        self.name = name
+        self.value = value
+        for key, value in kwargs.items():
+            setattr(self, key, value)
+
+    def execute(self):
+        os.environ[self.name] = str(self.value)
+
+
+class UnsetEnv(object):
+    def __init__(self, name, **kwargs):
+        self.name = name
+        for key, value in kwargs.items():
+            setattr(self, key, value)
+
+    def execute(self):
+        os.environ.pop(self.name, None)  # Avoid throwing if the variable was not set
+
+
+class AppendPath(object):
+    def __init__(self, name, path, **kwargs):
+        self.name = name
+        self.path = path
+        for key, value in kwargs.items():
+            setattr(self, key, value)
+
+    def execute(self):
+        environment_value = os.environ.get(self.name, '')
+        directories = environment_value.split(':') if environment_value else []
+        # TODO : Check if this is a valid directory name
+        directories.append(os.path.normpath(self.path))
+        os.environ[self.name] = ':'.join(directories)
+
+
+class PrependPath(object):
+    def __init__(self, name, path, **kwargs):
+        self.name = name
+        self.path = path
+        for key, value in kwargs.items():
+            setattr(self, key, value)
+
+    def execute(self):
+        environment_value = os.environ.get(self.name, '')
+        directories = environment_value.split(':') if environment_value else []
+        # TODO : Check if this is a valid directory name
+        directories = [os.path.normpath(self.path)] + directories
+        os.environ[self.name] = ':'.join(directories)
+
+
+class RemovePath(object):
+    def __init__(self, name, path, **kwargs):
+        self.name = name
+        self.path = path
+        for key, value in kwargs.items():
+            setattr(self, key, value)
+
+    def execute(self):
+        environment_value = os.environ.get(self.name, '')
+        directories = environment_value.split(':') if environment_value else []
+        directories = [os.path.normpath(x) for x in directories if x != os.path.normpath(self.path)]
+        os.environ[self.name] = ':'.join(directories)
+
+
+class EnvironmentModifications(object):
+    """
+    Keeps track of requests to modify the current environment
+    """
+
+    def __init__(self):
+        self.env_modifications = []
+
+    def __iter__(self):
+        return iter(self.env_modifications)
+
+    def set_env(self, name, value, **kwargs):
+        """
+        Stores in the current object a request to set an environment variable
+
+        Args:
+            name: name of the environment variable to be set
+            value: value of the environment variable
+        """
+        item = SetEnv(name, value, **kwargs)
+        self.env_modifications.append(item)
+
+    def unset_env(self, name, **kwargs):
+        """
+        Stores in the current object a request to unset an environment variable
+
+        Args:
+            name: name of the environment variable to be set
+        """
+        item = UnsetEnv(name, **kwargs)
+        self.env_modifications.append(item)
+
+    def append_path(self, name, path, **kwargs):
+        """
+        Stores in the current object a request to append a path to a path list
+
+        Args:
+            name: name of the path list in the environment
+            path: path to be appended
+        """
+        item = AppendPath(name, path, **kwargs)
+        self.env_modifications.append(item)
+
+    def prepend_path(self, name, path, **kwargs):
+        """
+        Same as `append_path`, but the path is pre-pended
+
+        Args:
+            name: name of the path list in the environment
+            path: path to be pre-pended
+        """
+        item = PrependPath(name, path, **kwargs)
+        self.env_modifications.append(item)
+
+    def remove_path(self, name, path, **kwargs):
+        """
+        Stores in the current object a request to remove a path from a path list
+
+        Args:
+            name: name of the path list in the environment
+            path: path to be removed
+        """
+        item = RemovePath(name, path, **kwargs)
+        self.env_modifications.append(item)
+
+
+def validate_environment_modifications(env):
+    modifications = collections.defaultdict(list)
+    for item in env:
+        modifications[item.name].append(item)
+    return modifications
+
+
+def apply_environment_modifications(env):
+    """
+    Modifies the current environment according to the request in env
+
+    Args:
+        env: object storing modifications to the environment
+    """
+    modifications = validate_environment_modifications(env)
+
+    # Cycle over the environment variables that will be modified
+    for variable, actions in modifications.items():
+        # Execute all the actions in the order they were issued
+        for x in actions:
+            x.execute()
diff --git a/lib/spack/spack/test/__init__.py b/lib/spack/spack/test/__init__.py
index d5d8b647650..cd842561e6c 100644
--- a/lib/spack/spack/test/__init__.py
+++ b/lib/spack/spack/test/__init__.py
@@ -66,7 +66,8 @@
               'database',
               'namespace_trie',
               'yaml',
-              'sbang']
+              'sbang',
+              'environment']
 
 
 def list_tests():
diff --git a/lib/spack/spack/test/environment.py b/lib/spack/spack/test/environment.py
new file mode 100644
index 00000000000..dff3863d322
--- /dev/null
+++ b/lib/spack/spack/test/environment.py
@@ -0,0 +1,50 @@
+import unittest
+import os
+from spack.environment import EnvironmentModifications, apply_environment_modifications
+
+
+class EnvironmentTest(unittest.TestCase):
+    def setUp(self):
+        os.environ.clear()
+        os.environ['UNSET_ME'] = 'foo'
+        os.environ['EMPTY_PATH_LIST'] = ''
+        os.environ['PATH_LIST'] = '/path/second:/path/third'
+        os.environ['REMOVE_PATH_LIST'] = '/a/b:/duplicate:/a/c:/remove/this:/a/d:/duplicate/:/f/g'
+
+    def test_set_env(self):
+        env = EnvironmentModifications()
+        env.set_env('A', 'dummy value')
+        env.set_env('B', 3)
+        apply_environment_modifications(env)
+        self.assertEqual('dummy value', os.environ['A'])
+        self.assertEqual(str(3), os.environ['B'])
+
+    def test_unset_env(self):
+        env = EnvironmentModifications()
+        self.assertEqual('foo', os.environ['UNSET_ME'])
+        env.unset_env('UNSET_ME')
+        apply_environment_modifications(env)
+        self.assertRaises(KeyError, os.environ.__getitem__, 'UNSET_ME')
+
+    def test_path_manipulation(self):
+        env = EnvironmentModifications()
+
+        env.append_path('PATH_LIST', '/path/last')
+        env.prepend_path('PATH_LIST', '/path/first')
+
+        env.append_path('EMPTY_PATH_LIST', '/path/middle')
+        env.append_path('EMPTY_PATH_LIST', '/path/last')
+        env.prepend_path('EMPTY_PATH_LIST', '/path/first')
+
+        env.append_path('NEWLY_CREATED_PATH_LIST', '/path/middle')
+        env.append_path('NEWLY_CREATED_PATH_LIST', '/path/last')
+        env.prepend_path('NEWLY_CREATED_PATH_LIST', '/path/first')
+
+        env.remove_path('REMOVE_PATH_LIST', '/remove/this')
+        env.remove_path('REMOVE_PATH_LIST', '/duplicate/')
+
+        apply_environment_modifications(env)
+        self.assertEqual('/path/first:/path/second:/path/third:/path/last', os.environ['PATH_LIST'])
+        self.assertEqual('/path/first:/path/middle:/path/last', os.environ['EMPTY_PATH_LIST'])
+        self.assertEqual('/path/first:/path/middle:/path/last', os.environ['NEWLY_CREATED_PATH_LIST'])
+        self.assertEqual('/a/b:/a/c:/a/d:/f/g', os.environ['REMOVE_PATH_LIST'])

From f20247ae55362424d1d5543840a21142017661af Mon Sep 17 00:00:00 2001
From: alalazo <massimiliano.culpo@googlemail.com>
Date: Tue, 15 Mar 2016 10:08:54 +0100
Subject: [PATCH 014/230] environment : refactoreded
 set_compiler_environment_variables

---
 lib/spack/spack/build_environment.py | 38 +++++++++++++++-------------
 lib/spack/spack/environment.py       | 17 ++++++++++++-
 lib/spack/spack/test/database.py     |  1 +
 lib/spack/spack/test/environment.py  |  9 +++++++
 4 files changed, 47 insertions(+), 18 deletions(-)

diff --git a/lib/spack/spack/build_environment.py b/lib/spack/spack/build_environment.py
index 392ba7ea4d5..e91a8a19977 100644
--- a/lib/spack/spack/build_environment.py
+++ b/lib/spack/spack/build_environment.py
@@ -35,6 +35,7 @@
 
 import spack
 from llnl.util.filesystem import *
+from spack.environment import EnvironmentModifications, apply_environment_modifications
 from spack.util.environment import *
 from spack.util.executable import Executable, which
 
@@ -83,30 +84,32 @@ def __call__(self, *args, **kwargs):
 
 
 def set_compiler_environment_variables(pkg):
-    assert(pkg.spec.concrete)
-    compiler = pkg.compiler
-
+    assert pkg.spec.concrete
     # Set compiler variables used by CMake and autotools
-    assert all(key in pkg.compiler.link_paths
-               for key in ('cc', 'cxx', 'f77', 'fc'))
+    assert all(key in pkg.compiler.link_paths for key in ('cc', 'cxx', 'f77', 'fc'))
 
+    # Populate an object with the list of environment modifications
+    # and return it
+    # TODO : add additional kwargs for better diagnostics, like requestor, ttyout, ttyerr, etc.
+    env = EnvironmentModifications()
     link_dir = spack.build_env_path
-    os.environ['CC']  = join_path(link_dir, pkg.compiler.link_paths['cc'])
-    os.environ['CXX'] = join_path(link_dir, pkg.compiler.link_paths['cxx'])
-    os.environ['F77'] = join_path(link_dir, pkg.compiler.link_paths['f77'])
-    os.environ['FC']  = join_path(link_dir, pkg.compiler.link_paths['fc'])
-
+    env.set_env('CC', join_path(link_dir, pkg.compiler.link_paths['cc']))
+    env.set_env('CXX', join_path(link_dir, pkg.compiler.link_paths['cxx']))
+    env.set_env('F77', join_path(link_dir, pkg.compiler.link_paths['f77']))
+    env.set_env('FC', join_path(link_dir, pkg.compiler.link_paths['fc']))
     # Set SPACK compiler variables so that our wrapper knows what to call
+    compiler = pkg.compiler
     if compiler.cc:
-        os.environ['SPACK_CC']  = compiler.cc
+        env.set_env('SPACK_CC', compiler.cc)
     if compiler.cxx:
-        os.environ['SPACK_CXX'] = compiler.cxx
+        env.set_env('SPACK_CXX', compiler.cxx)
     if compiler.f77:
-        os.environ['SPACK_F77'] = compiler.f77
+        env.set_env('SPACK_F77', compiler.f77)
     if compiler.fc:
-        os.environ['SPACK_FC']  = compiler.fc
+        env.set_env('SPACK_FC', compiler.fc)
 
-    os.environ['SPACK_COMPILER_SPEC'] = str(pkg.spec.compiler)
+    env.set_env('SPACK_COMPILER_SPEC', str(pkg.spec.compiler))
+    return env
 
 
 def set_build_environment_variables(pkg):
@@ -264,9 +267,10 @@ def parent_class_modules(cls):
 
 def setup_package(pkg):
     """Execute all environment setup routines."""
-    set_compiler_environment_variables(pkg)
+    env = EnvironmentModifications()
+    env.extend(set_compiler_environment_variables(pkg))
+    apply_environment_modifications(env)
     set_build_environment_variables(pkg)
-
     # If a user makes their own package repo, e.g.
     # spack.repos.mystuff.libelf.Libelf, and they inherit from
     # an existing class like spack.repos.original.libelf.Libelf,
diff --git a/lib/spack/spack/environment.py b/lib/spack/spack/environment.py
index 7d3d7af0de1..3b73f1c7a2a 100644
--- a/lib/spack/spack/environment.py
+++ b/lib/spack/spack/environment.py
@@ -73,12 +73,24 @@ class EnvironmentModifications(object):
     Keeps track of requests to modify the current environment
     """
 
-    def __init__(self):
+    def __init__(self, other=None):
         self.env_modifications = []
+        if other is not None:
+            self._check_other(other)
+            self.env_modifications.extend(other.env_modifications)
 
     def __iter__(self):
         return iter(self.env_modifications)
 
+    def extend(self, other):
+        self._check_other(other)
+        self.env_modifications.extend(other.env_modifications)
+
+    @staticmethod
+    def _check_other(other):
+        if not isinstance(other, EnvironmentModifications):
+            raise TypeError('other must be an instance of EnvironmentModifications')
+
     def set_env(self, name, value, **kwargs):
         """
         Stores in the current object a request to set an environment variable
@@ -138,6 +150,9 @@ def validate_environment_modifications(env):
     modifications = collections.defaultdict(list)
     for item in env:
         modifications[item.name].append(item)
+    # TODO : once we organized the modifications into a dictionary that maps an environment variable
+    # TODO : to a list of action to be done on it, we may easily spot inconsistencies and warn the user if
+    # TODO : something suspicious is happening
     return modifications
 
 
diff --git a/lib/spack/spack/test/database.py b/lib/spack/spack/test/database.py
index 9a57e1f03ea..ce6e8a0552b 100644
--- a/lib/spack/spack/test/database.py
+++ b/lib/spack/spack/test/database.py
@@ -26,6 +26,7 @@
 These tests check the database is functioning properly,
 both in memory and in its file
 """
+import os.path
 import multiprocessing
 import shutil
 import tempfile
diff --git a/lib/spack/spack/test/environment.py b/lib/spack/spack/test/environment.py
index dff3863d322..17061c8fd0e 100644
--- a/lib/spack/spack/test/environment.py
+++ b/lib/spack/spack/test/environment.py
@@ -48,3 +48,12 @@ def test_path_manipulation(self):
         self.assertEqual('/path/first:/path/middle:/path/last', os.environ['EMPTY_PATH_LIST'])
         self.assertEqual('/path/first:/path/middle:/path/last', os.environ['NEWLY_CREATED_PATH_LIST'])
         self.assertEqual('/a/b:/a/c:/a/d:/f/g', os.environ['REMOVE_PATH_LIST'])
+
+    def test_extra_arguments(self):
+        env = EnvironmentModifications()
+        env.set_env('A', 'dummy value', who='Pkg1')
+        apply_environment_modifications(env)
+        self.assertEqual('dummy value', os.environ['A'])
+
+    def test_copy(self):
+        pass

From bcea1df01ce145aea5e49eaaceb7a063b44ddf80 Mon Sep 17 00:00:00 2001
From: alalazo <massimiliano.culpo@googlemail.com>
Date: Tue, 15 Mar 2016 10:49:33 +0100
Subject: [PATCH 015/230] environment : refactoreded
 set_build_environment_variables

---
 lib/spack/spack/build_environment.py          | 52 ++++++++++---------
 lib/spack/spack/environment.py                |  3 ++
 .../builtin/packages/mvapich2/package.py      |  2 +-
 3 files changed, 31 insertions(+), 26 deletions(-)

diff --git a/lib/spack/spack/build_environment.py b/lib/spack/spack/build_environment.py
index e91a8a19977..770e191ac90 100644
--- a/lib/spack/spack/build_environment.py
+++ b/lib/spack/spack/build_environment.py
@@ -35,7 +35,7 @@
 
 import spack
 from llnl.util.filesystem import *
-from spack.environment import EnvironmentModifications, apply_environment_modifications
+from spack.environment import EnvironmentModifications, apply_environment_modifications, concatenate_paths
 from spack.util.environment import *
 from spack.util.executable import Executable, which
 
@@ -127,44 +127,45 @@ def set_build_environment_variables(pkg):
     # handled by putting one in the <build_env_path>/case-insensitive
     # directory.  Add that to the path too.
     env_paths = []
-    def add_env_path(path):
-        env_paths.append(path)
-        ci = join_path(path, 'case-insensitive')
-        if os.path.isdir(ci): env_paths.append(ci)
-    add_env_path(spack.build_env_path)
-    add_env_path(join_path(spack.build_env_path, pkg.compiler.name))
+    for item in [spack.build_env_path, join_path(spack.build_env_path, pkg.compiler.name)]:
+        env_paths.append(item)
+        ci = join_path(item, 'case-insensitive')
+        if os.path.isdir(ci):
+            env_paths.append(ci)
 
-    path_put_first("PATH", env_paths)
-    path_set(SPACK_ENV_PATH, env_paths)
+    env = EnvironmentModifications()
+    for item in reversed(env_paths):
+        env.prepend_path('PATH', item)
+    env.set_env(SPACK_ENV_PATH, concatenate_paths(env_paths))
 
-    # Prefixes of all of the package's dependencies go in
-    # SPACK_DEPENDENCIES
+    # Prefixes of all of the package's dependencies go in SPACK_DEPENDENCIES
     dep_prefixes = [d.prefix for d in pkg.spec.traverse(root=False)]
-    path_set(SPACK_DEPENDENCIES, dep_prefixes)
+    env.set_env(SPACK_DEPENDENCIES, concatenate_paths(dep_prefixes))
+    env.set_env('CMAKE_PREFIX_PATH', concatenate_paths(dep_prefixes))  # Add dependencies to CMAKE_PREFIX_PATH
 
     # Install prefix
-    os.environ[SPACK_PREFIX] = pkg.prefix
+    env.set_env(SPACK_PREFIX, pkg.prefix)
 
     # Install root prefix
-    os.environ[SPACK_INSTALL] = spack.install_path
+    env.set_env(SPACK_INSTALL, spack.install_path)
 
     # Remove these vars from the environment during build because they
     # can affect how some packages find libraries.  We want to make
     # sure that builds never pull in unintended external dependencies.
-    pop_keys(os.environ, "LD_LIBRARY_PATH", "LD_RUN_PATH", "DYLD_LIBRARY_PATH")
+    env.unset_env('LD_LIBRARY_PATH')
+    env.unset_env('LD_RUN_PATH')
+    env.unset_env('DYLD_LIBRARY_PATH')
 
     # Add bin directories from dependencies to the PATH for the build.
-    bin_dirs = ['%s/bin' % prefix for prefix in dep_prefixes]
-    path_put_first('PATH', [bin for bin in bin_dirs if os.path.isdir(bin)])
+    bin_dirs = reversed(filter(os.path.isdir, ['%s/bin' % prefix for prefix in dep_prefixes]))
+    for item in bin_dirs:
+        env.prepend_path('PATH', item)
 
     # Working directory for the spack command itself, for debug logs.
     if spack.debug:
-        os.environ[SPACK_DEBUG] = "TRUE"
-    os.environ[SPACK_SHORT_SPEC] = pkg.spec.short_spec
-    os.environ[SPACK_DEBUG_LOG_DIR] = spack.spack_working_dir
-
-    # Add dependencies to CMAKE_PREFIX_PATH
-    path_set("CMAKE_PREFIX_PATH", dep_prefixes)
+        env.set_env(SPACK_DEBUG, 'TRUE')
+    env.set_env(SPACK_SHORT_SPEC, pkg.spec.short_spec)
+    env.set_env(SPACK_DEBUG_LOG_DIR, spack.spack_working_dir)
 
     # Add any pkgconfig directories to PKG_CONFIG_PATH
     pkg_config_dirs = []
@@ -173,8 +174,9 @@ def add_env_path(path):
             pcdir = join_path(p, libdir, 'pkgconfig')
             if os.path.isdir(pcdir):
                 pkg_config_dirs.append(pcdir)
-    path_set("PKG_CONFIG_PATH", pkg_config_dirs)
+    env.set_env('PKG_CONFIG_PATH', concatenate_paths(pkg_config_dirs))
 
+    return env
 
 def set_module_variables_for_package(pkg, m):
     """Populate the module scope of install() with some useful functions.
@@ -269,8 +271,8 @@ def setup_package(pkg):
     """Execute all environment setup routines."""
     env = EnvironmentModifications()
     env.extend(set_compiler_environment_variables(pkg))
+    env.extend(set_build_environment_variables(pkg))
     apply_environment_modifications(env)
-    set_build_environment_variables(pkg)
     # If a user makes their own package repo, e.g.
     # spack.repos.mystuff.libelf.Libelf, and they inherit from
     # an existing class like spack.repos.original.libelf.Libelf,
diff --git a/lib/spack/spack/environment.py b/lib/spack/spack/environment.py
index 3b73f1c7a2a..18fef1ef12c 100644
--- a/lib/spack/spack/environment.py
+++ b/lib/spack/spack/environment.py
@@ -146,6 +146,9 @@ def remove_path(self, name, path, **kwargs):
         self.env_modifications.append(item)
 
 
+def concatenate_paths(paths):
+    return ':'.join(str(item) for item in paths)
+
 def validate_environment_modifications(env):
     modifications = collections.defaultdict(list)
     for item in env:
diff --git a/var/spack/repos/builtin/packages/mvapich2/package.py b/var/spack/repos/builtin/packages/mvapich2/package.py
index af5ed1b0888..e4e95f92af7 100644
--- a/var/spack/repos/builtin/packages/mvapich2/package.py
+++ b/var/spack/repos/builtin/packages/mvapich2/package.py
@@ -123,7 +123,7 @@ def set_network_type(self, spec, configure_args):
                 count += 1
         if count > 1:
             raise RuntimeError('network variants are mutually exclusive (only one can be selected at a time)')
-
+        network_options = []
         # From here on I can suppose that only one variant has been selected
         if self.enabled(Mvapich2.PSM) in spec:
             network_options = ["--with-device=ch3:psm"]

From c85888eb5763d453af7b7255b6d8c3461082362f Mon Sep 17 00:00:00 2001
From: alalazo <massimiliano.culpo@googlemail.com>
Date: Tue, 15 Mar 2016 13:36:41 +0100
Subject: [PATCH 016/230] package : added `environment_modifications`

---
 lib/spack/spack/build_environment.py          |  7 +++---
 lib/spack/spack/package.py                    |  4 ++++
 .../repos/builtin/packages/mpich/package.py   | 16 +++++++++-----
 .../packages/netlib-scalapack/package.py      |  3 +--
 .../repos/builtin/packages/openmpi/package.py | 14 +++++++-----
 .../repos/builtin/packages/python/package.py  | 20 +++++++++--------
 .../repos/builtin/packages/qt/package.py      | 12 +++++-----
 .../repos/builtin/packages/ruby/package.py    | 22 +++++++++++--------
 8 files changed, 58 insertions(+), 40 deletions(-)

diff --git a/lib/spack/spack/build_environment.py b/lib/spack/spack/build_environment.py
index 770e191ac90..d321a0e495e 100644
--- a/lib/spack/spack/build_environment.py
+++ b/lib/spack/spack/build_environment.py
@@ -178,6 +178,7 @@ def set_build_environment_variables(pkg):
 
     return env
 
+
 def set_module_variables_for_package(pkg, m):
     """Populate the module scope of install() with some useful functions.
        This makes things easier for package writers.
@@ -272,7 +273,6 @@ def setup_package(pkg):
     env = EnvironmentModifications()
     env.extend(set_compiler_environment_variables(pkg))
     env.extend(set_build_environment_variables(pkg))
-    apply_environment_modifications(env)
     # If a user makes their own package repo, e.g.
     # spack.repos.mystuff.libelf.Libelf, and they inherit from
     # an existing class like spack.repos.original.libelf.Libelf,
@@ -284,8 +284,9 @@ def setup_package(pkg):
 
     # Allow dependencies to set up environment as well.
     for dep_spec in pkg.spec.traverse(root=False):
-        dep_spec.package.setup_dependent_environment(
-            pkg.module, dep_spec, pkg.spec)
+        env.extend(dep_spec.package.environment_modifications(pkg.module, dep_spec, pkg.spec))
+        dep_spec.package.setup_dependent_environment(pkg.module, dep_spec, pkg.spec)
+    apply_environment_modifications(env)
 
 
 def fork(pkg, function):
diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py
index 696adaf8965..224d7f8f4b9 100644
--- a/lib/spack/spack/package.py
+++ b/lib/spack/spack/package.py
@@ -63,6 +63,7 @@
 import spack.url
 import spack.util.web
 import spack.fetch_strategy as fs
+from spack.environment import EnvironmentModifications
 from spack.version import *
 from spack.stage import Stage, ResourceStage, StageComposite
 from spack.util.compression import allowed_archive, extension
@@ -983,6 +984,9 @@ def module(self):
                           fromlist=[self.__class__.__name__])
 
 
+    def environment_modifications(self, module, spec, dependent_spec):
+        return EnvironmentModifications()
+
     def setup_dependent_environment(self, module, spec, dependent_spec):
         """Called before the install() method of dependents.
 
diff --git a/var/spack/repos/builtin/packages/mpich/package.py b/var/spack/repos/builtin/packages/mpich/package.py
index e2b3654c19a..c85e8febf39 100644
--- a/var/spack/repos/builtin/packages/mpich/package.py
+++ b/var/spack/repos/builtin/packages/mpich/package.py
@@ -46,14 +46,18 @@ class Mpich(Package):
     provides('mpi@:3.0', when='@3:')
     provides('mpi@:1.3', when='@1:')
 
+    def environment_modifications(self, module, spec, dependent_spec):
+        env = super(Mpich, self).environment_modifications(module, spec, dependent_spec)
+        env.set_env('MPICH_CC', os.environ['CC'])
+        env.set_env('MPICH_CXX', os.environ['CXX'])
+        env.set_env('MPICH_F77', os.environ['F77'])
+        env.set_env('MPICH_F90', os.environ['FC'])
+        env.set_env('MPICH_FC', os.environ['FC'])
+        return env
+
     def setup_dependent_environment(self, module, spec, dep_spec):
         """For dependencies, make mpicc's use spack wrapper."""
-        os.environ['MPICH_CC']  = os.environ['CC']
-        os.environ['MPICH_CXX'] = os.environ['CXX']
-        os.environ['MPICH_F77'] = os.environ['F77']
-        os.environ['MPICH_F90'] = os.environ['FC']
-        os.environ['MPICH_FC'] = os.environ['FC']
-
+        # FIXME : is this necessary ? Shouldn't this be part of a contract with MPI providers?
         module.mpicc = join_path(self.prefix.bin, 'mpicc')
 
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/netlib-scalapack/package.py b/var/spack/repos/builtin/packages/netlib-scalapack/package.py
index 22d538560e8..6dbf3674756 100644
--- a/var/spack/repos/builtin/packages/netlib-scalapack/package.py
+++ b/var/spack/repos/builtin/packages/netlib-scalapack/package.py
@@ -46,5 +46,4 @@ def setup_dependent_environment(self, module, spec, dependent_spec):
 
         spec['scalapack'].fc_link = '-L%s -lscalapack' % spec['scalapack'].prefix.lib
         spec['scalapack'].cc_link = spec['scalapack'].fc_link
-        spec['scalapack'].libraries = [join_path(spec['scalapack'].prefix.lib,
-                                                 'libscalapack%s' % lib_suffix)]
+        spec['scalapack'].libraries = [join_path(spec['scalapack'].prefix.lib, 'libscalapack%s' % lib_suffix)]
diff --git a/var/spack/repos/builtin/packages/openmpi/package.py b/var/spack/repos/builtin/packages/openmpi/package.py
index e4484af8c5e..83a3fe7a4f3 100644
--- a/var/spack/repos/builtin/packages/openmpi/package.py
+++ b/var/spack/repos/builtin/packages/openmpi/package.py
@@ -41,12 +41,14 @@ class Openmpi(Package):
     def url_for_version(self, version):
         return "http://www.open-mpi.org/software/ompi/v%s/downloads/openmpi-%s.tar.bz2" % (version.up_to(2), version)
 
-    def setup_dependent_environment(self, module, spec, dep_spec):
-        """For dependencies, make mpicc's use spack wrapper."""
-        os.environ['OMPI_CC'] = 'cc'
-        os.environ['OMPI_CXX'] = 'c++'
-        os.environ['OMPI_FC'] = 'f90'
-        os.environ['OMPI_F77'] = 'f77'
+    def environment_modifications(self, module, spec, dependent_spec):
+        env = super(Openmpi, self).environment_modifications(module, spec, dependent_spec)
+        # FIXME : the compilers should point to the current wrappers, not to generic cc etc.
+        env.set_env('OMPI_CC', 'cc')
+        env.set_env('OMPI_CXX', 'c++')
+        env.set_env('OMPI_FC', 'f90')
+        env.set_env('OMPI_F77', 'f77')
+        return env
 
     def install(self, spec, prefix):
         config_args = ["--prefix=%s" % prefix,
diff --git a/var/spack/repos/builtin/packages/python/package.py b/var/spack/repos/builtin/packages/python/package.py
index dd240d1ea0a..39ced0a1200 100644
--- a/var/spack/repos/builtin/packages/python/package.py
+++ b/var/spack/repos/builtin/packages/python/package.py
@@ -90,6 +90,17 @@ def site_packages_dir(self):
         return os.path.join(self.python_lib_dir, 'site-packages')
 
 
+    def environment_modifications(self, module, spec, dependent_spec):
+        env = super(Python, self).environment_modifications(module, spec, dependent_spec)
+        # Set PYTHONPATH to include site-packages dir for the
+        # extension and any other python extensions it depends on.
+        python_paths = []
+        for d in ext_spec.traverse():
+            if d.package.extends(self.spec):
+                python_paths.append(os.path.join(d.prefix, self.site_packages_dir))
+        env.set_env['PYTHONPATH'] = ':'.join(python_paths)
+
+
     def setup_dependent_environment(self, module, spec, ext_spec):
         """Called before python modules' install() methods.
 
@@ -111,15 +122,6 @@ def setup_dependent_environment(self, module, spec, ext_spec):
         # Make the site packages directory if it does not exist already.
         mkdirp(module.site_packages_dir)
 
-        # Set PYTHONPATH to include site-packages dir for the
-        # extension and any other python extensions it depends on.
-        python_paths = []
-        for d in ext_spec.traverse():
-            if d.package.extends(self.spec):
-                python_paths.append(os.path.join(d.prefix, self.site_packages_dir))
-        os.environ['PYTHONPATH'] = ':'.join(python_paths)
-
-
     # ========================================================================
     # Handle specifics of activating and deactivating python modules.
     # ========================================================================
diff --git a/var/spack/repos/builtin/packages/qt/package.py b/var/spack/repos/builtin/packages/qt/package.py
index 91afa420c17..373623cd959 100644
--- a/var/spack/repos/builtin/packages/qt/package.py
+++ b/var/spack/repos/builtin/packages/qt/package.py
@@ -52,11 +52,13 @@ class Qt(Package):
     depends_on("mesa", when='@4:+mesa')
     depends_on("libxcb")
 
-
-    def setup_dependent_environment(self, module, spec, dep_spec):
-        """Dependencies of Qt find it using the QTDIR environment variable."""
-        os.environ['QTDIR'] = self.prefix
-
+    def environment_modifications(self, module, spec, dep_spec):
+        """
+        Dependencies of Qt find it using the QTDIR environment variable
+        """
+        env = super(Qt, self).environment_modifications(module, spec, dep_spec)
+        env.set_env['QTDIR'] = self.prefix
+        return env
 
     def patch(self):
         if self.spec.satisfies('@4'):
diff --git a/var/spack/repos/builtin/packages/ruby/package.py b/var/spack/repos/builtin/packages/ruby/package.py
index 6b6242362cd..9ec0afa2683 100644
--- a/var/spack/repos/builtin/packages/ruby/package.py
+++ b/var/spack/repos/builtin/packages/ruby/package.py
@@ -15,10 +15,21 @@ class Ruby(Package):
 
     def install(self, spec, prefix):
         configure("--prefix=%s" % prefix)
-
         make()
         make("install")
 
+    def environment_modifications(self, module, spec, ext_spec):
+        env = super(Ruby, self).environment_modifications(module, spec, ext_spec)
+        # Set GEM_PATH to include dependent gem directories
+        ruby_paths = []
+        for d in ext_spec.traverse():
+            if d.package.extends(self.spec):
+                ruby_paths.append(d.prefix)
+        env.set_env('GEM_PATH', concatenate_paths(ruby_paths))
+        # The actual installation path for this gem
+        env.set_env('GEM_HOME', ext_spec.prefix)
+        return env
+
     def setup_dependent_environment(self, module, spec, ext_spec):
         """Called before ruby modules' install() methods.  Sets GEM_HOME
         and GEM_PATH to values appropriate for the package being built.
@@ -31,11 +42,4 @@ def setup_dependent_environment(self, module, spec, ext_spec):
         module.ruby = Executable(join_path(spec.prefix.bin, 'ruby'))
         module.gem = Executable(join_path(spec.prefix.bin, 'gem'))
 
-        # Set GEM_PATH to include dependent gem directories
-        ruby_paths = []
-        for d in ext_spec.traverse():
-            if d.package.extends(self.spec):
-                ruby_paths.append(d.prefix)
-        os.environ['GEM_PATH'] = ':'.join(ruby_paths)
-        # The actual installation path for this gem
-        os.environ['GEM_HOME'] = ext_spec.prefix
+

From 572cb93bf8131d222d2d08bca13fd9de6fded1f4 Mon Sep 17 00:00:00 2001
From: alalazo <massimiliano.culpo@googlemail.com>
Date: Tue, 15 Mar 2016 14:05:30 +0100
Subject: [PATCH 017/230] package : renamed `setup_dependent_environment` to
 `module_modifications`

---
 lib/spack/spack/build_environment.py                |  4 ++--
 lib/spack/spack/package.py                          |  4 ++--
 var/spack/repos/builtin/packages/mpich/package.py   |  6 +++---
 .../builtin/packages/netlib-scalapack/package.py    |  2 +-
 var/spack/repos/builtin/packages/openmpi/package.py |  4 ++--
 var/spack/repos/builtin/packages/python/package.py  | 10 ++++------
 var/spack/repos/builtin/packages/qt/package.py      |  7 ++-----
 var/spack/repos/builtin/packages/ruby/package.py    | 13 ++++++-------
 8 files changed, 22 insertions(+), 28 deletions(-)

diff --git a/lib/spack/spack/build_environment.py b/lib/spack/spack/build_environment.py
index d321a0e495e..e86a7c413a9 100644
--- a/lib/spack/spack/build_environment.py
+++ b/lib/spack/spack/build_environment.py
@@ -284,8 +284,8 @@ def setup_package(pkg):
 
     # Allow dependencies to set up environment as well.
     for dep_spec in pkg.spec.traverse(root=False):
-        env.extend(dep_spec.package.environment_modifications(pkg.module, dep_spec, pkg.spec))
-        dep_spec.package.setup_dependent_environment(pkg.module, dep_spec, pkg.spec)
+        dep_spec.package.module_modifications(pkg.module, dep_spec, pkg.spec)
+        env.extend(dep_spec.package.environment_modifications(pkg.spec))
     apply_environment_modifications(env)
 
 
diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py
index 224d7f8f4b9..c1a5c912be7 100644
--- a/lib/spack/spack/package.py
+++ b/lib/spack/spack/package.py
@@ -984,10 +984,10 @@ def module(self):
                           fromlist=[self.__class__.__name__])
 
 
-    def environment_modifications(self, module, spec, dependent_spec):
+    def environment_modifications(self, dependent_spec):
         return EnvironmentModifications()
 
-    def setup_dependent_environment(self, module, spec, dependent_spec):
+    def module_modifications(self, module, spec, dependent_spec):
         """Called before the install() method of dependents.
 
         Default implementation does nothing, but this can be
diff --git a/var/spack/repos/builtin/packages/mpich/package.py b/var/spack/repos/builtin/packages/mpich/package.py
index c85e8febf39..d298981c925 100644
--- a/var/spack/repos/builtin/packages/mpich/package.py
+++ b/var/spack/repos/builtin/packages/mpich/package.py
@@ -46,8 +46,8 @@ class Mpich(Package):
     provides('mpi@:3.0', when='@3:')
     provides('mpi@:1.3', when='@1:')
 
-    def environment_modifications(self, module, spec, dependent_spec):
-        env = super(Mpich, self).environment_modifications(module, spec, dependent_spec)
+    def environment_modifications(self, dependent_spec):
+        env = super(Mpich, self).environment_modifications(dependent_spec)
         env.set_env('MPICH_CC', os.environ['CC'])
         env.set_env('MPICH_CXX', os.environ['CXX'])
         env.set_env('MPICH_F77', os.environ['F77'])
@@ -55,7 +55,7 @@ def environment_modifications(self, module, spec, dependent_spec):
         env.set_env('MPICH_FC', os.environ['FC'])
         return env
 
-    def setup_dependent_environment(self, module, spec, dep_spec):
+    def module_modifications(self, module, spec, dep_spec):
         """For dependencies, make mpicc's use spack wrapper."""
         # FIXME : is this necessary ? Shouldn't this be part of a contract with MPI providers?
         module.mpicc = join_path(self.prefix.bin, 'mpicc')
diff --git a/var/spack/repos/builtin/packages/netlib-scalapack/package.py b/var/spack/repos/builtin/packages/netlib-scalapack/package.py
index 6dbf3674756..ecdea464420 100644
--- a/var/spack/repos/builtin/packages/netlib-scalapack/package.py
+++ b/var/spack/repos/builtin/packages/netlib-scalapack/package.py
@@ -40,7 +40,7 @@ def install(self, spec, prefix):
             make()
             make("install")
 
-    def setup_dependent_environment(self, module, spec, dependent_spec):
+    def module_modifications(self, module, spec, dependent_spec):
         # TODO treat OS that are not Linux...
         lib_suffix = '.so' if '+shared' in spec['scalapack'] else '.a'
 
diff --git a/var/spack/repos/builtin/packages/openmpi/package.py b/var/spack/repos/builtin/packages/openmpi/package.py
index 83a3fe7a4f3..3a141704576 100644
--- a/var/spack/repos/builtin/packages/openmpi/package.py
+++ b/var/spack/repos/builtin/packages/openmpi/package.py
@@ -41,8 +41,8 @@ class Openmpi(Package):
     def url_for_version(self, version):
         return "http://www.open-mpi.org/software/ompi/v%s/downloads/openmpi-%s.tar.bz2" % (version.up_to(2), version)
 
-    def environment_modifications(self, module, spec, dependent_spec):
-        env = super(Openmpi, self).environment_modifications(module, spec, dependent_spec)
+    def environment_modifications(self, dependent_spec):
+        env = super(Openmpi, self).environment_modifications(dependent_spec)
         # FIXME : the compilers should point to the current wrappers, not to generic cc etc.
         env.set_env('OMPI_CC', 'cc')
         env.set_env('OMPI_CXX', 'c++')
diff --git a/var/spack/repos/builtin/packages/python/package.py b/var/spack/repos/builtin/packages/python/package.py
index 39ced0a1200..307cec726b6 100644
--- a/var/spack/repos/builtin/packages/python/package.py
+++ b/var/spack/repos/builtin/packages/python/package.py
@@ -89,19 +89,17 @@ def python_include_dir(self):
     def site_packages_dir(self):
         return os.path.join(self.python_lib_dir, 'site-packages')
 
-
-    def environment_modifications(self, module, spec, dependent_spec):
-        env = super(Python, self).environment_modifications(module, spec, dependent_spec)
+    def environment_modifications(self, extension_spec):
+        env = super(Python, self).environment_modifications(extension_spec)
         # Set PYTHONPATH to include site-packages dir for the
         # extension and any other python extensions it depends on.
         python_paths = []
-        for d in ext_spec.traverse():
+        for d in extension_spec.traverse():
             if d.package.extends(self.spec):
                 python_paths.append(os.path.join(d.prefix, self.site_packages_dir))
         env.set_env['PYTHONPATH'] = ':'.join(python_paths)
 
-
-    def setup_dependent_environment(self, module, spec, ext_spec):
+    def module_modifications(self, module, spec, ext_spec):
         """Called before python modules' install() methods.
 
         In most cases, extensions will only need to have one line::
diff --git a/var/spack/repos/builtin/packages/qt/package.py b/var/spack/repos/builtin/packages/qt/package.py
index 373623cd959..8391ded3e0b 100644
--- a/var/spack/repos/builtin/packages/qt/package.py
+++ b/var/spack/repos/builtin/packages/qt/package.py
@@ -52,11 +52,8 @@ class Qt(Package):
     depends_on("mesa", when='@4:+mesa')
     depends_on("libxcb")
 
-    def environment_modifications(self, module, spec, dep_spec):
-        """
-        Dependencies of Qt find it using the QTDIR environment variable
-        """
-        env = super(Qt, self).environment_modifications(module, spec, dep_spec)
+    def environment_modifications(self, dependent_spec):
+        env = super(Qt, self).environment_modifications(dependent_spec)
         env.set_env['QTDIR'] = self.prefix
         return env
 
diff --git a/var/spack/repos/builtin/packages/ruby/package.py b/var/spack/repos/builtin/packages/ruby/package.py
index 9ec0afa2683..9caea30ef46 100644
--- a/var/spack/repos/builtin/packages/ruby/package.py
+++ b/var/spack/repos/builtin/packages/ruby/package.py
@@ -1,6 +1,5 @@
 from spack import *
-import spack
-import os
+
 
 class Ruby(Package):
     """A dynamic, open source programming language with a focus on 
@@ -18,19 +17,19 @@ def install(self, spec, prefix):
         make()
         make("install")
 
-    def environment_modifications(self, module, spec, ext_spec):
-        env = super(Ruby, self).environment_modifications(module, spec, ext_spec)
+    def environment_modifications(self, extension_spec):
+        env = super(Ruby, self).environment_modifications(extension_spec)
         # Set GEM_PATH to include dependent gem directories
         ruby_paths = []
-        for d in ext_spec.traverse():
+        for d in extension_spec.traverse():
             if d.package.extends(self.spec):
                 ruby_paths.append(d.prefix)
         env.set_env('GEM_PATH', concatenate_paths(ruby_paths))
         # The actual installation path for this gem
-        env.set_env('GEM_HOME', ext_spec.prefix)
+        env.set_env('GEM_HOME', extension_spec.prefix)
         return env
 
-    def setup_dependent_environment(self, module, spec, ext_spec):
+    def module_modifications(self, module, spec, ext_spec):
         """Called before ruby modules' install() methods.  Sets GEM_HOME
         and GEM_PATH to values appropriate for the package being built.
 

From cc3d9f4eb751fe028db5a074fc7bc52fbe0a962a Mon Sep 17 00:00:00 2001
From: alalazo <massimiliano.culpo@googlemail.com>
Date: Tue, 15 Mar 2016 15:09:35 +0100
Subject: [PATCH 018/230] environment : added test, modified docs

---
 lib/spack/spack/environment.py      | 61 ++++++++++++++++++++---------
 lib/spack/spack/package.py          | 45 +++++++++++++--------
 lib/spack/spack/test/environment.py | 10 ++++-
 lib/spack/spack/util/environment.py |  8 +---
 4 files changed, 80 insertions(+), 44 deletions(-)

diff --git a/lib/spack/spack/environment.py b/lib/spack/spack/environment.py
index 18fef1ef12c..5a68e10c997 100644
--- a/lib/spack/spack/environment.py
+++ b/lib/spack/spack/environment.py
@@ -3,33 +3,40 @@
 import collections
 
 
-class SetEnv(object):
-    def __init__(self, name, value, **kwargs):
-        self.name = name
-        self.value = value
+class AttributeHolder(object):
+    """
+    Policy that permits to store any kind of attribute on self. The attributes must be passed as key/value pairs
+    during the initialization of the instance.
+    """
+    def __init__(self, **kwargs):
         for key, value in kwargs.items():
             setattr(self, key, value)
 
+
+class SetEnv(AttributeHolder):
+    def __init__(self, name, value, **kwargs):
+        super(SetEnv, self).__init__(**kwargs)
+        self.name = name
+        self.value = value
+
     def execute(self):
         os.environ[self.name] = str(self.value)
 
 
-class UnsetEnv(object):
+class UnsetEnv(AttributeHolder):
     def __init__(self, name, **kwargs):
+        super(UnsetEnv, self).__init__(**kwargs)
         self.name = name
-        for key, value in kwargs.items():
-            setattr(self, key, value)
 
     def execute(self):
         os.environ.pop(self.name, None)  # Avoid throwing if the variable was not set
 
 
-class AppendPath(object):
+class AppendPath(AttributeHolder):
     def __init__(self, name, path, **kwargs):
+        super(AppendPath, self).__init__(**kwargs)
         self.name = name
         self.path = path
-        for key, value in kwargs.items():
-            setattr(self, key, value)
 
     def execute(self):
         environment_value = os.environ.get(self.name, '')
@@ -39,12 +46,11 @@ def execute(self):
         os.environ[self.name] = ':'.join(directories)
 
 
-class PrependPath(object):
+class PrependPath(AttributeHolder):
     def __init__(self, name, path, **kwargs):
+        super(PrependPath, self).__init__(**kwargs)
         self.name = name
         self.path = path
-        for key, value in kwargs.items():
-            setattr(self, key, value)
 
     def execute(self):
         environment_value = os.environ.get(self.name, '')
@@ -54,12 +60,11 @@ def execute(self):
         os.environ[self.name] = ':'.join(directories)
 
 
-class RemovePath(object):
+class RemovePath(AttributeHolder):
     def __init__(self, name, path, **kwargs):
+        super(RemovePath, self).__init__(**kwargs)
         self.name = name
         self.path = path
-        for key, value in kwargs.items():
-            setattr(self, key, value)
 
     def execute(self):
         environment_value = os.environ.get(self.name, '')
@@ -70,18 +75,26 @@ def execute(self):
 
 class EnvironmentModifications(object):
     """
-    Keeps track of requests to modify the current environment
+    Keeps track of requests to modify the current environment.
     """
 
     def __init__(self, other=None):
+        """
+        Initializes a new instance, copying commands from other if it is not None
+
+        Args:
+            other: another instance of EnvironmentModifications from which (optional)
+        """
         self.env_modifications = []
         if other is not None:
-            self._check_other(other)
-            self.env_modifications.extend(other.env_modifications)
+            self.extend(other)
 
     def __iter__(self):
         return iter(self.env_modifications)
 
+    def __len__(self):
+        return len(self.env_modifications)
+
     def extend(self, other):
         self._check_other(other)
         self.env_modifications.extend(other.env_modifications)
@@ -147,8 +160,18 @@ def remove_path(self, name, path, **kwargs):
 
 
 def concatenate_paths(paths):
+    """
+    Concatenates an iterable of paths into a column separated string
+
+    Args:
+        paths: iterable of paths
+
+    Returns:
+        column separated string
+    """
     return ':'.join(str(item) for item in paths)
 
+
 def validate_environment_modifications(env):
     modifications = collections.defaultdict(list)
     for item in env:
diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py
index c1a5c912be7..5d8258d4cf0 100644
--- a/lib/spack/spack/package.py
+++ b/lib/spack/spack/package.py
@@ -985,30 +985,41 @@ def module(self):
 
 
     def environment_modifications(self, dependent_spec):
+        """
+        Called before the install() method of dependents.
+
+        Return the list of environment modifications needed by dependents (or extensions). Default implementation does
+        nothing, but this can be overridden by an extendable package to set up the install environment for its
+        extensions. This is useful if there are some common steps to installing all extensions for a certain package.
+
+        Example :
+
+        1. Installing python modules generally requires `PYTHONPATH` to point to the lib/pythonX.Y/site-packages
+        directory in the module's install prefix.  This could set that variable.
+
+        2. A lot of Qt extensions need `QTDIR` set.  This can be used to do that.
+
+        Args:
+            dependent_spec: dependent (or extension) of this spec
+
+        Returns:
+            instance of environment modifications
+        """
         return EnvironmentModifications()
 
     def module_modifications(self, module, spec, dependent_spec):
-        """Called before the install() method of dependents.
+        """
+        Called before the install() method of dependents.
 
-        Default implementation does nothing, but this can be
-        overridden by an extendable package to set up the install
-        environment for its extensions.  This is useful if there are
-        some common steps to installing all extensions for a
+        Default implementation does nothing, but this can be overridden by an extendable package to set up the module of
+        its extensions. This is useful if there are some common steps to installing all extensions for a
         certain package.
 
-        Some examples:
-
-        1. Installing python modules generally requires PYTHONPATH to
-           point to the lib/pythonX.Y/site-packages directory in the
-           module's install prefix.  This could set that variable.
-
-        2. Extensions often need to invoke the 'python' interpreter
-           from the Python installation being extended.  This routine can
-           put a 'python' Execuable object in the module scope for the
-           extension package to simplify extension installs.
-
-        3. A lot of Qt extensions need QTDIR set.  This can be used to do that.
+        Example :
 
+        1. Extensions often need to invoke the 'python' interpreter from the Python installation being extended.
+        This routine can put a 'python' Executable object in the module scope for the extension package to simplify
+        extension installs.
         """
         pass
 
diff --git a/lib/spack/spack/test/environment.py b/lib/spack/spack/test/environment.py
index 17061c8fd0e..97581ecb76a 100644
--- a/lib/spack/spack/test/environment.py
+++ b/lib/spack/spack/test/environment.py
@@ -55,5 +55,11 @@ def test_extra_arguments(self):
         apply_environment_modifications(env)
         self.assertEqual('dummy value', os.environ['A'])
 
-    def test_copy(self):
-        pass
+    def test_extend(self):
+        env = EnvironmentModifications()
+        env.set_env('A', 'dummy value')
+        env.set_env('B', 3)
+        copy_construct = EnvironmentModifications(env)
+        self.assertEqual(len(copy_construct), 2)
+        for x, y in zip(env, copy_construct):
+            self.assertIs(x, y)
diff --git a/lib/spack/spack/util/environment.py b/lib/spack/spack/util/environment.py
index ae8e5708bef..00cda8d5084 100644
--- a/lib/spack/spack/util/environment.py
+++ b/lib/spack/spack/util/environment.py
@@ -40,11 +40,13 @@ def env_flag(name):
     return False
 
 
+# FIXME : remove this function ?
 def path_set(var_name, directories):
     path_str = ":".join(str(dir) for dir in directories)
     os.environ[var_name] = path_str
 
 
+# FIXME : remove this function ?
 def path_put_first(var_name, directories):
     """Puts the provided directories first in the path, adding them
        if they're not already there.
@@ -59,12 +61,6 @@ def path_put_first(var_name, directories):
     path_set(var_name, new_path)
 
 
-def pop_keys(dictionary, *keys):
-    for key in keys:
-        if key in dictionary:
-            dictionary.pop(key)
-
-
 def dump_environment(path):
     """Dump the current environment out to a file."""
     with open(path, 'w') as env_file:

From ccced9f290bc213561209db2479bccfb5605366d Mon Sep 17 00:00:00 2001
From: alalazo <massimiliano.culpo@googlemail.com>
Date: Tue, 15 Mar 2016 15:12:39 +0100
Subject: [PATCH 019/230] package : optimized imports

---
 lib/spack/spack/package.py | 41 ++++++++++++++++----------------------
 1 file changed, 17 insertions(+), 24 deletions(-)

diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py
index 5d8258d4cf0..042833964ac 100644
--- a/lib/spack/spack/package.py
+++ b/lib/spack/spack/package.py
@@ -34,41 +34,34 @@
 README.
 """
 import os
-import errno
 import re
-import shutil
-import time
-import itertools
-import subprocess
-import platform as py_platform
-import multiprocessing
-from urlparse import urlparse, urljoin
 import textwrap
-from StringIO import StringIO
+import time
 
 import llnl.util.tty as tty
-from llnl.util.tty.log import log_output
-from llnl.util.link_tree import LinkTree
-from llnl.util.filesystem import *
-from llnl.util.lang import *
-
 import spack
-import spack.error
-import spack.compilers
-import spack.mirror
-import spack.hooks
-import spack.directives
-import spack.repository
 import spack.build_environment
+import spack.compilers
+import spack.directives
+import spack.error
+import spack.fetch_strategy as fs
+import spack.hooks
+import spack.mirror
+import spack.repository
 import spack.url
 import spack.util.web
-import spack.fetch_strategy as fs
+from StringIO import StringIO
+from llnl.util.filesystem import *
+from llnl.util.lang import *
+from llnl.util.link_tree import LinkTree
+from llnl.util.tty.log import log_output
 from spack.environment import EnvironmentModifications
-from spack.version import *
 from spack.stage import Stage, ResourceStage, StageComposite
-from spack.util.compression import allowed_archive, extension
-from spack.util.executable import ProcessError
+from spack.util.compression import allowed_archive
 from spack.util.environment import dump_environment
+from spack.util.executable import ProcessError
+from spack.version import *
+from urlparse import urlparse
 
 """Allowed URL schemes for spack packages."""
 _ALLOWED_URL_SCHEMES = ["http", "https", "ftp", "file", "git"]

From c8cc6f4fc111d5dd2d55295e569a10cd5739ceee Mon Sep 17 00:00:00 2001
From: alalazo <massimiliano.culpo@googlemail.com>
Date: Tue, 15 Mar 2016 16:59:29 +0100
Subject: [PATCH 020/230] test : fix for python 2.6

---
 lib/spack/spack/test/environment.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/spack/spack/test/environment.py b/lib/spack/spack/test/environment.py
index 97581ecb76a..f44282d6f39 100644
--- a/lib/spack/spack/test/environment.py
+++ b/lib/spack/spack/test/environment.py
@@ -62,4 +62,4 @@ def test_extend(self):
         copy_construct = EnvironmentModifications(env)
         self.assertEqual(len(copy_construct), 2)
         for x, y in zip(env, copy_construct):
-            self.assertIs(x, y)
+            assert x is y

From b45ec3f04e3627dbe3633239560873ae01bf3beb Mon Sep 17 00:00:00 2001
From: alalazo <massimiliano.culpo@googlemail.com>
Date: Wed, 16 Mar 2016 10:55:28 +0100
Subject: [PATCH 021/230] environment : simplified modification of the
 environment

---
 lib/spack/spack/build_environment.py          | 12 ++--
 lib/spack/spack/cmd/module.py                 |  2 +-
 lib/spack/spack/environment.py                | 58 ++++++++++---------
 lib/spack/spack/test/environment.py           | 12 ++--
 lib/spack/spack/util/environment.py           |  2 +-
 .../repos/builtin/packages/python/package.py  |  1 +
 6 files changed, 47 insertions(+), 40 deletions(-)

diff --git a/lib/spack/spack/build_environment.py b/lib/spack/spack/build_environment.py
index e86a7c413a9..e5d256a2e01 100644
--- a/lib/spack/spack/build_environment.py
+++ b/lib/spack/spack/build_environment.py
@@ -35,7 +35,7 @@
 
 import spack
 from llnl.util.filesystem import *
-from spack.environment import EnvironmentModifications, apply_environment_modifications, concatenate_paths
+from spack.environment import EnvironmentModifications, concatenate_paths
 from spack.util.environment import *
 from spack.util.executable import Executable, which
 
@@ -283,10 +283,12 @@ def setup_package(pkg):
         set_module_variables_for_package(pkg, mod)
 
     # Allow dependencies to set up environment as well.
-    for dep_spec in pkg.spec.traverse(root=False):
-        dep_spec.package.module_modifications(pkg.module, dep_spec, pkg.spec)
-        env.extend(dep_spec.package.environment_modifications(pkg.spec))
-    apply_environment_modifications(env)
+    for dependency_spec in pkg.spec.traverse(root=False):
+        dependency_spec.package.module_modifications(pkg.module, dependency_spec, pkg.spec)
+        env.extend(dependency_spec.package.environment_modifications(pkg.spec))
+    # TODO : implement validation
+    #validate(env)
+    env.apply_modifications()
 
 
 def fork(pkg, function):
diff --git a/lib/spack/spack/cmd/module.py b/lib/spack/spack/cmd/module.py
index 1d6867c1d96..315d9fc9266 100644
--- a/lib/spack/spack/cmd/module.py
+++ b/lib/spack/spack/cmd/module.py
@@ -80,7 +80,7 @@ def module_find(mtype, spec_array):
     if not os.path.isfile(mod.file_name):
         tty.die("No %s module is installed for %s" % (mtype, spec))
 
-    print mod.use_name
+    print(mod.use_name)
 
 
 def module_refresh():
diff --git a/lib/spack/spack/environment.py b/lib/spack/spack/environment.py
index 5a68e10c997..b557bf0bbcf 100644
--- a/lib/spack/spack/environment.py
+++ b/lib/spack/spack/environment.py
@@ -158,41 +158,43 @@ def remove_path(self, name, path, **kwargs):
         item = RemovePath(name, path, **kwargs)
         self.env_modifications.append(item)
 
+    def group_by_name(self):
+        """
+        Returns a dict of the modifications grouped by variable name
+
+        Returns:
+            dict mapping the environment variable name to the modifications to be done on it
+        """
+        modifications = collections.defaultdict(list)
+        for item in self:
+            modifications[item.name].append(item)
+        return modifications
+
+    def clear(self):
+        """
+        Clears the current list of modifications
+        """
+        self.env_modifications.clear()
+
+    def apply_modifications(self):
+        """
+        Applies the modifications and clears the list
+        """
+        modifications = self.group_by_name()
+        # Apply the modifications to the environment variables one variable at a time
+        for name, actions in sorted(modifications.items()):
+            for x in actions:
+                x.execute()
+
 
 def concatenate_paths(paths):
     """
-    Concatenates an iterable of paths into a column separated string
+    Concatenates an iterable of paths into a  string of column separated paths
 
     Args:
         paths: iterable of paths
 
     Returns:
-        column separated string
+        string
     """
     return ':'.join(str(item) for item in paths)
-
-
-def validate_environment_modifications(env):
-    modifications = collections.defaultdict(list)
-    for item in env:
-        modifications[item.name].append(item)
-    # TODO : once we organized the modifications into a dictionary that maps an environment variable
-    # TODO : to a list of action to be done on it, we may easily spot inconsistencies and warn the user if
-    # TODO : something suspicious is happening
-    return modifications
-
-
-def apply_environment_modifications(env):
-    """
-    Modifies the current environment according to the request in env
-
-    Args:
-        env: object storing modifications to the environment
-    """
-    modifications = validate_environment_modifications(env)
-
-    # Cycle over the environment variables that will be modified
-    for variable, actions in modifications.items():
-        # Execute all the actions in the order they were issued
-        for x in actions:
-            x.execute()
diff --git a/lib/spack/spack/test/environment.py b/lib/spack/spack/test/environment.py
index f44282d6f39..d0b093b0543 100644
--- a/lib/spack/spack/test/environment.py
+++ b/lib/spack/spack/test/environment.py
@@ -1,6 +1,6 @@
 import unittest
 import os
-from spack.environment import EnvironmentModifications, apply_environment_modifications
+from spack.environment import EnvironmentModifications
 
 
 class EnvironmentTest(unittest.TestCase):
@@ -15,7 +15,7 @@ def test_set_env(self):
         env = EnvironmentModifications()
         env.set_env('A', 'dummy value')
         env.set_env('B', 3)
-        apply_environment_modifications(env)
+        env.apply_modifications()
         self.assertEqual('dummy value', os.environ['A'])
         self.assertEqual(str(3), os.environ['B'])
 
@@ -23,7 +23,7 @@ def test_unset_env(self):
         env = EnvironmentModifications()
         self.assertEqual('foo', os.environ['UNSET_ME'])
         env.unset_env('UNSET_ME')
-        apply_environment_modifications(env)
+        env.apply_modifications()
         self.assertRaises(KeyError, os.environ.__getitem__, 'UNSET_ME')
 
     def test_path_manipulation(self):
@@ -43,7 +43,7 @@ def test_path_manipulation(self):
         env.remove_path('REMOVE_PATH_LIST', '/remove/this')
         env.remove_path('REMOVE_PATH_LIST', '/duplicate/')
 
-        apply_environment_modifications(env)
+        env.apply_modifications()
         self.assertEqual('/path/first:/path/second:/path/third:/path/last', os.environ['PATH_LIST'])
         self.assertEqual('/path/first:/path/middle:/path/last', os.environ['EMPTY_PATH_LIST'])
         self.assertEqual('/path/first:/path/middle:/path/last', os.environ['NEWLY_CREATED_PATH_LIST'])
@@ -52,7 +52,9 @@ def test_path_manipulation(self):
     def test_extra_arguments(self):
         env = EnvironmentModifications()
         env.set_env('A', 'dummy value', who='Pkg1')
-        apply_environment_modifications(env)
+        for x in env:
+            assert hasattr(x, 'who')
+        env.apply_modifications()
         self.assertEqual('dummy value', os.environ['A'])
 
     def test_extend(self):
diff --git a/lib/spack/spack/util/environment.py b/lib/spack/spack/util/environment.py
index 00cda8d5084..1485992b0f1 100644
--- a/lib/spack/spack/util/environment.py
+++ b/lib/spack/spack/util/environment.py
@@ -64,5 +64,5 @@ def path_put_first(var_name, directories):
 def dump_environment(path):
     """Dump the current environment out to a file."""
     with open(path, 'w') as env_file:
-        for key,val in sorted(os.environ.items()):
+        for key, val in sorted(os.environ.items()):
             env_file.write("%s=%s\n" % (key, val))
diff --git a/var/spack/repos/builtin/packages/python/package.py b/var/spack/repos/builtin/packages/python/package.py
index 307cec726b6..2f9948d451c 100644
--- a/var/spack/repos/builtin/packages/python/package.py
+++ b/var/spack/repos/builtin/packages/python/package.py
@@ -98,6 +98,7 @@ def environment_modifications(self, extension_spec):
             if d.package.extends(self.spec):
                 python_paths.append(os.path.join(d.prefix, self.site_packages_dir))
         env.set_env['PYTHONPATH'] = ':'.join(python_paths)
+        return env
 
     def module_modifications(self, module, spec, ext_spec):
         """Called before python modules' install() methods.

From 597727f8bedc894330dfd26eab1a82859980f2f1 Mon Sep 17 00:00:00 2001
From: alalazo <massimiliano.culpo@googlemail.com>
Date: Wed, 16 Mar 2016 15:19:13 +0100
Subject: [PATCH 022/230] tclmodules : added hooks to process
 EnvironmentModifications objects

---
 lib/spack/spack/modules.py                    | 143 +++++++++++++-----
 .../repos/builtin/packages/mpich/package.py   |  25 ++-
 .../repos/builtin/packages/python/package.py  |  15 +-
 3 files changed, 133 insertions(+), 50 deletions(-)

diff --git a/lib/spack/spack/modules.py b/lib/spack/spack/modules.py
index c27043db8cd..1a0a0fd4d61 100644
--- a/lib/spack/spack/modules.py
+++ b/lib/spack/spack/modules.py
@@ -47,18 +47,18 @@
 __all__ = ['EnvModule', 'Dotkit', 'TclModule']
 
 import os
+import os.path
 import re
-import textwrap
 import shutil
+import textwrap
 from glob import glob
 
 import llnl.util.tty as tty
+import spack
+from spack.environment import *
 from llnl.util.filesystem import join_path, mkdirp
 
-import spack
-
-"""Registry of all types of modules.  Entries created by EnvModule's
-   metaclass."""
+# Registry of all types of modules.  Entries created by EnvModule's metaclass
 module_types = {}
 
 
@@ -79,6 +79,32 @@ def print_help():
             "")
 
 
+class PathInspector(object):
+    dirname2varname = {
+        'bin': ('PATH',),
+        'man': ('MANPATH',),
+        'lib': ('LIBRARY_PATH', 'LD_LIBRARY_PATH'),
+        'lib64': ('LIBRARY_PATH', 'LD_LIBRARY_PATH'),
+        'include': ('CPATH',),
+        'pkgconfig': ('PKG_CONFIG_PATH',)
+    }
+
+    def __call__(self, env, directory, names):
+        for name in names:
+            variables = PathInspector.dirname2varname.get(name, None)
+            if variables is None:
+                continue
+            absolute_path = join_path(os.path.abspath(directory), name)
+            for variable in variables:
+                env.prepend_path(variable, absolute_path)
+
+
+def inspect_path(path):
+    env, inspector = EnvironmentModifications(), PathInspector()
+    os.path.walk(path, inspector, env)
+    return env
+
+
 class EnvModule(object):
     name = 'env_module'
 
@@ -88,21 +114,27 @@ def __init__(cls, name, bases, dict):
             if cls.name != 'env_module':
                 module_types[cls.name] = cls
 
-
     def __init__(self, spec=None):
         # category in the modules system
         # TODO: come up with smarter category names.
         self.category = "spack"
 
-        # Descriptions for the module system's UI
-        self.short_description = ""
-        self.long_description = ""
-
         # dict pathname -> list of directories to be prepended to in
         # the module file.
         self._paths = None
         self.spec = spec
+        self.pkg = spec.package  # Just stored for convenience
 
+        # short description default is just the package + version
+        # packages can provide this optional attribute
+        self.short_description = spec.format("$_ $@")
+        if hasattr(self.pkg, 'short_description'):
+            self.short_description = self.pkg.short_description
+
+        # long description is the docstring with reduced whitespace.
+        self.long_description = None
+        if self.spec.package.__doc__:
+            self.long_description = re.sub(r'\s+', ' ', self.spec.package.__doc__)
 
     @property
     def paths(self):
@@ -130,26 +162,19 @@ def add_path(path_name, directory):
                     add_path(var, directory)
 
             # Add python path unless it's an actual python installation
-            # TODO: is there a better way to do this?
+            # TODO : is there a better way to do this?
+            # FIXME : add PYTHONPATH to every python package
             if self.spec.name != 'python':
                 site_packages = glob(join_path(self.spec.prefix.lib, "python*/site-packages"))
                 if site_packages:
                     add_path('PYTHONPATH', site_packages[0])
 
+            # FIXME : Same for GEM_PATH
             if self.spec.package.extends(spack.spec.Spec('ruby')):
-              add_path('GEM_PATH', self.spec.prefix)
-
-            # short description is just the package + version
-            # TODO: maybe packages can optionally provide it.
-            self.short_description = self.spec.format("$_ $@")
-
-            # long description is the docstring with reduced whitespace.
-            if self.spec.package.__doc__:
-                self.long_description = re.sub(r'\s+', ' ', self.spec.package.__doc__)
+                add_path('GEM_PATH', self.spec.prefix)
 
         return self._paths
 
-
     def write(self):
         """Write out a module file for this object."""
         module_dir = os.path.dirname(self.file_name)
@@ -160,9 +185,18 @@ def write(self):
         if not self.paths:
             return
 
-        with open(self.file_name, 'w') as f:
-            self._write(f)
+        # Construct the changes that needs to be done on the environment for
+        env = inspect_path(self.spec.prefix)
+        # FIXME : move the logic to inspection
+        env.prepend_path('CMAKE_PREFIX_PATH', self.spec.prefix)
+        # FIXME : decide how to distinguish between calls done in the installation and elsewhere
+        env.extend(self.spec.package.environment_modifications(None))
+        # site_specific = ...`
+        if not env:
+            return
 
+        with open(self.file_name, 'w') as f:
+            self._write(f, env)
 
     def _write(self, stream):
         """To be implemented by subclasses."""
@@ -175,14 +209,12 @@ def file_name(self):
            where this module lives."""
         raise NotImplementedError()
 
-
     @property
     def use_name(self):
         """Subclasses should implement this to return the name the
            module command uses to refer to the package."""
         raise NotImplementedError()
 
-
     def remove(self):
         mod_file = self.file_name
         if os.path.exists(mod_file):
@@ -205,7 +237,7 @@ def use_name(self):
                                  self.spec.compiler.version, 
                                  self.spec.dag_hash())
 
-    def _write(self, dk_file):
+    def _write(self, dk_file, env):
         # Category
         if self.category:
             dk_file.write('#c %s\n' % self.category)
@@ -231,6 +263,10 @@ def _write(self, dk_file):
 class TclModule(EnvModule):
     name = 'tcl'
     path = join_path(spack.share_path, "modules")
+    formats = {
+        PrependPath: 'prepend-path {0.name} \"{0.path}\"\n',
+        SetEnv: 'setenv {0.name} \"{0.value}\"\n'
+    }
 
     @property
     def file_name(self):
@@ -244,25 +280,56 @@ def use_name(self):
                                  self.spec.compiler.version, 
                                  self.spec.dag_hash())
 
+    def process_environment_command(self, env):
+        for command in env:
+            # FIXME : how should we handle errors here?
+            yield self.formats[type(command)].format(command)
 
-    def _write(self, m_file):
-        # TODO: cateogry?
-        m_file.write('#%Module1.0\n')
+    def _write(self, module_file, env):
+        """
+        Writes a TCL module file for this package
 
+        Args:
+            module_file: module file stream
+            env: list of environment modifications to be written in the module file
+        """
+        # TCL Modulefile header
+        module_file.write('#%Module1.0\n')
+        # TODO : category ?
         # Short description
         if self.short_description:
-            m_file.write('module-whatis \"%s\"\n\n' % self.short_description)
+            module_file.write('module-whatis \"%s\"\n\n' % self.short_description)
 
         # Long description
         if self.long_description:
-            m_file.write('proc ModulesHelp { } {\n')
+            module_file.write('proc ModulesHelp { } {\n')
             doc = re.sub(r'"', '\"', self.long_description)
-            m_file.write("puts stderr \"%s\"\n" % doc)
-            m_file.write('}\n\n')
+            module_file.write("puts stderr \"%s\"\n" % doc)
+            module_file.write('}\n\n')
 
-        # Path alterations
-        for var, dirs in self.paths.items():
-            for directory in dirs:
-                m_file.write("prepend-path %s \"%s\"\n" % (var, directory))
+        # Environment modifications
+        for line in self.process_environment_command(env):
+            module_file.write(line)
 
-        m_file.write("prepend-path CMAKE_PREFIX_PATH \"%s\"\n" % self.spec.prefix)
+    # FIXME : REMOVE
+    # def _write(self, m_file):
+    #     # TODO: cateogry?
+    #     m_file.write('#%Module1.0\n')
+    #
+    #     # Short description
+    #     if self.short_description:
+    #         m_file.write('module-whatis \"%s\"\n\n' % self.short_description)
+    #
+    #     # Long description
+    #     if self.long_description:
+    #         m_file.write('proc ModulesHelp { } {\n')
+    #         doc = re.sub(r'"', '\"', self.long_description)
+    #         m_file.write("puts stderr \"%s\"\n" % doc)
+    #         m_file.write('}\n\n')
+    #
+    #     # Path alterations
+    #     for var, dirs in self.paths.items():
+    #         for directory in dirs:
+    #             m_file.write("prepend-path %s \"%s\"\n" % (var, directory))
+    #
+    #     m_file.write("prepend-path CMAKE_PREFIX_PATH \"%s\"\n" % self.spec.prefix)
diff --git a/var/spack/repos/builtin/packages/mpich/package.py b/var/spack/repos/builtin/packages/mpich/package.py
index d298981c925..4c34d0308f5 100644
--- a/var/spack/repos/builtin/packages/mpich/package.py
+++ b/var/spack/repos/builtin/packages/mpich/package.py
@@ -25,6 +25,7 @@
 from spack import *
 import os
 
+
 class Mpich(Package):
     """MPICH is a high performance and widely portable implementation of
        the Message Passing Interface (MPI) standard."""
@@ -48,11 +49,25 @@ class Mpich(Package):
 
     def environment_modifications(self, dependent_spec):
         env = super(Mpich, self).environment_modifications(dependent_spec)
-        env.set_env('MPICH_CC', os.environ['CC'])
-        env.set_env('MPICH_CXX', os.environ['CXX'])
-        env.set_env('MPICH_F77', os.environ['F77'])
-        env.set_env('MPICH_F90', os.environ['FC'])
-        env.set_env('MPICH_FC', os.environ['FC'])
+
+        if dependent_spec is None:
+            # We are not using compiler wrappers
+            cc = self.compiler.cc
+            cxx = self.compiler.cxx
+            f77 = self.compiler.f77
+            f90 = fc = self.compiler.fc
+        else:
+            # Spack compiler wrappers
+            cc = os.environ['CC']
+            cxx = os.environ['CXX']
+            f77 = os.environ['F77']
+            f90 = fc = os.environ['FC']
+
+        env.set_env('MPICH_CC', cc)
+        env.set_env('MPICH_CXX', cxx)
+        env.set_env('MPICH_F77', f77)
+        env.set_env('MPICH_F90', f90)
+        env.set_env('MPICH_FC', fc)
         return env
 
     def module_modifications(self, module, spec, dep_spec):
diff --git a/var/spack/repos/builtin/packages/python/package.py b/var/spack/repos/builtin/packages/python/package.py
index 2f9948d451c..acb36517268 100644
--- a/var/spack/repos/builtin/packages/python/package.py
+++ b/var/spack/repos/builtin/packages/python/package.py
@@ -91,13 +91,14 @@ def site_packages_dir(self):
 
     def environment_modifications(self, extension_spec):
         env = super(Python, self).environment_modifications(extension_spec)
-        # Set PYTHONPATH to include site-packages dir for the
-        # extension and any other python extensions it depends on.
-        python_paths = []
-        for d in extension_spec.traverse():
-            if d.package.extends(self.spec):
-                python_paths.append(os.path.join(d.prefix, self.site_packages_dir))
-        env.set_env['PYTHONPATH'] = ':'.join(python_paths)
+        if extension_spec is not None:
+            # Set PYTHONPATH to include site-packages dir for the
+            # extension and any other python extensions it depends on.
+            python_paths = []
+            for d in extension_spec.traverse():
+                if d.package.extends(self.spec):
+                    python_paths.append(os.path.join(d.prefix, self.site_packages_dir))
+            env.set_env['PYTHONPATH'] = ':'.join(python_paths)
         return env
 
     def module_modifications(self, module, spec, ext_spec):

From ac762e95a6213e1514f29d3d6501e4a95dd3e1d4 Mon Sep 17 00:00:00 2001
From: alalazo <massimiliano.culpo@googlemail.com>
Date: Wed, 16 Mar 2016 16:23:02 +0100
Subject: [PATCH 023/230] modules : removed dead code

---
 lib/spack/spack/modules.py | 205 ++++++++++++-------------------------
 1 file changed, 66 insertions(+), 139 deletions(-)

diff --git a/lib/spack/spack/modules.py b/lib/spack/spack/modules.py
index 1a0a0fd4d61..b64a8b32266 100644
--- a/lib/spack/spack/modules.py
+++ b/lib/spack/spack/modules.py
@@ -22,14 +22,12 @@
 # along with this program; if not, write to the Free Software Foundation,
 # Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
-"""This module contains code for creating environment modules, which
-can include dotkits, tcl modules, lmod, and others.
+"""
+This module contains code for creating environment modules, which can include dotkits, tcl modules, lmod, and others.
 
-The various types of modules are installed by post-install hooks and
-removed after an uninstall by post-uninstall hooks.  This class
-consolidates the logic for creating an abstract description of the
-information that module systems need.  Currently that includes a
-number of directories to be appended to paths in the user's environment:
+The various types of modules are installed by post-install hooks and removed after an uninstall by post-uninstall hooks.
+This class consolidates the logic for creating an abstract description of the information that module systems need.
+Currently that includes a number of directories to be appended to paths in the user's environment:
 
   * /bin directories to be appended to PATH
   * /lib* directories for LD_LIBRARY_PATH
@@ -37,26 +35,23 @@
   * /man* and /share/man* directories for MANPATH
   * the package prefix for CMAKE_PREFIX_PATH
 
-This module also includes logic for coming up with unique names for
-the module files so that they can be found by the various
-shell-support files in $SPACK/share/spack/setup-env.*.
+This module also includes logic for coming up with unique names for the module files so that they can be found by the
+various shell-support files in $SPACK/share/spack/setup-env.*.
 
-Each hook in hooks/ implements the logic for writing its specific type
-of module file.
+Each hook in hooks/ implements the logic for writing its specific type of module file.
 """
-__all__ = ['EnvModule', 'Dotkit', 'TclModule']
-
 import os
 import os.path
 import re
 import shutil
 import textwrap
-from glob import glob
 
 import llnl.util.tty as tty
 import spack
-from spack.environment import *
 from llnl.util.filesystem import join_path, mkdirp
+from spack.environment import *
+
+__all__ = ['EnvModule', 'Dotkit', 'TclModule']
 
 # Registry of all types of modules.  Entries created by EnvModule's metaclass
 module_types = {}
@@ -79,34 +74,35 @@ def print_help():
             "")
 
 
-class PathInspector(object):
-    dirname2varname = {
-        'bin': ('PATH',),
-        'man': ('MANPATH',),
-        'lib': ('LIBRARY_PATH', 'LD_LIBRARY_PATH'),
-        'lib64': ('LIBRARY_PATH', 'LD_LIBRARY_PATH'),
-        'include': ('CPATH',),
-        'pkgconfig': ('PKG_CONFIG_PATH',)
-    }
-
-    def __call__(self, env, directory, names):
-        for name in names:
-            variables = PathInspector.dirname2varname.get(name, None)
-            if variables is None:
-                continue
-            absolute_path = join_path(os.path.abspath(directory), name)
-            for variable in variables:
-                env.prepend_path(variable, absolute_path)
-
-
 def inspect_path(path):
+    class PathInspector(object):
+        dirname2varname = {
+            'bin': ('PATH',),
+            'man': ('MANPATH',),
+            'lib': ('LIBRARY_PATH', 'LD_LIBRARY_PATH'),
+            'lib64': ('LIBRARY_PATH', 'LD_LIBRARY_PATH'),
+            'include': ('CPATH',),
+            'pkgconfig': ('PKG_CONFIG_PATH',)
+        }
+
+        def __call__(self, env, directory, names):
+            for name in names:
+                variables = PathInspector.dirname2varname.get(name, None)
+                if variables is None:
+                    continue
+                absolute_path = join_path(os.path.abspath(directory), name)
+                for variable in variables:
+                    env.prepend_path(variable, absolute_path)
+
     env, inspector = EnvironmentModifications(), PathInspector()
     os.path.walk(path, inspector, env)
+    env.prepend_path('CMAKE_PREFIX_PATH', path)
     return env
 
 
 class EnvModule(object):
     name = 'env_module'
+    formats = {}
 
     class __metaclass__(type):
         def __init__(cls, name, bases, dict):
@@ -119,9 +115,6 @@ def __init__(self, spec=None):
         # TODO: come up with smarter category names.
         self.category = "spack"
 
-        # dict pathname -> list of directories to be prepended to in
-        # the module file.
-        self._paths = None
         self.spec = spec
         self.pkg = spec.package  # Just stored for convenience
 
@@ -136,44 +129,21 @@ def __init__(self, spec=None):
         if self.spec.package.__doc__:
             self.long_description = re.sub(r'\s+', ' ', self.spec.package.__doc__)
 
-    @property
-    def paths(self):
-        if self._paths is None:
-            self._paths = {}
-
-            def add_path(path_name, directory):
-                path = self._paths.setdefault(path_name, [])
-                path.append(directory)
-
-            # Add paths if they exist.
-            for var, directory in [
-                    ('PATH', self.spec.prefix.bin),
-                    ('MANPATH', self.spec.prefix.man),
-                    ('MANPATH', self.spec.prefix.share_man),
-                    ('LIBRARY_PATH', self.spec.prefix.lib),
-                    ('LIBRARY_PATH', self.spec.prefix.lib64),
-                    ('LD_LIBRARY_PATH', self.spec.prefix.lib),
-                    ('LD_LIBRARY_PATH', self.spec.prefix.lib64),
-                    ('CPATH', self.spec.prefix.include),
-                    ('PKG_CONFIG_PATH', join_path(self.spec.prefix.lib, 'pkgconfig')),
-                    ('PKG_CONFIG_PATH', join_path(self.spec.prefix.lib64, 'pkgconfig'))]:
-
-                if os.path.isdir(directory):
-                    add_path(var, directory)
-
-            # Add python path unless it's an actual python installation
-            # TODO : is there a better way to do this?
-            # FIXME : add PYTHONPATH to every python package
-            if self.spec.name != 'python':
-                site_packages = glob(join_path(self.spec.prefix.lib, "python*/site-packages"))
-                if site_packages:
-                    add_path('PYTHONPATH', site_packages[0])
-
-            # FIXME : Same for GEM_PATH
-            if self.spec.package.extends(spack.spec.Spec('ruby')):
-                add_path('GEM_PATH', self.spec.prefix)
-
-        return self._paths
+    # @property
+    # def paths(self):
+    #         # Add python path unless it's an actual python installation
+    #         # TODO : is there a better way to do this?
+    #         # FIXME : add PYTHONPATH to every python package
+    #         if self.spec.name != 'python':
+    #             site_packages = glob(join_path(self.spec.prefix.lib, "python*/site-packages"))
+    #             if site_packages:
+    #                 add_path('PYTHONPATH', site_packages[0])
+    #
+    #         # FIXME : Same for GEM_PATH
+    #         if self.spec.package.extends(spack.spec.Spec('ruby')):
+    #             add_path('GEM_PATH', self.spec.prefix)
+    #
+    #     return self._paths
 
     def write(self):
         """Write out a module file for this object."""
@@ -181,14 +151,9 @@ def write(self):
         if not os.path.exists(module_dir):
             mkdirp(module_dir)
 
-        # If there are no paths, no need for a dotkit.
-        if not self.paths:
-            return
-
-        # Construct the changes that needs to be done on the environment for
+        # Environment modifications guessed by inspecting the installation prefix
         env = inspect_path(self.spec.prefix)
-        # FIXME : move the logic to inspection
-        env.prepend_path('CMAKE_PREFIX_PATH', self.spec.prefix)
+        # Package-specific environment modifications
         # FIXME : decide how to distinguish between calls done in the installation and elsewhere
         env.extend(self.spec.package.environment_modifications(None))
         # site_specific = ...`
@@ -196,12 +161,17 @@ def write(self):
             return
 
         with open(self.file_name, 'w') as f:
-            self._write(f, env)
+            self.write_header(f)
+            for line in self.process_environment_command(env):
+                f.write(line)
 
-    def _write(self, stream):
-        """To be implemented by subclasses."""
+    def write_header(self, stream):
         raise NotImplementedError()
 
+    def process_environment_command(self, env):
+        for command in env:
+            # FIXME : how should we handle errors here?
+            yield self.formats[type(command)].format(command)
 
     @property
     def file_name(self):
@@ -225,10 +195,14 @@ class Dotkit(EnvModule):
     name = 'dotkit'
     path = join_path(spack.share_path, "dotkit")
 
+    formats = {
+        PrependPath: 'dk_alter {0.name} {0.path}\n',
+        SetEnv: 'dk_setenv {0.name} {0.value}\n'
+    }
+
     @property
     def file_name(self):
-        return join_path(Dotkit.path, self.spec.architecture,
-                         '%s.dk' % self.use_name)
+        return join_path(Dotkit.path, self.spec.architecture, '%s.dk' % self.use_name)
 
     @property
     def use_name(self):
@@ -237,7 +211,7 @@ def use_name(self):
                                  self.spec.compiler.version, 
                                  self.spec.dag_hash())
 
-    def _write(self, dk_file, env):
+    def write_header(self, dk_file):
         # Category
         if self.category:
             dk_file.write('#c %s\n' % self.category)
@@ -251,18 +225,11 @@ def _write(self, dk_file, env):
             for line in textwrap.wrap(self.long_description, 72):
                 dk_file.write("#h %s\n" % line)
 
-        # Path alterations
-        for var, dirs in self.paths.items():
-            for directory in dirs:
-                dk_file.write("dk_alter %s %s\n" % (var, directory))
-
-        # Let CMake find this package.
-        dk_file.write("dk_alter CMAKE_PREFIX_PATH %s\n" % self.spec.prefix)
-
 
 class TclModule(EnvModule):
     name = 'tcl'
     path = join_path(spack.share_path, "modules")
+
     formats = {
         PrependPath: 'prepend-path {0.name} \"{0.path}\"\n',
         SetEnv: 'setenv {0.name} \"{0.value}\"\n'
@@ -272,7 +239,6 @@ class TclModule(EnvModule):
     def file_name(self):
         return join_path(TclModule.path, self.spec.architecture, self.use_name)
 
-
     @property
     def use_name(self):
       return "%s-%s-%s-%s-%s" % (self.spec.name, self.spec.version,
@@ -280,19 +246,7 @@ def use_name(self):
                                  self.spec.compiler.version, 
                                  self.spec.dag_hash())
 
-    def process_environment_command(self, env):
-        for command in env:
-            # FIXME : how should we handle errors here?
-            yield self.formats[type(command)].format(command)
-
-    def _write(self, module_file, env):
-        """
-        Writes a TCL module file for this package
-
-        Args:
-            module_file: module file stream
-            env: list of environment modifications to be written in the module file
-        """
+    def write_header(self, module_file):
         # TCL Modulefile header
         module_file.write('#%Module1.0\n')
         # TODO : category ?
@@ -306,30 +260,3 @@ def _write(self, module_file, env):
             doc = re.sub(r'"', '\"', self.long_description)
             module_file.write("puts stderr \"%s\"\n" % doc)
             module_file.write('}\n\n')
-
-        # Environment modifications
-        for line in self.process_environment_command(env):
-            module_file.write(line)
-
-    # FIXME : REMOVE
-    # def _write(self, m_file):
-    #     # TODO: cateogry?
-    #     m_file.write('#%Module1.0\n')
-    #
-    #     # Short description
-    #     if self.short_description:
-    #         m_file.write('module-whatis \"%s\"\n\n' % self.short_description)
-    #
-    #     # Long description
-    #     if self.long_description:
-    #         m_file.write('proc ModulesHelp { } {\n')
-    #         doc = re.sub(r'"', '\"', self.long_description)
-    #         m_file.write("puts stderr \"%s\"\n" % doc)
-    #         m_file.write('}\n\n')
-    #
-    #     # Path alterations
-    #     for var, dirs in self.paths.items():
-    #         for directory in dirs:
-    #             m_file.write("prepend-path %s \"%s\"\n" % (var, directory))
-    #
-    #     m_file.write("prepend-path CMAKE_PREFIX_PATH \"%s\"\n" % self.spec.prefix)

From f07d4c94393f6541d1a6afd9118d3f9c84bd08fc Mon Sep 17 00:00:00 2001
From: "Kelly (KT) Thompson" <kgt@lanl.gov>
Date: Wed, 16 Mar 2016 18:55:14 -0600
Subject: [PATCH 024/230] + Provide ~perl and ~shared variants.

---
 var/spack/repos/builtin/packages/graphviz/package.py | 11 +++++++++--
 1 file changed, 9 insertions(+), 2 deletions(-)

diff --git a/var/spack/repos/builtin/packages/graphviz/package.py b/var/spack/repos/builtin/packages/graphviz/package.py
index 7af7da1881a..2a2102bfcb6 100644
--- a/var/spack/repos/builtin/packages/graphviz/package.py
+++ b/var/spack/repos/builtin/packages/graphviz/package.py
@@ -7,6 +7,9 @@ class Graphviz(Package):
 
     version('2.38.0', '5b6a829b2ac94efcd5fa3c223ed6d3ae')
 
+    variant('perl', default=True, description='Disable if you have problems with the optional script language bindings')
+    variant('shared', default=True, description='Building static is required on AIX')
+
     parallel = False
 
     depends_on("swig")
@@ -14,8 +17,12 @@ class Graphviz(Package):
     depends_on("ghostscript")
 
     def install(self, spec, prefix):
-        configure("--prefix=%s" %prefix)
+        options = ['--prefix=%s' % prefix]
+        if '~perl' in spec:
+            options.append('--disable-perl')
+        if '~shared' in spec:
+            options.append('--enable-shared=no')
 
+        configure(*options)
         make()
         make("install")
-

From 9cdd79e33f8463699fcea0b668eafac1c9fae1d4 Mon Sep 17 00:00:00 2001
From: alalazo <massimiliano.culpo@googlemail.com>
Date: Thu, 17 Mar 2016 14:14:18 +0100
Subject: [PATCH 025/230] modules : restored previous logic for path inspection

---
 lib/spack/spack/modules.py | 50 ++++++++++++++++++++++----------------
 1 file changed, 29 insertions(+), 21 deletions(-)

diff --git a/lib/spack/spack/modules.py b/lib/spack/spack/modules.py
index b64a8b32266..7e395736e4f 100644
--- a/lib/spack/spack/modules.py
+++ b/lib/spack/spack/modules.py
@@ -74,29 +74,37 @@ def print_help():
             "")
 
 
-def inspect_path(path):
-    class PathInspector(object):
-        dirname2varname = {
-            'bin': ('PATH',),
-            'man': ('MANPATH',),
-            'lib': ('LIBRARY_PATH', 'LD_LIBRARY_PATH'),
-            'lib64': ('LIBRARY_PATH', 'LD_LIBRARY_PATH'),
-            'include': ('CPATH',),
-            'pkgconfig': ('PKG_CONFIG_PATH',)
-        }
+def inspect_path(prefix):
+    """
+    Inspects the prefix of an installation to search for common layouts. Issues a request to modify the environment
+    accordingly when an item is found.
 
-        def __call__(self, env, directory, names):
-            for name in names:
-                variables = PathInspector.dirname2varname.get(name, None)
-                if variables is None:
-                    continue
-                absolute_path = join_path(os.path.abspath(directory), name)
-                for variable in variables:
-                    env.prepend_path(variable, absolute_path)
+    Args:
+        prefix: prefix of the installation
 
-    env, inspector = EnvironmentModifications(), PathInspector()
-    os.path.walk(path, inspector, env)
-    env.prepend_path('CMAKE_PREFIX_PATH', path)
+    Returns:
+        instance of EnvironmentModifications containing the requested modifications
+    """
+    env = EnvironmentModifications()
+    # Inspect the prefix to check for the existence of common directories
+    prefix_inspections = {
+        'bin': ('PATH',),
+        'man': ('MANPATH',),
+        'lib': ('LIBRARY_PATH', 'LD_LIBRARY_PATH'),
+        'lib64': ('LIBRARY_PATH', 'LD_LIBRARY_PATH'),
+        'include': ('CPATH',)
+    }
+    for attribute, variables in prefix_inspections.items():
+        expected = getattr(prefix, attribute)
+        if os.path.isdir(expected):
+            for variable in variables:
+                env.prepend_path(variable, expected)
+    # PKGCONFIG
+    for expected in (join_path(prefix.lib, 'pkgconfig'), join_path(prefix.lib64, 'pkgconfig')):
+        if os.path.isdir(expected):
+            env.prepend_path('PKG_CONFIG_PATH', expected)
+    # CMake related variables
+    env.prepend_path('CMAKE_PREFIX_PATH', prefix)
     return env
 
 

From f0f0663d1b9ece1e2b0b0a8f720b1325eec443bb Mon Sep 17 00:00:00 2001
From: alalazo <massimiliano.culpo@googlemail.com>
Date: Thu, 17 Mar 2016 15:11:39 +0100
Subject: [PATCH 026/230] package : split `environment_modifications` into
 `setup_environment` and `setup_dependent_environment`. package : renamed
 `module_modifications` to `modify_module` for consistency

---
 lib/spack/spack/build_environment.py          |  4 +--
 lib/spack/spack/modules.py                    |  5 ++-
 lib/spack/spack/package.py                    |  9 +++--
 .../repos/builtin/packages/mpich/package.py   | 35 +++++++------------
 .../packages/netlib-scalapack/package.py      |  2 +-
 .../repos/builtin/packages/openmpi/package.py | 19 +++++-----
 .../repos/builtin/packages/python/package.py  | 25 ++++++-------
 .../repos/builtin/packages/qt/package.py      |  4 +--
 .../repos/builtin/packages/ruby/package.py    |  6 ++--
 9 files changed, 49 insertions(+), 60 deletions(-)

diff --git a/lib/spack/spack/build_environment.py b/lib/spack/spack/build_environment.py
index e5d256a2e01..68477145fef 100644
--- a/lib/spack/spack/build_environment.py
+++ b/lib/spack/spack/build_environment.py
@@ -284,8 +284,8 @@ def setup_package(pkg):
 
     # Allow dependencies to set up environment as well.
     for dependency_spec in pkg.spec.traverse(root=False):
-        dependency_spec.package.module_modifications(pkg.module, dependency_spec, pkg.spec)
-        env.extend(dependency_spec.package.environment_modifications(pkg.spec))
+        dependency_spec.package.modify_module(pkg.module, dependency_spec, pkg.spec)
+        dependency_spec.package.setup_dependent_environment(env, pkg.spec)
     # TODO : implement validation
     #validate(env)
     env.apply_modifications()
diff --git a/lib/spack/spack/modules.py b/lib/spack/spack/modules.py
index 7e395736e4f..09895d8c441 100644
--- a/lib/spack/spack/modules.py
+++ b/lib/spack/spack/modules.py
@@ -162,9 +162,8 @@ def write(self):
         # Environment modifications guessed by inspecting the installation prefix
         env = inspect_path(self.spec.prefix)
         # Package-specific environment modifications
-        # FIXME : decide how to distinguish between calls done in the installation and elsewhere
-        env.extend(self.spec.package.environment_modifications(None))
-        # site_specific = ...`
+        self.spec.package.setup_environment(env)
+        # TODO : implement site-specific modifications and filters
         if not env:
             return
 
diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py
index 042833964ac..8e56dd1f976 100644
--- a/lib/spack/spack/package.py
+++ b/lib/spack/spack/package.py
@@ -977,7 +977,7 @@ def module(self):
                           fromlist=[self.__class__.__name__])
 
 
-    def environment_modifications(self, dependent_spec):
+    def setup_environment(self, env):
         """
         Called before the install() method of dependents.
 
@@ -998,9 +998,12 @@ def environment_modifications(self, dependent_spec):
         Returns:
             instance of environment modifications
         """
-        return EnvironmentModifications()
+        pass
 
-    def module_modifications(self, module, spec, dependent_spec):
+    def setup_dependent_environment(self, env, dependent_spec):
+        self.setup_environment(env)
+
+    def modify_module(self, module, spec, dependent_spec):
         """
         Called before the install() method of dependents.
 
diff --git a/var/spack/repos/builtin/packages/mpich/package.py b/var/spack/repos/builtin/packages/mpich/package.py
index 4c34d0308f5..5af9b585ea8 100644
--- a/var/spack/repos/builtin/packages/mpich/package.py
+++ b/var/spack/repos/builtin/packages/mpich/package.py
@@ -47,30 +47,21 @@ class Mpich(Package):
     provides('mpi@:3.0', when='@3:')
     provides('mpi@:1.3', when='@1:')
 
-    def environment_modifications(self, dependent_spec):
-        env = super(Mpich, self).environment_modifications(dependent_spec)
+    def setup_environment(self, env):
+        env.set_env('MPICH_CC', self.compiler.cc)
+        env.set_env('MPICH_CXX', self.compiler.cxx)
+        env.set_env('MPICH_F77', self.compiler.f77)
+        env.set_env('MPICH_F90', self.compiler.fc)
+        env.set_env('MPICH_FC', self.compiler.fc)
 
-        if dependent_spec is None:
-            # We are not using compiler wrappers
-            cc = self.compiler.cc
-            cxx = self.compiler.cxx
-            f77 = self.compiler.f77
-            f90 = fc = self.compiler.fc
-        else:
-            # Spack compiler wrappers
-            cc = os.environ['CC']
-            cxx = os.environ['CXX']
-            f77 = os.environ['F77']
-            f90 = fc = os.environ['FC']
+    def setup_dependent_environment(self, env, dependent_spec):
+        env.set_env('MPICH_CC', spack_cc)
+        env.set_env('MPICH_CXX', spack_cxx)
+        env.set_env('MPICH_F77', spack_f77)
+        env.set_env('MPICH_F90', spack_f90)
+        env.set_env('MPICH_FC', spack_fc)
 
-        env.set_env('MPICH_CC', cc)
-        env.set_env('MPICH_CXX', cxx)
-        env.set_env('MPICH_F77', f77)
-        env.set_env('MPICH_F90', f90)
-        env.set_env('MPICH_FC', fc)
-        return env
-
-    def module_modifications(self, module, spec, dep_spec):
+    def modify_module(self, module, spec, dep_spec):
         """For dependencies, make mpicc's use spack wrapper."""
         # FIXME : is this necessary ? Shouldn't this be part of a contract with MPI providers?
         module.mpicc = join_path(self.prefix.bin, 'mpicc')
diff --git a/var/spack/repos/builtin/packages/netlib-scalapack/package.py b/var/spack/repos/builtin/packages/netlib-scalapack/package.py
index ecdea464420..7e7e5b2e2ee 100644
--- a/var/spack/repos/builtin/packages/netlib-scalapack/package.py
+++ b/var/spack/repos/builtin/packages/netlib-scalapack/package.py
@@ -40,7 +40,7 @@ def install(self, spec, prefix):
             make()
             make("install")
 
-    def module_modifications(self, module, spec, dependent_spec):
+    def modify_module(self, module, spec, dependent_spec):
         # TODO treat OS that are not Linux...
         lib_suffix = '.so' if '+shared' in spec['scalapack'] else '.a'
 
diff --git a/var/spack/repos/builtin/packages/openmpi/package.py b/var/spack/repos/builtin/packages/openmpi/package.py
index 3a141704576..7783ca87666 100644
--- a/var/spack/repos/builtin/packages/openmpi/package.py
+++ b/var/spack/repos/builtin/packages/openmpi/package.py
@@ -41,14 +41,17 @@ class Openmpi(Package):
     def url_for_version(self, version):
         return "http://www.open-mpi.org/software/ompi/v%s/downloads/openmpi-%s.tar.bz2" % (version.up_to(2), version)
 
-    def environment_modifications(self, dependent_spec):
-        env = super(Openmpi, self).environment_modifications(dependent_spec)
-        # FIXME : the compilers should point to the current wrappers, not to generic cc etc.
-        env.set_env('OMPI_CC', 'cc')
-        env.set_env('OMPI_CXX', 'c++')
-        env.set_env('OMPI_FC', 'f90')
-        env.set_env('OMPI_F77', 'f77')
-        return env
+    def setup_environment(self, env):
+        env.set_env('OMPI_CC', self.compiler.cc)
+        env.set_env('OMPI_CXX', self.compiler.cxx)
+        env.set_env('OMPI_FC', self.compiler.fc)
+        env.set_env('OMPI_F77', self.compiler.f77)
+
+    def setup_dependent_environment(self, env, dependent_spec):
+        env.set_env('OMPI_CC', spack_cc)
+        env.set_env('OMPI_CXX', spack_cxx)
+        env.set_env('OMPI_FC', spack_fc)
+        env.set_env('OMPI_F77', spack_f77)
 
     def install(self, spec, prefix):
         config_args = ["--prefix=%s" % prefix,
diff --git a/var/spack/repos/builtin/packages/python/package.py b/var/spack/repos/builtin/packages/python/package.py
index acb36517268..d47c1d1b2f3 100644
--- a/var/spack/repos/builtin/packages/python/package.py
+++ b/var/spack/repos/builtin/packages/python/package.py
@@ -89,24 +89,21 @@ def python_include_dir(self):
     def site_packages_dir(self):
         return os.path.join(self.python_lib_dir, 'site-packages')
 
-    def environment_modifications(self, extension_spec):
-        env = super(Python, self).environment_modifications(extension_spec)
-        if extension_spec is not None:
-            # Set PYTHONPATH to include site-packages dir for the
-            # extension and any other python extensions it depends on.
-            python_paths = []
-            for d in extension_spec.traverse():
-                if d.package.extends(self.spec):
-                    python_paths.append(os.path.join(d.prefix, self.site_packages_dir))
-            env.set_env['PYTHONPATH'] = ':'.join(python_paths)
-        return env
+    def setup_dependent_environment(self, env, extension_spec):
+        # Set PYTHONPATH to include site-packages dir for the extension and any other python extensions it depends on.
+        python_paths = []
+        for d in extension_spec.traverse():
+            if d.package.extends(self.spec):
+                python_paths.append(os.path.join(d.prefix, self.site_packages_dir))
+        env.set_env['PYTHONPATH'] = ':'.join(python_paths)
 
-    def module_modifications(self, module, spec, ext_spec):
-        """Called before python modules' install() methods.
+    def modify_module(self, module, spec, ext_spec):
+        """
+        Called before python modules' install() methods.
 
         In most cases, extensions will only need to have one line::
 
-            python('setup.py', 'install', '--prefix=%s' % prefix)
+        python('setup.py', 'install', '--prefix=%s' % prefix)
         """
         # Python extension builds can have a global python executable function
         if self.version >= Version("3.0.0") and self.version < Version("4.0.0"):
diff --git a/var/spack/repos/builtin/packages/qt/package.py b/var/spack/repos/builtin/packages/qt/package.py
index 0adf352be21..35b9d684624 100644
--- a/var/spack/repos/builtin/packages/qt/package.py
+++ b/var/spack/repos/builtin/packages/qt/package.py
@@ -55,10 +55,8 @@ class Qt(Package):
     depends_on("mesa", when='@4:+mesa')
     depends_on("libxcb")
 
-    def environment_modifications(self, dependent_spec):
-        env = super(Qt, self).environment_modifications(dependent_spec)
+    def setup_environment(self, env):
         env.set_env['QTDIR'] = self.prefix
-        return env
 
     def patch(self):
         if self.spec.satisfies('@4'):
diff --git a/var/spack/repos/builtin/packages/ruby/package.py b/var/spack/repos/builtin/packages/ruby/package.py
index 9caea30ef46..2d1da8c9af1 100644
--- a/var/spack/repos/builtin/packages/ruby/package.py
+++ b/var/spack/repos/builtin/packages/ruby/package.py
@@ -17,8 +17,7 @@ def install(self, spec, prefix):
         make()
         make("install")
 
-    def environment_modifications(self, extension_spec):
-        env = super(Ruby, self).environment_modifications(extension_spec)
+    def setup_dependent_environment(self, env, extension_spec):
         # Set GEM_PATH to include dependent gem directories
         ruby_paths = []
         for d in extension_spec.traverse():
@@ -27,9 +26,8 @@ def environment_modifications(self, extension_spec):
         env.set_env('GEM_PATH', concatenate_paths(ruby_paths))
         # The actual installation path for this gem
         env.set_env('GEM_HOME', extension_spec.prefix)
-        return env
 
-    def module_modifications(self, module, spec, ext_spec):
+    def modify_module(self, module, spec, ext_spec):
         """Called before ruby modules' install() methods.  Sets GEM_HOME
         and GEM_PATH to values appropriate for the package being built.
 

From 3da4d6664bbee38fde6faeffb39f889698ea320c Mon Sep 17 00:00:00 2001
From: alalazo <massimiliano.culpo@googlemail.com>
Date: Thu, 17 Mar 2016 15:38:08 +0100
Subject: [PATCH 027/230] environment : simplified hierarchy according to
 comments in review

---
 lib/spack/spack/environment.py      | 53 +++++++++--------------------
 lib/spack/spack/modules.py          | 10 +++---
 lib/spack/spack/package.py          |  1 +
 lib/spack/spack/test/environment.py |  2 +-
 lib/spack/spack/util/environment.py |  2 --
 5 files changed, 24 insertions(+), 44 deletions(-)

diff --git a/lib/spack/spack/environment.py b/lib/spack/spack/environment.py
index b557bf0bbcf..3ee917fcec6 100644
--- a/lib/spack/spack/environment.py
+++ b/lib/spack/spack/environment.py
@@ -3,73 +3,54 @@
 import collections
 
 
-class AttributeHolder(object):
-    """
-    Policy that permits to store any kind of attribute on self. The attributes must be passed as key/value pairs
-    during the initialization of the instance.
-    """
-    def __init__(self, **kwargs):
-        for key, value in kwargs.items():
-            setattr(self, key, value)
+class NameModifier(object):
+    def __init__(self, name, **kwargs):
+        self.name = name
+        self.args = {'name': name}
+        self.args.update(kwargs)
 
 
-class SetEnv(AttributeHolder):
+class NameValueModifier(object):
     def __init__(self, name, value, **kwargs):
-        super(SetEnv, self).__init__(**kwargs)
         self.name = name
         self.value = value
+        self.args = {'name': name, 'value': value}
+        self.args.update(kwargs)
 
+
+class SetEnv(NameValueModifier):
     def execute(self):
         os.environ[self.name] = str(self.value)
 
 
-class UnsetEnv(AttributeHolder):
-    def __init__(self, name, **kwargs):
-        super(UnsetEnv, self).__init__(**kwargs)
-        self.name = name
-
+class UnsetEnv(NameModifier):
     def execute(self):
         os.environ.pop(self.name, None)  # Avoid throwing if the variable was not set
 
 
-class AppendPath(AttributeHolder):
-    def __init__(self, name, path, **kwargs):
-        super(AppendPath, self).__init__(**kwargs)
-        self.name = name
-        self.path = path
-
+class AppendPath(NameValueModifier):
     def execute(self):
         environment_value = os.environ.get(self.name, '')
         directories = environment_value.split(':') if environment_value else []
         # TODO : Check if this is a valid directory name
-        directories.append(os.path.normpath(self.path))
+        directories.append(os.path.normpath(self.value))
         os.environ[self.name] = ':'.join(directories)
 
 
-class PrependPath(AttributeHolder):
-    def __init__(self, name, path, **kwargs):
-        super(PrependPath, self).__init__(**kwargs)
-        self.name = name
-        self.path = path
-
+class PrependPath(NameValueModifier):
     def execute(self):
         environment_value = os.environ.get(self.name, '')
         directories = environment_value.split(':') if environment_value else []
         # TODO : Check if this is a valid directory name
-        directories = [os.path.normpath(self.path)] + directories
+        directories = [os.path.normpath(self.value)] + directories
         os.environ[self.name] = ':'.join(directories)
 
 
-class RemovePath(AttributeHolder):
-    def __init__(self, name, path, **kwargs):
-        super(RemovePath, self).__init__(**kwargs)
-        self.name = name
-        self.path = path
-
+class RemovePath(NameValueModifier):
     def execute(self):
         environment_value = os.environ.get(self.name, '')
         directories = environment_value.split(':') if environment_value else []
-        directories = [os.path.normpath(x) for x in directories if x != os.path.normpath(self.path)]
+        directories = [os.path.normpath(x) for x in directories if x != os.path.normpath(self.value)]
         os.environ[self.name] = ':'.join(directories)
 
 
diff --git a/lib/spack/spack/modules.py b/lib/spack/spack/modules.py
index 09895d8c441..0f826c73634 100644
--- a/lib/spack/spack/modules.py
+++ b/lib/spack/spack/modules.py
@@ -178,7 +178,7 @@ def write_header(self, stream):
     def process_environment_command(self, env):
         for command in env:
             # FIXME : how should we handle errors here?
-            yield self.formats[type(command)].format(command)
+            yield self.formats[type(command)].format(**command.args)
 
     @property
     def file_name(self):
@@ -203,8 +203,8 @@ class Dotkit(EnvModule):
     path = join_path(spack.share_path, "dotkit")
 
     formats = {
-        PrependPath: 'dk_alter {0.name} {0.path}\n',
-        SetEnv: 'dk_setenv {0.name} {0.value}\n'
+        PrependPath: 'dk_alter {name} {value}\n',
+        SetEnv: 'dk_setenv {name} {value}\n'
     }
 
     @property
@@ -238,8 +238,8 @@ class TclModule(EnvModule):
     path = join_path(spack.share_path, "modules")
 
     formats = {
-        PrependPath: 'prepend-path {0.name} \"{0.path}\"\n',
-        SetEnv: 'setenv {0.name} \"{0.value}\"\n'
+        PrependPath: 'prepend-path {name} \"{value}\"\n',
+        SetEnv: 'setenv {name} \"{value}\"\n'
     }
 
     @property
diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py
index 8e56dd1f976..680b26d69a7 100644
--- a/lib/spack/spack/package.py
+++ b/lib/spack/spack/package.py
@@ -979,6 +979,7 @@ def module(self):
 
     def setup_environment(self, env):
         """
+
         Called before the install() method of dependents.
 
         Return the list of environment modifications needed by dependents (or extensions). Default implementation does
diff --git a/lib/spack/spack/test/environment.py b/lib/spack/spack/test/environment.py
index d0b093b0543..3e03760c016 100644
--- a/lib/spack/spack/test/environment.py
+++ b/lib/spack/spack/test/environment.py
@@ -53,7 +53,7 @@ def test_extra_arguments(self):
         env = EnvironmentModifications()
         env.set_env('A', 'dummy value', who='Pkg1')
         for x in env:
-            assert hasattr(x, 'who')
+            assert 'who' in x.args
         env.apply_modifications()
         self.assertEqual('dummy value', os.environ['A'])
 
diff --git a/lib/spack/spack/util/environment.py b/lib/spack/spack/util/environment.py
index 1485992b0f1..55e653fd2fb 100644
--- a/lib/spack/spack/util/environment.py
+++ b/lib/spack/spack/util/environment.py
@@ -40,13 +40,11 @@ def env_flag(name):
     return False
 
 
-# FIXME : remove this function ?
 def path_set(var_name, directories):
     path_str = ":".join(str(dir) for dir in directories)
     os.environ[var_name] = path_str
 
 
-# FIXME : remove this function ?
 def path_put_first(var_name, directories):
     """Puts the provided directories first in the path, adding them
        if they're not already there.

From 38c3c84969c25aaee8f643ff9770759c7e6d9c35 Mon Sep 17 00:00:00 2001
From: alalazo <massimiliano.culpo@googlemail.com>
Date: Thu, 17 Mar 2016 17:37:33 +0100
Subject: [PATCH 028/230] environment : added caller information

---
 lib/spack/spack/environment.py | 27 +++++++++++++++++++++++++--
 lib/spack/spack/modules.py     |  8 ++++++--
 2 files changed, 31 insertions(+), 4 deletions(-)

diff --git a/lib/spack/spack/environment.py b/lib/spack/spack/environment.py
index 3ee917fcec6..6d214595a3e 100644
--- a/lib/spack/spack/environment.py
+++ b/lib/spack/spack/environment.py
@@ -1,6 +1,7 @@
 import os
 import os.path
 import collections
+import inspect
 
 
 class NameModifier(object):
@@ -32,7 +33,6 @@ class AppendPath(NameValueModifier):
     def execute(self):
         environment_value = os.environ.get(self.name, '')
         directories = environment_value.split(':') if environment_value else []
-        # TODO : Check if this is a valid directory name
         directories.append(os.path.normpath(self.value))
         os.environ[self.name] = ':'.join(directories)
 
@@ -41,7 +41,6 @@ class PrependPath(NameValueModifier):
     def execute(self):
         environment_value = os.environ.get(self.name, '')
         directories = environment_value.split(':') if environment_value else []
-        # TODO : Check if this is a valid directory name
         directories = [os.path.normpath(self.value)] + directories
         os.environ[self.name] = ':'.join(directories)
 
@@ -57,6 +56,11 @@ def execute(self):
 class EnvironmentModifications(object):
     """
     Keeps track of requests to modify the current environment.
+
+    Each call to a method to modify the environment stores the extra information on the caller in the request:
+    - 'filename' : filename of the module where the caller is defined
+    - 'lineno': line number where the request occurred
+    - 'context' : line of code that issued the request that failed
     """
 
     def __init__(self, other=None):
@@ -85,6 +89,20 @@ def _check_other(other):
         if not isinstance(other, EnvironmentModifications):
             raise TypeError('other must be an instance of EnvironmentModifications')
 
+    def _get_outside_caller_attributes(self):
+        stack = inspect.stack()
+        try:
+            _, filename, lineno, _, context, index = stack[2]
+            context = context[index].strip()
+        except Exception:
+            filename, lineno, context = 'unknown file', 'unknown line', 'unknown context'
+        args = {
+            'filename': filename,
+            'lineno': lineno,
+            'context': context
+        }
+        return args
+
     def set_env(self, name, value, **kwargs):
         """
         Stores in the current object a request to set an environment variable
@@ -93,6 +111,7 @@ def set_env(self, name, value, **kwargs):
             name: name of the environment variable to be set
             value: value of the environment variable
         """
+        kwargs.update(self._get_outside_caller_attributes())
         item = SetEnv(name, value, **kwargs)
         self.env_modifications.append(item)
 
@@ -103,6 +122,7 @@ def unset_env(self, name, **kwargs):
         Args:
             name: name of the environment variable to be set
         """
+        kwargs.update(self._get_outside_caller_attributes())
         item = UnsetEnv(name, **kwargs)
         self.env_modifications.append(item)
 
@@ -114,6 +134,7 @@ def append_path(self, name, path, **kwargs):
             name: name of the path list in the environment
             path: path to be appended
         """
+        kwargs.update(self._get_outside_caller_attributes())
         item = AppendPath(name, path, **kwargs)
         self.env_modifications.append(item)
 
@@ -125,6 +146,7 @@ def prepend_path(self, name, path, **kwargs):
             name: name of the path list in the environment
             path: path to be pre-pended
         """
+        kwargs.update(self._get_outside_caller_attributes())
         item = PrependPath(name, path, **kwargs)
         self.env_modifications.append(item)
 
@@ -136,6 +158,7 @@ def remove_path(self, name, path, **kwargs):
             name: name of the path list in the environment
             path: path to be removed
         """
+        kwargs.update(self._get_outside_caller_attributes())
         item = RemovePath(name, path, **kwargs)
         self.env_modifications.append(item)
 
diff --git a/lib/spack/spack/modules.py b/lib/spack/spack/modules.py
index 0f826c73634..d192bbe004e 100644
--- a/lib/spack/spack/modules.py
+++ b/lib/spack/spack/modules.py
@@ -177,8 +177,12 @@ def write_header(self, stream):
 
     def process_environment_command(self, env):
         for command in env:
-            # FIXME : how should we handle errors here?
-            yield self.formats[type(command)].format(**command.args)
+            try:
+                yield self.formats[type(command)].format(**command.args)
+            except KeyError:
+                tty.warn('Cannot handle command of type {command} : skipping request'.format(command=type(command)))
+                tty.warn('{context} at {filename}:{lineno}'.format(**command.args))
+
 
     @property
     def file_name(self):

From e673127263a03e63d6a64840d1071a788f0c099e Mon Sep 17 00:00:00 2001
From: alalazo <massimiliano.culpo@googlemail.com>
Date: Thu, 17 Mar 2016 18:11:23 +0100
Subject: [PATCH 029/230] package : added documentation

---
 lib/spack/spack/package.py | 35 +++++++++++++++++++++--------------
 1 file changed, 21 insertions(+), 14 deletions(-)

diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py
index 680b26d69a7..d0b94dbbeb9 100644
--- a/lib/spack/spack/package.py
+++ b/lib/spack/spack/package.py
@@ -976,32 +976,41 @@ def module(self):
         return __import__(self.__class__.__module__,
                           fromlist=[self.__class__.__name__])
 
-
     def setup_environment(self, env):
         """
+        Appends in `env` the list of environment modifications needed to use this package outside of spack.
 
+        Default implementation does nothing, but this can be overridden if the package needs a particular environment.
+
+        Example :
+
+        1. A lot of Qt extensions need `QTDIR` set.  This can be used to do that.
+
+        Args:
+            env: list of environment modifications to be updated
+        """
+        pass
+
+    def setup_dependent_environment(self, env, dependent_spec):
+        """
         Called before the install() method of dependents.
 
-        Return the list of environment modifications needed by dependents (or extensions). Default implementation does
-        nothing, but this can be overridden by an extendable package to set up the install environment for its
-        extensions. This is useful if there are some common steps to installing all extensions for a certain package.
+        Appends in `env` the list of environment modifications needed by dependents (or extensions) during the
+        installation of a package. The default implementation delegates to `setup_environment`, but can be overridden
+        if the modifications to the environment happen to be different from the one needed to use the package outside
+        of spack.
+
+        This is useful if there are some common steps to installing all extensions for a certain package.
 
         Example :
 
         1. Installing python modules generally requires `PYTHONPATH` to point to the lib/pythonX.Y/site-packages
         directory in the module's install prefix.  This could set that variable.
 
-        2. A lot of Qt extensions need `QTDIR` set.  This can be used to do that.
-
         Args:
+            env: list of environment modifications to be updated
             dependent_spec: dependent (or extension) of this spec
-
-        Returns:
-            instance of environment modifications
         """
-        pass
-
-    def setup_dependent_environment(self, env, dependent_spec):
         self.setup_environment(env)
 
     def modify_module(self, module, spec, dependent_spec):
@@ -1020,12 +1029,10 @@ def modify_module(self, module, spec, dependent_spec):
         """
         pass
 
-
     def install(self, spec, prefix):
         """Package implementations override this with their own build configuration."""
         raise InstallError("Package %s provides no install method!" % self.name)
 
-
     def do_uninstall(self, force=False):
         if not self.installed:
             raise InstallError(str(self.spec) + " is not installed.")

From ac394718ec0aa67c468a8529b930eaade0bcbed1 Mon Sep 17 00:00:00 2001
From: alalazo <massimiliano.culpo@googlemail.com>
Date: Thu, 17 Mar 2016 18:22:07 +0100
Subject: [PATCH 030/230] python : implemented possible solution

---
 lib/spack/spack/package.py                          | 11 ++++++++++-
 var/spack/repos/builtin/packages/py-nose/package.py |  3 ++-
 2 files changed, 12 insertions(+), 2 deletions(-)

diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py
index d0b94dbbeb9..a7ab20137ea 100644
--- a/lib/spack/spack/package.py
+++ b/lib/spack/spack/package.py
@@ -37,6 +37,7 @@
 import re
 import textwrap
 import time
+import glob
 
 import llnl.util.tty as tty
 import spack
@@ -55,7 +56,6 @@
 from llnl.util.lang import *
 from llnl.util.link_tree import LinkTree
 from llnl.util.tty.log import log_output
-from spack.environment import EnvironmentModifications
 from spack.stage import Stage, ResourceStage, StageComposite
 from spack.util.compression import allowed_archive
 from spack.util.environment import dump_environment
@@ -1236,6 +1236,15 @@ def rpath_args(self):
         return " ".join("-Wl,-rpath,%s" % p for p in self.rpath)
 
 
+class PythonExtension(Package):
+    def setup_dependent_environment(self, env, dependent_spec):
+        pass
+
+    def setup_environment(self, env):
+        site_packages = glob.glob(join_path(self.spec.prefix.lib, "python*/site-packages"))
+        if site_packages:
+            env.prepend_path('PYTHONPATH', site_packages[0])
+
 def validate_package_url(url_string):
     """Determine whether spack can handle a particular URL or not."""
     url = urlparse(url_string)
diff --git a/var/spack/repos/builtin/packages/py-nose/package.py b/var/spack/repos/builtin/packages/py-nose/package.py
index e7c6cf0264b..e817b8eb513 100644
--- a/var/spack/repos/builtin/packages/py-nose/package.py
+++ b/var/spack/repos/builtin/packages/py-nose/package.py
@@ -1,6 +1,7 @@
 from spack import *
+from spack.package import PythonExtension
 
-class PyNose(Package):
+class PyNose(PythonExtension):
     """nose extends the test loading and running features of unittest,
     making it easier to write, find and run tests."""
 

From e55880904376847ce767770344059eef1ba7707c Mon Sep 17 00:00:00 2001
From: alalazo <massimiliano.culpo@googlemail.com>
Date: Thu, 17 Mar 2016 19:32:31 +0100
Subject: [PATCH 031/230] python : fixed typo

---
 var/spack/repos/builtin/packages/python/package.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/python/package.py b/var/spack/repos/builtin/packages/python/package.py
index d47c1d1b2f3..d46e1068b6c 100644
--- a/var/spack/repos/builtin/packages/python/package.py
+++ b/var/spack/repos/builtin/packages/python/package.py
@@ -95,7 +95,7 @@ def setup_dependent_environment(self, env, extension_spec):
         for d in extension_spec.traverse():
             if d.package.extends(self.spec):
                 python_paths.append(os.path.join(d.prefix, self.site_packages_dir))
-        env.set_env['PYTHONPATH'] = ':'.join(python_paths)
+        env.set_env('PYTHONPATH', ':'.join(python_paths))
 
     def modify_module(self, module, spec, ext_spec):
         """

From f3ea0420f80f418a0f3e628479c782f197e6a43e Mon Sep 17 00:00:00 2001
From: Erik Schnetter <schnetter@gmail.com>
Date: Thu, 17 Mar 2016 21:53:13 -0400
Subject: [PATCH 032/230] Import recent changes

---
 lib/spack/env/cc | 185 +++++++++++++++++------------------------------
 1 file changed, 65 insertions(+), 120 deletions(-)

diff --git a/lib/spack/env/cc b/lib/spack/env/cc
index df6795c2640..c6a09724e9b 100755
--- a/lib/spack/env/cc
+++ b/lib/spack/env/cc
@@ -65,7 +65,7 @@ function die {
 }
 
 for param in $parameters; do
-    if [ -z "${!param}" ]; then
+    if [[ -z ${!param} ]]; then
         die "Spack compiler must be run from spack!  Input $param was missing!"
     fi
 done
@@ -78,10 +78,11 @@ done
 # 'command' is set based on the input command to $SPACK_[CC|CXX|F77|F90]
 #
 # 'mode' is set to one of:
+#    cpp     preprocess
 #    cc      compile
+#    as      assemble
 #    ld      link
 #    ccld    compile & link
-#    cpp     preprocessor
 #    vcheck  version check
 #
 command=$(basename "$0")
@@ -131,6 +132,9 @@ if [ -z "$mode" ]; then
         if [ "$arg" = -E ]; then
             mode=cpp
             break
+        elif [ "$arg" = -S ]; then
+            mode=as
+            break
         elif [ "$arg" = -c ]; then
             mode=cc
             break
@@ -146,22 +150,25 @@ fi
 
 # Check that at least one of the real commands was actually selected,
 # otherwise we don't know what to execute.
-if [ -z "$command" ]; then
+if [[ -z $command ]]; then
     die "ERROR: Compiler '$SPACK_COMPILER_SPEC' does not support compiling $language programs."
 fi
 
+if [ "$mode" == vcheck ] ; then
+    exec ${command} "$@"
+fi
+
 # Save original command for debug logging
 input_command="$@"
 args=("$@")
 
-<<<<<<< HEAD
 # Dump parsed values for unit testing if asked for
 if [[ -n $SPACK_TEST_COMMAND ]]; then
 
     #
     # Now do real parsing of the command line args, trying hard to keep
-    # non-rpath linker arguments in the proper order w.r.t. other command
-    # line arguments.  This is important for things like groups.
+    # non-rpath linker arguments in the proper order w.r.t. other command line
+    # arguments.  This is important for things like groups.
     #
     includes=()
     libraries=()
@@ -188,32 +195,44 @@ if [[ -n $SPACK_TEST_COMMAND ]]; then
                 ;;
             -Wl,*)
                 arg="${1#-Wl,}"
-                if [ -z "$arg" ]; then shift; arg="$1"; fi
-                if [[ "$arg" = -rpath=* ]]; then
-                    rpaths+=("${arg#-rpath=}")
-                elif [[ "$arg" = -rpath ]]; then
+                # TODO: Handle multiple -Wl, continuations of -Wl,-rpath
+                if [[ $arg == -rpath=* ]]; then
+                    arg="${arg#-rpath=}"
+                    for rpath in ${arg//,/ }; do
+                        rpaths+=("$rpath")
+                    done
+                elif [[ $arg == -rpath,* ]]; then
+                    arg="${arg#-rpath,}"
+                    for rpath in ${arg//,/ }; do
+                        rpaths+=("$rpath")
+                    done
+                elif [[ $arg == -rpath ]]; then
                     shift; arg="$1"
-                    if [[ "$arg" != -Wl,* ]]; then
+                    if [[ $arg != '-Wl,'* ]]; then
                         die "-Wl,-rpath was not followed by -Wl,*"
                     fi
-                    rpaths+=("${arg#-Wl,}")
+                    arg="${arg#-Wl,}"
+                    for rpath in ${arg//,/ }; do
+                        rpaths+=("$rpath")
+                    done
                 else
                     other_args+=("-Wl,$arg")
                 fi
                 ;;
-            -Xlinker,*)
-                arg="${1#-Xlinker,}"
-                if [ -z "$arg" ]; then shift; arg="$1"; fi
-                if [[ "$arg" = -rpath=* ]]; then
+            -Xlinker)
+                shift; arg="$1";
+                if [[ $arg = -rpath=* ]]; then
                     rpaths+=("${arg#-rpath=}")
-                elif [[ "$arg" = -rpath ]]; then
+                elif [[ $arg = -rpath ]]; then
                     shift; arg="$1"
-                    if [[ "$arg" != -Xlinker,* ]]; then
-                        die "-Xlinker,-rpath was not followed by -Xlinker,*"
+                    if [[ $arg != -Xlinker ]]; then
+                        die "-Xlinker -rpath was not followed by -Xlinker <arg>"
                     fi
-                    rpaths+=("${arg#-Xlinker,}")
+                    shift; arg="$1"
+                    rpaths+=("$arg")
                 else
-                    other_args+=("-Xlinker,$arg")
+                    other_args+=("-Xlinker")
+                    other_args+=("$arg")
                 fi
                 ;;
             *)
@@ -222,88 +241,6 @@ if [[ -n $SPACK_TEST_COMMAND ]]; then
         esac
         shift
     done
-=======
-if [ "$mode" == vcheck ] ; then
-    exec ${command} "$@"
-fi
-
-#
-# Now do real parsing of the command line args, trying hard to keep
-# non-rpath linker arguments in the proper order w.r.t. other command
-# line arguments.  This is important for things like groups.
-#
-includes=()
-libraries=()
-libs=()
-rpaths=()
-other_args=()
-
-while [ -n "$1" ]; do
-    case "$1" in
-        -I*)
-            arg="${1#-I}"
-            if [ -z "$arg" ]; then shift; arg="$1"; fi
-            includes+=("$arg")
-            ;;
-        -L*)
-            arg="${1#-L}"
-            if [ -z "$arg" ]; then shift; arg="$1"; fi
-            libraries+=("$arg")
-            ;;
-        -l*)
-            arg="${1#-l}"
-            if [ -z "$arg" ]; then shift; arg="$1"; fi
-            libs+=("$arg")
-            ;;
-        -Wl,*)
-            arg="${1#-Wl,}"
-            # TODO: Handle multiple -Wl, continuations of -Wl,-rpath
-            if [[ $arg == -rpath=* ]]; then
-                arg="${arg#-rpath=}"
-                for rpath in ${arg//,/ }; do
-                    rpaths+=("$rpath")
-                done
-            elif [[ $arg == -rpath,* ]]; then
-                arg="${arg#-rpath,}"
-                for rpath in ${arg//,/ }; do
-                    rpaths+=("$rpath")
-                done
-            elif [[ $arg == -rpath ]]; then
-                shift; arg="$1"
-                if [[ $arg != '-Wl,'* ]]; then
-                    die "-Wl,-rpath was not followed by -Wl,*"
-                fi
-                arg="${arg#-Wl,}"
-                for rpath in ${arg//,/ }; do
-                    rpaths+=("$rpath")
-                done
-            else
-                other_args+=("-Wl,$arg")
-            fi
-            ;;
-        -Xlinker)
-            shift; arg="$1";
-            if [[ $arg = -rpath=* ]]; then
-                rpaths+=("${arg#-rpath=}")
-            elif [[ $arg = -rpath ]]; then
-                shift; arg="$1"
-                if [[ $arg != -Xlinker ]]; then
-                    die "-Xlinker -rpath was not followed by -Xlinker <arg>"
-                fi
-                shift; arg="$1"
-                rpaths+=("$arg")
-            else
-                other_args+=("-Xlinker")
-                other_args+=("$arg")
-            fi
-            ;;
-        *)
-            other_args+=("$1")
-            ;;
-    esac
-    shift
-done
->>>>>>> develop
 
     IFS=$'\n'
     case "$SPACK_TEST_COMMAND" in
@@ -329,8 +266,8 @@ done
             echo "${other_args[*]}"
             ;;
         *)
-            echo "ERROR: Unknown test command"
-            exit 1 ;;
+            die "ERROR: Unknown test command"
+            ;;
     esac
     exit
 fi
@@ -338,11 +275,14 @@ fi
 # Read spack dependencies from the path environment variable
 IFS=':' read -ra deps <<< "$SPACK_DEPENDENCIES"
 for dep in "${deps[@]}"; do
-    if [ -d "$dep/include" ]; then
-        args=("-I$dep/include" "${args[@]}")
+    if [[ -d $dep/include ]]; then
+        if [[ $mode = cpp || $mode = cc || $mode = as || $mode = ccld ]]; then
+            args=("-I$dep/include" "${args[@]}")
+        fi
     fi
 
-    if [ -d "$dep/lib" ]; then
+    if [[ -d $dep/lib ]]; then
+        # libraries+=("$dep/lib")
         if [[ $mode = ccld ]]; then
             args=("-L$dep/lib" "-Wl,-rpath,$dep/lib" "${args[@]}")
         elif [[ $mode = ld ]]; then
@@ -350,7 +290,7 @@ for dep in "${deps[@]}"; do
         fi
     fi
 
-    if [ -d "$dep/lib64" ]; then
+    if [[ -d $dep/lib64 ]]; then
         # libraries+=("$dep/lib64")
         if [[ $mode = ccld ]]; then
             args=("-L$dep/lib" "-Wl,-rpath,$dep/lib" "${args[@]}")
@@ -362,8 +302,18 @@ done
 
 # Include all -L's and prefix/whatever dirs in rpath
 if [[ $mode = ccld ]]; then
+    # for dir in "${libraries[@]}"; do
+    #     if [[ dir = $SPACK_INSTALL* ]]; then
+    #         args=("-Wl,-rpath,$dir" "${args[@]}")
+    #     fi
+    # done
     args=("-Wl,-rpath,$SPACK_PREFIX/lib" "-Wl,-rpath,$SPACK_PREFIX/lib64" "${args[@]}")
 elif [[ $mode = ld ]]; then
+    # for dir in "${libraries[@]}"; do
+    #     if [[ dir = $SPACK_INSTALL* ]]; then
+    #         args=("-rpath" "$dir" "${args[@]}")
+    #     fi
+    # done
     args=("-rpath" "$SPACK_PREFIX/lib" "-rpath" "$SPACK_PREFIX/lib64" "${args[@]}")
 fi
 
@@ -385,28 +335,23 @@ PATH=""
 for dir in "${env_path[@]}"; do
     remove=""
     for rm_dir in "${spack_env_dirs[@]}"; do
-        if [ "$dir" = "$rm_dir" ]; then remove=True; fi
+        if [[ $dir = $rm_dir ]]; then remove=True; fi
     done
-    if [ -z "$remove" ]; then
-        if [ -z "$PATH" ]; then
-            PATH="$dir"
-        else
-            PATH="$PATH:$dir"
-        fi
+    if [[ -z $remove ]]; then
+        PATH="${PATH:+$PATH:}$dir"
     fi
 done
 export PATH
 
-full_command=("$command")
-full_command+=("${args[@]}")
+full_command=("$command" "${args[@]}")
 
 #
 # Write the input and output commands to debug logs if it's asked for.
 #
-if [ "$SPACK_DEBUG" = "TRUE" ]; then
+if [[ $SPACK_DEBUG = TRUE ]]; then
     input_log="$SPACK_DEBUG_LOG_DIR/spack-cc-$SPACK_SHORT_SPEC.in.log"
     output_log="$SPACK_DEBUG_LOG_DIR/spack-cc-$SPACK_SHORT_SPEC.out.log"
-    echo "$input_command"     >> $input_log
+    echo "$input_command" >> $input_log
     echo "$mode       ${full_command[@]}" >> $output_log
 fi
 

From 4cf4bf3a0343fc93d6f0c14dd89956fa03b8f738 Mon Sep 17 00:00:00 2001
From: alalazo <massimiliano.culpo@googlemail.com>
Date: Fri, 18 Mar 2016 11:05:59 +0100
Subject: [PATCH 033/230] openssl : solved glitch to prevent spack to freeze
 when the network is unreachable

---
 .../repos/builtin/packages/openssl/package.py | 29 +++++++++++--------
 1 file changed, 17 insertions(+), 12 deletions(-)

diff --git a/var/spack/repos/builtin/packages/openssl/package.py b/var/spack/repos/builtin/packages/openssl/package.py
index 70afaf4038a..22d538531a5 100644
--- a/var/spack/repos/builtin/packages/openssl/package.py
+++ b/var/spack/repos/builtin/packages/openssl/package.py
@@ -1,4 +1,4 @@
-import urllib
+import urllib2
 import llnl.util.tty as tty
 
 from spack import *
@@ -37,17 +37,22 @@ def url_for_version(self, version):
             version_number = '.'.join([str(x) for x in version[:-1]])
             older_url = older.format(version_number=version_number, version_full=version)
             latest_url = latest.format(version=version)
-            response = urllib.urlopen(latest.format(version=version))
-            if response.getcode() == 404:
-                openssl_url = older_url
-                # Checks if we already warned the user for this particular version of OpenSSL.
-                # If not we display a warning message and mark this version
-                if not warnings_given_to_user.get(version, False):
-                    tty.warn('This installation depends on an old version of OpenSSL, which may have known security issues. ')
-                    tty.warn('Consider updating to the latest version of this package.')
-                    tty.warn('More details at {homepage}'.format(homepage=Openssl.homepage))
-                    warnings_given_to_user[version] = True
-            else:
+            try:
+                response = urllib2.urlopen(latest.format(version=version), timeout=5)
+                if response.getcode() == 404:
+                    openssl_url = older_url
+                    # Checks if we already warned the user for this particular version of OpenSSL.
+                    # If not we display a warning message and mark this version
+                    if not warnings_given_to_user.get(version, False):
+                        tty.warn('This installation depends on an old version of OpenSSL, which may have known security issues. ')
+                        tty.warn('Consider updating to the latest version of this package.')
+                        tty.warn('More details at {homepage}'.format(homepage=Openssl.homepage))
+                        warnings_given_to_user[version] = True
+                else:
+                    openssl_url = latest_url
+            except urllib2.URLError:
+                tty.warn('Cannot connect to network to retrieve OpenSSL version. Using default url.')
+                warnings_given_to_user[version] = True
                 openssl_url = latest_url
             # Store the computed URL
             openssl_urls[version] = openssl_url

From 3b24db92b5ea64814b1294fc6c9c982bbaa9b3c6 Mon Sep 17 00:00:00 2001
From: Erik Schnetter <schnetter@gmail.com>
Date: Thu, 17 Mar 2016 13:43:40 -0400
Subject: [PATCH 034/230] Update PAPI to 5.4.3

---
 var/spack/repos/builtin/packages/papi/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/papi/package.py b/var/spack/repos/builtin/packages/papi/package.py
index 910e0aa9f9a..53d69e28d90 100644
--- a/var/spack/repos/builtin/packages/papi/package.py
+++ b/var/spack/repos/builtin/packages/papi/package.py
@@ -13,6 +13,7 @@ class Papi(Package):
     homepage = "http://icl.cs.utk.edu/papi/index.html"
 
     url      = "http://icl.cs.utk.edu/projects/papi/downloads/papi-5.4.1.tar.gz"
+    version('5.4.3', '3211b5a5bb389fe692370f5cf4cc2412')
     version('5.4.1', '9134a99219c79767a11463a76b0b01a2')
     version('5.3.0', '367961dd0ab426e5ae367c2713924ffb')
 

From ec8cc2b52839007f0825815c8cfdee8f9a8629a6 Mon Sep 17 00:00:00 2001
From: alalazo <massimiliano.culpo@googlemail.com>
Date: Fri, 18 Mar 2016 14:40:53 +0100
Subject: [PATCH 035/230] PYTHONPATH : python patches methods for its
 extensions

---
 lib/spack/spack/build_environment.py          |  4 ++-
 lib/spack/spack/cmd/uninstall.py              | 12 +++----
 lib/spack/spack/directory_layout.py           |  2 +-
 lib/spack/spack/modules.py                    | 12 +++++--
 lib/spack/spack/package.py                    | 10 ------
 .../repos/builtin/packages/py-nose/package.py |  6 ++--
 .../repos/builtin/packages/python/package.py  | 34 +++++++++++++++++--
 7 files changed, 53 insertions(+), 27 deletions(-)

diff --git a/lib/spack/spack/build_environment.py b/lib/spack/spack/build_environment.py
index 68477145fef..c51fa584778 100644
--- a/lib/spack/spack/build_environment.py
+++ b/lib/spack/spack/build_environment.py
@@ -282,9 +282,11 @@ def setup_package(pkg):
     for mod in modules:
         set_module_variables_for_package(pkg, mod)
 
-    # Allow dependencies to set up environment as well.
+    # Allow dependencies to modify the module
     for dependency_spec in pkg.spec.traverse(root=False):
         dependency_spec.package.modify_module(pkg.module, dependency_spec, pkg.spec)
+    # Allow dependencies to set up environment as well
+    for dependency_spec in pkg.spec.traverse(root=False):
         dependency_spec.package.setup_dependent_environment(env, pkg.spec)
     # TODO : implement validation
     #validate(env)
diff --git a/lib/spack/spack/cmd/uninstall.py b/lib/spack/spack/cmd/uninstall.py
index d01aa2136b0..2fab8f6f2a1 100644
--- a/lib/spack/spack/cmd/uninstall.py
+++ b/lib/spack/spack/cmd/uninstall.py
@@ -79,7 +79,7 @@ def uninstall(parser, args):
                 try:
                     # should work if package is known to spack
                     pkgs.append(s.package)
-                except spack.repository.UnknownPackageError, e:
+                except spack.repository.UnknownPackageError as e:
                     # The package.py file has gone away -- but still
                     # want to uninstall.
                     spack.Package(s).do_uninstall(force=True)
@@ -94,11 +94,11 @@ def num_installed_deps(pkg):
         for pkg in pkgs:
             try:
                 pkg.do_uninstall(force=args.force)
-            except PackageStillNeededError, e:
+            except PackageStillNeededError as e:
                 tty.error("Will not uninstall %s" % e.spec.format("$_$@$%@$#", color=True))
-                print
-                print "The following packages depend on it:"
+                print()
+                print("The following packages depend on it:")
                 display_specs(e.dependents, long=True)
-                print
-                print "You can use spack uninstall -f to force this action."
+                print()
+                print("You can use spack uninstall -f to force this action.")
                 sys.exit(1)
diff --git a/lib/spack/spack/directory_layout.py b/lib/spack/spack/directory_layout.py
index 39ee4e203d6..da8f1aa1bc0 100644
--- a/lib/spack/spack/directory_layout.py
+++ b/lib/spack/spack/directory_layout.py
@@ -150,7 +150,7 @@ def remove_install_directory(self, spec):
         if os.path.exists(path):
             try:
                 shutil.rmtree(path)
-            except exceptions.OSError, e:
+            except exceptions.OSError as e:
                 raise RemoveFailedError(spec, path, e)
 
         path = os.path.dirname(path)
diff --git a/lib/spack/spack/modules.py b/lib/spack/spack/modules.py
index d192bbe004e..7303844229c 100644
--- a/lib/spack/spack/modules.py
+++ b/lib/spack/spack/modules.py
@@ -119,13 +119,13 @@ def __init__(cls, name, bases, dict):
                 module_types[cls.name] = cls
 
     def __init__(self, spec=None):
+        self.spec = spec
+        self.pkg = spec.package  # Just stored for convenience
+
         # category in the modules system
         # TODO: come up with smarter category names.
         self.category = "spack"
 
-        self.spec = spec
-        self.pkg = spec.package  # Just stored for convenience
-
         # short description default is just the package + version
         # packages can provide this optional attribute
         self.short_description = spec.format("$_ $@")
@@ -161,6 +161,12 @@ def write(self):
 
         # Environment modifications guessed by inspecting the installation prefix
         env = inspect_path(self.spec.prefix)
+
+        # Let the extendee modify their extensions before asking for package-specific modifications
+        for extendee in self.pkg.extendees:
+            extendee_spec = self.spec[extendee]
+            extendee_spec.package.modify_module(self.pkg, extendee_spec, self.spec)
+
         # Package-specific environment modifications
         self.spec.package.setup_environment(env)
         # TODO : implement site-specific modifications and filters
diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py
index 185e3ad2eea..72c84ec624f 100644
--- a/lib/spack/spack/package.py
+++ b/lib/spack/spack/package.py
@@ -1261,16 +1261,6 @@ def rpath_args(self):
         """Get the rpath args as a string, with -Wl,-rpath, for each element."""
         return " ".join("-Wl,-rpath,%s" % p for p in self.rpath)
 
-
-class PythonExtension(Package):
-    def setup_dependent_environment(self, env, dependent_spec):
-        pass
-
-    def setup_environment(self, env):
-        site_packages = glob.glob(join_path(self.spec.prefix.lib, "python*/site-packages"))
-        if site_packages:
-            env.prepend_path('PYTHONPATH', site_packages[0])
-
 def validate_package_url(url_string):
     """Determine whether spack can handle a particular URL or not."""
     url = urlparse(url_string)
diff --git a/var/spack/repos/builtin/packages/py-nose/package.py b/var/spack/repos/builtin/packages/py-nose/package.py
index e817b8eb513..4fee99098ed 100644
--- a/var/spack/repos/builtin/packages/py-nose/package.py
+++ b/var/spack/repos/builtin/packages/py-nose/package.py
@@ -1,12 +1,12 @@
 from spack import *
-from spack.package import PythonExtension
 
-class PyNose(PythonExtension):
+
+class PyNose(Package):
     """nose extends the test loading and running features of unittest,
     making it easier to write, find and run tests."""
 
     homepage = "https://pypi.python.org/pypi/nose"
-    url      = "https://pypi.python.org/packages/source/n/nose/nose-1.3.4.tar.gz"
+    url = "https://pypi.python.org/packages/source/n/nose/nose-1.3.4.tar.gz"
 
     version('1.3.4', '6ed7169887580ddc9a8e16048d38274d')
     version('1.3.6', '0ca546d81ca8309080fc80cb389e7a16')
diff --git a/var/spack/repos/builtin/packages/python/package.py b/var/spack/repos/builtin/packages/python/package.py
index d46e1068b6c..c445d26369e 100644
--- a/var/spack/repos/builtin/packages/python/package.py
+++ b/var/spack/repos/builtin/packages/python/package.py
@@ -1,11 +1,14 @@
+import functools
+import glob
+import inspect
 import os
 import re
 from contextlib import closing
-from llnl.util.lang import match_predicate
-from spack.util.environment import *
 
-from spack import *
 import spack
+from llnl.util.lang import match_predicate
+from spack import *
+from spack.util.environment import *
 
 
 class Python(Package):
@@ -111,6 +114,31 @@ def modify_module(self, module, spec, ext_spec):
         else:
             module.python = Executable(join_path(spec.prefix.bin, 'python'))
 
+        # The code below patches the any python extension to have good defaults for `setup_dependent_environment` and
+        # `setup_environment` only if the extension didn't override any of these functions explicitly.
+        def _setup_env(self, env):
+            site_packages = glob.glob(join_path(self.spec.prefix.lib, "python*/site-packages"))
+            if site_packages:
+                env.prepend_path('PYTHONPATH', site_packages[0])
+
+        def _setup_denv(self, env, extension_spec):
+            pass
+
+        pkg_cls = type(ext_spec.package)  # Retrieve the type we may want to patch
+        if 'python' in pkg_cls.extendees:
+            # List of overrides we are interested in
+            interesting_overrides = ['setup_environment', 'setup_dependent_environment']
+            overrides_found = [
+                (name, defining_cls) for name, _, defining_cls, _, in inspect.classify_class_attrs(pkg_cls)
+                if
+                name in interesting_overrides and  # The attribute has the right name
+                issubclass(defining_cls, Package) and defining_cls is not Package  # and is an actual override
+            ]
+            if not overrides_found:
+                # If no override were found go on patching
+                pkg_cls.setup_environment = functools.wraps(Package.setup_environment)(_setup_env)
+                pkg_cls.setup_dependent_environment = functools.wraps(Package.setup_dependent_environment)(_setup_denv)
+
         # Add variables for lib/pythonX.Y and lib/pythonX.Y/site-packages dirs.
         module.python_lib_dir     = os.path.join(ext_spec.prefix, self.python_lib_dir)
         module.python_include_dir = os.path.join(ext_spec.prefix, self.python_include_dir)

From 5f6f2d5f51fc3700dce13c6aa035943bbc42f6f7 Mon Sep 17 00:00:00 2001
From: alalazo <massimiliano.culpo@googlemail.com>
Date: Fri, 18 Mar 2016 14:42:24 +0100
Subject: [PATCH 036/230] Revert "openssl : solved glitch to prevent spack to
 freeze when the network is unreachable"

This reverts commit 4cf4bf3a0343fc93d6f0c14dd89956fa03b8f738.
---
 .../repos/builtin/packages/openssl/package.py | 29 ++++++++-----------
 1 file changed, 12 insertions(+), 17 deletions(-)

diff --git a/var/spack/repos/builtin/packages/openssl/package.py b/var/spack/repos/builtin/packages/openssl/package.py
index 22d538531a5..70afaf4038a 100644
--- a/var/spack/repos/builtin/packages/openssl/package.py
+++ b/var/spack/repos/builtin/packages/openssl/package.py
@@ -1,4 +1,4 @@
-import urllib2
+import urllib
 import llnl.util.tty as tty
 
 from spack import *
@@ -37,22 +37,17 @@ def url_for_version(self, version):
             version_number = '.'.join([str(x) for x in version[:-1]])
             older_url = older.format(version_number=version_number, version_full=version)
             latest_url = latest.format(version=version)
-            try:
-                response = urllib2.urlopen(latest.format(version=version), timeout=5)
-                if response.getcode() == 404:
-                    openssl_url = older_url
-                    # Checks if we already warned the user for this particular version of OpenSSL.
-                    # If not we display a warning message and mark this version
-                    if not warnings_given_to_user.get(version, False):
-                        tty.warn('This installation depends on an old version of OpenSSL, which may have known security issues. ')
-                        tty.warn('Consider updating to the latest version of this package.')
-                        tty.warn('More details at {homepage}'.format(homepage=Openssl.homepage))
-                        warnings_given_to_user[version] = True
-                else:
-                    openssl_url = latest_url
-            except urllib2.URLError:
-                tty.warn('Cannot connect to network to retrieve OpenSSL version. Using default url.')
-                warnings_given_to_user[version] = True
+            response = urllib.urlopen(latest.format(version=version))
+            if response.getcode() == 404:
+                openssl_url = older_url
+                # Checks if we already warned the user for this particular version of OpenSSL.
+                # If not we display a warning message and mark this version
+                if not warnings_given_to_user.get(version, False):
+                    tty.warn('This installation depends on an old version of OpenSSL, which may have known security issues. ')
+                    tty.warn('Consider updating to the latest version of this package.')
+                    tty.warn('More details at {homepage}'.format(homepage=Openssl.homepage))
+                    warnings_given_to_user[version] = True
+            else:
                 openssl_url = latest_url
             # Store the computed URL
             openssl_urls[version] = openssl_url

From 67ca2c704b9c367b41ce29342a06427e156a30e9 Mon Sep 17 00:00:00 2001
From: alalazo <massimiliano.culpo@googlemail.com>
Date: Fri, 18 Mar 2016 15:18:26 +0100
Subject: [PATCH 037/230] modules : fixed bug in `modify_module` arguments

---
 lib/spack/spack/modules.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/spack/spack/modules.py b/lib/spack/spack/modules.py
index 7303844229c..f5bf2138456 100644
--- a/lib/spack/spack/modules.py
+++ b/lib/spack/spack/modules.py
@@ -165,7 +165,7 @@ def write(self):
         # Let the extendee modify their extensions before asking for package-specific modifications
         for extendee in self.pkg.extendees:
             extendee_spec = self.spec[extendee]
-            extendee_spec.package.modify_module(self.pkg, extendee_spec, self.spec)
+            extendee_spec.package.modify_module(self.pkg.module, extendee_spec, self.spec)
 
         # Package-specific environment modifications
         self.spec.package.setup_environment(env)

From ccd90df62ffd69b5c3b4e1f8dbaf82146721a52a Mon Sep 17 00:00:00 2001
From: alalazo <massimiliano.culpo@googlemail.com>
Date: Fri, 18 Mar 2016 15:41:14 +0100
Subject: [PATCH 038/230] modules : turned category into a property (logic can
 be extended later)

---
 lib/spack/spack/modules.py | 15 +++++++++++----
 1 file changed, 11 insertions(+), 4 deletions(-)

diff --git a/lib/spack/spack/modules.py b/lib/spack/spack/modules.py
index f5bf2138456..bb1a444e5a6 100644
--- a/lib/spack/spack/modules.py
+++ b/lib/spack/spack/modules.py
@@ -122,10 +122,6 @@ def __init__(self, spec=None):
         self.spec = spec
         self.pkg = spec.package  # Just stored for convenience
 
-        # category in the modules system
-        # TODO: come up with smarter category names.
-        self.category = "spack"
-
         # short description default is just the package + version
         # packages can provide this optional attribute
         self.short_description = spec.format("$_ $@")
@@ -137,6 +133,17 @@ def __init__(self, spec=None):
         if self.spec.package.__doc__:
             self.long_description = re.sub(r'\s+', ' ', self.spec.package.__doc__)
 
+    @property
+    def category(self):
+        # Anything defined at the package level takes precedence
+        if hasattr(self.pkg, 'category'):
+            return self.pkg.category
+        # Extensions
+        for extendee in self.pkg.extendees:
+            return '{extendee} extension'.format(extendee=extendee)
+        # Not very descriptive fallback
+        return 'spack installed package'
+
     # @property
     # def paths(self):
     #         # Add python path unless it's an actual python installation

From 1e468c55414822365b4ba7f7c52fbfdb5f30d3b2 Mon Sep 17 00:00:00 2001
From: alalazo <massimiliano.culpo@googlemail.com>
Date: Fri, 18 Mar 2016 16:02:44 +0100
Subject: [PATCH 039/230] modules : added formats mapping

---
 lib/spack/spack/modules.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/lib/spack/spack/modules.py b/lib/spack/spack/modules.py
index bb1a444e5a6..0378110c8cb 100644
--- a/lib/spack/spack/modules.py
+++ b/lib/spack/spack/modules.py
@@ -256,7 +256,10 @@ class TclModule(EnvModule):
 
     formats = {
         PrependPath: 'prepend-path {name} \"{value}\"\n',
-        SetEnv: 'setenv {name} \"{value}\"\n'
+        AppendPath: 'append-path {name} \"{value}\"\n',
+        RemovePath: 'remove-path {name} \"{value}\"\n',
+        SetEnv: 'setenv {name} \"{value}\"\n',
+        UnsetEnv: 'unsetenv {name}\n'
     }
 
     @property

From 491babd5cd435fc307b6e977b850e4e64d2b0ccf Mon Sep 17 00:00:00 2001
From: alalazo <massimiliano.culpo@googlemail.com>
Date: Fri, 18 Mar 2016 17:09:20 +0100
Subject: [PATCH 040/230] env modifications : added a validation rule

---
 lib/spack/spack/build_environment.py |  6 +++---
 lib/spack/spack/environment.py       | 30 ++++++++++++++++++++++++++++
 2 files changed, 33 insertions(+), 3 deletions(-)

diff --git a/lib/spack/spack/build_environment.py b/lib/spack/spack/build_environment.py
index c51fa584778..59b234624cf 100644
--- a/lib/spack/spack/build_environment.py
+++ b/lib/spack/spack/build_environment.py
@@ -34,8 +34,9 @@
 import sys
 
 import spack
+import llnl.util.tty as tty
 from llnl.util.filesystem import *
-from spack.environment import EnvironmentModifications, concatenate_paths
+from spack.environment import EnvironmentModifications, concatenate_paths, validate
 from spack.util.environment import *
 from spack.util.executable import Executable, which
 
@@ -288,8 +289,7 @@ def setup_package(pkg):
     # Allow dependencies to set up environment as well
     for dependency_spec in pkg.spec.traverse(root=False):
         dependency_spec.package.setup_dependent_environment(env, pkg.spec)
-    # TODO : implement validation
-    #validate(env)
+    validate(env, tty.warn)
     env.apply_modifications()
 
 
diff --git a/lib/spack/spack/environment.py b/lib/spack/spack/environment.py
index 6d214595a3e..74aef57fe88 100644
--- a/lib/spack/spack/environment.py
+++ b/lib/spack/spack/environment.py
@@ -202,3 +202,33 @@ def concatenate_paths(paths):
         string
     """
     return ':'.join(str(item) for item in paths)
+
+
+def set_or_unset_not_first(variable, changes, errstream):
+    """
+    Check if we are going to set or unset something after other modifications have already been requested
+    """
+    indexes = [ii for ii, item in enumerate(changes) if ii != 0 and type(item) in [SetEnv, UnsetEnv]]
+    if indexes:
+        good = '\t    \t{context} at {filename}:{lineno}'
+        nogood = '\t--->\t{context} at {filename}:{lineno}'
+        errstream('Suspicious requests to set or unset the variable \'{var}\' found'.format(var=variable))
+        for ii, item in enumerate(changes):
+            print_format = nogood if ii in indexes else good
+            errstream(print_format.format(**item.args))
+
+
+def validate(env, errstream):
+    """
+    Validates the environment modifications to check for the presence of suspicious patterns. Prompts a warning for
+    everything that was found
+
+    Current checks:
+    - set or unset variables after other changes on the same variable
+
+    Args:
+        env: list of environment modifications
+    """
+    modifications = env.group_by_name()
+    for variable, list_of_changes in sorted(modifications.items()):
+        set_or_unset_not_first(variable, list_of_changes, errstream)

From 23f3f1adfe01f7b1301959e7e54584724679c7b3 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Fri, 18 Mar 2016 13:32:37 -0700
Subject: [PATCH 041/230] Make InstallError and ExternalPackageError visiible
 in packages.

---
 lib/spack/spack/__init__.py | 8 ++++++--
 lib/spack/spack/package.py  | 4 ++++
 2 files changed, 10 insertions(+), 2 deletions(-)

diff --git a/lib/spack/spack/__init__.py b/lib/spack/spack/__init__.py
index 0ba42bbbfcd..aee11f061f3 100644
--- a/lib/spack/spack/__init__.py
+++ b/lib/spack/spack/__init__.py
@@ -189,5 +189,9 @@
 from spack.util.executable import *
 __all__ += spack.util.executable.__all__
 
-from spack.package import install_dependency_symlinks, flatten_dependencies, DependencyConflictError
-__all__ += ['install_dependency_symlinks', 'flatten_dependencies', 'DependencyConflictError']
+from spack.package import \
+    install_dependency_symlinks, flatten_dependencies, DependencyConflictError, \
+    InstallError, ExternalPackageError
+__all__ += [
+    'install_dependency_symlinks', 'flatten_dependencies', 'DependencyConflictError',
+    'InstallError', 'ExternalPackageError']
diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py
index b488e4c49db..dafad0b184a 100644
--- a/lib/spack/spack/package.py
+++ b/lib/spack/spack/package.py
@@ -1351,6 +1351,10 @@ def __init__(self, message, long_msg=None):
         super(InstallError, self).__init__(message, long_msg)
 
 
+class ExternalPackageError(InstallError):
+    """Raised by install() when a package is only for external use."""
+
+
 class PackageStillNeededError(InstallError):
     """Raised when package is still needed by another on uninstall."""
     def __init__(self, spec, dependents):

From e9126baaabbfaa5e12641b3d44a5c5fd49e43ca3 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Fri, 18 Mar 2016 13:42:45 -0700
Subject: [PATCH 042/230] Add docs for InstallError.

---
 lib/spack/docs/packaging_guide.rst | 14 ++++++++++++++
 1 file changed, 14 insertions(+)

diff --git a/lib/spack/docs/packaging_guide.rst b/lib/spack/docs/packaging_guide.rst
index c1077e44977..519c0da2329 100644
--- a/lib/spack/docs/packaging_guide.rst
+++ b/lib/spack/docs/packaging_guide.rst
@@ -1844,6 +1844,20 @@ dedicated process.
 
 .. _prefix-objects:
 
+
+Failing the build
+----------------------
+
+Sometimes you don't want a package to successfully install unless some
+condition is true.  You can explicitly cause the build to fail from
+``install()`` by raising an ``InstallError``, for example:
+
+.. code-block:: python
+
+   if spec.architecture.startswith('darwin'):
+       raise InstallError('This package does not build on Mac OS X!')
+
+
 Prefix objects
 ----------------------
 

From f5f7d47be1a5fd8488ed4cdc692173fe136d9791 Mon Sep 17 00:00:00 2001
From: Erik Schnetter <schnetter@gmail.com>
Date: Sat, 19 Mar 2016 18:42:06 -0400
Subject: [PATCH 043/230] Support Bash "-u" mode

---
 share/spack/setup-env.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/share/spack/setup-env.sh b/share/spack/setup-env.sh
index 586a5b836b1..764af684001 100755
--- a/share/spack/setup-env.sh
+++ b/share/spack/setup-env.sh
@@ -141,7 +141,7 @@ function _spack_pathadd {
     fi
 
     # Do the actual prepending here.
-    eval "_pa_oldvalue=\$${_pa_varname}"
+    eval "_pa_oldvalue=\${${_pa_varname}:-}"
 
     if [ -d "$_pa_new_path" ] && [[ ":$_pa_oldvalue:" != *":$_pa_new_path:"* ]]; then
         if [ -n "$_pa_oldvalue" ]; then

From ed0b5e649dd6bc480e3faa6ffcca121eb9e264b8 Mon Sep 17 00:00:00 2001
From: "Kelly (KT) Thompson" <kgt@lanl.gov>
Date: Fri, 18 Mar 2016 15:54:26 -0600
Subject: [PATCH 044/230] + Provide fpic variant for netlib-lapack.

---
 var/spack/repos/builtin/packages/netlib-lapack/package.py | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/var/spack/repos/builtin/packages/netlib-lapack/package.py b/var/spack/repos/builtin/packages/netlib-lapack/package.py
index 741f4af4215..78c5a053fe5 100644
--- a/var/spack/repos/builtin/packages/netlib-lapack/package.py
+++ b/var/spack/repos/builtin/packages/netlib-lapack/package.py
@@ -20,13 +20,13 @@ class NetlibLapack(Package):
     version('3.3.1', 'd0d533ec9a5b74933c2a1e84eedc58b4')
 
     variant('shared', default=False, description="Build shared library version")
+    variant('fpic', default=False, description="Build with -fpic compiler option")
 
     # virtual dependency
     provides('lapack')
 
     # blas is a virtual dependency.
     depends_on('blas')
-
     depends_on('cmake')
 
     # Doesn't always build correctly in parallel
@@ -37,24 +37,23 @@ def get_blas_libs(self):
         blas = self.spec['netlib-blas']
         return [join_path(blas.prefix.lib, 'blas.a')]
 
-
     @when('^atlas')
     def get_blas_libs(self):
         blas = self.spec['atlas']
         return [join_path(blas.prefix.lib, l)
                 for l in ('libf77blas.a', 'libatlas.a')]
 
-
     def install(self, spec, prefix):
         blas_libs = ";".join(self.get_blas_libs())
         cmake_args = [".", '-DBLAS_LIBRARIES=' + blas_libs]
 
         if '+shared' in spec:
             cmake_args.append('-DBUILD_SHARED_LIBS=ON')
+        if '+fpic' in spec:
+            cmake_args.append('-DCMAKE_POSITION_INDEPENDENT_CODE=ON')
 
         cmake_args += std_cmake_args
 
         cmake(*cmake_args)
         make()
         make("install")
-

From 620c120503c8c23d10feb14e14d37dfc36f4befb Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Sat, 19 Mar 2016 19:32:44 +0100
Subject: [PATCH 045/230] fix openblas suffix for OS-X

---
 var/spack/repos/builtin/packages/openblas/package.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/var/spack/repos/builtin/packages/openblas/package.py b/var/spack/repos/builtin/packages/openblas/package.py
index e16d3fe89c1..781a1e2ec8f 100644
--- a/var/spack/repos/builtin/packages/openblas/package.py
+++ b/var/spack/repos/builtin/packages/openblas/package.py
@@ -1,4 +1,5 @@
 from spack import *
+import sys
 
 class Openblas(Package):
     """OpenBLAS: An optimized BLAS library"""
@@ -16,13 +17,14 @@ def install(self, spec, prefix):
         make('libs', 'netlib', 'shared', 'CC=cc', 'FC=f77')
         make('install', "PREFIX='%s'" % prefix)
 
+        lib_dsuffix = 'dylib' if sys.platform == 'darwin' else 'so'
         # Blas virtual package should provide blas.a and libblas.a
         with working_dir(prefix.lib):
             symlink('libopenblas.a', 'blas.a')
             symlink('libopenblas.a', 'libblas.a')
-            symlink('libopenblas.so', 'libblas.so')
+            symlink('libopenblas.%s' % lib_dsuffix, 'libblas.%s' % lib_dsuffix)
 
         # Lapack virtual package should provide liblapack.a
         with working_dir(prefix.lib):
             symlink('libopenblas.a', 'liblapack.a')
-            symlink('libopenblas.so', 'liblapack.so')
+            symlink('libopenblas.%s' % lib_dsuffix, 'liblapack.%s' % lib_dsuffix)

From 95ad2875b6bb4dc15eb43b44c1dbdd521c843119 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Sun, 20 Mar 2016 09:25:02 +0100
Subject: [PATCH 046/230] fix scalapack suffix for osx

---
 .../builtin/packages/netlib-scalapack/package.py      | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/var/spack/repos/builtin/packages/netlib-scalapack/package.py b/var/spack/repos/builtin/packages/netlib-scalapack/package.py
index 22d538560e8..a5b6eedafbe 100644
--- a/var/spack/repos/builtin/packages/netlib-scalapack/package.py
+++ b/var/spack/repos/builtin/packages/netlib-scalapack/package.py
@@ -1,8 +1,9 @@
 from spack import *
+import sys
 
 class NetlibScalapack(Package):
     """ScaLAPACK is a library of high-performance linear algebra routines for parallel distributed memory machines"""
-    
+
     homepage = "http://www.netlib.org/scalapack/"
     url      = "http://www.netlib.org/scalapack/scalapack-2.0.2.tgz"
 
@@ -32,17 +33,17 @@ def install(self, spec, prefix):
                 "-DCMAKE_C_FLAGS=-fPIC",
                 "-DCMAKE_Fortran_FLAGS=-fPIC"
             ])
-           
+
         options.extend(std_cmake_args)
-        
+
         with working_dir('spack-build', create=True):
             cmake('..', *options)
             make()
             make("install")
 
     def setup_dependent_environment(self, module, spec, dependent_spec):
-        # TODO treat OS that are not Linux...
-        lib_suffix = '.so' if '+shared' in spec['scalapack'] else '.a'
+        lib_dsuffix = '.dylib' if sys.platform == 'darwin' else '.so'
+        lib_suffix = lib_dsuffix if '+shared' in spec['scalapack'] else '.a'
 
         spec['scalapack'].fc_link = '-L%s -lscalapack' % spec['scalapack'].prefix.lib
         spec['scalapack'].cc_link = spec['scalapack'].fc_link

From db61a09cf14cc791d7692aac0329e8958b228fb6 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Fri, 18 Mar 2016 16:28:36 +0100
Subject: [PATCH 047/230] fix mumps: when installed with parmetis has to be
 linked with metis

---
 .../repos/builtin/packages/mumps/package.py   | 28 +++++++++++--------
 1 file changed, 16 insertions(+), 12 deletions(-)

diff --git a/var/spack/repos/builtin/packages/mumps/package.py b/var/spack/repos/builtin/packages/mumps/package.py
index 44a37903cc8..5c120c37df8 100644
--- a/var/spack/repos/builtin/packages/mumps/package.py
+++ b/var/spack/repos/builtin/packages/mumps/package.py
@@ -20,10 +20,10 @@ class Mumps(Package):
     variant('complex', default=True, description='Activate the compilation of cmumps and/or zmumps')
     variant('idx64', default=False, description='Use int64_t/integer*8 as default index type')
 
-    
+
     depends_on('scotch + esmumps', when='~ptscotch+scotch')
     depends_on('scotch + esmumps + mpi', when='+ptscotch')
-    depends_on('metis', when='~parmetis+metis')
+    depends_on('metis', when='+metis')
     depends_on('parmetis', when="+parmetis")
     depends_on('blas')
     depends_on('lapack')
@@ -38,11 +38,11 @@ class Mumps(Package):
     def write_makefile_inc(self):
         if ('+parmetis' in self.spec or '+ptscotch' in self.spec) and '+mpi' not in self.spec:
             raise RuntimeError('You cannot use the variants parmetis or ptscotch without mpi')
-        
+
         makefile_conf = ["LIBBLAS = -L%s -lblas" % self.spec['blas'].prefix.lib]
 
         orderings = ['-Dpord']
-        
+
         if '+ptscotch' in self.spec or '+scotch' in self.spec:
             join_lib = ' -l%s' % ('pt' if '+ptscotch' in self.spec else '')
             makefile_conf.extend(
@@ -54,15 +54,19 @@ def write_makefile_inc(self):
             if '+ptscotch' in self.spec:
                 orderings.append('-Dptscotch')
 
-        if '+parmetis' in self.spec or '+metis' in self.spec:
+        if '+parmetis' in self.spec and '+metis' in self.spec:
             libname = 'parmetis' if '+parmetis' in self.spec else 'metis'
             makefile_conf.extend(
-                ["IMETIS = -I%s" % self.spec[libname].prefix.include,
-                 "LMETIS = -L%s -l%s" % (self.spec[libname].prefix.lib, libname)])
+                ["IMETIS = -I%s" % self.spec['parmetis'].prefix.include,
+                 "LMETIS = -L%s -l%s -L%s -l%s" % (self.spec['parmetis'].prefix.lib, 'parmetis',self.spec['metis'].prefix.lib, 'metis')])
+
+            orderings.append('-Dparmetis')
+        elif '+metis' in self.spec:
+            makefile_conf.extend(
+                ["IMETIS = -I%s" % self.spec['metis'].prefix.include,
+                 "LMETIS = -L%s -l%s" % (self.spec['metis'].prefix.lib, 'metis')])
 
             orderings.append('-Dmetis')
-            if '+parmetis' in self.spec:
-                orderings.append('-Dparmetis')
 
         makefile_conf.append("ORDERINGSF = %s" % (' '.join(orderings)))
 
@@ -101,12 +105,12 @@ def write_makefile_inc(self):
         # compiler possible values are -DAdd_, -DAdd__ and/or -DUPPER
         makefile_conf.append("CDEFS   = -DAdd_")
 
-        
+
         makefile_inc_template = join_path(os.path.dirname(self.module.__file__),
                                           'Makefile.inc')
         with open(makefile_inc_template, "r") as fh:
             makefile_conf.extend(fh.read().split('\n'))
-        
+
         with working_dir('.'):
             with open("Makefile.inc", "w") as fh:
                 makefile_inc = '\n'.join(makefile_conf)
@@ -130,7 +134,7 @@ def install(self, spec, prefix):
                 make_libs.append('zexamples')
 
         self.write_makefile_inc()
-                
+
         make(*make_libs)
 
         install_tree('lib', prefix.lib)

From d493658a583231eeb778613cf7b6c8c8641c63a0 Mon Sep 17 00:00:00 2001
From: Cyrus Harrison <cyrush@llnl.gov>
Date: Sun, 20 Mar 2016 15:18:36 -0700
Subject: [PATCH 048/230] cmake package: add variant for openssl support

The openssl variant defaults to true to preserve spack's
current CMake configuration, which is using OpenSSL.

Signed-off-by: Cyrus Harrison <cyrush@llnl.gov>
---
 var/spack/repos/builtin/packages/cmake/package.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/var/spack/repos/builtin/packages/cmake/package.py b/var/spack/repos/builtin/packages/cmake/package.py
index cc93c7067c3..be930a90abe 100644
--- a/var/spack/repos/builtin/packages/cmake/package.py
+++ b/var/spack/repos/builtin/packages/cmake/package.py
@@ -38,6 +38,7 @@ class Cmake(Package):
     version('2.8.10.2', '097278785da7182ec0aea8769d06860c')
 
     variant('ncurses', default=True, description='Enables the build of the ncurses gui')
+    variant('openssl', default=True, description="Enables CMake's OpenSSL features")
     variant('qt', default=False, description='Enables the build of cmake-gui')
     variant('doc', default=False, description='Enables the generation of html and man page documentation')
 
@@ -77,8 +78,9 @@ def install(self, spec, prefix):
             options.append('--sphinx-html')
             options.append('--sphinx-man')
 
-        options.append('--')
-        options.append('-DCMAKE_USE_OPENSSL=ON')
+        if '+openssl' in spec:
+            options.append('--')
+            options.append('-DCMAKE_USE_OPENSSL=ON')
 
         configure(*options)
         make()

From bba66cbe2836e364b58a611a5a5f5ae0d9692df4 Mon Sep 17 00:00:00 2001
From: Cyrus Harrison <cyrush@llnl.gov>
Date: Sun, 20 Mar 2016 19:27:22 -0700
Subject: [PATCH 049/230] cmake: depend on openssl when openssl variant=true

---
 var/spack/repos/builtin/packages/cmake/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/cmake/package.py b/var/spack/repos/builtin/packages/cmake/package.py
index be930a90abe..1f93d39769b 100644
--- a/var/spack/repos/builtin/packages/cmake/package.py
+++ b/var/spack/repos/builtin/packages/cmake/package.py
@@ -43,6 +43,7 @@ class Cmake(Package):
     variant('doc', default=False, description='Enables the generation of html and man page documentation')
 
     depends_on('ncurses', when='+ncurses')
+    depends_on('openssl', when='+openssl')
     depends_on('qt', when='+qt')
     depends_on('python@2.7.11:', when='+doc')
     depends_on('py-sphinx', when='+doc')

From 7b283bfaffa5509915d91392878203bba8a8d2cb Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Mon, 21 Mar 2016 07:48:17 +0100
Subject: [PATCH 050/230] fix petsc on osx

---
 .../repos/builtin/packages/petsc/package.py   | 20 ++++++++++++++-----
 1 file changed, 15 insertions(+), 5 deletions(-)

diff --git a/var/spack/repos/builtin/packages/petsc/package.py b/var/spack/repos/builtin/packages/petsc/package.py
index efe172fc083..7239baaf7f5 100644
--- a/var/spack/repos/builtin/packages/petsc/package.py
+++ b/var/spack/repos/builtin/packages/petsc/package.py
@@ -61,14 +61,24 @@ def mpi_dependent_options(self):
                 errors = ['incompatible variants given'] + errors
                 raise RuntimeError('\n'.join(errors))
         else:
-            compiler_opts = [
-                '--with-mpi=1',
-                '--with-mpi-dir=%s' % self.spec['mpi'].prefix,
-            ]
+            if self.compiler.name == "clang":
+                compiler_opts = [
+                    '--with-mpi=1',
+                    '--with-cc=%s  -Qunused-arguments' % join_path(self.spec['mpi'].prefix.bin, 'mpicc'), # Avoid confusing PETSc config by clang: warning: argument unused during compilation
+                    '--with-cxx=%s -Qunused-arguments' % join_path(self.spec['mpi'].prefix.bin, 'mpic++'),
+                    '--with-fc=%s' % join_path(self.spec['mpi'].prefix.bin, 'mpif90'),
+                    '--with-f77=%s' % join_path(self.spec['mpi'].prefix.bin, 'mpif77'),
+                ]
+            else:
+                compiler_opts = [
+                    '--with-mpi=1',
+                    '--with-mpi-dir=%s' % self.spec['mpi'].prefix,
+                ]
         return compiler_opts
 
     def install(self, spec, prefix):
-        options = []
+        options = ['--with-debugging=0',
+                   '--with-ssl=0']
         options.extend(self.mpi_dependent_options())
         options.extend([
             '--with-precision=%s' % ('double' if '+double' in spec else 'single'),

From aef6d50b08daf893174046ba14c09a7019fe1212 Mon Sep 17 00:00:00 2001
From: alalazo <massimiliano.culpo@googlemail.com>
Date: Mon, 21 Mar 2016 09:23:25 +0100
Subject: [PATCH 051/230] uninstall : fixed typo (print statement vs. print
 function)

---
 lib/spack/spack/cmd/uninstall.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/lib/spack/spack/cmd/uninstall.py b/lib/spack/spack/cmd/uninstall.py
index 2fab8f6f2a1..1ece8386124 100644
--- a/lib/spack/spack/cmd/uninstall.py
+++ b/lib/spack/spack/cmd/uninstall.py
@@ -96,9 +96,9 @@ def num_installed_deps(pkg):
                 pkg.do_uninstall(force=args.force)
             except PackageStillNeededError as e:
                 tty.error("Will not uninstall %s" % e.spec.format("$_$@$%@$#", color=True))
-                print()
+                print('')
                 print("The following packages depend on it:")
                 display_specs(e.dependents, long=True)
-                print()
+                print('')
                 print("You can use spack uninstall -f to force this action.")
                 sys.exit(1)

From b926d8a0cdcf47de029e372cf15e281266930378 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Mon, 21 Mar 2016 14:33:00 +0100
Subject: [PATCH 052/230] build parmetis against external metis

---
 .../parmetis/enable_external_metis.patch      | 13 ++++++++++
 .../builtin/packages/parmetis/package.py      | 24 ++++---------------
 2 files changed, 17 insertions(+), 20 deletions(-)
 create mode 100644 var/spack/repos/builtin/packages/parmetis/enable_external_metis.patch

diff --git a/var/spack/repos/builtin/packages/parmetis/enable_external_metis.patch b/var/spack/repos/builtin/packages/parmetis/enable_external_metis.patch
new file mode 100644
index 00000000000..514781b8b88
--- /dev/null
+++ b/var/spack/repos/builtin/packages/parmetis/enable_external_metis.patch
@@ -0,0 +1,13 @@
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index ca945dd..1bf94e9 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -33,7 +33,7 @@ include_directories(${GKLIB_PATH})
+ include_directories(${METIS_PATH}/include)
+
+ # List of directories that cmake will look for CMakeLists.txt
+-add_subdirectory(${METIS_PATH}/libmetis ${CMAKE_BINARY_DIR}/libmetis)
++#add_subdirectory(${METIS_PATH}/libmetis ${CMAKE_BINARY_DIR}/libmetis)
+ add_subdirectory(include)
+ add_subdirectory(libparmetis)
+ add_subdirectory(programs)
diff --git a/var/spack/repos/builtin/packages/parmetis/package.py b/var/spack/repos/builtin/packages/parmetis/package.py
index c897dec7e44..3f18dd76b87 100644
--- a/var/spack/repos/builtin/packages/parmetis/package.py
+++ b/var/spack/repos/builtin/packages/parmetis/package.py
@@ -25,9 +25,6 @@
 
 from spack import *
 
-# FIXME : lot of code is duplicated from packages/metis/package.py . Inheriting from there may reduce
-# FIXME : the installation rules to just a few lines
-
 
 class Parmetis(Package):
     """
@@ -43,13 +40,11 @@ class Parmetis(Package):
     variant('debug', default=False, description='Builds the library in debug mode')
     variant('gdb', default=False, description='Enables gdb support')
 
-    variant('idx64', default=False, description='Use int64_t as default index type')
-    variant('double', default=False, description='Use double precision floating point types')
-
     depends_on('cmake @2.8:')  # build dependency
     depends_on('mpi')
 
-    # FIXME : this should conflict with metis as it builds its own version internally
+    patch('enable_external_metis.patch')
+    depends_on('metis')
 
     depends_on('gdb', when='+gdb')
 
@@ -63,8 +58,8 @@ def install(self, spec, prefix):
 
         # FIXME : Once a contract is defined, MPI compilers should be retrieved indirectly via spec['mpi'] in case
         # FIXME : they use a non-standard name
-        options.extend(['-DGKLIB_PATH:PATH={metis_source}/GKlib'.format(metis_source=metis_source),
-                        '-DMETIS_PATH:PATH={metis_source}'.format(metis_source=metis_source),
+        options.extend(['-DGKLIB_PATH:PATH={metis_source}/GKlib'.format(metis_source=metis_source), # still need headers from METIS source, and they are not installed with METIS. shame...
+                        '-DMETIS_PATH:PATH={metis_source}'.format(metis_source=spec['metis'].prefix),
                         '-DCMAKE_C_COMPILER:STRING=mpicc',
                         '-DCMAKE_CXX_COMPILER:STRING=mpicxx'])
 
@@ -78,18 +73,7 @@ def install(self, spec, prefix):
         if '+gdb' in spec:
             options.append('-DGDB:BOOL=ON')
 
-        metis_header = join_path(metis_source, 'include', 'metis.h')
-
-        if '+idx64' in spec:
-            filter_file('IDXTYPEWIDTH 32', 'IDXTYPEWIDTH 64', metis_header)
-
-        if '+double' in spec:
-            filter_file('REALTYPEWIDTH 32', 'REALTYPEWIDTH 64', metis_header)
-
         with working_dir(build_directory, create=True):
             cmake(source_directory, *options)
             make()
             make("install")
-            # Parmetis build system doesn't allow for an external metis to be used, but doesn't copy the required
-            # metis header either
-            install(metis_header, self.prefix.include)

From 3fcaf5b9031c3d55b152844b97cd432078340f4b Mon Sep 17 00:00:00 2001
From: alalazo <massimiliano.culpo@googlemail.com>
Date: Mon, 21 Mar 2016 14:47:05 +0100
Subject: [PATCH 053/230] llvm : update to 3.8.0

---
 var/spack/repos/builtin/packages/llvm/package.py | 15 +++++++++++++++
 1 file changed, 15 insertions(+)

diff --git a/var/spack/repos/builtin/packages/llvm/package.py b/var/spack/repos/builtin/packages/llvm/package.py
index 280e400f696..5c38b5b88c3 100644
--- a/var/spack/repos/builtin/packages/llvm/package.py
+++ b/var/spack/repos/builtin/packages/llvm/package.py
@@ -132,6 +132,21 @@ class Llvm(Package):
                         'llvm-libunwind' : 'http://llvm.org/svn/llvm-project/libunwind/trunk',
                         }
                   },
+                  {
+                    'version' : '3.8.0',
+                    'md5':'07a7a74f3c6bd65de4702bf941b511a0',
+                    'resources' : {
+                        'compiler-rt' : 'd6fcbe14352ffb708e4d1ac2e48bb025',
+                        'openmp' : '8fd7cc35d48051613cf1e750e9f22e40',
+                        'polly' : '1b3b20f52d34a4024e21a4ea7112caa7',
+                        'libcxx' : 'd6e0bdbbee39f7907ad74fd56d03b88a',
+                        'libcxxabi' : 'bbe6b4d72c7c5978550d370af529bcf7',
+                        'clang' : 'cc99e7019bb74e6459e80863606250c5',
+                        'clang-tools-extra' : 'c2344f50e0eea0b402f0092a80ddc036',
+                        'lldb' : 'a5da35ed9cc8c8817ee854e3dbfba00e',
+                        'llvm-libunwind' : '162ade468607f153cca12be90b5194fa',
+                        }
+                  },
                   {
                     'version' : '3.7.1',
                     'md5':'bf8b3a2c79e61212c5409041dfdbd319',

From 3a3443dff63167fc0331672871af4c0cc1fe5903 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Mon, 21 Mar 2016 15:14:48 +0100
Subject: [PATCH 054/230] parmetis patches by PETSc developers

---
 .../builtin/packages/parmetis/package.py      |  6 ++
 ...9fd0f408dc4d42c57f5c3ee6ace411eb222b.patch | 77 +++++++++++++++++++
 ...9d68aa1d6cbc70740d0f35024aae17f7d5cb.patch | 35 +++++++++
 3 files changed, 118 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/parmetis/pkg-parmetis-1c1a9fd0f408dc4d42c57f5c3ee6ace411eb222b.patch
 create mode 100644 var/spack/repos/builtin/packages/parmetis/pkg-parmetis-82409d68aa1d6cbc70740d0f35024aae17f7d5cb.patch

diff --git a/var/spack/repos/builtin/packages/parmetis/package.py b/var/spack/repos/builtin/packages/parmetis/package.py
index 3f18dd76b87..c691cf4191d 100644
--- a/var/spack/repos/builtin/packages/parmetis/package.py
+++ b/var/spack/repos/builtin/packages/parmetis/package.py
@@ -46,6 +46,12 @@ class Parmetis(Package):
     patch('enable_external_metis.patch')
     depends_on('metis')
 
+    # bug fixes from PETSc developers
+    # https://bitbucket.org/petsc/pkg-parmetis/commits/1c1a9fd0f408dc4d42c57f5c3ee6ace411eb222b/raw/
+    patch('pkg-parmetis-1c1a9fd0f408dc4d42c57f5c3ee6ace411eb222b.patch')
+    # https://bitbucket.org/petsc/pkg-parmetis/commits/82409d68aa1d6cbc70740d0f35024aae17f7d5cb/raw/
+    patch('pkg-parmetis-82409d68aa1d6cbc70740d0f35024aae17f7d5cb.patch')
+
     depends_on('gdb', when='+gdb')
 
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/parmetis/pkg-parmetis-1c1a9fd0f408dc4d42c57f5c3ee6ace411eb222b.patch b/var/spack/repos/builtin/packages/parmetis/pkg-parmetis-1c1a9fd0f408dc4d42c57f5c3ee6ace411eb222b.patch
new file mode 100644
index 00000000000..e6b8056c210
--- /dev/null
+++ b/var/spack/repos/builtin/packages/parmetis/pkg-parmetis-1c1a9fd0f408dc4d42c57f5c3ee6ace411eb222b.patch
@@ -0,0 +1,77 @@
+From 1c1a9fd0f408dc4d42c57f5c3ee6ace411eb222b Mon Sep 17 00:00:00 2001
+From: Jed Brown <jed@59A2.org>
+Date: Fri, 12 Oct 2012 15:45:10 -0500
+Subject: [PATCH] ParMetis bug fixes reported by John Fettig [petsc-maint
+ #133631]
+
+'''
+I have also reported to to Karypis but have received zero
+response and he hasn't released any updates to the original release
+either.  At least he approved my forum posting so that other people
+can see the bug and the fix.
+http://glaros.dtc.umn.edu/gkhome/node/837
+'''
+
+Hg-commit: 1c2b9fe39201d404b493885093b5992028b9b8d4
+---
+ libparmetis/xyzpart.c | 12 ++++++------
+ 1 file changed, 6 insertions(+), 6 deletions(-)
+
+diff --git a/libparmetis/xyzpart.c b/libparmetis/xyzpart.c
+index 3a2c289..63abfcb 100644
+--- a/libparmetis/xyzpart.c
++++ b/libparmetis/xyzpart.c
+@@ -104,7 +104,7 @@ void IRBinCoordinates(ctrl_t *ctrl, graph_t *graph, idx_t ndims, real_t *xyz,
+ 
+     for (i=0; i<nbins; i++)
+       emarkers[i] = gmin + (gmax-gmin)*i/nbins;
+-    emarkers[nbins] = gmax*(1.0+2.0*REAL_EPSILON);
++    emarkers[nbins] = gmax*(1.0+copysign(1.0,gmax)*2.0*REAL_EPSILON);
+ 
+     /* get into a iterative backet boundary refinement */
+     for (l=0; l<5; l++) {
+@@ -152,7 +152,7 @@ void IRBinCoordinates(ctrl_t *ctrl, graph_t *graph, idx_t ndims, real_t *xyz,
+         }
+       }
+       nemarkers[0]     = gmin;
+-      nemarkers[nbins] = gmax*(1.0+2.0*REAL_EPSILON);
++      nemarkers[nbins] = gmax*(1.0+copysign(1.0,gmax)*2.0*REAL_EPSILON);
+       rcopy(nbins+1, nemarkers, emarkers);
+     }
+ 
+@@ -218,7 +218,7 @@ void RBBinCoordinates(ctrl_t *ctrl, graph_t *graph, idx_t ndims, real_t *xyz,
+ 
+     emarkers[0] = gmin;
+     emarkers[1] = gsum/gnvtxs;
+-    emarkers[2] = gmax*(1.0+2.0*REAL_EPSILON);
++    emarkers[2] = gmax*(1.0+(gmax < 0 ? -1. : 1.)*2.0*REAL_EPSILON);
+     cnbins = 2;
+ 
+     /* get into a iterative backet boundary refinement */
+@@ -227,7 +227,7 @@ void RBBinCoordinates(ctrl_t *ctrl, graph_t *graph, idx_t ndims, real_t *xyz,
+       iset(cnbins, 0, lcounts);
+       rset(cnbins, 0, lsums);
+       for (j=0, i=0; i<nvtxs;) {
+-        if (cand[i].key < emarkers[j+1]) {
++        if (cand[i].key <= emarkers[j+1]) {
+           lcounts[j]++;
+           lsums[j] += cand[i].key;
+           i++;
+@@ -272,12 +272,12 @@ void RBBinCoordinates(ctrl_t *ctrl, graph_t *graph, idx_t ndims, real_t *xyz,
+       
+       rsorti(cnbins, nemarkers);
+       rcopy(cnbins, nemarkers, emarkers);
+-      emarkers[cnbins] = gmax*(1.0+2.0*REAL_EPSILON);
++      emarkers[cnbins] = gmax*(1.0+(gmax < 0 ? -1. : 1.)*2.0*REAL_EPSILON);
+     }
+ 
+     /* assign the coordinate to the appropriate bin */
+     for (j=0, i=0; i<nvtxs;) {
+-      if (cand[i].key < emarkers[j+1]) {
++      if (cand[i].key <= emarkers[j+1]) {
+         bxyz[cand[i].val*ndims+k] = j;
+         i++;
+       }
+-- 
+2.1.1.1.g1fb337f
+
diff --git a/var/spack/repos/builtin/packages/parmetis/pkg-parmetis-82409d68aa1d6cbc70740d0f35024aae17f7d5cb.patch b/var/spack/repos/builtin/packages/parmetis/pkg-parmetis-82409d68aa1d6cbc70740d0f35024aae17f7d5cb.patch
new file mode 100644
index 00000000000..9651d553478
--- /dev/null
+++ b/var/spack/repos/builtin/packages/parmetis/pkg-parmetis-82409d68aa1d6cbc70740d0f35024aae17f7d5cb.patch
@@ -0,0 +1,35 @@
+From 82409d68aa1d6cbc70740d0f35024aae17f7d5cb Mon Sep 17 00:00:00 2001
+From: Sean Farley <sean@mcs.anl.gov>
+Date: Tue, 20 Mar 2012 11:59:44 -0500
+Subject: [PATCH] parmetis: fix bug reported by jfettig; '<' to '<=' in xyzpart
+
+Hg-commit: 2dd2eae596acaabbc80e0ef875182616f868dbc2
+---
+ libparmetis/xyzpart.c | 4 ++--
+ 1 file changed, 2 insertions(+), 2 deletions(-)
+
+diff --git a/libparmetis/xyzpart.c b/libparmetis/xyzpart.c
+index 307aed9..3a2c289 100644
+--- a/libparmetis/xyzpart.c
++++ b/libparmetis/xyzpart.c
+@@ -111,7 +111,7 @@ void IRBinCoordinates(ctrl_t *ctrl, graph_t *graph, idx_t ndims, real_t *xyz,
+       /* determine bucket counts */
+       iset(nbins, 0, lcounts);
+       for (j=0, i=0; i<nvtxs;) {
+-        if (cand[i].key < emarkers[j+1]) {
++        if (cand[i].key <= emarkers[j+1]) {
+           lcounts[j]++;
+           i++;
+         }
+@@ -158,7 +158,7 @@ void IRBinCoordinates(ctrl_t *ctrl, graph_t *graph, idx_t ndims, real_t *xyz,
+ 
+     /* assign the coordinate to the appropriate bin */
+     for (j=0, i=0; i<nvtxs;) {
+-      if (cand[i].key < emarkers[j+1]) {
++      if (cand[i].key <= emarkers[j+1]) {
+         bxyz[cand[i].val*ndims+k] = j;
+         i++;
+       }
+-- 
+2.1.1.1.g1fb337f
+

From 7569204a53076f763cc713123b5e92551f647d7f Mon Sep 17 00:00:00 2001
From: alalazo <massimiliano.culpo@googlemail.com>
Date: Mon, 21 Mar 2016 16:18:02 +0100
Subject: [PATCH 055/230] llvm : does not support python 3

---
 var/spack/repos/builtin/packages/llvm/package.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/llvm/package.py b/var/spack/repos/builtin/packages/llvm/package.py
index 5c38b5b88c3..1d25d59e504 100644
--- a/var/spack/repos/builtin/packages/llvm/package.py
+++ b/var/spack/repos/builtin/packages/llvm/package.py
@@ -52,7 +52,7 @@ class Llvm(Package):
     depends_on('cmake @2.8.12.2:')
 
     # Universal dependency
-    depends_on('python@2.7:')
+    depends_on('python@2.7:2.8')  # Seems not to support python 3.X.Y
 
     # lldb dependencies
     depends_on('ncurses', when='+lldb')

From c5c92d50eb78673c635a7ed26145bf10a15c20cb Mon Sep 17 00:00:00 2001
From: Ben Boeckel <ben.boeckel@kitware.com>
Date: Mon, 21 Mar 2016 11:24:36 -0400
Subject: [PATCH 056/230] paraview: remove trailing whitespace

---
 var/spack/repos/builtin/packages/paraview/package.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/var/spack/repos/builtin/packages/paraview/package.py b/var/spack/repos/builtin/packages/paraview/package.py
index ccf2d14c06e..b3312736f16 100644
--- a/var/spack/repos/builtin/packages/paraview/package.py
+++ b/var/spack/repos/builtin/packages/paraview/package.py
@@ -37,11 +37,11 @@ class Paraview(Package):
     #depends_on('protobuf') # version mismatches?
     #depends_on('sqlite') # external version not supported
     depends_on('zlib')
-    
+
     def url_for_version(self, version):
         """Handle ParaView version-based custom URLs."""
         return self._url_str % (version.up_to(2), version)
-    
+
 
     def install(self, spec, prefix):
         with working_dir('spack-build', create=True):

From 8e77f1776020c2a6edf9eb284615d99c905821e9 Mon Sep 17 00:00:00 2001
From: Ben Boeckel <ben.boeckel@kitware.com>
Date: Mon, 21 Mar 2016 11:54:58 -0400
Subject: [PATCH 057/230] paraview: fix variant description typo

---
 var/spack/repos/builtin/packages/paraview/package.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/paraview/package.py b/var/spack/repos/builtin/packages/paraview/package.py
index b3312736f16..0c3c7c16214 100644
--- a/var/spack/repos/builtin/packages/paraview/package.py
+++ b/var/spack/repos/builtin/packages/paraview/package.py
@@ -16,7 +16,7 @@ class Paraview(Package):
 
     variant('osmesa', default=False, description='Enable OSMesa support')
     variant('qt', default=False, description='Enable Qt support')
-    variant('opengl2', default=False, description='Enable OPengl2 backend')
+    variant('opengl2', default=False, description='Enable OpenGL2 backend')
 
     depends_on('python', when='+python')
     depends_on('py-numpy', when='+python')

From 553fff270a13d40fb9a41569bebf5075a740d8ac Mon Sep 17 00:00:00 2001
From: Ben Boeckel <ben.boeckel@kitware.com>
Date: Mon, 21 Mar 2016 11:24:49 -0400
Subject: [PATCH 058/230] paraview: disallow python3

ParaView is not Python3-ready.
---
 var/spack/repos/builtin/packages/paraview/package.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/paraview/package.py b/var/spack/repos/builtin/packages/paraview/package.py
index 0c3c7c16214..c16054816c1 100644
--- a/var/spack/repos/builtin/packages/paraview/package.py
+++ b/var/spack/repos/builtin/packages/paraview/package.py
@@ -18,7 +18,7 @@ class Paraview(Package):
     variant('qt', default=False, description='Enable Qt support')
     variant('opengl2', default=False, description='Enable OpenGL2 backend')
 
-    depends_on('python', when='+python')
+    depends_on('python@2:2.7', when='+python')
     depends_on('py-numpy', when='+python')
     depends_on('py-matplotlib', when='+python')
     depends_on('tcl', when='+tcl')

From 953fb35f82c099936f833f31dcd292ffa1a3ec06 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Mon, 21 Mar 2016 18:00:32 +0100
Subject: [PATCH 059/230] add superlu_dist package

---
 .../builtin/packages/superlu-dist/package.py  | 63 +++++++++++++++++++
 1 file changed, 63 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/superlu-dist/package.py

diff --git a/var/spack/repos/builtin/packages/superlu-dist/package.py b/var/spack/repos/builtin/packages/superlu-dist/package.py
new file mode 100644
index 00000000000..c4c76909b35
--- /dev/null
+++ b/var/spack/repos/builtin/packages/superlu-dist/package.py
@@ -0,0 +1,63 @@
+from spack import *
+
+class SuperluDist(Package):
+    """A general purpose library for the direct solution of large, sparse, nonsymmetric systems of linear equations on high performance machines."""
+    homepage = "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/"
+    url      = "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/superlu_dist_4.1.tar.gz"
+
+    version('4.3', 'ee66c84e37b4f7cc557771ccc3dc43ae')
+    version('4.2', 'ae9fafae161f775fbac6eba11e530a65')
+    version('4.1', '4edee38cc29f687bd0c8eb361096a455')
+    version('4.0', 'c0b98b611df227ae050bc1635c6940e0')
+
+    depends_on ('mpi')
+    depends_on ('blas')
+    depends_on ('lapack')
+    depends_on ('parmetis')
+    depends_on ('metis')
+
+    def install(self, spec, prefix):
+        makefile_inc = []
+        makefile_inc.extend([
+            'PLAT         = _mac_x',
+            'DSuperLUroot = %s' % self.stage.source_path, #self.stage.path, prefix
+            'DSUPERLULIB  = $(DSuperLUroot)/lib/libsuperlu_dist.a',
+            'BLASDEF      = -DUSE_VENDOR_BLAS',
+            'BLASLIB      = -L%s -llapack %s -lblas' % (spec['lapack'].prefix.lib, spec['blas'].prefix.lib), # FIXME: avoid hardcoding blas/lapack lib names
+            'METISLIB     = -L%s -lmetis' % spec['metis'].prefix.lib,
+            'PARMETISLIB  = -L%s -lparmetis' % spec['parmetis'].prefix.lib,
+            'FLIBS        =',
+            'LIBS         = $(DSUPERLULIB) $(BLASLIB) $(PARMETISLIB) $(METISLIB)',
+            'ARCH         = ar',
+            'ARCHFLAGS    = cr',
+            'RANLIB       = true',
+            'CC           = mpicc', # FIXME avoid hardcoding MPI compiler names
+            'CFLAGS       = -fPIC -std=c99 -O2 -I%s -I%s' %(spec['parmetis'].prefix.include, spec['metis'].prefix.include),
+            'NOOPTS       = -fPIC -std=c99',
+            'FORTRAN      = mpif77',
+            'F90FLAGS     = -O2',
+            'LOADER       = mpif77',
+            'LOADOPTS     =',
+            'CDEFS        = -DAdd_'
+            ])
+
+        #with working_dir('src'):
+        with open('make.inc', 'w') as fh:
+            fh.write('\n'.join(makefile_inc))
+
+        make("lib", parallel=False)
+
+        # FIXME:
+        # cd "EXAMPLE" do
+        # system "make"
+
+        # need to install by hand
+        headers_location = join_path(self.prefix.include,'superlu_dist')
+        mkdirp(headers_location)
+        # FIXME: fetch all headers in the folder automatically
+        for header in ['Cnames.h','cublas_utils.h','dcomplex.h','html_mainpage.h','machines.h','old_colamd.h','psymbfact.h','superlu_ddefs.h','superlu_defs.h','superlu_enum_consts.h','superlu_zdefs.h','supermatrix.h','util_dist.h']:
+            superludist_header = join_path(self.stage.source_path, 'SRC/',header)
+            install(superludist_header, headers_location)
+
+        superludist_lib = join_path(self.stage.source_path, 'lib/libsuperlu_dist.a')
+        install(superludist_lib,self.prefix.lib)

From b79fce76cb4d412cf718b48b05d549470e4c55ab Mon Sep 17 00:00:00 2001
From: Matthew LeGendre <legendre1@llnl.gov>
Date: Mon, 21 Mar 2016 14:28:07 -0700
Subject: [PATCH 060/230] Fix issue 573 where Spack was ignoring user's
 compiler preference in concretization

---
 lib/spack/spack/concretize.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/lib/spack/spack/concretize.py b/lib/spack/spack/concretize.py
index 8083f919828..2e576743ec6 100644
--- a/lib/spack/spack/concretize.py
+++ b/lib/spack/spack/concretize.py
@@ -241,7 +241,7 @@ def concretize_compiler(self, spec):
             return False
 
         #Find the another spec that has a compiler, or the root if none do
-        other_spec = find_spec(spec, lambda(x) : x.compiler)
+        other_spec = spec if spec.compiler else find_spec(spec, lambda(x) : x.compiler)
         if not other_spec:
             other_spec = spec.root
         other_compiler = other_spec.compiler
@@ -288,7 +288,7 @@ def find_spec(spec, condition):
     if condition(spec):
         return spec
 
-    return None   # Nohting matched the condition.
+    return None   # Nothing matched the condition.
 
 
 def cmp_specs(lhs, rhs):

From 5d06daeb5eed28b4b91ba62a8f99165d87b5ef86 Mon Sep 17 00:00:00 2001
From: Matthew LeGendre <legendre1@llnl.gov>
Date: Mon, 21 Mar 2016 14:28:34 -0700
Subject: [PATCH 061/230] Add test for issue 573, child with compiler not
 respected in concretization

---
 lib/spack/spack/test/concretize.py | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/lib/spack/spack/test/concretize.py b/lib/spack/spack/test/concretize.py
index f264faf17a2..08cce096747 100644
--- a/lib/spack/spack/test/concretize.py
+++ b/lib/spack/spack/test/concretize.py
@@ -309,3 +309,10 @@ def test_find_spec_none(self):
                       Spec('d')),
                  Spec('e'))
         self.assertEqual(None, find_spec(s['b'], lambda s: '+foo' in s))
+
+
+    def test_compiler_child(self):
+        s = Spec('mpileaks%clang ^dyninst%gcc')
+        s.concretize()
+        self.assertTrue(s['mpileaks'].satisfies('%clang'))
+        self.assertTrue(s['dyninst'].satisfies('%gcc'))

From 48b35bb495bc154c64d23d1ad364506c4572b913 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Mon, 21 Mar 2016 00:11:18 -0700
Subject: [PATCH 062/230] Fix print function in uninstall.py

---
 lib/spack/spack/cmd/uninstall.py | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/lib/spack/spack/cmd/uninstall.py b/lib/spack/spack/cmd/uninstall.py
index 1ece8386124..350ef372cb6 100644
--- a/lib/spack/spack/cmd/uninstall.py
+++ b/lib/spack/spack/cmd/uninstall.py
@@ -22,6 +22,7 @@
 # along with this program; if not, write to the Free Software Foundation,
 # Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
+from __future__ import print_function
 import sys
 import argparse
 
@@ -63,12 +64,12 @@ def uninstall(parser, args):
             matching_specs = spack.installed_db.query(spec)
             if not args.all and len(matching_specs) > 1:
                 tty.error("%s matches multiple packages:" % spec)
-                print
+                print()
                 display_specs(matching_specs, long=True)
-                print
-                print "You can either:"
-                print "  a) Use a more specific spec, or"
-                print "  b) use spack uninstall -a to uninstall ALL matching specs."
+                print()
+                print("You can either:")
+                print("  a) Use a more specific spec, or")
+                print("  b) use spack uninstall -a to uninstall ALL matching specs.")
                 sys.exit(1)
 
             if len(matching_specs) == 0:

From e88df95b42fdcaa49552811853f8ca4ecc52cf9f Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Mon, 21 Mar 2016 00:35:13 -0700
Subject: [PATCH 063/230] Remove unused code from modules.py

---
 lib/spack/spack/modules.py | 30 ++++++++++--------------------
 1 file changed, 10 insertions(+), 20 deletions(-)

diff --git a/lib/spack/spack/modules.py b/lib/spack/spack/modules.py
index 0378110c8cb..4e98d500013 100644
--- a/lib/spack/spack/modules.py
+++ b/lib/spack/spack/modules.py
@@ -133,6 +133,7 @@ def __init__(self, spec=None):
         if self.spec.package.__doc__:
             self.long_description = re.sub(r'\s+', ' ', self.spec.package.__doc__)
 
+
     @property
     def category(self):
         # Anything defined at the package level takes precedence
@@ -144,21 +145,6 @@ def category(self):
         # Not very descriptive fallback
         return 'spack installed package'
 
-    # @property
-    # def paths(self):
-    #         # Add python path unless it's an actual python installation
-    #         # TODO : is there a better way to do this?
-    #         # FIXME : add PYTHONPATH to every python package
-    #         if self.spec.name != 'python':
-    #             site_packages = glob(join_path(self.spec.prefix.lib, "python*/site-packages"))
-    #             if site_packages:
-    #                 add_path('PYTHONPATH', site_packages[0])
-    #
-    #         # FIXME : Same for GEM_PATH
-    #         if self.spec.package.extends(spack.spec.Spec('ruby')):
-    #             add_path('GEM_PATH', self.spec.prefix)
-    #
-    #     return self._paths
 
     def write(self):
         """Write out a module file for this object."""
@@ -166,16 +152,20 @@ def write(self):
         if not os.path.exists(module_dir):
             mkdirp(module_dir)
 
-        # Environment modifications guessed by inspecting the installation prefix
+        # Environment modifications guessed by inspecting the
+        # installation prefix
         env = inspect_path(self.spec.prefix)
 
-        # Let the extendee modify their extensions before asking for package-specific modifications
+        # Let the extendee modify their extensions before asking for
+        # package-specific modifications
         for extendee in self.pkg.extendees:
             extendee_spec = self.spec[extendee]
-            extendee_spec.package.modify_module(self.pkg.module, extendee_spec, self.spec)
+            extendee_spec.package.modify_module(
+                self.pkg.module, extendee_spec, self.spec)
 
         # Package-specific environment modifications
         self.spec.package.setup_environment(env)
+
         # TODO : implement site-specific modifications and filters
         if not env:
             return
@@ -232,7 +222,7 @@ def file_name(self):
     def use_name(self):
       return "%s-%s-%s-%s-%s" % (self.spec.name, self.spec.version,
                                  self.spec.compiler.name,
-                                 self.spec.compiler.version, 
+                                 self.spec.compiler.version,
                                  self.spec.dag_hash())
 
     def write_header(self, dk_file):
@@ -270,7 +260,7 @@ def file_name(self):
     def use_name(self):
       return "%s-%s-%s-%s-%s" % (self.spec.name, self.spec.version,
                                  self.spec.compiler.name,
-                                 self.spec.compiler.version, 
+                                 self.spec.compiler.version,
                                  self.spec.dag_hash())
 
     def write_header(self, module_file):

From 439d47b4e45c674ab9aa4ebd0c2bfaf6911ade60 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Mon, 21 Mar 2016 01:48:18 -0700
Subject: [PATCH 064/230] Refactor environment setup.

- Gave setup_environment and setup_dependent_environment more similar
  signatures. They now allows editing the Spack env and the runtime
  env for *this* package and dependents, respectively.

- modify_module renamed to setup_dependent_python_module for symmetry
  with setup_dependent_environment and to avoid confusion with
  environment modules.

- removed need for patching Package objects at runtime.

- adjust packages to reflect these changes.
---
 lib/spack/spack/build_environment.py          |  35 +++--
 lib/spack/spack/modules.py                    |   3 +-
 lib/spack/spack/package.py                    | 120 ++++++++++++++----
 .../repos/builtin/packages/mpich/package.py   |   9 +-
 .../packages/netlib-scalapack/package.py      |   2 +-
 .../repos/builtin/packages/openmpi/package.py |  16 +--
 .../repos/builtin/packages/python/package.py  |  39 ++----
 .../repos/builtin/packages/qt/package.py      |  10 +-
 .../repos/builtin/packages/ruby/package.py    |  12 +-
 9 files changed, 150 insertions(+), 96 deletions(-)

diff --git a/lib/spack/spack/build_environment.py b/lib/spack/spack/build_environment.py
index 59b234624cf..5688d47e2d3 100644
--- a/lib/spack/spack/build_environment.py
+++ b/lib/spack/spack/build_environment.py
@@ -84,7 +84,7 @@ def __call__(self, *args, **kwargs):
         return super(MakeExecutable, self).__call__(*args, **kwargs)
 
 
-def set_compiler_environment_variables(pkg):
+def set_compiler_environment_variables(pkg, env):
     assert pkg.spec.concrete
     # Set compiler variables used by CMake and autotools
     assert all(key in pkg.compiler.link_paths for key in ('cc', 'cxx', 'f77', 'fc'))
@@ -92,7 +92,6 @@ def set_compiler_environment_variables(pkg):
     # Populate an object with the list of environment modifications
     # and return it
     # TODO : add additional kwargs for better diagnostics, like requestor, ttyout, ttyerr, etc.
-    env = EnvironmentModifications()
     link_dir = spack.build_env_path
     env.set_env('CC', join_path(link_dir, pkg.compiler.link_paths['cc']))
     env.set_env('CXX', join_path(link_dir, pkg.compiler.link_paths['cxx']))
@@ -113,7 +112,7 @@ def set_compiler_environment_variables(pkg):
     return env
 
 
-def set_build_environment_variables(pkg):
+def set_build_environment_variables(pkg, env):
     """
     This ensures a clean install environment when we build packages
     """
@@ -134,7 +133,6 @@ def set_build_environment_variables(pkg):
         if os.path.isdir(ci):
             env_paths.append(ci)
 
-    env = EnvironmentModifications()
     for item in reversed(env_paths):
         env.prepend_path('PATH', item)
     env.set_env(SPACK_ENV_PATH, concatenate_paths(env_paths))
@@ -180,7 +178,7 @@ def set_build_environment_variables(pkg):
     return env
 
 
-def set_module_variables_for_package(pkg, m):
+def set_module_variables_for_package(pkg, module):
     """Populate the module scope of install() with some useful functions.
        This makes things easier for package writers.
     """
@@ -190,6 +188,8 @@ def set_module_variables_for_package(pkg, m):
         jobs = 1
     elif pkg.make_jobs:
         jobs = pkg.make_jobs
+
+    m = module
     m.make_jobs = jobs
 
     # TODO: make these build deps that can be installed if not found.
@@ -271,9 +271,12 @@ def parent_class_modules(cls):
 
 def setup_package(pkg):
     """Execute all environment setup routines."""
-    env = EnvironmentModifications()
-    env.extend(set_compiler_environment_variables(pkg))
-    env.extend(set_build_environment_variables(pkg))
+    spack_env = EnvironmentModifications()
+    run_env   = EnvironmentModifications()
+
+    set_compiler_environment_variables(pkg, spack_env)
+    set_build_environment_variables(pkg, spack_env)
+
     # If a user makes their own package repo, e.g.
     # spack.repos.mystuff.libelf.Libelf, and they inherit from
     # an existing class like spack.repos.original.libelf.Libelf,
@@ -285,12 +288,20 @@ def setup_package(pkg):
 
     # Allow dependencies to modify the module
     for dependency_spec in pkg.spec.traverse(root=False):
-        dependency_spec.package.modify_module(pkg.module, dependency_spec, pkg.spec)
+        dpkg = dependency_spec.package
+        dpkg.setup_dependent_python_module(pkg.module, pkg.spec)
+
     # Allow dependencies to set up environment as well
     for dependency_spec in pkg.spec.traverse(root=False):
-        dependency_spec.package.setup_dependent_environment(env, pkg.spec)
-    validate(env, tty.warn)
-    env.apply_modifications()
+        dpkg = dependency_spec.package
+        dpkg.setup_dependent_environment(spack_env, run_env, pkg.spec)
+
+    # Allow the package to apply some settings.
+    pkg.setup_environment(spack_env, run_env)
+
+    # Make sure nothing's strange about the Spack environment.
+    validate(spack_env, tty.warn)
+    spack_env.apply_modifications()
 
 
 def fork(pkg, function):
diff --git a/lib/spack/spack/modules.py b/lib/spack/spack/modules.py
index 4e98d500013..05c93cd3e65 100644
--- a/lib/spack/spack/modules.py
+++ b/lib/spack/spack/modules.py
@@ -164,7 +164,8 @@ def write(self):
                 self.pkg.module, extendee_spec, self.spec)
 
         # Package-specific environment modifications
-        self.spec.package.setup_environment(env)
+        spack_env = EnvironmentModifications()
+        self.spec.package.setup_environment(spack_env, env)
 
         # TODO : implement site-specific modifications and filters
         if not env:
diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py
index acad5a28f6c..9d8ac87bd70 100644
--- a/lib/spack/spack/package.py
+++ b/lib/spack/spack/package.py
@@ -1002,56 +1002,120 @@ def module(self):
         return __import__(self.__class__.__module__,
                           fromlist=[self.__class__.__name__])
 
-    def setup_environment(self, env):
-        """
-        Appends in `env` the list of environment modifications needed to use this package outside of spack.
+    def setup_environment(self, spack_env, run_env):
+        """Set up the compile and runtime environemnts for a package.
 
-        Default implementation does nothing, but this can be overridden if the package needs a particular environment.
+        `spack_env` and `run_env` are `EnvironmentModifications`
+        objects.  Package authors can call methods on them to alter
+        the environment within Spack and at runtime.
 
-        Example :
+        Both `spack_env` and `run_env` are applied within the build
+        process, before this package's `install()` method is called.
 
-        1. A lot of Qt extensions need `QTDIR` set.  This can be used to do that.
+        Modifications in `run_env` will *also* be added to the
+        generated environment modules for this package.
+
+        Default implementation does nothing, but this can be
+        overridden if the package needs a particular environment.
+
+        Examples:
+
+            1. Qt extensions need `QTDIR` set.
 
         Args:
-            env: list of environment modifications to be updated
+            spack_env (EnvironmentModifications): list of
+                modifications to be applied when this package is built
+                within Spack.
+
+            run_env (EnvironmentModifications): list of environment
+                changes to be applied when this package is run outside
+                of Spack.
+
         """
         pass
 
-    def setup_dependent_environment(self, env, dependent_spec):
-        """
-        Called before the install() method of dependents.
 
-        Appends in `env` the list of environment modifications needed by dependents (or extensions) during the
-        installation of a package. The default implementation delegates to `setup_environment`, but can be overridden
-        if the modifications to the environment happen to be different from the one needed to use the package outside
-        of spack.
+    def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
+        """Set up the environment of packages that depend on this one.
 
-        This is useful if there are some common steps to installing all extensions for a certain package.
+        This is similar to `setup_environment`, but it is used to
+        modify the compile and runtime environments of packages that
+        *depend* on this one. This gives packages like Python and
+        others that follow the extension model a way to implement
+        common environment or compile-time settings for dependencies.
+
+        By default, this delegates to self.setup_environment()
 
         Example :
 
-        1. Installing python modules generally requires `PYTHONPATH` to point to the lib/pythonX.Y/site-packages
-        directory in the module's install prefix.  This could set that variable.
+            1. Installing python modules generally requires
+              `PYTHONPATH` to point to the lib/pythonX.Y/site-packages
+              directory in the module's install prefix.  This could
+              set that variable.
 
         Args:
-            env: list of environment modifications to be updated
-            dependent_spec: dependent (or extension) of this spec
-        """
-        self.setup_environment(env)
 
-    def modify_module(self, module, spec, dependent_spec):
+            spack_env (EnvironmentModifications): list of
+                modifications to be applied when the dependent package
+                is bulit within Spack.
+
+            run_env (EnvironmentModifications): list of environment
+                changes to be applied when the dependent package is
+                run outside of Spack.
+
+            dependent_spec (Spec): The spec of the dependent package
+                about to be built. This allows the extendee (self) to
+                query the dependent's state. Note that *this*
+                package's spec is available as `self.spec`.
+
+        This is useful if there are some common steps to installing
+        all extensions for a certain package.
+
         """
+        self.setup_environment(spack_env, run_env)
+
+
+    def setup_dependent_python_module(self, module, dependent_spec):
+        """Set up Python module-scope variables for dependent packages.
+
         Called before the install() method of dependents.
 
-        Default implementation does nothing, but this can be overridden by an extendable package to set up the module of
-        its extensions. This is useful if there are some common steps to installing all extensions for a
-        certain package.
+        Default implementation does nothing, but this can be
+        overridden by an extendable package to set up the module of
+        its extensions. This is useful if there are some common steps
+        to installing all extensions for a certain package.
 
         Example :
 
-        1. Extensions often need to invoke the 'python' interpreter from the Python installation being extended.
-        This routine can put a 'python' Executable object in the module scope for the extension package to simplify
-        extension installs.
+            1. Extensions often need to invoke the `python`
+               interpreter from the Python installation being
+               extended.  This routine can put a 'python' Executable
+               object in the module scope for the extension package to
+               simplify extension installs.
+
+            2. MPI compilers could set some variables in the
+               dependent's scope that point to `mpicc`, `mpicxx`,
+               etc., allowing them to be called by common names
+               regardless of which MPI is used.
+
+            3. BLAS/LAPACK implementations can set some variables
+               indicating the path to their libraries, since these
+               paths differ by BLAS/LAPACK implementation.
+
+        Args:
+
+            module (module): The Python `module` object of the
+                dependent package. Packages can use this to set
+                module-scope variables for the dependent to use.
+
+            dependent_spec (Spec): The spec of the dependent package
+                about to be built. This allows the extendee (self) to
+                query the dependent's state.  Note that *this*
+                package's spec is available as `self.spec`.
+
+        This is useful if there are some common steps to installing
+        all extensions for a certain package.
+
         """
         pass
 
diff --git a/var/spack/repos/builtin/packages/mpich/package.py b/var/spack/repos/builtin/packages/mpich/package.py
index 5af9b585ea8..90b5d42eab4 100644
--- a/var/spack/repos/builtin/packages/mpich/package.py
+++ b/var/spack/repos/builtin/packages/mpich/package.py
@@ -47,13 +47,6 @@ class Mpich(Package):
     provides('mpi@:3.0', when='@3:')
     provides('mpi@:1.3', when='@1:')
 
-    def setup_environment(self, env):
-        env.set_env('MPICH_CC', self.compiler.cc)
-        env.set_env('MPICH_CXX', self.compiler.cxx)
-        env.set_env('MPICH_F77', self.compiler.f77)
-        env.set_env('MPICH_F90', self.compiler.fc)
-        env.set_env('MPICH_FC', self.compiler.fc)
-
     def setup_dependent_environment(self, env, dependent_spec):
         env.set_env('MPICH_CC', spack_cc)
         env.set_env('MPICH_CXX', spack_cxx)
@@ -61,7 +54,7 @@ def setup_dependent_environment(self, env, dependent_spec):
         env.set_env('MPICH_F90', spack_f90)
         env.set_env('MPICH_FC', spack_fc)
 
-    def modify_module(self, module, spec, dep_spec):
+    def setup_dependent_python_module(self, module, spec, dep_spec):
         """For dependencies, make mpicc's use spack wrapper."""
         # FIXME : is this necessary ? Shouldn't this be part of a contract with MPI providers?
         module.mpicc = join_path(self.prefix.bin, 'mpicc')
diff --git a/var/spack/repos/builtin/packages/netlib-scalapack/package.py b/var/spack/repos/builtin/packages/netlib-scalapack/package.py
index 36f506f7cdf..62abfcc48e3 100644
--- a/var/spack/repos/builtin/packages/netlib-scalapack/package.py
+++ b/var/spack/repos/builtin/packages/netlib-scalapack/package.py
@@ -40,7 +40,7 @@ def install(self, spec, prefix):
             make()
             make("install")
 
-    def modify_module(self, module, spec, dependent_spec):
+    def setup_dependent_python_module(self, module, spec, dependent_spec):
         lib_dsuffix = '.dylib' if sys.platform == 'darwin' else '.so'
         lib_suffix = lib_dsuffix if '+shared' in spec['scalapack'] else '.a'
 
diff --git a/var/spack/repos/builtin/packages/openmpi/package.py b/var/spack/repos/builtin/packages/openmpi/package.py
index 7783ca87666..c91a13e3760 100644
--- a/var/spack/repos/builtin/packages/openmpi/package.py
+++ b/var/spack/repos/builtin/packages/openmpi/package.py
@@ -41,17 +41,13 @@ class Openmpi(Package):
     def url_for_version(self, version):
         return "http://www.open-mpi.org/software/ompi/v%s/downloads/openmpi-%s.tar.bz2" % (version.up_to(2), version)
 
-    def setup_environment(self, env):
-        env.set_env('OMPI_CC', self.compiler.cc)
-        env.set_env('OMPI_CXX', self.compiler.cxx)
-        env.set_env('OMPI_FC', self.compiler.fc)
-        env.set_env('OMPI_F77', self.compiler.f77)
 
-    def setup_dependent_environment(self, env, dependent_spec):
-        env.set_env('OMPI_CC', spack_cc)
-        env.set_env('OMPI_CXX', spack_cxx)
-        env.set_env('OMPI_FC', spack_fc)
-        env.set_env('OMPI_F77', spack_f77)
+    def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
+        spack_env.set_env('OMPI_CC', spack_cc)
+        spack_env.set_env('OMPI_CXX', spack_cxx)
+        spack_env.set_env('OMPI_FC', spack_fc)
+        spack_env.set_env('OMPI_F77', spack_f77)
+
 
     def install(self, spec, prefix):
         config_args = ["--prefix=%s" % prefix,
diff --git a/var/spack/repos/builtin/packages/python/package.py b/var/spack/repos/builtin/packages/python/package.py
index c445d26369e..593a27708c8 100644
--- a/var/spack/repos/builtin/packages/python/package.py
+++ b/var/spack/repos/builtin/packages/python/package.py
@@ -92,13 +92,21 @@ def python_include_dir(self):
     def site_packages_dir(self):
         return os.path.join(self.python_lib_dir, 'site-packages')
 
-    def setup_dependent_environment(self, env, extension_spec):
-        # Set PYTHONPATH to include site-packages dir for the extension and any other python extensions it depends on.
+
+    def setup_dependent_environment(self, spack_env, run_env, extension_spec):
+        # TODO: do this only for actual extensions.
+
+        # Set PYTHONPATH to include site-packages dir for the
+        # extension and any other python extensions it depends on.
         python_paths = []
         for d in extension_spec.traverse():
             if d.package.extends(self.spec):
                 python_paths.append(os.path.join(d.prefix, self.site_packages_dir))
-        env.set_env('PYTHONPATH', ':'.join(python_paths))
+
+        pythonpath = ':'.join(python_paths)
+        spack_env.set_env('PYTHONPATH', pythonpath)
+        run_env.set_env('PYTHONPATH', pythonpath)
+
 
     def modify_module(self, module, spec, ext_spec):
         """
@@ -114,31 +122,6 @@ def modify_module(self, module, spec, ext_spec):
         else:
             module.python = Executable(join_path(spec.prefix.bin, 'python'))
 
-        # The code below patches the any python extension to have good defaults for `setup_dependent_environment` and
-        # `setup_environment` only if the extension didn't override any of these functions explicitly.
-        def _setup_env(self, env):
-            site_packages = glob.glob(join_path(self.spec.prefix.lib, "python*/site-packages"))
-            if site_packages:
-                env.prepend_path('PYTHONPATH', site_packages[0])
-
-        def _setup_denv(self, env, extension_spec):
-            pass
-
-        pkg_cls = type(ext_spec.package)  # Retrieve the type we may want to patch
-        if 'python' in pkg_cls.extendees:
-            # List of overrides we are interested in
-            interesting_overrides = ['setup_environment', 'setup_dependent_environment']
-            overrides_found = [
-                (name, defining_cls) for name, _, defining_cls, _, in inspect.classify_class_attrs(pkg_cls)
-                if
-                name in interesting_overrides and  # The attribute has the right name
-                issubclass(defining_cls, Package) and defining_cls is not Package  # and is an actual override
-            ]
-            if not overrides_found:
-                # If no override were found go on patching
-                pkg_cls.setup_environment = functools.wraps(Package.setup_environment)(_setup_env)
-                pkg_cls.setup_dependent_environment = functools.wraps(Package.setup_dependent_environment)(_setup_denv)
-
         # Add variables for lib/pythonX.Y and lib/pythonX.Y/site-packages dirs.
         module.python_lib_dir     = os.path.join(ext_spec.prefix, self.python_lib_dir)
         module.python_include_dir = os.path.join(ext_spec.prefix, self.python_include_dir)
diff --git a/var/spack/repos/builtin/packages/qt/package.py b/var/spack/repos/builtin/packages/qt/package.py
index 35b9d684624..039aeb3c314 100644
--- a/var/spack/repos/builtin/packages/qt/package.py
+++ b/var/spack/repos/builtin/packages/qt/package.py
@@ -55,8 +55,14 @@ class Qt(Package):
     depends_on("mesa", when='@4:+mesa')
     depends_on("libxcb")
 
-    def setup_environment(self, env):
-        env.set_env['QTDIR'] = self.prefix
+
+    def setup_environment(self, spack_env, env):
+        env.set_env('QTDIR', self.prefix)
+
+
+    def setup_dependent_environment(self, spack_env, run_env, dspec):
+        spack_env.set_env('QTDIR', self.prefix)
+
 
     def patch(self):
         if self.spec.satisfies('@4'):
diff --git a/var/spack/repos/builtin/packages/ruby/package.py b/var/spack/repos/builtin/packages/ruby/package.py
index 2d1da8c9af1..39f65f51d2c 100644
--- a/var/spack/repos/builtin/packages/ruby/package.py
+++ b/var/spack/repos/builtin/packages/ruby/package.py
@@ -2,7 +2,7 @@
 
 
 class Ruby(Package):
-    """A dynamic, open source programming language with a focus on 
+    """A dynamic, open source programming language with a focus on
     simplicity and productivity."""
 
     homepage = "https://www.ruby-lang.org/"
@@ -17,15 +17,17 @@ def install(self, spec, prefix):
         make()
         make("install")
 
-    def setup_dependent_environment(self, env, extension_spec):
+    def setup_dependent_environment(self, spack_env, run_env, extension_spec):
+        # TODO: do this only for actual extensions.
         # Set GEM_PATH to include dependent gem directories
         ruby_paths = []
         for d in extension_spec.traverse():
             if d.package.extends(self.spec):
                 ruby_paths.append(d.prefix)
-        env.set_env('GEM_PATH', concatenate_paths(ruby_paths))
+
+        spack_env.set_env('GEM_PATH', concatenate_paths(ruby_paths))
         # The actual installation path for this gem
-        env.set_env('GEM_HOME', extension_spec.prefix)
+        spack_env.set_env('GEM_HOME', extension_spec.prefix)
 
     def modify_module(self, module, spec, ext_spec):
         """Called before ruby modules' install() methods.  Sets GEM_HOME
@@ -38,5 +40,3 @@ def modify_module(self, module, spec, ext_spec):
         # Ruby extension builds have global ruby and gem functions
         module.ruby = Executable(join_path(spec.prefix.bin, 'ruby'))
         module.gem = Executable(join_path(spec.prefix.bin, 'gem'))
-
-

From b1516f64eb75c108eded1e9ee7e0480a4552236a Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Mon, 21 Mar 2016 02:21:31 -0700
Subject: [PATCH 065/230] Rename some environment methods to be less
 repetitive, add set_path.

---
 lib/spack/spack/build_environment.py          | 45 ++++++++++---------
 lib/spack/spack/environment.py                | 22 ++++++++-
 lib/spack/spack/test/environment.py           | 22 +++++----
 .../repos/builtin/packages/mpich/package.py   | 10 ++---
 .../repos/builtin/packages/openmpi/package.py |  8 ++--
 .../repos/builtin/packages/python/package.py  |  4 +-
 .../repos/builtin/packages/qt/package.py      |  4 +-
 .../repos/builtin/packages/ruby/package.py    |  5 ++-
 8 files changed, 73 insertions(+), 47 deletions(-)

diff --git a/lib/spack/spack/build_environment.py b/lib/spack/spack/build_environment.py
index 5688d47e2d3..fc5b7d6207f 100644
--- a/lib/spack/spack/build_environment.py
+++ b/lib/spack/spack/build_environment.py
@@ -36,7 +36,7 @@
 import spack
 import llnl.util.tty as tty
 from llnl.util.filesystem import *
-from spack.environment import EnvironmentModifications, concatenate_paths, validate
+from spack.environment import EnvironmentModifications, validate
 from spack.util.environment import *
 from spack.util.executable import Executable, which
 
@@ -93,22 +93,23 @@ def set_compiler_environment_variables(pkg, env):
     # and return it
     # TODO : add additional kwargs for better diagnostics, like requestor, ttyout, ttyerr, etc.
     link_dir = spack.build_env_path
-    env.set_env('CC', join_path(link_dir, pkg.compiler.link_paths['cc']))
-    env.set_env('CXX', join_path(link_dir, pkg.compiler.link_paths['cxx']))
-    env.set_env('F77', join_path(link_dir, pkg.compiler.link_paths['f77']))
-    env.set_env('FC', join_path(link_dir, pkg.compiler.link_paths['fc']))
+    env.set('CC', join_path(link_dir, pkg.compiler.link_paths['cc']))
+    env.set('CXX', join_path(link_dir, pkg.compiler.link_paths['cxx']))
+    env.set('F77', join_path(link_dir, pkg.compiler.link_paths['f77']))
+    env.set('FC', join_path(link_dir, pkg.compiler.link_paths['fc']))
+
     # Set SPACK compiler variables so that our wrapper knows what to call
     compiler = pkg.compiler
     if compiler.cc:
-        env.set_env('SPACK_CC', compiler.cc)
+        env.set('SPACK_CC', compiler.cc)
     if compiler.cxx:
-        env.set_env('SPACK_CXX', compiler.cxx)
+        env.set('SPACK_CXX', compiler.cxx)
     if compiler.f77:
-        env.set_env('SPACK_F77', compiler.f77)
+        env.set('SPACK_F77', compiler.f77)
     if compiler.fc:
-        env.set_env('SPACK_FC', compiler.fc)
+        env.set('SPACK_FC', compiler.fc)
 
-    env.set_env('SPACK_COMPILER_SPEC', str(pkg.spec.compiler))
+    env.set('SPACK_COMPILER_SPEC', str(pkg.spec.compiler))
     return env
 
 
@@ -135,25 +136,25 @@ def set_build_environment_variables(pkg, env):
 
     for item in reversed(env_paths):
         env.prepend_path('PATH', item)
-    env.set_env(SPACK_ENV_PATH, concatenate_paths(env_paths))
+    env.set_path(SPACK_ENV_PATH, env_paths)
 
     # Prefixes of all of the package's dependencies go in SPACK_DEPENDENCIES
     dep_prefixes = [d.prefix for d in pkg.spec.traverse(root=False)]
-    env.set_env(SPACK_DEPENDENCIES, concatenate_paths(dep_prefixes))
-    env.set_env('CMAKE_PREFIX_PATH', concatenate_paths(dep_prefixes))  # Add dependencies to CMAKE_PREFIX_PATH
+    env.set_path(SPACK_DEPENDENCIES, dep_prefixes)
+    env.set_path('CMAKE_PREFIX_PATH', dep_prefixes)  # Add dependencies to CMAKE_PREFIX_PATH
 
     # Install prefix
-    env.set_env(SPACK_PREFIX, pkg.prefix)
+    env.set(SPACK_PREFIX, pkg.prefix)
 
     # Install root prefix
-    env.set_env(SPACK_INSTALL, spack.install_path)
+    env.set(SPACK_INSTALL, spack.install_path)
 
     # Remove these vars from the environment during build because they
     # can affect how some packages find libraries.  We want to make
     # sure that builds never pull in unintended external dependencies.
-    env.unset_env('LD_LIBRARY_PATH')
-    env.unset_env('LD_RUN_PATH')
-    env.unset_env('DYLD_LIBRARY_PATH')
+    env.unset('LD_LIBRARY_PATH')
+    env.unset('LD_RUN_PATH')
+    env.unset('DYLD_LIBRARY_PATH')
 
     # Add bin directories from dependencies to the PATH for the build.
     bin_dirs = reversed(filter(os.path.isdir, ['%s/bin' % prefix for prefix in dep_prefixes]))
@@ -162,9 +163,9 @@ def set_build_environment_variables(pkg, env):
 
     # Working directory for the spack command itself, for debug logs.
     if spack.debug:
-        env.set_env(SPACK_DEBUG, 'TRUE')
-    env.set_env(SPACK_SHORT_SPEC, pkg.spec.short_spec)
-    env.set_env(SPACK_DEBUG_LOG_DIR, spack.spack_working_dir)
+        env.set(SPACK_DEBUG, 'TRUE')
+    env.set(SPACK_SHORT_SPEC, pkg.spec.short_spec)
+    env.set(SPACK_DEBUG_LOG_DIR, spack.spack_working_dir)
 
     # Add any pkgconfig directories to PKG_CONFIG_PATH
     pkg_config_dirs = []
@@ -173,7 +174,7 @@ def set_build_environment_variables(pkg, env):
             pcdir = join_path(p, libdir, 'pkgconfig')
             if os.path.isdir(pcdir):
                 pkg_config_dirs.append(pcdir)
-    env.set_env('PKG_CONFIG_PATH', concatenate_paths(pkg_config_dirs))
+    env.set_path('PKG_CONFIG_PATH', pkg_config_dirs)
 
     return env
 
diff --git a/lib/spack/spack/environment.py b/lib/spack/spack/environment.py
index 74aef57fe88..72aafa4e2d6 100644
--- a/lib/spack/spack/environment.py
+++ b/lib/spack/spack/environment.py
@@ -29,6 +29,12 @@ def execute(self):
         os.environ.pop(self.name, None)  # Avoid throwing if the variable was not set
 
 
+class SetPath(NameValueModifier):
+    def execute(self):
+        string_path = concatenate_paths(self.value)
+        os.environ[self.name] = string_path
+
+
 class AppendPath(NameValueModifier):
     def execute(self):
         environment_value = os.environ.get(self.name, '')
@@ -103,7 +109,7 @@ def _get_outside_caller_attributes(self):
         }
         return args
 
-    def set_env(self, name, value, **kwargs):
+    def set(self, name, value, **kwargs):
         """
         Stores in the current object a request to set an environment variable
 
@@ -115,7 +121,7 @@ def set_env(self, name, value, **kwargs):
         item = SetEnv(name, value, **kwargs)
         self.env_modifications.append(item)
 
-    def unset_env(self, name, **kwargs):
+    def unset(self, name, **kwargs):
         """
         Stores in the current object a request to unset an environment variable
 
@@ -126,6 +132,18 @@ def unset_env(self, name, **kwargs):
         item = UnsetEnv(name, **kwargs)
         self.env_modifications.append(item)
 
+    def set_path(self, name, elts, **kwargs):
+        """
+        Stores a request to set a path generated from a list.
+
+        Args:
+            name: name o the environment variable to be set.
+            elts: elements of the path to set.
+        """
+        kwargs.update(self._get_outside_caller_attributes())
+        item = SetPath(name, elts, **kwargs)
+        self.env_modifications.append(item)
+
     def append_path(self, name, path, **kwargs):
         """
         Stores in the current object a request to append a path to a path list
diff --git a/lib/spack/spack/test/environment.py b/lib/spack/spack/test/environment.py
index 3e03760c016..6c8f5ea43c3 100644
--- a/lib/spack/spack/test/environment.py
+++ b/lib/spack/spack/test/environment.py
@@ -11,21 +11,27 @@ def setUp(self):
         os.environ['PATH_LIST'] = '/path/second:/path/third'
         os.environ['REMOVE_PATH_LIST'] = '/a/b:/duplicate:/a/c:/remove/this:/a/d:/duplicate/:/f/g'
 
-    def test_set_env(self):
+    def test_set(self):
         env = EnvironmentModifications()
-        env.set_env('A', 'dummy value')
-        env.set_env('B', 3)
+        env.set('A', 'dummy value')
+        env.set('B', 3)
         env.apply_modifications()
         self.assertEqual('dummy value', os.environ['A'])
         self.assertEqual(str(3), os.environ['B'])
 
-    def test_unset_env(self):
+    def test_unset(self):
         env = EnvironmentModifications()
         self.assertEqual('foo', os.environ['UNSET_ME'])
-        env.unset_env('UNSET_ME')
+        env.unset('UNSET_ME')
         env.apply_modifications()
         self.assertRaises(KeyError, os.environ.__getitem__, 'UNSET_ME')
 
+    def test_set_path(self):
+        env = EnvironmentModifications()
+        env.set_path('A', ['foo', 'bar', 'baz'])
+        env.apply_modifications()
+        self.assertEqual('foo:bar:baz', os.environ['A'])
+
     def test_path_manipulation(self):
         env = EnvironmentModifications()
 
@@ -51,7 +57,7 @@ def test_path_manipulation(self):
 
     def test_extra_arguments(self):
         env = EnvironmentModifications()
-        env.set_env('A', 'dummy value', who='Pkg1')
+        env.set('A', 'dummy value', who='Pkg1')
         for x in env:
             assert 'who' in x.args
         env.apply_modifications()
@@ -59,8 +65,8 @@ def test_extra_arguments(self):
 
     def test_extend(self):
         env = EnvironmentModifications()
-        env.set_env('A', 'dummy value')
-        env.set_env('B', 3)
+        env.set('A', 'dummy value')
+        env.set('B', 3)
         copy_construct = EnvironmentModifications(env)
         self.assertEqual(len(copy_construct), 2)
         for x, y in zip(env, copy_construct):
diff --git a/var/spack/repos/builtin/packages/mpich/package.py b/var/spack/repos/builtin/packages/mpich/package.py
index 90b5d42eab4..c4d9940bb72 100644
--- a/var/spack/repos/builtin/packages/mpich/package.py
+++ b/var/spack/repos/builtin/packages/mpich/package.py
@@ -48,11 +48,11 @@ class Mpich(Package):
     provides('mpi@:1.3', when='@1:')
 
     def setup_dependent_environment(self, env, dependent_spec):
-        env.set_env('MPICH_CC', spack_cc)
-        env.set_env('MPICH_CXX', spack_cxx)
-        env.set_env('MPICH_F77', spack_f77)
-        env.set_env('MPICH_F90', spack_f90)
-        env.set_env('MPICH_FC', spack_fc)
+        env.set('MPICH_CC', spack_cc)
+        env.set('MPICH_CXX', spack_cxx)
+        env.set('MPICH_F77', spack_f77)
+        env.set('MPICH_F90', spack_f90)
+        env.set('MPICH_FC', spack_fc)
 
     def setup_dependent_python_module(self, module, spec, dep_spec):
         """For dependencies, make mpicc's use spack wrapper."""
diff --git a/var/spack/repos/builtin/packages/openmpi/package.py b/var/spack/repos/builtin/packages/openmpi/package.py
index c91a13e3760..9a127f18123 100644
--- a/var/spack/repos/builtin/packages/openmpi/package.py
+++ b/var/spack/repos/builtin/packages/openmpi/package.py
@@ -43,10 +43,10 @@ def url_for_version(self, version):
 
 
     def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
-        spack_env.set_env('OMPI_CC', spack_cc)
-        spack_env.set_env('OMPI_CXX', spack_cxx)
-        spack_env.set_env('OMPI_FC', spack_fc)
-        spack_env.set_env('OMPI_F77', spack_f77)
+        spack_env.set('OMPI_CC', spack_cc)
+        spack_env.set('OMPI_CXX', spack_cxx)
+        spack_env.set('OMPI_FC', spack_fc)
+        spack_env.set('OMPI_F77', spack_f77)
 
 
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/python/package.py b/var/spack/repos/builtin/packages/python/package.py
index 593a27708c8..4f55bc803ea 100644
--- a/var/spack/repos/builtin/packages/python/package.py
+++ b/var/spack/repos/builtin/packages/python/package.py
@@ -104,8 +104,8 @@ def setup_dependent_environment(self, spack_env, run_env, extension_spec):
                 python_paths.append(os.path.join(d.prefix, self.site_packages_dir))
 
         pythonpath = ':'.join(python_paths)
-        spack_env.set_env('PYTHONPATH', pythonpath)
-        run_env.set_env('PYTHONPATH', pythonpath)
+        spack_env.set('PYTHONPATH', pythonpath)
+        run_env.set('PYTHONPATH', pythonpath)
 
 
     def modify_module(self, module, spec, ext_spec):
diff --git a/var/spack/repos/builtin/packages/qt/package.py b/var/spack/repos/builtin/packages/qt/package.py
index 039aeb3c314..d08e8e81e1a 100644
--- a/var/spack/repos/builtin/packages/qt/package.py
+++ b/var/spack/repos/builtin/packages/qt/package.py
@@ -57,11 +57,11 @@ class Qt(Package):
 
 
     def setup_environment(self, spack_env, env):
-        env.set_env('QTDIR', self.prefix)
+        env.set('QTDIR', self.prefix)
 
 
     def setup_dependent_environment(self, spack_env, run_env, dspec):
-        spack_env.set_env('QTDIR', self.prefix)
+        spack_env.set('QTDIR', self.prefix)
 
 
     def patch(self):
diff --git a/var/spack/repos/builtin/packages/ruby/package.py b/var/spack/repos/builtin/packages/ruby/package.py
index 39f65f51d2c..7ff1898ce91 100644
--- a/var/spack/repos/builtin/packages/ruby/package.py
+++ b/var/spack/repos/builtin/packages/ruby/package.py
@@ -25,9 +25,10 @@ def setup_dependent_environment(self, spack_env, run_env, extension_spec):
             if d.package.extends(self.spec):
                 ruby_paths.append(d.prefix)
 
-        spack_env.set_env('GEM_PATH', concatenate_paths(ruby_paths))
+        spack_env.set_path('GEM_PATH', ruby_paths)
+
         # The actual installation path for this gem
-        spack_env.set_env('GEM_HOME', extension_spec.prefix)
+        spack_env.set('GEM_HOME', extension_spec.prefix)
 
     def modify_module(self, module, spec, ext_spec):
         """Called before ruby modules' install() methods.  Sets GEM_HOME

From 4b46e21685b557188d8738bf11af2e0195c14046 Mon Sep 17 00:00:00 2001
From: "Kelly (KT) Thompson" <kgt@lanl.gov>
Date: Mon, 21 Mar 2016 19:55:54 -0600
Subject: [PATCH 066/230] + Provide package numdiff.

---
 .../repos/builtin/packages/numdiff/package.py | 41 +++++++++++++++++++
 1 file changed, 41 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/numdiff/package.py

diff --git a/var/spack/repos/builtin/packages/numdiff/package.py b/var/spack/repos/builtin/packages/numdiff/package.py
new file mode 100644
index 00000000000..a51f6206cf1
--- /dev/null
+++ b/var/spack/repos/builtin/packages/numdiff/package.py
@@ -0,0 +1,41 @@
+##############################################################################
+# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License (as published by
+# the Free Software Foundation) version 2.1 dated February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with this program; if not, write to the Free Software Foundation,
+# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+class Numdiff(Package):
+    """Numdiff is a little program that can be used to compare putatively
+    similar files line by line and field by field, ignoring small numeric
+    differences or/and different numeric formats."""
+
+    homepage  = 'https://www.nongnu.org/numdiff'
+    url       = 'http://nongnu.askapache.com/numdiff/numdiff-5.8.1.tar.gz'
+
+    version('5.8.1',    'a295eb391f6cb1578209fc6b4f9d994e')
+
+    def install(self, spec, prefix):
+        options = ['--prefix=%s' % prefix]
+        configure(*options)
+        make()
+        make('install')

From 7ec450912dc71915205857da75bb418ffc3d0904 Mon Sep 17 00:00:00 2001
From: "Kelly (KT) Thompson" <kgt@lanl.gov>
Date: Mon, 21 Mar 2016 21:14:03 -0600
Subject: [PATCH 067/230] + Provide subversion and required packages apr and
 apr-util. + Installation of subversion may need to be modified to include
 python and perl   bindings. I have provided comments to this end, but the
 code is not active.

---
 .../packages/apr-util/apr-util.new/package.py | 44 ++++++++++++++
 .../builtin/packages/apr/apr.new/package.py   | 51 ++++++++++++++++
 .../subversion/subversion.new/package.py      | 59 +++++++++++++++++++
 .../repos/builtin/packages/swig/package.py    |  5 +-
 4 files changed, 158 insertions(+), 1 deletion(-)
 create mode 100644 var/spack/repos/builtin/packages/apr-util/apr-util.new/package.py
 create mode 100644 var/spack/repos/builtin/packages/apr/apr.new/package.py
 create mode 100644 var/spack/repos/builtin/packages/subversion/subversion.new/package.py

diff --git a/var/spack/repos/builtin/packages/apr-util/apr-util.new/package.py b/var/spack/repos/builtin/packages/apr-util/apr-util.new/package.py
new file mode 100644
index 00000000000..8f19c84d225
--- /dev/null
+++ b/var/spack/repos/builtin/packages/apr-util/apr-util.new/package.py
@@ -0,0 +1,44 @@
+##############################################################################
+# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License (as published by
+# the Free Software Foundation) version 2.1 dated February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with this program; if not, write to the Free Software Foundation,
+# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+class AprUtil(Package):
+    """Apache Portable Runtime Utility"""
+    homepage  = 'https://apr.apache.org/'
+    url       = 'http://archive.apache.org/dist/apr/apr-util-1.5.4.tar.gz'
+
+    version('1.5.4',    '866825c04da827c6e5f53daff5569f42')
+
+    depends_on('apr')
+
+    def install(self, spec, prefix):
+
+        # configure, build, install:
+        options = ['--prefix=%s' % prefix]
+        options.append('--with-apr=%s' % spec['apr'].prefix)
+
+        configure(*options)
+        make()
+        make('install')
diff --git a/var/spack/repos/builtin/packages/apr/apr.new/package.py b/var/spack/repos/builtin/packages/apr/apr.new/package.py
new file mode 100644
index 00000000000..5cbbad350bd
--- /dev/null
+++ b/var/spack/repos/builtin/packages/apr/apr.new/package.py
@@ -0,0 +1,51 @@
+##############################################################################
+# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License (as published by
+# the Free Software Foundation) version 2.1 dated February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with this program; if not, write to the Free Software Foundation,
+# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+class Apr(Package):
+    """Apache portable runtime."""
+    homepage  = 'https://apr.apache.org/'
+    url       = 'http://archive.apache.org/dist/apr/apr-1.5.2.tar.gz'
+
+    version('1.5.2',    '98492e965963f852ab29f9e61b2ad700')
+
+    #variant('ncurses', default=True, description='Enables the build of the ncurses gui')
+    #variant('qt', default=False, description='Enables the build of cmake-gui')
+    #variant('doc', default=False, description='Enables the generation of html and man page documentation')
+
+    #depends_on('ncurses', when='+ncurses')
+    #depends_on('qt', when='+qt')
+    #depends_on('python@2.7.11:', when='+doc')
+    #depends_on('py-sphinx', when='+doc')
+
+    #def url_for_version(self, version):
+    #    """Handle CMake's version-based custom URLs."""
+    #    return 'https://cmake.org/files/v%s/cmake-%s.tar.gz' % (version.up_to(2), version)
+
+    def install(self, spec, prefix):
+        options = ['--prefix=%s' % prefix]
+        configure(*options)
+        make()
+        make('install')
diff --git a/var/spack/repos/builtin/packages/subversion/subversion.new/package.py b/var/spack/repos/builtin/packages/subversion/subversion.new/package.py
new file mode 100644
index 00000000000..b1c3380238a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/subversion/subversion.new/package.py
@@ -0,0 +1,59 @@
+##############################################################################
+# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License (as published by
+# the Free Software Foundation) version 2.1 dated February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with this program; if not, write to the Free Software Foundation,
+# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+#import os
+
+class Subversion(Package):
+    """Apache Subversion - an open source version control system."""
+    homepage  = 'https://subversion.apache.org/'
+    url       = 'http://archive.apache.org/dist/subversion/subversion-1.8.13.tar.gz'
+
+    version('1.8.13',    '8065b3698d799507fb72dd7926ed32b6')
+    version('1.9.3',     'a92bcfaec4e5038f82c74a7b5bbd2f46')
+
+    depends_on('apr')
+    depends_on('apr-util')
+    depends_on('zlib')
+    depends_on('sqlite')
+    #depends_on('swig')
+
+    def install(self, spec, prefix):
+
+        # configure, build, install:
+        # Ref: http://www.linuxfromscratch.org/blfs/view/svn/general/subversion.html
+        options = ['--prefix=%s' % prefix]
+        options.append('--with-apr=%s' % spec['apr'].prefix)
+        options.append('--with-apr-util=%s' % spec['apr-util'].prefix)
+        options.append('--with-zlib=%s' % spec['zlib'].prefix)
+        options.append('--with-sqlite=%s' % spec['sqlite'].prefix)
+        #options.append('--with-swig=%s' % spec['swig'].prefix)
+
+        configure(*options)
+        make()
+        make('install')
+        #make('swig-py') # python bindings
+        #make('install-swig-py')
+        #make('swig-pl') # perl bindings
+        #make('install-swig-pl')
diff --git a/var/spack/repos/builtin/packages/swig/package.py b/var/spack/repos/builtin/packages/swig/package.py
index 8d46c4fe465..de6055e9656 100644
--- a/var/spack/repos/builtin/packages/swig/package.py
+++ b/var/spack/repos/builtin/packages/swig/package.py
@@ -36,11 +36,14 @@ class Swig(Package):
     homepage = "http://www.swig.org"
     url      = "http://prdownloads.sourceforge.net/swig/swig-3.0.2.tar.gz"
 
-    version('3.0.2', '62f9b0d010cef36a13a010dc530d0d41')
+    version('3.0.8',  'c96a1d5ecb13d38604d7e92148c73c97')
+    version('3.0.2',  '62f9b0d010cef36a13a010dc530d0d41')
+    version('2.0.12', 'c3fb0b2d710cc82ed0154b91e43085a4')
 
     depends_on('pcre')
 
     def install(self, spec, prefix):
         configure("--prefix=%s" % prefix)
+
         make()
         make("install")

From 23bf70296e4a02f49c301b1b744055802b1e8dc1 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Tue, 22 Mar 2016 09:22:42 +0100
Subject: [PATCH 068/230] arpack: add a patch for 3.3

---
 .../repos/builtin/packages/arpack-ng/package.py   |  4 ++++
 .../builtin/packages/arpack-ng/pdlamch10.patch    | 15 +++++++++++++++
 2 files changed, 19 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/arpack-ng/pdlamch10.patch

diff --git a/var/spack/repos/builtin/packages/arpack-ng/package.py b/var/spack/repos/builtin/packages/arpack-ng/package.py
index 0b49d142024..614071cf534 100644
--- a/var/spack/repos/builtin/packages/arpack-ng/package.py
+++ b/var/spack/repos/builtin/packages/arpack-ng/package.py
@@ -35,6 +35,10 @@ class ArpackNg(Package):
     variant('shared', default=True, description='Enables the build of shared libraries')
     variant('mpi', default=False, description='Activates MPI support')
 
+    # The function pdlamch10 does not set the return variable. This is fixed upstream
+    # see https://github.com/opencollab/arpack-ng/issues/34
+    patch('pdlamch10.patch', when='@3.3:')
+
     depends_on('blas')
     depends_on('lapack')
     depends_on('mpi', when='+mpi')
diff --git a/var/spack/repos/builtin/packages/arpack-ng/pdlamch10.patch b/var/spack/repos/builtin/packages/arpack-ng/pdlamch10.patch
new file mode 100644
index 00000000000..922828909f8
--- /dev/null
+++ b/var/spack/repos/builtin/packages/arpack-ng/pdlamch10.patch
@@ -0,0 +1,15 @@
+diff --git a/PARPACK/SRC/MPI/pdlamch10.f b/PARPACK/SRC/MPI/pdlamch10.f
+index 6571da9..2882c2e 100644
+--- a/PARPACK/SRC/MPI/pdlamch10.f
++++ b/PARPACK/SRC/MPI/pdlamch10.f
+@@ -86,8 +86,8 @@
+           TEMP = TEMP1
+       END IF
+ *
+-      PDLAMCH = TEMP
++      PDLAMCH10 = TEMP
+ *
+-*     End of PDLAMCH
++*     End of PDLAMCH10
+ *
+       END

From aca8b5c89de7058ab58f2eb3392e8b023b16fe8a Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Tue, 22 Mar 2016 09:27:00 +0100
Subject: [PATCH 069/230] move suite sparse to a proper folder

---
 .../builtin/packages/{SuiteSparse => suite-sparse}/package.py     | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename var/spack/repos/builtin/packages/{SuiteSparse => suite-sparse}/package.py (100%)

diff --git a/var/spack/repos/builtin/packages/SuiteSparse/package.py b/var/spack/repos/builtin/packages/suite-sparse/package.py
similarity index 100%
rename from var/spack/repos/builtin/packages/SuiteSparse/package.py
rename to var/spack/repos/builtin/packages/suite-sparse/package.py

From 3c5a1605d5e3cba881b743bf561f0966b1a3ad8b Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Tue, 22 Mar 2016 09:27:39 +0100
Subject: [PATCH 070/230] adjust the class name for suite sparse

---
 var/spack/repos/builtin/packages/suite-sparse/package.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/var/spack/repos/builtin/packages/suite-sparse/package.py b/var/spack/repos/builtin/packages/suite-sparse/package.py
index 6e130d118fe..b57f9967c30 100644
--- a/var/spack/repos/builtin/packages/suite-sparse/package.py
+++ b/var/spack/repos/builtin/packages/suite-sparse/package.py
@@ -1,7 +1,7 @@
 from spack import *
 
 
-class Suitesparse(Package):
+class SuiteSparse(Package):
     """
     SuiteSparse is a suite of sparse matrix algorithms
     """
@@ -24,4 +24,3 @@ def install(self, spec, prefix):
         # FIXME : this actually uses the current workaround
         # FIXME : (blas / lapack always provide libblas and liblapack as aliases)
         make('install', 'INSTALL=%s' % prefix, 'BLAS=-lblas', 'LAPACK=-llapack')
-

From cb97e8dd9301e5bbc6752caed2f4861a2a06f494 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Tue, 22 Mar 2016 09:43:10 +0100
Subject: [PATCH 071/230] adjust eigen and octave to use new names of suite
 sparse

---
 var/spack/repos/builtin/packages/eigen/package.py  | 2 +-
 var/spack/repos/builtin/packages/octave/package.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/var/spack/repos/builtin/packages/eigen/package.py b/var/spack/repos/builtin/packages/eigen/package.py
index e40046b4529..8d6e672f86c 100644
--- a/var/spack/repos/builtin/packages/eigen/package.py
+++ b/var/spack/repos/builtin/packages/eigen/package.py
@@ -48,7 +48,7 @@ class Eigen(Package):
     depends_on('metis', when='+metis')
     depends_on('scotch', when='+scotch')
     depends_on('fftw', when='+fftw')
-    depends_on('SuiteSparse', when='+suitesparse')
+    depends_on('suite-sparse', when='+suitesparse')
     depends_on('mpfr@2.3.0:')  # Eigen 3.2.7 requires at least 2.3.0
     depends_on('gmp')
 
diff --git a/var/spack/repos/builtin/packages/octave/package.py b/var/spack/repos/builtin/packages/octave/package.py
index 38b355159dd..6e99c236520 100644
--- a/var/spack/repos/builtin/packages/octave/package.py
+++ b/var/spack/repos/builtin/packages/octave/package.py
@@ -62,7 +62,7 @@ class Octave(Package):
     depends_on('qrupdate',    when='+qrupdate')
     #depends_on('qscintilla',  when='+qscintilla) # TODO: add package
     depends_on('qt',          when='+qt')
-    depends_on('SuiteSparse', when='+suitesparse')
+    depends_on('suite-sparse',when='+suitesparse')
     depends_on('zlib',        when='+zlib')
 
 

From a26992ef55fed958c15b45b989fc0a4d57f02251 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Tue, 22 Mar 2016 01:56:16 -0700
Subject: [PATCH 072/230] Change from PR #552: rename
 setup_dependent_python_module -> setup_dependent_package

- Fixed in package.py
- Fixed wrong prototypes in packages that use it.
- Fixed build_environment to set module variables properly
  - added hacky fix to ensure spec/package consistency in build processes.
  - Need to think about defensive spec copy done by `Repo.get`.  May be
    time to think about an immutable spec implementation.
---
 lib/spack/spack/build_environment.py          | 52 ++++++++++++++-----
 lib/spack/spack/package.py                    |  2 +-
 .../repos/builtin/packages/mpich/package.py   |  2 +-
 .../packages/netlib-scalapack/package.py      | 22 ++++----
 4 files changed, 52 insertions(+), 26 deletions(-)

diff --git a/lib/spack/spack/build_environment.py b/lib/spack/spack/build_environment.py
index fc5b7d6207f..119a255a349 100644
--- a/lib/spack/spack/build_environment.py
+++ b/lib/spack/spack/build_environment.py
@@ -225,7 +225,7 @@ def set_module_variables_for_package(pkg, module):
     m.spack_cc  = join_path(link_dir, pkg.compiler.link_paths['cc'])
     m.spack_cxx = join_path(link_dir, pkg.compiler.link_paths['cxx'])
     m.spack_f77 = join_path(link_dir, pkg.compiler.link_paths['f77'])
-    m.spack_f90 = join_path(link_dir, pkg.compiler.link_paths['fc'])
+    m.spack_fc  = join_path(link_dir, pkg.compiler.link_paths['fc'])
 
     # Emulate some shell commands for convenience
     m.pwd          = os.getcwd
@@ -270,32 +270,56 @@ def parent_class_modules(cls):
     return result
 
 
+def setup_module_variables_for_dag(pkg):
+    """Set module-scope variables for all packages in the DAG."""
+    for spec in pkg.spec.traverse(order='post'):
+        # If a user makes their own package repo, e.g.
+        # spack.repos.mystuff.libelf.Libelf, and they inherit from
+        # an existing class like spack.repos.original.libelf.Libelf,
+        # then set the module variables for both classes so the
+        # parent class can still use them if it gets called.
+        spkg = spec.package
+        modules = parent_class_modules(spkg.__class__)
+        for mod in modules:
+            set_module_variables_for_package(spkg, mod)
+        set_module_variables_for_package(spkg, spkg.module)
+
+
 def setup_package(pkg):
     """Execute all environment setup routines."""
     spack_env = EnvironmentModifications()
     run_env   = EnvironmentModifications()
 
+    # Before proceeding, ensure that specs and packages are consistent
+    #
+    # This is a confusing behavior due to how packages are
+    # constructed.  `setup_dependent_package` may set attributes on
+    # specs in the DAG for use by other packages' install
+    # method. However, spec.package will look up a package via
+    # spack.repo, which defensively copies specs into packages.  This
+    # code ensures that all packages in the DAG have pieces of the
+    # same spec object at build time.
+    #
+    # This is safe for the build process, b/c the build process is a
+    # throwaway environment, but it is kind of dirty.
+    #
+    # TODO: Think about how to avoid this fix and do something cleaner.
+    for s in pkg.spec.traverse(): s.package.spec = s
+
     set_compiler_environment_variables(pkg, spack_env)
     set_build_environment_variables(pkg, spack_env)
-
-    # If a user makes their own package repo, e.g.
-    # spack.repos.mystuff.libelf.Libelf, and they inherit from
-    # an existing class like spack.repos.original.libelf.Libelf,
-    # then set the module variables for both classes so the
-    # parent class can still use them if it gets called.
-    modules = parent_class_modules(pkg.__class__)
-    for mod in modules:
-        set_module_variables_for_package(pkg, mod)
+    setup_module_variables_for_dag(pkg)
 
     # Allow dependencies to modify the module
-    for dependency_spec in pkg.spec.traverse(root=False):
+    spec = pkg.spec
+    for dependency_spec in spec.traverse(root=False):
         dpkg = dependency_spec.package
-        dpkg.setup_dependent_python_module(pkg.module, pkg.spec)
+        dpkg.setup_dependent_package(pkg.module, spec)
 
     # Allow dependencies to set up environment as well
-    for dependency_spec in pkg.spec.traverse(root=False):
+    for dependency_spec in spec.traverse(root=False):
         dpkg = dependency_spec.package
-        dpkg.setup_dependent_environment(spack_env, run_env, pkg.spec)
+        dpkg.setup_dependent_environment(spack_env, run_env, spec)
 
     # Allow the package to apply some settings.
     pkg.setup_environment(spack_env, run_env)
diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py
index 9d8ac87bd70..9af32218374 100644
--- a/lib/spack/spack/package.py
+++ b/lib/spack/spack/package.py
@@ -1075,7 +1075,7 @@ def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
         self.setup_environment(spack_env, run_env)
 
 
-    def setup_dependent_python_module(self, module, dependent_spec):
+    def setup_dependent_package(self, module, dependent_spec):
         """Set up Python module-scope variables for dependent packages.
 
         Called before the install() method of dependents.
diff --git a/var/spack/repos/builtin/packages/mpich/package.py b/var/spack/repos/builtin/packages/mpich/package.py
index c4d9940bb72..b20dc8dd60c 100644
--- a/var/spack/repos/builtin/packages/mpich/package.py
+++ b/var/spack/repos/builtin/packages/mpich/package.py
@@ -54,7 +54,7 @@ def setup_dependent_environment(self, env, dependent_spec):
         env.set('MPICH_F90', spack_f90)
         env.set('MPICH_FC', spack_fc)
 
-    def setup_dependent_python_module(self, module, spec, dep_spec):
+    def setup_dependent_package(self, module, dep_spec):
         """For dependencies, make mpicc's use spack wrapper."""
         # FIXME : is this necessary ? Shouldn't this be part of a contract with MPI providers?
         module.mpicc = join_path(self.prefix.bin, 'mpicc')
diff --git a/var/spack/repos/builtin/packages/netlib-scalapack/package.py b/var/spack/repos/builtin/packages/netlib-scalapack/package.py
index 62abfcc48e3..c3e6822cdfe 100644
--- a/var/spack/repos/builtin/packages/netlib-scalapack/package.py
+++ b/var/spack/repos/builtin/packages/netlib-scalapack/package.py
@@ -1,4 +1,5 @@
 from spack import *
+import sys
 
 class NetlibScalapack(Package):
     """ScaLAPACK is a library of high-performance linear algebra routines for parallel distributed memory machines"""
@@ -11,16 +12,16 @@ class NetlibScalapack(Package):
     version('2.0.0', '9e76ae7b291be27faaad47cfc256cbfe')
     # versions before 2.0.0 are not using cmake and requires blacs as
     # a separated package
-    
+
     variant('shared', default=True, description='Build the shared library version')
     variant('fpic', default=False, description="Build with -fpic compiler option")
-    
+
     provides('scalapack')
-    
+
     depends_on('mpi')
     depends_on('lapack')
-    
-    def install(self, spec, prefix):       
+
+    def install(self, spec, prefix):
         options = [
             "-DBUILD_SHARED_LIBS:BOOL=%s" % ('ON' if '+shared' in spec else 'OFF'),
             "-DBUILD_STATIC_LIBS:BOOL=%s" % ('OFF' if '+shared' in spec else 'ON'),
@@ -40,10 +41,11 @@ def install(self, spec, prefix):
             make()
             make("install")
 
-    def setup_dependent_python_module(self, module, spec, dependent_spec):
+    def setup_dependent_package(self, module, dependent_spec):
+        spec = self.spec
         lib_dsuffix = '.dylib' if sys.platform == 'darwin' else '.so'
-        lib_suffix = lib_dsuffix if '+shared' in spec['scalapack'] else '.a'
+        lib_suffix = lib_dsuffix if '+shared' in spec else '.a'
 
-        spec['scalapack'].fc_link = '-L%s -lscalapack' % spec['scalapack'].prefix.lib
-        spec['scalapack'].cc_link = spec['scalapack'].fc_link
-        spec['scalapack'].libraries = [join_path(spec['scalapack'].prefix.lib, 'libscalapack%s' % lib_suffix)]
+        spec.fc_link = '-L%s -lscalapack' % spec.prefix.lib
+        spec.cc_link = spec.fc_link
+        spec.libraries = [join_path(spec.prefix.lib, 'libscalapack%s' % lib_suffix)]

From 6eb97a30a36f0a0f072826d473a641dd143345ed Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Tue, 22 Mar 2016 14:24:27 +0100
Subject: [PATCH 073/230] arpack: fix for +mpi variant

---
 var/spack/repos/builtin/packages/arpack-ng/package.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/arpack-ng/package.py b/var/spack/repos/builtin/packages/arpack-ng/package.py
index 614071cf534..dd86b17a53a 100644
--- a/var/spack/repos/builtin/packages/arpack-ng/package.py
+++ b/var/spack/repos/builtin/packages/arpack-ng/package.py
@@ -50,7 +50,10 @@ def install(self, spec, prefix):
         options = ['--prefix=%s' % prefix]
 
         if '+mpi' in spec:
-            options.append('--enable-mpi')
+            options.extend([
+                '--enable-mpi',
+                'F77=mpif77' #FIXME: avoid hardcoding MPI wrapper names
+            ])
 
         if '~shared' in spec:
             options.append('--enable-shared=no')

From d25026b74936f9988cdaf701258c937b3965c106 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Tue, 22 Mar 2016 16:26:16 +0100
Subject: [PATCH 074/230] add OCE package

---
 .../repos/builtin/packages/oce/package.py     | 47 +++++++++++++++++++
 1 file changed, 47 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/oce/package.py

diff --git a/var/spack/repos/builtin/packages/oce/package.py b/var/spack/repos/builtin/packages/oce/package.py
new file mode 100644
index 00000000000..06acb96736e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/oce/package.py
@@ -0,0 +1,47 @@
+from spack import *
+import platform
+
+class Oce(Package):
+    """
+    Open CASCADE Community Edition:
+    patches/improvements/experiments contributed by users over the official Open CASCADE library.
+    """
+    homepage = "https://github.com/tpaviot/oce"
+    url      = "https://github.com/tpaviot/oce/archive/OCE-0.17.tar.gz"
+
+    version('0.17.1', '36c67b87093c675698b483454258af91')
+    version('0.17'  , 'f1a89395c4b0d199bea3db62b85f818d')
+    version('0.16.1', '4d591b240c9293e879f50d86a0cb2bb3')
+    version('0.16'  , '7a4b4df5a104d75a537e25e7dd387eca')
+    version('0.15'  , '7ec541a1c350ca8a684f74980e48801c')
+
+    depends_on('cmake@2.8:')
+
+    def install(self, spec, prefix):
+        options = []
+        options.extend(std_cmake_args)
+        options.extend([
+            '-DOCE_INSTALL_PREFIX=%s' % prefix,
+            '-DOCE_BUILD_SHARED_LIB:BOOL=ON',
+            '-DOCE_BUILD_TYPE:STRING=Release',
+            '-DOCE_DATAEXCHANGE:BOOL=ON',
+            '-DOCE_DISABLE_X11:BOOL=ON',
+            '-DOCE_DRAW:BOOL=OFF',
+            '-DOCE_MODEL:BOOL=ON',
+            '-DOCE_MULTITHREAD_LIBRARY:STRING=NONE', # FIXME: add tbb
+            '-DOCE_OCAF:BOOL=ON',
+            '-DOCE_USE_TCL_TEST_FRAMEWORK:BOOL=OFF',
+            '-DOCE_VISUALISATION:BOOL=OFF',
+            '-DOCE_WITH_FREEIMAGE:BOOL=OFF',
+            '-DOCE_WITH_GL2PS:BOOL=OFF',
+            '-DOCE_WITH_OPENCL:BOOL=OFF'
+        ])
+
+        if platform.system() == 'Darwin':
+            options.extend([
+                '-DOCE_OSX_USE_COCOA:BOOL=ON',
+            ])
+
+        cmake('.', *options)
+
+        make("install/strip")

From 1f8d79b69ab005a6a372ff34806525148c0ed854 Mon Sep 17 00:00:00 2001
From: "Kelly (KT) Thompson" <kgt@lanl.gov>
Date: Tue, 22 Mar 2016 09:33:49 -0600
Subject: [PATCH 075/230] + Provide a ~perl variant to support building on
 systems w/o the perl-devel   package installed.

---
 var/spack/repos/builtin/packages/graphviz/package.py | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/var/spack/repos/builtin/packages/graphviz/package.py b/var/spack/repos/builtin/packages/graphviz/package.py
index 2a2102bfcb6..84bd696af2b 100644
--- a/var/spack/repos/builtin/packages/graphviz/package.py
+++ b/var/spack/repos/builtin/packages/graphviz/package.py
@@ -8,7 +8,6 @@ class Graphviz(Package):
     version('2.38.0', '5b6a829b2ac94efcd5fa3c223ed6d3ae')
 
     variant('perl', default=True, description='Disable if you have problems with the optional script language bindings')
-    variant('shared', default=True, description='Building static is required on AIX')
 
     parallel = False
 
@@ -20,8 +19,6 @@ def install(self, spec, prefix):
         options = ['--prefix=%s' % prefix]
         if '~perl' in spec:
             options.append('--disable-perl')
-        if '~shared' in spec:
-            options.append('--enable-shared=no')
 
         configure(*options)
         make()

From 7618dc504cb58e115a0a95b130bcfc485cd8341d Mon Sep 17 00:00:00 2001
From: Erik Schnetter <schnetter@gmail.com>
Date: Tue, 22 Mar 2016 19:17:39 +0100
Subject: [PATCH 076/230] temporary fix Hypre for OSX by building static lib by
 default

---
 var/spack/repos/builtin/packages/hypre/package.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/var/spack/repos/builtin/packages/hypre/package.py b/var/spack/repos/builtin/packages/hypre/package.py
index 242ee100d7a..8d93d48d1f6 100644
--- a/var/spack/repos/builtin/packages/hypre/package.py
+++ b/var/spack/repos/builtin/packages/hypre/package.py
@@ -1,5 +1,5 @@
 from spack import *
-import os
+import os, sys
 
 class Hypre(Package):
     """Hypre is a library of high performance preconditioners that
@@ -12,7 +12,8 @@ class Hypre(Package):
     version('2.10.1', 'dc048c4cabb3cd549af72591474ad674')
     version('2.10.0b', '768be38793a35bb5d055905b271f5b8e')
 
-    variant('shared', default=True, description="Build shared library version (disables static library)")
+    # hypre does not know how to build shared libraries on Darwin
+    variant('shared', default=sys.platform!='darwin', description="Build shared library version (disables static library)")
 
     depends_on("mpi")
     depends_on("blas")

From e56f5c4d6b4626a428b3c209f00eff59cd37b22f Mon Sep 17 00:00:00 2001
From: Cyrus Harrison <cyrush@llnl.gov>
Date: Tue, 22 Mar 2016 16:59:40 +0100
Subject: [PATCH 077/230] add Intel TBB package

---
 .../repos/builtin/packages/tbb/package.py     | 79 +++++++++++++++++++
 1 file changed, 79 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/tbb/package.py

diff --git a/var/spack/repos/builtin/packages/tbb/package.py b/var/spack/repos/builtin/packages/tbb/package.py
new file mode 100644
index 00000000000..56ffe4c27c6
--- /dev/null
+++ b/var/spack/repos/builtin/packages/tbb/package.py
@@ -0,0 +1,79 @@
+from spack import *
+import os
+import glob
+
+class Tbb(Package):
+    """Widely used C++ template library for task parallelism.
+    Intel Threading Building Blocks (Intel TBB) lets you easily write parallel
+    C++ programs that take full advantage of multicore performance, that are
+    portable and composable, and that have future-proof scalability.
+    """
+    homepage = "http://www.threadingbuildingblocks.org/"
+
+    # Only version-specific URL's work for TBB
+    version('4.4.3', '80707e277f69d9b20eeebdd7a5f5331137868ce1', url='https://www.threadingbuildingblocks.org/sites/default/files/software_releases/source/tbb44_20160128oss_src_0.tgz')
+
+    def coerce_to_spack(self,tbb_build_subdir):
+        for compiler in ["icc","gcc","clang"]:
+              fs = glob.glob(join_path(tbb_build_subdir,"*.%s.inc" % compiler ))
+              for f in fs:
+                  lines = open(f).readlines()
+                  of = open(f,"w")
+                  for l in lines:
+                      if l.strip().startswith("CPLUS ="):
+                        of.write("# coerced to spack\n")
+                        of.write("CPLUS = $(CXX)\n")
+                      elif l.strip().startswith("CPLUS ="):
+                        of.write("# coerced to spack\n")
+                        of.write("CONLY = $(CC)\n")
+                      else:
+                        of.write(l);
+
+    def install(self, spec, prefix):
+        #
+        # we need to follow TBB's compiler selection logic to get the proper build + link flags
+        # but we still need to use spack's compiler wrappers
+        # to accomplish this, we do two things:
+        #
+        # * Look at the spack spec to determine which compiler we should pass to tbb's Makefile
+        #
+        # * patch tbb's build system to use the compiler wrappers (CC, CXX) for
+        #    icc, gcc, clang
+        #    (see coerce_to_spack())
+        #
+        self.coerce_to_spack("build")
+
+        if spec.satisfies('%clang'):
+            tbb_compiler = "clang"
+        elif spec.satisfies('%intel'):
+            tbb_compiler = "icc"
+        else:
+            tbb_compiler = "gcc"
+
+
+        mkdirp(prefix)
+        mkdirp(prefix.lib)
+
+        #
+        # tbb does not have a configure script or make install target
+        # we simply call make, and try to put the pieces together
+        #
+        make("compiler=%s"  %(tbb_compiler))
+
+        # install headers to {prefix}/include
+        install_tree('include',prefix.include)
+
+        # install libs to {prefix}/lib
+        tbb_lib_names = ["libtbb",
+                         "libtbbmalloc",
+                         "libtbbmalloc_proxy"]
+
+        for lib_name in tbb_lib_names:
+            # install release libs
+            fs = glob.glob(join_path("build","*release",lib_name + ".*"))
+            for f in fs:
+                install(f, prefix.lib)
+            # install debug libs if they exist
+            fs = glob.glob(join_path("build","*debug",lib_name + "_debug.*"))
+            for f in fs:
+                install(f, prefix.lib)

From 1eb7b8cf4624910121ac66996f17a212ed2cfc91 Mon Sep 17 00:00:00 2001
From: "Kelly (KT) Thompson" <kgt@lanl.gov>
Date: Tue, 22 Mar 2016 12:31:27 -0600
Subject: [PATCH 078/230] + Add a validate function that refuses to build
 numdiff if arch is darwin-x86_64.

---
 .../repos/builtin/packages/numdiff/package.py     | 15 +++++++++++++++
 1 file changed, 15 insertions(+)

diff --git a/var/spack/repos/builtin/packages/numdiff/package.py b/var/spack/repos/builtin/packages/numdiff/package.py
index a51f6206cf1..91286127fbb 100644
--- a/var/spack/repos/builtin/packages/numdiff/package.py
+++ b/var/spack/repos/builtin/packages/numdiff/package.py
@@ -34,7 +34,22 @@ class Numdiff(Package):
 
     version('5.8.1',    'a295eb391f6cb1578209fc6b4f9d994e')
 
+    def validate(self, spec):
+        """
+        Checks if we are attempting to build on an incompatible
+        architecture.
+
+        Ref. https://github.com/davydden/homebrew-dealiisuite/blob/master/numdiff.rb#L13-L15.
+
+        :param spec: spec of the package
+        :raises RuntimeError: in case of inconsistencies.
+        """
+
+        if spec.satisfies("=darwin-x86_64"):
+            raise RuntimeError(msg)
+
     def install(self, spec, prefix):
+        self.validate(spec)
         options = ['--prefix=%s' % prefix]
         configure(*options)
         make()

From 5f68e14d3bd90e4a71f6366a328dcc97fc6e8a92 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Tue, 22 Mar 2016 19:41:31 +0100
Subject: [PATCH 079/230] add gettext package

---
 .../repos/builtin/packages/gettext/package.py | 30 +++++++++++++++++++
 1 file changed, 30 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/gettext/package.py

diff --git a/var/spack/repos/builtin/packages/gettext/package.py b/var/spack/repos/builtin/packages/gettext/package.py
new file mode 100644
index 00000000000..05712d7392c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/gettext/package.py
@@ -0,0 +1,30 @@
+from spack import *
+
+class Gettext(Package):
+    """GNU internationalization (i18n) and localization (l10n) library."""
+    homepage = "https://www.gnu.org/software/gettext/"
+    url      = "http://ftpmirror.gnu.org/gettext/gettext-0.19.7.tar.xz"
+
+    version('0.19.7', 'f81e50556da41b44c1d59ac93474dca5')
+
+    def install(self, spec, prefix):
+        options = ['--disable-dependency-tracking',
+                   '--disable-silent-rules',
+                   '--disable-debug',
+                   '--prefix=%s' % prefix,
+                   '--with-included-gettext',
+                   '--with-included-glib',
+                   '--with-included-libcroco',
+                   '--with-included-libunistring',
+                   '--with-emacs',
+                   '--with-lispdir=%s/emacs/site-lisp/gettext' % prefix.share,
+                   '--disable-java',
+                   '--disable-csharp',
+                   '--without-git', # Don't use VCS systems to create these archives
+                   '--without-cvs',
+                   '--without-xz']
+
+        configure(*options)
+
+        make()
+        make("install")

From fd1784369a20650c3fc6f84d57ed4e6be59afc44 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Tue, 22 Mar 2016 19:50:15 +0100
Subject: [PATCH 080/230] add muparser package

---
 .../repos/builtin/packages/muparser/package.py | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/muparser/package.py

diff --git a/var/spack/repos/builtin/packages/muparser/package.py b/var/spack/repos/builtin/packages/muparser/package.py
new file mode 100644
index 00000000000..a1a9ff90e53
--- /dev/null
+++ b/var/spack/repos/builtin/packages/muparser/package.py
@@ -0,0 +1,18 @@
+from spack import *
+
+class Muparser(Package):
+    """C++ math expression parser library."""
+    homepage = "http://muparser.beltoforion.de/"
+    url      = "https://github.com/beltoforion/muparser/archive/v2.2.5.tar.gz"
+
+    version('2.2.5', '02dae671aa5ad955fdcbcd3fee313fb7')
+
+    def install(self, spec, prefix):
+        options = ['--disable-debug',
+                   '--disable-dependency-tracking',
+                   '--prefix=%s' % prefix]
+
+        configure(*options)
+
+        make()
+        make("install")

From d05e4581c9d249c0736d8d58b394860ca05f8402 Mon Sep 17 00:00:00 2001
From: Joseph Ciurej <ciurej1@llnl.gov>
Date: Tue, 22 Mar 2016 12:31:26 -0700
Subject: [PATCH 081/230] Added the '+silex' variant to the Silo package. Added
 a number of different versions to the Silo package.

---
 .../repos/builtin/packages/silo/package.py    | 23 ++++++++++++++-----
 1 file changed, 17 insertions(+), 6 deletions(-)

diff --git a/var/spack/repos/builtin/packages/silo/package.py b/var/spack/repos/builtin/packages/silo/package.py
index d1aed78e0e8..b7894e4d2bd 100644
--- a/var/spack/repos/builtin/packages/silo/package.py
+++ b/var/spack/repos/builtin/packages/silo/package.py
@@ -5,24 +5,35 @@ class Silo(Package):
        data to binary, disk files."""
 
     homepage = "http://wci.llnl.gov/simulation/computer-codes/silo"
-    url      = "https://wci.llnl.gov/content/assets/docs/simulation/computer-codes/silo/silo-4.8/silo-4.8.tar.gz"
+    base_url = "https://wci.llnl.gov/content/assets/docs/simulation/computer-codes/silo"
 
+    version('4.10.2', '9ceac777a2f2469ac8cef40f4fab49c8')
+    version('4.9', 'a83eda4f06761a86726e918fc55e782a')
     version('4.8', 'b1cbc0e7ec435eb656dc4b53a23663c9')
 
     variant('fortran', default=True, description='Enable Fortran support')
+    variant('silex', default=False, description='Builds Silex, a GUI for viewing Silo files')
 
-    depends_on("hdf5")
+    depends_on('hdf5')
+    depends_on('qt', when='+silex')
 
     def install(self, spec, prefix):
         config_args = [
             '--enable-fortran' if '+fortran' in spec else '--disable-fortran',
+            '--enable-silex' if '+silex' in spec else '--disable-silex',
         ]
 
+        if '+silex' in spec:
+            config_args.append('--with-Qt-dir=%s' % spec['qt'].prefix)
+
         configure(
-            "--prefix=%s" % prefix,
-            "--with-hdf5=%s,%s" % (spec['hdf5'].prefix.include, spec['hdf5'].prefix.lib),
-            "--with-zlib=%s,%s" % (spec['zlib'].prefix.include, spec['zlib'].prefix.lib),
+            '--prefix=%s' % prefix,
+            '--with-hdf5=%s,%s' % (spec['hdf5'].prefix.include, spec['hdf5'].prefix.lib),
+            '--with-zlib=%s,%s' % (spec['zlib'].prefix.include, spec['zlib'].prefix.lib),
             *config_args)
 
         make()
-        make("install")
+        make('install')
+
+    def url_for_version(self, version):
+        return '%s/silo-%s/silo-%s.tar.gz' % (Silo.base_url, version, version)

From 1728a0c3e60d55d1181f14ef5a677b1652a0680b Mon Sep 17 00:00:00 2001
From: Joseph Ciurej <ciurej1@llnl.gov>
Date: Tue, 22 Mar 2016 12:33:11 -0700
Subject: [PATCH 082/230] Updated the 'crypto++' package to use an improved URL
 formation scheme (inspired by changes made to the 'Silo' package).

---
 var/spack/repos/builtin/packages/cryptopp/package.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/var/spack/repos/builtin/packages/cryptopp/package.py b/var/spack/repos/builtin/packages/cryptopp/package.py
index 1693c4b160f..743a3ac70f4 100644
--- a/var/spack/repos/builtin/packages/cryptopp/package.py
+++ b/var/spack/repos/builtin/packages/cryptopp/package.py
@@ -8,8 +8,8 @@ class Cryptopp(Package):
        public-key encryption (RSA, DSA), and a few obsolete/historical encryption
        algorithms (MD5, Panama)."""
 
-    homepage = "http://www.cryptopp.com/"
-    url      = "http://www.cryptopp.com/cryptopp563.zip"
+    homepage = "http://www.cryptopp.com"
+    base_url = "http://www.cryptopp.com"
 
     version('5.6.3', '3c5b70e2ec98b7a24988734446242d07')
     version('5.6.2', '7ed022585698df48e65ce9218f6c6a67')
@@ -28,4 +28,4 @@ def url_for_version(self, version):
         version_tuple = tuple(v for v in iter(version))
         version_string = reduce(lambda vs, nv: vs + str(nv), version_tuple, "")
 
-        return "%scryptopp%s.zip" % (Cryptopp.homepage, version_string)
+        return '%s/cryptopp%s.zip' % (Cryptopp.base_url, version_string)

From 27f337aa11104a6e625db6e40f8d9414954123ee Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Tue, 22 Mar 2016 11:44:38 +0100
Subject: [PATCH 083/230] petsc: set PETSC_DIR in dependent_env

---
 var/spack/repos/builtin/packages/petsc/package.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/var/spack/repos/builtin/packages/petsc/package.py b/var/spack/repos/builtin/packages/petsc/package.py
index 7239baaf7f5..3dd117eed11 100644
--- a/var/spack/repos/builtin/packages/petsc/package.py
+++ b/var/spack/repos/builtin/packages/petsc/package.py
@@ -100,3 +100,7 @@ def install(self, spec, prefix):
         # PETSc has its own way of doing parallel make.
         make('MAKE_NP=%s' % make_jobs, parallel=False)
         make("install")
+
+    def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
+        # set up PETSC_DIR for everyone using PETSc package
+        spack_env.set('PETSC_DIR', self.prefix)

From 24264eb00e4f4e3661ea1a28e9cbe3a97cd69580 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Tue, 22 Mar 2016 11:45:18 +0100
Subject: [PATCH 084/230] add slepc package

---
 .../repos/builtin/packages/slepc/package.py   | 49 +++++++++++++++++++
 1 file changed, 49 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/slepc/package.py

diff --git a/var/spack/repos/builtin/packages/slepc/package.py b/var/spack/repos/builtin/packages/slepc/package.py
new file mode 100644
index 00000000000..8b5f24394f6
--- /dev/null
+++ b/var/spack/repos/builtin/packages/slepc/package.py
@@ -0,0 +1,49 @@
+import os
+from spack import *
+
+
+class Slepc(Package):
+    """
+    Scalable Library for Eigenvalue Computations.
+    """
+
+    homepage = "http://www.grycap.upv.es/slepc"
+    url = "http://slepc.upv.es/download/download.php?filename=slepc-3.6.2.tar.gz"
+
+    version('3.6.2', '2ab4311bed26ccf7771818665991b2ea3a9b15f97e29fd13911ab1293e8e65df')
+
+    variant('arpack', default=False, description='Enables Arpack wrappers')
+
+    depends_on('petsc')
+    depends_on('arpack-ng~mpi',when='+arpack^petsc~mpi')
+    depends_on('arpack-ng+mpi',when='+arpack^petsc+mpi')
+
+    def install(self, spec, prefix):
+        # set SLEPC_DIR for installation
+        os.environ['SLEPC_DIR'] = self.stage.source_path
+
+        options = []
+
+        if '+arpack' in spec:
+            options.extend([
+                '--with-arpack-dir=%s' % spec['arpack-ng'].prefix.lib,
+            ])
+            if 'arpack-ng~mpi' in spec:
+                options.extend([
+                    '--with-arpack-flags=-larpack'
+                ])
+            else:
+                options.extend([
+                    '--with-arpack-flags=-lparpack,-larpack'
+                ])
+
+        configure('--prefix=%s' % prefix, *options)
+
+        make('MAKE_NP=%s' % make_jobs, parallel=False)
+        #FIXME:
+        # make('test')
+        make('install')
+
+    def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
+        # set up SLEPC_DIR for everyone using SLEPc package
+        spack_env.set('SLEPC_DIR', self.prefix)

From 6c8d51f403213cf3a49373d4dca03fac565a73b4 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Tue, 22 Mar 2016 22:58:14 +0100
Subject: [PATCH 085/230] add p4est package

---
 .../repos/builtin/packages/p4est/package.py   | 34 +++++++++++++++++++
 1 file changed, 34 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/p4est/package.py

diff --git a/var/spack/repos/builtin/packages/p4est/package.py b/var/spack/repos/builtin/packages/p4est/package.py
new file mode 100644
index 00000000000..1e2969fe642
--- /dev/null
+++ b/var/spack/repos/builtin/packages/p4est/package.py
@@ -0,0 +1,34 @@
+from spack import *
+
+class P4est(Package):
+    """Dynamic management of a collection (a forest) of adaptive octrees in parallel"""
+    homepage = "http://www.p4est.org"
+    url      = "http://p4est.github.io/release/p4est-1.1.tar.gz"
+
+    version('1.1', '37ba7f4410958cfb38a2140339dbf64f')
+
+    # disable by default to make it work on frontend of clusters
+    variant('tests', default=False, description='Run small tests')
+
+    depends_on('mpi')
+
+    def install(self, spec, prefix):
+        options = ['--enable-mpi',
+                   '--enable-shared',
+                   '--disable-vtk-binary',
+                   '--without-blas',
+                   'CPPFLAGS=-DSC_LOG_PRIORITY=SC_LP_ESSENTIAL',
+                   'CFLAGS=-O2',
+                   'CC=%s' % join_path(self.spec['mpi'].prefix.bin, 'mpicc'), # TODO: use ENV variables or MPI class wrappers
+                   'CXX=%s' % join_path(self.spec['mpi'].prefix.bin, 'mpic++'),
+                   'FC=%s' % join_path(self.spec['mpi'].prefix.bin, 'mpif90'),
+                   'F77=%s' % join_path(self.spec['mpi'].prefix.bin, 'mpif77'),
+                  ]
+
+        configure('--prefix=%s' % prefix, *options)
+
+        make()
+        if '+tests' in self.spec:
+            make("check")
+
+        make("install")

From 0ee993569f8f47f5ca94873bc779d98639e9a1b4 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Tue, 22 Mar 2016 23:04:59 +0100
Subject: [PATCH 086/230] add deal.ii package

---
 .../repos/builtin/packages/dealii/package.py  | 67 +++++++++++++++++++
 1 file changed, 67 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/dealii/package.py

diff --git a/var/spack/repos/builtin/packages/dealii/package.py b/var/spack/repos/builtin/packages/dealii/package.py
new file mode 100644
index 00000000000..cddf5cd98ba
--- /dev/null
+++ b/var/spack/repos/builtin/packages/dealii/package.py
@@ -0,0 +1,67 @@
+from spack import *
+
+class Dealii(Package):
+    """C++ software library providing well-documented tools to build finite element codes for a broad variety of PDEs."""
+    homepage = "https://www.dealii.org"
+    url      = "https://github.com/dealii/dealii/releases/download/v8.4.0/dealii-8.4.0.tar.gz"
+
+    version('8.4.0', 'ac5dbf676096ff61e092ce98c80c2b00')
+
+    depends_on ("cmake")
+    depends_on ("blas")
+    depends_on ("lapack")
+    depends_on ("mpi")
+
+    #depends_on ("arpack")
+    depends_on ("boost")
+    #depends_on ("doxygen")
+    depends_on ("hdf5+mpi")
+    depends_on ("metis")
+    #depends_on "muparser"
+    depends_on ("netcdf")
+    #depends_on ("numdiff")
+    #depends_on ("oce")
+    depends_on ("p4est")
+    depends_on ("parmetis")
+    depends_on ("petsc")
+    #depends_on ("slepc")
+    depends_on ("SuiteSparse")
+    #depends_on "tbb"
+    depends_on ("trilinos")
+
+    def install(self, spec, prefix):
+        options = []
+        options.extend(std_cmake_args)
+
+        # CMAKE_BUILD_TYPE should be DebugRelease | Debug | Release
+        for word in options[:]:
+            if word.startswith('-DCMAKE_BUILD_TYPE'):
+                options.remove(word)
+
+        options.extend([
+            '-DCMAKE_BUILD_TYPE=DebugRelease',
+            '-DDEAL_II_WITH_THREADS:BOOL=ON'
+            '-DDEAL_II_WITH_MPI:BOOL=ON',
+            '-DCMAKE_C_COMPILER=%s' % join_path(self.spec['mpi'].prefix.bin, 'mpicc'),
+            '-DCMAKE_CXX_COMPILER=%s' % join_path(self.spec['mpi'].prefix.bin, 'mpic++'),
+            '-DCMAKE_Fortran_COMPILER=%s' % join_path(self.spec['mpi'].prefix.bin, 'mpif90'),
+            #'-DARPACK_DIR=%s' %  ,
+            '-DBOOST_DIR=%s' % spec['boost'].prefix,
+            '-DHDF5_DIR=%s' % spec['hdf5'].prefix,
+            '-DMETIS_DIR=%s' % spec['metis'].prefix,
+            #'-DMUPARSER_DIR=%s '
+            '-DNETCDF_DIR=%s' % spec['netcdf'].prefix,
+            #'-DOPENCASCADE_DIR=
+            '-DP4EST_DIR=%s' % spec['p4est'].prefix,
+            '-DPETSC_DIR=%s' % spec['petsc'].prefix,
+            #'-DSLEPC_DIR=
+            '-DUMFPACK_DIR=%s' % spec['SuiteSparse'].prefix,
+            #'-DTBB_DIR=%s'
+            '-DTRILINOS_DIR=%s' % spec['trilinos'].prefix
+        ])
+
+        cmake('.', *options)
+
+        make()
+        make("test")
+        make("install")

From 474db2085e223b8226a6ae799232bb2fede3efde Mon Sep 17 00:00:00 2001
From: Joseph Ciurej <ciurej1@llnl.gov>
Date: Tue, 22 Mar 2016 15:55:54 -0700
Subject: [PATCH 087/230] Simplified the 'url_for_version' function for the
 'Crypto++' package.

---
 var/spack/repos/builtin/packages/cryptopp/package.py | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/var/spack/repos/builtin/packages/cryptopp/package.py b/var/spack/repos/builtin/packages/cryptopp/package.py
index 743a3ac70f4..bc83cb2b651 100644
--- a/var/spack/repos/builtin/packages/cryptopp/package.py
+++ b/var/spack/repos/builtin/packages/cryptopp/package.py
@@ -25,7 +25,5 @@ def install(self, spec, prefix):
         install('libcryptopp.a', prefix.lib)
 
     def url_for_version(self, version):
-        version_tuple = tuple(v for v in iter(version))
-        version_string = reduce(lambda vs, nv: vs + str(nv), version_tuple, "")
-
+        version_string = str(version).replace('.', '')
         return '%s/cryptopp%s.zip' % (Cryptopp.base_url, version_string)

From 5b3c96a9bb0ba6501512c93dcdb26510e796314e Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Wed, 23 Mar 2016 08:07:45 +0100
Subject: [PATCH 088/230] fix superlu-dist lib installation

---
 var/spack/repos/builtin/packages/superlu-dist/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/superlu-dist/package.py b/var/spack/repos/builtin/packages/superlu-dist/package.py
index c4c76909b35..9a94de8ba50 100644
--- a/var/spack/repos/builtin/packages/superlu-dist/package.py
+++ b/var/spack/repos/builtin/packages/superlu-dist/package.py
@@ -54,6 +54,7 @@ def install(self, spec, prefix):
         # need to install by hand
         headers_location = join_path(self.prefix.include,'superlu_dist')
         mkdirp(headers_location)
+        mkdirp(prefix.lib)
         # FIXME: fetch all headers in the folder automatically
         for header in ['Cnames.h','cublas_utils.h','dcomplex.h','html_mainpage.h','machines.h','old_colamd.h','psymbfact.h','superlu_ddefs.h','superlu_defs.h','superlu_enum_consts.h','superlu_zdefs.h','supermatrix.h','util_dist.h']:
             superludist_header = join_path(self.stage.source_path, 'SRC/',header)

From c4134ee71e43a6a2a38822e25cc72ca73efdcfea Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Wed, 23 Mar 2016 00:36:32 -0700
Subject: [PATCH 089/230] Fix #608: broken numpy build.

- Failed to catch all instances of modify_module when it was renamed
  to setup_dependent_package.

- Refactored remaining modify_module calls.

- Also modified Python's setup_dependent_package slightly: only
  creates empty site-packages directory for Python extensions now, not
  for all dependents.
---
 lib/spack/spack/modules.py                         |  4 ++--
 lib/spack/spack/preferred_packages.py              |  4 +++-
 var/spack/repos/builtin/packages/python/package.py | 11 ++++++-----
 var/spack/repos/builtin/packages/ruby/package.py   |  6 +++---
 4 files changed, 14 insertions(+), 11 deletions(-)

diff --git a/lib/spack/spack/modules.py b/lib/spack/spack/modules.py
index 05c93cd3e65..8ed98e5d38f 100644
--- a/lib/spack/spack/modules.py
+++ b/lib/spack/spack/modules.py
@@ -160,8 +160,8 @@ def write(self):
         # package-specific modifications
         for extendee in self.pkg.extendees:
             extendee_spec = self.spec[extendee]
-            extendee_spec.package.modify_module(
-                self.pkg.module, extendee_spec, self.spec)
+            extendee_spec.package.setup_dependent_package(
+                self.pkg.module, self.spec)
 
         # Package-specific environment modifications
         spack_env = EnvironmentModifications()
diff --git a/lib/spack/spack/preferred_packages.py b/lib/spack/spack/preferred_packages.py
index 4d8526c75fa..f0a5382dc91 100644
--- a/lib/spack/spack/preferred_packages.py
+++ b/lib/spack/spack/preferred_packages.py
@@ -150,7 +150,9 @@ def spec_has_preferred_provider(self, pkgname, provider_str):
     def version_compare(self, pkgname, a, b):
         """Return less-than-0, 0, or greater than 0 if version a of pkgname is
            respecively less-than, equal-to, or greater-than version b of pkgname.
-           One version is less-than another if it is preferred over the other."""
+           Versions marked 'preferred=True' in package.py take precedence over any
+           versions not marked preferred.
+        """
         return self._spec_compare(pkgname, 'version', a, b, True, None)
 
 
diff --git a/var/spack/repos/builtin/packages/python/package.py b/var/spack/repos/builtin/packages/python/package.py
index 4f55bc803ea..6d9030805b1 100644
--- a/var/spack/repos/builtin/packages/python/package.py
+++ b/var/spack/repos/builtin/packages/python/package.py
@@ -108,7 +108,7 @@ def setup_dependent_environment(self, spack_env, run_env, extension_spec):
         run_env.set('PYTHONPATH', pythonpath)
 
 
-    def modify_module(self, module, spec, ext_spec):
+    def setup_dependent_package(self, module, ext_spec):
         """
         Called before python modules' install() methods.
 
@@ -118,17 +118,18 @@ def modify_module(self, module, spec, ext_spec):
         """
         # Python extension builds can have a global python executable function
         if self.version >= Version("3.0.0") and self.version < Version("4.0.0"):
-            module.python = Executable(join_path(spec.prefix.bin, 'python3'))
+            module.python = Executable(join_path(self.spec.prefix.bin, 'python3'))
         else:
-            module.python = Executable(join_path(spec.prefix.bin, 'python'))
+            module.python = Executable(join_path(self.spec.prefix.bin, 'python'))
 
         # Add variables for lib/pythonX.Y and lib/pythonX.Y/site-packages dirs.
         module.python_lib_dir     = os.path.join(ext_spec.prefix, self.python_lib_dir)
         module.python_include_dir = os.path.join(ext_spec.prefix, self.python_include_dir)
         module.site_packages_dir  = os.path.join(ext_spec.prefix, self.site_packages_dir)
 
-        # Make the site packages directory if it does not exist already.
-        mkdirp(module.site_packages_dir)
+        # Make the site packages directory for extensions, if it does not exist already.
+        if ext_spec.package.is_extension:
+            mkdirp(module.site_packages_dir)
 
     # ========================================================================
     # Handle specifics of activating and deactivating python modules.
diff --git a/var/spack/repos/builtin/packages/ruby/package.py b/var/spack/repos/builtin/packages/ruby/package.py
index 7ff1898ce91..e13677e4d22 100644
--- a/var/spack/repos/builtin/packages/ruby/package.py
+++ b/var/spack/repos/builtin/packages/ruby/package.py
@@ -30,7 +30,7 @@ def setup_dependent_environment(self, spack_env, run_env, extension_spec):
         # The actual installation path for this gem
         spack_env.set('GEM_HOME', extension_spec.prefix)
 
-    def modify_module(self, module, spec, ext_spec):
+    def setup_dependent_package(self, module, ext_spec):
         """Called before ruby modules' install() methods.  Sets GEM_HOME
         and GEM_PATH to values appropriate for the package being built.
 
@@ -39,5 +39,5 @@ def modify_module(self, module, spec, ext_spec):
             gem('install', '<gem-name>.gem')
         """
         # Ruby extension builds have global ruby and gem functions
-        module.ruby = Executable(join_path(spec.prefix.bin, 'ruby'))
-        module.gem = Executable(join_path(spec.prefix.bin, 'gem'))
+        module.ruby = Executable(join_path(self.spec.prefix.bin, 'ruby'))
+        module.gem = Executable(join_path(self.spec.prefix.bin, 'gem'))

From 01918a6f4891ab985b8619daaadc1bf484e4db17 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Wed, 23 Mar 2016 05:26:51 +0100
Subject: [PATCH 090/230] fix MUMPS build on OSX (set parallel=False)

---
 var/spack/repos/builtin/packages/mumps/package.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/mumps/package.py b/var/spack/repos/builtin/packages/mumps/package.py
index 5c120c37df8..5a254dfd00e 100644
--- a/var/spack/repos/builtin/packages/mumps/package.py
+++ b/var/spack/repos/builtin/packages/mumps/package.py
@@ -135,7 +135,8 @@ def install(self, spec, prefix):
 
         self.write_makefile_inc()
 
-        make(*make_libs)
+        # Build fails in parallel, at least on OS-X
+        make(*make_libs, parallel=False)
 
         install_tree('lib', prefix.lib)
         install_tree('include', prefix.include)

From 38350ae33d29e108803cebdf13b90b6898947328 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Wed, 23 Mar 2016 01:32:54 -0700
Subject: [PATCH 091/230] resurrect preferred=True option for packages lost in
 merge of externals support.

- Pyton 2.7.11 is preferred again.
---
 lib/spack/spack/concretize.py         | 4 ++++
 lib/spack/spack/preferred_packages.py | 4 +---
 lib/spack/spack/test/concretize.py    | 9 +++++++++
 3 files changed, 14 insertions(+), 3 deletions(-)

diff --git a/lib/spack/spack/concretize.py b/lib/spack/spack/concretize.py
index 2e576743ec6..ed9bf798682 100644
--- a/lib/spack/spack/concretize.py
+++ b/lib/spack/spack/concretize.py
@@ -159,6 +159,10 @@ def concretize_version(self, spec):
              if any(v.satisfies(sv) for sv in spec.versions)],
             cmp=cmp_versions)
 
+        def prefer_key(v):
+            return pkg.versions.get(Version(v)).get('preferred', False)
+        valid_versions.sort(key=prefer_key, reverse=True)
+
         if valid_versions:
             spec.versions = ver([valid_versions[0]])
         else:
diff --git a/lib/spack/spack/preferred_packages.py b/lib/spack/spack/preferred_packages.py
index f0a5382dc91..4d8526c75fa 100644
--- a/lib/spack/spack/preferred_packages.py
+++ b/lib/spack/spack/preferred_packages.py
@@ -150,9 +150,7 @@ def spec_has_preferred_provider(self, pkgname, provider_str):
     def version_compare(self, pkgname, a, b):
         """Return less-than-0, 0, or greater than 0 if version a of pkgname is
            respecively less-than, equal-to, or greater-than version b of pkgname.
-           Versions marked 'preferred=True' in package.py take precedence over any
-           versions not marked preferred.
-        """
+           One version is less-than another if it is preferred over the other."""
         return self._spec_compare(pkgname, 'version', a, b, True, None)
 
 
diff --git a/lib/spack/spack/test/concretize.py b/lib/spack/spack/test/concretize.py
index 08cce096747..9cd8c969aed 100644
--- a/lib/spack/spack/test/concretize.py
+++ b/lib/spack/spack/test/concretize.py
@@ -24,6 +24,7 @@
 ##############################################################################
 import spack
 from spack.spec import Spec, CompilerSpec
+from spack.version import ver
 from spack.concretize import find_spec
 from spack.test.mock_packages_test import *
 
@@ -77,6 +78,14 @@ def test_concretize_variant(self):
         self.check_concretize('mpich')
 
 
+    def test_concretize_preferred_version(self):
+        spec = self.check_concretize('python')
+        self.assertEqual(spec.versions, ver('2.7.11'))
+
+        spec = self.check_concretize('python@3.5.1')
+        self.assertEqual(spec.versions, ver('3.5.1'))
+
+
     def test_concretize_with_virtual(self):
         self.check_concretize('mpileaks ^mpi')
         self.check_concretize('mpileaks ^mpi@:1.1')

From cc582dd4b435ba06dc140b1ca96b688871e36abb Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Wed, 23 Mar 2016 02:02:49 -0700
Subject: [PATCH 092/230] Add mock python package.

---
 .../builtin.mock/packages/python/package.py   | 43 +++++++++++++++++++
 1 file changed, 43 insertions(+)
 create mode 100644 var/spack/repos/builtin.mock/packages/python/package.py

diff --git a/var/spack/repos/builtin.mock/packages/python/package.py b/var/spack/repos/builtin.mock/packages/python/package.py
new file mode 100644
index 00000000000..c5fed52f534
--- /dev/null
+++ b/var/spack/repos/builtin.mock/packages/python/package.py
@@ -0,0 +1,43 @@
+##############################################################################
+# Copyright (c) 2013-2015, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License (as published by
+# the Free Software Foundation) version 2.1 dated February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with this program; if not, write to the Free Software Foundation,
+# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+class Python(Package):
+    """Dummy Python package to demonstrate preferred versions."""
+    homepage = "http://www.python.org"
+    url      = "http://www.python.org/ftp/python/2.7.8/Python-2.7.8.tgz"
+
+    extendable = True
+
+    version('3.5.1', 'be78e48cdfc1a7ad90efff146dce6cfe')
+    version('3.5.0', 'a56c0c0b45d75a0ec9c6dee933c41c36')
+    version('2.7.11', '6b6076ec9e93f05dd63e47eb9c15728b', preferred=True)
+    version('2.7.10', 'd7547558fd673bd9d38e2108c6b42521')
+    version('2.7.9', '5eebcaa0030dc4061156d3429657fb83')
+    version('2.7.8', 'd4bca0159acb0b44a781292b5231936f')
+
+    def install(self, spec, prefix):
+        pass
+

From 0fbdb3f65d234d6ed8f77d3732c134962ad47b35 Mon Sep 17 00:00:00 2001
From: alalazo <massimiliano.culpo@googlemail.com>
Date: Wed, 23 Mar 2016 15:43:16 +0100
Subject: [PATCH 093/230] modules : added configuration file with disable
 keyword

---
 lib/spack/spack/config.py  | 28 +++++++++++++++++++++++++---
 lib/spack/spack/modules.py | 12 ++++++++++--
 2 files changed, 35 insertions(+), 5 deletions(-)

diff --git a/lib/spack/spack/config.py b/lib/spack/spack/config.py
index 6afd69b3ac7..6ef79c70b15 100644
--- a/lib/spack/spack/config.py
+++ b/lib/spack/spack/config.py
@@ -237,7 +237,29 @@
                                 'type' : 'object',
                                 'default' : {},
                             }
-                        },},},},},}
+                        },},},},},},
+    'modules': {
+        '$schema': 'http://json-schema.org/schema#',
+        'title': 'Spack module file configuration file schema',
+        'type': 'object',
+        'additionalProperties': False,
+        'patternProperties': {
+            r'modules:?': {
+                'type': 'object',
+                'default': {},
+                'additionalProperties': False,
+                'properties': {
+                    'disable': {
+                        'type': 'array',
+                        'default': [],
+                        'items': {
+                            'type': 'string'
+                        }
+                    }
+                }
+            },
+        },
+    },
 }
 
 """OrderedDict of config scopes keyed by name.
@@ -405,11 +427,11 @@ def _read_config_file(filename, schema):
             validate_section(data, schema)
         return data
 
-    except MarkedYAMLError, e:
+    except MarkedYAMLError as e:
         raise ConfigFileError(
             "Error parsing yaml%s: %s" % (str(e.context_mark), e.problem))
 
-    except IOError, e:
+    except IOError as e:
         raise ConfigFileError(
             "Error reading configuration file %s: %s" % (filename, str(e)))
 
diff --git a/lib/spack/spack/modules.py b/lib/spack/spack/modules.py
index 8ed98e5d38f..639f1101b82 100644
--- a/lib/spack/spack/modules.py
+++ b/lib/spack/spack/modules.py
@@ -48,6 +48,7 @@
 
 import llnl.util.tty as tty
 import spack
+import spack.config
 from llnl.util.filesystem import join_path, mkdirp
 from spack.environment import *
 
@@ -57,6 +58,13 @@
 module_types = {}
 
 
+def read_configuration_file():
+    f = spack.config.get_config('modules')
+    f.setdefault('disable', [])  # Default : disable nothing
+    return f
+
+CONFIGURATION = read_configuration_file()
+
 def print_help():
     """For use by commands to tell user how to activate shell support."""
 
@@ -115,8 +123,8 @@ class EnvModule(object):
     class __metaclass__(type):
         def __init__(cls, name, bases, dict):
             type.__init__(cls, name, bases, dict)
-            if cls.name != 'env_module':
-                module_types[cls.name] = cls
+            if cls.name != 'env_module' and cls.name not in CONFIGURATION['disable']:
+                    module_types[cls.name] = cls
 
     def __init__(self, spec=None):
         self.spec = spec

From d93f2b335d5a5198b943cc6293a1d24d614c979b Mon Sep 17 00:00:00 2001
From: alalazo <massimiliano.culpo@googlemail.com>
Date: Wed, 23 Mar 2016 16:04:36 +0100
Subject: [PATCH 094/230] modules : fixed annoying indent

---
 lib/spack/spack/modules.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/spack/spack/modules.py b/lib/spack/spack/modules.py
index 639f1101b82..d354c8bb715 100644
--- a/lib/spack/spack/modules.py
+++ b/lib/spack/spack/modules.py
@@ -124,7 +124,7 @@ class __metaclass__(type):
         def __init__(cls, name, bases, dict):
             type.__init__(cls, name, bases, dict)
             if cls.name != 'env_module' and cls.name not in CONFIGURATION['disable']:
-                    module_types[cls.name] = cls
+                module_types[cls.name] = cls
 
     def __init__(self, spec=None):
         self.spec = spec

From 34a8f0c96bc50870f20f094d95b403b2bb19487d Mon Sep 17 00:00:00 2001
From: alalazo <massimiliano.culpo@googlemail.com>
Date: Wed, 23 Mar 2016 17:01:52 +0100
Subject: [PATCH 095/230] espresso : fixes #454

---
 var/spack/repos/builtin/packages/espresso/package.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/var/spack/repos/builtin/packages/espresso/package.py b/var/spack/repos/builtin/packages/espresso/package.py
index a2bf58f585b..59f362ab46c 100644
--- a/var/spack/repos/builtin/packages/espresso/package.py
+++ b/var/spack/repos/builtin/packages/espresso/package.py
@@ -32,6 +32,10 @@ def check_variants(self, spec):
         if '+elpa' in spec and ('~mpi' in spec or '~scalapack' in spec):
             raise RuntimeError(error.format(variant='elpa'))
 
+    def setup_environment(self, spack_env, run_env):
+        # Espresso copies every executable in prefix without creating sub-folders
+        run_env.prepend_path('PATH', self.prefix)
+
     def install(self, spec, prefix):
         self.check_variants(spec)
 

From 4e5dfc8b18ed30e261fe6b6dd014c8991937934d Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Wed, 23 Mar 2016 19:40:16 +0100
Subject: [PATCH 096/230] fix missing (depricated) _dggsvd_ and _sggsvd_ in
 Openblas 0.2.16

---
 var/spack/repos/builtin/packages/openblas/package.py | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/openblas/package.py b/var/spack/repos/builtin/packages/openblas/package.py
index 781a1e2ec8f..1d10f217c45 100644
--- a/var/spack/repos/builtin/packages/openblas/package.py
+++ b/var/spack/repos/builtin/packages/openblas/package.py
@@ -6,6 +6,7 @@ class Openblas(Package):
     homepage = "http://www.openblas.net"
     url      = "http://github.com/xianyi/OpenBLAS/archive/v0.2.15.tar.gz"
 
+    version('0.2.17', '664a12807f2a2a7cda4781e3ab2ae0e1')
     version('0.2.16', 'fef46ab92463bdbb1479dcec594ef6dc')
     version('0.2.15', 'b1190f3d3471685f17cfd1ec1d252ac9')
 
@@ -14,7 +15,14 @@ class Openblas(Package):
     provides('lapack')
 
     def install(self, spec, prefix):
-        make('libs', 'netlib', 'shared', 'CC=cc', 'FC=f77')
+        extra=[]
+        if spec.satisfies('@0.2.16'):
+            extra.extend([
+                'BUILD_LAPACK_DEPRECATED=1' # fix missing _dggsvd_ and _sggsvd_
+            ])
+
+        make('libs', 'netlib', 'shared', 'CC=cc', 'FC=f77',*extra)
+        make("tests")
         make('install', "PREFIX='%s'" % prefix)
 
         lib_dsuffix = 'dylib' if sys.platform == 'darwin' else 'so'

From f095e619b985a9271ff96cd469086d4654edf489 Mon Sep 17 00:00:00 2001
From: alalazo <massimiliano.culpo@googlemail.com>
Date: Thu, 24 Mar 2016 09:31:28 +0100
Subject: [PATCH 097/230] module files configuration : enable/disable logic is
 now positive

---
 lib/spack/spack/config.py  | 2 +-
 lib/spack/spack/modules.py | 9 ++-------
 2 files changed, 3 insertions(+), 8 deletions(-)

diff --git a/lib/spack/spack/config.py b/lib/spack/spack/config.py
index 6ef79c70b15..14e5aaf4fb6 100644
--- a/lib/spack/spack/config.py
+++ b/lib/spack/spack/config.py
@@ -249,7 +249,7 @@
                 'default': {},
                 'additionalProperties': False,
                 'properties': {
-                    'disable': {
+                    'enable': {
                         'type': 'array',
                         'default': [],
                         'items': {
diff --git a/lib/spack/spack/modules.py b/lib/spack/spack/modules.py
index d354c8bb715..6c32937c3cc 100644
--- a/lib/spack/spack/modules.py
+++ b/lib/spack/spack/modules.py
@@ -57,13 +57,8 @@
 # Registry of all types of modules.  Entries created by EnvModule's metaclass
 module_types = {}
 
+CONFIGURATION = spack.config.get_config('modules')
 
-def read_configuration_file():
-    f = spack.config.get_config('modules')
-    f.setdefault('disable', [])  # Default : disable nothing
-    return f
-
-CONFIGURATION = read_configuration_file()
 
 def print_help():
     """For use by commands to tell user how to activate shell support."""
@@ -123,7 +118,7 @@ class EnvModule(object):
     class __metaclass__(type):
         def __init__(cls, name, bases, dict):
             type.__init__(cls, name, bases, dict)
-            if cls.name != 'env_module' and cls.name not in CONFIGURATION['disable']:
+            if cls.name != 'env_module' and cls.name in CONFIGURATION['enable']:
                 module_types[cls.name] = cls
 
     def __init__(self, spec=None):

From e4adc675e58222f3082f167e709e3819beafd474 Mon Sep 17 00:00:00 2001
From: alalazo <massimiliano.culpo@googlemail.com>
Date: Thu, 24 Mar 2016 10:04:02 +0100
Subject: [PATCH 098/230] module files configuration : added default
 configuration

---
 etc/spack/modules.yaml | 8 ++++++++
 1 file changed, 8 insertions(+)
 create mode 100644 etc/spack/modules.yaml

diff --git a/etc/spack/modules.yaml b/etc/spack/modules.yaml
new file mode 100644
index 00000000000..aa2a2c3fe29
--- /dev/null
+++ b/etc/spack/modules.yaml
@@ -0,0 +1,8 @@
+# -------------------------------------------------------------------------
+# This is the default spack module files generation configuration.
+#
+# Changes to this file will affect all users of this spack install,
+# although users can override these settings in their ~/.spack/modules.yaml.
+# -------------------------------------------------------------------------
+modules:
+  enable: ['tcl', 'dotkit']

From 9b8b17b6f1ec22ce4ac2115e5f7687beba21dd19 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Thu, 24 Mar 2016 10:36:02 +0100
Subject: [PATCH 099/230] fix parmetis on Ubuntu with GNU compilers by linking
 to lm

---
 .../builtin/packages/parmetis/link-to-lm.patch     | 14 ++++++++++++++
 .../repos/builtin/packages/parmetis/package.py     |  2 ++
 2 files changed, 16 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/parmetis/link-to-lm.patch

diff --git a/var/spack/repos/builtin/packages/parmetis/link-to-lm.patch b/var/spack/repos/builtin/packages/parmetis/link-to-lm.patch
new file mode 100644
index 00000000000..faa809231e1
--- /dev/null
+++ b/var/spack/repos/builtin/packages/parmetis/link-to-lm.patch
@@ -0,0 +1,14 @@
+diff --git a/libparmetis/CMakeLists.txt b/libparmetis/CMakeLists.txt
+index 9cfc8a7..dfc0125 100644
+--- a/libparmetis/CMakeLists.txt
++++ b/libparmetis/CMakeLists.txt
+@@ -5,7 +5,7 @@ file(GLOB parmetis_sources *.c)
+ # Create libparmetis
+ add_library(parmetis ${ParMETIS_LIBRARY_TYPE} ${parmetis_sources})
+ # Link with metis and MPI libraries.
+-target_link_libraries(parmetis metis ${MPI_LIBRARIES})
++target_link_libraries(parmetis metis ${MPI_LIBRARIES} "-lm")
+ set_target_properties(parmetis PROPERTIES LINK_FLAGS "${MPI_LINK_FLAGS}")
+
+ install(TARGETS parmetis
+
diff --git a/var/spack/repos/builtin/packages/parmetis/package.py b/var/spack/repos/builtin/packages/parmetis/package.py
index c691cf4191d..bc71fb72991 100644
--- a/var/spack/repos/builtin/packages/parmetis/package.py
+++ b/var/spack/repos/builtin/packages/parmetis/package.py
@@ -52,6 +52,8 @@ class Parmetis(Package):
     # https://bitbucket.org/petsc/pkg-parmetis/commits/82409d68aa1d6cbc70740d0f35024aae17f7d5cb/raw/
     patch('pkg-parmetis-82409d68aa1d6cbc70740d0f35024aae17f7d5cb.patch')
 
+    patch('link-to-lm.patch')
+
     depends_on('gdb', when='+gdb')
 
     def install(self, spec, prefix):

From 758a9c9096bd6c306f2dba0e40b46544dcec1992 Mon Sep 17 00:00:00 2001
From: alalazo <massimiliano.culpo@googlemail.com>
Date: Wed, 23 Mar 2016 11:18:11 +0100
Subject: [PATCH 100/230] python extensions : create PYTHONPATH in module files

---
 lib/spack/spack/modules.py                         | 10 +++++-----
 var/spack/repos/builtin/packages/python/package.py |  5 ++++-
 2 files changed, 9 insertions(+), 6 deletions(-)

diff --git a/lib/spack/spack/modules.py b/lib/spack/spack/modules.py
index 6c32937c3cc..d45fdde7035 100644
--- a/lib/spack/spack/modules.py
+++ b/lib/spack/spack/modules.py
@@ -161,13 +161,13 @@ def write(self):
 
         # Let the extendee modify their extensions before asking for
         # package-specific modifications
-        for extendee in self.pkg.extendees:
-            extendee_spec = self.spec[extendee]
-            extendee_spec.package.setup_dependent_package(
-                self.pkg.module, self.spec)
+        spack_env = EnvironmentModifications()
+        for item in self.pkg.extendees:
+            package = self.spec[item].package
+            package.setup_dependent_package(self.pkg.module, self.spec)
+            package.setup_dependent_environment(spack_env, env, self.spec)
 
         # Package-specific environment modifications
-        spack_env = EnvironmentModifications()
         self.spec.package.setup_environment(spack_env, env)
 
         # TODO : implement site-specific modifications and filters
diff --git a/var/spack/repos/builtin/packages/python/package.py b/var/spack/repos/builtin/packages/python/package.py
index 6d9030805b1..f5237c3b578 100644
--- a/var/spack/repos/builtin/packages/python/package.py
+++ b/var/spack/repos/builtin/packages/python/package.py
@@ -105,7 +105,10 @@ def setup_dependent_environment(self, spack_env, run_env, extension_spec):
 
         pythonpath = ':'.join(python_paths)
         spack_env.set('PYTHONPATH', pythonpath)
-        run_env.set('PYTHONPATH', pythonpath)
+
+        # For run time environment set only the path for extension_spec and prepend it to PYTHONPATH
+        if extension_spec.package.extends(self.spec):
+            run_env.prepend_path('PYTHONPATH', os.path.join(extension_spec.prefix, self.site_packages_dir))
 
 
     def setup_dependent_package(self, module, ext_spec):

From 8643e2191357dd6f53bfafdfd51f43b770e2137c Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Thu, 24 Mar 2016 12:34:58 -0500
Subject: [PATCH 101/230] Simplified NumPy dependencies

---
 .../builtin/packages/py-numpy/package.py      | 37 ++++++++++++++-----
 .../builtin/packages/py-scipy/package.py      |  5 ++-
 2 files changed, 31 insertions(+), 11 deletions(-)

diff --git a/var/spack/repos/builtin/packages/py-numpy/package.py b/var/spack/repos/builtin/packages/py-numpy/package.py
index 03548111863..a08e612df6c 100644
--- a/var/spack/repos/builtin/packages/py-numpy/package.py
+++ b/var/spack/repos/builtin/packages/py-numpy/package.py
@@ -1,24 +1,43 @@
 from spack import *
 
 class PyNumpy(Package):
-    """array processing for numbers, strings, records, and objects."""
-    homepage = "https://pypi.python.org/pypi/numpy"
+    """NumPy is the fundamental package for scientific computing with Python.
+    It contains among other things: a powerful N-dimensional array object,
+    sophisticated (broadcasting) functions, tools for integrating C/C++ and
+    Fortran code, and useful linear algebra, Fourier transform, and random
+    number capabilities"""
+    homepage = "http://www.numpy.org/"
     url      = "https://pypi.python.org/packages/source/n/numpy/numpy-1.9.1.tar.gz"
 
-    version('1.9.1', '78842b73560ec378142665e712ae4ad9')
-    version('1.9.2', 'a1ed53432dbcd256398898d35bc8e645')
+    version('1.10.4', 'aed294de0aa1ac7bd3f9745f4f1968ad')
+    version('1.9.2',  'a1ed53432dbcd256398898d35bc8e645')
+    version('1.9.1',  '78842b73560ec378142665e712ae4ad9')
 
-    variant('blas', default=True)
+
+    variant('blas',   default=True)
+    variant('lapack', default=True)
 
     extends('python')
     depends_on('py-nose')
-    depends_on('netlib-blas+fpic', when='+blas')
-    depends_on('netlib-lapack+shared', when='+blas')
+    depends_on('blas',   when='+blas')
+    depends_on('lapack', when='+lapack')
 
     def install(self, spec, prefix):
+        libraries    = []
+        library_dirs = []
+
         if '+blas' in spec:
+            libraries.append('blas')
+            library_dirs.append(spec['blas'].prefix.lib)
+        if '+lapack' in spec:
+            libraries.append('lapack')
+            library_dirs.append(spec['lapack'].prefix.lib)
+
+        if '+blas' in spec or '+lapack' in spec:
             with open('site.cfg', 'w') as f:
                 f.write('[DEFAULT]\n')
-                f.write('libraries=lapack,blas\n')
-                f.write('library_dirs=%s/lib:%s/lib\n' % (spec['blas'].prefix, spec['lapack'].prefix))
+                f.write('libraries=%s\n'    % ','.join(libraries))
+                f.write('library_dirs=%s\n' % ':'.join(library_dirs))
+
         python('setup.py', 'install', '--prefix=%s' % prefix)
+
diff --git a/var/spack/repos/builtin/packages/py-scipy/package.py b/var/spack/repos/builtin/packages/py-scipy/package.py
index 3a1124cc15a..c2161c90c43 100644
--- a/var/spack/repos/builtin/packages/py-scipy/package.py
+++ b/var/spack/repos/builtin/packages/py-scipy/package.py
@@ -2,11 +2,12 @@
 
 class PyScipy(Package):
     """Scientific Library for Python."""
-    homepage = "https://pypi.python.org/pypi/scipy"
+    homepage = "http://www.scipy.org/"
     url      = "https://pypi.python.org/packages/source/s/scipy/scipy-0.15.0.tar.gz"
 
-    version('0.15.0', '639112f077f0aeb6d80718dc5019dc7a')
+    version('0.17.0', '5ff2971e1ce90e762c59d2cd84837224')
     version('0.15.1', 'be56cd8e60591d6332aac792a5880110')
+    version('0.15.0', '639112f077f0aeb6d80718dc5019dc7a')
 
     extends('python')
     depends_on('py-nose')

From 254f65f2994de32da8681c24838beb32bbbc5fe1 Mon Sep 17 00:00:00 2001
From: Alfredo Gimenez <gimenez1@llnl.gov>
Date: Thu, 24 Mar 2016 10:48:38 -0700
Subject: [PATCH 102/230] Remove incorrect sanity check for libelf

---
 var/spack/repos/builtin/packages/libelf/package.py | 2 --
 1 file changed, 2 deletions(-)

diff --git a/var/spack/repos/builtin/packages/libelf/package.py b/var/spack/repos/builtin/packages/libelf/package.py
index 9f16708af5b..29bc21b65c4 100644
--- a/var/spack/repos/builtin/packages/libelf/package.py
+++ b/var/spack/repos/builtin/packages/libelf/package.py
@@ -38,8 +38,6 @@ class Libelf(Package):
 
     provides('elf')
 
-    sanity_check_is_file = 'include/libelf.h'
-
     def install(self, spec, prefix):
         configure("--prefix=" + prefix,
                   "--enable-shared",

From 9985816642bad10008f45583a7d715761a6ae03d Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Thu, 24 Mar 2016 14:49:41 -0500
Subject: [PATCH 103/230] Fix spack info indentation

---
 lib/spack/spack/cmd/info.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/lib/spack/spack/cmd/info.py b/lib/spack/spack/cmd/info.py
index e7abe7f4a59..c93db55c63c 100644
--- a/lib/spack/spack/cmd/info.py
+++ b/lib/spack/spack/cmd/info.py
@@ -52,7 +52,7 @@ def print_text_info(pkg):
     print "Safe versions:  "
 
     if not pkg.versions:
-        print("None")
+        print("    None")
     else:
         pad = padder(pkg.versions, 4)
         for v in reversed(sorted(pkg.versions)):
@@ -62,7 +62,7 @@ def print_text_info(pkg):
     print
     print "Variants:"
     if not pkg.variants:
-        print "None"
+        print "    None"
     else:
         pad = padder(pkg.variants, 4)
 

From 7fb463abb9b912f9a5bcb6e810b733f0b8bc1672 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Thu, 24 Mar 2016 20:23:13 +0100
Subject: [PATCH 104/230] install GKlib headers along with METIS

---
 .../metis/install_gklib_defs_rename.patch     | 22 +++++++++++++++++++
 .../repos/builtin/packages/metis/package.py   | 13 +++++++++--
 2 files changed, 33 insertions(+), 2 deletions(-)
 create mode 100644 var/spack/repos/builtin/packages/metis/install_gklib_defs_rename.patch

diff --git a/var/spack/repos/builtin/packages/metis/install_gklib_defs_rename.patch b/var/spack/repos/builtin/packages/metis/install_gklib_defs_rename.patch
new file mode 100644
index 00000000000..b182b167b90
--- /dev/null
+++ b/var/spack/repos/builtin/packages/metis/install_gklib_defs_rename.patch
@@ -0,0 +1,22 @@
+# HG changeset patch
+# User Sean Farley <sean@mcs.anl.gov>
+# Date 1332269671 18000
+#      Tue Mar 20 13:54:31 2012 -0500
+# Node ID b95c0c2e1d8bf8e3273f7d45e856f0c0127d998e
+# Parent  88049269953c67c3fdcc4309bf901508a875f0dc
+cmake: add gklib headers to install into include
+
+diff -r 88049269953c -r b95c0c2e1d8b libmetis/CMakeLists.txt
+Index: libmetis/CMakeLists.txt
+===================================================================
+--- a/libmetis/CMakeLists.txt Tue Mar 20 13:54:29 2012 -0500
++++ b/libmetis/CMakeLists.txt Tue Mar 20 13:54:31 2012 -0500
+@@ -12,6 +12,8 @@ endif()
+ if(METIS_INSTALL)
+   install(TARGETS metis
+     LIBRARY DESTINATION lib
+     RUNTIME DESTINATION lib
+     ARCHIVE DESTINATION lib)
++  install(FILES gklib_defs.h DESTINATION include)
++  install(FILES gklib_rename.h DESTINATION include)
+ endif()
diff --git a/var/spack/repos/builtin/packages/metis/package.py b/var/spack/repos/builtin/packages/metis/package.py
index bbfc4de7d1d..68b9f6fd306 100644
--- a/var/spack/repos/builtin/packages/metis/package.py
+++ b/var/spack/repos/builtin/packages/metis/package.py
@@ -24,7 +24,7 @@
 ##############################################################################
 
 from spack import *
-
+import glob
 
 class Metis(Package):
     """
@@ -49,6 +49,8 @@ class Metis(Package):
 
     depends_on('gdb', when='+gdb')
 
+    patch('install_gklib_defs_rename.patch')
+
     def install(self, spec, prefix):
 
         options = []
@@ -80,4 +82,11 @@ def install(self, spec, prefix):
         with working_dir(build_directory, create=True):
             cmake(source_directory, *options)
             make()
-            make("install")
\ No newline at end of file
+            make("install")
+
+            # install GKlib headers, which will be needed for ParMETIS
+            GKlib_dist = join_path(prefix.include,'GKlib')
+            mkdirp(GKlib_dist)
+            fs = glob.glob(join_path(source_directory,'GKlib',"*.h"))
+            for f in fs:
+                install(f, GKlib_dist)

From 0d4d201b70c57359f041807df0a2f58b47be78d6 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Thu, 24 Mar 2016 21:22:58 +0100
Subject: [PATCH 105/230] patch parmetis to use external GKlib

---
 .../parmetis/enable_external_metis.patch      | 48 +++++++++++++++++--
 .../builtin/packages/parmetis/package.py      |  2 +-
 2 files changed, 46 insertions(+), 4 deletions(-)

diff --git a/var/spack/repos/builtin/packages/parmetis/enable_external_metis.patch b/var/spack/repos/builtin/packages/parmetis/enable_external_metis.patch
index 514781b8b88..8b05ecc872f 100644
--- a/var/spack/repos/builtin/packages/parmetis/enable_external_metis.patch
+++ b/var/spack/repos/builtin/packages/parmetis/enable_external_metis.patch
@@ -1,13 +1,55 @@
 diff --git a/CMakeLists.txt b/CMakeLists.txt
-index ca945dd..1bf94e9 100644
+index ca945dd..5995e42 100644
 --- a/CMakeLists.txt
 +++ b/CMakeLists.txt
+@@ -23,7 +23,7 @@ else()
+   set(ParMETIS_LIBRARY_TYPE STATIC)
+ endif()
+ 
+-include(${GKLIB_PATH}/GKlibSystem.cmake)
++include_directories(${GKLIB_PATH})
+ 
+ # List of paths that the compiler will search for header files.
+ # i.e., the -I equivalent
 @@ -33,7 +33,7 @@ include_directories(${GKLIB_PATH})
  include_directories(${METIS_PATH}/include)
-
+ 
  # List of directories that cmake will look for CMakeLists.txt
 -add_subdirectory(${METIS_PATH}/libmetis ${CMAKE_BINARY_DIR}/libmetis)
-+#add_subdirectory(${METIS_PATH}/libmetis ${CMAKE_BINARY_DIR}/libmetis)
++# add_subdirectory(${METIS_PATH}/libmetis ${CMAKE_BINARY_DIR}/libmetis)
  add_subdirectory(include)
  add_subdirectory(libparmetis)
  add_subdirectory(programs)
+diff --git a/libparmetis/parmetislib.h b/libparmetis/parmetislib.h
+index c1daeeb..07511f6 100644
+--- a/libparmetis/parmetislib.h
++++ b/libparmetis/parmetislib.h
+@@ -20,13 +20,12 @@
+ 
+ #include <parmetis.h>
+ 
+-#include "../metis/libmetis/gklib_defs.h"
++#include <gklib_defs.h>
+ 
+-#include <mpi.h> 
++#include <mpi.h>
+ 
+ #include <rename.h>
+ #include <defs.h>
+ #include <struct.h>
+ #include <macros.h>
+ #include <proto.h>
+-
+diff --git a/programs/parmetisbin.h b/programs/parmetisbin.h
+index e26cd2d..d156480 100644
+--- a/programs/parmetisbin.h
++++ b/programs/parmetisbin.h
+@@ -19,7 +19,7 @@
+ #include <GKlib.h>
+ #include <parmetis.h>
+ 
+-#include "../metis/libmetis/gklib_defs.h"
++#include <gklib_defs.h>
+ #include "../libparmetis/rename.h"
+ #include "../libparmetis/defs.h"
+ #include "../libparmetis/struct.h"
diff --git a/var/spack/repos/builtin/packages/parmetis/package.py b/var/spack/repos/builtin/packages/parmetis/package.py
index bc71fb72991..5c97a836f9b 100644
--- a/var/spack/repos/builtin/packages/parmetis/package.py
+++ b/var/spack/repos/builtin/packages/parmetis/package.py
@@ -66,7 +66,7 @@ def install(self, spec, prefix):
 
         # FIXME : Once a contract is defined, MPI compilers should be retrieved indirectly via spec['mpi'] in case
         # FIXME : they use a non-standard name
-        options.extend(['-DGKLIB_PATH:PATH={metis_source}/GKlib'.format(metis_source=metis_source), # still need headers from METIS source, and they are not installed with METIS. shame...
+        options.extend(['-DGKLIB_PATH:PATH={metis_source}/GKlib'.format(metis_source=spec['metis'].prefix.include),
                         '-DMETIS_PATH:PATH={metis_source}'.format(metis_source=spec['metis'].prefix),
                         '-DCMAKE_C_COMPILER:STRING=mpicc',
                         '-DCMAKE_CXX_COMPILER:STRING=mpicxx'])

From 03c8a91f6a647849f0251496f361da9574a98c22 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Thu, 24 Mar 2016 22:33:10 +0100
Subject: [PATCH 106/230] parmetis: avoid hardcoding -lm; use same approach as
 in METIS

---
 .../parmetis/enable_external_metis.patch      | 20 +++++++++++++++++--
 .../packages/parmetis/link-to-lm.patch        | 14 -------------
 .../builtin/packages/parmetis/package.py      |  2 --
 3 files changed, 18 insertions(+), 18 deletions(-)
 delete mode 100644 var/spack/repos/builtin/packages/parmetis/link-to-lm.patch

diff --git a/var/spack/repos/builtin/packages/parmetis/enable_external_metis.patch b/var/spack/repos/builtin/packages/parmetis/enable_external_metis.patch
index 8b05ecc872f..e4f27294836 100644
--- a/var/spack/repos/builtin/packages/parmetis/enable_external_metis.patch
+++ b/var/spack/repos/builtin/packages/parmetis/enable_external_metis.patch
@@ -1,5 +1,5 @@
 diff --git a/CMakeLists.txt b/CMakeLists.txt
-index ca945dd..5995e42 100644
+index ca945dd..aff8b5f 100644
 --- a/CMakeLists.txt
 +++ b/CMakeLists.txt
 @@ -23,7 +23,7 @@ else()
@@ -16,10 +16,26 @@ index ca945dd..5995e42 100644
  
  # List of directories that cmake will look for CMakeLists.txt
 -add_subdirectory(${METIS_PATH}/libmetis ${CMAKE_BINARY_DIR}/libmetis)
-+# add_subdirectory(${METIS_PATH}/libmetis ${CMAKE_BINARY_DIR}/libmetis)
++find_library(METIS_LIBRARY metis PATHS ${METIS_PATH}/lib)
  add_subdirectory(include)
  add_subdirectory(libparmetis)
  add_subdirectory(programs)
+diff --git a/libparmetis/CMakeLists.txt b/libparmetis/CMakeLists.txt
+index 9cfc8a7..e0c4de7 100644
+--- a/libparmetis/CMakeLists.txt
++++ b/libparmetis/CMakeLists.txt
+@@ -5,7 +5,10 @@ file(GLOB parmetis_sources *.c)
+ # Create libparmetis
+ add_library(parmetis ${ParMETIS_LIBRARY_TYPE} ${parmetis_sources})
+ # Link with metis and MPI libraries.
+-target_link_libraries(parmetis metis ${MPI_LIBRARIES})
++target_link_libraries(parmetis ${METIS_LIBRARY} ${MPI_LIBRARIES})
++if(UNIX)
++  target_link_libraries(parmetis m)
++endif()
+ set_target_properties(parmetis PROPERTIES LINK_FLAGS "${MPI_LINK_FLAGS}")
+ 
+ install(TARGETS parmetis
 diff --git a/libparmetis/parmetislib.h b/libparmetis/parmetislib.h
 index c1daeeb..07511f6 100644
 --- a/libparmetis/parmetislib.h
diff --git a/var/spack/repos/builtin/packages/parmetis/link-to-lm.patch b/var/spack/repos/builtin/packages/parmetis/link-to-lm.patch
deleted file mode 100644
index faa809231e1..00000000000
--- a/var/spack/repos/builtin/packages/parmetis/link-to-lm.patch
+++ /dev/null
@@ -1,14 +0,0 @@
-diff --git a/libparmetis/CMakeLists.txt b/libparmetis/CMakeLists.txt
-index 9cfc8a7..dfc0125 100644
---- a/libparmetis/CMakeLists.txt
-+++ b/libparmetis/CMakeLists.txt
-@@ -5,7 +5,7 @@ file(GLOB parmetis_sources *.c)
- # Create libparmetis
- add_library(parmetis ${ParMETIS_LIBRARY_TYPE} ${parmetis_sources})
- # Link with metis and MPI libraries.
--target_link_libraries(parmetis metis ${MPI_LIBRARIES})
-+target_link_libraries(parmetis metis ${MPI_LIBRARIES} "-lm")
- set_target_properties(parmetis PROPERTIES LINK_FLAGS "${MPI_LINK_FLAGS}")
-
- install(TARGETS parmetis
-
diff --git a/var/spack/repos/builtin/packages/parmetis/package.py b/var/spack/repos/builtin/packages/parmetis/package.py
index 5c97a836f9b..f5b8b6de919 100644
--- a/var/spack/repos/builtin/packages/parmetis/package.py
+++ b/var/spack/repos/builtin/packages/parmetis/package.py
@@ -52,8 +52,6 @@ class Parmetis(Package):
     # https://bitbucket.org/petsc/pkg-parmetis/commits/82409d68aa1d6cbc70740d0f35024aae17f7d5cb/raw/
     patch('pkg-parmetis-82409d68aa1d6cbc70740d0f35024aae17f7d5cb.patch')
 
-    patch('link-to-lm.patch')
-
     depends_on('gdb', when='+gdb')
 
     def install(self, spec, prefix):

From fdd7e91ba078bea4f0fec1859124baaa8261fa2c Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Thu, 24 Mar 2016 12:49:56 +0100
Subject: [PATCH 107/230] add shared variant to mumps (needed for Trilinos)
 plus tests

---
 .../repos/builtin/packages/mumps/Makefile.inc |  5 +--
 .../repos/builtin/packages/mumps/package.py   | 45 ++++++++++++++++---
 2 files changed, 41 insertions(+), 9 deletions(-)

diff --git a/var/spack/repos/builtin/packages/mumps/Makefile.inc b/var/spack/repos/builtin/packages/mumps/Makefile.inc
index 2e6a041878c..22d8f5518a5 100644
--- a/var/spack/repos/builtin/packages/mumps/Makefile.inc
+++ b/var/spack/repos/builtin/packages/mumps/Makefile.inc
@@ -8,12 +8,9 @@ IORDERINGSF = $(ISCOTCH)
 IORDERINGSC = $(IMETIS) $(IPORD) $(ISCOTCH)
 
 PLAT    =
-LIBEXT  = .a
-OUTC    = -o 
+OUTC    = -o
 OUTF    = -o
 RM = /bin/rm -f
-AR = ar vr 
-RANLIB = ranlib
 
 INCSEQ  = -I$(topdir)/libseq
 LIBSEQ  = -L$(topdir)/libseq -lmpiseq
diff --git a/var/spack/repos/builtin/packages/mumps/package.py b/var/spack/repos/builtin/packages/mumps/package.py
index 5a254dfd00e..2801d4194dc 100644
--- a/var/spack/repos/builtin/packages/mumps/package.py
+++ b/var/spack/repos/builtin/packages/mumps/package.py
@@ -1,6 +1,5 @@
 from spack import *
-import os
-
+import os, sys
 
 class Mumps(Package):
     """MUMPS: a MUltifrontal Massively Parallel sparse direct Solver"""
@@ -19,6 +18,7 @@ class Mumps(Package):
     variant('float', default=True, description='Activate the compilation of smumps')
     variant('complex', default=True, description='Activate the compilation of cmumps and/or zmumps')
     variant('idx64', default=False, description='Use int64_t/integer*8 as default index type')
+    variant('shared', default=True, description='Build shared libraries')
 
 
     depends_on('scotch + esmumps', when='~ptscotch+scotch')
@@ -105,6 +105,27 @@ def write_makefile_inc(self):
         # compiler possible values are -DAdd_, -DAdd__ and/or -DUPPER
         makefile_conf.append("CDEFS   = -DAdd_")
 
+        if '+shared' in self.spec:
+            if sys.platform == 'darwin':
+                # Building dylibs with mpif90 causes segfaults on 10.8 and 10.10. Use gfortran. (Homebrew)
+                makefile_conf.extend([
+                    'LIBEXT=.dylib',
+                    'AR=%s -dynamiclib -undefined dynamic_lookup -o ' % os.environ['FC'],
+                    'RANLIB=echo'
+                ])
+            else:
+                makefile_conf.extend([
+                    'LIBEXT=.so',
+                    'AR=$(FL) -shared -o',
+                    'RANLIB=echo'
+                ])
+        else:
+            makefile_conf.extend([
+                'LIBEXT  = .a',
+                'AR = ar vr',
+                'RANLIB = ranlib'
+            ])
+
 
         makefile_inc_template = join_path(os.path.dirname(self.module.__file__),
                                           'Makefile.inc')
@@ -121,7 +142,7 @@ def write_makefile_inc(self):
     def install(self, spec, prefix):
         make_libs = []
 
-        # the coice to compile ?examples is to have kind of a sanity
+        # the choice to compile ?examples is to have kind of a sanity
         # check on the libraries generated.
         if '+float' in spec:
             make_libs.append('sexamples')
@@ -135,10 +156,24 @@ def install(self, spec, prefix):
 
         self.write_makefile_inc()
 
-        # Build fails in parallel, at least on OS-X
+        # Build fails in parallel
         make(*make_libs, parallel=False)
 
         install_tree('lib', prefix.lib)
         install_tree('include', prefix.include)
         if '~mpi' in spec:
-            install('libseq/libmpiseq.a', prefix.lib)
+            lib_dsuffix = '.dylib' if sys.platform == 'darwin' else '.so'
+            lib_suffix = lib_dsuffix if '+shared' in spec else '.a'
+            install('libseq/libmpiseq%s' % lib_suffix, prefix.lib)
+
+        # FIXME: extend the tests to mpirun -np 2 (or alike) when build with MPI
+        # FIXME: use something like numdiff to compare blessed output with the current
+        with working_dir('examples'):
+            if '+float' in spec:
+                os.system('./ssimpletest < input_simpletest_real')
+                if '+complex' in spec:
+                    os.system('./csimpletest < input_simpletest_real')
+            if '+double' in spec:
+                os.system('./dsimpletest < input_simpletest_real')
+                if '+complex' in spec:
+                    os.system('./zsimpletest < input_simpletest_cmplx')

From 540e57f02686bad7125a951d14784e8fcc896e26 Mon Sep 17 00:00:00 2001
From: Josh Sixsmith <josh.sixsmith@gmail.com>
Date: Fri, 25 Mar 2016 18:27:02 +1100
Subject: [PATCH 108/230] Upload of GDAL, kealib, openjpeg, py-tuiview package
 builds.

---
 .../repos/builtin/packages/gdal/package.py    | 69 +++++++++++++++++++
 .../repos/builtin/packages/kealib/package.py  | 35 ++++++++++
 .../builtin/packages/openjpeg/package.py      | 26 +++++++
 .../builtin/packages/py-tuiview/package.py    | 19 +++++
 4 files changed, 149 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/gdal/package.py
 create mode 100644 var/spack/repos/builtin/packages/kealib/package.py
 create mode 100644 var/spack/repos/builtin/packages/openjpeg/package.py
 create mode 100644 var/spack/repos/builtin/packages/py-tuiview/package.py

diff --git a/var/spack/repos/builtin/packages/gdal/package.py b/var/spack/repos/builtin/packages/gdal/package.py
new file mode 100644
index 00000000000..4f1f1ec2dd1
--- /dev/null
+++ b/var/spack/repos/builtin/packages/gdal/package.py
@@ -0,0 +1,69 @@
+from spack import *
+
+class Gdal(Package):
+    """
+    GDAL is a translator library for raster and vector geospatial
+    data formats that is released under an X/MIT style Open Source
+    license by the Open Source Geospatial Foundation. As a library,
+    it presents a single raster abstract data model and vector
+    abstract data model to the calling application for all supported
+    formats. It also comes with a variety of useful command line
+    utilities for data translation and processing
+    """
+
+    homepage   = "http://www.gdal.org/"
+    url        = "http://download.osgeo.org/gdal/2.0.2/gdal-2.0.2.tar.gz"
+    list_url   = "http://download.osgeo.org/gdal/"
+    list_depth = 2
+
+    version('2.0.2', '573865f3f59ba7b4f8f4cddf223b52a5')
+
+    extends('python')
+
+    variant('hdf5', default=False, description='Enable HDF5 support')
+    variant('hdf', default=False, description='Enable HDF4 support')
+    variant('openjpeg', default=False, description='Enable JPEG2000 support')
+    variant('geos', default=False, description='Enable GEOS support')
+    variant('kea', default=False, description='Enable KEA support')
+    variant('netcdf', default=False, description='Enable netcdf support')
+
+    depends_on('swig')
+    depends_on("hdf5", when='+hdf5')
+    depends_on("hdf", when='+hdf')
+    depends_on("openjpeg", when='+openjpeg')
+    depends_on("geos", when='+geos')
+    depends_on("kealib", when='+kea')
+    depends_on("netcdf", when='+netcdf')
+    depends_on("libtiff")
+    depends_on("libpng")
+    depends_on("zlib")
+    depends_on("proj")
+    depends_on("py-numpy")
+
+    parallel = False
+
+    def install(self, spec, prefix):
+        args = []
+        args.append("--prefix=%s" % prefix)
+        args.append("--with-liblzma=yes")
+        args.append("--with-zlib=%s" % spec['zlib'].prefix)
+        args.append("--with-python=%s" % spec['python'].prefix.bin + "/python")
+        args.append("--without-libtool")
+
+        if '+geos' in spec:
+            args.append('--with-geos=yes')
+        if '+hdf' in spec:
+            args.append('--with-hdf4=%s' % spec['hdf'].prefix)
+        if '+hdf5' in spec:
+            args.append('--with-hdf5=%s' % spec['hdf5'].prefix)
+        if '+openjpeg' in spec:
+            args.append('--with-openjpeg=%s' % spec['openjpeg'].prefix)
+        if '+kea' in spec:
+            args.append('--with-kea=yes')
+        if '+netcdf' in spec:
+            args.append('--with-netcdf=%s' % spec['netcdf'].prefix)
+
+        configure(*args)
+
+        make()
+        make("install")
diff --git a/var/spack/repos/builtin/packages/kealib/package.py b/var/spack/repos/builtin/packages/kealib/package.py
new file mode 100644
index 00000000000..475d21e1d80
--- /dev/null
+++ b/var/spack/repos/builtin/packages/kealib/package.py
@@ -0,0 +1,35 @@
+from spack import *
+
+class Kealib(Package):
+    """An HDF5 Based Raster File Format
+    
+    KEALib provides an implementation of the GDAL data model.
+    The format supports raster attribute tables, image pyramids,
+    meta-data and in-built statistics while also handling very
+    large files and compression throughout.
+    
+    Based on the HDF5 standard, it also provides a base from which
+    other formats can be derived and is a good choice for long
+    term data archiving. An independent software library (libkea)
+    provides complete access to the KEA image format and a GDAL
+    driver allowing KEA images to be used from any GDAL supported software.
+    
+    Development work on this project has been funded by Landcare Research.
+    """
+    homepage = "http://kealib.org/"
+    url      = "https://bitbucket.org/chchrsc/kealib/get/kealib-1.4.5.tar.gz"
+
+    version('1.4.5', '112e9c42d980b2d2987a3c15d0833a5d')
+
+    depends_on("hdf5")
+
+    def install(self, spec, prefix):
+        with working_dir('trunk', create=False):
+            cmake_args = []
+            cmake_args.append("-DCMAKE_INSTALL_PREFIX=%s" % prefix)
+            cmake_args.append("-DHDF5_INCLUDE_DIR=%s" % spec['hdf5'].prefix.include)
+            cmake_args.append("-DHDF5_LIB_PATH=%s" % spec['hdf5'].prefix.lib)
+            cmake('.', *cmake_args)
+
+            make()
+            make("install")
diff --git a/var/spack/repos/builtin/packages/openjpeg/package.py b/var/spack/repos/builtin/packages/openjpeg/package.py
new file mode 100644
index 00000000000..afec197d112
--- /dev/null
+++ b/var/spack/repos/builtin/packages/openjpeg/package.py
@@ -0,0 +1,26 @@
+from spack import *
+
+class Openjpeg(Package):
+    """
+    OpenJPEG is an open-source JPEG 2000 codec written in C language.
+    It has been developed in order to promote the use of JPEG 2000, a
+    still-image compression standard from the Joint Photographic
+    Experts Group (JPEG).
+    Since April 2015, it is officially recognized by ISO/IEC and
+    ITU-T as a JPEG 2000 Reference Software.
+    """
+    homepage = "https://github.com/uclouvain/openjpeg"
+    url      = "https://github.com/uclouvain/openjpeg/archive/version.2.1.tar.gz"
+
+    version('2.1'  , '3e1c451c087f8462955426da38aa3b3d')
+    version('2.0.1', '105876ed43ff7dbb2f90b41b5a43cfa5')
+    version('2.0'  , 'cdf266530fee8af87454f15feb619609')
+    version('1.5.2', '545f98923430369a6b046ef3632ef95c')
+    version('1.5.1', 'd774e4b5a0db5f0f171c4fc0aabfa14e')
+
+
+    def install(self, spec, prefix):
+        cmake('.', *std_cmake_args)
+
+        make()
+        make("install")
diff --git a/var/spack/repos/builtin/packages/py-tuiview/package.py b/var/spack/repos/builtin/packages/py-tuiview/package.py
new file mode 100644
index 00000000000..984b4196b19
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-tuiview/package.py
@@ -0,0 +1,19 @@
+from spack import *
+
+class PyTuiview(Package):
+    """
+       TuiView is a lightweight raster GIS with powerful raster attribute
+       table manipulation abilities.
+    """
+    homepage = "https://bitbucket.org/chchrsc/tuiview"
+    url      = "https://bitbucket.org/chchrsc/tuiview/get/tuiview-1.1.7.tar.gz"
+
+    version('1.1.7', '4b3b38a820cc239c8ab4a181ac5d4c30')
+
+    extends("python")
+    depends_on("py-pyqt")
+    depends_on("py-numpy")
+    depends_on("gdal")
+
+    def install(self, spec, prefix):
+        python('setup.py', 'install', '--prefix=%s' % prefix)

From fd67da607e5476b767071dc37af66af6fd492452 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Fri, 25 Mar 2016 08:32:14 +0100
Subject: [PATCH 109/230] make netcdf link against Spack's curl

---
 var/spack/repos/builtin/packages/netcdf/package.py | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/var/spack/repos/builtin/packages/netcdf/package.py b/var/spack/repos/builtin/packages/netcdf/package.py
index 227362399a9..b60a2c4e9a3 100644
--- a/var/spack/repos/builtin/packages/netcdf/package.py
+++ b/var/spack/repos/builtin/packages/netcdf/package.py
@@ -43,6 +43,13 @@ def install(self, spec, prefix):
             "--enable-dap"
         ]
 
+        # Make sure Netcdf links against Spack's curl
+        # Otherwise it may pick up system's curl, which could lead to link errors:
+        # /usr/lib/x86_64-linux-gnu/libcurl.so: undefined reference to `SSL_CTX_use_certificate_chain_file@OPENSSL_1.0.0'
+        LIBS.append("-lcurl")
+        CPPFLAGS.append("-I%s" % spec['curl'].prefix.include)
+        LDFLAGS.append ("-L%s" % spec['curl'].prefix.lib)
+
         if '+mpi' in spec:
             config_args.append('--enable-parallel4')
 

From 3e39daeb12aa13a3f3f975ff315143bc3f13a2b4 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Fri, 25 Mar 2016 09:56:24 +0100
Subject: [PATCH 110/230] add fPIC to MUMPS when building shared libs

---
 var/spack/repos/builtin/packages/mumps/package.py | 15 +++++++++------
 1 file changed, 9 insertions(+), 6 deletions(-)

diff --git a/var/spack/repos/builtin/packages/mumps/package.py b/var/spack/repos/builtin/packages/mumps/package.py
index 2801d4194dc..b295857ab59 100644
--- a/var/spack/repos/builtin/packages/mumps/package.py
+++ b/var/spack/repos/builtin/packages/mumps/package.py
@@ -70,6 +70,9 @@ def write_makefile_inc(self):
 
         makefile_conf.append("ORDERINGSF = %s" % (' '.join(orderings)))
 
+        # when building shared libs need -fPIC, otherwise
+        # /usr/bin/ld: graph.o: relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
+        fpic = '-fPIC' if '+shared' in self.spec else ''
         # TODO: test this part, it needs a full blas, scalapack and
         # partitionning environment with 64bit integers
         if '+idx64' in self.spec:
@@ -77,14 +80,14 @@ def write_makefile_inc(self):
                 # the fortran compilation flags most probably are
                 # working only for intel and gnu compilers this is
                 # perhaps something the compiler should provide
-                ['OPTF    = -O  -DALLOW_NON_INIT %s' % '-fdefault-integer-8' if self.compiler.name == "gcc" else '-i8',
-                 'OPTL    = -O ',
-                 'OPTC    = -O -DINTSIZE64'])
+                ['OPTF    = %s -O  -DALLOW_NON_INIT %s' % (fpic,'-fdefault-integer-8' if self.compiler.name == "gcc" else '-i8'),
+                 'OPTL    = %s -O ' % fpic,
+                 'OPTC    = %s -O -DINTSIZE64' % fpic])
         else:
             makefile_conf.extend(
-                ['OPTF    = -O  -DALLOW_NON_INIT',
-                 'OPTL    = -O ',
-                 'OPTC    = -O '])
+                ['OPTF    = %s -O  -DALLOW_NON_INIT' % fpic,
+                 'OPTL    = %s -O ' % fpic,
+                 'OPTC    = %s -O ' % fpic])
 
 
         if '+mpi' in self.spec:

From 83fea631f1765d4641cde8af2c5c931b22e4ee33 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Tue, 22 Mar 2016 23:04:17 +0100
Subject: [PATCH 111/230] extend trilinos

---
 .../builtin/packages/trilinos/package.py      | 32 ++++++++++++++++---
 1 file changed, 28 insertions(+), 4 deletions(-)

diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py
index edc40476e30..22c7ab6d61c 100644
--- a/var/spack/repos/builtin/packages/trilinos/package.py
+++ b/var/spack/repos/builtin/packages/trilinos/package.py
@@ -1,5 +1,5 @@
 from spack import *
-
+import os
 
 class Trilinos(Package):
     """
@@ -10,6 +10,7 @@ class Trilinos(Package):
     homepage = "https://trilinos.org/"
     url = "http://trilinos.csbsju.edu/download/files/trilinos-12.2.1-Source.tar.gz"
 
+    version('12.6.1', 'adcf2d3aab74cdda98f88fee19cd1442604199b0515ee3da4d80cbe8f37d00e4')
     version('12.4.2', '7c830f7f0f68b8ad324690603baf404e')
     version('12.2.1', '6161926ea247863c690e927687f83be9')
     version('12.0.1', 'bd99741d047471e127b8296b2ec08017')
@@ -39,15 +40,38 @@ def install(self, spec, prefix):
         options.extend(std_cmake_args)
 
         options.extend(['-DTrilinos_ENABLE_ALL_PACKAGES:BOOL=ON',
+                        '-DTrilinos_ENABLE_ALL_OPTIONAL_PACKAGES:BOOL=ON',
                         '-DTrilinos_ENABLE_TESTS:BOOL=OFF',
                         '-DTrilinos_ENABLE_EXAMPLES:BOOL=OFF',
                         '-DCMAKE_BUILD_TYPE:STRING=%s' % ('Debug' if '+debug' in spec else 'Release'),
                         '-DBUILD_SHARED_LIBS:BOOL=%s' % ('ON' if '+shared' in spec else 'OFF'),
-                        '-DTPL_ENABLE_MPI:STRING=ON',
-                        '-DBLAS_LIBRARY_DIRS:PATH=%s' % spec['blas'].prefix,
-                        '-DLAPACK_LIBRARY_DIRS:PATH=%s' % spec['lapack'].prefix
+                        '-DTPL_ENABLE_MPI:BOOL=ON',
+                        '-DMPI_BASE_DIR:PATH=%s' % spec['mpi'].prefix,
+                        '-DTPL_ENABLE_BLAS=ON',
+                        '-DBLAS_LIBRARY_NAMES=blas',
+                        '-DBLAS_LIBRARY_DIRS=/usr/lib', # % spec['blas'].prefix,
+                        '-DTPL_ENABLE_LAPACK=ON',
+                        '-DLAPACK_LIBRARY_NAMES=lapack',
+                        '-DLAPACK_LIBRARY_DIRS=/usr/lib', # % spec['lapack'].prefix,
+                        '-DTPL_ENABLE_Boost:BOOL=ON',
+                        '-DBOOST_BASE_DIR:PATH=%s' % spec['boost'].prefix,
+                        '-DTrilinos_ENABLE_Fortran=OFF',
+                        '-DTrilinos_ENABLE_EXPLICIT_INSTANTIATION:BOOL=ON',
+                        '-DTrilinos_ENABLE_CXX11:BOOL=ON',
+                        '-DTrilinos_CXX11_FLAGS=-std=c++11'
                         ])
 
+        # disable due to compiler / config errors:
+        options.extend(['-DTrilinos_ENABLE_SEACAS=OFF',
+                        '-DTrilinos_ENABLE_Pike=OFF',
+                        '-DTrilinos_ENABLE_STK=OFF'
+                        ])
+
+        if self.compiler.name == "clang":
+            os.environ['CPPFLAGS']="-Qunused-arguments"
+
+        #os.environ['LDFLAGS']="lgfortran"
+
         with working_dir('spack-build', create=True):
             cmake('..', *options)
             make()

From 30ba96e58fe699e92902ce53a87b5e1cfb756d6f Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Tue, 22 Mar 2016 23:56:18 +0100
Subject: [PATCH 112/230] same

---
 .../builtin/packages/trilinos/package.py      | 84 ++++++++++++++++---
 1 file changed, 74 insertions(+), 10 deletions(-)

diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py
index 22c7ab6d61c..7b913031e3d 100644
--- a/var/spack/repos/builtin/packages/trilinos/package.py
+++ b/var/spack/repos/builtin/packages/trilinos/package.py
@@ -2,8 +2,7 @@
 import os
 
 class Trilinos(Package):
-    """
-    The Trilinos Project is an effort to develop algorithms and enabling technologies within an object-oriented
+    """The Trilinos Project is an effort to develop algorithms and enabling technologies within an object-oriented
     software framework for the solution of large-scale, complex multi-physics engineering and scientific problems.
     A unique design feature of Trilinos is its focus on packages.
     """
@@ -28,10 +27,19 @@ class Trilinos(Package):
     depends_on('matio')
     depends_on('glm')
     depends_on('swig')
+    depends_on('metis')
+    depends_on('suite-sparse')
+    depends_on('tbb')
 
     # MPI related dependencies
     depends_on('mpi')
     depends_on('netcdf+mpi')
+    depends_on('parmetis')
+    depends_on('mumps+metis+parmetis')
+    depends_on('scalapack')
+    depends_on('superlu-dist')
+    depends_on('hypre')
+    depends_on('hdf5+mpi')
 
     depends_on('python') #  Needs py-numpy activated
 
@@ -49,23 +57,79 @@ def install(self, spec, prefix):
                         '-DMPI_BASE_DIR:PATH=%s' % spec['mpi'].prefix,
                         '-DTPL_ENABLE_BLAS=ON',
                         '-DBLAS_LIBRARY_NAMES=blas',
-                        '-DBLAS_LIBRARY_DIRS=/usr/lib', # % spec['blas'].prefix,
+                        '-DBLAS_LIBRARY_DIRS=/usr/lib', # % spec['blas'].prefix, #FIXME
                         '-DTPL_ENABLE_LAPACK=ON',
                         '-DLAPACK_LIBRARY_NAMES=lapack',
-                        '-DLAPACK_LIBRARY_DIRS=/usr/lib', # % spec['lapack'].prefix,
+                        '-DLAPACK_LIBRARY_DIRS=/usr/lib', # % spec['lapack'].prefix, #FIXME
                         '-DTPL_ENABLE_Boost:BOOL=ON',
                         '-DBOOST_BASE_DIR:PATH=%s' % spec['boost'].prefix,
-                        '-DTrilinos_ENABLE_Fortran=OFF',
+                        '-DTrilinos_ENABLE_Fortran=OFF', # FIXME
                         '-DTrilinos_ENABLE_EXPLICIT_INSTANTIATION:BOOL=ON',
                         '-DTrilinos_ENABLE_CXX11:BOOL=ON',
-                        '-DTrilinos_CXX11_FLAGS=-std=c++11'
+                        '-DTrilinos_CXX11_FLAGS=-std=c++11',
+                        '-DTPL_ENABLE_Netcdf:BOOL=ON',
+                        '-DTPL_ENABLE_HYPRE:BOOL=ON',
+                        '-DTPL_ENABLE_HDF5:BOOL=ON',
+                        '-DTPL_ENABLE_TBB:BOOL=ON'
                         ])
 
+        # Amesos, conflicting types of double and complex SLU_D
+        # see https://trilinos.org/pipermail/trilinos-users/2015-March/004731.html
+        # and https://trilinos.org/pipermail/trilinos-users/2015-March/004802.html
+        options.extend([
+            '-DTeuchos_ENABLE_COMPLEX:BOOL=OFF',
+            '-DKokkosTSQR_ENABLE_Complex:BOOL=OFF'
+        ])
+
+        # suite-sparse related
+        options.extend([
+            '-DTPL_ENABLE_Cholmod:BOOL=ON',
+            '-DTPL_ENABLE_UMFPACK:BOOL=ON',
+            '-DUMFPACK_LIBRARY_NAMES=umfpack;amd;colamd;cholmod;suitesparseconfig'
+        ])
+
+        # metis / parmetis
+        options.extend([
+            '-DTPL_ENABLE_METIS:BOOL=ON',
+            '-DMETIS_LIBRARY_DIRS=%s' % spec['metis'].prefix.lib,
+            '-DMETIS_LIBRARY_NAMES=metis',
+            '-DTPL_METIS_INCLUDE_DIRS=%s' % spec['metis'].prefix.include,
+            '-DTPL_ENABLE_ParMETIS:BOOL=ON',
+            '-DParMETIS_LIBRARY_DIRS=%s;%s' % (spec['parmetis'].prefix.lib,spec['metis'].prefix.lib),
+            '-DParMETIS_LIBRARY_NAMES=parmetis;metis',
+            '-DTPL_ParMETIS_INCLUDE_DIRS=%s' % spec['parmetis'].prefix.include
+        ])
+
+        # mumps
+        options.extend([
+            '-DTPL_ENABLE_MUMPS:BOOL=ON"',
+            '-DMUMPS_LIBRARY_DIRS=%s' % spec['mumps'].prefix.lib,
+            '-DMUMPS_LIBRARY_NAMES=dmumps;mumps_common;pord' # order is important!
+        ])
+
+        # scalapack
+        options.extend([
+            '-DTPL_ENABLE_SCALAPACK:BOOL=ON',
+            '-DSCALAPACK_LIBRARY_NAMES=scalapack' # FIXME: for MKL it's mkl_scalapack_lp64;mkl_blacs_mpich_lp64
+        ])
+
+        # superlu_dist
+        options.extend([
+            '-DTPL_ENABLE_SuperLUDist:BOOL=ON',
+            '-DSuperLUDist_INCLUDE_DIRS=%s' % spec['superlu_dist'].prefix.include
+        ])
+        if spec.satisfies('^superlu-dist@4.0:'):
+            options.extend([
+                '-DHAVE_SUPERLUDIST_LUSTRUCTINIT_2ARG:BOOL=ON'
+            ])
+
+
         # disable due to compiler / config errors:
-        options.extend(['-DTrilinos_ENABLE_SEACAS=OFF',
-                        '-DTrilinos_ENABLE_Pike=OFF',
-                        '-DTrilinos_ENABLE_STK=OFF'
-                        ])
+        options.extend([
+            '-DTrilinos_ENABLE_SEACAS=OFF',
+            '-DTrilinos_ENABLE_Pike=OFF',
+            '-DTrilinos_ENABLE_STK=OFF'
+        ])
 
         if self.compiler.name == "clang":
             os.environ['CPPFLAGS']="-Qunused-arguments"

From 76006fc346c7880b03356c1cf9d00bab2fdeac45 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Wed, 23 Mar 2016 05:30:48 +0100
Subject: [PATCH 113/230] fix typo

---
 var/spack/repos/builtin/packages/trilinos/package.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py
index 7b913031e3d..7d7613d2b53 100644
--- a/var/spack/repos/builtin/packages/trilinos/package.py
+++ b/var/spack/repos/builtin/packages/trilinos/package.py
@@ -116,7 +116,7 @@ def install(self, spec, prefix):
         # superlu_dist
         options.extend([
             '-DTPL_ENABLE_SuperLUDist:BOOL=ON',
-            '-DSuperLUDist_INCLUDE_DIRS=%s' % spec['superlu_dist'].prefix.include
+            '-DSuperLUDist_INCLUDE_DIRS=%s' % spec['superlu-dist'].prefix.include
         ])
         if spec.satisfies('^superlu-dist@4.0:'):
             options.extend([

From 18db930866b2024b242ea7c825851d7a56b27247 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Wed, 23 Mar 2016 07:09:58 +0100
Subject: [PATCH 114/230] rearrange

---
 .../repos/builtin/packages/trilinos/package.py | 18 ++++++++----------
 1 file changed, 8 insertions(+), 10 deletions(-)

diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py
index 7d7613d2b53..063d179c7eb 100644
--- a/var/spack/repos/builtin/packages/trilinos/package.py
+++ b/var/spack/repos/builtin/packages/trilinos/package.py
@@ -73,14 +73,6 @@ def install(self, spec, prefix):
                         '-DTPL_ENABLE_TBB:BOOL=ON'
                         ])
 
-        # Amesos, conflicting types of double and complex SLU_D
-        # see https://trilinos.org/pipermail/trilinos-users/2015-March/004731.html
-        # and https://trilinos.org/pipermail/trilinos-users/2015-March/004802.html
-        options.extend([
-            '-DTeuchos_ENABLE_COMPLEX:BOOL=OFF',
-            '-DKokkosTSQR_ENABLE_Complex:BOOL=OFF'
-        ])
-
         # suite-sparse related
         options.extend([
             '-DTPL_ENABLE_Cholmod:BOOL=ON',
@@ -113,7 +105,14 @@ def install(self, spec, prefix):
             '-DSCALAPACK_LIBRARY_NAMES=scalapack' # FIXME: for MKL it's mkl_scalapack_lp64;mkl_blacs_mpich_lp64
         ])
 
-        # superlu_dist
+        # superlu_dist:
+        # Amesos, conflicting types of double and complex SLU_D
+        # see https://trilinos.org/pipermail/trilinos-users/2015-March/004731.html
+        # and https://trilinos.org/pipermail/trilinos-users/2015-March/004802.html
+        options.extend([
+            '-DTeuchos_ENABLE_COMPLEX:BOOL=OFF',
+            '-DKokkosTSQR_ENABLE_Complex:BOOL=OFF'
+        ])
         options.extend([
             '-DTPL_ENABLE_SuperLUDist:BOOL=ON',
             '-DSuperLUDist_INCLUDE_DIRS=%s' % spec['superlu-dist'].prefix.include
@@ -123,7 +122,6 @@ def install(self, spec, prefix):
                 '-DHAVE_SUPERLUDIST_LUSTRUCTINIT_2ARG:BOOL=ON'
             ])
 
-
         # disable due to compiler / config errors:
         options.extend([
             '-DTrilinos_ENABLE_SEACAS=OFF',

From b91a155e8d996c9e51da7f75d4e106469ba488e6 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Wed, 23 Mar 2016 07:10:31 +0100
Subject: [PATCH 115/230] more specific about dependencies

---
 var/spack/repos/builtin/packages/trilinos/package.py | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py
index 063d179c7eb..2937ed4c381 100644
--- a/var/spack/repos/builtin/packages/trilinos/package.py
+++ b/var/spack/repos/builtin/packages/trilinos/package.py
@@ -62,7 +62,7 @@ def install(self, spec, prefix):
                         '-DLAPACK_LIBRARY_NAMES=lapack',
                         '-DLAPACK_LIBRARY_DIRS=/usr/lib', # % spec['lapack'].prefix, #FIXME
                         '-DTPL_ENABLE_Boost:BOOL=ON',
-                        '-DBOOST_BASE_DIR:PATH=%s' % spec['boost'].prefix,
+                        '-DBoost_BASE_DIR:PATH=%s' % spec['boost'].prefix,
                         '-DTrilinos_ENABLE_Fortran=OFF', # FIXME
                         '-DTrilinos_ENABLE_EXPLICIT_INSTANTIATION:BOOL=ON',
                         '-DTrilinos_ENABLE_CXX11:BOOL=ON',
@@ -76,7 +76,9 @@ def install(self, spec, prefix):
         # suite-sparse related
         options.extend([
             '-DTPL_ENABLE_Cholmod:BOOL=ON',
+            '-DCholmod_BASE_DIR:PATH=%s' % spec['suite-sparse'].prefix,
             '-DTPL_ENABLE_UMFPACK:BOOL=ON',
+            '-D_UMFPACK_BASE_DIR:PATH=%s' % spec['suite-sparse'].prefix,
             '-DUMFPACK_LIBRARY_NAMES=umfpack;amd;colamd;cholmod;suitesparseconfig'
         ])
 
@@ -94,7 +96,7 @@ def install(self, spec, prefix):
 
         # mumps
         options.extend([
-            '-DTPL_ENABLE_MUMPS:BOOL=ON"',
+            '-DTPL_ENABLE_MUMPS:BOOL=ON',
             '-DMUMPS_LIBRARY_DIRS=%s' % spec['mumps'].prefix.lib,
             '-DMUMPS_LIBRARY_NAMES=dmumps;mumps_common;pord' # order is important!
         ])
@@ -115,6 +117,7 @@ def install(self, spec, prefix):
         ])
         options.extend([
             '-DTPL_ENABLE_SuperLUDist:BOOL=ON',
+            '-DSuperLUDist_BASE_DIR:PATH=%s' % spec['superlu-dist'].prefix,
             '-DSuperLUDist_INCLUDE_DIRS=%s' % spec['superlu-dist'].prefix.include
         ])
         if spec.satisfies('^superlu-dist@4.0:'):

From b6a35716ce3e02e1a3661e2433986ad637b65d0c Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Wed, 23 Mar 2016 07:33:28 +0100
Subject: [PATCH 116/230] same

---
 var/spack/repos/builtin/packages/trilinos/package.py | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py
index 2937ed4c381..b31cf880bca 100644
--- a/var/spack/repos/builtin/packages/trilinos/package.py
+++ b/var/spack/repos/builtin/packages/trilinos/package.py
@@ -43,6 +43,8 @@ class Trilinos(Package):
 
     depends_on('python') #  Needs py-numpy activated
 
+    patch('umfpack_from_suitesparse.patch')
+
     def install(self, spec, prefix):
         options = []
         options.extend(std_cmake_args)
@@ -76,9 +78,11 @@ def install(self, spec, prefix):
         # suite-sparse related
         options.extend([
             '-DTPL_ENABLE_Cholmod:BOOL=ON',
-            '-DCholmod_BASE_DIR:PATH=%s' % spec['suite-sparse'].prefix,
+            '-DCholmod_LIBRARY_DIRS=%s' % spec['suite-sparse'].prefix.lib,
+            '-DCholmod_INCLUDE_DIRS:PATH=%s' % spec['suite-sparse'].prefix.include,
             '-DTPL_ENABLE_UMFPACK:BOOL=ON',
-            '-D_UMFPACK_BASE_DIR:PATH=%s' % spec['suite-sparse'].prefix,
+            '-D_UMFPACK_LIBRARY_DIRS:PATH=%s' % spec['suite-sparse'].prefix.lib,
+            '-D_UMFPACK_INCLUDE_DIRS:PATH=%s' % spec['suite-sparse'].prefix.include,
             '-DUMFPACK_LIBRARY_NAMES=umfpack;amd;colamd;cholmod;suitesparseconfig'
         ])
 
@@ -117,7 +121,7 @@ def install(self, spec, prefix):
         ])
         options.extend([
             '-DTPL_ENABLE_SuperLUDist:BOOL=ON',
-            '-DSuperLUDist_BASE_DIR:PATH=%s' % spec['superlu-dist'].prefix,
+            '-DSuperLUDist_LIBRARY_DIRS=%s' % spec['superlu-dist'].prefix.lib,
             '-DSuperLUDist_INCLUDE_DIRS=%s' % spec['superlu-dist'].prefix.include
         ])
         if spec.satisfies('^superlu-dist@4.0:'):

From 45b4895888a2abb3cf11ecf2b26b7940a9f89b5a Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Wed, 23 Mar 2016 07:34:22 +0100
Subject: [PATCH 117/230] patch

---
 .../packages/trilinos/umfpack_from_suitesparse.patch | 12 ++++++++++++
 1 file changed, 12 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/trilinos/umfpack_from_suitesparse.patch

diff --git a/var/spack/repos/builtin/packages/trilinos/umfpack_from_suitesparse.patch b/var/spack/repos/builtin/packages/trilinos/umfpack_from_suitesparse.patch
new file mode 100644
index 00000000000..9defc555276
--- /dev/null
+++ b/var/spack/repos/builtin/packages/trilinos/umfpack_from_suitesparse.patch
@@ -0,0 +1,12 @@
+diff --git a/cmake/TPLs/FindTPLUMFPACK.cmake b/cmake/TPLs/FindTPLUMFPACK.cmake
+index 963eb71..998cd02 100644
+--- a/cmake/TPLs/FindTPLUMFPACK.cmake
++++ b/cmake/TPLs/FindTPLUMFPACK.cmake
+@@ -55,6 +55,6 @@
+
+
+ TRIBITS_TPL_FIND_INCLUDE_DIRS_AND_LIBRARIES( UMFPACK
+-  REQUIRED_HEADERS umfpack.h amd.h UFconfig.h
++  REQUIRED_HEADERS umfpack.h amd.h SuiteSparse_config.h
+   REQUIRED_LIBS_NAMES umfpack amd
+   )

From bc3314a57d43963416f709a94967ae8e1758c458 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Wed, 23 Mar 2016 08:05:18 +0100
Subject: [PATCH 118/230] more and more

---
 .../repos/builtin/packages/trilinos/package.py     | 14 ++++++++------
 1 file changed, 8 insertions(+), 6 deletions(-)

diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py
index b31cf880bca..77ae6f818da 100644
--- a/var/spack/repos/builtin/packages/trilinos/package.py
+++ b/var/spack/repos/builtin/packages/trilinos/package.py
@@ -64,7 +64,8 @@ def install(self, spec, prefix):
                         '-DLAPACK_LIBRARY_NAMES=lapack',
                         '-DLAPACK_LIBRARY_DIRS=/usr/lib', # % spec['lapack'].prefix, #FIXME
                         '-DTPL_ENABLE_Boost:BOOL=ON',
-                        '-DBoost_BASE_DIR:PATH=%s' % spec['boost'].prefix,
+                        '-DBoost_INCLUDE_DIRS:PATH=%s' % spec['boost'].prefix.include,
+                        '-DBoost_LIBRARY_DIRS:PATH=%s' % spec['boost'].prefix.lib,
                         '-DTrilinos_ENABLE_Fortran=OFF', # FIXME
                         '-DTrilinos_ENABLE_EXPLICIT_INSTANTIATION:BOOL=ON',
                         '-DTrilinos_ENABLE_CXX11:BOOL=ON',
@@ -77,12 +78,13 @@ def install(self, spec, prefix):
 
         # suite-sparse related
         options.extend([
-            '-DTPL_ENABLE_Cholmod:BOOL=ON',
-            '-DCholmod_LIBRARY_DIRS=%s' % spec['suite-sparse'].prefix.lib,
-            '-DCholmod_INCLUDE_DIRS:PATH=%s' % spec['suite-sparse'].prefix.include,
+            '-DTPL_ENABLE_Cholmod:BOOL=OFF', # FIXME: Trilinos seems to be looking for static libs only, patch CMake TPL file?
+            #'-DTPL_ENABLE_Cholmod:BOOL=ON',
+            #'-DCholmod_LIBRARY_DIRS:PATH=%s' % spec['suite-sparse'].prefix.lib,
+            #'-DCholmod_INCLUDE_DIRS:PATH=%s' % spec['suite-sparse'].prefix.include,
             '-DTPL_ENABLE_UMFPACK:BOOL=ON',
-            '-D_UMFPACK_LIBRARY_DIRS:PATH=%s' % spec['suite-sparse'].prefix.lib,
-            '-D_UMFPACK_INCLUDE_DIRS:PATH=%s' % spec['suite-sparse'].prefix.include,
+            '-DUMFPACK_LIBRARY_DIRS:PATH=%s' % spec['suite-sparse'].prefix.lib,
+            '-DUMFPACK_INCLUDE_DIRS:PATH=%s' % spec['suite-sparse'].prefix.include,
             '-DUMFPACK_LIBRARY_NAMES=umfpack;amd;colamd;cholmod;suitesparseconfig'
         ])
 

From 2162627f35f98dc7f07cd34a6593f71d74095955 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Wed, 23 Mar 2016 08:13:19 +0100
Subject: [PATCH 119/230] more

---
 var/spack/repos/builtin/packages/trilinos/package.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py
index 77ae6f818da..532db69cc24 100644
--- a/var/spack/repos/builtin/packages/trilinos/package.py
+++ b/var/spack/repos/builtin/packages/trilinos/package.py
@@ -124,7 +124,7 @@ def install(self, spec, prefix):
         options.extend([
             '-DTPL_ENABLE_SuperLUDist:BOOL=ON',
             '-DSuperLUDist_LIBRARY_DIRS=%s' % spec['superlu-dist'].prefix.lib,
-            '-DSuperLUDist_INCLUDE_DIRS=%s' % spec['superlu-dist'].prefix.include
+            '-DSuperLUDist_INCLUDE_DIRS=%s/superlu_dist' % spec['superlu-dist'].prefix.include # superlu_dist and superlu have the same header names :-( In order to avoid conflicts, try to keep "dist" version headers in a subfolder
         ])
         if spec.satisfies('^superlu-dist@4.0:'):
             options.extend([

From 88a7a23132a379e526220324b8493d3be870f7e6 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Wed, 23 Mar 2016 08:46:23 +0100
Subject: [PATCH 120/230] even more

---
 .../repos/builtin/packages/trilinos/package.py   | 16 ++++++++++------
 1 file changed, 10 insertions(+), 6 deletions(-)

diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py
index 532db69cc24..13794ae930a 100644
--- a/var/spack/repos/builtin/packages/trilinos/package.py
+++ b/var/spack/repos/builtin/packages/trilinos/package.py
@@ -36,7 +36,7 @@ class Trilinos(Package):
     depends_on('netcdf+mpi')
     depends_on('parmetis')
     depends_on('mumps+metis+parmetis')
-    depends_on('scalapack')
+    # depends_on('scalapack') # see FIXME below
     depends_on('superlu-dist')
     depends_on('hypre')
     depends_on('hdf5+mpi')
@@ -49,6 +49,7 @@ def install(self, spec, prefix):
         options = []
         options.extend(std_cmake_args)
 
+        mpi_bin = spec['mpi'].prefix.bin
         options.extend(['-DTrilinos_ENABLE_ALL_PACKAGES:BOOL=ON',
                         '-DTrilinos_ENABLE_ALL_OPTIONAL_PACKAGES:BOOL=ON',
                         '-DTrilinos_ENABLE_TESTS:BOOL=OFF',
@@ -73,7 +74,12 @@ def install(self, spec, prefix):
                         '-DTPL_ENABLE_Netcdf:BOOL=ON',
                         '-DTPL_ENABLE_HYPRE:BOOL=ON',
                         '-DTPL_ENABLE_HDF5:BOOL=ON',
-                        '-DTPL_ENABLE_TBB:BOOL=ON'
+                        '-DTPL_ENABLE_TBB:BOOL=ON',
+                        # Need to use MPI wrappers, otherwise: Undefined symbols for architecture x86_64: "_mpi_abort_","_mpi_allgatherv_", etc from MUMPS
+                        '-DCMAKE_C_COMPILER=%s' % join_path(mpi_bin,'mpicc'), # FIXME: dont hardcode compiler name
+                        '-DCMAKE_CXX_COMPILER=%s' % join_path(mpi_bin,'mpicxx'),
+                        '-DCMAKE_Fortran_COMPILER=%s' % join_path(mpi_bin,'mpicxx'),
+                        '-DTrilinos_EXTRA_LINK_FLAGS:STRING=-lgfortran'
                         ])
 
         # suite-sparse related
@@ -109,8 +115,8 @@ def install(self, spec, prefix):
 
         # scalapack
         options.extend([
-            '-DTPL_ENABLE_SCALAPACK:BOOL=ON',
-            '-DSCALAPACK_LIBRARY_NAMES=scalapack' # FIXME: for MKL it's mkl_scalapack_lp64;mkl_blacs_mpich_lp64
+            '-DTPL_ENABLE_SCALAPACK:BOOL=OFF', #FIXME: Undefined symbols for architecture x86_64: "_blacs_gridinfo__", referenced from: Amesos_Scalapack::RedistributeA() in Amesos_Scalapack.cpp.o
+            #'-DSCALAPACK_LIBRARY_NAMES=scalapack' # FIXME: for MKL it's mkl_scalapack_lp64;mkl_blacs_mpich_lp64
         ])
 
         # superlu_dist:
@@ -141,8 +147,6 @@ def install(self, spec, prefix):
         if self.compiler.name == "clang":
             os.environ['CPPFLAGS']="-Qunused-arguments"
 
-        #os.environ['LDFLAGS']="lgfortran"
-
         with working_dir('spack-build', create=True):
             cmake('..', *options)
             make()

From 7e4e2c988ab4e5163469395ace204d9f332a9675 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Wed, 23 Mar 2016 08:48:25 +0100
Subject: [PATCH 121/230] minor

---
 var/spack/repos/builtin/packages/trilinos/package.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py
index 13794ae930a..c915d8eb1a6 100644
--- a/var/spack/repos/builtin/packages/trilinos/package.py
+++ b/var/spack/repos/builtin/packages/trilinos/package.py
@@ -78,7 +78,7 @@ def install(self, spec, prefix):
                         # Need to use MPI wrappers, otherwise: Undefined symbols for architecture x86_64: "_mpi_abort_","_mpi_allgatherv_", etc from MUMPS
                         '-DCMAKE_C_COMPILER=%s' % join_path(mpi_bin,'mpicc'), # FIXME: dont hardcode compiler name
                         '-DCMAKE_CXX_COMPILER=%s' % join_path(mpi_bin,'mpicxx'),
-                        '-DCMAKE_Fortran_COMPILER=%s' % join_path(mpi_bin,'mpicxx'),
+                        '-DCMAKE_Fortran_COMPILER=%s' % join_path(mpi_bin,'mpif90'),
                         '-DTrilinos_EXTRA_LINK_FLAGS:STRING=-lgfortran'
                         ])
 

From 50e4b609c688b573ef882a079e2d45a83966f94c Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Wed, 23 Mar 2016 09:11:26 +0100
Subject: [PATCH 122/230] minor

---
 var/spack/repos/builtin/packages/trilinos/package.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py
index c915d8eb1a6..3622548ecea 100644
--- a/var/spack/repos/builtin/packages/trilinos/package.py
+++ b/var/spack/repos/builtin/packages/trilinos/package.py
@@ -52,6 +52,7 @@ def install(self, spec, prefix):
         mpi_bin = spec['mpi'].prefix.bin
         options.extend(['-DTrilinos_ENABLE_ALL_PACKAGES:BOOL=ON',
                         '-DTrilinos_ENABLE_ALL_OPTIONAL_PACKAGES:BOOL=ON',
+                        '-DTrilinos_VERBOSE_CONFIGURE:BOOL=OFF',
                         '-DTrilinos_ENABLE_TESTS:BOOL=OFF',
                         '-DTrilinos_ENABLE_EXAMPLES:BOOL=OFF',
                         '-DCMAKE_BUILD_TYPE:STRING=%s' % ('Debug' if '+debug' in spec else 'Release'),
@@ -145,7 +146,9 @@ def install(self, spec, prefix):
         ])
 
         if self.compiler.name == "clang":
-            os.environ['CPPFLAGS']="-Qunused-arguments"
+            options.extend([
+                '-DCMAKE_EXE_LINKER_FLAGS:STRING=-Qunused-arguments'
+            ])
 
         with working_dir('spack-build', create=True):
             cmake('..', *options)

From 2fb599ea86c82e3395d8402db116a3a25fed0c73 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Wed, 23 Mar 2016 09:16:51 +0100
Subject: [PATCH 123/230] minor

---
 var/spack/repos/builtin/packages/trilinos/package.py | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py
index 3622548ecea..82681e004c0 100644
--- a/var/spack/repos/builtin/packages/trilinos/package.py
+++ b/var/spack/repos/builtin/packages/trilinos/package.py
@@ -55,7 +55,7 @@ def install(self, spec, prefix):
                         '-DTrilinos_VERBOSE_CONFIGURE:BOOL=OFF',
                         '-DTrilinos_ENABLE_TESTS:BOOL=OFF',
                         '-DTrilinos_ENABLE_EXAMPLES:BOOL=OFF',
-                        '-DCMAKE_BUILD_TYPE:STRING=%s' % ('Debug' if '+debug' in spec else 'Release'),
+                        '-DCMAKE_BUILD_TYPE:STRING=%s' % ('DEBUG' if '+debug' in spec else 'RELEASE'),
                         '-DBUILD_SHARED_LIBS:BOOL=%s' % ('ON' if '+shared' in spec else 'OFF'),
                         '-DTPL_ENABLE_MPI:BOOL=ON',
                         '-DMPI_BASE_DIR:PATH=%s' % spec['mpi'].prefix,
@@ -83,6 +83,11 @@ def install(self, spec, prefix):
                         '-DTrilinos_EXTRA_LINK_FLAGS:STRING=-lgfortran'
                         ])
 
+        # for build-debug only:
+        options.extend([
+            '-DCMAKE_VERBOSE_MAKEFILE:BOOL=TRUE'
+        ])
+
         # suite-sparse related
         options.extend([
             '-DTPL_ENABLE_Cholmod:BOOL=OFF', # FIXME: Trilinos seems to be looking for static libs only, patch CMake TPL file?

From eb5b0767aa20b46932c36203595c124b7463a444 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Wed, 23 Mar 2016 09:45:33 +0100
Subject: [PATCH 124/230] remove gfortran as we have libnotfound...

---
 var/spack/repos/builtin/packages/trilinos/package.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py
index 82681e004c0..bb6f0951909 100644
--- a/var/spack/repos/builtin/packages/trilinos/package.py
+++ b/var/spack/repos/builtin/packages/trilinos/package.py
@@ -80,7 +80,7 @@ def install(self, spec, prefix):
                         '-DCMAKE_C_COMPILER=%s' % join_path(mpi_bin,'mpicc'), # FIXME: dont hardcode compiler name
                         '-DCMAKE_CXX_COMPILER=%s' % join_path(mpi_bin,'mpicxx'),
                         '-DCMAKE_Fortran_COMPILER=%s' % join_path(mpi_bin,'mpif90'),
-                        '-DTrilinos_EXTRA_LINK_FLAGS:STRING=-lgfortran'
+                        # '-DTrilinos_EXTRA_LINK_FLAGS:STRING=-lgfortran' # FIXME 
                         ])
 
         # for build-debug only:

From 7897f10126f0f8389326c9e723d73021f654ea6a Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Wed, 23 Mar 2016 13:04:43 +0100
Subject: [PATCH 125/230] fiddle with fortran

---
 .../builtin/packages/trilinos/package.py      | 21 ++++++++++++-------
 1 file changed, 14 insertions(+), 7 deletions(-)

diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py
index bb6f0951909..f6f24e967e9 100644
--- a/var/spack/repos/builtin/packages/trilinos/package.py
+++ b/var/spack/repos/builtin/packages/trilinos/package.py
@@ -68,7 +68,7 @@ def install(self, spec, prefix):
                         '-DTPL_ENABLE_Boost:BOOL=ON',
                         '-DBoost_INCLUDE_DIRS:PATH=%s' % spec['boost'].prefix.include,
                         '-DBoost_LIBRARY_DIRS:PATH=%s' % spec['boost'].prefix.lib,
-                        '-DTrilinos_ENABLE_Fortran=OFF', # FIXME
+                        # '-DTrilinos_ENABLE_Fortran=OFF', # FIXME
                         '-DTrilinos_ENABLE_EXPLICIT_INSTANTIATION:BOOL=ON',
                         '-DTrilinos_ENABLE_CXX11:BOOL=ON',
                         '-DTrilinos_CXX11_FLAGS=-std=c++11',
@@ -79,10 +79,17 @@ def install(self, spec, prefix):
                         # Need to use MPI wrappers, otherwise: Undefined symbols for architecture x86_64: "_mpi_abort_","_mpi_allgatherv_", etc from MUMPS
                         '-DCMAKE_C_COMPILER=%s' % join_path(mpi_bin,'mpicc'), # FIXME: dont hardcode compiler name
                         '-DCMAKE_CXX_COMPILER=%s' % join_path(mpi_bin,'mpicxx'),
-                        '-DCMAKE_Fortran_COMPILER=%s' % join_path(mpi_bin,'mpif90'),
-                        # '-DTrilinos_EXTRA_LINK_FLAGS:STRING=-lgfortran' # FIXME 
+                        '-DCMAKE_Fortran_COMPILER=%s' % join_path(mpi_bin,'mpif90')
                         ])
 
+        # Fortran lib
+        libgfortran = os.path.dirname (os.popen('%s --print-file-name libgfortran.a' % join_path(mpi_bin,'mpif90') ).read())
+        #os.environ['LDFLAGS'] = '-L%s -lgfortran' % libgfortran
+        options.extend([
+            '-DTrilinos_EXTRA_LINK_FLAGS:STRING=-lgfortran',
+            '-DCMAKE_EXE_LINKER_FLAGS:STRING=-L%s -lgfortran' % libgfortran
+        ])
+
         # for build-debug only:
         options.extend([
             '-DCMAKE_VERBOSE_MAKEFILE:BOOL=TRUE'
@@ -150,10 +157,10 @@ def install(self, spec, prefix):
             '-DTrilinos_ENABLE_STK=OFF'
         ])
 
-        if self.compiler.name == "clang":
-            options.extend([
-                '-DCMAKE_EXE_LINKER_FLAGS:STRING=-Qunused-arguments'
-            ])
+        #if self.compiler.name == "clang":
+        #    options.extend([
+        #        '-DCMAKE_EXE_LINKER_FLAGS:STRING=-Qunused-arguments'
+        #    ])
 
         with working_dir('spack-build', create=True):
             cmake('..', *options)

From fade526ae4e748a9454fd56c07ef7bc1fca38423 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Wed, 23 Mar 2016 16:58:59 +0100
Subject: [PATCH 126/230] remove tbb

---
 var/spack/repos/builtin/packages/trilinos/package.py | 2 --
 1 file changed, 2 deletions(-)

diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py
index f6f24e967e9..12212360a0d 100644
--- a/var/spack/repos/builtin/packages/trilinos/package.py
+++ b/var/spack/repos/builtin/packages/trilinos/package.py
@@ -29,7 +29,6 @@ class Trilinos(Package):
     depends_on('swig')
     depends_on('metis')
     depends_on('suite-sparse')
-    depends_on('tbb')
 
     # MPI related dependencies
     depends_on('mpi')
@@ -75,7 +74,6 @@ def install(self, spec, prefix):
                         '-DTPL_ENABLE_Netcdf:BOOL=ON',
                         '-DTPL_ENABLE_HYPRE:BOOL=ON',
                         '-DTPL_ENABLE_HDF5:BOOL=ON',
-                        '-DTPL_ENABLE_TBB:BOOL=ON',
                         # Need to use MPI wrappers, otherwise: Undefined symbols for architecture x86_64: "_mpi_abort_","_mpi_allgatherv_", etc from MUMPS
                         '-DCMAKE_C_COMPILER=%s' % join_path(mpi_bin,'mpicc'), # FIXME: dont hardcode compiler name
                         '-DCMAKE_CXX_COMPILER=%s' % join_path(mpi_bin,'mpicxx'),

From e51fe2934e0189aa5c33c8663819d23e7706f809 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Wed, 23 Mar 2016 17:38:36 +0100
Subject: [PATCH 127/230] fiddle more

---
 var/spack/repos/builtin/packages/trilinos/package.py | 11 ++---------
 1 file changed, 2 insertions(+), 9 deletions(-)

diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py
index 12212360a0d..fb14e1f36cb 100644
--- a/var/spack/repos/builtin/packages/trilinos/package.py
+++ b/var/spack/repos/builtin/packages/trilinos/package.py
@@ -67,7 +67,6 @@ def install(self, spec, prefix):
                         '-DTPL_ENABLE_Boost:BOOL=ON',
                         '-DBoost_INCLUDE_DIRS:PATH=%s' % spec['boost'].prefix.include,
                         '-DBoost_LIBRARY_DIRS:PATH=%s' % spec['boost'].prefix.lib,
-                        # '-DTrilinos_ENABLE_Fortran=OFF', # FIXME
                         '-DTrilinos_ENABLE_EXPLICIT_INSTANTIATION:BOOL=ON',
                         '-DTrilinos_ENABLE_CXX11:BOOL=ON',
                         '-DTrilinos_CXX11_FLAGS=-std=c++11',
@@ -82,10 +81,9 @@ def install(self, spec, prefix):
 
         # Fortran lib
         libgfortran = os.path.dirname (os.popen('%s --print-file-name libgfortran.a' % join_path(mpi_bin,'mpif90') ).read())
-        #os.environ['LDFLAGS'] = '-L%s -lgfortran' % libgfortran
         options.extend([
-            '-DTrilinos_EXTRA_LINK_FLAGS:STRING=-lgfortran',
-            '-DCMAKE_EXE_LINKER_FLAGS:STRING=-L%s -lgfortran' % libgfortran
+            '-DTrilinos_EXTRA_LINK_FLAGS:STRING=-L%s/ -lgfortran' % libgfortran,
+            '-DTrilinos_ENABLE_Fortran=OFF' # FIXME: otherwise VerifyFortranC fails as it does not contain -lgfortran , issues with IMPLICIT_LINK_LIBRARIES in CMakeFiles/CMake(C|CXX|Fortran)Compiler.cmake?
         ])
 
         # for build-debug only:
@@ -155,11 +153,6 @@ def install(self, spec, prefix):
             '-DTrilinos_ENABLE_STK=OFF'
         ])
 
-        #if self.compiler.name == "clang":
-        #    options.extend([
-        #        '-DCMAKE_EXE_LINKER_FLAGS:STRING=-Qunused-arguments'
-        #    ])
-
         with working_dir('spack-build', create=True):
             cmake('..', *options)
             make()

From 3f12a51759fcdd3b11867cb849fc2aa81a4941ef Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Wed, 23 Mar 2016 19:35:49 +0100
Subject: [PATCH 128/230] keep fiddling

---
 .../repos/builtin/packages/trilinos/package.py  | 17 +++++++++++------
 1 file changed, 11 insertions(+), 6 deletions(-)

diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py
index fb14e1f36cb..cdc2bf2379f 100644
--- a/var/spack/repos/builtin/packages/trilinos/package.py
+++ b/var/spack/repos/builtin/packages/trilinos/package.py
@@ -1,6 +1,11 @@
 from spack import *
 import os
 
+# Trilinos is complicated to build, as an inspiration a couple of links to other repositories which build it:
+# https://github.com/hpcugent/easybuild-easyblocks/blob/master/easybuild/easyblocks/t/trilinos.py#L111
+# https://github.com/koecher/candi/blob/master/deal.II-toolchain/packages/trilinos.package
+# https://gitlab.com/configurations/cluster-config/blob/master/trilinos.sh
+# https://github.com/Homebrew/homebrew-science/blob/master/trilinos.rb
 class Trilinos(Package):
     """The Trilinos Project is an effort to develop algorithms and enabling technologies within an object-oriented
     software framework for the solution of large-scale, complex multi-physics engineering and scientific problems.
@@ -59,11 +64,11 @@ def install(self, spec, prefix):
                         '-DTPL_ENABLE_MPI:BOOL=ON',
                         '-DMPI_BASE_DIR:PATH=%s' % spec['mpi'].prefix,
                         '-DTPL_ENABLE_BLAS=ON',
-                        '-DBLAS_LIBRARY_NAMES=blas',
-                        '-DBLAS_LIBRARY_DIRS=/usr/lib', # % spec['blas'].prefix, #FIXME
+                        '-DBLAS_LIBRARY_NAMES=blas', # FIXME: for Intel, Clang+GNU, GNU; easybuild add gfortran here...
+                        '-DBLAS_LIBRARY_DIRS=%s' % spec['blas'].prefix.lib,
                         '-DTPL_ENABLE_LAPACK=ON',
                         '-DLAPACK_LIBRARY_NAMES=lapack',
-                        '-DLAPACK_LIBRARY_DIRS=/usr/lib', # % spec['lapack'].prefix, #FIXME
+                        '-DLAPACK_LIBRARY_DIRS=%s' % spec['lapack'].prefix,
                         '-DTPL_ENABLE_Boost:BOOL=ON',
                         '-DBoost_INCLUDE_DIRS:PATH=%s' % spec['boost'].prefix.include,
                         '-DBoost_LIBRARY_DIRS:PATH=%s' % spec['boost'].prefix.lib,
@@ -74,9 +79,9 @@ def install(self, spec, prefix):
                         '-DTPL_ENABLE_HYPRE:BOOL=ON',
                         '-DTPL_ENABLE_HDF5:BOOL=ON',
                         # Need to use MPI wrappers, otherwise: Undefined symbols for architecture x86_64: "_mpi_abort_","_mpi_allgatherv_", etc from MUMPS
-                        '-DCMAKE_C_COMPILER=%s' % join_path(mpi_bin,'mpicc'), # FIXME: dont hardcode compiler name
-                        '-DCMAKE_CXX_COMPILER=%s' % join_path(mpi_bin,'mpicxx'),
-                        '-DCMAKE_Fortran_COMPILER=%s' % join_path(mpi_bin,'mpif90')
+                        #'-DCMAKE_C_COMPILER=%s' % join_path(mpi_bin,'mpicc'), # FIXME: dont hardcode compiler name
+                        #'-DCMAKE_CXX_COMPILER=%s' % join_path(mpi_bin,'mpicxx'),
+                        #'-DCMAKE_Fortran_COMPILER=%s' % join_path(mpi_bin,'mpif90')
                         ])
 
         # Fortran lib

From 8c9f88761384d16c77aa9cbee55cc501712c7b12 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Thu, 24 Mar 2016 12:45:43 +0100
Subject: [PATCH 129/230] finally builds

---
 var/spack/repos/builtin/packages/trilinos/package.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py
index cdc2bf2379f..b80123838ac 100644
--- a/var/spack/repos/builtin/packages/trilinos/package.py
+++ b/var/spack/repos/builtin/packages/trilinos/package.py
@@ -39,7 +39,7 @@ class Trilinos(Package):
     depends_on('mpi')
     depends_on('netcdf+mpi')
     depends_on('parmetis')
-    depends_on('mumps+metis+parmetis')
+    depends_on('mumps+metis+parmetis+shared') # build errors with static libs
     # depends_on('scalapack') # see FIXME below
     depends_on('superlu-dist')
     depends_on('hypre')

From df995c4ef850338823b3a5a5c2ee3b12e05a33b1 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Thu, 24 Mar 2016 12:57:22 +0100
Subject: [PATCH 130/230] minor cleanup

---
 .../repos/builtin/packages/trilinos/package.py     | 14 +++++---------
 1 file changed, 5 insertions(+), 9 deletions(-)

diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py
index b80123838ac..f2e9c37caac 100644
--- a/var/spack/repos/builtin/packages/trilinos/package.py
+++ b/var/spack/repos/builtin/packages/trilinos/package.py
@@ -77,24 +77,20 @@ def install(self, spec, prefix):
                         '-DTrilinos_CXX11_FLAGS=-std=c++11',
                         '-DTPL_ENABLE_Netcdf:BOOL=ON',
                         '-DTPL_ENABLE_HYPRE:BOOL=ON',
-                        '-DTPL_ENABLE_HDF5:BOOL=ON',
-                        # Need to use MPI wrappers, otherwise: Undefined symbols for architecture x86_64: "_mpi_abort_","_mpi_allgatherv_", etc from MUMPS
-                        #'-DCMAKE_C_COMPILER=%s' % join_path(mpi_bin,'mpicc'), # FIXME: dont hardcode compiler name
-                        #'-DCMAKE_CXX_COMPILER=%s' % join_path(mpi_bin,'mpicxx'),
-                        #'-DCMAKE_Fortran_COMPILER=%s' % join_path(mpi_bin,'mpif90')
+                        '-DTPL_ENABLE_HDF5:BOOL=ON'
                         ])
 
         # Fortran lib
         libgfortran = os.path.dirname (os.popen('%s --print-file-name libgfortran.a' % join_path(mpi_bin,'mpif90') ).read())
         options.extend([
             '-DTrilinos_EXTRA_LINK_FLAGS:STRING=-L%s/ -lgfortran' % libgfortran,
-            '-DTrilinos_ENABLE_Fortran=OFF' # FIXME: otherwise VerifyFortranC fails as it does not contain -lgfortran , issues with IMPLICIT_LINK_LIBRARIES in CMakeFiles/CMake(C|CXX|Fortran)Compiler.cmake?
+            '-DTrilinos_ENABLE_Fortran=OFF' # FIXME: otherwise CMake's VerifyFortranC fails as it does not contain -lgfortran
         ])
 
         # for build-debug only:
-        options.extend([
-            '-DCMAKE_VERBOSE_MAKEFILE:BOOL=TRUE'
-        ])
+        # options.extend([
+        #    '-DCMAKE_VERBOSE_MAKEFILE:BOOL=TRUE'
+        # ])
 
         # suite-sparse related
         options.extend([

From 0fc9326a4cc742e7a06cc1bb4192d0dfd008880d Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Thu, 24 Mar 2016 13:23:56 +0100
Subject: [PATCH 131/230] add variants

---
 .../builtin/packages/trilinos/package.py      | 111 +++++++++++-------
 1 file changed, 69 insertions(+), 42 deletions(-)

diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py
index f2e9c37caac..2e119581e11 100644
--- a/var/spack/repos/builtin/packages/trilinos/package.py
+++ b/var/spack/repos/builtin/packages/trilinos/package.py
@@ -22,8 +22,15 @@ class Trilinos(Package):
     version('11.14.2', 'a43590cf896c677890d75bfe75bc6254')
     version('11.14.1', '40febc57f76668be8b6a77b7607bb67f')
 
-    variant('shared', default=True, description='Enables the build of shared libraries')
-    variant('debug', default=False, description='Builds a debug version of the libraries')
+    variant('metis',        default=True,  description='Compile with METIS')
+    variant('parmetis',     default=True,  description='Compile with ParMETIS')
+    variant('mumps',        default=True,  description='Compile with support for MUMPS solvers')
+    variant('superlu-dist', default=True,  description='Compile with SuperluDist solvers')
+    variant('hypre',        default=True,  description='Compile with Hypre preconditioner')
+    variant('hdf5',         default=True,  description='Compile with HDF5')
+    variant('suite-sparse', default=True,  description='Compile with SuiteSparse solvers')
+    variant('shared',       default=True,  description='Enables the build of shared libraries')
+    variant('debug',        default=False, description='Builds a debug version of the libraries')
 
     # Everything should be compiled with -fpic
     depends_on('blas')
@@ -49,7 +56,23 @@ class Trilinos(Package):
 
     patch('umfpack_from_suitesparse.patch')
 
+    # check that the combination of variants makes sense
+    def variants_check(self):
+        if '+parmetis' in self.spec and '+metis' not in self.spec:
+            raise RuntimeError('You cannot use the variant parmetis without metis')
+
+        if '+mumps' in self.spec and '+parmetis' not in self.spec:
+            raise RuntimeError('You cannot use the variant mumps without parmetis')
+
+        if '+superlu-dist' in self.spec and self.spec.satisfies('@:11.4.3'):
+            # For Trilinos v11 we need to force SuperLUDist=OFF,
+            # since only the deprecated SuperLUDist v3.3 together with an Amesos patch
+            # is working.
+            raise RuntimeError('The superlu-dist variant can only be used with Trilinos @12.0.1:')
+
     def install(self, spec, prefix):
+        self.variants_check()
+
         options = []
         options.extend(std_cmake_args)
 
@@ -93,35 +116,38 @@ def install(self, spec, prefix):
         # ])
 
         # suite-sparse related
-        options.extend([
-            '-DTPL_ENABLE_Cholmod:BOOL=OFF', # FIXME: Trilinos seems to be looking for static libs only, patch CMake TPL file?
-            #'-DTPL_ENABLE_Cholmod:BOOL=ON',
-            #'-DCholmod_LIBRARY_DIRS:PATH=%s' % spec['suite-sparse'].prefix.lib,
-            #'-DCholmod_INCLUDE_DIRS:PATH=%s' % spec['suite-sparse'].prefix.include,
-            '-DTPL_ENABLE_UMFPACK:BOOL=ON',
-            '-DUMFPACK_LIBRARY_DIRS:PATH=%s' % spec['suite-sparse'].prefix.lib,
-            '-DUMFPACK_INCLUDE_DIRS:PATH=%s' % spec['suite-sparse'].prefix.include,
-            '-DUMFPACK_LIBRARY_NAMES=umfpack;amd;colamd;cholmod;suitesparseconfig'
-        ])
+        if '+suite-sparse' in spec:
+            options.extend([
+                '-DTPL_ENABLE_Cholmod:BOOL=OFF', # FIXME: Trilinos seems to be looking for static libs only, patch CMake TPL file?
+                #'-DTPL_ENABLE_Cholmod:BOOL=ON',
+                #'-DCholmod_LIBRARY_DIRS:PATH=%s' % spec['suite-sparse'].prefix.lib,
+                #'-DCholmod_INCLUDE_DIRS:PATH=%s' % spec['suite-sparse'].prefix.include,
+                '-DTPL_ENABLE_UMFPACK:BOOL=ON',
+                '-DUMFPACK_LIBRARY_DIRS:PATH=%s' % spec['suite-sparse'].prefix.lib,
+                '-DUMFPACK_INCLUDE_DIRS:PATH=%s' % spec['suite-sparse'].prefix.include,
+                '-DUMFPACK_LIBRARY_NAMES=umfpack;amd;colamd;cholmod;suitesparseconfig'
+            ])
 
         # metis / parmetis
-        options.extend([
-            '-DTPL_ENABLE_METIS:BOOL=ON',
-            '-DMETIS_LIBRARY_DIRS=%s' % spec['metis'].prefix.lib,
-            '-DMETIS_LIBRARY_NAMES=metis',
-            '-DTPL_METIS_INCLUDE_DIRS=%s' % spec['metis'].prefix.include,
-            '-DTPL_ENABLE_ParMETIS:BOOL=ON',
-            '-DParMETIS_LIBRARY_DIRS=%s;%s' % (spec['parmetis'].prefix.lib,spec['metis'].prefix.lib),
-            '-DParMETIS_LIBRARY_NAMES=parmetis;metis',
-            '-DTPL_ParMETIS_INCLUDE_DIRS=%s' % spec['parmetis'].prefix.include
-        ])
+        if '+parmetis' in spec: # metis is required, see variants_check()
+            options.extend([
+                '-DTPL_ENABLE_METIS:BOOL=ON',
+                '-DMETIS_LIBRARY_DIRS=%s' % spec['metis'].prefix.lib,
+                '-DMETIS_LIBRARY_NAMES=metis',
+                '-DTPL_METIS_INCLUDE_DIRS=%s' % spec['metis'].prefix.include,
+                '-DTPL_ENABLE_ParMETIS:BOOL=ON',
+                '-DParMETIS_LIBRARY_DIRS=%s;%s' % (spec['parmetis'].prefix.lib,spec['metis'].prefix.lib),
+                '-DParMETIS_LIBRARY_NAMES=parmetis;metis',
+                '-DTPL_ParMETIS_INCLUDE_DIRS=%s' % spec['parmetis'].prefix.include
+            ])
 
         # mumps
-        options.extend([
-            '-DTPL_ENABLE_MUMPS:BOOL=ON',
-            '-DMUMPS_LIBRARY_DIRS=%s' % spec['mumps'].prefix.lib,
-            '-DMUMPS_LIBRARY_NAMES=dmumps;mumps_common;pord' # order is important!
-        ])
+        if '+mumps' in spec:
+            options.extend([
+                '-DTPL_ENABLE_MUMPS:BOOL=ON',
+                '-DMUMPS_LIBRARY_DIRS=%s' % spec['mumps'].prefix.lib,
+                '-DMUMPS_LIBRARY_NAMES=dmumps;mumps_common;pord' # order is important!
+            ])
 
         # scalapack
         options.extend([
@@ -129,23 +155,24 @@ def install(self, spec, prefix):
             #'-DSCALAPACK_LIBRARY_NAMES=scalapack' # FIXME: for MKL it's mkl_scalapack_lp64;mkl_blacs_mpich_lp64
         ])
 
-        # superlu_dist:
-        # Amesos, conflicting types of double and complex SLU_D
-        # see https://trilinos.org/pipermail/trilinos-users/2015-March/004731.html
-        # and https://trilinos.org/pipermail/trilinos-users/2015-March/004802.html
-        options.extend([
-            '-DTeuchos_ENABLE_COMPLEX:BOOL=OFF',
-            '-DKokkosTSQR_ENABLE_Complex:BOOL=OFF'
-        ])
-        options.extend([
-            '-DTPL_ENABLE_SuperLUDist:BOOL=ON',
-            '-DSuperLUDist_LIBRARY_DIRS=%s' % spec['superlu-dist'].prefix.lib,
-            '-DSuperLUDist_INCLUDE_DIRS=%s/superlu_dist' % spec['superlu-dist'].prefix.include # superlu_dist and superlu have the same header names :-( In order to avoid conflicts, try to keep "dist" version headers in a subfolder
-        ])
-        if spec.satisfies('^superlu-dist@4.0:'):
+        # superlu-dist:
+        if '+superlu-dist' in spec:
+            # Amesos, conflicting types of double and complex SLU_D
+            # see https://trilinos.org/pipermail/trilinos-users/2015-March/004731.html
+            # and https://trilinos.org/pipermail/trilinos-users/2015-March/004802.html
             options.extend([
-                '-DHAVE_SUPERLUDIST_LUSTRUCTINIT_2ARG:BOOL=ON'
+                '-DTeuchos_ENABLE_COMPLEX:BOOL=OFF',
+                '-DKokkosTSQR_ENABLE_Complex:BOOL=OFF'
             ])
+            options.extend([
+                '-DTPL_ENABLE_SuperLUDist:BOOL=ON',
+                '-DSuperLUDist_LIBRARY_DIRS=%s' % spec['superlu-dist'].prefix.lib,
+                '-DSuperLUDist_INCLUDE_DIRS=%s/superlu_dist' % spec['superlu-dist'].prefix.include # superlu_dist and superlu have the same header names :-( In order to avoid conflicts, try to keep "dist" version headers in a subfolder
+            ])
+            if spec.satisfies('^superlu-dist@4.0:'):
+                options.extend([
+                    '-DHAVE_SUPERLUDIST_LUSTRUCTINIT_2ARG:BOOL=ON'
+                ])
 
         # disable due to compiler / config errors:
         options.extend([

From 416fcd081013afa8349d311909d50b21d9685674 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Thu, 24 Mar 2016 13:33:00 +0100
Subject: [PATCH 132/230] same

---
 .../repos/builtin/packages/trilinos/package.py  | 17 +++++++++--------
 1 file changed, 9 insertions(+), 8 deletions(-)

diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py
index 2e119581e11..3beadeb7980 100644
--- a/var/spack/repos/builtin/packages/trilinos/package.py
+++ b/var/spack/repos/builtin/packages/trilinos/package.py
@@ -29,6 +29,7 @@ class Trilinos(Package):
     variant('hypre',        default=True,  description='Compile with Hypre preconditioner')
     variant('hdf5',         default=True,  description='Compile with HDF5')
     variant('suite-sparse', default=True,  description='Compile with SuiteSparse solvers')
+    variant('python',       default=True,  description='Build python wrappers')
     variant('shared',       default=True,  description='Enables the build of shared libraries')
     variant('debug',        default=False, description='Builds a debug version of the libraries')
 
@@ -39,20 +40,20 @@ class Trilinos(Package):
     depends_on('matio')
     depends_on('glm')
     depends_on('swig')
-    depends_on('metis')
-    depends_on('suite-sparse')
+    depends_on('metis',when='+metis')
+    depends_on('suite-sparse',when='+suite-sparse')
 
     # MPI related dependencies
     depends_on('mpi')
     depends_on('netcdf+mpi')
-    depends_on('parmetis')
-    depends_on('mumps+metis+parmetis+shared') # build errors with static libs
+    depends_on('parmetis',when='+parmetis')
+    depends_on('mumps+metis+parmetis+shared',when='+mumps') # build errors with static libs
     # depends_on('scalapack') # see FIXME below
-    depends_on('superlu-dist')
-    depends_on('hypre')
-    depends_on('hdf5+mpi')
+    depends_on('superlu-dist',when='+superlu-dist')
+    depends_on('hypre',when='+hypre')
+    depends_on('hdf5+mpi',when='+hdf5')
 
-    depends_on('python') #  Needs py-numpy activated
+    depends_on('python',when='+python') #  Needs py-numpy activated
 
     patch('umfpack_from_suitesparse.patch')
 

From c33a63cabc8dcd8c71fc87de60a883cef4a4dae2 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Thu, 24 Mar 2016 13:47:07 +0100
Subject: [PATCH 133/230] fix python installation

---
 var/spack/repos/builtin/packages/trilinos/package.py | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py
index 3beadeb7980..886893b639c 100644
--- a/var/spack/repos/builtin/packages/trilinos/package.py
+++ b/var/spack/repos/builtin/packages/trilinos/package.py
@@ -186,3 +186,14 @@ def install(self, spec, prefix):
             cmake('..', *options)
             make()
             make('install')
+
+            # When trilinos is built with Python, libpytrilinos is included through
+            # cmake configure files. Namely, Trilinos_LIBRARIES in TrilinosConfig.cmake
+            # contains pytrilinos. This leads to a run-time error:
+            # Symbol not found: _PyBool_Type
+            # and prevents Trilinos to be used in any C++ code, which links executable
+            # against the libraries listed in Trilinos_LIBRARIES.
+            # See https://github.com/Homebrew/homebrew-science/issues/2148#issuecomment-103614509
+            # A workaround it to remove PyTrilinos from the COMPONENTS_LIST :
+            if '+python' in self.spec:
+                filter_file(r'(?:SET\(COMPONENTS_LIST.*)(PyTrilinos;)(?:.*)',  '',  '%s/cmake/Trilinos/TrilinosConfig.cmake' % prefix.lib)

From d096b155f45d97775affa2bdda640a22823cb73e Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Thu, 24 Mar 2016 19:41:37 +0100
Subject: [PATCH 134/230] fix filter_file

---
 var/spack/repos/builtin/packages/trilinos/package.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py
index 886893b639c..3967d0ef0ed 100644
--- a/var/spack/repos/builtin/packages/trilinos/package.py
+++ b/var/spack/repos/builtin/packages/trilinos/package.py
@@ -196,4 +196,4 @@ def install(self, spec, prefix):
             # See https://github.com/Homebrew/homebrew-science/issues/2148#issuecomment-103614509
             # A workaround it to remove PyTrilinos from the COMPONENTS_LIST :
             if '+python' in self.spec:
-                filter_file(r'(?:SET\(COMPONENTS_LIST.*)(PyTrilinos;)(?:.*)',  '',  '%s/cmake/Trilinos/TrilinosConfig.cmake' % prefix.lib)
+                filter_file(r'(SET\(COMPONENTS_LIST.*)(PyTrilinos;)(.*)',  (r'\1\3'),  '%s/cmake/Trilinos/TrilinosConfig.cmake' % prefix.lib)

From 7f2db8c26793abb1977dbccd2ae8a3a1b5a46568 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Fri, 25 Mar 2016 11:54:51 +0100
Subject: [PATCH 135/230] fix w GCC 4.8 on Ubuntu but broke w GCC 5.3/Clang on
 OSX

---
 .../builtin/packages/trilinos/package.py      | 26 ++++++++++++++-----
 1 file changed, 19 insertions(+), 7 deletions(-)

diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py
index 3967d0ef0ed..1f1601e5376 100644
--- a/var/spack/repos/builtin/packages/trilinos/package.py
+++ b/var/spack/repos/builtin/packages/trilinos/package.py
@@ -48,7 +48,7 @@ class Trilinos(Package):
     depends_on('netcdf+mpi')
     depends_on('parmetis',when='+parmetis')
     depends_on('mumps+metis+parmetis+shared',when='+mumps') # build errors with static libs
-    # depends_on('scalapack') # see FIXME below
+    depends_on('scalapack')
     depends_on('superlu-dist',when='+superlu-dist')
     depends_on('hypre',when='+hypre')
     depends_on('hdf5+mpi',when='+hdf5')
@@ -108,13 +108,13 @@ def install(self, spec, prefix):
         libgfortran = os.path.dirname (os.popen('%s --print-file-name libgfortran.a' % join_path(mpi_bin,'mpif90') ).read())
         options.extend([
             '-DTrilinos_EXTRA_LINK_FLAGS:STRING=-L%s/ -lgfortran' % libgfortran,
-            '-DTrilinos_ENABLE_Fortran=OFF' # FIXME: otherwise CMake's VerifyFortranC fails as it does not contain -lgfortran
+            '-DTrilinos_ENABLE_Fortran=ON' # FIXME: otherwise CMake's VerifyFortranC fails as it does not contain -lgfortran
         ])
 
         # for build-debug only:
-        # options.extend([
-        #    '-DCMAKE_VERBOSE_MAKEFILE:BOOL=TRUE'
-        # ])
+        options.extend([
+           '-DCMAKE_VERBOSE_MAKEFILE:BOOL=TRUE'
+        ])
 
         # suite-sparse related
         if '+suite-sparse' in spec:
@@ -144,16 +144,22 @@ def install(self, spec, prefix):
 
         # mumps
         if '+mumps' in spec:
+            # FIXME:
+            # since we use mumps with MPI, it will certainly be build against Scalapack.
+            # Add scalapack lib here as well. 
+            # This likely won't be need if Trilinos would compile with Scalapack
             options.extend([
                 '-DTPL_ENABLE_MUMPS:BOOL=ON',
                 '-DMUMPS_LIBRARY_DIRS=%s' % spec['mumps'].prefix.lib,
                 '-DMUMPS_LIBRARY_NAMES=dmumps;mumps_common;pord' # order is important!
+#                '-DMUMPS_LIBRARY_DIRS=%s;%s' % (spec['mumps'].prefix.lib,spec['scalapack'].prefix.lib),
+#                '-DMUMPS_LIBRARY_NAMES=dmumps;mumps_common;pord;scalapack' # order is important!
             ])
 
         # scalapack
         options.extend([
-            '-DTPL_ENABLE_SCALAPACK:BOOL=OFF', #FIXME: Undefined symbols for architecture x86_64: "_blacs_gridinfo__", referenced from: Amesos_Scalapack::RedistributeA() in Amesos_Scalapack.cpp.o
-            #'-DSCALAPACK_LIBRARY_NAMES=scalapack' # FIXME: for MKL it's mkl_scalapack_lp64;mkl_blacs_mpich_lp64
+            '-DTPL_ENABLE_SCALAPACK:BOOL=ON', #FIXME: Undefined symbols for architecture x86_64: "_blacs_gridinfo__", referenced from: Amesos_Scalapack::RedistributeA() in Amesos_Scalapack.cpp.o
+            '-DSCALAPACK_LIBRARY_NAMES=scalapack' # FIXME: for MKL it's mkl_scalapack_lp64;mkl_blacs_mpich_lp64
         ])
 
         # superlu-dist:
@@ -175,6 +181,12 @@ def install(self, spec, prefix):
                     '-DHAVE_SUPERLUDIST_LUSTRUCTINIT_2ARG:BOOL=ON'
                 ])
 
+        # python
+        if '~python' in spec:
+            options.extend([
+                '-DTrilinos_ENABLE_PyTrilinos:BOOL=OFF'
+            ])
+
         # disable due to compiler / config errors:
         options.extend([
             '-DTrilinos_ENABLE_SEACAS=OFF',

From 828aeefb1d4e09deb0694c61397a3097bda85ccb Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Fri, 25 Mar 2016 12:01:00 +0100
Subject: [PATCH 136/230] minor cleanup

---
 var/spack/repos/builtin/packages/trilinos/package.py | 12 +++---------
 1 file changed, 3 insertions(+), 9 deletions(-)

diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py
index 1f1601e5376..1dba2b8db39 100644
--- a/var/spack/repos/builtin/packages/trilinos/package.py
+++ b/var/spack/repos/builtin/packages/trilinos/package.py
@@ -88,7 +88,7 @@ def install(self, spec, prefix):
                         '-DTPL_ENABLE_MPI:BOOL=ON',
                         '-DMPI_BASE_DIR:PATH=%s' % spec['mpi'].prefix,
                         '-DTPL_ENABLE_BLAS=ON',
-                        '-DBLAS_LIBRARY_NAMES=blas', # FIXME: for Intel, Clang+GNU, GNU; easybuild add gfortran here...
+                        '-DBLAS_LIBRARY_NAMES=blas', # FIXME: don't hardcode names
                         '-DBLAS_LIBRARY_DIRS=%s' % spec['blas'].prefix.lib,
                         '-DTPL_ENABLE_LAPACK=ON',
                         '-DLAPACK_LIBRARY_NAMES=lapack',
@@ -108,7 +108,7 @@ def install(self, spec, prefix):
         libgfortran = os.path.dirname (os.popen('%s --print-file-name libgfortran.a' % join_path(mpi_bin,'mpif90') ).read())
         options.extend([
             '-DTrilinos_EXTRA_LINK_FLAGS:STRING=-L%s/ -lgfortran' % libgfortran,
-            '-DTrilinos_ENABLE_Fortran=ON' # FIXME: otherwise CMake's VerifyFortranC fails as it does not contain -lgfortran
+            '-DTrilinos_ENABLE_Fortran=ON'
         ])
 
         # for build-debug only:
@@ -144,21 +144,15 @@ def install(self, spec, prefix):
 
         # mumps
         if '+mumps' in spec:
-            # FIXME:
-            # since we use mumps with MPI, it will certainly be build against Scalapack.
-            # Add scalapack lib here as well. 
-            # This likely won't be need if Trilinos would compile with Scalapack
             options.extend([
                 '-DTPL_ENABLE_MUMPS:BOOL=ON',
                 '-DMUMPS_LIBRARY_DIRS=%s' % spec['mumps'].prefix.lib,
                 '-DMUMPS_LIBRARY_NAMES=dmumps;mumps_common;pord' # order is important!
-#                '-DMUMPS_LIBRARY_DIRS=%s;%s' % (spec['mumps'].prefix.lib,spec['scalapack'].prefix.lib),
-#                '-DMUMPS_LIBRARY_NAMES=dmumps;mumps_common;pord;scalapack' # order is important!
             ])
 
         # scalapack
         options.extend([
-            '-DTPL_ENABLE_SCALAPACK:BOOL=ON', #FIXME: Undefined symbols for architecture x86_64: "_blacs_gridinfo__", referenced from: Amesos_Scalapack::RedistributeA() in Amesos_Scalapack.cpp.o
+            '-DTPL_ENABLE_SCALAPACK:BOOL=ON',
             '-DSCALAPACK_LIBRARY_NAMES=scalapack' # FIXME: for MKL it's mkl_scalapack_lp64;mkl_blacs_mpich_lp64
         ])
 

From 21e81e92a9ac88bd498bd65aa9b77a43c27da881 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Fri, 25 Mar 2016 12:05:48 +0100
Subject: [PATCH 137/230] try to disable VerifyFortranC tests on Darwin

---
 var/spack/repos/builtin/packages/trilinos/package.py | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py
index 1dba2b8db39..0c7d8a79673 100644
--- a/var/spack/repos/builtin/packages/trilinos/package.py
+++ b/var/spack/repos/builtin/packages/trilinos/package.py
@@ -110,6 +110,13 @@ def install(self, spec, prefix):
             '-DTrilinos_EXTRA_LINK_FLAGS:STRING=-L%s/ -lgfortran' % libgfortran,
             '-DTrilinos_ENABLE_Fortran=ON'
         ])
+        # FIXME:
+        # VerifyFortranC test of CMake does not contain -lgfortran and thus fails.
+        # This could be GCC/CMake related, but appears at least on OSX with Clang@7.0.2 and GNU Fortran@5.3.0
+        if sys.platform == 'darwin':
+            options.extend([
+                '-DTrilinos_SKIP_FORTRANCINTERFACE_VERIFY_TEST:BOOL=TRUE'
+            ])
 
         # for build-debug only:
         options.extend([

From 26a72619aed8684019ab331889b276b8883b76c8 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Fri, 25 Mar 2016 12:42:26 +0100
Subject: [PATCH 138/230] add missing sys

---
 var/spack/repos/builtin/packages/trilinos/package.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py
index 0c7d8a79673..e077dfbbfd1 100644
--- a/var/spack/repos/builtin/packages/trilinos/package.py
+++ b/var/spack/repos/builtin/packages/trilinos/package.py
@@ -1,5 +1,5 @@
 from spack import *
-import os
+import os, sys
 
 # Trilinos is complicated to build, as an inspiration a couple of links to other repositories which build it:
 # https://github.com/hpcugent/easybuild-easyblocks/blob/master/easybuild/easyblocks/t/trilinos.py#L111

From 5172f09b9f966a3f1be438bab972a0267cccc73b Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Fri, 25 Mar 2016 16:47:48 +0100
Subject: [PATCH 139/230] builds on OSX again (modulo CC wrappers are solved)

---
 .../builtin/packages/trilinos/package.py      | 19 ++++++++++++-------
 1 file changed, 12 insertions(+), 7 deletions(-)

diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py
index e077dfbbfd1..3003b4ab53f 100644
--- a/var/spack/repos/builtin/packages/trilinos/package.py
+++ b/var/spack/repos/builtin/packages/trilinos/package.py
@@ -113,15 +113,15 @@ def install(self, spec, prefix):
         # FIXME:
         # VerifyFortranC test of CMake does not contain -lgfortran and thus fails.
         # This could be GCC/CMake related, but appears at least on OSX with Clang@7.0.2 and GNU Fortran@5.3.0
-        if sys.platform == 'darwin':
-            options.extend([
-                '-DTrilinos_SKIP_FORTRANCINTERFACE_VERIFY_TEST:BOOL=TRUE'
-            ])
+        #if sys.platform == 'darwin':
+        #    options.extend([
+        #        '-DTrilinos_SKIP_FORTRANCINTERFACE_VERIFY_TEST:BOOL=TRUE'
+        #    ])
 
         # for build-debug only:
-        options.extend([
-           '-DCMAKE_VERBOSE_MAKEFILE:BOOL=TRUE'
-        ])
+        #options.extend([
+        #   '-DCMAKE_VERBOSE_MAKEFILE:BOOL=TRUE'
+        #])
 
         # suite-sparse related
         if '+suite-sparse' in spec:
@@ -194,6 +194,11 @@ def install(self, spec, prefix):
             '-DTrilinos_ENABLE_Pike=OFF',
             '-DTrilinos_ENABLE_STK=OFF'
         ])
+        if sys.platform == 'darwin':
+            options.extend([
+                '-DTrilinos_ENABLE_FEI=OFF'
+            ])
+
 
         with working_dir('spack-build', create=True):
             cmake('..', *options)

From eec50b524bdf9e04f9e3536bc389ce633133373b Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Fri, 25 Mar 2016 16:58:14 +0100
Subject: [PATCH 140/230] minor cleanup

---
 .../builtin/packages/trilinos/package.py      | 46 ++++++++++++++-----
 1 file changed, 35 insertions(+), 11 deletions(-)

diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py
index 3003b4ab53f..b1caca96ff7 100644
--- a/var/spack/repos/builtin/packages/trilinos/package.py
+++ b/var/spack/repos/builtin/packages/trilinos/package.py
@@ -28,6 +28,7 @@ class Trilinos(Package):
     variant('superlu-dist', default=True,  description='Compile with SuperluDist solvers')
     variant('hypre',        default=True,  description='Compile with Hypre preconditioner')
     variant('hdf5',         default=True,  description='Compile with HDF5')
+    variant('scalapack',    default=True,  description='Compile with Scalapack')
     variant('suite-sparse', default=True,  description='Compile with SuiteSparse solvers')
     variant('python',       default=True,  description='Build python wrappers')
     variant('shared',       default=True,  description='Enables the build of shared libraries')
@@ -110,13 +111,6 @@ def install(self, spec, prefix):
             '-DTrilinos_EXTRA_LINK_FLAGS:STRING=-L%s/ -lgfortran' % libgfortran,
             '-DTrilinos_ENABLE_Fortran=ON'
         ])
-        # FIXME:
-        # VerifyFortranC test of CMake does not contain -lgfortran and thus fails.
-        # This could be GCC/CMake related, but appears at least on OSX with Clang@7.0.2 and GNU Fortran@5.3.0
-        #if sys.platform == 'darwin':
-        #    options.extend([
-        #        '-DTrilinos_SKIP_FORTRANCINTERFACE_VERIFY_TEST:BOOL=TRUE'
-        #    ])
 
         # for build-debug only:
         #options.extend([
@@ -135,6 +129,11 @@ def install(self, spec, prefix):
                 '-DUMFPACK_INCLUDE_DIRS:PATH=%s' % spec['suite-sparse'].prefix.include,
                 '-DUMFPACK_LIBRARY_NAMES=umfpack;amd;colamd;cholmod;suitesparseconfig'
             ])
+        else:
+            options.extend([
+                '-DTPL_ENABLE_Cholmod:BOOL=OFF',
+                '-DTPL_ENABLE_UMFPACK:BOOL=OFF',
+            ])
 
         # metis / parmetis
         if '+parmetis' in spec: # metis is required, see variants_check()
@@ -148,6 +147,11 @@ def install(self, spec, prefix):
                 '-DParMETIS_LIBRARY_NAMES=parmetis;metis',
                 '-DTPL_ParMETIS_INCLUDE_DIRS=%s' % spec['parmetis'].prefix.include
             ])
+        else:
+            options.extend([
+                '-DTPL_ENABLE_METIS:BOOL=OFF',
+                '-DTPL_ENABLE_ParMETIS:BOOL=OFF',
+            ])
 
         # mumps
         if '+mumps' in spec:
@@ -156,12 +160,22 @@ def install(self, spec, prefix):
                 '-DMUMPS_LIBRARY_DIRS=%s' % spec['mumps'].prefix.lib,
                 '-DMUMPS_LIBRARY_NAMES=dmumps;mumps_common;pord' # order is important!
             ])
+        else:
+            options.extend([
+                '-DTPL_ENABLE_MUMPS:BOOL=OFF',
+            ])
 
         # scalapack
-        options.extend([
-            '-DTPL_ENABLE_SCALAPACK:BOOL=ON',
-            '-DSCALAPACK_LIBRARY_NAMES=scalapack' # FIXME: for MKL it's mkl_scalapack_lp64;mkl_blacs_mpich_lp64
-        ])
+        if '+scalapack' in spec:
+            options.extend([
+                '-DTPL_ENABLE_SCALAPACK:BOOL=ON',
+                '-DSCALAPACK_LIBRARY_NAMES=scalapack' # FIXME: for MKL it's mkl_scalapack_lp64;mkl_blacs_mpich_lp64
+            ])
+        else:
+            options.extend([
+                '-DTPL_ENABLE_SCALAPACK:BOOL=OFF',
+            ])
+
 
         # superlu-dist:
         if '+superlu-dist' in spec:
@@ -181,12 +195,22 @@ def install(self, spec, prefix):
                 options.extend([
                     '-DHAVE_SUPERLUDIST_LUSTRUCTINIT_2ARG:BOOL=ON'
                 ])
+        else:
+            options.extend([
+                '-DTPL_ENABLE_SuperLUDist:BOOL=OFF',
+            ])
+
 
         # python
         if '~python' in spec:
             options.extend([
                 '-DTrilinos_ENABLE_PyTrilinos:BOOL=OFF'
             ])
+        else:
+            options.extend([
+                '-DTrilinos_ENABLE_PyTrilinos:BOOL=ON'
+            ])
+
 
         # disable due to compiler / config errors:
         options.extend([

From 6699399e5191004ed924b9a8916ec1ae61223000 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Fri, 25 Mar 2016 17:00:42 +0100
Subject: [PATCH 141/230] add when to depends_on scalapack

---
 var/spack/repos/builtin/packages/trilinos/package.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py
index b1caca96ff7..8b664051371 100644
--- a/var/spack/repos/builtin/packages/trilinos/package.py
+++ b/var/spack/repos/builtin/packages/trilinos/package.py
@@ -49,7 +49,7 @@ class Trilinos(Package):
     depends_on('netcdf+mpi')
     depends_on('parmetis',when='+parmetis')
     depends_on('mumps+metis+parmetis+shared',when='+mumps') # build errors with static libs
-    depends_on('scalapack')
+    depends_on('scalapack',when='+scalapack')
     depends_on('superlu-dist',when='+superlu-dist')
     depends_on('hypre',when='+hypre')
     depends_on('hdf5+mpi',when='+hdf5')

From c7011d21aa95145c7b3978f4220b211e39c9ecf2 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Fri, 25 Mar 2016 22:15:39 +0100
Subject: [PATCH 142/230] update dependencies. Builds fine on OSX

---
 .../repos/builtin/packages/dealii/package.py  | 32 +++++++++----------
 1 file changed, 16 insertions(+), 16 deletions(-)

diff --git a/var/spack/repos/builtin/packages/dealii/package.py b/var/spack/repos/builtin/packages/dealii/package.py
index cddf5cd98ba..5a50481b9b8 100644
--- a/var/spack/repos/builtin/packages/dealii/package.py
+++ b/var/spack/repos/builtin/packages/dealii/package.py
@@ -12,21 +12,21 @@ class Dealii(Package):
     depends_on ("lapack")
     depends_on ("mpi")
 
-    #depends_on ("arpack")
+    depends_on ("arpack-ng")
     depends_on ("boost")
-    #depends_on ("doxygen")
-    depends_on ("hdf5+mpi")
+    depends_on ("doxygen")
+    depends_on ("hdf5+mpi~cxx") #FIXME NetCDF declares dependency with ~cxx, why?
     depends_on ("metis")
-    #depends_on "muparser"
+    depends_on ("muparser")
     depends_on ("netcdf")
-    #depends_on ("numdiff")
-    #depends_on ("oce")
+    #depends_on ("numdiff") #FIXME
+    depends_on ("oce")
     depends_on ("p4est")
     depends_on ("parmetis")
     depends_on ("petsc")
-    #depends_on ("slepc")
-    depends_on ("SuiteSparse")
-    #depends_on "tbb"
+    depends_on ("slepc")
+    depends_on ("suite-sparse")
+    depends_on ("tbb")
     depends_on ("trilinos")
 
     def install(self, spec, prefix):
@@ -42,21 +42,21 @@ def install(self, spec, prefix):
             '-DCMAKE_BUILD_TYPE=DebugRelease',
             '-DDEAL_II_WITH_THREADS:BOOL=ON'
             '-DDEAL_II_WITH_MPI:BOOL=ON',
-            '-DCMAKE_C_COMPILER=%s' % join_path(self.spec['mpi'].prefix.bin, 'mpicc'),
+            '-DCMAKE_C_COMPILER=%s' % join_path(self.spec['mpi'].prefix.bin, 'mpicc'), # FIXME: avoid hardcoding mpi wrappers names
             '-DCMAKE_CXX_COMPILER=%s' % join_path(self.spec['mpi'].prefix.bin, 'mpic++'),
             '-DCMAKE_Fortran_COMPILER=%s' % join_path(self.spec['mpi'].prefix.bin, 'mpif90'),
-            #'-DARPACK_DIR=%s' %  ,
+            '-DARPACK_DIR=%s' % spec['arpack-ng'].prefix,
             '-DBOOST_DIR=%s' % spec['boost'].prefix,
             '-DHDF5_DIR=%s' % spec['hdf5'].prefix,
             '-DMETIS_DIR=%s' % spec['metis'].prefix,
-            #'-DMUPARSER_DIR=%s '
+            '-DMUPARSER_DIR=%s ' % spec['muparser'].prefix,
             '-DNETCDF_DIR=%s' % spec['netcdf'].prefix,
-            #'-DOPENCASCADE_DIR=
+            '-DOPENCASCADE_DIR=%s' % spec['oce'].prefix,
             '-DP4EST_DIR=%s' % spec['p4est'].prefix,
             '-DPETSC_DIR=%s' % spec['petsc'].prefix,
-            #'-DSLEPC_DIR=
-            '-DUMFPACK_DIR=%s' % spec['SuiteSparse'].prefix,
-            #'-DTBB_DIR=%s'
+            '-DSLEPC_DIR=%s' % spec['slepc'].prefix,
+            '-DUMFPACK_DIR=%s' % spec['suite-sparse'].prefix,
+            '-DTBB_DIR=%s' % spec['tbb'].prefix,
             '-DTRILINOS_DIR=%s' % spec['trilinos'].prefix
         ])
 

From 497adc3b42191c000323c55aae5da32fab901265 Mon Sep 17 00:00:00 2001
From: Elizabeth F <rpf2116@columbia.edu>
Date: Fri, 25 Mar 2016 22:45:19 -0400
Subject: [PATCH 143/230] Added new version; old versions don't work with
 Python3.

---
 var/spack/repos/builtin/packages/py-cython/package.py | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/var/spack/repos/builtin/packages/py-cython/package.py b/var/spack/repos/builtin/packages/py-cython/package.py
index 68eb735ad93..4d728fa8fbd 100644
--- a/var/spack/repos/builtin/packages/py-cython/package.py
+++ b/var/spack/repos/builtin/packages/py-cython/package.py
@@ -3,10 +3,13 @@
 class PyCython(Package):
     """The Cython compiler for writing C extensions for the Python language."""
     homepage = "https://pypi.python.org/pypi/cython"
-    url      = "https://pypi.python.org/packages/source/C/Cython/cython-0.22.tar.gz"
+    url      = "https://pypi.python.org/packages/source/C/Cython/Cython-0.22.tar.gz"
 
-    version('0.21.2', 'd21adb870c75680dc857cd05d41046a4')
+    version('0.23.4', '157df1f69bcec6b56fd97e0f2e057f6e')
+
+    # These versions contain illegal Python3 code...
     version('0.22', '1ae25add4ef7b63ee9b4af697300d6b6')
+    version('0.21.2', 'd21adb870c75680dc857cd05d41046a4')
 
     extends('python')
 

From f603c82e814ebc59ba03b0b83be86f1a4bfcbd94 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Sat, 26 Mar 2016 18:43:55 +0100
Subject: [PATCH 144/230] qualify Amesos link errors

---
 var/spack/repos/builtin/packages/trilinos/package.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py
index 8b664051371..0ba7a51b8b9 100644
--- a/var/spack/repos/builtin/packages/trilinos/package.py
+++ b/var/spack/repos/builtin/packages/trilinos/package.py
@@ -48,7 +48,7 @@ class Trilinos(Package):
     depends_on('mpi')
     depends_on('netcdf+mpi')
     depends_on('parmetis',when='+parmetis')
-    depends_on('mumps+metis+parmetis+shared',when='+mumps') # build errors with static libs
+    depends_on('mumps+metis+parmetis+shared',when='+mumps') # Amesos link errors with static: "__gfortran_adjustl", referenced from: _dmumps_ in libdmumps.a(dmumps_driver.o) "_mpi_abort_", referenced from: _mumps_abort_ in libmumps_common.a(tools_common.o)
     depends_on('scalapack',when='+scalapack')
     depends_on('superlu-dist',when='+superlu-dist')
     depends_on('hypre',when='+hypre')

From 965ce633c311e2bcb765f5e9900f0da6205f9c23 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Sat, 26 Mar 2016 18:51:59 +0100
Subject: [PATCH 145/230] cleanup variants

---
 .../builtin/packages/trilinos/package.py      | 40 ++++++-------------
 1 file changed, 13 insertions(+), 27 deletions(-)

diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py
index 0ba7a51b8b9..48bffc65e0d 100644
--- a/var/spack/repos/builtin/packages/trilinos/package.py
+++ b/var/spack/repos/builtin/packages/trilinos/package.py
@@ -22,13 +22,11 @@ class Trilinos(Package):
     version('11.14.2', 'a43590cf896c677890d75bfe75bc6254')
     version('11.14.1', '40febc57f76668be8b6a77b7607bb67f')
 
-    variant('metis',        default=True,  description='Compile with METIS')
-    variant('parmetis',     default=True,  description='Compile with ParMETIS')
+    variant('metis',        default=True,  description='Compile with METIS and ParMETIS')
     variant('mumps',        default=True,  description='Compile with support for MUMPS solvers')
     variant('superlu-dist', default=True,  description='Compile with SuperluDist solvers')
     variant('hypre',        default=True,  description='Compile with Hypre preconditioner')
     variant('hdf5',         default=True,  description='Compile with HDF5')
-    variant('scalapack',    default=True,  description='Compile with Scalapack')
     variant('suite-sparse', default=True,  description='Compile with SuiteSparse solvers')
     variant('python',       default=True,  description='Build python wrappers')
     variant('shared',       default=True,  description='Enables the build of shared libraries')
@@ -47,9 +45,9 @@ class Trilinos(Package):
     # MPI related dependencies
     depends_on('mpi')
     depends_on('netcdf+mpi')
-    depends_on('parmetis',when='+parmetis')
-    depends_on('mumps+metis+parmetis+shared',when='+mumps') # Amesos link errors with static: "__gfortran_adjustl", referenced from: _dmumps_ in libdmumps.a(dmumps_driver.o) "_mpi_abort_", referenced from: _mumps_abort_ in libmumps_common.a(tools_common.o)
-    depends_on('scalapack',when='+scalapack')
+    depends_on('parmetis',when='+metis')
+    depends_on('mumps+mpi+metis+parmetis+shared',when='+mumps') # Amesos link errors with static: "__gfortran_adjustl", referenced from: _dmumps_ in libdmumps.a(dmumps_driver.o) "_mpi_abort_", referenced from: _mumps_abort_ in libmumps_common.a(tools_common.o)
+    depends_on('scalapack',when='+mumps')
     depends_on('superlu-dist',when='+superlu-dist')
     depends_on('hypre',when='+hypre')
     depends_on('hdf5+mpi',when='+hdf5')
@@ -60,11 +58,8 @@ class Trilinos(Package):
 
     # check that the combination of variants makes sense
     def variants_check(self):
-        if '+parmetis' in self.spec and '+metis' not in self.spec:
-            raise RuntimeError('You cannot use the variant parmetis without metis')
-
-        if '+mumps' in self.spec and '+parmetis' not in self.spec:
-            raise RuntimeError('You cannot use the variant mumps without parmetis')
+        if '+mumps' in self.spec and '+metis' not in self.spec:
+            raise RuntimeError('You cannot use the variant mumps without metis')
 
         if '+superlu-dist' in self.spec and self.spec.satisfies('@:11.4.3'):
             # For Trilinos v11 we need to force SuperLUDist=OFF,
@@ -136,7 +131,7 @@ def install(self, spec, prefix):
             ])
 
         # metis / parmetis
-        if '+parmetis' in spec: # metis is required, see variants_check()
+        if '+metis' in spec:
             options.extend([
                 '-DTPL_ENABLE_METIS:BOOL=ON',
                 '-DMETIS_LIBRARY_DIRS=%s' % spec['metis'].prefix.lib,
@@ -153,30 +148,21 @@ def install(self, spec, prefix):
                 '-DTPL_ENABLE_ParMETIS:BOOL=OFF',
             ])
 
-        # mumps
+        # mumps / scalapack
         if '+mumps' in spec:
             options.extend([
                 '-DTPL_ENABLE_MUMPS:BOOL=ON',
                 '-DMUMPS_LIBRARY_DIRS=%s' % spec['mumps'].prefix.lib,
-                '-DMUMPS_LIBRARY_NAMES=dmumps;mumps_common;pord' # order is important!
-            ])
-        else:
-            options.extend([
-                '-DTPL_ENABLE_MUMPS:BOOL=OFF',
-            ])
-
-        # scalapack
-        if '+scalapack' in spec:
-            options.extend([
+                '-DMUMPS_LIBRARY_NAMES=dmumps;mumps_common;pord', # order is important!
                 '-DTPL_ENABLE_SCALAPACK:BOOL=ON',
                 '-DSCALAPACK_LIBRARY_NAMES=scalapack' # FIXME: for MKL it's mkl_scalapack_lp64;mkl_blacs_mpich_lp64
             ])
         else:
             options.extend([
+                '-DTPL_ENABLE_MUMPS:BOOL=OFF',
                 '-DTPL_ENABLE_SCALAPACK:BOOL=OFF',
             ])
 
-
         # superlu-dist:
         if '+superlu-dist' in spec:
             # Amesos, conflicting types of double and complex SLU_D
@@ -202,13 +188,13 @@ def install(self, spec, prefix):
 
 
         # python
-        if '~python' in spec:
+        if '+python' in spec:
             options.extend([
-                '-DTrilinos_ENABLE_PyTrilinos:BOOL=OFF'
+                '-DTrilinos_ENABLE_PyTrilinos:BOOL=ON'
             ])
         else:
             options.extend([
-                '-DTrilinos_ENABLE_PyTrilinos:BOOL=ON'
+                '-DTrilinos_ENABLE_PyTrilinos:BOOL=OFF'
             ])
 
 

From 9c391bbda1c8379dd60cf21d82779db704183f32 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Sat, 26 Mar 2016 20:52:08 +0100
Subject: [PATCH 146/230] minor changes to variants

---
 var/spack/repos/builtin/packages/dealii/package.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/var/spack/repos/builtin/packages/dealii/package.py b/var/spack/repos/builtin/packages/dealii/package.py
index 5a50481b9b8..19bb3814be5 100644
--- a/var/spack/repos/builtin/packages/dealii/package.py
+++ b/var/spack/repos/builtin/packages/dealii/package.py
@@ -12,7 +12,7 @@ class Dealii(Package):
     depends_on ("lapack")
     depends_on ("mpi")
 
-    depends_on ("arpack-ng")
+    depends_on ("arpack-ng+mpi")
     depends_on ("boost")
     depends_on ("doxygen")
     depends_on ("hdf5+mpi~cxx") #FIXME NetCDF declares dependency with ~cxx, why?
@@ -23,7 +23,7 @@ class Dealii(Package):
     depends_on ("oce")
     depends_on ("p4est")
     depends_on ("parmetis")
-    depends_on ("petsc")
+    depends_on ("petsc+mpi")
     depends_on ("slepc")
     depends_on ("suite-sparse")
     depends_on ("tbb")

From 11ca06b1045283e2c89dc84a91ceb88fcadb6163 Mon Sep 17 00:00:00 2001
From: Elizabeth F <rpf2116@columbia.edu>
Date: Sat, 26 Mar 2016 20:35:34 -0400
Subject: [PATCH 147/230] Added new py-cython version

---
 var/spack/repos/builtin/packages/py-cython/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/py-cython/package.py b/var/spack/repos/builtin/packages/py-cython/package.py
index 4d728fa8fbd..072355026e1 100644
--- a/var/spack/repos/builtin/packages/py-cython/package.py
+++ b/var/spack/repos/builtin/packages/py-cython/package.py
@@ -5,6 +5,7 @@ class PyCython(Package):
     homepage = "https://pypi.python.org/pypi/cython"
     url      = "https://pypi.python.org/packages/source/C/Cython/Cython-0.22.tar.gz"
 
+    version('0.23.5', '66b62989a67c55af016c916da36e7514')
     version('0.23.4', '157df1f69bcec6b56fd97e0f2e057f6e')
 
     # These versions contain illegal Python3 code...

From 9b130e1d199bcff10903e981bd7592ed941d0107 Mon Sep 17 00:00:00 2001
From: citibeth <rpf2116@columbia.edu>
Date: Sat, 26 Mar 2016 20:42:35 -0400
Subject: [PATCH 148/230] Added googletest package.

---
 .../builtin/packages/googletest/package.py    | 40 +++++++++++++++++++
 1 file changed, 40 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/googletest/package.py

diff --git a/var/spack/repos/builtin/packages/googletest/package.py b/var/spack/repos/builtin/packages/googletest/package.py
new file mode 100644
index 00000000000..ed27afa10ce
--- /dev/null
+++ b/var/spack/repos/builtin/packages/googletest/package.py
@@ -0,0 +1,40 @@
+# FIXME:
+# This is a template package file for Spack.  We've conveniently
+# put "FIXME" labels next to all the things you'll want to change.
+#
+# Once you've edited all the FIXME's, delete this whole message,
+# save this file, and test out your package like this:
+#
+#     spack install googletest
+#
+# You can always get back here to change things with:
+#
+#     spack edit googletest
+#
+# See the spack documentation for more information on building
+# packages.
+#
+from spack import *
+
+class Googletest(Package):
+    """Google test framework for C++.  Also called gtest."""
+    homepage = "https://github.com/google/googletest"
+    url      = "https://github.com/google/googletest/tarball/release-1.7.0"
+
+    version('1.7.0', '5eaf03ed925a47b37c8e1d559eb19bc4')
+
+    depends_on("cmake")
+
+    def install(self, spec, prefix):
+        which('cmake')('.', *std_cmake_args)
+
+        make()
+
+        # Google Test doesn't have a make install
+        # We have to do our own install here.
+	install_tree('include', prefix.include)
+
+        mkdirp(prefix.lib)
+	install('./libgtest.a', '%s' % prefix.lib)
+	install('./libgtest_main.a', '%s' % prefix.lib)
+

From a82a587b3298ffec0c11ddf1c9639c6de228fa6a Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Sun, 27 Mar 2016 06:17:43 +0200
Subject: [PATCH 149/230] lower requirement on mumps

---
 var/spack/repos/builtin/packages/trilinos/package.py | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py
index 48bffc65e0d..e8c4bcd7e21 100644
--- a/var/spack/repos/builtin/packages/trilinos/package.py
+++ b/var/spack/repos/builtin/packages/trilinos/package.py
@@ -46,7 +46,7 @@ class Trilinos(Package):
     depends_on('mpi')
     depends_on('netcdf+mpi')
     depends_on('parmetis',when='+metis')
-    depends_on('mumps+mpi+metis+parmetis+shared',when='+mumps') # Amesos link errors with static: "__gfortran_adjustl", referenced from: _dmumps_ in libdmumps.a(dmumps_driver.o) "_mpi_abort_", referenced from: _mumps_abort_ in libmumps_common.a(tools_common.o)
+    depends_on('mumps+mpi+shared',when='+mumps') # Amesos link errors with static: "__gfortran_adjustl", referenced from: _dmumps_ in libdmumps.a(dmumps_driver.o) "_mpi_abort_", referenced from: _mumps_abort_ in libmumps_common.a(tools_common.o)
     depends_on('scalapack',when='+mumps')
     depends_on('superlu-dist',when='+superlu-dist')
     depends_on('hypre',when='+hypre')
@@ -58,9 +58,6 @@ class Trilinos(Package):
 
     # check that the combination of variants makes sense
     def variants_check(self):
-        if '+mumps' in self.spec and '+metis' not in self.spec:
-            raise RuntimeError('You cannot use the variant mumps without metis')
-
         if '+superlu-dist' in self.spec and self.spec.satisfies('@:11.4.3'):
             # For Trilinos v11 we need to force SuperLUDist=OFF,
             # since only the deprecated SuperLUDist v3.3 together with an Amesos patch

From 9cff241ad52ba628a0bdad47cee98bbbf6ba5511 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Sun, 27 Mar 2016 10:39:09 +0200
Subject: [PATCH 150/230] fix install name on Darwin

---
 var/spack/repos/builtin/packages/trilinos/package.py | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py
index e8c4bcd7e21..72f904d8aa8 100644
--- a/var/spack/repos/builtin/packages/trilinos/package.py
+++ b/var/spack/repos/builtin/packages/trilinos/package.py
@@ -1,5 +1,5 @@
 from spack import *
-import os, sys
+import os, sys, glob
 
 # Trilinos is complicated to build, as an inspiration a couple of links to other repositories which build it:
 # https://github.com/hpcugent/easybuild-easyblocks/blob/master/easybuild/easyblocks/t/trilinos.py#L111
@@ -222,3 +222,10 @@ def install(self, spec, prefix):
             # A workaround it to remove PyTrilinos from the COMPONENTS_LIST :
             if '+python' in self.spec:
                 filter_file(r'(SET\(COMPONENTS_LIST.*)(PyTrilinos;)(.*)',  (r'\1\3'),  '%s/cmake/Trilinos/TrilinosConfig.cmake' % prefix.lib)
+
+            # The shared libraries are not installed correctly on Darwin; correct this
+            if (sys.platform == 'darwin') and ('+shared' in spec):
+                fs = glob.glob(join_path(prefix.lib,"*.dylib"))
+                install_name_tool = which('install_name_tool')
+                for f in fs:
+                    install_name_tool('-id',f,f)

From 69ebc8173e1843ea570d78ac27465b0ea32c753d Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Sun, 27 Mar 2016 16:04:13 +0200
Subject: [PATCH 151/230] use global tool to fix install_name

---
 var/spack/repos/builtin/packages/trilinos/package.py | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py
index 72f904d8aa8..6608f64ea72 100644
--- a/var/spack/repos/builtin/packages/trilinos/package.py
+++ b/var/spack/repos/builtin/packages/trilinos/package.py
@@ -225,7 +225,4 @@ def install(self, spec, prefix):
 
             # The shared libraries are not installed correctly on Darwin; correct this
             if (sys.platform == 'darwin') and ('+shared' in spec):
-                fs = glob.glob(join_path(prefix.lib,"*.dylib"))
-                install_name_tool = which('install_name_tool')
-                for f in fs:
-                    install_name_tool('-id',f,f)
+                fix_darwin_install_name(prefix.lib)

From cc42391e0fa6eda490c4aeffcbfbae584f077db3 Mon Sep 17 00:00:00 2001
From: citibeth <rpf2116@columbia.edu>
Date: Sun, 27 Mar 2016 11:06:10 -0400
Subject: [PATCH 152/230] Added py-netcdf

---
 .../repos/builtin/packages/py-netcdf/package.py  | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/py-netcdf/package.py

diff --git a/var/spack/repos/builtin/packages/py-netcdf/package.py b/var/spack/repos/builtin/packages/py-netcdf/package.py
new file mode 100644
index 00000000000..7faa15ad253
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-netcdf/package.py
@@ -0,0 +1,16 @@
+from spack import *
+
+class PyNetcdf(Package):
+    """Python interface to the netCDF Library."""
+    homepage = "http://unidata.github.io/netcdf4-python"
+    url      = "https://github.com/Unidata/netcdf4-python/tarball/v1.2.3.1rel"
+
+    version('1.2.3.1', '4fc4320d4f2a77b894ebf8da1c9895af')
+
+    extends('python')
+    depends_on('py-numpy')
+    depends_on('py-cython')
+    depends_on('netcdf')
+
+    def install(self, spec, prefix):
+        python('setup.py', 'install', '--prefix=%s' % prefix)

From 439d3b3ddb4e53721b216bd19bec1e8fa16faf89 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Sun, 27 Mar 2016 17:38:25 +0200
Subject: [PATCH 153/230] mumps: add install_name / soname

---
 var/spack/repos/builtin/packages/mumps/package.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/var/spack/repos/builtin/packages/mumps/package.py b/var/spack/repos/builtin/packages/mumps/package.py
index b295857ab59..26440ab7c81 100644
--- a/var/spack/repos/builtin/packages/mumps/package.py
+++ b/var/spack/repos/builtin/packages/mumps/package.py
@@ -113,13 +113,13 @@ def write_makefile_inc(self):
                 # Building dylibs with mpif90 causes segfaults on 10.8 and 10.10. Use gfortran. (Homebrew)
                 makefile_conf.extend([
                     'LIBEXT=.dylib',
-                    'AR=%s -dynamiclib -undefined dynamic_lookup -o ' % os.environ['FC'],
+                    'AR=%s -dynamiclib -Wl,-install_name -Wl,%s/$(notdir $@) -undefined dynamic_lookup -o ' % (os.environ['FC'],prefix.lib),
                     'RANLIB=echo'
                 ])
             else:
                 makefile_conf.extend([
                     'LIBEXT=.so',
-                    'AR=$(FL) -shared -o',
+                    'AR=$(FL) -shared -Wl,-soname -Wl,%s/$(notdir $@) -o' % prefix.lib,
                     'RANLIB=echo'
                 ])
         else:

From b0b882cbb3d903a85413acb0439a02d6ac9e26fc Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Sat, 26 Mar 2016 00:56:19 -0700
Subject: [PATCH 154/230] Speed up directives  by skipping debug info in stack
 traversal.

- `caller_locals()` doesn't need debug info, only frame locals.
- `get_calling_module()` doesn't either.

- Changed calls to `inspect.stack()` -> `inspect.stack(0)`
---
 lib/spack/llnl/util/lang.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/lib/spack/llnl/util/lang.py b/lib/spack/llnl/util/lang.py
index 13d301f84e6..3b4e2c8352a 100644
--- a/lib/spack/llnl/util/lang.py
+++ b/lib/spack/llnl/util/lang.py
@@ -117,7 +117,8 @@ def caller_locals():
        scope.  Yes, this is some black magic, and yes it's useful
        for implementing things like depends_on and provides.
     """
-    stack = inspect.stack()
+    # Passing zero here skips line context for speed.
+    stack = inspect.stack(0)
     try:
         return stack[2][0].f_locals
     finally:
@@ -128,7 +129,8 @@ def get_calling_module_name():
     """Make sure that the caller is a class definition, and return the
        enclosing module's name.
     """
-    stack = inspect.stack()
+    # Passing zero here skips line context for speed.
+    stack = inspect.stack(0)
     try:
         # Make sure locals contain __module__
         caller_locals = stack[2][0].f_locals

From dce590fb21af844230727b283f6c8bf759ea805c Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Sat, 26 Mar 2016 19:59:02 -0700
Subject: [PATCH 155/230] Add a dso_suffix variable to build_environment

- Consolidate this in one place so that we don't have to do it in every build.

- Will update further once better OS support is committed.  Shoudl
  really be an attribute of the forthcoming `Platform` class.
---
 lib/spack/spack/build_environment.py | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/lib/spack/spack/build_environment.py b/lib/spack/spack/build_environment.py
index 119a255a349..640db0c1d16 100644
--- a/lib/spack/spack/build_environment.py
+++ b/lib/spack/spack/build_environment.py
@@ -59,6 +59,11 @@
 SPACK_DEBUG_LOG_DIR    = 'SPACK_DEBUG_LOG_DIR'
 
 
+# Platform-specific library suffix.
+dso_suffix = 'dylib' if sys.platform == 'darwin' else 'so'
+
+
+
 class MakeExecutable(Executable):
     """Special callable executable object for make so the user can
        specify parallel or not on a per-invocation basis.  Using
@@ -246,6 +251,9 @@ def set_module_variables_for_package(pkg, module):
     # a Prefix object.
     m.prefix  = pkg.prefix
 
+    # Platform-specific library suffix.
+    m.dso_suffix = dso_suffix
+
 
 def get_rpaths(pkg):
     """Get a list of all the rpaths for a package."""

From cde33205827edbed988ec4548c983ff93e9445c6 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Sat, 26 Mar 2016 20:00:28 -0700
Subject: [PATCH 156/230] Add a method to find the containing directory of a
 library.

---
 lib/spack/llnl/util/filesystem.py | 17 ++++++++++++++++-
 1 file changed, 16 insertions(+), 1 deletion(-)

diff --git a/lib/spack/llnl/util/filesystem.py b/lib/spack/llnl/util/filesystem.py
index c4665c284cf..92f9ca29834 100644
--- a/lib/spack/llnl/util/filesystem.py
+++ b/lib/spack/llnl/util/filesystem.py
@@ -27,7 +27,7 @@
            'force_remove', 'join_path', 'ancestor', 'can_access', 'filter_file',
            'FileFilter', 'change_sed_delimiter', 'is_exe', 'force_symlink',
            'set_executable', 'copy_mode', 'unset_executable_mode',
-           'remove_dead_links', 'remove_linked_tree']
+           'remove_dead_links', 'remove_linked_tree', 'find_library_path']
 
 import os
 import sys
@@ -392,3 +392,18 @@ def remove_linked_tree(path):
             os.unlink(path)
         else:
             shutil.rmtree(path, True)
+
+
+def find_library_path(libname, *paths):
+    """Searches for a file called <libname> in each path.
+
+    Return:
+      directory where the library was found, if found.  None otherwise.
+
+    """
+    for path in paths:
+        library = join_path(path, libname)
+        if os.path.exists(library):
+            return path
+    return None
+

From 66bb71534b3ab7eaf7b27743efc0ecf9763e4982 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Sat, 26 Mar 2016 20:02:08 -0700
Subject: [PATCH 157/230] Better blas/lapack and scipy packages: more robust,
 added `shared` variants.

- py-scipy now builds with netlib-lapack, openblas, and atlas.
- started a convention for passing lib info from blas/lapack implementations.

- Improved netlib-lapack:
  - Also build static libs when `shared` variant is enabled.
  - Enable CBLAS  build
    - needed minor patch to build correctly.

- Added `shared` variant to OpenBLAS.
  - Made OpenBLAS build properly shared and static.
---
 .../builtin/packages/netlib-lapack/package.py | 40 ++++++++++++--
 .../builtin/packages/openblas/package.py      | 52 +++++++++++++++----
 .../builtin/packages/py-scipy/package.py      | 12 +++--
 3 files changed, 88 insertions(+), 16 deletions(-)

diff --git a/var/spack/repos/builtin/packages/netlib-lapack/package.py b/var/spack/repos/builtin/packages/netlib-lapack/package.py
index c4b7ce3b048..05436332ac5 100644
--- a/var/spack/repos/builtin/packages/netlib-lapack/package.py
+++ b/var/spack/repos/builtin/packages/netlib-lapack/package.py
@@ -31,8 +31,16 @@ class NetlibLapack(Package):
     depends_on('cmake')
     depends_on('blas', when='+external-blas')
 
-    def install(self, spec, prefix):
-        cmake_args = ['-DBUILD_SHARED_LIBS:BOOL=%s' % ('ON' if '+shared' in spec else 'OFF'),
+
+    def patch(self):
+        # Fix cblas CMakeLists.txt -- has wrong case for subdirectory name.
+        filter_file('${CMAKE_CURRENT_SOURCE_DIR}/CMAKE/',
+                    '${CMAKE_CURRENT_SOURCE_DIR}/cmake/', 'CBLAS/CMakeLists.txt', string=True)
+
+
+    def install_one(self, spec, prefix, shared):
+        cmake_args = ['-DBUILD_SHARED_LIBS:BOOL=%s' % ('ON' if shared else 'OFF'),
+                      '-DCBLAS=ON', # always build CBLAS
                       '-DCMAKE_BUILD_TYPE:STRING=%s' % ('Debug' if '+debug' in spec else 'Release'),
                       '-DLAPACKE:BOOL=%s' % ('ON' if '+lapacke' in spec else 'OFF')]
         if '+external-blas' in spec:
@@ -45,7 +53,33 @@ def install(self, spec, prefix):
 
         cmake_args.extend(std_cmake_args)
 
-        with working_dir('spack-build', create=True):
+        build_dir = 'spack-build' + ('-shared' if shared else '-static')
+        with working_dir(build_dir, create=True):
             cmake('..', *cmake_args)
             make()
             make("install")
+
+
+    def install(self, spec, prefix):
+        # Always build static libraries.
+        self.install_one(spec, prefix, False)
+
+        # Build shared libraries if requested.
+        if '+shared' in spec:
+            self.install_one(spec, prefix, True)
+
+
+    def setup_dependent_package(self, module, dspec):
+        # This is WIP for a prototype interface for virtual packages.
+        # We can update this as more builds start depending on BLAS/LAPACK.
+        libdir = find_library_path('libblas.a', self.prefix.lib64, self.prefix.lib)
+
+        self.spec.blas_static_lib   = join_path(libdir, 'libblas.a')
+        self.spec.lapack_static_lib = join_path(libdir, 'liblapack.a')
+
+        if '+shared' in self.spec:
+            self.spec.blas_shared_lib   = join_path(libdir, 'libblas.%s' % dso_suffix)
+            self.spec.lapack_shared_lib = join_path(libdir, 'liblapack.%s' % dso_suffix)
+
+
+
diff --git a/var/spack/repos/builtin/packages/openblas/package.py b/var/spack/repos/builtin/packages/openblas/package.py
index 1d10f217c45..4ec829a85b0 100644
--- a/var/spack/repos/builtin/packages/openblas/package.py
+++ b/var/spack/repos/builtin/packages/openblas/package.py
@@ -1,5 +1,6 @@
 from spack import *
 import sys
+import os
 
 class Openblas(Package):
     """OpenBLAS: An optimized BLAS library"""
@@ -10,29 +11,60 @@ class Openblas(Package):
     version('0.2.16', 'fef46ab92463bdbb1479dcec594ef6dc')
     version('0.2.15', 'b1190f3d3471685f17cfd1ec1d252ac9')
 
+    variant('shared', default=True, description="Build shared libraries as well as static libs.")
+
     # virtual dependency
     provides('blas')
     provides('lapack')
 
+
     def install(self, spec, prefix):
-        extra=[]
+        make_defs = ['CC=%s' % spack_cc,
+                     'FC=%s' % spack_fc]
+
+        make_targets = ['libs', 'netlib']
+
+        # Build shared if variant is set.
+        if '+shared' in spec:
+            make_targets += ['shared']
+        else:
+            make_defs += ['NO_SHARED=1']
+
+        # fix missing _dggsvd_ and _sggsvd_
         if spec.satisfies('@0.2.16'):
-            extra.extend([
-                'BUILD_LAPACK_DEPRECATED=1' # fix missing _dggsvd_ and _sggsvd_
-            ])
+            make_defs += ['BUILD_LAPACK_DEPRECATED=1']
 
-        make('libs', 'netlib', 'shared', 'CC=cc', 'FC=f77',*extra)
-        make("tests")
-        make('install', "PREFIX='%s'" % prefix)
+        make_args = make_defs + make_targets
+        make(*make_args)
+
+        make("tests", *make_defs)
+
+        # no quotes around prefix (spack doesn't use a shell)
+        make('install', "PREFIX=%s" % prefix, *make_defs)
 
-        lib_dsuffix = 'dylib' if sys.platform == 'darwin' else 'so'
         # Blas virtual package should provide blas.a and libblas.a
         with working_dir(prefix.lib):
             symlink('libopenblas.a', 'blas.a')
             symlink('libopenblas.a', 'libblas.a')
-            symlink('libopenblas.%s' % lib_dsuffix, 'libblas.%s' % lib_dsuffix)
+            if '+shared' in spec:
+                symlink('libopenblas.%s' % dso_suffix, 'libblas.%s' % dso_suffix)
 
         # Lapack virtual package should provide liblapack.a
         with working_dir(prefix.lib):
             symlink('libopenblas.a', 'liblapack.a')
-            symlink('libopenblas.%s' % lib_dsuffix, 'liblapack.%s' % lib_dsuffix)
+            if '+shared' in spec:
+                symlink('libopenblas.%s' % dso_suffix, 'liblapack.%s' % dso_suffix)
+
+
+    def setup_dependent_package(self, module, dspec):
+        # This is WIP for a prototype interface for virtual packages.
+        # We can update this as more builds start depending on BLAS/LAPACK.
+        libdir = find_library_path('libopenblas.a', self.prefix.lib64, self.prefix.lib)
+
+        self.spec.blas_static_lib   = join_path(libdir, 'libopenblas.a')
+        self.spec.lapack_static_lib = self.spec.blas_static_lib
+
+        if '+shared' in self.spec:
+            self.spec.blas_shared_lib   = join_path(libdir, 'libopenblas.%s' % dso_suffix)
+            self.spec.lapack_shared_lib = self.spec.blas_shared_lib
+
diff --git a/var/spack/repos/builtin/packages/py-scipy/package.py b/var/spack/repos/builtin/packages/py-scipy/package.py
index c2161c90c43..4d47c641eec 100644
--- a/var/spack/repos/builtin/packages/py-scipy/package.py
+++ b/var/spack/repos/builtin/packages/py-scipy/package.py
@@ -11,9 +11,15 @@ class PyScipy(Package):
 
     extends('python')
     depends_on('py-nose')
-    depends_on('py-numpy')
-    depends_on('blas')
-    depends_on('lapack')
+    depends_on('py-numpy+blas+lapack')
 
     def install(self, spec, prefix):
+        if 'atlas' in spec:
+            # libatlas.so actually isn't always installed, but this
+            # seems to make the build autodetect things correctly.
+            env['ATLAS'] = join_path(spec['atlas'].prefix.lib, 'libatlas.' + dso_suffix)
+        else:
+            env['BLAS']   = spec['blas'].blas_shared_lib
+            env['LAPACK'] = spec['lapack'].lapack_shared_lib
+
         python('setup.py', 'install', '--prefix=%s' % prefix)

From e049fc2840ba81cdff2ca7edd798c5e961ae94e9 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Sun, 27 Mar 2016 11:47:20 -0700
Subject: [PATCH 158/230] Run post-install hoooks before build stage is
 removed.

- Build will properly fail when post-install hoooks fail.

- Post-install hooks have a proper working directory set now.
---
 lib/spack/spack/package.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py
index 9af32218374..c17bec4a146 100644
--- a/lib/spack/spack/package.py
+++ b/lib/spack/spack/package.py
@@ -926,6 +926,9 @@ def build_process():
                      install(env_path, env_install_path)
                      dump_packages(self.spec, packages_dir)
 
+                # Run post install hooks before build stage is removed.
+                spack.hooks.post_install(self)
+
             # Stop timer.
             self._total_time = time.time() - start_time
             build_time = self._total_time - self._fetch_time
@@ -954,9 +957,6 @@ def build_process():
         # the database, so that we don't need to re-read from file.
         spack.installed_db.add(self.spec, self.prefix)
 
-        # Once everything else is done, run post install hooks
-        spack.hooks.post_install(self)
-
 
     def sanity_check_prefix(self):
         """This function checks whether install succeeded."""

From 20600b8cac9488ff416397de374c2d3dacf4afe4 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Sun, 27 Mar 2016 21:03:18 +0200
Subject: [PATCH 159/230] add tests and netcdf-cxx4

---
 .../repos/builtin/packages/dealii/package.py  | 38 ++++++++++++++++++-
 1 file changed, 36 insertions(+), 2 deletions(-)

diff --git a/var/spack/repos/builtin/packages/dealii/package.py b/var/spack/repos/builtin/packages/dealii/package.py
index 19bb3814be5..1d4c8002884 100644
--- a/var/spack/repos/builtin/packages/dealii/package.py
+++ b/var/spack/repos/builtin/packages/dealii/package.py
@@ -1,4 +1,5 @@
 from spack import *
+import shutil
 
 class Dealii(Package):
     """C++ software library providing well-documented tools to build finite element codes for a broad variety of PDEs."""
@@ -18,7 +19,7 @@ class Dealii(Package):
     depends_on ("hdf5+mpi~cxx") #FIXME NetCDF declares dependency with ~cxx, why?
     depends_on ("metis")
     depends_on ("muparser")
-    depends_on ("netcdf")
+    depends_on ("netcdf-cxx4")
     #depends_on ("numdiff") #FIXME
     depends_on ("oce")
     depends_on ("p4est")
@@ -50,7 +51,7 @@ def install(self, spec, prefix):
             '-DHDF5_DIR=%s' % spec['hdf5'].prefix,
             '-DMETIS_DIR=%s' % spec['metis'].prefix,
             '-DMUPARSER_DIR=%s ' % spec['muparser'].prefix,
-            '-DNETCDF_DIR=%s' % spec['netcdf'].prefix,
+            '-DNETCDF_DIR=%s' % spec['netcdf-cxx4'].prefix,
             '-DOPENCASCADE_DIR=%s' % spec['oce'].prefix,
             '-DP4EST_DIR=%s' % spec['p4est'].prefix,
             '-DPETSC_DIR=%s' % spec['petsc'].prefix,
@@ -65,3 +66,36 @@ def install(self, spec, prefix):
         make()
         make("test")
         make("install")
+
+        # run some MPI examples with different solvers from PETSc and Trilinos
+        env['DEAL_II_DIR'] = prefix
+        # take bare-bones step-3
+        with working_dir('examples/step-3'):
+            cmake('.')
+            make('release')
+            make('run',parallel=False)
+
+        # take step-40 which can use both PETSc and Trilinos
+        # FIXME: switch step-40 to MPI run
+        with working_dir('examples/step-40'):
+            # list the number of cycles to speed up
+            filter_file(r'(const unsigned int n_cycles = 8;)',  ('const unsigned int n_cycles = 2;'), 'step-40.cc')
+            cmake('.')
+            make('release')
+            make('run',parallel=False)
+
+            # change Linear Algebra to Trilinos
+            filter_file(r'(#define USE_PETSC_LA.*)',  (''), 'step-40.cc')
+            make('release')
+            make('run',parallel=False)
+
+        with working_dir('examples/step-36'):
+            cmake('.')
+            make('release')
+            make('run',parallel=False)
+
+        with working_dir('examples/step-54'):
+            cmake('.')
+            make('release')
+            # FIXME
+            # make('run',parallel=False)

From 5695e4c03d6c98fc187ec405923cd1dcf2fbdff6 Mon Sep 17 00:00:00 2001
From: Glenn Johnson <glenn-johnson@uiowa.edu>
Date: Sun, 27 Mar 2016 15:37:52 -0500
Subject: [PATCH 160/230] Wrap the long description of an environment module so
 it is more readable.

---
 lib/spack/spack/modules.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/lib/spack/spack/modules.py b/lib/spack/spack/modules.py
index d45fdde7035..f6a11c92e31 100644
--- a/lib/spack/spack/modules.py
+++ b/lib/spack/spack/modules.py
@@ -278,6 +278,6 @@ def write_header(self, module_file):
         # Long description
         if self.long_description:
             module_file.write('proc ModulesHelp { } {\n')
-            doc = re.sub(r'"', '\"', self.long_description)
-            module_file.write("puts stderr \"%s\"\n" % doc)
+            for line in textwrap.wrap(self.long_description, 72):
+                module_file.write("puts stderr \"%s\"\n" % line)
             module_file.write('}\n\n')

From fc73e93b50a708ecfa2395a636bc32161c9d3051 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Sun, 27 Mar 2016 23:47:43 +0200
Subject: [PATCH 161/230] rework netcdf

---
 var/spack/repos/builtin/packages/dealii/package.py | 12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)

diff --git a/var/spack/repos/builtin/packages/dealii/package.py b/var/spack/repos/builtin/packages/dealii/package.py
index 1d4c8002884..baedd155efa 100644
--- a/var/spack/repos/builtin/packages/dealii/package.py
+++ b/var/spack/repos/builtin/packages/dealii/package.py
@@ -1,5 +1,5 @@
 from spack import *
-import shutil
+import sys
 
 class Dealii(Package):
     """C++ software library providing well-documented tools to build finite element codes for a broad variety of PDEs."""
@@ -39,6 +39,7 @@ def install(self, spec, prefix):
             if word.startswith('-DCMAKE_BUILD_TYPE'):
                 options.remove(word)
 
+        dsuf = 'dylib' if sys.platform == 'darwin' else 'so'
         options.extend([
             '-DCMAKE_BUILD_TYPE=DebugRelease',
             '-DDEAL_II_WITH_THREADS:BOOL=ON'
@@ -51,7 +52,14 @@ def install(self, spec, prefix):
             '-DHDF5_DIR=%s' % spec['hdf5'].prefix,
             '-DMETIS_DIR=%s' % spec['metis'].prefix,
             '-DMUPARSER_DIR=%s ' % spec['muparser'].prefix,
-            '-DNETCDF_DIR=%s' % spec['netcdf-cxx4'].prefix,
+            # since Netcdf is spread among two, need to do it by hand:
+            '-DNETCDF_FOUND=true',
+            '-DNETCDF_LIBRARIES=%s;%s' %
+                (join_path(spec['netcdf-cxx4'].prefix.lib,'libnetcdf_c++4.%s' % dsuf),
+                 join_path(spec['netcdf'].prefix.lib,'libnetcdf.%s' % dsuf)),
+            '-DNETCDF_INCLUDE_DIRS=%s;%s' %
+                (spec['netcdf-cxx4'].prefix.include,
+                 spec['netcdf'].prefix.include),
             '-DOPENCASCADE_DIR=%s' % spec['oce'].prefix,
             '-DP4EST_DIR=%s' % spec['p4est'].prefix,
             '-DPETSC_DIR=%s' % spec['petsc'].prefix,

From ccd155572fc8ef066b93424e90a74f9bb8fcf435 Mon Sep 17 00:00:00 2001
From: citibeth <rpf2116@columbia.edu>
Date: Sun, 27 Mar 2016 18:18:54 -0400
Subject: [PATCH 162/230] Removed redundant package py-libxml2.  Use libxml2
 instead.

---
 .../repos/builtin/packages/py-libxml2/package.py  | 15 ---------------
 1 file changed, 15 deletions(-)
 delete mode 100644 var/spack/repos/builtin/packages/py-libxml2/package.py

diff --git a/var/spack/repos/builtin/packages/py-libxml2/package.py b/var/spack/repos/builtin/packages/py-libxml2/package.py
deleted file mode 100644
index 59005428e4d..00000000000
--- a/var/spack/repos/builtin/packages/py-libxml2/package.py
+++ /dev/null
@@ -1,15 +0,0 @@
-from spack import *
-
-class PyLibxml2(Package):
-    """A Python wrapper around libxml2."""
-    homepage = "https://xmlsoft.org/python.html"
-    url      = "ftp://xmlsoft.org/libxml2/python/libxml2-python-2.6.21.tar.gz"
-
-    version('2.6.21', '229dd2b3d110a77defeeaa73af83f7f3')
-
-    extends('python')
-    depends_on('libxml2')
-    depends_on('libxslt')
-
-    def install(self, spec, prefix):
-        python('setup.py', 'install', '--prefix=%s' % prefix)

From 7eca1284c81c3efc5a87b8a174a0974811656b3e Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Sun, 27 Mar 2016 08:59:25 +0200
Subject: [PATCH 163/230] metis/parmetis/boost/oce/scalapack: correct
 install_name on Darwin via a global function.

---
 lib/spack/llnl/util/filesystem.py             | 30 ++++++++++-
 .../repos/builtin/packages/boost/package.py   | 50 ++++++++++---------
 .../repos/builtin/packages/metis/package.py   |  6 ++-
 .../packages/netlib-scalapack/package.py      |  5 ++
 .../repos/builtin/packages/oce/package.py     |  6 ++-
 .../builtin/packages/parmetis/package.py      |  6 ++-
 6 files changed, 76 insertions(+), 27 deletions(-)

diff --git a/lib/spack/llnl/util/filesystem.py b/lib/spack/llnl/util/filesystem.py
index c4665c284cf..46ca03bec40 100644
--- a/lib/spack/llnl/util/filesystem.py
+++ b/lib/spack/llnl/util/filesystem.py
@@ -27,9 +27,10 @@
            'force_remove', 'join_path', 'ancestor', 'can_access', 'filter_file',
            'FileFilter', 'change_sed_delimiter', 'is_exe', 'force_symlink',
            'set_executable', 'copy_mode', 'unset_executable_mode',
-           'remove_dead_links', 'remove_linked_tree']
+           'remove_dead_links', 'remove_linked_tree', 'fix_darwin_install_name']
 
 import os
+import glob
 import sys
 import re
 import shutil
@@ -38,6 +39,7 @@
 import getpass
 from contextlib import contextmanager, closing
 from tempfile import NamedTemporaryFile
+import subprocess
 
 import llnl.util.tty as tty
 from spack.util.compression import ALLOWED_ARCHIVE_TYPES
@@ -392,3 +394,29 @@ def remove_linked_tree(path):
             os.unlink(path)
         else:
             shutil.rmtree(path, True)
+
+def fix_darwin_install_name(path):
+    """
+    Fix install name of dynamic libraries on Darwin to have full path.
+    There are two parts of this task:
+    (i) use install_name('-id',...) to change install name of a single lib;
+    (ii) use install_name('-change',...) to change the cross linking between libs.
+    The function assumes that all libraries are in one folder and currently won't
+    follow subfolders.
+
+    Args:
+        path: directory in which .dylib files are alocated
+
+    """
+    libs = glob.glob(join_path(path,"*.dylib"))
+    for lib in libs:
+        # fix install name first:
+        subprocess.Popen(["install_name_tool", "-id",lib,lib], stdout=subprocess.PIPE).communicate()[0]
+        long_deps = subprocess.Popen(["otool", "-L",lib], stdout=subprocess.PIPE).communicate()[0].split('\n')
+        deps = [dep.partition(' ')[0][1::] for dep in long_deps[2:-1]]
+        # fix all dependencies:
+        for dep in deps:
+            for loc in libs:
+                if dep == os.path.basename(loc):
+                    subprocess.Popen(["install_name_tool", "-change",dep,loc,lib], stdout=subprocess.PIPE).communicate()[0]
+                    break
diff --git a/var/spack/repos/builtin/packages/boost/package.py b/var/spack/repos/builtin/packages/boost/package.py
index fb1f5daee7f..82ce6fbb744 100644
--- a/var/spack/repos/builtin/packages/boost/package.py
+++ b/var/spack/repos/builtin/packages/boost/package.py
@@ -1,5 +1,6 @@
 from spack import *
 import spack
+import sys
 
 class Boost(Package):
     """Boost provides free peer-reviewed portable C++ source
@@ -45,34 +46,34 @@ class Boost(Package):
     version('1.34.1', '2d938467e8a448a2c9763e0a9f8ca7e5')
     version('1.34.0', 'ed5b9291ffad776f8757a916e1726ad0')
 
-    default_install_libs = set(['atomic', 
-        'chrono', 
-        'date_time', 
-        'filesystem', 
+    default_install_libs = set(['atomic',
+        'chrono',
+        'date_time',
+        'filesystem',
         'graph',
         'iostreams',
         'locale',
         'log',
-        'math', 
+        'math',
         'program_options',
-        'random', 
-        'regex', 
-        'serialization', 
-        'signals', 
-        'system', 
-        'test', 
-        'thread', 
+        'random',
+        'regex',
+        'serialization',
+        'signals',
+        'system',
+        'test',
+        'thread',
         'wave'])
 
-    # mpi/python are not installed by default because they pull in many 
-    # dependencies and/or because there is a great deal of customization 
+    # mpi/python are not installed by default because they pull in many
+    # dependencies and/or because there is a great deal of customization
     # possible (and it would be difficult to choose sensible defaults)
     default_noinstall_libs = set(['mpi', 'python'])
 
     all_libs = default_install_libs | default_noinstall_libs
 
     for lib in all_libs:
-        variant(lib, default=(lib not in default_noinstall_libs), 
+        variant(lib, default=(lib not in default_noinstall_libs),
             description="Compile with {0} library".format(lib))
 
     variant('debug', default=False, description='Switch to the debug version of Boost')
@@ -124,9 +125,9 @@ def determine_bootstrap_options(self, spec, withLibs, options):
 
         with open('user-config.jam', 'w') as f:
             compiler_wrapper = join_path(spack.build_env_path, 'c++')
-            f.write("using {0} : : {1} ;\n".format(boostToolsetId, 
+            f.write("using {0} : : {1} ;\n".format(boostToolsetId,
                 compiler_wrapper))
-            
+
             if '+mpi' in spec:
                 f.write('using mpi : %s ;\n' %
                     join_path(spec['mpi'].prefix.bin, 'mpicxx'))
@@ -155,7 +156,7 @@ def determine_b2_options(self, spec, options):
         linkTypes = ['static']
         if '+shared' in spec:
             linkTypes.append('shared')
-        
+
         threadingOpts = []
         if '+multithreaded' in spec:
             threadingOpts.append('multi')
@@ -163,12 +164,12 @@ def determine_b2_options(self, spec, options):
             threadingOpts.append('single')
         if not threadingOpts:
             raise RuntimeError("At least one of {singlethreaded, multithreaded} must be enabled")
-        
+
         options.extend([
             'toolset=%s' % self.determine_toolset(spec),
             'link=%s' % ','.join(linkTypes),
             '--layout=tagged'])
-        
+
         return threadingOpts
 
     def install(self, spec, prefix):
@@ -177,14 +178,14 @@ def install(self, spec, prefix):
             if "+{0}".format(lib) in spec:
                 withLibs.append(lib)
         if not withLibs:
-            # if no libraries are specified for compilation, then you dont have 
+            # if no libraries are specified for compilation, then you dont have
             # to configure/build anything, just copy over to the prefix directory.
             src = join_path(self.stage.source_path, 'boost')
             mkdirp(join_path(prefix, 'include'))
             dst = join_path(prefix, 'include', 'boost')
             install_tree(src, dst)
             return
-    
+
         # to make Boost find the user-config.jam
         env['BOOST_BUILD_PATH'] = './'
 
@@ -207,4 +208,7 @@ def install(self, spec, prefix):
         # Boost.MPI if the threading options are not separated.
         for threadingOpt in threadingOpts:
             b2('install', 'threading=%s' % threadingOpt, *b2_options)
-        
+
+        # The shared libraries are not installed correctly on Darwin; correct this
+        if (sys.platform == 'darwin') and ('+shared' in spec):
+            fix_darwin_install_name(prefix.lib)
diff --git a/var/spack/repos/builtin/packages/metis/package.py b/var/spack/repos/builtin/packages/metis/package.py
index 68b9f6fd306..9301135f9f3 100644
--- a/var/spack/repos/builtin/packages/metis/package.py
+++ b/var/spack/repos/builtin/packages/metis/package.py
@@ -24,7 +24,7 @@
 ##############################################################################
 
 from spack import *
-import glob
+import glob,sys
 
 class Metis(Package):
     """
@@ -90,3 +90,7 @@ def install(self, spec, prefix):
             fs = glob.glob(join_path(source_directory,'GKlib',"*.h"))
             for f in fs:
                 install(f, GKlib_dist)
+
+            # The shared library is not installed correctly on Darwin; correct this
+            if (sys.platform == 'darwin') and ('+shared' in spec):
+                fix_darwin_install_name(prefix.lib)
diff --git a/var/spack/repos/builtin/packages/netlib-scalapack/package.py b/var/spack/repos/builtin/packages/netlib-scalapack/package.py
index c3e6822cdfe..d59f8e41fec 100644
--- a/var/spack/repos/builtin/packages/netlib-scalapack/package.py
+++ b/var/spack/repos/builtin/packages/netlib-scalapack/package.py
@@ -41,6 +41,11 @@ def install(self, spec, prefix):
             make()
             make("install")
 
+        # The shared libraries are not installed correctly on Darwin; correct this
+        if (sys.platform == 'darwin') and ('+shared' in spec):
+            fix_darwin_install_name(prefix.lib)
+
+
     def setup_dependent_package(self, module, dependent_spec):
         spec = self.spec
         lib_dsuffix = '.dylib' if sys.platform == 'darwin' else '.so'
diff --git a/var/spack/repos/builtin/packages/oce/package.py b/var/spack/repos/builtin/packages/oce/package.py
index 06acb96736e..4d5081ac9d4 100644
--- a/var/spack/repos/builtin/packages/oce/package.py
+++ b/var/spack/repos/builtin/packages/oce/package.py
@@ -1,5 +1,5 @@
 from spack import *
-import platform
+import platform, sys
 
 class Oce(Package):
     """
@@ -45,3 +45,7 @@ def install(self, spec, prefix):
         cmake('.', *options)
 
         make("install/strip")
+
+        # The shared libraries are not installed correctly on Darwin; correct this
+        if (sys.platform == 'darwin'):
+            fix_darwin_install_name(prefix.lib)
diff --git a/var/spack/repos/builtin/packages/parmetis/package.py b/var/spack/repos/builtin/packages/parmetis/package.py
index f5b8b6de919..ff4370aa4b4 100644
--- a/var/spack/repos/builtin/packages/parmetis/package.py
+++ b/var/spack/repos/builtin/packages/parmetis/package.py
@@ -24,7 +24,7 @@
 ##############################################################################
 
 from spack import *
-
+import sys
 
 class Parmetis(Package):
     """
@@ -83,3 +83,7 @@ def install(self, spec, prefix):
             cmake(source_directory, *options)
             make()
             make("install")
+
+            # The shared library is not installed correctly on Darwin; correct this
+            if (sys.platform == 'darwin') and ('+shared' in spec):
+                fix_darwin_install_name(prefix.lib)

From 3bd550d6a2ceb279743aae626c6a3a614519d2f5 Mon Sep 17 00:00:00 2001
From: Elizabeth F <rpf2116@columbia.edu>
Date: Sun, 27 Mar 2016 18:27:06 -0400
Subject: [PATCH 164/230] GEOS Python extension did not compile with Python3.

---
 .../repos/builtin/packages/geos/package.py    | 24 +++++++++++++++----
 1 file changed, 20 insertions(+), 4 deletions(-)

diff --git a/var/spack/repos/builtin/packages/geos/package.py b/var/spack/repos/builtin/packages/geos/package.py
index 4a2657e32f2..030703f286e 100644
--- a/var/spack/repos/builtin/packages/geos/package.py
+++ b/var/spack/repos/builtin/packages/geos/package.py
@@ -1,4 +1,5 @@
 from spack import *
+import os
 
 class Geos(Package):
     """GEOS (Geometry Engine - Open Source) is a C++ port of the Java
@@ -10,6 +11,10 @@ class Geos(Package):
     homepage = "http://trac.osgeo.org/geos/"
     url      = "http://download.osgeo.org/geos/geos-3.4.2.tar.bz2"
 
+    # Verison 3.5.0 supports Autotools and CMake
+    version('3.5.0', '136842690be7f504fba46b3c539438dd')
+
+    # Versions through 3.4.2 have CMake, but only Autotools is supported
     version('3.4.2', 'fc5df2d926eb7e67f988a43a92683bae')
     version('3.4.1', '4c930dec44c45c49cd71f3e0931ded7e')
     version('3.4.0', 'e41318fc76b5dc764a69d43ac6b18488')
@@ -21,11 +26,22 @@ class Geos(Package):
     version('3.3.4', '1bb9f14d57ef06ffa41cb1d67acb55a1')
     version('3.3.3', '8454e653d7ecca475153cc88fd1daa26')
 
-    extends('python')
-    depends_on('swig')
+#    # Python3 is not supported.
+#    variant('python', default=False, description='Enable Python support')
+
+#    extends('python', when='+python')
+#    depends_on('python', when='+python')
+#    depends_on('swig', when='+python')
 
     def install(self, spec, prefix):
-        configure("--prefix=%s" % prefix,
-                  "--enable-python")
+        args = ["--prefix=%s" % prefix]
+#        if '+python' in spec:
+#            os.environ['PYTHON'] = join_path(spec['python'].prefix, 'bin',
+#                'python' if spec['python'].version[:1][0] <= 2 else 'python3')
+#            os.environ['SWIG'] = join_path(spec['swig'].prefix, 'bin', 'swig')
+#
+#            args.append("--enable-python")
+
+        configure(*args)
         make()
         make("install")

From 9c894f59354bafd9cd45e874be599dc8535e426e Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Mon, 28 Mar 2016 10:19:25 +0200
Subject: [PATCH 165/230] new package: netcdf-cxx

---
 .../repos/builtin/packages/netcdf-cxx/package.py  | 15 +++++++++++++++
 1 file changed, 15 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/netcdf-cxx/package.py

diff --git a/var/spack/repos/builtin/packages/netcdf-cxx/package.py b/var/spack/repos/builtin/packages/netcdf-cxx/package.py
new file mode 100644
index 00000000000..5334dfb853a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/netcdf-cxx/package.py
@@ -0,0 +1,15 @@
+from spack import *
+
+class NetcdfCxx(Package):
+    """C++ compatibility bindings for NetCDF"""
+    homepage = "http://www.unidata.ucar.edu/software/netcdf"
+    url      = "http://www.unidata.ucar.edu/downloads/netcdf/ftp/netcdf-cxx-4.2.tar.gz"
+
+    version('4.2', 'd32b20c00f144ae6565d9e98d9f6204c')
+
+    depends_on('netcdf')
+
+    def install(self, spec, prefix):
+        configure('--prefix=%s' % prefix)
+        make()
+        make("install")

From 97cdd7947894b3b631e2a209f0573ed839eb7b8a Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Mon, 28 Mar 2016 10:49:20 +0200
Subject: [PATCH 166/230] fix netcdf

---
 var/spack/repos/builtin/packages/dealii/package.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/var/spack/repos/builtin/packages/dealii/package.py b/var/spack/repos/builtin/packages/dealii/package.py
index baedd155efa..486aa6e4a4d 100644
--- a/var/spack/repos/builtin/packages/dealii/package.py
+++ b/var/spack/repos/builtin/packages/dealii/package.py
@@ -19,7 +19,7 @@ class Dealii(Package):
     depends_on ("hdf5+mpi~cxx") #FIXME NetCDF declares dependency with ~cxx, why?
     depends_on ("metis")
     depends_on ("muparser")
-    depends_on ("netcdf-cxx4")
+    depends_on ("netcdf-cxx")
     #depends_on ("numdiff") #FIXME
     depends_on ("oce")
     depends_on ("p4est")
@@ -55,10 +55,10 @@ def install(self, spec, prefix):
             # since Netcdf is spread among two, need to do it by hand:
             '-DNETCDF_FOUND=true',
             '-DNETCDF_LIBRARIES=%s;%s' %
-                (join_path(spec['netcdf-cxx4'].prefix.lib,'libnetcdf_c++4.%s' % dsuf),
+                (join_path(spec['netcdf-cxx'].prefix.lib,'libnetcdf_c++.%s' % dsuf),
                  join_path(spec['netcdf'].prefix.lib,'libnetcdf.%s' % dsuf)),
             '-DNETCDF_INCLUDE_DIRS=%s;%s' %
-                (spec['netcdf-cxx4'].prefix.include,
+                (spec['netcdf-cxx'].prefix.include,
                  spec['netcdf'].prefix.include),
             '-DOPENCASCADE_DIR=%s' % spec['oce'].prefix,
             '-DP4EST_DIR=%s' % spec['p4est'].prefix,

From e00cab75bd6721ac49bb6199d77ad99df80556a9 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Mon, 28 Mar 2016 12:12:55 +0200
Subject: [PATCH 167/230] more elaborated tests/direct solvers

---
 .../repos/builtin/packages/dealii/package.py  | 42 ++++++++++++++++++-
 1 file changed, 41 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/dealii/package.py b/var/spack/repos/builtin/packages/dealii/package.py
index 486aa6e4a4d..9ac1572b95a 100644
--- a/var/spack/repos/builtin/packages/dealii/package.py
+++ b/var/spack/repos/builtin/packages/dealii/package.py
@@ -77,7 +77,13 @@ def install(self, spec, prefix):
 
         # run some MPI examples with different solvers from PETSc and Trilinos
         env['DEAL_II_DIR'] = prefix
+        print('=====================================')
+        print('============ EXAMPLES ===============')
+        print('=====================================')
         # take bare-bones step-3
+        print('=====================================')
+        print('============ Step-3 =================')
+        print('=====================================')
         with working_dir('examples/step-3'):
             cmake('.')
             make('release')
@@ -86,22 +92,56 @@ def install(self, spec, prefix):
         # take step-40 which can use both PETSc and Trilinos
         # FIXME: switch step-40 to MPI run
         with working_dir('examples/step-40'):
+            print('=====================================')
+            print('========== Step-40 PETSc ============')
+            print('=====================================')
             # list the number of cycles to speed up
             filter_file(r'(const unsigned int n_cycles = 8;)',  ('const unsigned int n_cycles = 2;'), 'step-40.cc')
             cmake('.')
             make('release')
             make('run',parallel=False)
 
+            print('=====================================')
+            print('========= Step-40 Trilinos ==========')
+            print('=====================================')
             # change Linear Algebra to Trilinos
-            filter_file(r'(#define USE_PETSC_LA.*)',  (''), 'step-40.cc')
+            filter_file(r'(\/\/ #define FORCE_USE_OF_TRILINOS.*)',  ('#define FORCE_USE_OF_TRILINOS'), 'step-40.cc')
             make('release')
             make('run',parallel=False)
 
+            print('=====================================')
+            print('=== Step-40 Trilinos SuperluDist ====')
+            print('=====================================')
+            # change to direct solvers
+            filter_file(r'(LA::SolverCG solver\(solver_control\);)',  ('TrilinosWrappers::SolverDirect::AdditionalData data(false,"Amesos_Superludist"); TrilinosWrappers::SolverDirect solver(solver_control,data);'), 'step-40.cc')
+            filter_file(r'(LA::MPI::PreconditionAMG preconditioner;)',  (''), 'step-40.cc')
+            filter_file(r'(LA::MPI::PreconditionAMG::AdditionalData data;)',  (''), 'step-40.cc')
+            filter_file(r'(preconditioner.initialize\(system_matrix, data\);)',  (''), 'step-40.cc')
+            filter_file(r'(solver\.solve \(system_matrix, completely_distributed_solution, system_rhs,)',  ('solver.solve (system_matrix, completely_distributed_solution, system_rhs);'), 'step-40.cc')
+            filter_file(r'(preconditioner\);)',  (''), 'step-40.cc')
+
+            make('release')
+            make('run',paralle=False)
+
+            print('=====================================')
+            print('====== Step-40 Trilinos MUMPS =======')
+            print('=====================================')
+            # switch to Mumps
+            filter_file(r'(Amesos_Superludist)',  ('Amesos_Mumps'), 'step-40.cc')
+            make('release')
+            make('run',parallel=False)
+
+        print('=====================================')
+        print('============ Step-36 ================')
+        print('=====================================')
         with working_dir('examples/step-36'):
             cmake('.')
             make('release')
             make('run',parallel=False)
 
+        print('=====================================')
+        print('============ Step-54 ================')
+        print('=====================================')
         with working_dir('examples/step-54'):
             cmake('.')
             make('release')

From f3dd889d4462d14c9f0233540bccbf6a9720bcf0 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Mon, 28 Mar 2016 03:51:05 -0700
Subject: [PATCH 168/230] Fix bug with lib64 RPATH setting in cc.

---
 lib/spack/env/cc | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/lib/spack/env/cc b/lib/spack/env/cc
index c6a09724e9b..17740250d14 100755
--- a/lib/spack/env/cc
+++ b/lib/spack/env/cc
@@ -293,9 +293,9 @@ for dep in "${deps[@]}"; do
     if [[ -d $dep/lib64 ]]; then
         # libraries+=("$dep/lib64")
         if [[ $mode = ccld ]]; then
-            args=("-L$dep/lib" "-Wl,-rpath,$dep/lib" "${args[@]}")
+            args=("-L$dep/lib64" "-Wl,-rpath,$dep/lib64" "${args[@]}")
         elif [[ $mode = ld ]]; then
-            args=("-L$dep/lib" "-rpath" "$dep/lib" "${args[@]}")
+            args=("-L$dep/lib64" "-rpath" "$dep/lib64" "${args[@]}")
         fi
     fi
 done

From d8579a5b80efd8b09e5332a922dee533f2a0a55e Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Mon, 28 Mar 2016 03:51:41 -0700
Subject: [PATCH 169/230] Simplify cc: Remove old logic and add better tests.

- removed a lot of old logic that was only still needed for tests.

- Added better unit tests for dependency RPATH, -L, and -I args

- tests now check whether the compiler omits -I args in link mode.
---
 lib/spack/env/cc           | 138 ++++---------------------------------
 lib/spack/spack/test/cc.py | 127 +++++++++++++++++++++++++++++-----
 2 files changed, 123 insertions(+), 142 deletions(-)

diff --git a/lib/spack/env/cc b/lib/spack/env/cc
index 17740250d14..4217159a25c 100755
--- a/lib/spack/env/cc
+++ b/lib/spack/env/cc
@@ -114,7 +114,9 @@ case "$command" in
         ;;
 esac
 
-# If any of the arguments below is present then the mode is vcheck. In vcheck mode nothing is added in terms of extra search paths or libraries
+# If any of the arguments below is present then the mode is vcheck. In
+# vcheck mode nothing is added in terms of extra search paths or
+# libraries
 if [ -z "$mode" ]; then
     for arg in "$@"; do
         if [ "$arg" = -v -o "$arg" = -V -o "$arg" = --version -o "$arg" = -dumpversion ]; then
@@ -125,7 +127,6 @@ if [ -z "$mode" ]; then
 fi
 
 # Finish setting up the mode.
-
 if [ -z "$mode" ]; then
     mode=ccld
     for arg in "$@"; do
@@ -162,127 +163,18 @@ fi
 input_command="$@"
 args=("$@")
 
-# Dump parsed values for unit testing if asked for
-if [[ -n $SPACK_TEST_COMMAND ]]; then
-
-    #
-    # Now do real parsing of the command line args, trying hard to keep
-    # non-rpath linker arguments in the proper order w.r.t. other command line
-    # arguments.  This is important for things like groups.
-    #
-    includes=()
-    libraries=()
-    libs=()
-    rpaths=()
-    other_args=()
-
-    while [ -n "$1" ]; do
-        case "$1" in
-            -I*)
-                arg="${1#-I}"
-                if [ -z "$arg" ]; then shift; arg="$1"; fi
-                includes+=("$arg")
-                ;;
-            -L*)
-                arg="${1#-L}"
-                if [ -z "$arg" ]; then shift; arg="$1"; fi
-                libraries+=("$arg")
-                ;;
-            -l*)
-                arg="${1#-l}"
-                if [ -z "$arg" ]; then shift; arg="$1"; fi
-                libs+=("$arg")
-                ;;
-            -Wl,*)
-                arg="${1#-Wl,}"
-                # TODO: Handle multiple -Wl, continuations of -Wl,-rpath
-                if [[ $arg == -rpath=* ]]; then
-                    arg="${arg#-rpath=}"
-                    for rpath in ${arg//,/ }; do
-                        rpaths+=("$rpath")
-                    done
-                elif [[ $arg == -rpath,* ]]; then
-                    arg="${arg#-rpath,}"
-                    for rpath in ${arg//,/ }; do
-                        rpaths+=("$rpath")
-                    done
-                elif [[ $arg == -rpath ]]; then
-                    shift; arg="$1"
-                    if [[ $arg != '-Wl,'* ]]; then
-                        die "-Wl,-rpath was not followed by -Wl,*"
-                    fi
-                    arg="${arg#-Wl,}"
-                    for rpath in ${arg//,/ }; do
-                        rpaths+=("$rpath")
-                    done
-                else
-                    other_args+=("-Wl,$arg")
-                fi
-                ;;
-            -Xlinker)
-                shift; arg="$1";
-                if [[ $arg = -rpath=* ]]; then
-                    rpaths+=("${arg#-rpath=}")
-                elif [[ $arg = -rpath ]]; then
-                    shift; arg="$1"
-                    if [[ $arg != -Xlinker ]]; then
-                        die "-Xlinker -rpath was not followed by -Xlinker <arg>"
-                    fi
-                    shift; arg="$1"
-                    rpaths+=("$arg")
-                else
-                    other_args+=("-Xlinker")
-                    other_args+=("$arg")
-                fi
-                ;;
-            *)
-                other_args+=("$1")
-                ;;
-        esac
-        shift
-    done
-
-    IFS=$'\n'
-    case "$SPACK_TEST_COMMAND" in
-        dump-includes)   echo "${includes[*]}";;
-        dump-libraries)  echo "${libraries[*]}";;
-        dump-libs)       echo "${libs[*]}";;
-        dump-rpaths)     echo "${rpaths[*]}";;
-        dump-other-args) echo "${other_args[*]}";;
-        dump-all)
-            echo "INCLUDES:"
-            echo "${includes[*]}"
-            echo
-            echo "LIBRARIES:"
-            echo "${libraries[*]}"
-            echo
-            echo "LIBS:"
-            echo "${libs[*]}"
-            echo
-            echo "RPATHS:"
-            echo "${rpaths[*]}"
-            echo
-            echo "ARGS:"
-            echo "${other_args[*]}"
-            ;;
-        *)
-            die "ERROR: Unknown test command"
-            ;;
-    esac
-    exit
-fi
-
 # Read spack dependencies from the path environment variable
 IFS=':' read -ra deps <<< "$SPACK_DEPENDENCIES"
 for dep in "${deps[@]}"; do
+    # Prepend include directories
     if [[ -d $dep/include ]]; then
         if [[ $mode = cpp || $mode = cc || $mode = as || $mode = ccld ]]; then
             args=("-I$dep/include" "${args[@]}")
         fi
     fi
 
+    # Prepend lib and RPATH directories
     if [[ -d $dep/lib ]]; then
-        # libraries+=("$dep/lib")
         if [[ $mode = ccld ]]; then
             args=("-L$dep/lib" "-Wl,-rpath,$dep/lib" "${args[@]}")
         elif [[ $mode = ld ]]; then
@@ -290,8 +182,8 @@ for dep in "${deps[@]}"; do
         fi
     fi
 
+    # Prepend lib64 and RPATH directories
     if [[ -d $dep/lib64 ]]; then
-        # libraries+=("$dep/lib64")
         if [[ $mode = ccld ]]; then
             args=("-L$dep/lib64" "-Wl,-rpath,$dep/lib64" "${args[@]}")
         elif [[ $mode = ld ]]; then
@@ -302,18 +194,8 @@ done
 
 # Include all -L's and prefix/whatever dirs in rpath
 if [[ $mode = ccld ]]; then
-    # for dir in "${libraries[@]}"; do
-    #     if [[ dir = $SPACK_INSTALL* ]]; then
-    #         args=("-Wl,-rpath,$dir" "${args[@]}")
-    #     fi
-    # done
     args=("-Wl,-rpath,$SPACK_PREFIX/lib" "-Wl,-rpath,$SPACK_PREFIX/lib64" "${args[@]}")
 elif [[ $mode = ld ]]; then
-    # for dir in "${libraries[@]}"; do
-    #     if [[ dir = $SPACK_INSTALL* ]]; then
-    #         args=("-rpath" "$dir" "${args[@]}")
-    #     fi
-    # done
     args=("-rpath" "$SPACK_PREFIX/lib" "-rpath" "$SPACK_PREFIX/lib64" "${args[@]}")
 fi
 
@@ -345,6 +227,14 @@ export PATH
 
 full_command=("$command" "${args[@]}")
 
+# In test command mode, write out full command for Spack tests.
+if [[ $SPACK_TEST_COMMAND = dump-args ]]; then
+    echo "${full_command[@]}"
+    exit
+elif [[ -n $SPACK_TEST_COMMAND ]]; then
+    die "ERROR: Unknown test command"
+fi
+
 #
 # Write the input and output commands to debug logs if it's asked for.
 #
diff --git a/lib/spack/spack/test/cc.py b/lib/spack/spack/test/cc.py
index f3f6d4a22e6..0b1aeb2a8fe 100644
--- a/lib/spack/spack/test/cc.py
+++ b/lib/spack/spack/test/cc.py
@@ -28,6 +28,8 @@
 """
 import os
 import unittest
+import tempfile
+import shutil
 
 from llnl.util.filesystem import *
 import spack
@@ -55,13 +57,40 @@ def setUp(self):
         self.ld = Executable(join_path(spack.build_env_path, "ld"))
         self.cpp = Executable(join_path(spack.build_env_path, "cpp"))
 
-        os.environ['SPACK_CC'] = "/bin/mycc"
-        os.environ['SPACK_PREFIX'] = "/usr"
+        self.realcc = "/bin/mycc"
+        self.prefix = "/spack-test-prefix"
+
+        os.environ['SPACK_CC'] = self.realcc
+        os.environ['SPACK_PREFIX'] = self.prefix
         os.environ['SPACK_ENV_PATH']="test"
         os.environ['SPACK_DEBUG_LOG_DIR'] = "."
         os.environ['SPACK_COMPILER_SPEC'] = "gcc@4.4.7"
         os.environ['SPACK_SHORT_SPEC'] = "foo@1.2"
 
+        # Make some fake dependencies
+        self.tmp_deps = tempfile.mkdtemp()
+        self.dep1 = join_path(self.tmp_deps, 'dep1')
+        self.dep2 = join_path(self.tmp_deps, 'dep2')
+        self.dep3 = join_path(self.tmp_deps, 'dep3')
+        self.dep4 = join_path(self.tmp_deps, 'dep4')
+
+        mkdirp(join_path(self.dep1, 'include'))
+        mkdirp(join_path(self.dep1, 'lib'))
+
+        mkdirp(join_path(self.dep2, 'lib64'))
+
+        mkdirp(join_path(self.dep3, 'include'))
+        mkdirp(join_path(self.dep3, 'lib64'))
+
+        mkdirp(join_path(self.dep4, 'include'))
+
+        if 'SPACK_DEPENDENCIES' in os.environ:
+            del os.environ['SPACK_DEPENDENCIES']
+
+
+    def tearDown(self):
+        shutil.rmtree(self.tmp_deps, True)
+
 
     def check_cc(self, command, args, expected):
         os.environ['SPACK_TEST_COMMAND'] = command
@@ -92,6 +121,10 @@ def test_cpp_mode(self):
         self.check_cpp('dump-mode', [], "cpp")
 
 
+    def test_as_mode(self):
+        self.check_cc('dump-mode', ['-S'], "as")
+
+
     def test_ccld_mode(self):
         self.check_cc('dump-mode', [], "ccld")
         self.check_cc('dump-mode', ['foo.c', '-o', 'foo'], "ccld")
@@ -104,27 +137,85 @@ def test_ld_mode(self):
         self.check_ld('dump-mode', ['foo.o', 'bar.o', 'baz.o', '-o', 'foo', '-Wl,-rpath,foo'], "ld")
 
 
-    def test_includes(self):
-        self.check_cc('dump-includes', test_command,
-                      "\n".join(["/test/include", "/other/include"]))
+    def test_dep_rpath(self):
+        """Ensure RPATHs for root package are added."""
+        self.check_cc('dump-args', test_command,
+                      self.realcc + ' ' +
+                      '-Wl,-rpath,' + self.prefix + '/lib ' +
+                      '-Wl,-rpath,' + self.prefix + '/lib64 ' +
+                      ' '.join(test_command))
 
 
-    def test_libraries(self):
-        self.check_cc('dump-libraries', test_command,
-                      "\n".join(["/test/lib", "/other/lib"]))
+    def test_dep_include(self):
+        """Ensure a single dependency include directory is added."""
+        os.environ['SPACK_DEPENDENCIES'] = self.dep4
+        self.check_cc('dump-args', test_command,
+                      self.realcc + ' ' +
+                      '-Wl,-rpath,' + self.prefix + '/lib ' +
+                      '-Wl,-rpath,' + self.prefix + '/lib64 ' +
+                      '-I' + self.dep4 + '/include ' +
+                      ' '.join(test_command))
 
 
-    def test_libs(self):
-        self.check_cc('dump-libs', test_command,
-                      "\n".join(["lib1", "lib2", "lib3", "lib4"]))
+    def test_dep_lib(self):
+        """Ensure a single dependency RPATH is added."""
+        os.environ['SPACK_DEPENDENCIES'] = self.dep2
+        self.check_cc('dump-args', test_command,
+                      self.realcc + ' ' +
+                      '-Wl,-rpath,' + self.prefix + '/lib ' +
+                      '-Wl,-rpath,' + self.prefix + '/lib64 ' +
+                      '-L' + self.dep2 + '/lib64 ' +
+                      '-Wl,-rpath,' + self.dep2 + '/lib64 ' +
+                      ' '.join(test_command))
 
 
-    def test_rpaths(self):
-        self.check_cc('dump-rpaths', test_command,
-                      "\n".join(["/first/rpath", "/second/rpath", "/third/rpath", "/fourth/rpath"]))
+    def test_all_deps(self):
+        """Ensure includes and RPATHs for all deps are added. """
+        os.environ['SPACK_DEPENDENCIES'] = ':'.join([
+            self.dep1, self.dep2, self.dep3, self.dep4])
+
+        # This is probably more constrained than it needs to be; it
+        # checks order within prepended args and doesn't strictly have
+        # to.  We could loosen that if it becomes necessary
+        self.check_cc('dump-args', test_command,
+                      self.realcc + ' ' +
+                      '-Wl,-rpath,' + self.prefix + '/lib ' +
+                      '-Wl,-rpath,' + self.prefix + '/lib64 ' +
+
+                      '-I' + self.dep4 + '/include ' +
+
+                      '-L' + self.dep3 + '/lib64 ' +
+                      '-Wl,-rpath,' + self.dep3 + '/lib64 ' +
+                      '-I' + self.dep3 + '/include ' +
+
+                      '-L' + self.dep2 + '/lib64 ' +
+                      '-Wl,-rpath,' + self.dep2 + '/lib64 ' +
+
+                      '-L' + self.dep1 + '/lib ' +
+                      '-Wl,-rpath,' + self.dep1 + '/lib ' +
+                      '-I' + self.dep1 + '/include ' +
+
+                      ' '.join(test_command))
 
 
-    def test_other_args(self):
-        self.check_cc('dump-other-args', test_command,
-                      "\n".join(["arg1", "-Wl,--start-group", "arg2", "arg3", "arg4",
-                                 "-Wl,--end-group", "arg5", "arg6"]))
+    def test_ld_deps(self):
+        """Ensure no (extra) -I args or -Wl, are passed in ld mode."""
+        os.environ['SPACK_DEPENDENCIES'] = ':'.join([
+            self.dep1, self.dep2, self.dep3, self.dep4])
+
+        self.check_ld('dump-args', test_command,
+                      'ld ' +
+                      '-rpath ' + self.prefix + '/lib ' +
+                      '-rpath ' + self.prefix + '/lib64 ' +
+
+                      '-L' + self.dep3 + '/lib64 ' +
+                      '-rpath ' + self.dep3 + '/lib64 ' +
+
+                      '-L' + self.dep2 + '/lib64 ' +
+                      '-rpath ' + self.dep2 + '/lib64 ' +
+
+                      '-L' + self.dep1 + '/lib ' +
+                      '-rpath ' + self.dep1 + '/lib ' +
+
+                      ' '.join(test_command))
+

From 0da545ecac1c57a04abf814c9fed4f9929726ff5 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Mon, 28 Mar 2016 13:16:08 +0200
Subject: [PATCH 170/230] tell amesos that we use mumps 5

---
 .../repos/builtin/packages/trilinos/package.py    | 15 +++++++++++++--
 1 file changed, 13 insertions(+), 2 deletions(-)

diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py
index 6608f64ea72..90b7bff1492 100644
--- a/var/spack/repos/builtin/packages/trilinos/package.py
+++ b/var/spack/repos/builtin/packages/trilinos/package.py
@@ -6,6 +6,9 @@
 # https://github.com/koecher/candi/blob/master/deal.II-toolchain/packages/trilinos.package
 # https://gitlab.com/configurations/cluster-config/blob/master/trilinos.sh
 # https://github.com/Homebrew/homebrew-science/blob/master/trilinos.rb
+# and some relevant documentation/examples:
+# https://trilinos.org/docs/dev/packages/amesos2/doc/html/classAmesos2_1_1MUMPS.html
+# https://github.com/trilinos/Trilinos/issues/175
 class Trilinos(Package):
     """The Trilinos Project is an effort to develop algorithms and enabling technologies within an object-oriented
     software framework for the solution of large-scale, complex multi-physics engineering and scientific problems.
@@ -46,7 +49,7 @@ class Trilinos(Package):
     depends_on('mpi')
     depends_on('netcdf+mpi')
     depends_on('parmetis',when='+metis')
-    depends_on('mumps+mpi+shared',when='+mumps') # Amesos link errors with static: "__gfortran_adjustl", referenced from: _dmumps_ in libdmumps.a(dmumps_driver.o) "_mpi_abort_", referenced from: _mumps_abort_ in libmumps_common.a(tools_common.o)
+    depends_on('mumps@5.0:+mpi+shared',when='+mumps') # Amesos link errors with static: "__gfortran_adjustl", referenced from: _dmumps_ in libdmumps.a(dmumps_driver.o) "_mpi_abort_", referenced from: _mumps_abort_ in libmumps_common.a(tools_common.o)
     depends_on('scalapack',when='+mumps')
     depends_on('superlu-dist',when='+superlu-dist')
     depends_on('hypre',when='+hypre')
@@ -67,6 +70,7 @@ def variants_check(self):
     def install(self, spec, prefix):
         self.variants_check()
 
+        cxx_flags = []
         options = []
         options.extend(std_cmake_args)
 
@@ -91,7 +95,6 @@ def install(self, spec, prefix):
                         '-DBoost_LIBRARY_DIRS:PATH=%s' % spec['boost'].prefix.lib,
                         '-DTrilinos_ENABLE_EXPLICIT_INSTANTIATION:BOOL=ON',
                         '-DTrilinos_ENABLE_CXX11:BOOL=ON',
-                        '-DTrilinos_CXX11_FLAGS=-std=c++11',
                         '-DTPL_ENABLE_Netcdf:BOOL=ON',
                         '-DTPL_ENABLE_HYPRE:BOOL=ON',
                         '-DTPL_ENABLE_HDF5:BOOL=ON'
@@ -154,6 +157,10 @@ def install(self, spec, prefix):
                 '-DTPL_ENABLE_SCALAPACK:BOOL=ON',
                 '-DSCALAPACK_LIBRARY_NAMES=scalapack' # FIXME: for MKL it's mkl_scalapack_lp64;mkl_blacs_mpich_lp64
             ])
+            # see https://github.com/trilinos/Trilinos/blob/master/packages/amesos/README-MUMPS
+            cxx_flags.extend([
+                '-DMUMPS_5_0'
+            ])
         else:
             options.extend([
                 '-DTPL_ENABLE_MUMPS:BOOL=OFF',
@@ -194,6 +201,10 @@ def install(self, spec, prefix):
                 '-DTrilinos_ENABLE_PyTrilinos:BOOL=OFF'
             ])
 
+        # collect CXX flags:
+        options.extend([
+            '-DCMAKE_CXX_FLAGS:STRING=%s' % (' '.join(cxx_flags)),
+        ])
 
         # disable due to compiler / config errors:
         options.extend([

From 5eefca43e75d2df1c2f859d199f7bb37e7142993 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Mon, 28 Mar 2016 14:35:01 +0200
Subject: [PATCH 171/230] petsc: extend variants by mumps, complex and debug

---
 .../repos/builtin/packages/petsc/package.py   | 31 ++++++++++++-------
 1 file changed, 19 insertions(+), 12 deletions(-)

diff --git a/var/spack/repos/builtin/packages/petsc/package.py b/var/spack/repos/builtin/packages/petsc/package.py
index 3dd117eed11..dd3d2aa1626 100644
--- a/var/spack/repos/builtin/packages/petsc/package.py
+++ b/var/spack/repos/builtin/packages/petsc/package.py
@@ -17,14 +17,17 @@ class Petsc(Package):
     version('3.5.1', 'a557e029711ebf425544e117ffa44d8f')
     version('3.4.4', '7edbc68aa6d8d6a3295dd5f6c2f6979d')
 
-    variant('shared', default=True, description='Enables the build of shared libraries')
-    variant('mpi', default=True, description='Activates MPI support')
-    variant('double', default=True, description='Switches between single and double precision')
+    variant('shared',  default=True,  description='Enables the build of shared libraries')
+    variant('mpi',     default=True,  description='Activates MPI support')
+    variant('double',  default=True,  description='Switches between single and double precision')
+    variant('complex', default=False, description='Build with complex numbers')
+    variant('debug',   default=False, description='Compile in debug mode')
 
-    variant('metis', default=True, description='Activates support for metis and parmetis')
-    variant('hdf5', default=True, description='Activates support for HDF5 (only parallel)')
-    variant('boost', default=True, description='Activates support for Boost')
-    variant('hypre', default=True, description='Activates support for Hypre')
+    variant('metis',   default=True,  description='Activates support for metis and parmetis')
+    variant('hdf5',    default=True,  description='Activates support for HDF5 (only parallel)')
+    variant('boost',   default=True,  description='Activates support for Boost')
+    variant('hypre',   default=True,  description='Activates support for Hypre (only parallel)')
+    variant('mumps',   default=True,  description='Activates support for MUMPS (only parallel)')
 
     # Virtual dependencies
     depends_on('blas')
@@ -40,7 +43,10 @@ class Petsc(Package):
 
     depends_on('hdf5+mpi', when='+hdf5+mpi')
     depends_on('parmetis', when='+metis+mpi')
-    depends_on('hypre',    when='+hypre+mpi')
+    depends_on('hypre',    when='+hypre+mpi~complex') # Hypre does not support complex numbers
+
+    depends_on('mumps+mpi', when='+mumps+mpi')
+    depends_on('scalapack', when='+mumps+mpi')
 
     def mpi_dependent_options(self):
         if '~mpi' in self.spec:
@@ -55,7 +61,7 @@ def mpi_dependent_options(self):
             # If mpi is disabled (~mpi), it's an error to have any of these enabled.
             # This generates a list of any such errors.
             errors = [error_message_fmt.format(library=x)
-                      for x in ('hdf5', 'hypre', 'parmetis')
+                      for x in ('hdf5', 'hypre', 'parmetis','mumps')
                       if ('+'+x) in self.spec]
             if errors:
                 errors = ['incompatible variants given'] + errors
@@ -77,16 +83,17 @@ def mpi_dependent_options(self):
         return compiler_opts
 
     def install(self, spec, prefix):
-        options = ['--with-debugging=0',
-                   '--with-ssl=0']
+        options = ['--with-ssl=0']
         options.extend(self.mpi_dependent_options())
         options.extend([
             '--with-precision=%s' % ('double' if '+double' in spec else 'single'),
+            '--with-scalar-type=%s' % ('complex' if '+complex' in spec else 'real'),
             '--with-shared-libraries=%s' % ('1' if '+shared' in spec else '0'),
+            '--with-debugging=%s' % ('1' if '+debug' in spec else '0'),
             '--with-blas-lapack-dir=%s' % spec['lapack'].prefix
         ])
         # Activates library support if needed
-        for library in ('metis', 'boost', 'hdf5', 'hypre', 'parmetis'):
+        for library in ('metis', 'boost', 'hdf5', 'hypre', 'parmetis','mumps','scalapack'):
             options.append(
                 '--with-{library}={value}'.format(library=library, value=('1' if library in spec else '0'))
             )

From dd60cc326c12bfa8434b68afec72f4b68c18a94c Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Mon, 28 Mar 2016 17:52:22 +0200
Subject: [PATCH 172/230] adopt modifed superlu and hypre

---
 var/spack/repos/builtin/packages/trilinos/package.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py
index 90b7bff1492..b2dc8df0ea1 100644
--- a/var/spack/repos/builtin/packages/trilinos/package.py
+++ b/var/spack/repos/builtin/packages/trilinos/package.py
@@ -52,7 +52,7 @@ class Trilinos(Package):
     depends_on('mumps@5.0:+mpi+shared',when='+mumps') # Amesos link errors with static: "__gfortran_adjustl", referenced from: _dmumps_ in libdmumps.a(dmumps_driver.o) "_mpi_abort_", referenced from: _mumps_abort_ in libmumps_common.a(tools_common.o)
     depends_on('scalapack',when='+mumps')
     depends_on('superlu-dist',when='+superlu-dist')
-    depends_on('hypre',when='+hypre')
+    depends_on('hypre~internal-superlu',when='+hypre')
     depends_on('hdf5+mpi',when='+hdf5')
 
     depends_on('python',when='+python') #  Needs py-numpy activated
@@ -179,7 +179,7 @@ def install(self, spec, prefix):
             options.extend([
                 '-DTPL_ENABLE_SuperLUDist:BOOL=ON',
                 '-DSuperLUDist_LIBRARY_DIRS=%s' % spec['superlu-dist'].prefix.lib,
-                '-DSuperLUDist_INCLUDE_DIRS=%s/superlu_dist' % spec['superlu-dist'].prefix.include # superlu_dist and superlu have the same header names :-( In order to avoid conflicts, try to keep "dist" version headers in a subfolder
+                '-DSuperLUDist_INCLUDE_DIRS=%s' % spec['superlu-dist'].prefix.include
             ])
             if spec.satisfies('^superlu-dist@4.0:'):
                 options.extend([

From 207215980b05e4916e05ded8b05044b3edbe92c0 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Mon, 28 Mar 2016 17:54:27 +0200
Subject: [PATCH 173/230] make hypre and hdf5 be ON/OFF

---
 var/spack/repos/builtin/packages/trilinos/package.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py
index b2dc8df0ea1..eb3bd1e0ee4 100644
--- a/var/spack/repos/builtin/packages/trilinos/package.py
+++ b/var/spack/repos/builtin/packages/trilinos/package.py
@@ -96,8 +96,8 @@ def install(self, spec, prefix):
                         '-DTrilinos_ENABLE_EXPLICIT_INSTANTIATION:BOOL=ON',
                         '-DTrilinos_ENABLE_CXX11:BOOL=ON',
                         '-DTPL_ENABLE_Netcdf:BOOL=ON',
-                        '-DTPL_ENABLE_HYPRE:BOOL=ON',
-                        '-DTPL_ENABLE_HDF5:BOOL=ON'
+                        '-DTPL_ENABLE_HYPRE:BOOL=%s' % ('ON' if '+hypre' in spec else 'OFF'),,
+                        '-DTPL_ENABLE_HDF5:BOOL=%s' % ('ON' if '+hdf5' in spec else 'OFF'),
                         ])
 
         # Fortran lib

From 4e87cf9d7492133d30675a64703b91ec6992ca00 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Mon, 28 Mar 2016 18:00:34 +0200
Subject: [PATCH 174/230] fix extra comma

---
 var/spack/repos/builtin/packages/trilinos/package.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py
index eb3bd1e0ee4..71c0be61c38 100644
--- a/var/spack/repos/builtin/packages/trilinos/package.py
+++ b/var/spack/repos/builtin/packages/trilinos/package.py
@@ -96,7 +96,7 @@ def install(self, spec, prefix):
                         '-DTrilinos_ENABLE_EXPLICIT_INSTANTIATION:BOOL=ON',
                         '-DTrilinos_ENABLE_CXX11:BOOL=ON',
                         '-DTPL_ENABLE_Netcdf:BOOL=ON',
-                        '-DTPL_ENABLE_HYPRE:BOOL=%s' % ('ON' if '+hypre' in spec else 'OFF'),,
+                        '-DTPL_ENABLE_HYPRE:BOOL=%s' % ('ON' if '+hypre' in spec else 'OFF'),
                         '-DTPL_ENABLE_HDF5:BOOL=%s' % ('ON' if '+hdf5' in spec else 'OFF'),
                         ])
 

From 09e77812b67d92094bea8dae54617e3e02ebaa61 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Mon, 28 Mar 2016 17:49:20 +0200
Subject: [PATCH 175/230] fix installation of superlu_dist headers and add it
 as a dependency to petsc; add a variant to hypre to disable internal superlu

---
 .../repos/builtin/packages/hypre/package.py   |  5 +++++
 .../repos/builtin/packages/petsc/package.py   | 21 ++++++++++++++++---
 .../builtin/packages/superlu-dist/package.py  | 11 +++++-----
 3 files changed, 29 insertions(+), 8 deletions(-)

diff --git a/var/spack/repos/builtin/packages/hypre/package.py b/var/spack/repos/builtin/packages/hypre/package.py
index 8d93d48d1f6..0e995532933 100644
--- a/var/spack/repos/builtin/packages/hypre/package.py
+++ b/var/spack/repos/builtin/packages/hypre/package.py
@@ -14,6 +14,8 @@ class Hypre(Package):
 
     # hypre does not know how to build shared libraries on Darwin
     variant('shared', default=sys.platform!='darwin', description="Build shared library version (disables static library)")
+    # SuperluDist have conflicting headers with those in Hypre
+    variant('internal-superlu', default=True, description="Use internal Superlu routines")
 
     depends_on("mpi")
     depends_on("blas")
@@ -38,6 +40,9 @@ def install(self, spec, prefix):
         if '+shared' in self.spec:
             configure_args.append("--enable-shared")
 
+        if '~internal-superlu' in self.spec:
+            configure_args.append("--without-superlu")
+
         # Hypre's source is staged under ./src so we'll have to manually
         # cd into it.
         with working_dir("src"):
diff --git a/var/spack/repos/builtin/packages/petsc/package.py b/var/spack/repos/builtin/packages/petsc/package.py
index dd3d2aa1626..e9b7c8a732c 100644
--- a/var/spack/repos/builtin/packages/petsc/package.py
+++ b/var/spack/repos/builtin/packages/petsc/package.py
@@ -28,6 +28,7 @@ class Petsc(Package):
     variant('boost',   default=True,  description='Activates support for Boost')
     variant('hypre',   default=True,  description='Activates support for Hypre (only parallel)')
     variant('mumps',   default=True,  description='Activates support for MUMPS (only parallel)')
+    variant('superlu-dist', default=True, description='Activates support for SuperluDist (only parallel)')
 
     # Virtual dependencies
     depends_on('blas')
@@ -43,8 +44,11 @@ class Petsc(Package):
 
     depends_on('hdf5+mpi', when='+hdf5+mpi')
     depends_on('parmetis', when='+metis+mpi')
-    depends_on('hypre',    when='+hypre+mpi~complex') # Hypre does not support complex numbers
-
+    # Hypre does not support complex numbers.
+    # Also PETSc prefer to build it without internal superlu, likely due to conflict in headers
+    # see https://bitbucket.org/petsc/petsc/src/90564b43f6b05485163c147b464b5d6d28cde3ef/config/BuildSystem/config/packages/hypre.py
+    depends_on('hypre~internal-superlu', when='+hypre+mpi~complex')
+    depends_on('superlu-dist', when='+superlu-dist+mpi')
     depends_on('mumps+mpi', when='+mumps+mpi')
     depends_on('scalapack', when='+mumps+mpi')
 
@@ -61,7 +65,7 @@ def mpi_dependent_options(self):
             # If mpi is disabled (~mpi), it's an error to have any of these enabled.
             # This generates a list of any such errors.
             errors = [error_message_fmt.format(library=x)
-                      for x in ('hdf5', 'hypre', 'parmetis','mumps')
+                      for x in ('hdf5', 'hypre', 'parmetis','mumps','superlu-dist')
                       if ('+'+x) in self.spec]
             if errors:
                 errors = ['incompatible variants given'] + errors
@@ -101,6 +105,17 @@ def install(self, spec, prefix):
                 options.append(
                     '--with-{library}-dir={path}'.format(library=library, path=spec[library].prefix)
                 )
+        # PETSc does not pick up SuperluDist from the dir as they look for superlu_dist_4.1.a
+        if 'superlu-dist' in spec:
+            options.extend([
+                '--with-superlu_dist-include=%s' % spec['superlu-dist'].prefix.include,
+                '--with-superlu_dist-lib=%s' % join_path(spec['superlu-dist'].prefix.lib, 'libsuperlu_dist.a'),
+                '--with-superlu_dist=1'
+            ])
+        else:
+            options.append(
+                '--with-superlu_dist=0'
+            )
 
         configure('--prefix=%s' % prefix, *options)
 
diff --git a/var/spack/repos/builtin/packages/superlu-dist/package.py b/var/spack/repos/builtin/packages/superlu-dist/package.py
index 9a94de8ba50..ddcb7f92252 100644
--- a/var/spack/repos/builtin/packages/superlu-dist/package.py
+++ b/var/spack/repos/builtin/packages/superlu-dist/package.py
@@ -1,4 +1,5 @@
 from spack import *
+import glob
 
 class SuperluDist(Package):
     """A general purpose library for the direct solution of large, sparse, nonsymmetric systems of linear equations on high performance machines."""
@@ -52,13 +53,13 @@ def install(self, spec, prefix):
         # system "make"
 
         # need to install by hand
-        headers_location = join_path(self.prefix.include,'superlu_dist')
+        headers_location = self.prefix.include
         mkdirp(headers_location)
         mkdirp(prefix.lib)
-        # FIXME: fetch all headers in the folder automatically
-        for header in ['Cnames.h','cublas_utils.h','dcomplex.h','html_mainpage.h','machines.h','old_colamd.h','psymbfact.h','superlu_ddefs.h','superlu_defs.h','superlu_enum_consts.h','superlu_zdefs.h','supermatrix.h','util_dist.h']:
-            superludist_header = join_path(self.stage.source_path, 'SRC/',header)
-            install(superludist_header, headers_location)
+
+        headers = glob.glob(join_path(self.stage.source_path, 'SRC','*.h'))
+        for h in headers:
+            install(h,headers_location)
 
         superludist_lib = join_path(self.stage.source_path, 'lib/libsuperlu_dist.a')
         install(superludist_lib,self.prefix.lib)

From a14527ec0619151d6defc909a46aefd2a9378cb7 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Mon, 28 Mar 2016 15:34:25 -0700
Subject: [PATCH 176/230] Add command to compiler input log.

---
 lib/spack/env/cc | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/spack/env/cc b/lib/spack/env/cc
index 4217159a25c..68cd8514f44 100755
--- a/lib/spack/env/cc
+++ b/lib/spack/env/cc
@@ -241,7 +241,7 @@ fi
 if [[ $SPACK_DEBUG = TRUE ]]; then
     input_log="$SPACK_DEBUG_LOG_DIR/spack-cc-$SPACK_SHORT_SPEC.in.log"
     output_log="$SPACK_DEBUG_LOG_DIR/spack-cc-$SPACK_SHORT_SPEC.out.log"
-    echo "$input_command" >> $input_log
+    echo "$command $input_command" >> $input_log
     echo "$mode       ${full_command[@]}" >> $output_log
 fi
 

From f9bcce6a683b1d948190b9927254e3ee29d3606c Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Tue, 29 Mar 2016 09:19:24 +0200
Subject: [PATCH 177/230] turn off python by default

---
 var/spack/repos/builtin/packages/trilinos/package.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py
index 71c0be61c38..0ab4addd52a 100644
--- a/var/spack/repos/builtin/packages/trilinos/package.py
+++ b/var/spack/repos/builtin/packages/trilinos/package.py
@@ -31,7 +31,8 @@ class Trilinos(Package):
     variant('hypre',        default=True,  description='Compile with Hypre preconditioner')
     variant('hdf5',         default=True,  description='Compile with HDF5')
     variant('suite-sparse', default=True,  description='Compile with SuiteSparse solvers')
-    variant('python',       default=True,  description='Build python wrappers')
+    # not everyone has py-numpy activated, keep it disabled by default to avoid configure errors
+    variant('python',       default=False, description='Build python wrappers')
     variant('shared',       default=True,  description='Enables the build of shared libraries')
     variant('debug',        default=False, description='Builds a debug version of the libraries')
 
@@ -55,7 +56,7 @@ class Trilinos(Package):
     depends_on('hypre~internal-superlu',when='+hypre')
     depends_on('hdf5+mpi',when='+hdf5')
 
-    depends_on('python',when='+python') #  Needs py-numpy activated
+    depends_on('python',when='+python')
 
     patch('umfpack_from_suitesparse.patch')
 

From 7753d823cbe1d1983957fb948bf095d624d76b7c Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Tue, 29 Mar 2016 09:27:55 +0200
Subject: [PATCH 178/230] add a comment on static mumps

---
 var/spack/repos/builtin/packages/trilinos/package.py | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py
index 0ab4addd52a..6223848c689 100644
--- a/var/spack/repos/builtin/packages/trilinos/package.py
+++ b/var/spack/repos/builtin/packages/trilinos/package.py
@@ -7,7 +7,6 @@
 # https://gitlab.com/configurations/cluster-config/blob/master/trilinos.sh
 # https://github.com/Homebrew/homebrew-science/blob/master/trilinos.rb
 # and some relevant documentation/examples:
-# https://trilinos.org/docs/dev/packages/amesos2/doc/html/classAmesos2_1_1MUMPS.html
 # https://github.com/trilinos/Trilinos/issues/175
 class Trilinos(Package):
     """The Trilinos Project is an effort to develop algorithms and enabling technologies within an object-oriented
@@ -50,7 +49,14 @@ class Trilinos(Package):
     depends_on('mpi')
     depends_on('netcdf+mpi')
     depends_on('parmetis',when='+metis')
-    depends_on('mumps@5.0:+mpi+shared',when='+mumps') # Amesos link errors with static: "__gfortran_adjustl", referenced from: _dmumps_ in libdmumps.a(dmumps_driver.o) "_mpi_abort_", referenced from: _mumps_abort_ in libmumps_common.a(tools_common.o)
+    # Trilinos' Tribits config system is limited which makes it
+    # very tricky to link Amesos with static MUMPS, see
+    # https://trilinos.org/docs/dev/packages/amesos2/doc/html/classAmesos2_1_1MUMPS.html
+    # One could work it out by getting linking flags from mpif90 --showme:link (or alike)
+    # and adding results to -DTrilinos_EXTRA_LINK_FLAGS
+    # together with Blas and Lapack and ScaLAPACK and Blacs and -lgfortran and
+    # it may work at the end. But let's avoid all this by simply using shared libs
+    depends_on('mumps@5.0:+mpi+shared',when='+mumps')
     depends_on('scalapack',when='+mumps')
     depends_on('superlu-dist',when='+superlu-dist')
     depends_on('hypre~internal-superlu',when='+hypre')

From 63c3feb79e7e4022e5565deb9f2749fa9732e7d2 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Tue, 29 Mar 2016 09:41:57 +0200
Subject: [PATCH 179/230] minor fixes to hypre and muparser on Linux

---
 var/spack/repos/builtin/packages/hypre/package.py    | 3 +++
 var/spack/repos/builtin/packages/muparser/package.py | 2 +-
 2 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/hypre/package.py b/var/spack/repos/builtin/packages/hypre/package.py
index 0e995532933..4b915daa687 100644
--- a/var/spack/repos/builtin/packages/hypre/package.py
+++ b/var/spack/repos/builtin/packages/hypre/package.py
@@ -42,6 +42,9 @@ def install(self, spec, prefix):
 
         if '~internal-superlu' in self.spec:
             configure_args.append("--without-superlu")
+            # MLI and FEI do not build without superlu on Linux
+            configure_args.append("--without-mli")
+            configure_args.append("--without-fei")
 
         # Hypre's source is staged under ./src so we'll have to manually
         # cd into it.
diff --git a/var/spack/repos/builtin/packages/muparser/package.py b/var/spack/repos/builtin/packages/muparser/package.py
index a1a9ff90e53..19ca8ce2874 100644
--- a/var/spack/repos/builtin/packages/muparser/package.py
+++ b/var/spack/repos/builtin/packages/muparser/package.py
@@ -14,5 +14,5 @@ def install(self, spec, prefix):
 
         configure(*options)
 
-        make()
+        make(parallel=False)
         make("install")

From f80e839ff48809a5ba8b7343d2378133a3fbce82 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Tue, 29 Mar 2016 02:58:05 -0700
Subject: [PATCH 180/230] Handle Darwin's ld -r option properly

- ld -r doesn't work with RPATH on OS X.

- for GNU ld, the -r option only means 'relocatable',
  and doesn't affect RPATH.

- This adds special handling to omit RPATHs for ld -r on OS X
---
 lib/spack/env/cc | 35 +++++++++++++++++++++++++++--------
 1 file changed, 27 insertions(+), 8 deletions(-)

diff --git a/lib/spack/env/cc b/lib/spack/env/cc
index 68cd8514f44..2eb6f46afe5 100755
--- a/lib/spack/env/cc
+++ b/lib/spack/env/cc
@@ -85,6 +85,10 @@ done
 #    ccld    compile & link
 #    vcheck  version check
 #
+# Depending on the mode, we may or may not add extra rpaths.
+# This variable controls whether they are added.
+add_rpaths=true
+
 command=$(basename "$0")
 case "$command" in
     cc|c89|c99|gcc|clang|icc|pgcc|xlc)
@@ -108,6 +112,17 @@ case "$command" in
         ;;
     ld)
         mode=ld
+
+        # Darwin's linker has a -r argument that merges object files
+        # together. It doesn't work with -rpath.
+        if [[ $OSTYPE = darwin* ]]; then
+            for arg in "$@"; do
+                if [ "$arg" = -r ]; then
+                    add_rpaths=false
+                    break
+	            fi
+            done
+        fi
         ;;
     *)
         die "Unkown compiler: $command"
@@ -176,27 +191,31 @@ for dep in "${deps[@]}"; do
     # Prepend lib and RPATH directories
     if [[ -d $dep/lib ]]; then
         if [[ $mode = ccld ]]; then
-            args=("-L$dep/lib" "-Wl,-rpath,$dep/lib" "${args[@]}")
+            $add_rpaths && args=("-Wl,-rpath,$dep/lib" "${args[@]}")
+            args=("-L$dep/lib" "${args[@]}")
         elif [[ $mode = ld ]]; then
-            args=("-L$dep/lib" "-rpath" "$dep/lib" "${args[@]}")
+            $add_rpaths && args=("-rpath" "$dep/lib" "${args[@]}")
+            args=("-L$dep/lib" "${args[@]}")
         fi
     fi
 
     # Prepend lib64 and RPATH directories
     if [[ -d $dep/lib64 ]]; then
         if [[ $mode = ccld ]]; then
-            args=("-L$dep/lib64" "-Wl,-rpath,$dep/lib64" "${args[@]}")
+            $add_rpaths && args=("-Wl,-rpath,$dep/lib64" "${args[@]}")
+            args=("-L$dep/lib64" "${args[@]}")
         elif [[ $mode = ld ]]; then
-            args=("-L$dep/lib64" "-rpath" "$dep/lib64" "${args[@]}")
+            $add_rpaths && args=("-rpath" "$dep/lib64" "${args[@]}")
+            args=("-L$dep/lib64" "${args[@]}")
         fi
     fi
 done
 
 # Include all -L's and prefix/whatever dirs in rpath
 if [[ $mode = ccld ]]; then
-    args=("-Wl,-rpath,$SPACK_PREFIX/lib" "-Wl,-rpath,$SPACK_PREFIX/lib64" "${args[@]}")
+    $add_rpaths && args=("-Wl,-rpath,$SPACK_PREFIX/lib" "-Wl,-rpath,$SPACK_PREFIX/lib64" "${args[@]}")
 elif [[ $mode = ld ]]; then
-    args=("-rpath" "$SPACK_PREFIX/lib" "-rpath" "$SPACK_PREFIX/lib64" "${args[@]}")
+    $add_rpaths && args=("-rpath" "$SPACK_PREFIX/lib" "-rpath" "$SPACK_PREFIX/lib64" "${args[@]}")
 fi
 
 #
@@ -241,8 +260,8 @@ fi
 if [[ $SPACK_DEBUG = TRUE ]]; then
     input_log="$SPACK_DEBUG_LOG_DIR/spack-cc-$SPACK_SHORT_SPEC.in.log"
     output_log="$SPACK_DEBUG_LOG_DIR/spack-cc-$SPACK_SHORT_SPEC.out.log"
-    echo "$command $input_command" >> $input_log
-    echo "$mode       ${full_command[@]}" >> $output_log
+    echo "[$mode] $command $input_command" >> $input_log
+    echo "[$mode] ${full_command[@]}" >> $output_log
 fi
 
 exec "${full_command[@]}"

From ccc1b23bea57a9c8a31ab1f4e9b739b54440466b Mon Sep 17 00:00:00 2001
From: Patrick Gartung <gartung@fnal.gov>
Date: Mon, 28 Mar 2016 16:28:29 -0500
Subject: [PATCH 181/230] this allows gcc4.9.3 to build on OSX10

---
 .../packages/gcc/darwin/gcc-4.9.patch1        | 42 +++++++++++++++++++
 .../packages/gcc/darwin/gcc-4.9.patch2        | 28 +++++++++++++
 .../repos/builtin/packages/gcc/package.py     | 12 +++++-
 3 files changed, 81 insertions(+), 1 deletion(-)
 create mode 100644 var/spack/repos/builtin/packages/gcc/darwin/gcc-4.9.patch1
 create mode 100644 var/spack/repos/builtin/packages/gcc/darwin/gcc-4.9.patch2

diff --git a/var/spack/repos/builtin/packages/gcc/darwin/gcc-4.9.patch1 b/var/spack/repos/builtin/packages/gcc/darwin/gcc-4.9.patch1
new file mode 100644
index 00000000000..444e292786d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/gcc/darwin/gcc-4.9.patch1
@@ -0,0 +1,42 @@
+diff --git a/gcc/configure b/gcc/configure
+index 9523773..52b0bf7 100755
+--- a/gcc/configure
++++ b/gcc/configure
+@@ -24884,7 +24884,7 @@ if test "${gcc_cv_as_ix86_filds+set}" = set; then :
+ else
+   gcc_cv_as_ix86_filds=no
+   if test x$gcc_cv_as != x; then
+-    $as_echo 'filds mem; fists mem' > conftest.s
++    $as_echo 'filds (%ebp); fists (%ebp)' > conftest.s
+     if { ac_try='$gcc_cv_as $gcc_cv_as_flags  -o conftest.o conftest.s >&5'
+   { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$ac_try\""; } >&5
+   (eval $ac_try) 2>&5
+@@ -24915,7 +24915,7 @@ if test "${gcc_cv_as_ix86_fildq+set}" = set; then :
+ else
+   gcc_cv_as_ix86_fildq=no
+   if test x$gcc_cv_as != x; then
+-    $as_echo 'fildq mem; fistpq mem' > conftest.s
++    $as_echo 'fildq (%ebp); fistpq (%ebp)' > conftest.s
+     if { ac_try='$gcc_cv_as $gcc_cv_as_flags  -o conftest.o conftest.s >&5'
+   { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$ac_try\""; } >&5
+   (eval $ac_try) 2>&5
+diff --git a/gcc/configure.ac b/gcc/configure.ac
+index 68b0ee8..bd53978 100644
+--- a/gcc/configure.ac
++++ b/gcc/configure.ac
+@@ -3869,13 +3869,13 @@ foo:	nop
+ 
+     gcc_GAS_CHECK_FEATURE([filds and fists mnemonics],
+        gcc_cv_as_ix86_filds,,,
+-       [filds mem; fists mem],,
++       [filds (%ebp); fists (%ebp)],,
+        [AC_DEFINE(HAVE_AS_IX86_FILDS, 1,
+          [Define if your assembler uses filds and fists mnemonics.])])
+ 
+     gcc_GAS_CHECK_FEATURE([fildq and fistpq mnemonics],
+        gcc_cv_as_ix86_fildq,,,
+-       [fildq mem; fistpq mem],,
++       [fildq (%ebp); fistpq (%ebp)],,
+        [AC_DEFINE(HAVE_AS_IX86_FILDQ, 1,
+          [Define if your assembler uses fildq and fistq mnemonics.])])
+ 
diff --git a/var/spack/repos/builtin/packages/gcc/darwin/gcc-4.9.patch2 b/var/spack/repos/builtin/packages/gcc/darwin/gcc-4.9.patch2
new file mode 100644
index 00000000000..b065997f453
--- /dev/null
+++ b/var/spack/repos/builtin/packages/gcc/darwin/gcc-4.9.patch2
@@ -0,0 +1,28 @@
+From 82f81877458ea372176eabb5de36329431dce99b Mon Sep 17 00:00:00 2001
+From: Iain Sandoe <iain@codesourcery.com>
+Date: Sat, 21 Dec 2013 00:30:18 +0000
+Subject: [PATCH] don't try to mark local symbols as no-dead-strip
+
+---
+ gcc/config/darwin.c | 5 +++++
+ 1 file changed, 5 insertions(+)
+
+diff --git a/gcc/config/darwin.c b/gcc/config/darwin.c
+index 40804b8..0080299 100644
+--- a/gcc/config/darwin.c
++++ b/gcc/config/darwin.c
+@@ -1259,6 +1259,11 @@ darwin_encode_section_info (tree decl, rtx rtl, int first ATTRIBUTE_UNUSED)
+ void
+ darwin_mark_decl_preserved (const char *name)
+ {
++  /* Actually we shouldn't mark any local symbol this way, but for now
++     this only happens with ObjC meta-data.  */
++  if (darwin_label_is_anonymous_local_objc_name (name))
++    return;
++
+   fprintf (asm_out_file, "\t.no_dead_strip ");
+   assemble_name (asm_out_file, name);
+   fputc ('\n', asm_out_file);
+-- 
+2.2.1
+
diff --git a/var/spack/repos/builtin/packages/gcc/package.py b/var/spack/repos/builtin/packages/gcc/package.py
index 232d0020df4..6043b622793 100644
--- a/var/spack/repos/builtin/packages/gcc/package.py
+++ b/var/spack/repos/builtin/packages/gcc/package.py
@@ -27,6 +27,7 @@
 from contextlib import closing
 from glob import glob
 import sys
+import os
 
 class Gcc(Package):
     """The GNU Compiler Collection includes front ends for C, C++,
@@ -63,6 +64,9 @@ class Gcc(Package):
     # TODO: integrate these libraries.
     #depends_on("ppl")
     #depends_on("cloog")
+    if sys.platform == 'darwin':
+        patch('darwin/gcc-4.9.patch1', when='@4.9.3')
+        patch('darwin/gcc-4.9.patch2', when='@4.9.3')
 
     def install(self, spec, prefix):
         # libjava/configure needs a minor fix to install into spack paths.
@@ -70,6 +74,7 @@ def install(self, spec, prefix):
             string=True)
 
         enabled_languages = set(('c', 'c++', 'fortran', 'java', 'objc'))
+
         if spec.satisfies("@4.7.1:") and sys.platform != 'darwin':
             enabled_languages.add('go')
 
@@ -101,12 +106,17 @@ def install(self, spec, prefix):
             isl_options = ["--with-isl=%s" % spec['isl'].prefix]
             options.extend(isl_options)
 
+        if sys.platform == 'darwin' :
+            darwin_options = [ "--with-build-config=bootstrap-debug" ]
+            options.extend(darwin_options)
+
         build_dir = join_path(self.stage.path, 'spack-build')
         configure = Executable( join_path(self.stage.source_path, 'configure') )
         with working_dir(build_dir, create=True):
             # Rest of install is straightforward.
             configure(*options)
-            make()
+            if sys.platform == 'darwin' : make("bootstrap")
+            else: make()
             make("install")
 
         self.write_rpath_specs()

From dfc5cf288c1017ef62390489cb534848aef5a9a6 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Tue, 29 Mar 2016 04:35:41 -0700
Subject: [PATCH 182/230] Fix bug in restage

- Restage previously only removed the source directory from the stage.
- Now removes any other directories in stage as well.
---
 lib/spack/spack/fetch_strategy.py | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/lib/spack/spack/fetch_strategy.py b/lib/spack/spack/fetch_strategy.py
index 0d0a7db8a91..4ea87bea7ea 100644
--- a/lib/spack/spack/fetch_strategy.py
+++ b/lib/spack/spack/fetch_strategy.py
@@ -289,8 +289,14 @@ def reset(self):
         if not self.archive_file:
             raise NoArchiveFileError("Tried to reset URLFetchStrategy before fetching",
                                      "Failed on reset() for URL %s" % self.url)
-        if self.stage.source_path:
-            shutil.rmtree(self.stage.source_path, ignore_errors=True)
+
+        # Remove everythigng but the archive from the stage
+        for filename in os.listdir(self.stage.path):
+            abspath = os.path.join(self.stage.path, filename)
+            if abspath != self.archive_file:
+                shutil.rmtree(abspath, ignore_errors=True)
+
+        # Expand the archive again
         self.expand()
 
     def __repr__(self):

From ad402ff85bc4150aa49fb394929b062b40b27604 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Mon, 21 Mar 2016 22:36:31 +0100
Subject: [PATCH 183/230] astyle@2.04: add new package

---
 .../repos/builtin/packages/astyle/package.py    | 17 +++++++++++++++++
 1 file changed, 17 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/astyle/package.py

diff --git a/var/spack/repos/builtin/packages/astyle/package.py b/var/spack/repos/builtin/packages/astyle/package.py
new file mode 100644
index 00000000000..7260fd74a1d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/astyle/package.py
@@ -0,0 +1,17 @@
+from spack import *
+import os
+
+class Astyle(Package):
+    """A Free, Fast, and Small Automatic Formatter for C, C++, C++/CLI, Objective-C, C#, and Java Source Code."""
+    homepage = "http://astyle.sourceforge.net/"
+    url      = "http://downloads.sourceforge.net/project/astyle/astyle/astyle%202.04/astyle_2.04_linux.tar.gz"
+
+    version('2.04', '30b1193a758b0909d06e7ee8dd9627f6')
+
+    def install(self, spec, prefix):
+
+        with working_dir('src'):
+            make('-f',
+                join_path(self.stage.source_path,'build','clang','Makefile'),
+                parallel=False)
+            install(join_path(self.stage.source_path, 'src','bin','astyle'), self.prefix.bin)

From d96ea5ba0075c63e8cd042337a1d99225b92b2d5 Mon Sep 17 00:00:00 2001
From: Patrick Gartung <gartung@fnal.gov>
Date: Tue, 29 Mar 2016 12:20:11 -0500
Subject: [PATCH 184/230] add modules package and have setup script find it if
 built

---
 share/spack/setup-env.sh                      | 10 ++++++++
 .../repos/builtin/packages/modules/package.py | 25 +++++++++++++++++++
 2 files changed, 35 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/modules/package.py

diff --git a/share/spack/setup-env.sh b/share/spack/setup-env.sh
index 764af684001..529517ff834 100755
--- a/share/spack/setup-env.sh
+++ b/share/spack/setup-env.sh
@@ -176,3 +176,13 @@ _spack_pathadd PATH       "${_sp_prefix%/}/bin"
 _sp_sys_type=$(spack-python -c 'print(spack.architecture.sys_type())')
 _spack_pathadd DK_NODE    "${_sp_share_dir%/}/dotkit/$_sp_sys_type"
 _spack_pathadd MODULEPATH "${_sp_share_dir%/}/modules/$_sp_sys_type"
+
+#
+# Use spack built modules package if available
+# for system that does not have it
+#
+
+_modules_install_path=$(command spack location -i modules)
+if [ -n "$_modules_install_path" ] ; then
+    . $_modules_install_path/Modules/init/sh
+fi
diff --git a/var/spack/repos/builtin/packages/modules/package.py b/var/spack/repos/builtin/packages/modules/package.py
new file mode 100644
index 00000000000..b014ee460c2
--- /dev/null
+++ b/var/spack/repos/builtin/packages/modules/package.py
@@ -0,0 +1,25 @@
+from spack import *
+
+class Modules(Package):
+    """ The Environment Modules package provides for the dynamic modification of a user's environment via modulefiles. """
+
+    homepage = "http://modules.sf.net"
+    url      = "http://downloads.sourceforge.net/project/modules/Modules/modules-3.2.10/modules-3.2.10.tar.gz"
+
+    version('3.2.10', '8b097fdcb90c514d7540bb55a3cb90fb')
+
+    depends_on("tcl")
+
+    def install(self, spec, prefix):
+
+	options = ['--prefix=%s' % prefix, 
+                   '--disable-debug',
+                   '--disable-dependency-tracking',
+                   '--disable-silent-rules',
+                   '--disable-versioning', 
+                   '--datarootdir=%s' % prefix.share,
+                   'CPPFLAGS=-DUSE_INTERP_ERRORLINE']
+
+        configure(*options)
+        make()
+        make("install")

From 4ddba5f7edd97c8c17781368edc5b9a0db74417d Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Tue, 29 Mar 2016 14:47:16 -0500
Subject: [PATCH 185/230] Add CUDA and HOOMD-blue packages

---
 .../repos/builtin/packages/cuda/package.py    | 42 ++++++++++++
 .../builtin/packages/hoomd-blue/package.py    | 67 +++++++++++++++++++
 2 files changed, 109 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/cuda/package.py
 create mode 100644 var/spack/repos/builtin/packages/hoomd-blue/package.py

diff --git a/var/spack/repos/builtin/packages/cuda/package.py b/var/spack/repos/builtin/packages/cuda/package.py
new file mode 100644
index 00000000000..547b43d6d26
--- /dev/null
+++ b/var/spack/repos/builtin/packages/cuda/package.py
@@ -0,0 +1,42 @@
+from spack import *
+from glob import glob
+import os
+
+class Cuda(Package):
+    """CUDA is a parallel computing platform and programming model invented by
+    NVIDIA. It enables dramatic increases in computing performance by harnessing
+    the power of the graphics processing unit (GPU).
+
+    Note: NVIDIA does not provide a download URL for CUDA so you will need to
+    download it yourself. Go to https://developer.nvidia.com/cuda-downloads
+    and select your Operating System, Architecture, Distribution, and Version.
+    For the Installer Type, select runfile and click Download. Spack will search
+    your current directory for this file. Alternatively, add this file to a
+    mirror so that Spack can find it. For instructions on how to set up a mirror,
+    see http://software.llnl.gov/spack/mirrors.html"""
+
+    homepage = "http://www.nvidia.com/object/cuda_home_new.html"
+    url      = "file://%s/cuda_7.5.18_linux.run" % os.getcwd()
+
+    version('7.5.18', '4b3bcecf0dfc35928a0898793cf3e4c6', expand=False)
+
+    def install(self, spec, prefix):
+        runfile = glob(os.path.join(self.stage.path, 'cuda*.run'))[0]
+        chmod = which('chmod')
+        chmod('+x', runfile)
+        runfile = which(runfile)
+
+        # Note: NVIDIA does not officially support many newer versions of compilers.
+        # For example, on CentOS 6, you must use GCC 4.4.7 or older.
+        # The --override flag disables these checks. See:
+        # http://docs.nvidia.com/cuda/cuda-installation-guide-linux/#system-requirements
+        # for details.
+
+        runfile(
+            '--silent',   # disable interactive prompts
+            '--verbose',  # create verbose log file
+            '--override', # ignore compiler checks
+            '--toolkit',  # install CUDA Toolkit
+            '--toolkitpath=%s' % prefix
+        )
+
diff --git a/var/spack/repos/builtin/packages/hoomd-blue/package.py b/var/spack/repos/builtin/packages/hoomd-blue/package.py
new file mode 100644
index 00000000000..97ce9c0cf0f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/hoomd-blue/package.py
@@ -0,0 +1,67 @@
+from spack import *
+import os
+
+class HoomdBlue(Package):
+    """HOOMD-blue is a general-purpose particle simulation toolkit. It scales
+    from a single CPU core to thousands of GPUs.
+
+    You define particle initial conditions and interactions in a high-level
+    python script. Then tell HOOMD-blue how you want to execute the job and it
+    takes care of the rest. Python job scripts give you unlimited flexibility
+    to create custom initialization routines, control simulation parameters,
+    and perform in situ analysis."""
+
+    homepage = "https://codeblue.umich.edu/hoomd-blue/index.html"
+    url      = "https://bitbucket.org/glotzer/hoomd-blue/get/v1.3.3.tar.bz2"
+
+    version('1.3.3', '1469ef4531dc14b579c0acddbfe6a273')
+
+    variant('mpi',  default=False, description='Compile with MPI enabled')
+    variant('cuda', default=False, description='Compile with CUDA Toolkit')
+    variant('doc',  default=False, description='Generate documentation')
+
+    extends('python')
+    depends_on('py-numpy')
+    depends_on('boost+python')
+    depends_on('cmake')
+    depends_on('mpi', when='+mpi')
+    depends_on('cuda', when='+cuda')
+    depends_on('doxygen', when='+doc')
+
+    def install(self, spec, prefix):
+
+        cmake_args = [
+            '-DPYTHON_EXECUTABLE=%s/python' % spec['python'].prefix.bin,
+            '-DBOOST_ROOT=%s'               % spec['boost' ].prefix
+        ]
+
+        # MPI support
+        if '+mpi' in spec:
+            os.environ['MPI_HOME'] = spec['mpi'].prefix
+            cmake_args.append('-DENABLE_MPI=ON')
+        else:
+            cmake_args.append('-DENABLE_MPI=OFF')
+
+        # CUDA support
+        if '+cuda' in spec:
+            cmake_args.append('-DENABLE_CUDA=ON')
+        else:
+            cmake_args.append('-DENABLE_CUDA=OFF')
+
+        # CUDA-aware MPI library support
+        if '+cuda' in spec and '+mpi' in spec:
+            cmake_args.append('-DENABLE_MPI_CUDA=ON')
+        else:
+            cmake_args.append('-DENABLE_MPI_CUDA=OFF')
+
+        # Documentation
+        if '+doc' in spec:
+            cmake_args.append('-DENABLE_DOXYGEN=ON')
+        else:
+            cmake_args.append('-DENABLE_DOXYGEN=OFF')
+
+        cmake_args.extend(std_cmake_args)
+        cmake('.', *cmake_args)
+
+        make()
+        make("install")

From abee9c83b440b8341be6df1f07c7c5f1bef9dd89 Mon Sep 17 00:00:00 2001
From: Elizabeth Fischer <rpf2116@columbia.edu>
Date: Tue, 29 Mar 2016 17:26:34 -0400
Subject: [PATCH 186/230] Removed googletest FIXME...

---
 .../repos/builtin/packages/googletest/package.py | 16 ----------------
 1 file changed, 16 deletions(-)

diff --git a/var/spack/repos/builtin/packages/googletest/package.py b/var/spack/repos/builtin/packages/googletest/package.py
index ed27afa10ce..663b758747b 100644
--- a/var/spack/repos/builtin/packages/googletest/package.py
+++ b/var/spack/repos/builtin/packages/googletest/package.py
@@ -1,19 +1,3 @@
-# FIXME:
-# This is a template package file for Spack.  We've conveniently
-# put "FIXME" labels next to all the things you'll want to change.
-#
-# Once you've edited all the FIXME's, delete this whole message,
-# save this file, and test out your package like this:
-#
-#     spack install googletest
-#
-# You can always get back here to change things with:
-#
-#     spack edit googletest
-#
-# See the spack documentation for more information on building
-# packages.
-#
 from spack import *
 
 class Googletest(Package):

From a4eff6de3faa3624a529015ea4cf5ebb1af41484 Mon Sep 17 00:00:00 2001
From: "Kelly (KT) Thompson" <kgt@lanl.gov>
Date: Tue, 29 Mar 2016 17:10:49 -0600
Subject: [PATCH 187/230] + New version of cmake (3.5.1).

---
 var/spack/repos/builtin/packages/cmake/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/cmake/package.py b/var/spack/repos/builtin/packages/cmake/package.py
index 1f93d39769b..91a4e3b415f 100644
--- a/var/spack/repos/builtin/packages/cmake/package.py
+++ b/var/spack/repos/builtin/packages/cmake/package.py
@@ -30,6 +30,7 @@ class Cmake(Package):
     homepage  = 'https://www.cmake.org'
     url       = 'https://cmake.org/files/v3.4/cmake-3.4.3.tar.gz'
 
+    version('3.5.1',    'ca051f4a66375c89d1a524e726da0296')
     version('3.5.0',    '33c5d09d4c33d4ffcc63578a6ba8777e')
     version('3.4.3',    '4cb3ff35b2472aae70f542116d616e63')
     version('3.4.0',    'cd3034e0a44256a0917e254167217fc8')

From 98bb151d85fc35389e0b76eaac90448fa688aa6c Mon Sep 17 00:00:00 2001
From: "Gregory L. Lee" <lee218@surface86.llnl.gov>
Date: Tue, 29 Mar 2016 20:25:56 -0700
Subject: [PATCH 188/230] updated geos version

---
 var/spack/repos/builtin/packages/dbus/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/dbus/package.py b/var/spack/repos/builtin/packages/dbus/package.py
index 294b0de54ea..422f5a19eba 100644
--- a/var/spack/repos/builtin/packages/dbus/package.py
+++ b/var/spack/repos/builtin/packages/dbus/package.py
@@ -13,6 +13,7 @@ class Dbus(Package):
     homepage = "http://dbus.freedesktop.org/"
     url      = "http://dbus.freedesktop.org/releases/dbus/dbus-1.8.8.tar.gz"
 
+    version('1.11.2', '957a07f066f3730d2bb3ea0932f0081b')
     version('1.9.0', 'ec6895a4d5c0637b01f0d0e7689e2b36')
     version('1.8.8', 'b9f4a18ee3faa1e07c04aa1d83239c43')
     version('1.8.6', '6a08ba555d340e9dfe2d623b83c0eea8')

From 5b6eefbf0417668c19e4c898c31cf56764d5bc2b Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Wed, 30 Mar 2016 11:30:35 +0200
Subject: [PATCH 189/230] add variants and extra dependencies

---
 .../repos/builtin/packages/dealii/package.py  | 178 ++++++++++++++----
 1 file changed, 141 insertions(+), 37 deletions(-)

diff --git a/var/spack/repos/builtin/packages/dealii/package.py b/var/spack/repos/builtin/packages/dealii/package.py
index 9ac1572b95a..396601356cf 100644
--- a/var/spack/repos/builtin/packages/dealii/package.py
+++ b/var/spack/repos/builtin/packages/dealii/package.py
@@ -8,27 +8,48 @@ class Dealii(Package):
 
     version('8.4.0', 'ac5dbf676096ff61e092ce98c80c2b00')
 
-    depends_on ("cmake")
-    depends_on ("blas")
-    depends_on ("lapack")
-    depends_on ("mpi")
+    variant('mpi',      default=True, description='Compile with MPI')
+    variant('arpack',   default=True, description='Compile with Arpack and PArpack (only with MPI)')
+    variant('doxygen',  default=True, description='Compile with Doxygen documentation')
+    variant('hdf5',     default=True, description='Compile with HDF5 (only with MPI)')
+    variant('metis',    default=True, description='Compile with Metis or ParMetis')
+    variant('netcdf',   default=True, description='Compile with Netcdf (only with MPI)')
+    variant('oce',      default=True, description='Compile with OCE')
+    variant('p4est',    default=True, description='Compile with P4est (only with MPI)')
+    variant('petsc',    default=True, description='Compile with Petsc (only with MPI)')
+    variant('slepc',    default=True, description='Compile with Slepc (only with Petsc and MPI)')
+    variant('trilinos', default=True, description='Compile with Trilinos (only with MPI)')
 
-    depends_on ("arpack-ng+mpi")
-    depends_on ("boost")
-    depends_on ("doxygen")
-    depends_on ("hdf5+mpi~cxx") #FIXME NetCDF declares dependency with ~cxx, why?
-    depends_on ("metis")
+    # required dependencies, light version
+    depends_on ("blas")
+    depends_on ("boost",     when='~mpi')
+    depends_on ("boost+mpi", when='+mpi')
+    depends_on ("bzip2")
+    depends_on ("cmake")
+    depends_on ("lapack")
     depends_on ("muparser")
-    depends_on ("netcdf-cxx")
-    #depends_on ("numdiff") #FIXME
-    depends_on ("oce")
-    depends_on ("p4est")
-    depends_on ("parmetis")
-    depends_on ("petsc+mpi")
-    depends_on ("slepc")
     depends_on ("suite-sparse")
     depends_on ("tbb")
-    depends_on ("trilinos")
+    depends_on ("zlib")
+
+    # optional dependencies
+    depends_on ("mpi", when="+mpi")
+    depends_on ("arpack-ng+mpi", when='+arpack+mpi')
+    depends_on ("doxygen", when='+doxygen')
+    depends_on ("hdf5+mpi~cxx", when='+hdf5+mpi') #FIXME NetCDF declares dependency with ~cxx, why?
+    depends_on ("metis", when='+metis')
+    depends_on ("netcdf+mpi", when="+netcdf+mpi")
+    depends_on ("netcdf-cxx", when='+netcdf+mpi')
+    depends_on ("oce", when='+oce')
+    depends_on ("p4est", when='+p4est+mpi')
+    depends_on ("parmetis", when='+metis+mpi')
+    depends_on ("petsc+mpi", when='+petsc+mpi')
+    depends_on ("slepc", when='+slepc+petsc+mpi')
+    depends_on ("trilinos", when='+trilinos+mpi')
+
+    # developer dependnecies
+    #depends_on ("numdiff") #FIXME
+    #depends_on ("astyle") #FIXME
 
     def install(self, spec, prefix):
         options = []
@@ -42,33 +63,116 @@ def install(self, spec, prefix):
         dsuf = 'dylib' if sys.platform == 'darwin' else 'so'
         options.extend([
             '-DCMAKE_BUILD_TYPE=DebugRelease',
-            '-DDEAL_II_WITH_THREADS:BOOL=ON'
-            '-DDEAL_II_WITH_MPI:BOOL=ON',
-            '-DCMAKE_C_COMPILER=%s' % join_path(self.spec['mpi'].prefix.bin, 'mpicc'), # FIXME: avoid hardcoding mpi wrappers names
-            '-DCMAKE_CXX_COMPILER=%s' % join_path(self.spec['mpi'].prefix.bin, 'mpic++'),
-            '-DCMAKE_Fortran_COMPILER=%s' % join_path(self.spec['mpi'].prefix.bin, 'mpif90'),
-            '-DARPACK_DIR=%s' % spec['arpack-ng'].prefix,
+            '-DDEAL_II_COMPONENT_EXAMPLES=ON',
+            '-DDEAL_II_WITH_THREADS:BOOL=ON',
             '-DBOOST_DIR=%s' % spec['boost'].prefix,
-            '-DHDF5_DIR=%s' % spec['hdf5'].prefix,
-            '-DMETIS_DIR=%s' % spec['metis'].prefix,
+            '-DBZIP2_DIR=%s' % spec['bzip2'].prefix,
+            # CMake's FindBlas/Lapack may pickup system's blas/lapack instead of Spack's.
+            # Be more specific to avoid this.
+            # Note that both lapack and blas are provided in -DLAPACK_XYZ variables
+            '-DLAPACK_FOUND=true',
+            '-DLAPACK_INCLUDE_DIRS=%s;%s' %
+                (spec['lapack'].prefix.include,
+                 spec['blas'].prefix.include),
+            '-DLAPACK_LIBRARIES=%s;%s' %
+                (join_path(spec['lapack'].prefix.lib,'liblapack.%s' % dsuf), # FIXME don't hardcode names
+                 join_path(spec['blas'].prefix.lib,'libblas.%s' % dsuf)),    # FIXME don't hardcode names
             '-DMUPARSER_DIR=%s ' % spec['muparser'].prefix,
-            # since Netcdf is spread among two, need to do it by hand:
-            '-DNETCDF_FOUND=true',
-            '-DNETCDF_LIBRARIES=%s;%s' %
-                (join_path(spec['netcdf-cxx'].prefix.lib,'libnetcdf_c++.%s' % dsuf),
-                 join_path(spec['netcdf'].prefix.lib,'libnetcdf.%s' % dsuf)),
-            '-DNETCDF_INCLUDE_DIRS=%s;%s' %
-                (spec['netcdf-cxx'].prefix.include,
-                 spec['netcdf'].prefix.include),
-            '-DOPENCASCADE_DIR=%s' % spec['oce'].prefix,
             '-DP4EST_DIR=%s' % spec['p4est'].prefix,
-            '-DPETSC_DIR=%s' % spec['petsc'].prefix,
-            '-DSLEPC_DIR=%s' % spec['slepc'].prefix,
             '-DUMFPACK_DIR=%s' % spec['suite-sparse'].prefix,
             '-DTBB_DIR=%s' % spec['tbb'].prefix,
-            '-DTRILINOS_DIR=%s' % spec['trilinos'].prefix
+            '-DZLIB_DIR=%s' % spec['zlib'].prefix
         ])
 
+        # MPI
+        if '+mpi' in spec:
+            options.extend([
+                '-DDEAL_II_WITH_MPI:BOOL=ON',
+                '-DCMAKE_C_COMPILER=%s' % join_path(self.spec['mpi'].prefix.bin, 'mpicc'), # FIXME: avoid hardcoding mpi wrappers names
+                '-DCMAKE_CXX_COMPILER=%s' % join_path(self.spec['mpi'].prefix.bin, 'mpic++'),
+                '-DCMAKE_Fortran_COMPILER=%s' % join_path(self.spec['mpi'].prefix.bin, 'mpif90'),
+            ])
+        else:
+            options.extend([
+                '-DDEAL_II_WITH_MPI:BOOL=OFF',
+            ])
+
+        # Optional dependencies for which librariy names are the same as CMake variables
+        for library in ('hdf5', 'p4est','petsc', 'slepc','trilinos','metis','parmetis'):
+            if library in spec:
+                options.extend([
+                    '-D{library}_DIR={value}'.format(library=library.upper(), value=spec[library].prefix),
+                    '-DDEAL_II_WITH_{library}:BOOL=ON'.format(library=library.upper())
+                ])
+            else:
+                options.extend([
+                    '-DDEAL_II_WITH_{library}:BOOL=OFF'.format(library=library.upper())
+                ])
+
+        # doxygen
+        options.extend([
+            '-DDEAL_II_COMPONENT_DOCUMENTATION=%s' % ('ON' if '+doxygen' in spec else 'OFF'),
+        ])
+
+
+        # arpack
+        if '+arpack' in spec:
+            options.extend([
+                '-DARPACK_DIR=%s' % spec['arpack-ng'].prefix,
+                '-DDEAL_II_WITH_ARPACK=ON',
+                '-DDEAL_II_ARPACK_WITH_PARPACK=ON'
+            ])
+        else:
+            options.extend([
+                '-DDEAL_II_WITH_ARPACK=OFF'
+            ])
+
+        # # metis
+        # if '+metis' in spec:
+        #
+        #     if 'mpi' in spec:
+        #         options.extend([
+        #             '-DMETIS_DIR=%s' % spec['parmetis'].prefix,
+        #         ])
+        #     else:
+        #         options.extend([
+        #             '-DMETIS_DIR=%s' % spec['metis'].prefix,
+        #         ])
+        #     options.extend([
+        #         '-DDEAL_II_WITH_METIS=ON'
+        #     ])
+        # else:
+        #     options.extend([
+        #         '-DDEAL_II_WITH_METIS=OFF'
+        #     ])
+
+        # since Netcdf is spread among two, need to do it by hand:
+        if '+netcdf' in spec:
+            options.extend([
+                '-DNETCDF_FOUND=true',
+                '-DNETCDF_LIBRARIES=%s;%s' %
+                    (join_path(spec['netcdf-cxx'].prefix.lib,'libnetcdf_c++.%s' % dsuf),
+                    join_path(spec['netcdf'].prefix.lib,'libnetcdf.%s' % dsuf)),
+                '-DNETCDF_INCLUDE_DIRS=%s;%s' %
+                    (spec['netcdf-cxx'].prefix.include,
+                    spec['netcdf'].prefix.include),
+            ])
+        else:
+            options.extend([
+                '-DDEAL_II_WITH_NETCDF=OFF'
+            ])
+
+        # Open Cascade
+        if '+oce' in spec:
+            options.extend([
+                '-DOPENCASCADE_DIR=%s' % spec['oce'].prefix,
+                '-DDEAL_II_WITH_OPENCASCADE=ON'
+            ])
+        else:
+            options.extend([
+                '-DDEAL_II_WITH_OPENCASCADE=OFF'
+            ])
+
         cmake('.', *options)
 
         make()

From bafc6cebe1ca37116badc1baf60e88564eb01614 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Wed, 30 Mar 2016 12:00:21 +0200
Subject: [PATCH 190/230] doxygen off by default

---
 .../repos/builtin/packages/dealii/package.py  | 22 +++++++++----------
 1 file changed, 11 insertions(+), 11 deletions(-)

diff --git a/var/spack/repos/builtin/packages/dealii/package.py b/var/spack/repos/builtin/packages/dealii/package.py
index 396601356cf..907aa333567 100644
--- a/var/spack/repos/builtin/packages/dealii/package.py
+++ b/var/spack/repos/builtin/packages/dealii/package.py
@@ -8,17 +8,17 @@ class Dealii(Package):
 
     version('8.4.0', 'ac5dbf676096ff61e092ce98c80c2b00')
 
-    variant('mpi',      default=True, description='Compile with MPI')
-    variant('arpack',   default=True, description='Compile with Arpack and PArpack (only with MPI)')
-    variant('doxygen',  default=True, description='Compile with Doxygen documentation')
-    variant('hdf5',     default=True, description='Compile with HDF5 (only with MPI)')
-    variant('metis',    default=True, description='Compile with Metis or ParMetis')
-    variant('netcdf',   default=True, description='Compile with Netcdf (only with MPI)')
-    variant('oce',      default=True, description='Compile with OCE')
-    variant('p4est',    default=True, description='Compile with P4est (only with MPI)')
-    variant('petsc',    default=True, description='Compile with Petsc (only with MPI)')
-    variant('slepc',    default=True, description='Compile with Slepc (only with Petsc and MPI)')
-    variant('trilinos', default=True, description='Compile with Trilinos (only with MPI)')
+    variant('mpi',      default=True,  description='Compile with MPI')
+    variant('arpack',   default=True,  description='Compile with Arpack and PArpack (only with MPI)')
+    variant('doxygen',  default=False, description='Compile with Doxygen documentation')
+    variant('hdf5',     default=True,  description='Compile with HDF5 (only with MPI)')
+    variant('metis',    default=True,  description='Compile with Metis or ParMetis')
+    variant('netcdf',   default=True,  description='Compile with Netcdf (only with MPI)')
+    variant('oce',      default=True,  description='Compile with OCE')
+    variant('p4est',    default=True,  description='Compile with P4est (only with MPI)')
+    variant('petsc',    default=True,  description='Compile with Petsc (only with MPI)')
+    variant('slepc',    default=True,  description='Compile with Slepc (only with Petsc and MPI)')
+    variant('trilinos', default=True,  description='Compile with Trilinos (only with MPI)')
 
     # required dependencies, light version
     depends_on ("blas")

From 9e9f5d01ad43e9b00262a12d1fd1225ac368581d Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Wed, 30 Mar 2016 11:59:13 +0200
Subject: [PATCH 191/230] doxygen: add missing dependencies

---
 var/spack/repos/builtin/packages/doxygen/package.py | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/var/spack/repos/builtin/packages/doxygen/package.py b/var/spack/repos/builtin/packages/doxygen/package.py
index 3d4a4e47a78..3a1deba9e14 100644
--- a/var/spack/repos/builtin/packages/doxygen/package.py
+++ b/var/spack/repos/builtin/packages/doxygen/package.py
@@ -4,6 +4,7 @@
 #------------------------------------------------------------------------------
 
 from spack import *
+import sys
 
 class Doxygen(Package):
     """Doxygen is the de facto standard tool for generating documentation
@@ -17,6 +18,10 @@ class Doxygen(Package):
     version('1.8.10', '79767ccd986f12a0f949015efb5f058f')
 
     depends_on("cmake@2.8.12:")
+    # flex does not build on OSX, but it's provided there anyway
+    depends_on("flex", sys.platform != 'darwin')
+    depends_on("bison", sys.platform != 'darwin')
+
 
     def install(self, spec, prefix):
         cmake('.', *std_cmake_args)

From 2abdd71b414b4f551e927edb7304b4dcc053d09e Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Wed, 30 Mar 2016 15:19:29 +0200
Subject: [PATCH 192/230] add dev version and conditionals for tests; remove
 parmetis

---
 .../repos/builtin/packages/dealii/package.py  | 62 +++++++------------
 1 file changed, 24 insertions(+), 38 deletions(-)

diff --git a/var/spack/repos/builtin/packages/dealii/package.py b/var/spack/repos/builtin/packages/dealii/package.py
index 907aa333567..32dfb33c6d0 100644
--- a/var/spack/repos/builtin/packages/dealii/package.py
+++ b/var/spack/repos/builtin/packages/dealii/package.py
@@ -7,12 +7,13 @@ class Dealii(Package):
     url      = "https://github.com/dealii/dealii/releases/download/v8.4.0/dealii-8.4.0.tar.gz"
 
     version('8.4.0', 'ac5dbf676096ff61e092ce98c80c2b00')
+    version('dev', git='https://github.com/dealii/dealii.git')
 
     variant('mpi',      default=True,  description='Compile with MPI')
     variant('arpack',   default=True,  description='Compile with Arpack and PArpack (only with MPI)')
     variant('doxygen',  default=False, description='Compile with Doxygen documentation')
     variant('hdf5',     default=True,  description='Compile with HDF5 (only with MPI)')
-    variant('metis',    default=True,  description='Compile with Metis or ParMetis')
+    variant('metis',    default=True,  description='Compile with Metis')
     variant('netcdf',   default=True,  description='Compile with Netcdf (only with MPI)')
     variant('oce',      default=True,  description='Compile with OCE')
     variant('p4est',    default=True,  description='Compile with P4est (only with MPI)')
@@ -42,7 +43,6 @@ class Dealii(Package):
     depends_on ("netcdf-cxx", when='+netcdf+mpi')
     depends_on ("oce", when='+oce')
     depends_on ("p4est", when='+p4est+mpi')
-    depends_on ("parmetis", when='+metis+mpi')
     depends_on ("petsc+mpi", when='+petsc+mpi')
     depends_on ("slepc", when='+slepc+petsc+mpi')
     depends_on ("trilinos", when='+trilinos+mpi')
@@ -98,7 +98,7 @@ def install(self, spec, prefix):
             ])
 
         # Optional dependencies for which librariy names are the same as CMake variables
-        for library in ('hdf5', 'p4est','petsc', 'slepc','trilinos','metis','parmetis'):
+        for library in ('hdf5', 'p4est','petsc', 'slepc','trilinos','metis'):
             if library in spec:
                 options.extend([
                     '-D{library}_DIR={value}'.format(library=library.upper(), value=spec[library].prefix),
@@ -127,25 +127,6 @@ def install(self, spec, prefix):
                 '-DDEAL_II_WITH_ARPACK=OFF'
             ])
 
-        # # metis
-        # if '+metis' in spec:
-        #
-        #     if 'mpi' in spec:
-        #         options.extend([
-        #             '-DMETIS_DIR=%s' % spec['parmetis'].prefix,
-        #         ])
-        #     else:
-        #         options.extend([
-        #             '-DMETIS_DIR=%s' % spec['metis'].prefix,
-        #         ])
-        #     options.extend([
-        #         '-DDEAL_II_WITH_METIS=ON'
-        #     ])
-        # else:
-        #     options.extend([
-        #         '-DDEAL_II_WITH_METIS=OFF'
-        #     ])
-
         # since Netcdf is spread among two, need to do it by hand:
         if '+netcdf' in spec:
             options.extend([
@@ -202,16 +183,18 @@ def install(self, spec, prefix):
             # list the number of cycles to speed up
             filter_file(r'(const unsigned int n_cycles = 8;)',  ('const unsigned int n_cycles = 2;'), 'step-40.cc')
             cmake('.')
-            make('release')
-            make('run',parallel=False)
+            if '^petsc' in spec:
+                make('release')
+                make('run',parallel=False)
 
             print('=====================================')
             print('========= Step-40 Trilinos ==========')
             print('=====================================')
             # change Linear Algebra to Trilinos
             filter_file(r'(\/\/ #define FORCE_USE_OF_TRILINOS.*)',  ('#define FORCE_USE_OF_TRILINOS'), 'step-40.cc')
-            make('release')
-            make('run',parallel=False)
+            if '^trilinos+hypre' in spec:
+                make('release')
+                make('run',parallel=False)
 
             print('=====================================')
             print('=== Step-40 Trilinos SuperluDist ====')
@@ -223,31 +206,34 @@ def install(self, spec, prefix):
             filter_file(r'(preconditioner.initialize\(system_matrix, data\);)',  (''), 'step-40.cc')
             filter_file(r'(solver\.solve \(system_matrix, completely_distributed_solution, system_rhs,)',  ('solver.solve (system_matrix, completely_distributed_solution, system_rhs);'), 'step-40.cc')
             filter_file(r'(preconditioner\);)',  (''), 'step-40.cc')
-
-            make('release')
-            make('run',paralle=False)
+            if '^trilinos+superlu-dist' in spec:
+                make('release')
+                make('run',paralle=False)
 
             print('=====================================')
             print('====== Step-40 Trilinos MUMPS =======')
             print('=====================================')
             # switch to Mumps
             filter_file(r'(Amesos_Superludist)',  ('Amesos_Mumps'), 'step-40.cc')
-            make('release')
-            make('run',parallel=False)
+            if '^trilinos+mumps' in spec:
+                make('release')
+                make('run',parallel=False)
 
         print('=====================================')
         print('============ Step-36 ================')
         print('=====================================')
         with working_dir('examples/step-36'):
-            cmake('.')
-            make('release')
-            make('run',parallel=False)
+            if 'slepc' in spec:
+                cmake('.')
+                make('release')
+                make('run',parallel=False)
 
         print('=====================================')
         print('============ Step-54 ================')
         print('=====================================')
         with working_dir('examples/step-54'):
-            cmake('.')
-            make('release')
-            # FIXME
-            # make('run',parallel=False)
+            if 'oce' in spec:
+                cmake('.')
+                make('release')
+                if sys.platform != 'darwin': #FIXME
+                    make('run',parallel=False)

From 5b1ef64e31a56877f6859820ca7a79dd51f6fe84 Mon Sep 17 00:00:00 2001
From: "Kelly (KT) Thompson" <kgt@lanl.gov>
Date: Wed, 30 Mar 2016 09:33:00 -0600
Subject: [PATCH 193/230] + Provide basic instructions for providing subversion
 w/o additional language bindings.

---
 .../apr-util/{apr-util.new => }/package.py    |  0
 .../packages/apr/{apr.new => }/package.py     | 13 ----------
 .../{subversion.new => }/package.py           | 24 ++++++++++++++++---
 3 files changed, 21 insertions(+), 16 deletions(-)
 rename var/spack/repos/builtin/packages/apr-util/{apr-util.new => }/package.py (100%)
 rename var/spack/repos/builtin/packages/apr/{apr.new => }/package.py (71%)
 rename var/spack/repos/builtin/packages/subversion/{subversion.new => }/package.py (78%)

diff --git a/var/spack/repos/builtin/packages/apr-util/apr-util.new/package.py b/var/spack/repos/builtin/packages/apr-util/package.py
similarity index 100%
rename from var/spack/repos/builtin/packages/apr-util/apr-util.new/package.py
rename to var/spack/repos/builtin/packages/apr-util/package.py
diff --git a/var/spack/repos/builtin/packages/apr/apr.new/package.py b/var/spack/repos/builtin/packages/apr/package.py
similarity index 71%
rename from var/spack/repos/builtin/packages/apr/apr.new/package.py
rename to var/spack/repos/builtin/packages/apr/package.py
index 5cbbad350bd..8a440766ece 100644
--- a/var/spack/repos/builtin/packages/apr/apr.new/package.py
+++ b/var/spack/repos/builtin/packages/apr/package.py
@@ -31,19 +31,6 @@ class Apr(Package):
 
     version('1.5.2',    '98492e965963f852ab29f9e61b2ad700')
 
-    #variant('ncurses', default=True, description='Enables the build of the ncurses gui')
-    #variant('qt', default=False, description='Enables the build of cmake-gui')
-    #variant('doc', default=False, description='Enables the generation of html and man page documentation')
-
-    #depends_on('ncurses', when='+ncurses')
-    #depends_on('qt', when='+qt')
-    #depends_on('python@2.7.11:', when='+doc')
-    #depends_on('py-sphinx', when='+doc')
-
-    #def url_for_version(self, version):
-    #    """Handle CMake's version-based custom URLs."""
-    #    return 'https://cmake.org/files/v%s/cmake-%s.tar.gz' % (version.up_to(2), version)
-
     def install(self, spec, prefix):
         options = ['--prefix=%s' % prefix]
         configure(*options)
diff --git a/var/spack/repos/builtin/packages/subversion/subversion.new/package.py b/var/spack/repos/builtin/packages/subversion/package.py
similarity index 78%
rename from var/spack/repos/builtin/packages/subversion/subversion.new/package.py
rename to var/spack/repos/builtin/packages/subversion/package.py
index b1c3380238a..5db1c3eb92d 100644
--- a/var/spack/repos/builtin/packages/subversion/subversion.new/package.py
+++ b/var/spack/repos/builtin/packages/subversion/package.py
@@ -37,7 +37,13 @@ class Subversion(Package):
     depends_on('apr-util')
     depends_on('zlib')
     depends_on('sqlite')
+
+    # Optional: We need swig if we want the Perl, Python or Ruby
+    # bindings.
     #depends_on('swig')
+    #depends_on('python')
+    #depends_on('perl')
+    #depends_on('ruby')
 
     def install(self, spec, prefix):
 
@@ -53,7 +59,19 @@ def install(self, spec, prefix):
         configure(*options)
         make()
         make('install')
-        #make('swig-py') # python bindings
-        #make('install-swig-py')
-        #make('swig-pl') # perl bindings
+
+        # python bindings
+        #make('swig-py',
+        #     'swig-pydir=/usr/lib/python2.7/site-packages/libsvn',
+        #     'swig_pydir_extra=/usr/lib/python2.7/site-packages/svn')
+        #make('install-swig-py',
+        #     'swig-pydir=/usr/lib/python2.7/site-packages/libsvn',
+        #     'swig_pydir_extra=/usr/lib/python2.7/site-packages/svn')
+
+        # perl bindings
+        #make('swig-pl')
         #make('install-swig-pl')
+
+        # ruby bindings
+        #make('swig-rb')
+        #make('isntall-swig-rb')

From a7ceacb991b2a3b0caba8da41a39e045912f9e22 Mon Sep 17 00:00:00 2001
From: "Kelly (KT) Thompson" <kgt@lanl.gov>
Date: Wed, 30 Mar 2016 09:47:31 -0600
Subject: [PATCH 194/230] + Changes to swig are not needed with this PR.

---
 var/spack/repos/builtin/packages/swig/package.py | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/var/spack/repos/builtin/packages/swig/package.py b/var/spack/repos/builtin/packages/swig/package.py
index de6055e9656..8d46c4fe465 100644
--- a/var/spack/repos/builtin/packages/swig/package.py
+++ b/var/spack/repos/builtin/packages/swig/package.py
@@ -36,14 +36,11 @@ class Swig(Package):
     homepage = "http://www.swig.org"
     url      = "http://prdownloads.sourceforge.net/swig/swig-3.0.2.tar.gz"
 
-    version('3.0.8',  'c96a1d5ecb13d38604d7e92148c73c97')
-    version('3.0.2',  '62f9b0d010cef36a13a010dc530d0d41')
-    version('2.0.12', 'c3fb0b2d710cc82ed0154b91e43085a4')
+    version('3.0.2', '62f9b0d010cef36a13a010dc530d0d41')
 
     depends_on('pcre')
 
     def install(self, spec, prefix):
         configure("--prefix=%s" % prefix)
-
         make()
         make("install")

From bc309e42d8f4d5c536ea43dc01a8356bf0aba3f2 Mon Sep 17 00:00:00 2001
From: Glenn Johnson <glenn-johnson@uiowa.edu>
Date: Wed, 30 Mar 2016 11:00:18 -0500
Subject: [PATCH 195/230] New package, py-bottleneck.

---
 .../builtin/packages/py-bottleneck/package.py      | 14 ++++++++++++++
 1 file changed, 14 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/py-bottleneck/package.py

diff --git a/var/spack/repos/builtin/packages/py-bottleneck/package.py b/var/spack/repos/builtin/packages/py-bottleneck/package.py
new file mode 100644
index 00000000000..0aa4208b4de
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-bottleneck/package.py
@@ -0,0 +1,14 @@
+from spack import *
+
+class PyBottleneck(Package):
+    """Bottleneck is a collection of fast NumPy array functions written in Cython."""
+    homepage = "https://pypi.python.org/pypi/Bottleneck/1.0.0"
+    url      = "https://pypi.python.org/packages/source/B/Bottleneck/Bottleneck-1.0.0.tar.gz"
+
+    version('1.0.0', '380fa6f275bd24f27e7cf0e0d752f5d2')
+
+    extends('python', ignore=r'bin/f2py$')
+    depends_on('py-numpy')
+
+    def install(self, spec, prefix):
+        python('setup.py', 'install', '--prefix=%s' % prefix)

From 5c95977dccef17a3cceb741d39f94aa075a0a9c4 Mon Sep 17 00:00:00 2001
From: Glenn Johnson <glenn-johnson@uiowa.edu>
Date: Wed, 30 Mar 2016 11:06:04 -0500
Subject: [PATCH 196/230] Added version 15.0.1

---
 var/spack/repos/builtin/packages/py-virtualenv/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/py-virtualenv/package.py b/var/spack/repos/builtin/packages/py-virtualenv/package.py
index 037a6fc59fe..09303d37b43 100644
--- a/var/spack/repos/builtin/packages/py-virtualenv/package.py
+++ b/var/spack/repos/builtin/packages/py-virtualenv/package.py
@@ -8,6 +8,7 @@ class PyVirtualenv(Package):
 
     version('1.11.6', 'f61cdd983d2c4e6aeabb70b1060d6f49')
     version('13.0.1', '1ffc011bde6667f0e37ecd976f4934db')
+    version('15.0.1', '28d76a0d9cbd5dc42046dd14e76a6ecc')
 
     extends('python')
     depends_on('py-setuptools')

From 3b19cc303fae89eed11581d7cdfe2ab8e9d469ef Mon Sep 17 00:00:00 2001
From: Glenn Johnson <glenn-johnson@uiowa.edu>
Date: Wed, 30 Mar 2016 11:08:28 -0500
Subject: [PATCH 197/230] Added version 1.10.0.

---
 var/spack/repos/builtin/packages/py-six/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/py-six/package.py b/var/spack/repos/builtin/packages/py-six/package.py
index 05c5bd00a98..df277100f77 100644
--- a/var/spack/repos/builtin/packages/py-six/package.py
+++ b/var/spack/repos/builtin/packages/py-six/package.py
@@ -6,6 +6,7 @@ class PySix(Package):
     url      = "https://pypi.python.org/packages/source/s/six/six-1.9.0.tar.gz"
 
     version('1.9.0', '476881ef4012262dfc8adc645ee786c4')
+    version('1.10.0', '34eed507548117b2ab523ab14b2f8b55')
 
     extends('python')
     depends_on('py-setuptools')

From 9153e03e5ce5bdd5161aa4b493854208040fcf3d Mon Sep 17 00:00:00 2001
From: Glenn Johnson <glenn-johnson@uiowa.edu>
Date: Wed, 30 Mar 2016 11:09:47 -0500
Subject: [PATCH 198/230] Added version 20.5.

---
 var/spack/repos/builtin/packages/py-setuptools/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/py-setuptools/package.py b/var/spack/repos/builtin/packages/py-setuptools/package.py
index 26c048bfd42..c6d9be1add7 100644
--- a/var/spack/repos/builtin/packages/py-setuptools/package.py
+++ b/var/spack/repos/builtin/packages/py-setuptools/package.py
@@ -9,6 +9,7 @@ class PySetuptools(Package):
     version('16.0', '0ace0b96233516fc5f7c857d086aa3ad')
     version('18.1', 'f72e87f34fbf07f299f6cb46256a0b06')
     version('19.2', '78353b1f80375ca5e088f4b4627ffe03')
+    version('20.5', 'fadc1e1123ddbe31006e5e43e927362b')
 
     extends('python')
 

From 42729d9cceafaf2382455f9e765cbc261dc41578 Mon Sep 17 00:00:00 2001
From: Glenn Johnson <glenn-johnson@uiowa.edu>
Date: Wed, 30 Mar 2016 11:10:32 -0500
Subject: [PATCH 199/230] Added version 2016.3.

---
 var/spack/repos/builtin/packages/py-pytz/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/py-pytz/package.py b/var/spack/repos/builtin/packages/py-pytz/package.py
index da6311a784a..060cf0cde41 100644
--- a/var/spack/repos/builtin/packages/py-pytz/package.py
+++ b/var/spack/repos/builtin/packages/py-pytz/package.py
@@ -7,6 +7,7 @@ class PyPytz(Package):
 
     version('2014.10', 'eb1cb941a20c5b751352c52486aa1dd7')
     version('2015.4', '417a47b1c432d90333e42084a605d3d8')
+    version('2016.3', 'abae92c3301b27bd8a9f56b14f52cb29')
 
     extends('python')
 

From 17075736a0ff4f8f677527664e37d55b39cbfe93 Mon Sep 17 00:00:00 2001
From: Glenn Johnson <glenn-johnson@uiowa.edu>
Date: Wed, 30 Mar 2016 11:16:11 -0500
Subject: [PATCH 200/230] Add version 2.5.2.

---
 var/spack/repos/builtin/packages/py-dateutil/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/py-dateutil/package.py b/var/spack/repos/builtin/packages/py-dateutil/package.py
index 0a17f2f2d24..b67e91ace60 100644
--- a/var/spack/repos/builtin/packages/py-dateutil/package.py
+++ b/var/spack/repos/builtin/packages/py-dateutil/package.py
@@ -7,6 +7,7 @@ class PyDateutil(Package):
 
     version('2.4.0', '75714163bb96bedd07685cdb2071b8bc')
     version('2.4.2', '4ef68e1c485b09e9f034e10473e5add2')
+    version('2.5.2', 'eafe168e8f404bf384514f5116eedbb6')
 
     extends('python')
     depends_on('py-setuptools')

From 8948cb100be21034b7e4bc78b7383fa73005a03a Mon Sep 17 00:00:00 2001
From: Glenn Johnson <glenn-johnson@uiowa.edu>
Date: Wed, 30 Mar 2016 11:16:35 -0500
Subject: [PATCH 201/230] Add version 1.3.7.

---
 var/spack/repos/builtin/packages/py-nose/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/py-nose/package.py b/var/spack/repos/builtin/packages/py-nose/package.py
index 4fee99098ed..c2c2b52e03e 100644
--- a/var/spack/repos/builtin/packages/py-nose/package.py
+++ b/var/spack/repos/builtin/packages/py-nose/package.py
@@ -10,6 +10,7 @@ class PyNose(Package):
 
     version('1.3.4', '6ed7169887580ddc9a8e16048d38274d')
     version('1.3.6', '0ca546d81ca8309080fc80cb389e7a16')
+    version('1.3.7', '4d3ad0ff07b61373d2cefc89c5d0b20b')
 
     extends('python', ignore=r'bin/nosetests.*$')
     depends_on('py-setuptools')

From f3b353f5f95c21641d4bee274393879e3a068c3c Mon Sep 17 00:00:00 2001
From: Glenn Johnson <glenn-johnson@uiowa.edu>
Date: Wed, 30 Mar 2016 11:17:24 -0500
Subject: [PATCH 202/230] Add 'bin/f2py' to ignore so activation works.

---
 var/spack/repos/builtin/packages/py-matplotlib/package.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/py-matplotlib/package.py b/var/spack/repos/builtin/packages/py-matplotlib/package.py
index 2167735fb89..45e77dd6313 100644
--- a/var/spack/repos/builtin/packages/py-matplotlib/package.py
+++ b/var/spack/repos/builtin/packages/py-matplotlib/package.py
@@ -12,7 +12,7 @@ class PyMatplotlib(Package):
     variant('gui', default=False, description='Enable GUI')
     variant('ipython', default=False, description='Enable ipython support')
 
-    extends('python', ignore=r'bin/nosetests.*$|bin/pbr$')
+    extends('python', ignore=r'bin/nosetests.*$|bin/pbr$|bin/f2py$')
 
     depends_on('py-pyside', when='+gui')
     depends_on('py-ipython', when='+ipython')

From e7ae983b41943939a20ca4964824b166833c282b Mon Sep 17 00:00:00 2001
From: Glenn Johnson <glenn-johnson@uiowa.edu>
Date: Wed, 30 Mar 2016 11:20:27 -0500
Subject: [PATCH 203/230] Added version 2.5. Added 'bin/f2py' to ignore so that
 activation works.

---
 var/spack/repos/builtin/packages/py-numexpr/package.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/py-numexpr/package.py b/var/spack/repos/builtin/packages/py-numexpr/package.py
index 89f8a525b12..081a79dec68 100644
--- a/var/spack/repos/builtin/packages/py-numexpr/package.py
+++ b/var/spack/repos/builtin/packages/py-numexpr/package.py
@@ -7,8 +7,9 @@ class PyNumexpr(Package):
     url      = "https://pypi.python.org/packages/source/n/numexpr/numexpr-2.4.6.tar.gz"
 
     version('2.4.6', '17ac6fafc9ea1ce3eb970b9abccb4fbd')
+    version('2.5', '84f66cced45ba3e30dcf77a937763aaa')
 
-    extends('python')
+    extends('python', ignore=r'bin/f2py$')
     depends_on('py-numpy')
 
     def install(self, spec, prefix):

From 78be85c84f89d861086c04e4fcc4fa70c21d0a5f Mon Sep 17 00:00:00 2001
From: Glenn Johnson <glenn-johnson@uiowa.edu>
Date: Wed, 30 Mar 2016 11:21:17 -0500
Subject: [PATCH 204/230] Added version 1.11.0.

---
 var/spack/repos/builtin/packages/py-numpy/package.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/var/spack/repos/builtin/packages/py-numpy/package.py b/var/spack/repos/builtin/packages/py-numpy/package.py
index a08e612df6c..40988fb44a7 100644
--- a/var/spack/repos/builtin/packages/py-numpy/package.py
+++ b/var/spack/repos/builtin/packages/py-numpy/package.py
@@ -9,6 +9,7 @@ class PyNumpy(Package):
     homepage = "http://www.numpy.org/"
     url      = "https://pypi.python.org/packages/source/n/numpy/numpy-1.9.1.tar.gz"
 
+    version('1.11.0', 'bc56fb9fc2895aa4961802ffbdb31d0b')
     version('1.10.4', 'aed294de0aa1ac7bd3f9745f4f1968ad')
     version('1.9.2',  'a1ed53432dbcd256398898d35bc8e645')
     version('1.9.1',  '78842b73560ec378142665e712ae4ad9')

From 8ae84cfabaf22e52b01911c909b2d2342b75f3d9 Mon Sep 17 00:00:00 2001
From: Glenn Johnson <glenn-johnson@uiowa.edu>
Date: Wed, 30 Mar 2016 11:21:38 -0500
Subject: [PATCH 205/230] This commit updates pandas and fixes dependencies.
 Added version 0.18.0. Added 'bin/f2py' to ignore so that activation works.

Removed unneccessary dependencies on
- libdrm
- libpciaccess
- llvm
- mesa

Added recommended dependencies from the pandas project site.
http://pandas.pydata.org/pandas-docs/stable/install.html
- py-numexpr
- py-bottleneck

The py-bottleneck is a new package that is also in this branch.

Removed optional dependencies
- py-scipy
- py-matplotlib

While those are most likely desired to be in the same python stack as
pandas they are not required by pandas.
---
 var/spack/repos/builtin/packages/py-pandas/package.py | 11 ++++-------
 1 file changed, 4 insertions(+), 7 deletions(-)

diff --git a/var/spack/repos/builtin/packages/py-pandas/package.py b/var/spack/repos/builtin/packages/py-pandas/package.py
index 5b9997faa94..2320b1f92f3 100644
--- a/var/spack/repos/builtin/packages/py-pandas/package.py
+++ b/var/spack/repos/builtin/packages/py-pandas/package.py
@@ -8,18 +8,15 @@ class PyPandas(Package):
 
     version('0.16.0', 'bfe311f05dc0c351f8955fbd1e296e73')
     version('0.16.1', 'fac4f25748f9610a3e00e765474bdea8')
+    version('0.18.0', 'f143762cd7a59815e348adf4308d2cf6')
 
-    extends('python')
+    extends('python', ignore=r'bin/f2py$')
     depends_on('py-dateutil')
     depends_on('py-numpy')
-    depends_on('py-matplotlib')
-    depends_on('py-scipy')
     depends_on('py-setuptools')
     depends_on('py-pytz')
-    depends_on('libdrm')
-    depends_on('libpciaccess')
-    depends_on('llvm')
-    depends_on('mesa')
+    depends_on('py-numexpr')
+    depends_on('py-bottleneck')
 
     def install(self, spec, prefix):
         python('setup.py', 'install', '--prefix=%s' % prefix)

From 9519f3d988d4f83cd3edf9bbdd90080559ba9549 Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Wed, 30 Mar 2016 11:46:58 -0500
Subject: [PATCH 206/230] Fix MPI-CUDA bug

---
 var/spack/repos/builtin/packages/cuda/package.py    | 11 ++++++-----
 .../repos/builtin/packages/hoomd-blue/package.py    | 13 +++++++++----
 2 files changed, 15 insertions(+), 9 deletions(-)

diff --git a/var/spack/repos/builtin/packages/cuda/package.py b/var/spack/repos/builtin/packages/cuda/package.py
index 547b43d6d26..eca371d05ae 100644
--- a/var/spack/repos/builtin/packages/cuda/package.py
+++ b/var/spack/repos/builtin/packages/cuda/package.py
@@ -16,9 +16,12 @@ class Cuda(Package):
     see http://software.llnl.gov/spack/mirrors.html"""
 
     homepage = "http://www.nvidia.com/object/cuda_home_new.html"
-    url      = "file://%s/cuda_7.5.18_linux.run" % os.getcwd()
 
-    version('7.5.18', '4b3bcecf0dfc35928a0898793cf3e4c6', expand=False)
+    version('7.5.18', '4b3bcecf0dfc35928a0898793cf3e4c6', expand=False,
+            url="file://%s/cuda_7.5.18_linux.run"    % os.getcwd())
+    version('6.5.14', '90b1b8f77313600cc294d9271741f4da', expand=False,
+            url="file://%s/cuda_6.5.14_linux_64.run" % os.getcwd())
+
 
     def install(self, spec, prefix):
         runfile = glob(os.path.join(self.stage.path, 'cuda*.run'))[0]
@@ -27,15 +30,13 @@ def install(self, spec, prefix):
         runfile = which(runfile)
 
         # Note: NVIDIA does not officially support many newer versions of compilers.
-        # For example, on CentOS 6, you must use GCC 4.4.7 or older.
-        # The --override flag disables these checks. See:
+        # For example, on CentOS 6, you must use GCC 4.4.7 or older. See:
         # http://docs.nvidia.com/cuda/cuda-installation-guide-linux/#system-requirements
         # for details.
 
         runfile(
             '--silent',   # disable interactive prompts
             '--verbose',  # create verbose log file
-            '--override', # ignore compiler checks
             '--toolkit',  # install CUDA Toolkit
             '--toolkitpath=%s' % prefix
         )
diff --git a/var/spack/repos/builtin/packages/hoomd-blue/package.py b/var/spack/repos/builtin/packages/hoomd-blue/package.py
index 97ce9c0cf0f..32fdff94267 100644
--- a/var/spack/repos/builtin/packages/hoomd-blue/package.py
+++ b/var/spack/repos/builtin/packages/hoomd-blue/package.py
@@ -49,10 +49,14 @@ def install(self, spec, prefix):
             cmake_args.append('-DENABLE_CUDA=OFF')
 
         # CUDA-aware MPI library support
-        if '+cuda' in spec and '+mpi' in spec:
-            cmake_args.append('-DENABLE_MPI_CUDA=ON')
-        else:
-            cmake_args.append('-DENABLE_MPI_CUDA=OFF')
+        #if '+cuda' in spec and '+mpi' in spec:
+        #    cmake_args.append('-DENABLE_MPI_CUDA=ON')
+        #else:
+        #    cmake_args.append('-DENABLE_MPI_CUDA=OFF')
+
+        # There may be a bug in the MPI-CUDA code. See:
+        # https://groups.google.com/forum/#!msg/hoomd-users/2griTESmc5I/E69s_M5fDwAJ
+        cmake_args.append('-DENABLE_MPI_CUDA=OFF')
 
         # Documentation
         if '+doc' in spec:
@@ -64,4 +68,5 @@ def install(self, spec, prefix):
         cmake('.', *cmake_args)
 
         make()
+        make("test")
         make("install")

From b909da759d7b6d0443a97c13ba1c97118acd3e7a Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Wed, 30 Mar 2016 19:26:03 +0200
Subject: [PATCH 207/230] petsc: remove no longer needed -Qunused-arguments
 hack

---
 .../repos/builtin/packages/petsc/package.py     | 17 ++++-------------
 1 file changed, 4 insertions(+), 13 deletions(-)

diff --git a/var/spack/repos/builtin/packages/petsc/package.py b/var/spack/repos/builtin/packages/petsc/package.py
index e9b7c8a732c..5c1fc6cc924 100644
--- a/var/spack/repos/builtin/packages/petsc/package.py
+++ b/var/spack/repos/builtin/packages/petsc/package.py
@@ -71,19 +71,10 @@ def mpi_dependent_options(self):
                 errors = ['incompatible variants given'] + errors
                 raise RuntimeError('\n'.join(errors))
         else:
-            if self.compiler.name == "clang":
-                compiler_opts = [
-                    '--with-mpi=1',
-                    '--with-cc=%s  -Qunused-arguments' % join_path(self.spec['mpi'].prefix.bin, 'mpicc'), # Avoid confusing PETSc config by clang: warning: argument unused during compilation
-                    '--with-cxx=%s -Qunused-arguments' % join_path(self.spec['mpi'].prefix.bin, 'mpic++'),
-                    '--with-fc=%s' % join_path(self.spec['mpi'].prefix.bin, 'mpif90'),
-                    '--with-f77=%s' % join_path(self.spec['mpi'].prefix.bin, 'mpif77'),
-                ]
-            else:
-                compiler_opts = [
-                    '--with-mpi=1',
-                    '--with-mpi-dir=%s' % self.spec['mpi'].prefix,
-                ]
+            compiler_opts = [
+                '--with-mpi=1',
+                '--with-mpi-dir=%s' % self.spec['mpi'].prefix,
+            ]
         return compiler_opts
 
     def install(self, spec, prefix):

From 01657e6991197c999180c2fec367fc75e59fba15 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Wed, 30 Mar 2016 11:41:25 -0700
Subject: [PATCH 208/230] Make suite-sparse use spack compilers.

---
 .../repos/builtin/packages/suite-sparse/package.py   | 12 +++++++++++-
 1 file changed, 11 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/suite-sparse/package.py b/var/spack/repos/builtin/packages/suite-sparse/package.py
index b57f9967c30..c2196dcec4d 100644
--- a/var/spack/repos/builtin/packages/suite-sparse/package.py
+++ b/var/spack/repos/builtin/packages/suite-sparse/package.py
@@ -23,4 +23,14 @@ def install(self, spec, prefix):
 
         # FIXME : this actually uses the current workaround
         # FIXME : (blas / lapack always provide libblas and liblapack as aliases)
-        make('install', 'INSTALL=%s' % prefix, 'BLAS=-lblas', 'LAPACK=-llapack')
+        make('install', 'INSTALL=%s' % prefix,
+
+             # inject Spack compiler wrappers
+             'AUTOCC=no',
+             'CC=cc',
+             'CXX=c++',
+             'F77=f77',
+
+             # BLAS arguments require path to libraries
+             'BLAS=-lblas',
+             'LAPACK=-llapack')

From 5506e89aa9f45b94a7b16a24e24e3c081fdf1e38 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Wed, 30 Mar 2016 21:41:23 +0200
Subject: [PATCH 209/230] rename variant doxygen to doc

---
 var/spack/repos/builtin/packages/dealii/package.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/var/spack/repos/builtin/packages/dealii/package.py b/var/spack/repos/builtin/packages/dealii/package.py
index 32dfb33c6d0..7aaf33380e6 100644
--- a/var/spack/repos/builtin/packages/dealii/package.py
+++ b/var/spack/repos/builtin/packages/dealii/package.py
@@ -11,7 +11,7 @@ class Dealii(Package):
 
     variant('mpi',      default=True,  description='Compile with MPI')
     variant('arpack',   default=True,  description='Compile with Arpack and PArpack (only with MPI)')
-    variant('doxygen',  default=False, description='Compile with Doxygen documentation')
+    variant('doc',      default=False, description='Compile with documentation')
     variant('hdf5',     default=True,  description='Compile with HDF5 (only with MPI)')
     variant('metis',    default=True,  description='Compile with Metis')
     variant('netcdf',   default=True,  description='Compile with Netcdf (only with MPI)')
@@ -36,7 +36,7 @@ class Dealii(Package):
     # optional dependencies
     depends_on ("mpi", when="+mpi")
     depends_on ("arpack-ng+mpi", when='+arpack+mpi')
-    depends_on ("doxygen", when='+doxygen')
+    depends_on ("doxygen", when='+doc')
     depends_on ("hdf5+mpi~cxx", when='+hdf5+mpi') #FIXME NetCDF declares dependency with ~cxx, why?
     depends_on ("metis", when='+metis')
     depends_on ("netcdf+mpi", when="+netcdf+mpi")
@@ -111,7 +111,7 @@ def install(self, spec, prefix):
 
         # doxygen
         options.extend([
-            '-DDEAL_II_COMPONENT_DOCUMENTATION=%s' % ('ON' if '+doxygen' in spec else 'OFF'),
+            '-DDEAL_II_COMPONENT_DOCUMENTATION=%s' % ('ON' if '+doc' in spec else 'OFF'),
         ])
 
 

From dbb25bfeed7113cbd6be090df52b97fcc10588e1 Mon Sep 17 00:00:00 2001
From: Ben Boeckel <mathstuf@gmail.com>
Date: Wed, 30 Mar 2016 16:17:52 -0400
Subject: [PATCH 210/230] ninja: fix installation on OS X

The cp -t flag is a GNU-ism. Instead, add a trailing slash to bindir to
ensure that it is not treated as a file.
---
 var/spack/repos/builtin/packages/ninja/package.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/var/spack/repos/builtin/packages/ninja/package.py b/var/spack/repos/builtin/packages/ninja/package.py
index 9e6bf4e358d..0722dd49a64 100644
--- a/var/spack/repos/builtin/packages/ninja/package.py
+++ b/var/spack/repos/builtin/packages/ninja/package.py
@@ -16,7 +16,7 @@ def install(self, spec, prefix):
 
         cp = which('cp')
 
-        bindir = os.path.join(prefix, 'bin')
+        bindir = os.path.join(prefix, 'bin/')
         mkdir(bindir)
-        cp('-a', '-t', bindir, 'ninja')
-        cp('-ra', 'misc', prefix)
+        cp('-a', 'ninja', bindir)
+        cp('-a', 'misc', prefix)

From d1a3adfcf09fb489acce9d29b2f9494df5f5d848 Mon Sep 17 00:00:00 2001
From: "Kelly (KT) Thompson" <kgt@lanl.gov>
Date: Wed, 30 Mar 2016 14:25:44 -0600
Subject: [PATCH 211/230] + Make --disable-perl the default configure option.

---
 var/spack/repos/builtin/packages/graphviz/package.py | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/var/spack/repos/builtin/packages/graphviz/package.py b/var/spack/repos/builtin/packages/graphviz/package.py
index 84bd696af2b..a45cd8743ee 100644
--- a/var/spack/repos/builtin/packages/graphviz/package.py
+++ b/var/spack/repos/builtin/packages/graphviz/package.py
@@ -7,7 +7,11 @@ class Graphviz(Package):
 
     version('2.38.0', '5b6a829b2ac94efcd5fa3c223ed6d3ae')
 
-    variant('perl', default=True, description='Disable if you have problems with the optional script language bindings')
+    # By default disable optional Perl language support to prevent build issues
+    # related to missing Perl packages. If spack begins support for Perl in the
+    # future, this package can be updated to depend_on('perl') and the
+    # ncecessary devel packages.
+    variant('perl', default=False, description='Disable if you have problems with the optional script language bindings')
 
     parallel = False
 
@@ -17,7 +21,7 @@ class Graphviz(Package):
 
     def install(self, spec, prefix):
         options = ['--prefix=%s' % prefix]
-        if '~perl' in spec:
+        if not '+perl' in spec:
             options.append('--disable-perl')
 
         configure(*options)

From 4ab362ae17da96db2a5fb7bacb3035824817c15d Mon Sep 17 00:00:00 2001
From: "Kelly (KT) Thompson" <kgt@lanl.gov>
Date: Wed, 30 Mar 2016 14:27:23 -0600
Subject: [PATCH 212/230] + Fix variant description.

---
 var/spack/repos/builtin/packages/graphviz/package.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/graphviz/package.py b/var/spack/repos/builtin/packages/graphviz/package.py
index a45cd8743ee..ecf92620d4a 100644
--- a/var/spack/repos/builtin/packages/graphviz/package.py
+++ b/var/spack/repos/builtin/packages/graphviz/package.py
@@ -11,7 +11,7 @@ class Graphviz(Package):
     # related to missing Perl packages. If spack begins support for Perl in the
     # future, this package can be updated to depend_on('perl') and the
     # ncecessary devel packages.
-    variant('perl', default=False, description='Disable if you have problems with the optional script language bindings')
+    variant('perl', default=False, description='Enable if you need the optional Perl language bindings.')
 
     parallel = False
 

From 2bc43f7f3724e86c3ff8875ce0c91178cbc31a6f Mon Sep 17 00:00:00 2001
From: Ben Boeckel <mathstuf@gmail.com>
Date: Wed, 30 Mar 2016 16:44:08 -0400
Subject: [PATCH 213/230] docs: add a link to the spack repo in the PR section

---
 README.md | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 8664953c0cc..1977a4fee96 100644
--- a/README.md
+++ b/README.md
@@ -59,7 +59,8 @@ can join it here:
 
 At the moment, contributing to Spack is relatively simple.  Just send us
 a [pull request](https://help.github.com/articles/using-pull-requests/).
-When you send your request, make ``develop`` the destination branch.
+When you send your request, make ``develop`` the destination branch on the
+[Spack repository](https://github.com/LLNL/spack).
 
 Spack is using a rough approximation of the [Git
 Flow](http://nvie.com/posts/a-successful-git-branching-model/)

From f1a0619821fc4c4aaa0a13b114ecaf8ca35b1ce9 Mon Sep 17 00:00:00 2001
From: Ben Boeckel <mathstuf@gmail.com>
Date: Wed, 30 Mar 2016 17:19:29 -0400
Subject: [PATCH 214/230] mpich: disable fortran without a fortran compiler

---
 var/spack/repos/builtin/packages/mpich/package.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/var/spack/repos/builtin/packages/mpich/package.py b/var/spack/repos/builtin/packages/mpich/package.py
index b20dc8dd60c..2d7955e08d3 100644
--- a/var/spack/repos/builtin/packages/mpich/package.py
+++ b/var/spack/repos/builtin/packages/mpich/package.py
@@ -78,6 +78,9 @@ def install(self, spec, prefix):
         if not self.compiler.fc:
             config_args.append("--disable-fc")
 
+        if not self.compiler.fc and not self.compiler.f77:
+            config_args.append("--disable-fortran")
+
         configure(*config_args)
         make()
         make("install")

From 2ad5d2ea2a280dd81a254458fcfb465073aef8da Mon Sep 17 00:00:00 2001
From: "Kelly (KT) Thompson" <kgt@lanl.gov>
Date: Wed, 30 Mar 2016 15:40:04 -0600
Subject: [PATCH 215/230] + For darwin, add a dependency on gettext. This
 change was recommended in the discussion for PR#601.

---
 var/spack/repos/builtin/packages/numdiff/package.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/var/spack/repos/builtin/packages/numdiff/package.py b/var/spack/repos/builtin/packages/numdiff/package.py
index a51f6206cf1..e72c60fadbe 100644
--- a/var/spack/repos/builtin/packages/numdiff/package.py
+++ b/var/spack/repos/builtin/packages/numdiff/package.py
@@ -23,6 +23,7 @@
 # Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 from spack import *
+import sys
 
 class Numdiff(Package):
     """Numdiff is a little program that can be used to compare putatively
@@ -34,6 +35,8 @@ class Numdiff(Package):
 
     version('5.8.1',    'a295eb391f6cb1578209fc6b4f9d994e')
 
+    depends_on('gettext', sys.platform=='darwin')
+
     def install(self, spec, prefix):
         options = ['--prefix=%s' % prefix]
         configure(*options)

From a364ab0d0f5ac226ba9d5a519f2da8ab7a09a846 Mon Sep 17 00:00:00 2001
From: "Kelly (KT) Thompson" <kgt@lanl.gov>
Date: Wed, 30 Mar 2016 17:12:32 -0600
Subject: [PATCH 216/230] libpng depends on zlib.

---
 var/spack/repos/builtin/packages/libpng/package.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/var/spack/repos/builtin/packages/libpng/package.py b/var/spack/repos/builtin/packages/libpng/package.py
index e02b08663e0..73c8c623414 100644
--- a/var/spack/repos/builtin/packages/libpng/package.py
+++ b/var/spack/repos/builtin/packages/libpng/package.py
@@ -9,6 +9,8 @@ class Libpng(Package):
     version('1.6.15', '829a256f3de9307731d4f52dc071916d')
     version('1.6.14', '2101b3de1d5f348925990f9aa8405660')
 
+    depends_on('zlib')
+
     def install(self, spec, prefix):
         configure("--prefix=%s" % prefix)
         make()

From a88c15e1010ccadd2f81de9edac48b140d70f9f1 Mon Sep 17 00:00:00 2001
From: "Kelly (KT) Thompson" <kgt@lanl.gov>
Date: Wed, 30 Mar 2016 21:18:04 -0600
Subject: [PATCH 217/230] + libdrm depends_on libpciaccess.  Use spack provided
 libpciaccess.

---
 var/spack/repos/builtin/packages/libdrm/package.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/libdrm/package.py b/var/spack/repos/builtin/packages/libdrm/package.py
index 00736b7811a..d5d779f7967 100644
--- a/var/spack/repos/builtin/packages/libdrm/package.py
+++ b/var/spack/repos/builtin/packages/libdrm/package.py
@@ -2,7 +2,7 @@
 
 class Libdrm(Package):
     """A userspace  library for  accessing the  DRM, direct
-    rendering  manager, on  Linux,  BSD and  other  operating 
+    rendering  manager, on  Linux,  BSD and  other  operating
     systems that support the  ioctl interface."""
 
     homepage = "http://dri.freedesktop.org/libdrm/" # no real website...
@@ -11,6 +11,8 @@ class Libdrm(Package):
     version('2.4.59', '105ac7af1afcd742d402ca7b4eb168b6')
     version('2.4.33', '86e4e3debe7087d5404461e0032231c8')
 
+    depends_on('libpciaccess')
+
     def install(self, spec, prefix):
         configure("--prefix=%s" % prefix)
 

From 44b89474453bf80fd603eb5ea5b629b0d9dff123 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Wed, 30 Mar 2016 23:33:57 -0700
Subject: [PATCH 218/230] arpack-ng needs an extra libtoolize to build.

---
 var/spack/repos/builtin/packages/arpack-ng/package.py | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/var/spack/repos/builtin/packages/arpack-ng/package.py b/var/spack/repos/builtin/packages/arpack-ng/package.py
index dd86b17a53a..6b152f78631 100644
--- a/var/spack/repos/builtin/packages/arpack-ng/package.py
+++ b/var/spack/repos/builtin/packages/arpack-ng/package.py
@@ -41,10 +41,17 @@ class ArpackNg(Package):
 
     depends_on('blas')
     depends_on('lapack')
+    depends_on('automake')
+    depends_on('autoconf')
+    depends_on('libtool@2.4.2:')
+
     depends_on('mpi', when='+mpi')
 
     def install(self, spec, prefix):
         # Apparently autotools are not bootstrapped
+        # TODO: switch to use the CMake build in the next version
+        # rather than bootstrapping.
+        which('libtoolize')()
         bootstrap = Executable('./bootstrap')
 
         options = ['--prefix=%s' % prefix]

From 397e0d1368d8f6077cb7ea59ee953b993ef3d244 Mon Sep 17 00:00:00 2001
From: Mayeul d'Avezac <mdavezac@gmail.com>
Date: Thu, 31 Mar 2016 10:12:20 +0100
Subject: [PATCH 219/230] Fixes #454 in a simpler way than 34a8f0c

Rather than mess with the environment, have espresso install into the
right directory (prefix/bin).
---
 var/spack/repos/builtin/packages/espresso/package.py | 8 ++------
 1 file changed, 2 insertions(+), 6 deletions(-)

diff --git a/var/spack/repos/builtin/packages/espresso/package.py b/var/spack/repos/builtin/packages/espresso/package.py
index 59f362ab46c..167bb38e381 100644
--- a/var/spack/repos/builtin/packages/espresso/package.py
+++ b/var/spack/repos/builtin/packages/espresso/package.py
@@ -24,7 +24,7 @@ class Espresso(Package):
     depends_on('fftw~mpi', when='~mpi')
     depends_on('fftw+mpi', when='+mpi')
     depends_on('scalapack', when='+scalapack+mpi')  # TODO : + mpi needed to avoid false dependencies installation
-    
+
     def check_variants(self, spec):
         error = 'you cannot ask for \'+{variant}\' when \'+mpi\' is not active'
         if '+scalapack' in spec and '~mpi' in spec:
@@ -32,14 +32,10 @@ def check_variants(self, spec):
         if '+elpa' in spec and ('~mpi' in spec or '~scalapack' in spec):
             raise RuntimeError(error.format(variant='elpa'))
 
-    def setup_environment(self, spack_env, run_env):
-        # Espresso copies every executable in prefix without creating sub-folders
-        run_env.prepend_path('PATH', self.prefix)
-
     def install(self, spec, prefix):
         self.check_variants(spec)
 
-        options = ['-prefix=%s' % prefix]
+        options = ['-prefix=%s' % prefix.bin]
 
         if '+mpi' in spec:
             options.append('--enable-parallel')

From 7430f9142fc3fc590232a21a193321be9de33df7 Mon Sep 17 00:00:00 2001
From: Mayeul d'Avezac <mdavezac@gmail.com>
Date: Thu, 31 Mar 2016 10:16:40 +0100
Subject: [PATCH 220/230] Can install espresso on OS/X

Espresso uses unix utility `find dir -name \*.x` to determine the executable to
install. On OS/X, it also finds a bunch of debug symbols associated
with the exectuble. These files have the same name, but are in a
different directory. So the install process is done by hand in the
package.py file, for OS/X.
---
 var/spack/repos/builtin/packages/espresso/package.py | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/var/spack/repos/builtin/packages/espresso/package.py b/var/spack/repos/builtin/packages/espresso/package.py
index 167bb38e381..0dad57a9f61 100644
--- a/var/spack/repos/builtin/packages/espresso/package.py
+++ b/var/spack/repos/builtin/packages/espresso/package.py
@@ -33,6 +33,7 @@ def check_variants(self, spec):
             raise RuntimeError(error.format(variant='elpa'))
 
     def install(self, spec, prefix):
+        from glob import glob
         self.check_variants(spec)
 
         options = ['-prefix=%s' % prefix.bin]
@@ -61,5 +62,11 @@ def install(self, spec, prefix):
 
         configure(*options)
         make('all')
-        make('install')        
+
+        if spec.architecture.startswith('darwin'):
+            mkdirp(prefix.bin)
+            for filename in glob("bin/*.x"):
+                install(filename, prefix.bin)
+        else:
+            make('install')
 

From 6d0b4a28abf8216ed141dac80a6779f6a51f03f1 Mon Sep 17 00:00:00 2001
From: Denis Davydov <davydden@gmail.com>
Date: Thu, 31 Mar 2016 09:39:37 +0200
Subject: [PATCH 221/230] oce: fix bugs related to NULL pointers and compiler
 optimisation

---
 .../repos/builtin/packages/dealii/package.py  |   3 +-
 .../repos/builtin/packages/oce/null.patch     | 482 ++++++++++++++++++
 .../repos/builtin/packages/oce/package.py     |  22 +-
 3 files changed, 502 insertions(+), 5 deletions(-)
 create mode 100644 var/spack/repos/builtin/packages/oce/null.patch

diff --git a/var/spack/repos/builtin/packages/dealii/package.py b/var/spack/repos/builtin/packages/dealii/package.py
index 7aaf33380e6..0b76db3827a 100644
--- a/var/spack/repos/builtin/packages/dealii/package.py
+++ b/var/spack/repos/builtin/packages/dealii/package.py
@@ -235,5 +235,4 @@ def install(self, spec, prefix):
             if 'oce' in spec:
                 cmake('.')
                 make('release')
-                if sys.platform != 'darwin': #FIXME
-                    make('run',parallel=False)
+                make('run',parallel=False)
diff --git a/var/spack/repos/builtin/packages/oce/null.patch b/var/spack/repos/builtin/packages/oce/null.patch
new file mode 100644
index 00000000000..42a3f0e44f3
--- /dev/null
+++ b/var/spack/repos/builtin/packages/oce/null.patch
@@ -0,0 +1,482 @@
+From 61cb965b9ffeca419005bc15e635e67589c421dd Mon Sep 17 00:00:00 2001
+From: Martin Siggel <martin.siggel@dlr.de>
+Date: Thu, 28 Jan 2016 19:05:00 +0100
+Subject: [PATCH] Workaround clang optimizations for null references
+
+OCCT/OCE includes some evil code that uses NULL references,
+which are normally not possible. Clang removes code in
+branches like if(&myNullRef==NULL) as it assumes this can
+never be true. This fix was inspired from the mantis issue
+http://tracker.dev.opencascade.org/view.php?id=26042. This
+code will be fixed in OCCT 7, but we might require the fix
+for earlier releases as well.
+
+Fixes issue #576
+---
+ inc/PLib.hxx                               |  2 +-
+ src/BSplCLib/BSplCLib.cxx                  | 16 ++++++-------
+ src/BSplCLib/BSplCLib_2.cxx                |  6 ++---
+ src/BSplCLib/BSplCLib_CurveComputation.gxx | 26 ++++++++++-----------
+ src/BSplSLib/BSplSLib.cxx                  | 36 +++++++++++++++---------------
+ src/BSplSLib/BSplSLib_BzSyntaxes.cxx       |  2 +-
+ src/PLib/PLib.cxx                          | 10 ++++-----
+ 7 files changed, 49 insertions(+), 49 deletions(-)
+
+diff --git a/inc/PLib.hxx b/inc/PLib.hxx
+index 7513234..52b1f84 100644
+--- a/inc/PLib.hxx
++++ b/inc/PLib.hxx
+@@ -343,6 +343,6 @@ friend class PLib_DoubleJacobiPolynomial;
+ 
+ 
+ 
+-
++#define IS_NULL_REF(ref) ((reinterpret_cast<size_t>(&ref) & 0xFFFFFF) == 0)
+ 
+ #endif // _PLib_HeaderFile
+diff --git a/src/BSplCLib/BSplCLib.cxx b/src/BSplCLib/BSplCLib.cxx
+index 683e4ab..2a2d9ea 100644
+--- a/src/BSplCLib/BSplCLib.cxx
++++ b/src/BSplCLib/BSplCLib.cxx
+@@ -298,7 +298,7 @@ void BSplCLib::LocateParameter
+  Standard_Real&                 NewU) 
+ {
+   Standard_Integer first,last;
+-  if (&Mults) {
++  if (!IS_NULL_REF(Mults)) {
+     if (Periodic) {
+       first = Knots.Lower();
+       last  = Knots.Upper();
+@@ -1434,7 +1434,7 @@ void BSplCLib::BuildKnots(const Standard_Integer         Degree,
+   const Standard_Real * pkn = &Knots(KLower);
+   pkn -= KLower;
+   Standard_Real *knot = &LK;
+-  if (&Mults == NULL) {
++  if (IS_NULL_REF(Mults)) {
+     switch (Degree) {
+     case 1 : {
+       Standard_Integer j = Index    ;
+@@ -1672,7 +1672,7 @@ Standard_Boolean  BSplCLib::PrepareInsertKnots
+  const Standard_Real            Tolerance,
+  const Standard_Boolean         Add)
+ {
+-  Standard_Boolean addflat = &AddMults == NULL;
++  Standard_Boolean addflat = IS_NULL_REF(AddMults);
+   
+   Standard_Integer first,last;
+   if (Periodic) {
+@@ -1856,7 +1856,7 @@ void BSplCLib::InsertKnots
+  const Standard_Real            Tolerance,
+  const Standard_Boolean         Add)
+ {
+-  Standard_Boolean addflat  = &AddMults == NULL;
++  Standard_Boolean addflat  = IS_NULL_REF(AddMults);
+   
+   Standard_Integer i,k,mult,firstmult;
+   Standard_Integer index,kn,curnk,curk;
+@@ -3902,7 +3902,7 @@ void BSplCLib::Resolution(      Standard_Real&        Poles,
+   num_poles = FlatKnots.Length() - Deg1;
+   switch (ArrayDimension) {
+   case 2 : {
+-    if (&Weights != NULL) {
++    if (!IS_NULL_REF(Weights)) {
+       const Standard_Real * WG = &Weights(Weights.Lower());
+       min_weights = WG[0];
+       
+@@ -3970,7 +3970,7 @@ void BSplCLib::Resolution(      Standard_Real&        Poles,
+     break;
+   }
+   case 3 : {
+-    if (&Weights != NULL) {
++    if (!IS_NULL_REF(Weights)) {
+       const Standard_Real * WG = &Weights(Weights.Lower());
+       min_weights = WG[0];
+       
+@@ -4047,7 +4047,7 @@ void BSplCLib::Resolution(      Standard_Real&        Poles,
+     break;
+   }
+   case 4 : {
+-    if (&Weights != NULL) {
++    if (!IS_NULL_REF(Weights)) {
+       const Standard_Real * WG = &Weights(Weights.Lower());
+       min_weights = WG[0];
+       
+@@ -4134,7 +4134,7 @@ void BSplCLib::Resolution(      Standard_Real&        Poles,
+   }
+     default : {
+       Standard_Integer kk;
+-      if (&Weights != NULL) {
++      if (!IS_NULL_REF(Weights)) {
+ 	const Standard_Real * WG = &Weights(Weights.Lower());
+ 	min_weights = WG[0];
+ 	
+diff --git a/src/BSplCLib/BSplCLib_2.cxx b/src/BSplCLib/BSplCLib_2.cxx
+index 35c4639..653b7cd 100644
+--- a/src/BSplCLib/BSplCLib_2.cxx
++++ b/src/BSplCLib/BSplCLib_2.cxx
+@@ -70,7 +70,7 @@ void  BSplCLib::BuildEval(const Standard_Integer         Degree,
+   Standard_Integer i;
+   Standard_Integer ip = PLower + Index - 1;
+   Standard_Real w, *pole = &LP;
+-  if (&Weights == NULL) {
++  if (IS_NULL_REF(Weights)) {
+     
+     for (i = 0; i <= Degree; i++) {
+       ip++;
+@@ -115,13 +115,13 @@ static void PrepareEval
+   
+   // make the knots
+   BSplCLib::BuildKnots(Degree,index,Periodic,Knots,Mults,*dc.knots);
+-  if (&Mults == NULL)
++  if (IS_NULL_REF(Mults))
+     index -= Knots.Lower() + Degree;
+   else
+     index = BSplCLib::PoleIndex(Degree,index,Periodic,Mults);
+   
+   // check truly rational
+-  rational = (&Weights != NULL);
++  rational = (!IS_NULL_REF(Weights));
+   if (rational) {
+     Standard_Integer WLower = Weights.Lower() + index;
+     rational = BSplCLib::IsRational(Weights, WLower, WLower + Degree);
+diff --git a/src/BSplCLib/BSplCLib_CurveComputation.gxx b/src/BSplCLib/BSplCLib_CurveComputation.gxx
+index e71b4e0..9d42643 100644
+--- a/src/BSplCLib/BSplCLib_CurveComputation.gxx
++++ b/src/BSplCLib/BSplCLib_CurveComputation.gxx
+@@ -92,7 +92,7 @@ Standard_Boolean BSplCLib::RemoveKnot
+  TColStd_Array1OfInteger&       NewMults,
+  const Standard_Real            Tolerance) 
+ {
+-  Standard_Boolean rational = &Weights  != NULL;
++  Standard_Boolean rational = !IS_NULL_REF(Weights);
+   Standard_Integer dim;
+   dim = Dimension_gen;
+   if (rational) dim++;
+@@ -133,7 +133,7 @@ void BSplCLib::InsertKnots
+  const Standard_Real            Epsilon,
+  const Standard_Boolean         Add) 
+ {
+-  Standard_Boolean rational = &Weights  != NULL;
++  Standard_Boolean rational = !IS_NULL_REF(Weights);
+   Standard_Integer dim;
+   dim = Dimension_gen;
+   if (rational) dim++;
+@@ -222,7 +222,7 @@ void BSplCLib::IncreaseDegree
+  TColStd_Array1OfReal&           NewKnots,
+  TColStd_Array1OfInteger&        NewMults) 
+ {
+-  Standard_Boolean rational = &Weights  != NULL;
++  Standard_Boolean rational = !IS_NULL_REF(Weights);
+   Standard_Integer dim;
+   dim = Dimension_gen;
+   if (rational) dim++;
+@@ -256,7 +256,7 @@ void  BSplCLib::Unperiodize
+  Array1OfPoints&          NewPoles,
+  TColStd_Array1OfReal&    NewWeights)
+ {
+-  Standard_Boolean rational = &Weights  != NULL;
++  Standard_Boolean rational = !IS_NULL_REF(Weights);
+   Standard_Integer dim;
+   dim = Dimension_gen;
+   if (rational) dim++;
+@@ -292,7 +292,7 @@ void BSplCLib::Trimming(const Standard_Integer         Degree,
+ 			Array1OfPoints&          NewPoles,
+ 			TColStd_Array1OfReal&    NewWeights)
+ {
+-  Standard_Boolean rational = &Weights  != NULL;
++  Standard_Boolean rational = !IS_NULL_REF(Weights);
+   Standard_Integer dim;
+   dim = Dimension_gen;
+   if (rational) dim++;
+@@ -339,7 +339,7 @@ void  BSplCLib::BuildEval(const Standard_Integer         Degree,
+   Standard_Integer PUpper = Poles.Upper();
+   Standard_Integer i;
+   Standard_Integer ip = PLower + Index - 1;
+-  if (&Weights == NULL) {
++  if (IS_NULL_REF(Weights)) {
+     for (i = 0; i <= Degree; i++) {
+       ip++;
+       if (ip > PUpper) ip = PLower;
+@@ -384,13 +384,13 @@ static void PrepareEval
+ 
+   // make the knots
+   BSplCLib::BuildKnots(Degree,index,Periodic,Knots,Mults,*dc.knots);
+-  if (&Mults == NULL)
++  if (IS_NULL_REF(Mults))
+     index -= Knots.Lower() + Degree;
+   else
+     index = BSplCLib::PoleIndex(Degree,index,Periodic,Mults);
+   
+   // check truly rational
+-  rational = (&Weights != NULL);
++  rational = (!IS_NULL_REF(Weights));
+   if (rational) {
+     Standard_Integer WLower = Weights.Lower() + index;
+     rational = BSplCLib::IsRational(Weights, WLower, WLower + Degree);
+@@ -741,7 +741,7 @@ void  BSplCLib::CacheD0(const Standard_Real                  Parameter,
+ 		       Degree * Dimension_gen,
+ 		       PArray[0],
+ 		       myPoint[0]) ;
+-  if (&WeightsArray != NULL) {
++  if (!IS_NULL_REF(WeightsArray)) {
+     Standard_Real *
+       WArray = (Standard_Real *) &WeightsArray(WeightsArray.Lower()) ;
+     PLib::NoDerivativeEvalPolynomial(NewParameter,
+@@ -798,7 +798,7 @@ void  BSplCLib::CacheD1(const Standard_Real                  Parameter,
+ 
+   ModifyCoords (LocalPDerivatives + Dimension_gen, /= SpanLenght);
+   
+-  if (&WeightsArray != NULL) {
++  if (!IS_NULL_REF(WeightsArray)) {
+     Standard_Real *
+       WArray = (Standard_Real *) &WeightsArray(WeightsArray.Lower()) ;
+     PLib::EvalPolynomial(NewParameter,
+@@ -878,7 +878,7 @@ void  BSplCLib::CacheD2(const Standard_Real                  Parameter,
+     Index += Dimension_gen;
+   }
+ 
+-  if (&WeightsArray != NULL) {
++  if (!IS_NULL_REF(WeightsArray)) {
+     Standard_Real *
+       WArray = (Standard_Real *) &WeightsArray(WeightsArray.Lower()) ;
+     
+@@ -971,7 +971,7 @@ void  BSplCLib::CacheD3(const Standard_Real                  Parameter,
+     Index  += Dimension_gen;
+   }
+   
+-  if (&WeightsArray != NULL) {
++  if (!IS_NULL_REF(WeightsArray)) {
+     Standard_Real *
+       WArray = (Standard_Real *) &WeightsArray(WeightsArray.Lower()) ;
+     
+@@ -1081,7 +1081,7 @@ void BSplCLib::BuildCache
+       LocalValue *= SpanDomain / (Standard_Real) ii ;
+     }
+ 
+-    if (&Weights != NULL) { 
++    if (!IS_NULL_REF(Weights)) {
+       for (ii = 1 ; ii <= Degree + 1 ; ii++)
+ 	CacheWeights(ii) = 0.0e0 ;
+       CacheWeights(1) = 1.0e0 ;
+diff --git a/src/BSplSLib/BSplSLib.cxx b/src/BSplSLib/BSplSLib.cxx
+index 5ad633c..07040d5 100644
+--- a/src/BSplSLib/BSplSLib.cxx
++++ b/src/BSplSLib/BSplSLib.cxx
+@@ -309,12 +309,12 @@ static Standard_Boolean  PrepareEval (const Standard_Real            U,
+     BSplCLib::BuildKnots(UDegree,uindex,UPer,UKnots,UMults,*dc.knots1);
+     BSplCLib::BuildKnots(VDegree,vindex,VPer,VKnots,VMults,*dc.knots2);
+     
+-    if (&UMults == NULL)
++    if (IS_NULL_REF(UMults))
+       uindex -= UKLower + UDegree;
+     else
+       uindex  = BSplCLib::PoleIndex(UDegree,uindex,UPer,UMults);
+ 
+-    if (&VMults == NULL)
++    if (IS_NULL_REF(VMults))
+       vindex -= VKLower + VDegree;
+     else
+       vindex  = BSplCLib::PoleIndex(VDegree,vindex,VPer,VMults);
+@@ -460,12 +460,12 @@ static Standard_Boolean  PrepareEval (const Standard_Real            U,
+     BSplCLib::BuildKnots(UDegree,uindex,UPer,UKnots,UMults,*dc.knots2);
+     BSplCLib::BuildKnots(VDegree,vindex,VPer,VKnots,VMults,*dc.knots1);
+ 
+-    if (&UMults == NULL)
++    if (IS_NULL_REF(UMults))
+       uindex -= UKLower + UDegree;
+     else
+       uindex  = BSplCLib::PoleIndex(UDegree,uindex,UPer,UMults);
+ 
+-    if (&VMults == NULL)
++    if (IS_NULL_REF(VMults))
+       vindex -= VKLower + VDegree;
+     else
+       vindex  = BSplCLib::PoleIndex(VDegree,vindex,VPer,VMults);
+@@ -1299,7 +1299,7 @@ void  BSplSLib::Iso(const Standard_Real            Param,
+ {
+   Standard_Integer index = 0;
+   Standard_Real    u = Param;
+-  Standard_Boolean rational = &Weights != NULL;
++  Standard_Boolean rational = !IS_NULL_REF(Weights);
+   Standard_Integer dim = rational ? 4 : 3;
+   
+   // compute local knots
+@@ -1307,7 +1307,7 @@ void  BSplSLib::Iso(const Standard_Real            Param,
+   NCollection_LocalArray<Standard_Real> locknots1 (2*Degree);  
+   BSplCLib::LocateParameter(Degree,Knots,Mults,u,Periodic,index,u);
+   BSplCLib::BuildKnots(Degree,index,Periodic,Knots,Mults,*locknots1);
+-  if (&Mults == NULL)
++  if (IS_NULL_REF(Mults))
+     index -= Knots.Lower() + Degree;
+   else
+     index = BSplCLib::PoleIndex(Degree,index,Periodic,Mults);
+@@ -1381,7 +1381,7 @@ void  BSplSLib::Iso(const Standard_Real            Param,
+   }
+   
+   // if the input is not rational but weights are wanted
+-  if (!rational && (&CWeights != NULL)) {
++  if (!rational && (!IS_NULL_REF(CWeights))) {
+ 
+     for (i = CWeights.Lower(); i <= CWeights.Upper(); i++)
+       CWeights(i) = 1.;
+@@ -1741,7 +1741,7 @@ void  BSplSLib::InsertKnots(const Standard_Boolean         UDirection,
+ 			    const Standard_Real            Epsilon, 
+ 			    const Standard_Boolean         Add )
+ {
+-  Standard_Boolean rational = &Weights != NULL;
++  Standard_Boolean rational = !IS_NULL_REF(Weights);
+   Standard_Integer dim = 3;
+   if (rational) dim++;
+   
+@@ -1787,7 +1787,7 @@ Standard_Boolean  BSplSLib::RemoveKnot
+  TColStd_Array1OfInteger& NewMults,
+  const Standard_Real            Tolerance)
+ {
+-  Standard_Boolean rational = &Weights != NULL;
++  Standard_Boolean rational = !IS_NULL_REF(Weights);
+   Standard_Integer dim = 3;
+   if (rational) dim++;
+   
+@@ -1834,7 +1834,7 @@ void  BSplSLib::IncreaseDegree
+  TColStd_Array1OfReal&    NewKnots, 
+  TColStd_Array1OfInteger& NewMults)
+ {
+-  Standard_Boolean rational = &Weights != NULL;
++  Standard_Boolean rational = !IS_NULL_REF(Weights);
+   Standard_Integer dim = 3;
+   if (rational) dim++;
+   
+@@ -1876,7 +1876,7 @@ void  BSplSLib::Unperiodize
+  TColgp_Array2OfPnt&      NewPoles,
+  TColStd_Array2OfReal&    NewWeights)
+ {
+-  Standard_Boolean rational = &Weights != NULL;
++  Standard_Boolean rational = !IS_NULL_REF(Weights);
+   Standard_Integer dim = 3;
+   if (rational) dim++;
+   
+@@ -1929,7 +1929,7 @@ void BSplSLib::BuildCache
+   Standard_Boolean rational,rational_u,rational_v,flag_u_or_v;                  
+   Standard_Integer kk,d1,d1p1,d2,d2p1,ii,jj,iii,jjj,Index;
+   Standard_Real u1,min_degree_domain,max_degree_domain,f,factor[2],u2;
+-  if (&Weights != NULL) 
++  if (!IS_NULL_REF(Weights))
+     rational_u = rational_v = Standard_True;
+   else
+     rational_u = rational_v = Standard_False;
+@@ -2025,7 +2025,7 @@ void BSplSLib::BuildCache
+       }
+       factor[0] *= max_degree_domain / (Standard_Real) (iii) ;
+     }
+-    if (&Weights != NULL) {
++    if (!IS_NULL_REF(Weights)) {
+       //
+       // means that PrepareEval did found out that the surface was 
+       // locally polynomial but since the surface is constructed
+@@ -2110,7 +2110,7 @@ void  BSplSLib::CacheD0(const Standard_Real                  UParameter,
+ 		       (min_degree << 1) + min_degree,
+ 		       locpoles[0],
+ 		       myPoint[0]) ;
+-  if (&WeightsArray != NULL) {
++  if (!IS_NULL_REF(WeightsArray)) {
+     dimension = min_degree + 1 ;
+     Standard_Real *
+       WArray = (Standard_Real *) 
+@@ -2190,7 +2190,7 @@ void  BSplSLib::CacheD1(const Standard_Real                  UParameter,
+   // the coefficients
+   //
+   //
+-  if (&WeightsArray != NULL) {
++  if (!IS_NULL_REF(WeightsArray)) {
+ 
+     local_poles_array            [0][0][0] = 0.0e0 ;
+     local_poles_array            [0][0][1] = 0.0e0 ;
+@@ -2275,7 +2275,7 @@ void  BSplSLib::CacheD1(const Standard_Real                  UParameter,
+ 		       locpoles[dimension],
+ 		       local_poles_array[1][0][0]) ;
+   
+-  if (&WeightsArray != NULL) {
++  if (!IS_NULL_REF(WeightsArray)) {
+     dimension = min_degree + 1 ;
+     Standard_Real *
+       WArray = (Standard_Real *) 
+@@ -2435,7 +2435,7 @@ void  BSplSLib::CacheD2(const Standard_Real                  UParameter,
+   // the coefficients
+   //
+   //
+-  if (&WeightsArray != NULL) {
++  if (!IS_NULL_REF(WeightsArray)) {
+     
+     local_poles_and_weights_array[0][0][0] = 0.0e0 ;
+     local_poles_and_weights_array[0][0][1] = 0.0e0 ;
+@@ -2564,7 +2564,7 @@ void  BSplSLib::CacheD2(const Standard_Real                  UParameter,
+ 		       locpoles[dimension + dimension],
+ 		       local_poles_array[2][0][0]) ;
+   
+-  if (&WeightsArray != NULL) {
++  if (!IS_NULL_REF(WeightsArray)) {
+     dimension = min_degree + 1 ;
+     Standard_Real *
+       WArray = (Standard_Real *) 
+diff --git a/src/BSplSLib/BSplSLib_BzSyntaxes.cxx b/src/BSplSLib/BSplSLib_BzSyntaxes.cxx
+index 0faf6b6..f2c0f74 100644
+--- a/src/BSplSLib/BSplSLib_BzSyntaxes.cxx
++++ b/src/BSplSLib/BSplSLib_BzSyntaxes.cxx
+@@ -68,7 +68,7 @@ void BSplSLib::PolesCoefficients (const TColgp_Array2OfPnt& Poles,
+ 			 biduflatknots,bidvflatknots,
+ 			 Poles,Weights,
+ 			 CPoles,CWeights);
+-    if (&Weights == NULL) {
++    if (IS_NULL_REF(Weights)) {
+       
+       for (ii = 1; ii <= uclas; ii++) {
+ 	
+diff --git a/src/PLib/PLib.cxx b/src/PLib/PLib.cxx
+index 23fa302..7ee231f 100644
+--- a/src/PLib/PLib.cxx
++++ b/src/PLib/PLib.cxx
+@@ -2427,7 +2427,7 @@ void PLib::CoefficientsPoles (const Standard_Integer      dim,
+ 			      TColStd_Array1OfReal&       Poles, 
+ 			      TColStd_Array1OfReal&       Weights)
+ {
+-  Standard_Boolean rat = &WCoefs != NULL;
++  Standard_Boolean rat = !IS_NULL_REF(WCoefs);
+   Standard_Integer loc = Coefs.Lower();
+   Standard_Integer lop = Poles.Lower();
+   Standard_Integer lowc=0;
+@@ -2550,7 +2550,7 @@ void PLib::Trimming(const Standard_Real U1,
+   Standard_Integer indc, indw=0;
+   Standard_Integer upc = Coefs.Upper() - dim + 1, upw=0;
+   Standard_Integer len = Coefs.Length()/dim;
+-  Standard_Boolean rat = &WCoefs != NULL;
++  Standard_Boolean rat = !IS_NULL_REF(WCoefs);
+ 
+   if (rat) {
+     if(len != WCoefs.Length())
+@@ -2607,7 +2607,7 @@ void PLib::CoefficientsPoles (const TColgp_Array2OfPnt&   Coefs,
+ 			      TColgp_Array2OfPnt&         Poles,
+ 			      TColStd_Array2OfReal&       Weights) 
+ {
+-  Standard_Boolean rat = (&WCoefs != NULL);
++  Standard_Boolean rat = (!IS_NULL_REF(WCoefs));
+   Standard_Integer LowerRow  = Poles.LowerRow();
+   Standard_Integer UpperRow  = Poles.UpperRow();
+   Standard_Integer LowerCol  = Poles.LowerCol();
+@@ -2701,7 +2701,7 @@ void PLib::UTrimming(const Standard_Real U1,
+ 		     TColgp_Array2OfPnt& Coeffs, 
+ 		     TColStd_Array2OfReal& WCoeffs)
+ {
+-  Standard_Boolean rat = &WCoeffs != NULL;
++  Standard_Boolean rat = !IS_NULL_REF(WCoeffs);
+   Standard_Integer lr = Coeffs.LowerRow();
+   Standard_Integer ur = Coeffs.UpperRow();
+   Standard_Integer lc = Coeffs.LowerCol();
+@@ -2735,7 +2735,7 @@ void PLib::VTrimming(const Standard_Real V1,
+ 		     TColgp_Array2OfPnt& Coeffs, 
+ 		     TColStd_Array2OfReal& WCoeffs)
+ {
+-  Standard_Boolean rat = &WCoeffs != NULL;
++  Standard_Boolean rat = !IS_NULL_REF(WCoeffs);
+   Standard_Integer lr = Coeffs.LowerRow();
+   Standard_Integer ur = Coeffs.UpperRow();
+   Standard_Integer lc = Coeffs.LowerCol();
\ No newline at end of file
diff --git a/var/spack/repos/builtin/packages/oce/package.py b/var/spack/repos/builtin/packages/oce/package.py
index 4d5081ac9d4..3fe6638e66c 100644
--- a/var/spack/repos/builtin/packages/oce/package.py
+++ b/var/spack/repos/builtin/packages/oce/package.py
@@ -13,9 +13,20 @@ class Oce(Package):
     version('0.17'  , 'f1a89395c4b0d199bea3db62b85f818d')
     version('0.16.1', '4d591b240c9293e879f50d86a0cb2bb3')
     version('0.16'  , '7a4b4df5a104d75a537e25e7dd387eca')
-    version('0.15'  , '7ec541a1c350ca8a684f74980e48801c')
+
+    variant('tbb', default=True, description='Build with Intel Threading Building Blocks')
 
     depends_on('cmake@2.8:')
+    depends_on('tbb', when='+tbb')
+
+    # There is a bug in OCE which appears with Clang (version?) or GCC 6.0
+    # and has to do with compiler optimization, see
+    # https://github.com/tpaviot/oce/issues/576
+    # http://tracker.dev.opencascade.org/view.php?id=26042
+    # https://github.com/tpaviot/oce/issues/605
+    # https://github.com/tpaviot/oce/commit/61cb965b9ffeca419005bc15e635e67589c421dd.patch
+    patch('null.patch',when='@0.16:0.17.1')
+
 
     def install(self, spec, prefix):
         options = []
@@ -23,12 +34,12 @@ def install(self, spec, prefix):
         options.extend([
             '-DOCE_INSTALL_PREFIX=%s' % prefix,
             '-DOCE_BUILD_SHARED_LIB:BOOL=ON',
-            '-DOCE_BUILD_TYPE:STRING=Release',
+            '-DCMAKE_BUILD_TYPE:STRING=Release',
             '-DOCE_DATAEXCHANGE:BOOL=ON',
             '-DOCE_DISABLE_X11:BOOL=ON',
             '-DOCE_DRAW:BOOL=OFF',
             '-DOCE_MODEL:BOOL=ON',
-            '-DOCE_MULTITHREAD_LIBRARY:STRING=NONE', # FIXME: add tbb
+            '-DOCE_MULTITHREAD_LIBRARY:STRING=%s' % ('TBB' if '+tbb' in spec else 'NONE'),
             '-DOCE_OCAF:BOOL=ON',
             '-DOCE_USE_TCL_TEST_FRAMEWORK:BOOL=OFF',
             '-DOCE_VISUALISATION:BOOL=OFF',
@@ -46,6 +57,11 @@ def install(self, spec, prefix):
 
         make("install/strip")
 
+        # OCE tests build is brocken at least on Darwin.
+        # Unit tests are linked against libTKernel.10.dylib isntead of /full/path/libTKernel.10.dylib
+        # see https://github.com/tpaviot/oce/issues/612
+        # make("test")
+
         # The shared libraries are not installed correctly on Darwin; correct this
         if (sys.platform == 'darwin'):
             fix_darwin_install_name(prefix.lib)

From 0bcfd095362c5d04b9add7ebc882b74fad68f9dd Mon Sep 17 00:00:00 2001
From: Dhanannjay Deo <dhanannjay.deo@kitware.com>
Date: Fri, 25 Mar 2016 13:25:29 -0400
Subject: [PATCH 222/230] add: VTK lastest versions

---
 var/spack/repos/builtin/packages/vtk/package.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/var/spack/repos/builtin/packages/vtk/package.py b/var/spack/repos/builtin/packages/vtk/package.py
index 4a27a8fedba..aeb03fe0a37 100644
--- a/var/spack/repos/builtin/packages/vtk/package.py
+++ b/var/spack/repos/builtin/packages/vtk/package.py
@@ -7,6 +7,10 @@ class Vtk(Package):
     homepage = "http://www.vtk.org"
     url      = "http://www.vtk.org/files/release/6.1/VTK-6.1.0.tar.gz"
 
+    version("7.0.0", "5fe35312db5fb2341139b8e4955c367d", url="http://www.vtk.org/files/release/7.0/VTK-7.0.0.tar.gz")
+
+    version("6.3.0", '0231ca4840408e9dd60af48b314c5b6d', url="http://www.vtk.org/files/release/6.3/VTK-6.3.0.tar.gz")
+
     version('6.1.0', '25e4dfb3bad778722dcaec80cd5dab7d')
 
     depends_on("qt")

From 123996aad0c58bab7de6f615159b2fd7b44c7369 Mon Sep 17 00:00:00 2001
From: Dhanannjay Deo <dhanannjay.deo@kitware.com>
Date: Thu, 31 Mar 2016 10:29:47 -0400
Subject: [PATCH 223/230] Fix build for vtk6.1.0

---
 var/spack/repos/builtin/packages/vtk/package.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/var/spack/repos/builtin/packages/vtk/package.py b/var/spack/repos/builtin/packages/vtk/package.py
index aeb03fe0a37..b29d52d0f03 100644
--- a/var/spack/repos/builtin/packages/vtk/package.py
+++ b/var/spack/repos/builtin/packages/vtk/package.py
@@ -39,6 +39,10 @@ def install(self, spec, prefix):
             if spec['qt'].satisfies('@5'):
                 cmake_args.append("-DVTK_QT_VERSION:STRING=5")
 
+            if spec.satisfies("@6.1.0"):
+                cmake_args.append("-DCMAKE_C_FLAGS=-DGLX_GLXEXT_LEGACY")
+                cmake_args.append("-DCMAKE_CXX_FLAGS=-DGLX_GLXEXT_LEGACY")
+
             cmake(*cmake_args)
             make()
             make("install")

From 3b0311a1e484a4f731d1cc6448dc6804410ecb3c Mon Sep 17 00:00:00 2001
From: Dhanannjay Deo <dhanannjay.deo@kitware.com>
Date: Thu, 31 Mar 2016 10:30:32 -0400
Subject: [PATCH 224/230] Add variant opengl2, which is ON by default

Needed for visit which depends on vtk@6.1.0~opengl2
---
 var/spack/repos/builtin/packages/vtk/package.py | 10 ++++++++++
 1 file changed, 10 insertions(+)

diff --git a/var/spack/repos/builtin/packages/vtk/package.py b/var/spack/repos/builtin/packages/vtk/package.py
index b29d52d0f03..24382af406c 100644
--- a/var/spack/repos/builtin/packages/vtk/package.py
+++ b/var/spack/repos/builtin/packages/vtk/package.py
@@ -15,7 +15,15 @@ class Vtk(Package):
 
     depends_on("qt")
 
+    # VTK7 defaults to OpenGL2 rendering backend
+    variant('opengl2', default=True, description='Build with OpenGL instead of OpenGL2 as rendering backend')
+
     def install(self, spec, prefix):
+        def feature_to_bool(feature, on='ON', off='OFF'):
+            if feature in spec:
+                return on
+            return off
+
         with working_dir('spack-build', create=True):
             cmake_args = [
                 "..",
@@ -43,6 +51,8 @@ def install(self, spec, prefix):
                 cmake_args.append("-DCMAKE_C_FLAGS=-DGLX_GLXEXT_LEGACY")
                 cmake_args.append("-DCMAKE_CXX_FLAGS=-DGLX_GLXEXT_LEGACY")
 
+            cmake_args.append('-DVTK_RENDERING_BACKEND:STRING=%s' % feature_to_bool('+opengl2', 'OpenGL2', 'OpenGL'))
+
             cmake(*cmake_args)
             make()
             make("install")

From a0902ad8d8a8c629eb921b8701332385d622bc12 Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Thu, 31 Mar 2016 11:04:29 -0500
Subject: [PATCH 225/230] Change variant defaults and add comment

---
 var/spack/repos/builtin/packages/cuda/package.py       | 6 +++++-
 var/spack/repos/builtin/packages/hoomd-blue/package.py | 7 ++++---
 2 files changed, 9 insertions(+), 4 deletions(-)

diff --git a/var/spack/repos/builtin/packages/cuda/package.py b/var/spack/repos/builtin/packages/cuda/package.py
index eca371d05ae..ea083d8651d 100644
--- a/var/spack/repos/builtin/packages/cuda/package.py
+++ b/var/spack/repos/builtin/packages/cuda/package.py
@@ -13,7 +13,11 @@ class Cuda(Package):
     For the Installer Type, select runfile and click Download. Spack will search
     your current directory for this file. Alternatively, add this file to a
     mirror so that Spack can find it. For instructions on how to set up a mirror,
-    see http://software.llnl.gov/spack/mirrors.html"""
+    see http://software.llnl.gov/spack/mirrors.html
+
+    Note: This package does not currently install the drivers necessary to run
+    CUDA. These will need to be installed manually. See:
+    http://docs.nvidia.com/cuda/cuda-getting-started-guide-for-linux for details."""
 
     homepage = "http://www.nvidia.com/object/cuda_home_new.html"
 
diff --git a/var/spack/repos/builtin/packages/hoomd-blue/package.py b/var/spack/repos/builtin/packages/hoomd-blue/package.py
index 32fdff94267..d310b7687a5 100644
--- a/var/spack/repos/builtin/packages/hoomd-blue/package.py
+++ b/var/spack/repos/builtin/packages/hoomd-blue/package.py
@@ -16,9 +16,9 @@ class HoomdBlue(Package):
 
     version('1.3.3', '1469ef4531dc14b579c0acddbfe6a273')
 
-    variant('mpi',  default=False, description='Compile with MPI enabled')
-    variant('cuda', default=False, description='Compile with CUDA Toolkit')
-    variant('doc',  default=False, description='Generate documentation')
+    variant('mpi',  default=True, description='Compile with MPI enabled')
+    variant('cuda', default=True, description='Compile with CUDA Toolkit')
+    variant('doc',  default=True, description='Generate documentation')
 
     extends('python')
     depends_on('py-numpy')
@@ -56,6 +56,7 @@ def install(self, spec, prefix):
 
         # There may be a bug in the MPI-CUDA code. See:
         # https://groups.google.com/forum/#!msg/hoomd-users/2griTESmc5I/E69s_M5fDwAJ
+        # This prevented "make test" from passing for me.
         cmake_args.append('-DENABLE_MPI_CUDA=OFF')
 
         # Documentation

From 63f824b218af9fcea4c13d7bef8b1d8ff31d09b2 Mon Sep 17 00:00:00 2001
From: Tom Scogland <scogland1@llnl.gov>
Date: Wed, 30 Dec 2015 11:53:27 -0800
Subject: [PATCH 226/230] add a path argument to the stage command

Allow users to use spack to stage a, potentially complex, package into a
given path.  This is nice for packages with multiple resources that must
be placed, for example LLVM with all sub-projects.
---
 lib/spack/spack/cmd/stage.py | 8 +++++++-
 lib/spack/spack/package.py   | 8 ++++++--
 2 files changed, 13 insertions(+), 3 deletions(-)

diff --git a/lib/spack/spack/cmd/stage.py b/lib/spack/spack/cmd/stage.py
index 5786780efb4..749fa908686 100644
--- a/lib/spack/spack/cmd/stage.py
+++ b/lib/spack/spack/cmd/stage.py
@@ -35,6 +35,9 @@ def setup_parser(subparser):
     subparser.add_argument(
         '-n', '--no-checksum', action='store_true', dest='no_checksum',
         help="Do not check downloaded packages against checksum")
+    subparser.add_argument(
+        '-p', '--path', dest='path',
+        help="Path to stage package, does not add to spack tree")
 
     subparser.add_argument(
         'specs', nargs=argparse.REMAINDER, help="specs of packages to stage")
@@ -50,4 +53,7 @@ def stage(parser, args):
     specs = spack.cmd.parse_specs(args.specs, concretize=True)
     for spec in specs:
         package = spack.repo.get(spec)
-        package.do_stage()
+        if args.path:
+            package.do_stage(path=args.path)
+        else:
+            package.do_stage()
diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py
index 9af32218374..ce314b7b0a5 100644
--- a/lib/spack/spack/package.py
+++ b/lib/spack/spack/package.py
@@ -709,14 +709,18 @@ def do_fetch(self, mirror_only=False):
         if spack.do_checksum and self.version in self.versions:
             self.stage.check()
 
-
-    def do_stage(self, mirror_only=False):
+    def do_stage(self, mirror_only=False, path=None):
         """Unpacks the fetched tarball, then changes into the expanded tarball
            directory."""
+
         if not self.spec.concrete:
             raise ValueError("Can only stage concrete packages.")
 
         self.do_fetch(mirror_only)
+
+        if path is not None:
+            self.stage.path = path
+
         self.stage.expand_archive()
         self.stage.chdir_to_source()
 

From 5d2151ed645f853a083cd445ae8631f9ed987559 Mon Sep 17 00:00:00 2001
From: Tom Scogland <scogland1@llnl.gov>
Date: Thu, 31 Mar 2016 10:20:55 -0700
Subject: [PATCH 227/230] reworked to deal with stage.path as property

This version actually pulls the path through the package to deliver it
to each stage on creation when passed through the command.  This is
necessary due to the new StageComposite class that makes setting the
path directly on the stage impractical, it also takes the logic out of
package for the most part, which seems like an improvement.
---
 lib/spack/spack/cmd/stage.py |  5 ++---
 lib/spack/spack/package.py   | 15 +++++++--------
 lib/spack/spack/stage.py     |  7 +++++--
 3 files changed, 14 insertions(+), 13 deletions(-)

diff --git a/lib/spack/spack/cmd/stage.py b/lib/spack/spack/cmd/stage.py
index 749fa908686..975bb54ef75 100644
--- a/lib/spack/spack/cmd/stage.py
+++ b/lib/spack/spack/cmd/stage.py
@@ -54,6 +54,5 @@ def stage(parser, args):
     for spec in specs:
         package = spack.repo.get(spec)
         if args.path:
-            package.do_stage(path=args.path)
-        else:
-            package.do_stage()
+            package.path = args.path
+        package.do_stage()
diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py
index ce314b7b0a5..9dcfbee6616 100644
--- a/lib/spack/spack/package.py
+++ b/lib/spack/spack/package.py
@@ -335,6 +335,9 @@ def __init__(self, spec):
         if '.' in self.name:
             self.name = self.name[self.name.rindex('.') + 1:]
 
+        # Allow custom staging paths for packages
+        self.path=None
+
         # Sanity check attributes required by Spack directives.
         spack.directives.ensure_dicts(type(self))
 
@@ -445,7 +448,8 @@ def _make_resource_stage(self, root_stage, fetcher, resource):
         resource_stage_folder = self._resource_stage(resource)
         resource_mirror = join_path(self.name, os.path.basename(fetcher.url))
         stage = ResourceStage(resource.fetcher, root=root_stage, resource=resource,
-                              name=resource_stage_folder, mirror_path=resource_mirror)
+                              name=resource_stage_folder, mirror_path=resource_mirror,
+                              path=self.path)
         return stage
 
     def _make_root_stage(self, fetcher):
@@ -455,7 +459,7 @@ def _make_root_stage(self, fetcher):
         s = self.spec
         stage_name = "%s-%s-%s" % (s.name, s.version, s.dag_hash())
         # Build the composite stage
-        stage = Stage(fetcher, mirror_path=mp, name=stage_name)
+        stage = Stage(fetcher, mirror_path=mp, name=stage_name, path=self.path)
         return stage
 
     def _make_stage(self):
@@ -709,18 +713,13 @@ def do_fetch(self, mirror_only=False):
         if spack.do_checksum and self.version in self.versions:
             self.stage.check()
 
-    def do_stage(self, mirror_only=False, path=None):
+    def do_stage(self, mirror_only=False):
         """Unpacks the fetched tarball, then changes into the expanded tarball
            directory."""
-
         if not self.spec.concrete:
             raise ValueError("Can only stage concrete packages.")
 
         self.do_fetch(mirror_only)
-
-        if path is not None:
-            self.stage.path = path
-
         self.stage.expand_archive()
         self.stage.chdir_to_source()
 
diff --git a/lib/spack/spack/stage.py b/lib/spack/spack/stage.py
index f88f82fc2d6..d711752c208 100644
--- a/lib/spack/spack/stage.py
+++ b/lib/spack/spack/stage.py
@@ -89,7 +89,7 @@ class Stage(object):
     """
 
     def __init__(self, url_or_fetch_strategy,
-                 name=None, mirror_path=None, keep=False):
+                 name=None, mirror_path=None, keep=False, path=None):
         """Create a stage object.
            Parameters:
              url_or_fetch_strategy
@@ -135,7 +135,10 @@ def __init__(self, url_or_fetch_strategy,
 
         # Try to construct here a temporary name for the stage directory
         # If this is a named stage, then construct a named path.
-        self.path = join_path(spack.stage_path, self.name)
+        if path is not None:
+            self.path = path
+        else:
+            self.path = join_path(spack.stage_path, self.name)
 
         # Flag to decide whether to delete the stage folder on exit or not
         self.keep = keep

From a670408617b76777d35185aa554eeaf3892e0188 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Thu, 31 Mar 2016 11:34:00 -0700
Subject: [PATCH 228/230] Quick fix for pkg diff.

---
 lib/spack/spack/cmd/pkg.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/lib/spack/spack/cmd/pkg.py b/lib/spack/spack/cmd/pkg.py
index cf478d3763e..20a3fc5fc22 100644
--- a/lib/spack/spack/cmd/pkg.py
+++ b/lib/spack/spack/cmd/pkg.py
@@ -77,7 +77,8 @@ def get_git():
 
 def list_packages(rev):
     git = get_git()
-    relpath = spack.packages_path[len(spack.prefix + os.path.sep):] + os.path.sep
+    pkgpath = os.path.join(spack.packages_path, 'packages')
+    relpath = pkgpath[len(spack.prefix + os.path.sep):] + os.path.sep
     output = git('ls-tree', '--full-tree', '--name-only', rev, relpath,
                  output=str)
     return sorted(line[len(relpath):] for line in output.split('\n') if line)

From 66038ef729b5fb8d2efadc48c87a868370ca23c5 Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Thu, 31 Mar 2016 13:34:56 -0500
Subject: [PATCH 229/230] Add url_for_version function and gtk variant

---
 .../repos/builtin/packages/qt/package.py      | 70 ++++++++++++-------
 1 file changed, 44 insertions(+), 26 deletions(-)

diff --git a/var/spack/repos/builtin/packages/qt/package.py b/var/spack/repos/builtin/packages/qt/package.py
index d08e8e81e1a..ab094690422 100644
--- a/var/spack/repos/builtin/packages/qt/package.py
+++ b/var/spack/repos/builtin/packages/qt/package.py
@@ -1,41 +1,31 @@
-import os
 from spack import *
 import os
 
 class Qt(Package):
     """Qt is a comprehensive cross-platform C++ application framework."""
-    homepage = "http://qt.io"
-    list_url   = 'http://download.qt-project.org/official_releases/qt/'
-    list_depth = 2
+    homepage = 'http://qt.io'
+    url      = 'http://download.qt.io/archive/qt/5.5/5.5.1/single/qt-everywhere-opensource-src-5.5.1.tar.gz'
 
-    version('5.4.2', 'fa1c4d819b401b267eb246a543a63ea5',
-            url='http://download.qt-project.org/official_releases/qt/5.4/5.4.2/single/qt-everywhere-opensource-src-5.4.2.tar.gz')
+    version('5.5.1',  '59f0216819152b77536cf660b015d784')
+    version('5.4.2',  'fa1c4d819b401b267eb246a543a63ea5')
+    version('5.4.0',  'e8654e4b37dd98039ba20da7a53877e6')
+    version('5.3.2',  'febb001129927a70174467ecb508a682')
+    version('5.2.1',  'a78408c887c04c34ce615da690e0b4c8')
+    version('4.8.6',  '2edbe4d6c2eff33ef91732602f3518eb')
+    version('3.3.8b', '9f05b4125cfe477cc52c9742c3c09009')
 
-    version('5.4.0', 'e8654e4b37dd98039ba20da7a53877e6',
-            url='http://download.qt-project.org/official_releases/qt/5.4/5.4.0/single/qt-everywhere-opensource-src-5.4.0.tar.gz')
-
-    version('5.3.2', 'febb001129927a70174467ecb508a682',
-            url='http://download.qt.io/archive/qt/5.3/5.3.2/single/qt-everywhere-opensource-src-5.3.2.tar.gz')
-
-    version('5.2.1', 'a78408c887c04c34ce615da690e0b4c8',
-            url='http://download.qt.io/archive/qt/5.2/5.2.1/single/qt-everywhere-opensource-src-5.2.1.tar.gz')
-
-    version('4.8.6', '2edbe4d6c2eff33ef91732602f3518eb',
-            url="http://download.qt-project.org/official_releases/qt/4.8/4.8.6/qt-everywhere-opensource-src-4.8.6.tar.gz")
-
-    version('3.3.8b', '9f05b4125cfe477cc52c9742c3c09009',
-            url="http://download.qt.io/archive/qt/3/qt-x11-free-3.3.8b.tar.gz")
-
-    variant('mesa', default=False, description='depend on mesa')
     # Add patch for compile issues with qt3 found with use in the OpenSpeedShop project
-    variant('krellpatch', default=False, description="build with openspeedshop based patch.")
+    variant('krellpatch', default=False, description="Build with openspeedshop based patch.")
+    variant('mesa',       default=False, description="Depend on mesa.")
+    variant('gtk',        default=False, description="Build with gtkplus.")
+
     patch('qt3krell.patch', when='@3.3.8b+krellpatch')
 
     # Use system openssl for security.
     #depends_on("openssl")
 
     depends_on("glib")
-    depends_on("gtkplus")
+    depends_on("gtkplus", when='+gtk')
     depends_on("libxml2")
     depends_on("zlib")
     depends_on("dbus", when='@4:')
@@ -56,6 +46,34 @@ class Qt(Package):
     depends_on("libxcb")
 
 
+    def url_for_version(self, version):
+        url = "http://download.qt.io/archive/qt/"
+
+        if version >= Version('5'):
+            url += "%s/%s/single/qt-everywhere-opensource-src-%s.tar.gz" % \
+                    (version.up_to(2), version, version)
+        elif version >= Version('4.8'):
+            url += "%s/%s/qt-everywhere-opensource-src-%s.tar.gz" % \
+                    (version.up_to(2), version, version)
+        elif version >= Version('4.6'):
+            url += "%s/qt-everywhere-opensource-src-%s.tar.gz" % \
+                    (version.up_to(2), version)
+        elif version >= Version('4.0'):
+            url += "%s/qt-x11-opensource-src-%s.tar.gz" % \
+                    (version.up_to(2), version)
+        elif version >= Version('3'):
+            url += "%s/qt-x11-free-%s.tar.gz" % \
+                    (version.up_to(1), version)
+        elif version >= Version('2.1'):
+            url += "%s/qt-x11-%s.tar.gz" % \
+                    (version.up_to(1), version)
+        else:
+            url += "%s/qt-%s.tar.gz" % \
+                    (version.up_to(1), version)
+
+        return url
+
+
     def setup_environment(self, spack_env, env):
         env.set('QTDIR', self.prefix)
 
@@ -88,7 +106,7 @@ def common_config_args(self):
             '-v',
             '-opensource',
             '-opengl',
-            "-release",
+            '-release',
             '-shared',
             '-confirm-license',
             '-openssl-linked',
@@ -97,7 +115,7 @@ def common_config_args(self):
             '-no-openvg',
             '-no-pch',
             # NIS is deprecated in more recent glibc
-            "-no-nis"]
+            '-no-nis']
     # Don't disable all the database drivers, but should
     # really get them into spack at some point.
 

From 87b70e2cb45660c5c037dfce963c5dc946b2daf5 Mon Sep 17 00:00:00 2001
From: Patrick Gartung <gartung@fnal.gov>
Date: Thu, 31 Mar 2016 14:07:03 -0500
Subject: [PATCH 230/230] remove the part I added to setup-env.sh as this does
 not work unless the modules package is already built.

---
 share/spack/setup-env.sh | 10 ----------
 1 file changed, 10 deletions(-)

diff --git a/share/spack/setup-env.sh b/share/spack/setup-env.sh
index 529517ff834..764af684001 100755
--- a/share/spack/setup-env.sh
+++ b/share/spack/setup-env.sh
@@ -176,13 +176,3 @@ _spack_pathadd PATH       "${_sp_prefix%/}/bin"
 _sp_sys_type=$(spack-python -c 'print(spack.architecture.sys_type())')
 _spack_pathadd DK_NODE    "${_sp_share_dir%/}/dotkit/$_sp_sys_type"
 _spack_pathadd MODULEPATH "${_sp_share_dir%/}/modules/$_sp_sys_type"
-
-#
-# Use spack built modules package if available
-# for system that does not have it
-#
-
-_modules_install_path=$(command spack location -i modules)
-if [ -n "$_modules_install_path" ] ; then
-    . $_modules_install_path/Modules/init/sh
-fi