Merge branch 'develop' of https://github.com/scalability-llnl/spack into issues/gcc

Conflicts:
	var/spack/packages/gcc/package.py

GCC : removed dependency on libelf. Removed isl variant

README.md

@@ -1,5 +1,5 @@
-Spack
+![image](share/spack/logo/spack-logo-text-64.png "Spack")
-===========
+============
 
 Spack is a package management tool designed to support multiple
 versions and configurations of software on a wide variety of platforms
@@ -13,7 +13,7 @@ can coexist on the same system.
 Most importantly, Spack is simple. It offers a simple spec syntax so
 that users can specify versions and configuration options
 concisely. Spack is also simple for package authors: package files are
-writtin in pure Python, and specs allow package authors to write a
+written in pure Python, and specs allow package authors to write a
 single build script for many different builds of the same package.
 
 See the
@@ -62,21 +62,9 @@ latest stable release.
 
 Authors
 ----------------
-Spack was written by Todd Gamblin, tgamblin@llnl.gov.
+Many thanks go to Spack's [contributors](https://github.com/scalability-llnl/spack/graphs/contributors).
 
-Significant contributions were also made by:
+Spack was originally written by Todd Gamblin, tgamblin@llnl.gov.
-
-  * David Beckingsale
-  * David Boehme
-  * Alfredo Gimenez
-  * Luc Jaulmes
-  * Matt Legendre
-  * Greg Lee
-  * Adam Moody
-  * Saravan Pantham
-  * Joachim Protze
-  * Bob Robey
-  * Justin Too
 
 Release
 ----------------

bin/spack

@@ -118,7 +118,7 @@ def main():
 
     # If the user asked for it, don't check ssl certs.
     if args.insecure:
-        tty.warn("You asked for --insecure, which does not check SSL certificates or checksums.")
+        tty.warn("You asked for --insecure, which does not check SSL certificates.")
         spack.curl.add_default_arg('-k')
 
     # Try to load the particular command asked for and run it

lib/spack/docs/conf.py

@@ -149,7 +149,7 @@
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the
 # documentation.
-#html_theme_options = [('show_copyright', False)]
+html_theme_options = { 'logo_only' : True }
 
 # Add any paths that contain custom themes here, relative to this directory.
 html_theme_path = ["_themes"]
@@ -163,12 +163,12 @@
 
 # The name of an image file (relative to this directory) to place at the top
 # of the sidebar.
-#html_logo = None
+html_logo = '../../../share/spack/logo/spack-logo-white-text-48.png'
 
 # The name of an image file (within the static path) to use as favicon of the
 # docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
 # pixels large.
-#html_favicon = None
+html_favicon = '../../../share/spack/logo/favicon.ico'
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,

lib/spack/llnl/util/tty/colify.py

@@ -33,8 +33,7 @@
 from StringIO import StringIO
 
 from llnl.util.tty import terminal_size
-from llnl.util.tty.color import clen
+from llnl.util.tty.color import clen, cextra
-
 
 class ColumnConfig:
     def __init__(self, cols):
@@ -42,7 +41,6 @@ def __init__(self, cols):
         self.line_length = 0
         self.valid = True
         self.widths = [0] * cols   # does not include ansi colors
-        self.cwidths = [0] * cols  # includes ansi colors
 
     def __repr__(self):
         attrs = [(a,getattr(self, a)) for a in dir(self) if not a.startswith("__")]
@@ -66,8 +64,6 @@ def config_variable_cols(elts, console_width, padding, cols=0):
     # Get a bound on the most columns we could possibly have.
     # 'clen' ignores length of ansi color sequences.
     lengths = [clen(e) for e in elts]
-    clengths = [len(e) for e in elts]
-
     max_cols = max(1, console_width / (min(lengths) + padding))
     max_cols = min(len(elts), max_cols)
 
@@ -85,7 +81,6 @@ def config_variable_cols(elts, console_width, padding, cols=0):
                 if conf.widths[col] < (length + p):
                     conf.line_length += length + p - conf.widths[col]
                     conf.widths[col]  = length + p
-                    conf.cwidths[col] = clengths[i] + p
                     conf.valid = (conf.line_length < console_width)
 
     try:
@@ -118,7 +113,6 @@ def config_uniform_cols(elts, console_width, padding, cols=0):
 
     config = ColumnConfig(cols)
     config.widths = [max_len] * cols
-    config.cwidths = [max_clen] * cols
 
     return config
 
@@ -147,9 +141,6 @@ def colify(elts, **options):
     method=<string>   Method to use to fit columns.  Options are variable or uniform.
                       Variable-width columns are tighter, uniform columns are all the
                       same width and fit less data on the screen.
-
-    len=<func>        Function to use for calculating string length.
-                      Useful for ignoring ansi color. Default is 'len'.
     """
     # Get keyword arguments or set defaults
     cols         = options.pop("cols", 0)
@@ -199,9 +190,6 @@ def colify(elts, **options):
         raise ValueError("method must be one of: " + allowed_methods)
 
     cols = config.cols
-    formats = ["%%-%ds" % width for width in config.cwidths[:-1]]
-    formats.append("%s")  # last column has no trailing space
-
     rows = (len(elts) + cols - 1) / cols
     rows_last_col = len(elts) % rows
 
@@ -209,7 +197,9 @@ def colify(elts, **options):
         output.write(" " * indent)
         for col in xrange(cols):
             elt = col * rows + row
-            output.write(formats[col] % elts[elt])
+            width = config.widths[col] + cextra(elts[elt])
+            fmt = '%%-%ds' % width
+            output.write(fmt % elts[elt])
 
         output.write("\n")
         row += 1

lib/spack/llnl/util/tty/color.py

@@ -158,6 +158,11 @@ def clen(string):
     return len(re.sub(r'\033[^m]*m', '', string))
 
 
+def cextra(string):
+    """"Length of extra color characters in a string"""
+    return len(''.join(re.findall(r'\033[^m]*m', string)))
+
+
 def cwrite(string, stream=sys.stdout, color=None):
     """Replace all color expressions in string with ANSI control
        codes and write the result to the stream.  If color is

lib/spack/spack/__init__.py

@@ -27,24 +27,26 @@
 from llnl.util.filesystem import *
 
 # This lives in $prefix/lib/spack/spack/__file__
-prefix = ancestor(__file__, 4)
+spack_root = ancestor(__file__, 4)
 
 # The spack script itself
-spack_file = join_path(prefix, "bin", "spack")
+spack_file = join_path(spack_root, "bin", "spack")
 
 # spack directory hierarchy
-etc_path       = join_path(prefix, "etc")
+lib_path       = join_path(spack_root, "lib", "spack")
-lib_path       = join_path(prefix, "lib", "spack")
 build_env_path = join_path(lib_path, "env")
 module_path    = join_path(lib_path, "spack")
 compilers_path = join_path(module_path, "compilers")
 test_path      = join_path(module_path, "test")
 hooks_path     = join_path(module_path, "hooks")
-var_path       = join_path(prefix, "var", "spack")
+var_path       = join_path(spack_root, "var", "spack")
 stage_path     = join_path(var_path, "stage")
+share_path     = join_path(spack_root, "share", "spack")
+
+prefix = spack_root
 opt_path       = join_path(prefix, "opt")
 install_path   = join_path(opt_path, "spack")
-share_path     = join_path(prefix, "share", "spack")
+etc_path       = join_path(prefix, "etc")
 
 #
 # Set up the packages database.

lib/spack/spack/cmd/info.py

@@ -65,11 +65,21 @@ def print_text_info(pkg):
         print "None"
     else:
         pad = padder(pkg.variants, 4)
+
+        maxv = max(len(v) for v in sorted(pkg.variants))
+        fmt = "%%-%ss%%-10s%%s" % (maxv + 4)
+
+        print "    " + fmt % ('Name',   'Default',   'Description')
+        print
         for name in sorted(pkg.variants):
             v = pkg.variants[name]
-            print "    %s%s" % (
+            default = 'on' if v.default else 'off'
-                pad(('+' if v.default else '-') + name + ':'),
+
-                "\n".join(textwrap.wrap(v.description)))
+            lines = textwrap.wrap(v.description)
+            lines[1:] = ["      " + (" " * maxv) + l for l in lines[1:]]
+            desc = "\n".join(lines)
+
+            print "    " + fmt % (name, default, desc)
 
     print
     print "Dependencies:"

lib/spack/spack/directory_layout.py

@@ -187,14 +187,9 @@ def hidden_file_paths(self):
 
     def relative_path_for_spec(self, spec):
         _check_concrete(spec)
-        enabled_variants = (
+        dir_name = "%s-%s-%s" % (
-            '-' + v.name for v in spec.variants.values()
-            if v.enabled)
-
-        dir_name = "%s-%s%s-%s" % (
             spec.name,
             spec.version,
-            ''.join(enabled_variants),
             spec.dag_hash(self.hash_len))
 
         path = join_path(

lib/spack/spack/package.py

@@ -438,9 +438,16 @@ def stage(self):
             raise ValueError("Can only get a stage for a concrete package.")
 
         if self._stage is None:
+            # Construct a mirror path (TODO: get this out of package.py)
             mp = spack.mirror.mirror_archive_path(self.spec)
-            self._stage = Stage(
+
-                self.fetcher, mirror_path=mp, name=self.spec.short_spec)
+            # Construct a path where the stage should build..
+            s = self.spec
+            stage_name = "%s-%s-%s" % (s.name, s.version, s.dag_hash())
+
+            # Build the stage
+            self._stage = Stage(self.fetcher, mirror_path=mp, name=stage_name)
+
         return self._stage
 
 

var/spack/packages/activeharmony/package.py

@@ -0,0 +1,15 @@
+from spack import *
+
+class Activeharmony(Package):
+    """Active Harmony: a framework for auto-tuning (the automated search for values to improve the performance of a target application)."""
+    homepage = "http://www.dyninst.org/harmony"
+    url      = "http://www.dyninst.org/sites/default/files/downloads/harmony/ah-4.5.tar.gz"
+
+    version('4.5', 'caee5b864716d376e2c25d739251b2a9')
+
+    def install(self, spec, prefix):
+        make("CFLAGS=-O3")
+        make("install", 'PREFIX=%s' % prefix)
+
+from spack import *
+

var/spack/packages/binutils/package.py

@@ -10,8 +10,20 @@ class Binutils(Package):
     version('2.23.2', '4f8fa651e35ef262edc01d60fb45702e')
     version('2.20.1', '2b9dc8f2b7dbd5ec5992c6e29de0b764')
 
-    def install(self, spec, prefix):
+    variant('libiberty', default=False, description='Also install libiberty.')
-        configure("--prefix=%s" % prefix)
 
+    def install(self, spec, prefix):
+        configure_args = [
+            '--prefix=%s' % prefix,
+            '--disable-dependency-tracking',
+            '--enable-interwork',
+            '--enable-multilib',
+            '--enable-64-bit-bfd',
+            '--enable-targets=all']
+
+        if '+libiberty' in spec:
+            configure_args.append('--enable-install-libiberty')
+
+        configure(*configure_args)
         make()
         make("install")

var/spack/packages/boost/package.py

@@ -14,6 +14,10 @@ class Boost(Package):
     list_url = "http://sourceforge.net/projects/boost/files/boost/"
     list_depth = 2
 
+    version('1.59.0', '6aa9a5c6a4ca1016edd0ed1178e3cb87')
+    version('1.58.0', 'b8839650e61e9c1c0a89f371dd475546')
+    version('1.57.0', '1be49befbdd9a5ce9def2983ba3e7b76')
+    version('1.56.0', 'a744cf167b05d72335f27c88115f211d')
     version('1.55.0', 'd6eef4b4cacb2183f2bf265a5a03a354')
     version('1.54.0', '15cb8c0803064faef0c4ddf5bc5ca279')
     version('1.53.0', 'a00d22605d5dbcfb4c9936a9b35bc4c2')

var/spack/packages/bowtie2/bowtie2-2.5.patch

@@ -0,0 +1,16 @@
+--- Makefile	2015-02-26 10:50:00.000000000 -0800
++++ Makefile.new	2015-07-29 18:03:59.891357399 -0700
+@@ -22,10 +22,10 @@
+ #
+ 
+ INC =
+-GCC_PREFIX = $(shell dirname `which gcc`)
++GCC_PREFIX =
+ GCC_SUFFIX =
+-CC = $(GCC_PREFIX)/gcc$(GCC_SUFFIX)
+-CPP = $(GCC_PREFIX)/g++$(GCC_SUFFIX)
++CC = cc 
++CPP = c++
+ CXX = $(CPP)
+ HEADERS = $(wildcard *.h)
+ BOWTIE_MM = 1

var/spack/packages/bowtie2/package.py

@@ -0,0 +1,24 @@
+from spack import *
+from glob import glob
+class Bowtie2(Package):
+    """Description"""
+    homepage = "bowtie-bio.sourceforge.net/bowtie2/index.shtml"
+    version('2.2.5','51fa97a862d248d7ee660efc1147c75f', url = "http://downloads.sourceforge.net/project/bowtie-bio/bowtie2/2.2.5/bowtie2-2.2.5-source.zip")
+
+    patch('bowtie2-2.5.patch',when='@2.2.5', level=0)
+
+    def install(self, spec, prefix):
+        make()
+        mkdirp(prefix.bin)
+        for bow in glob("bowtie2*"):
+            install(bow, prefix.bin)
+        # install('bowtie2',prefix.bin)
+        # install('bowtie2-align-l',prefix.bin)
+        # install('bowtie2-align-s',prefix.bin)
+        # install('bowtie2-build',prefix.bin)
+        # install('bowtie2-build-l',prefix.bin)
+        # install('bowtie2-build-s',prefix.bin)
+        # install('bowtie2-inspect',prefix.bin)
+        # install('bowtie2-inspect-l',prefix.bin)
+        # install('bowtie2-inspect-s',prefix.bin)
+

var/spack/packages/bzip2/package.py

@@ -22,8 +22,10 @@ def install(self, spec, prefix):
 
         bzip2_exe = join_path(prefix.bin, 'bzip2')
         install('bzip2-shared', bzip2_exe)
-        for libfile in glob('libbz2.so*'):
+        for i, libfile in enumerate(glob('libbz2.so*')):
             install(libfile, prefix.lib)
+            if i == 0:
+                symlink(join_path(prefix.lib, libfile), join_path(prefix.lib, 'libbz2.so'))
 
         bunzip2 = join_path(prefix.bin, 'bunzip2')
         remove(bunzip2)

var/spack/packages/doxygen/package.py

@@ -0,0 +1,25 @@
+#------------------------------------------------------------------------------
+# Author: Justin Too <justin@doubleotoo.com>
+# Date: September 11, 2015
+#------------------------------------------------------------------------------
+
+from spack import *
+
+class Doxygen(Package):
+    """Doxygen is the de facto standard tool for generating documentation
+    from annotated C++ sources, but it also supports other popular programming
+    languages such as C, Objective-C, C#, PHP, Java, Python, IDL (Corba,
+    Microsoft, and UNO/OpenOffice flavors), Fortran, VHDL, Tcl, and to some extent D..
+    """
+    homepage = "http://www.stack.nl/~dimitri/doxygen/"
+    url      = "http://ftp.stack.nl/pub/users/dimitri/doxygen-1.8.10.src.tar.gz"
+
+    version('1.8.10', '79767ccd986f12a0f949015efb5f058f')
+
+    depends_on("cmake@2.8.12:")
+
+    def install(self, spec, prefix):
+        cmake('.', *std_cmake_args)
+
+        make()
+        make("install")

var/spack/packages/fish/package.py

@@ -0,0 +1,18 @@
+from spack import *
+
+class Fish(Package):
+    """fish is a smart and user-friendly command line shell for OS X, Linux, and
+    the rest of the family.
+    """
+
+    homepage = "http://fishshell.com/"
+    url      = "http://fishshell.com/files/2.2.0/fish-2.2.0.tar.gz"
+    list_url = homepage
+
+    version('2.2.0', 'a76339fd14ce2ec229283c53e805faac48c3e99d9e3ede9d82c0554acfc7b77a')
+
+    def install(self, spec, prefix):
+        configure('--prefix=%s' % prefix)
+
+        make()
+        make("install")

var/spack/packages/gcc/package.py

@@ -47,17 +47,15 @@ class Gcc(Package):
     version('4.5.4', '27e459c2566b8209ab064570e1b378f7')
     
     variant('binutils', default=False, description='Add a dependency on binutils')
-    variant('libelf', default=False, description='Add a dependency on libelf')
-    variant('isl', default=True, description='Add a dependency on isl')
     
     depends_on("mpfr")
     depends_on("gmp")
     depends_on("mpc")     # when @4.5:
-    depends_on("libelf", when='+libelf')
+    depends_on("libelf")
-    depends_on("binutils",when="+binutils")
+    depends_on("binutils~libiberty", when="+binutils")
 
     # Save these until we can do optional deps.
-    depends_on("isl", when='@5.0:+isl')
+    depends_on("isl", when='@5.0:')
     #depends_on("ppl")
     #depends_on("cloog")
 

var/spack/packages/gflags/package.py

@@ -0,0 +1,21 @@
+import os
+from spack import *
+
+class Gflags(Package):
+    """The gflags package contains a C++ library that implements
+    commandline flags processing. It includes built-in support for
+    standard types such as string and the ability to define flags
+    in the source file in which they are used. Online documentation
+    available at: https://gflags.github.io/gflags/"""
+
+    homepage = "https://gflags.github.io/gflags"
+    url      = "https://github.com/gflags/gflags/archive/v2.1.2.tar.gz"
+
+    version('2.1.2', 'ac432de923f9de1e9780b5254884599f')
+
+    def install(self, spec, prefix):
+        cmake("-DCMAKE_INSTALL_PREFIX=" + prefix,
+              "-DBUILD_SHARED_LIBS=ON")
+        make()
+        make("test")
+        make("install")

var/spack/packages/glm/package.py

@@ -0,0 +1,19 @@
+from spack import *
+
+
+class Glm(Package):
+    """
+    OpenGL Mathematics (GLM) is a header only C++ mathematics library for graphics software based on
+    the OpenGL Shading Language (GLSL) specification.
+    """
+
+    homepage = "https://github.com/g-truc/glm"
+    url = "https://github.com/g-truc/glm/archive/0.9.7.1.tar.gz"
+
+    version('0.9.7.1', '61af6639cdf652d1cdd7117190afced8')
+
+    def install(self, spec, prefix):
+        with working_dir('spack-build', create=True):
+            cmake('..', *std_cmake_args)
+            make()
+            make("install")

var/spack/packages/glog/package.py

@@ -0,0 +1,15 @@
+import os
+from spack import *
+
+class Glog(Package):
+    """C++ implementation of the Google logging module."""
+
+    homepage = "https://github.com/google/glog"
+    url      = "https://github.com/google/glog/archive/v0.3.3.tar.gz"
+
+    version('0.3.3', 'c1f86af27bd9c73186730aa957607ed0')
+
+    def install(self, spec, prefix):
+        configure("--prefix=" + prefix)
+        make()
+        make("install")

var/spack/packages/hdf5/package.py

@@ -11,6 +11,7 @@ class Hdf5(Package):
     list_url = "http://www.hdfgroup.org/ftp/HDF5/releases"
     list_depth = 3
     
+    version('1.8.15', '03cccb5b33dbe975fdcd8ae9dc021f24')
     version('1.8.13', 'c03426e9e77d7766944654280b467289')
 
     depends_on("mpi")

var/spack/packages/leveldb/package.py

@@ -0,0 +1,29 @@
+import os
+import glob
+from spack import *
+
+class Leveldb(Package):
+    """LevelDB is a fast key-value storage library written at Google
+    that provides an ordered mapping from string keys to string values."""
+
+    homepage = "https://github.com/google/leveldb"
+    url      = "https://github.com/google/leveldb/archive/v1.18.tar.gz"
+
+    version('1.18', '73770de34a2a5ab34498d2e05b2b7fa0')
+
+    depends_on("snappy")
+
+    def install(self, spec, prefix):
+        make()
+
+        mkdirp(prefix.include)
+        mkdirp(prefix.lib)
+
+        cp = which('cp')
+
+        # cp --preserve=links libleveldb.* prefix/lib
+        args = glob.glob('libleveldb.*')
+        args.append(prefix + '/lib')
+        cp('--preserve=links', *args)
+
+        cp('-r', 'include/leveldb', prefix + '/include')

var/spack/packages/libffi/package.py

@@ -6,11 +6,12 @@ class Libffi(Package):
     to call any function specified by a call interface description at
     run time."""
     homepage = "https://sourceware.org/libffi/"
-    url      = "ftp://sourceware.org/pub/libffi/libffi-3.1.tar.gz"
     
-    version('3.1', 'f5898b29bbfd70502831a212d9249d10')
+    version('3.2.1','83b89587607e3eb65c70d361f13bab43',url = "ftp://sourceware.org/pub/libffi/libffi-3.2.1.tar.gz")
+    #version('3.1', 'f5898b29bbfd70502831a212d9249d10',url = "ftp://sourceware.org/pub/libffi/libffi-3.1.tar.gz") # Has a bug $(lib64) instead of ${lib64} in libffi.pc
 
     def install(self, spec, prefix):
         configure("--prefix=%s" % prefix)
         make()
         make("install")
+

var/spack/packages/libxcb/package.py

@@ -10,7 +10,7 @@ class Libxcb(Package):
     url      = "http://xcb.freedesktop.org/dist/libxcb-1.11.tar.gz"
 
     version('1.11', '1698dd837d7e6e94d029dbe8b3a82deb')
-
+    version('1.11.1', '118623c15a96b08622603a71d8789bf3')
     depends_on("python")
     depends_on("xcb-proto")
 

var/spack/packages/lmdb/package.py

@@ -0,0 +1,39 @@
+import os
+from spack import *
+
+class Lmdb(Package):
+    """Read-only mirror of official repo on openldap.org. Issues and
+    pull requests here are ignored. Use OpenLDAP ITS for issues.
+    http://www.openldap.org/software/repo.html"""
+
+
+    homepage = "http://www.openldap.org/software/repo.html"
+    url      = "https://github.com/LMDB/lmdb/archive/LMDB_0.9.16.tar.gz"
+
+    version('0.9.16', '0de89730b8f3f5711c2b3a4ba517b648')
+
+    def install(self, spec, prefix):
+        os.chdir('libraries/liblmdb')
+
+        make()
+
+        mkdirp(prefix.bin)
+        mkdirp(prefix + '/man/man1')
+        mkdirp(prefix.lib)
+        mkdirp(prefix.include)
+
+        bins = ['mdb_stat', 'mdb_copy', 'mdb_dump', 'mdb_load']
+        for f in bins:
+            install(f, prefix.bin)
+
+        mans = ['mdb_stat.1', 'mdb_copy.1', 'mdb_dump.1', 'mdb_load.1']
+        for f in mans:
+            install(f, prefix + '/man/man1')
+
+        libs = ['liblmdb.a', 'liblmdb.so']
+        for f in libs:
+            install(f, prefix.lib)
+
+        includes = ['lmdb.h']
+        for f in includes:
+            install(f, prefix.include)

var/spack/packages/matio/package.py

@@ -0,0 +1,15 @@
+from spack import *
+
+
+class Matio(Package):
+    """matio is an C library for reading and writing Matlab MAT files"""
+    homepage = "http://sourceforge.net/projects/matio/"
+    url = "http://downloads.sourceforge.net/project/matio/matio/1.5.2/matio-1.5.2.tar.gz"
+
+    version('1.5.2', '85b007b99916c63791f28398f6a4c6f1')
+
+    def install(self, spec, prefix):
+        configure('--prefix=%s' % prefix)
+
+        make()
+        make("install")

var/spack/packages/mpich/package.py

@@ -33,10 +33,15 @@ class Mpich(Package):
     list_url   = "http://www.mpich.org/static/downloads/"
     list_depth = 2
 
+    version('3.1.4', '2ab544607986486562e076b83937bba2')
+    version('3.1.3', '93cb17f91ac758cbf9174ecb03563778')
+    version('3.1.2', '7fbf4b81dcb74b07ae85939d1ceee7f1')
+    version('3.1.1', '40dc408b1e03cc36d80209baaa2d32b7')
+    version('3.1', '5643dd176499bfb7d25079aaff25f2ec')
     version('3.0.4', '9c5d5d4fe1e17dd12153f40bc5b6dbc0')
 
-    provides('mpi@:3', when='@3:')
+    provides('mpi@:3.0', when='@3:')
-    provides('mpi@:1', when='@1:')
+    provides('mpi@:1.3', when='@1:')
 
     def setup_dependent_environment(self, module, spec, dep_spec):
         """For dependencies, make mpicc's use spack wrapper."""

var/spack/packages/ncdu/package.py

@@ -0,0 +1,28 @@
+from spack import *
+
+class Ncdu(Package):
+    """
+    Ncdu is a disk usage analyzer with an ncurses interface. It is designed
+    to find space hogs on a remote server where you don't have an entire
+    gaphical setup available, but it is a useful tool even on regular desktop
+    systems. Ncdu aims to be fast, simple and easy to use, and should be able
+    to run in any minimal POSIX-like environment with ncurses installed.
+    """
+
+    homepage = "http://dev.yorhel.nl/ncdu"
+    url      = "http://dev.yorhel.nl/download/ncdu-1.11.tar.gz"
+
+    version('1.11', '9e44240a5356b029f05f0e70a63c4d12')
+    version('1.10', '7535decc8d54eca811493e82d4bfab2d')
+    version('1.9' , '93258079db897d28bb8890e2db89b1fb')
+    version('1.8' , '94d7a821f8a0d7ba8ef3dd926226f7d5')
+    version('1.7' , '172047c29d232724cc62e773e82e592a')
+
+    depends_on("ncurses")
+
+    def install(self, spec, prefix):
+        configure('--prefix=%s' % prefix,
+            '--with-ncurses=%s' % spec['ncurses'])
+
+        make()
+        make("install")

var/spack/packages/netcdf/netcdf-4.3.3-mpi.patch

@@ -0,0 +1,25 @@
+diff -Nur netcdf-4.3.3/CMakeLists.txt netcdf-4.3.3.mpi/CMakeLists.txt
+--- netcdf-4.3.3/CMakeLists.txt	2015-02-12 16:44:35.000000000 -0500
++++ netcdf-4.3.3.mpi/CMakeLists.txt	2015-10-14 16:44:41.176300658 -0400
+@@ -753,6 +753,7 @@
+     SET(USE_PARALLEL OFF CACHE BOOL "")
+     MESSAGE(STATUS "Cannot find HDF5 library built with parallel support. Disabling parallel build.")
+   ELSE()
++    FIND_PACKAGE(MPI REQUIRED)
+     SET(USE_PARALLEL ON CACHE BOOL "")
+     SET(STATUS_PARALLEL "ON")
+   ENDIF()
+diff -Nur netcdf-4.3.3/liblib/CMakeLists.txt netcdf-4.3.3.mpi/liblib/CMakeLists.txt
+--- netcdf-4.3.3/liblib/CMakeLists.txt	2015-02-12 16:44:35.000000000 -0500
++++ netcdf-4.3.3.mpi/liblib/CMakeLists.txt	2015-10-14 16:44:57.757793634 -0400
+@@ -71,6 +71,10 @@
+   SET(TLL_LIBS ${TLL_LIBS} ${CURL_LIBRARY})
+ ENDIF()
+ 
++IF(USE_PARALLEL)
++  SET(TLL_LIBS ${TLL_LIBS} ${MPI_C_LIBRARIES})
++ENDIF()
++
+ IF(USE_HDF4)
+   SET(TLL_LIBS ${TLL_LIBS} ${HDF4_LIBRARIES})
+ ENDIF()

var/spack/packages/netcdf/package.py

@@ -10,19 +10,18 @@ class Netcdf(Package):
 
     version('4.3.3', '5fbd0e108a54bd82cb5702a73f56d2ae')
 
+    patch('netcdf-4.3.3-mpi.patch')
+
     # Dependencies:
         # >HDF5
     depends_on("hdf5")
 
     def install(self, spec, prefix):
-        configure(
+        with working_dir('spack-build', create=True):
-		"--prefix=%s" % prefix, 
+            cmake('..',
-		"--disable-dap", # Disable DAP.
+                "-DCMAKE_INSTALL_PREFIX:PATH=%s" % prefix,
-		"--disable-shared", # Don't build shared libraries (use static libs).
+                "-DENABLE_DAP:BOOL=OFF", # Disable DAP.
-		"CPPFLAGS=-I%s/include" % spec['hdf5'].prefix, # Link HDF5's include dir.
+                "-DBUILD_SHARED_LIBS:BOOL=OFF") # Don't build shared libraries (use static libs).
-		"LDFLAGS=-L%s/lib" % spec['hdf5'].prefix) # Link HDF5's lib dir.
 
+            make()
             make("install")
-
-	# Check the newly installed netcdf package. Currently disabled.
-	# make("check")

var/spack/packages/openmpi/package.py

@@ -11,15 +11,19 @@ class Openmpi(Package):
 
     homepage = "http://www.open-mpi.org"
 
-    version('1.8.2', 'ab538ed8e328079d566fc797792e016e',
+    version('1.10.0', '280cf952de68369cebaca886c5ce0304',
-            url='http://www.open-mpi.org/software/ompi/v1.8/downloads/openmpi-1.8.2.tar.gz')
+            url = "http://www.open-mpi.org/software/ompi/v1.10/downloads/openmpi-1.10.0.tar.bz2")
+    version('1.8.8', '0dab8e602372da1425e9242ae37faf8c',
+            url = 'http://www.open-mpi.org/software/ompi/v1.8/downloads/openmpi-1.8.8.tar.bz2')
     version('1.6.5', '03aed2a4aa4d0b27196962a2a65fc475',
             url = "http://www.open-mpi.org/software/ompi/v1.6/downloads/openmpi-1.6.5.tar.bz2")
 
     patch('ad_lustre_rwcontig_open_source.patch', when="@1.6.5")
     patch('llnl-platforms.patch', when="@1.6.5")
 
-    provides('mpi@:2')
+    provides('mpi@:2.2', when='@1.6.5')    # Open MPI 1.6.5 supports MPI-2.2
+    provides('mpi@:3.0', when='@1.8.8')    # Open MPI 1.8.8 supports MPI-3.0
+    provides('mpi@:3.0', when='@1.10.0')   # Open MPI 1.10.0 supports MPI-3.0
 
     def install(self, spec, prefix):
         config_args = ["--prefix=%s" % prefix]

var/spack/packages/protobuf/package.py

@@ -0,0 +1,16 @@
+import os
+from spack import *
+
+class Protobuf(Package):
+    """Google's data interchange format."""
+
+    homepage = "https://developers.google.com/protocol-buffers"
+    url      = "https://github.com/google/protobuf/releases/download/v2.5.0/protobuf-2.5.0.tar.bz2"
+
+    version('2.5.0', 'a72001a9067a4c2c4e0e836d0f92ece4')
+
+    def install(self, spec, prefix):
+        configure("--prefix=" + prefix)
+        make()
+        make("check")
+        make("install")

var/spack/packages/samtools/package.py

@@ -0,0 +1,18 @@
+from spack import *
+
+class Samtools(Package):
+    """SAM Tools provide various utilities for manipulating alignments in the SAM format, 
+       including sorting, merging, indexing and generating
+       alignments in a per-position format"""
+
+    homepage = "www.htslib.org"
+    version('1.2','988ec4c3058a6ceda36503eebecd4122',url = "https://github.com/samtools/samtools/releases/download/1.2/samtools-1.2.tar.bz2")
+
+    depends_on("zlib")
+    depends_on("mpc")
+    parallel=False
+    patch("samtools1.2.patch",level=0)
+
+    def install(self, spec, prefix):
+        make("prefix=%s" % prefix, "install")
+

var/spack/packages/samtools/samtools1.2.patch

@@ -0,0 +1,20 @@
+--- Makefile	2015-02-03 08:27:34.000000000 -0800
++++ Makefile.new	2015-07-21 10:38:27.881406892 -0700
+@@ -26,7 +26,7 @@
+ CFLAGS   = -g -Wall -O2
+ LDFLAGS  =
+ LDLIBS   =
+-DFLAGS=     -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1
++DFLAGS=     -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0
+ LOBJS=      bam_aux.o bam.o bam_import.o sam.o \
+             sam_header.o bam_plbuf.o
+ AOBJS=      bam_index.o bam_plcmd.o sam_view.o \
+@@ -37,7 +37,7 @@
+             faidx.o stats.o stats_isize.o bam_flags.o bam_split.o \
+             bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o
+ INCLUDES=   -I. -I$(HTSDIR)
+-LIBCURSES=  -lcurses # -lXCurses
++#LIBCURSES=  -lcurses # -lXCurses
+ 
+ prefix      = /usr/local
+ exec_prefix = $(prefix)

var/spack/packages/scr/package.py

@@ -28,12 +28,14 @@ class Scr(Package):
     """SCR caches checkpoint data in storage on the compute nodes of a
        Linux cluster to provide a fast, scalable checkpoint/restart
        capability for MPI codes"""
+
     homepage = "https://computation.llnl.gov/project/scr/"
-    url      = "http://downloads.sourceforge.net/project/scalablecr/releases/scr-1.1-7.tar.gz"
 
     depends_on("mpi")
+#    depends_on("dtcmp")
 
-    version('1.1-7', 'a5930e9ab27d1b7049447c2fd7734ebd')
+    version('1.1-7', 'a5930e9ab27d1b7049447c2fd7734ebd', url='http://downloads.sourceforge.net/project/scalablecr/releases/scr-1.1-7.tar.gz')
+    version('1.1.8', '6a0f11ad18e27fcfc00a271ff587b06e', url='https://github.com/hpc/scr/releases/download/v1.1.8/scr-1.1.8.tar.gz')
 
     def install(self, spec, prefix):
         configure("--prefix=" + prefix,

var/spack/packages/snappy/package.py

@@ -0,0 +1,15 @@
+import os
+from spack import *
+
+class Snappy(Package):
+    """A fast compressor/decompressor: https://code.google.com/p/snappy"""
+
+    homepage = "https://code.google.com/p/snappy"
+    url      = "https://github.com/google/snappy/releases/download/1.1.3/snappy-1.1.3.tar.gz"
+
+    version('1.1.3', '7358c82f133dc77798e4c2062a749b73')
+
+    def install(self, spec, prefix):
+        configure("--prefix=" + prefix)
+        make()
+        make("install")

var/spack/packages/swig/package.py

@@ -38,6 +38,8 @@ class Swig(Package):
 
     version('3.0.2', '62f9b0d010cef36a13a010dc530d0d41')
 
+    depends_on('pcre')
+
     def install(self, spec, prefix):
         configure("--prefix=%s" % prefix)
         make()

var/spack/packages/trilinos/package.py

@@ -0,0 +1,50 @@
+from spack import *
+
+
+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.
+    A unique design feature of Trilinos is its focus on packages.
+    """
+    homepage = "https://trilinos.org/"
+    url = "http://trilinos.csbsju.edu/download/files/trilinos-12.2.1-Source.tar.gz"
+
+    version('12.2.1', '6161926ea247863c690e927687f83be9')
+    version('12.0.1', 'bd99741d047471e127b8296b2ec08017')
+    version('11.14.3', '2f4f83f8333e4233c57d0f01c4b57426')
+    version('11.14.2', 'a43590cf896c677890d75bfe75bc6254')
+    version('11.14.1', '40febc57f76668be8b6a77b7607bb67f')
+
+    variant('mpi', default=True, description='Add a dependency on MPI and enables MPI dependent packages')
+
+    # Everything should be compiled with -fpic
+    depends_on('blas')
+    depends_on('lapack')
+    depends_on('boost')
+    depends_on('netcdf')
+    depends_on('matio')
+    depends_on('glm')
+    depends_on('swig')
+    depends_on('mpi', when='+mpi')
+
+    def install(self, spec, prefix):
+
+        options = [
+            '-DTrilinos_ENABLE_ALL_PACKAGES:BOOL=ON',
+            '-DTrilinos_ENABLE_TESTS:BOOL=OFF',
+            '-DTrilinos_ENABLE_EXAMPLES:BOOL=OFF',
+            '-DBUILD_SHARED_LIBS:BOOL=ON',
+            '-DBLAS_LIBRARY_DIRS:PATH=%s' % spec['blas'].prefix,
+            '-DLAPACK_LIBRARY_DIRS:PATH=%s' % spec['lapack'].prefix
+        ]
+        if '+mpi' in spec:
+            mpi_options = ['-DTPL_ENABLE_MPI:BOOL=ON']
+            options.extend(mpi_options)
+
+        # -DCMAKE_INSTALL_PREFIX and all the likes...
+        options.extend(std_cmake_args)
+        with working_dir('spack-build', create=True):
+            cmake('..', *options)
+            make()
+            make('install')