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merge from develop

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This commit is contained in:
Peter Scheibel 2016-03-31 12:56:34 -07:00
commit 9eb314fcaa
115 changed files with 3976 additions and 852 deletions
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3
README.md
View File

@ -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/)

8
etc/spack/modules.yaml Normal file
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@ -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']

14
lib/spack/docs/packaging_guide.rst
View File

@ -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
----------------------

231
lib/spack/env/cc vendored
View File

@ -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
@ -78,12 +78,17 @@ done
# 'command' is set based on the input command to $SPACK_[CC|CXX|F77|F90]
#
# 'mode' is set to one of:
# cpp preprocess
# cc compile
# as assemble
# ld link
# ccld compile & link
# cpp preprocessor
# vcheck version check
#
# Depending on the mode, we may or may not add extra rpaths.
# This variable controls whether they are added.
add_rpaths=true
command=$(basename "$0")
case "$command" in
cc|c89|c99|gcc|clang|icc|pgcc|xlc)
@ -107,13 +112,26 @@ 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: $command"
;;
esac
# If any of the arguments below is present then the mode is vcheck. In vcheck mode nothing is added in terms of extra search paths or libraries
# If any of the arguments below is present then the mode is vcheck. In
# vcheck mode nothing is added in terms of extra search paths or
# libraries
if [ -z "$mode" ]; then
for arg in "$@"; do
if [ "$arg" = -v -o "$arg" = -V -o "$arg" = --version -o "$arg" = -dumpversion ]; then
@ -124,13 +142,15 @@ if [ -z "$mode" ]; then
fi
# Finish setting up the mode.
if [ -z "$mode" ]; then
mode=ccld
for arg in "$@"; do
if [ "$arg" = -E ]; then
mode=cpp
break
elif [ "$arg" = -S ]; then
mode=as
break
elif [ "$arg" = -c ]; then
mode=cc
break
@ -146,168 +166,56 @@ fi
# Check that at least one of the real commands was actually selected,
# otherwise we don't know what to execute.
if [ -z "$command" ]; then
if [[ -z $command ]]; then
die "ERROR: Compiler '$SPACK_COMPILER_SPEC' does not support compiling $language programs."
fi
# Save original command for debug logging
input_command="$@"
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+=("$1")
;;
esac
shift
done
# Dump parsed values for unit testing if asked for
if [ -n "$SPACK_TEST_COMMAND" ]; then
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[*]}"
;;
*)
echo "ERROR: Unknown test command"
exit 1 ;;
esac
exit
fi
# Save original command for debug logging
input_command="$@"
args=("$@")
# 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")
# Prepend include directories
if [[ -d $dep/include ]]; then
if [[ $mode = cpp || $mode = cc || $mode = as || $mode = ccld ]]; then
args=("-I$dep/include" "${args[@]}")
fi
fi
if [ -d "$dep/lib" ]; then
libraries+=("$dep/lib")
rpaths+=("$dep/lib")
# Prepend lib and RPATH directories
if [[ -d $dep/lib ]]; then
if [[ $mode = ccld ]]; then
$add_rpaths && args=("-Wl,-rpath,$dep/lib" "${args[@]}")
args=("-L$dep/lib" "${args[@]}")
elif [[ $mode = ld ]]; then
$add_rpaths && args=("-rpath" "$dep/lib" "${args[@]}")
args=("-L$dep/lib" "${args[@]}")
fi
fi
if [ -d "$dep/lib64" ]; then
libraries+=("$dep/lib64")
rpaths+=("$dep/lib64")
# Prepend lib64 and RPATH directories
if [[ -d $dep/lib64 ]]; then
if [[ $mode = ccld ]]; then
$add_rpaths && args=("-Wl,-rpath,$dep/lib64" "${args[@]}")
args=("-L$dep/lib64" "${args[@]}")
elif [[ $mode = ld ]]; then
$add_rpaths && args=("-rpath" "$dep/lib64" "${args[@]}")
args=("-L$dep/lib64" "${args[@]}")
fi
fi
done
# Include all -L's and prefix/whatever dirs in rpath
for dir in "${libraries[@]}"; do
[[ dir = $SPACK_INSTALL* ]] && rpaths+=("$dir")
done
rpaths+=("$SPACK_PREFIX/lib")
rpaths+=("$SPACK_PREFIX/lib64")
# 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
$add_rpaths && args=("-Wl,-rpath,$SPACK_PREFIX/lib" "-Wl,-rpath,$SPACK_PREFIX/lib64" "${args[@]}")
elif [[ $mode = ld ]]; then
$add_rpaths && args=("-rpath" "$SPACK_PREFIX/lib" "-rpath" "$SPACK_PREFIX/lib64" "${args[@]}")
fi
#
@ -323,34 +231,37 @@ 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=("$command" "${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 $SPACK_TEST_COMMAND ]]; then
die "ERROR: Unknown test command"
fi
#
# Write the input and output commands to debug logs if it's asked for.
#
if [ "$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" >> $input_log
echo "$mode ${full_command[@]}" >> $output_log
echo "[$mode] $command $input_command" >> $input_log
echo "[$mode] ${full_command[@]}" >> $output_log
fi
exec "${full_command[@]}"

46
lib/spack/llnl/util/filesystem.py
View File

@ -27,9 +27,11 @@
'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',
'fix_darwin_install_name']
import os
import glob
import sys
import re
import shutil
@ -38,6 +40,7 @@
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 +395,44 @@ 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
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

6
lib/spack/llnl/util/lang.py
View File

@ -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

8
lib/spack/spack/__init__.py
View File

@ -193,5 +193,9 @@
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']

192
lib/spack/spack/build_environment.py
View File

@ -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 +27,18 @@
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
import llnl.util.tty as tty
from llnl.util.filesystem import *
from spack.environment import EnvironmentModifications, validate
from spack.util.environment import *
from spack.util.executable import Executable, which
#
# This can be set by the user to globally disable parallel builds.
@ -58,6 +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
@ -83,85 +89,88 @@ def __call__(self, *args, **kwargs):
return super(MakeExecutable, self).__call__(*args, **kwargs)
def set_compiler_environment_variables(pkg):
assert(pkg.spec.concrete)
compiler = pkg.compiler
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'))
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.
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('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:
os.environ['SPACK_CC'] = compiler.cc
env.set('SPACK_CC', compiler.cc)
if compiler.cxx:
os.environ['SPACK_CXX'] = compiler.cxx
env.set('SPACK_CXX', compiler.cxx)
if compiler.f77:
os.environ['SPACK_F77'] = compiler.f77
env.set('SPACK_F77', compiler.f77)
if compiler.fc:
os.environ['SPACK_FC'] = compiler.fc
env.set('SPACK_FC', compiler.fc)
os.environ['SPACK_COMPILER_SPEC'] = str(pkg.spec.compiler)
env.set('SPACK_COMPILER_SPEC', str(pkg.spec.compiler))
return env
def set_build_environment_variables(pkg):
"""This ensures a clean install environment when we build packages.
def set_build_environment_variables(pkg, env):
"""
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
# 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)
for item in reversed(env_paths):
env.prepend_path('PATH', item)
env.set_path(SPACK_ENV_PATH, 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_path(SPACK_DEPENDENCIES, dep_prefixes)
env.set_path('CMAKE_PREFIX_PATH', dep_prefixes) # Add dependencies to CMAKE_PREFIX_PATH
# Install prefix
os.environ[SPACK_PREFIX] = pkg.prefix
env.set(SPACK_PREFIX, pkg.prefix)
# Install root prefix
os.environ[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.
pop_keys(os.environ, "LD_LIBRARY_PATH", "LD_RUN_PATH", "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 = ['%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(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 = []
@ -170,10 +179,12 @@ 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_path('PKG_CONFIG_PATH', pkg_config_dirs)
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.
"""
@ -183,6 +194,8 @@ 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.
@ -217,7 +230,7 @@ def set_module_variables_for_package(pkg, m):
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
@ -238,6 +251,9 @@ def set_module_variables_for_package(pkg, m):
# 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."""
@ -262,24 +278,63 @@ def parent_class_modules(cls):
return result
def setup_package(pkg):
"""Execute all environment setup routines."""
set_compiler_environment_variables(pkg)
set_build_environment_variables(pkg)
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.
modules = parent_class_modules(pkg.__class__)
spkg = spec.package
modules = parent_class_modules(spkg.__class__)
for mod in modules:
set_module_variables_for_package(pkg, mod)
set_module_variables_for_package(spkg, mod)
set_module_variables_for_package(spkg, spkg.module)
# 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)
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)
setup_module_variables_for_dag(pkg)
# Allow dependencies to modify the module
spec = pkg.spec
for dependency_spec in spec.traverse(root=False):
dpkg = dependency_spec.package
dpkg.setup_dependent_package(pkg.module, spec)
# Allow dependencies to set up environment as well
for dependency_spec in spec.traverse(root=False):
dpkg = dependency_spec.package
dpkg.setup_dependent_environment(spack_env, run_env, 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):
@ -296,9 +351,9 @@ 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 to print
@ -308,11 +363,11 @@ def child_fun():
"""
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 +378,7 @@ 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 +393,7 @@ 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):

2
lib/spack/spack/cmd/module.py
View File

@ -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():

3
lib/spack/spack/cmd/pkg.py
View File

@ -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)

5
lib/spack/spack/cmd/stage.py
View File

@ -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 +53,6 @@ def stage(parser, args):
specs = spack.cmd.parse_specs(args.specs, concretize=True)
for spec in specs:
package = spack.repo.get(spec)
if args.path:
package.path = args.path
package.do_stage()

23
lib/spack/spack/cmd/uninstall.py
View File

@ -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:
@ -79,7 +80,7 @@ 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 +95,11 @@ 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)

8
lib/spack/spack/concretize.py
View File

@ -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:
@ -241,7 +245,7 @@ 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 +292,7 @@ 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):

28
lib/spack/spack/config.py
View File

@ -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': {
'enable': {
'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)))

2
lib/spack/spack/directory_layout.py
View File

@ -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)

252
lib/spack/spack/environment.py Normal file
View File

@ -0,0 +1,252 @@
import os
import os.path
import collections
import inspect
class NameModifier(object):
def __init__(self, name, **kwargs):
self.name = name
self.args = {'name': name}
self.args.update(kwargs)
class NameValueModifier(object):
def __init__(self, name, value, **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(NameModifier):
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, '')
directories = environment_value.split(':') if environment_value else []
directories.append(os.path.normpath(self.value))
os.environ[self.name] = ':'.join(directories)
class PrependPath(NameValueModifier):
def execute(self):
environment_value = os.environ.get(self.name, '')
directories = environment_value.split(':') if environment_value else []
directories = [os.path.normpath(self.value)] + directories
os.environ[self.name] = ':'.join(directories)
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.value)]
os.environ[self.name] = ':'.join(directories)
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):
"""
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.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)
@staticmethod
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(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
"""
kwargs.update(self._get_outside_caller_attributes())
item = SetEnv(name, value, **kwargs)
self.env_modifications.append(item)
def unset(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
"""
kwargs.update(self._get_outside_caller_attributes())
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
Args:
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)
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
"""
kwargs.update(self._get_outside_caller_attributes())
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
"""
kwargs.update(self._get_outside_caller_attributes())
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 string of column separated paths
Args:
paths: iterable of paths
Returns:
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)

10
lib/spack/spack/fetch_strategy.py
View File

@ -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):

235
lib/spack/spack/modules.py
View File

@ -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
@ -37,30 +35,30 @@
* /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 textwrap
import shutil
from glob import glob
import textwrap
import llnl.util.tty as tty
from llnl.util.filesystem import join_path, mkdirp
import spack
import spack.config
from llnl.util.filesystem import join_path, mkdirp
from spack.environment import *
"""Registry of all types of modules. Entries created by EnvModule's
metaclass."""
__all__ = ['EnvModule', 'Dotkit', 'TclModule']
# Registry of all types of modules. Entries created by EnvModule's metaclass
module_types = {}
CONFIGURATION = spack.config.get_config('modules')
def print_help():
"""For use by commands to tell user how to activate shell support."""
@ -79,75 +77,76 @@ def print_help():
"")
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.
Args:
prefix: prefix of the installation
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
class EnvModule(object):
name = 'env_module'
formats = {}
class __metaclass__(type):
def __init__(cls, name, bases, dict):
type.__init__(cls, name, bases, dict)
if cls.name != 'env_module':
if cls.name != 'env_module' and cls.name in CONFIGURATION['enable']:
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
@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?
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])
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("$_ $@")
# short description default is just the package + version
# packages can provide this optional attribute
self.short_description = spec.format("$_ $@")
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__)
return self._paths
@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'
def write(self):
@ -156,18 +155,41 @@ 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:
# 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
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
self.spec.package.setup_environment(spack_env, env)
# TODO : implement site-specific modifications and filters
if not env:
return
with open(self.file_name, 'w') as f:
self._write(f)
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:
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):
@ -175,14 +197,12 @@ 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):
@ -193,10 +213,14 @@ class Dotkit(EnvModule):
name = 'dotkit'
path = join_path(spack.share_path, "dotkit")
formats = {
PrependPath: 'dk_alter {name} {value}\n',
SetEnv: 'dk_setenv {name} {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):
@ -205,7 +229,7 @@ def use_name(self):
self.spec.compiler.version,
self.spec.dag_hash())
def _write(self, dk_file):
def write_header(self, dk_file):
# Category
if self.category:
dk_file.write('#c %s\n' % self.category)
@ -219,24 +243,23 @@ def _write(self, dk_file):
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 {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
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,
@ -244,25 +267,17 @@ def use_name(self):
self.spec.compiler.version,
self.spec.dag_hash())
def _write(self, m_file):
# TODO: cateogry?
m_file.write('#%Module1.0\n')
def write_header(self, 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')
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)
module_file.write('proc ModulesHelp { } {\n')
for line in textwrap.wrap(self.long_description, 72):
module_file.write("puts stderr \"%s\"\n" % line)
module_file.write('}\n\n')

181
lib/spack/spack/package.py
View File

@ -34,40 +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 glob
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 spack.version import *
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.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"]
@ -341,6 +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))
@ -459,7 +456,8 @@ 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):
@ -469,7 +467,7 @@ 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):
@ -942,6 +940,9 @@ 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
@ -970,9 +971,6 @@ 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."""
@ -1018,38 +1016,127 @@ def module(self):
return __import__(self.__class__.__module__,
fromlist=[self.__class__.__name__])
def setup_environment(self, spack_env, run_env):
"""Set up the compile and runtime environemnts for a package.
def setup_dependent_environment(self, module, spec, dependent_spec):
"""Called before the install() method of dependents.
`spack_env` and `run_env` are `EnvironmentModifications`
objects. Package authors can call methods on them to alter
the environment within Spack and at runtime.
Both `spack_env` and `run_env` are applied within the build
process, before this package's `install()` method is called.
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 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.
overridden if the package needs a particular environment.
Some examples:
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.
1. Qt extensions need `QTDIR` set.
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.
Args:
spack_env (EnvironmentModifications): list of
modifications to be applied when this package is built
within Spack.
3. A lot of Qt extensions need QTDIR set. This can be used to do that.
run_env (EnvironmentModifications): list of environment
changes to be applied when this package is run outside
of Spack.
"""
pass
def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
"""Set up the environment of packages that depend on this one.
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.
Args:
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_package(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.
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.
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
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.")
@ -1361,6 +1448,10 @@ 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):

5
lib/spack/spack/stage.py
View File

@ -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
@ -135,6 +135,9 @@ 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.
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

3
lib/spack/spack/test/__init__.py
View File

@ -66,7 +66,8 @@
'database',
'namespace_trie',
'yaml',
'sbang']
'sbang',
'environment']
def list_tests():

127
lib/spack/spack/test/cc.py
View File

@ -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))

16
lib/spack/spack/test/concretize.py
View File

@ -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')
@ -309,3 +318,10 @@ 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'))

1
lib/spack/spack/test/database.py
View File

@ -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

73
lib/spack/spack/test/environment.py Normal file
View File

@ -0,0 +1,73 @@
import unittest
import os
from spack.environment import EnvironmentModifications
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(self):
env = EnvironmentModifications()
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(self):
env = EnvironmentModifications()
self.assertEqual('foo', os.environ['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()
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/')
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'])
self.assertEqual('/a/b:/a/c:/a/d:/f/g', os.environ['REMOVE_PATH_LIST'])
def test_extra_arguments(self):
env = EnvironmentModifications()
env.set('A', 'dummy value', who='Pkg1')
for x in env:
assert 'who' in x.args
env.apply_modifications()
self.assertEqual('dummy value', os.environ['A'])
def test_extend(self):
env = EnvironmentModifications()
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):
assert x is y

6
lib/spack/spack/util/environment.py
View File

@ -59,12 +59,6 @@ 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:

2
share/spack/setup-env.sh
View File

@ -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

43
var/spack/repos/builtin.mock/packages/python/package.py Normal file
View File

@ -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

44
var/spack/repos/builtin/packages/apr-util/package.py Normal file
View File

@ -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')

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@ -0,0 +1,38 @@
##############################################################################
# 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')
def install(self, spec, prefix):
options = ['--prefix=%s' % prefix]
configure(*options)
make()
make('install')

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@ -35,18 +35,32 @@ 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('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]
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')

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@ -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

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@ -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)

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@ -1,31 +1,36 @@
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.
variant('shared', default=True, description='Builds shared library')
# provides('blas')
provides('blas')
provides('lapack')
parallel = False
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 +38,21 @@ 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')

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@ -1,5 +1,9 @@
from spack import *
import spack
import sys
import os
import sys
class Boost(Package):
"""Boost provides free peer-reviewed portable C++ source
@ -172,6 +176,16 @@ def determine_b2_options(self, spec, options):
return threadingOpts
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']
withLibs = list()
for lib in Boost.all_libs:
if "+{0}".format(lib) in spec:
@ -208,3 +222,6 @@ def install(self, spec, prefix):
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)

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@ -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')
@ -38,10 +39,12 @@ 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')
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')
@ -77,6 +80,7 @@ def install(self, spec, prefix):
options.append('--sphinx-html')
options.append('--sphinx-man')
if '+openssl' in spec:
options.append('--')
options.append('-DCMAKE_USE_OPENSSL=ON')

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@ -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')
@ -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, "")
return "%scryptopp%s.zip" % (Cryptopp.homepage, version_string)
version_string = str(version).replace('.', '')
return '%s/cryptopp%s.zip' % (Cryptopp.base_url, version_string)

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@ -0,0 +1,47 @@
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
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"
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]
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. See:
# http://docs.nvidia.com/cuda/cuda-installation-guide-linux/#system-requirements
# for details.
runfile(
'--silent', # disable interactive prompts
'--verbose', # create verbose log file
'--toolkit', # install CUDA Toolkit
'--toolkitpath=%s' % prefix
)

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@ -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')

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@ -0,0 +1,238 @@
from spack import *
import sys
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')
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('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)')
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")
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 ("suite-sparse")
depends_on ("tbb")
depends_on ("zlib")
# optional dependencies
depends_on ("mpi", when="+mpi")
depends_on ("arpack-ng+mpi", when='+arpack+mpi')
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")
depends_on ("netcdf-cxx", when='+netcdf+mpi')
depends_on ("oce", when='+oce')
depends_on ("p4est", when='+p4est+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 = []
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)
dsuf = 'dylib' if sys.platform == 'darwin' else 'so'
options.extend([
'-DCMAKE_BUILD_TYPE=DebugRelease',
'-DDEAL_II_COMPONENT_EXAMPLES=ON',
'-DDEAL_II_WITH_THREADS:BOOL=ON',
'-DBOOST_DIR=%s' % spec['boost'].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,
'-DP4EST_DIR=%s' % spec['p4est'].prefix,
'-DUMFPACK_DIR=%s' % spec['suite-sparse'].prefix,
'-DTBB_DIR=%s' % spec['tbb'].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'):
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 '+doc' 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'
])
# 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()
make("test")
make("install")
# 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')
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'):
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('.')
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')
if '^trilinos+hypre' in spec:
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')
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')
if '^trilinos+mumps' in spec:
make('release')
make('run',parallel=False)
print('=====================================')
print('============ Step-36 ================')
print('=====================================')
with working_dir('examples/step-36'):
if 'slepc' in spec:
cmake('.')
make('release')
make('run',parallel=False)
print('=====================================')
print('============ Step-54 ================')
print('=====================================')
with working_dir('examples/step-54'):
if 'oce' in spec:
cmake('.')
make('release')
make('run',parallel=False)

5
var/spack/repos/builtin/packages/doxygen/package.py
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@ -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)

2
var/spack/repos/builtin/packages/eigen/package.py
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@ -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')

9
var/spack/repos/builtin/packages/espresso/package.py
View File

@ -33,9 +33,10 @@ 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]
options = ['-prefix=%s' % prefix.bin]
if '+mpi' in spec:
options.append('--enable-parallel')
@ -61,5 +62,11 @@ def install(self, spec, prefix):
configure(*options)
make('all')
if spec.architecture.startswith('darwin'):
mkdirp(prefix.bin)
for filename in glob("bin/*.x"):
install(filename, prefix.bin)
else:
make('install')

42
var/spack/repos/builtin/packages/gcc/darwin/gcc-4.9.patch1 Normal file
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@ -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.])])

28
var/spack/repos/builtin/packages/gcc/darwin/gcc-4.9.patch2 Normal file
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@ -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

45
var/spack/repos/builtin/packages/gcc/package.py
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@ -26,6 +26,8 @@
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++,
@ -47,24 +49,33 @@ 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("isl", when='@5.0:')
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')
# 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.
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:"):
if spec.satisfies("@4.7.1:") and sys.platform != 'darwin':
enabled_languages.add('go')
# Generic options to compile GCC
@ -76,15 +87,18 @@ 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
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",
"--with-as=%s/bin/as" % spec['binutils'].prefix]
options.extend(binutils_options)
# Isl
@ -92,12 +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()
@ -114,7 +133,8 @@ 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'))
@ -124,5 +144,6 @@ 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)

69
var/spack/repos/builtin/packages/gdal/package.py Normal file
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@ -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")

24
var/spack/repos/builtin/packages/geos/package.py
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@ -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")

30
var/spack/repos/builtin/packages/gettext/package.py Normal file
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@ -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")

24
var/spack/repos/builtin/packages/googletest/package.py Normal file
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@ -0,0 +1,24 @@
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)

12
var/spack/repos/builtin/packages/graphviz/package.py
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@ -7,6 +7,12 @@ class Graphviz(Package):
version('2.38.0', '5b6a829b2ac94efcd5fa3c223ed6d3ae')
# 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='Enable if you need the optional Perl language bindings.')
parallel = False
depends_on("swig")
@ -14,8 +20,10 @@ class Graphviz(Package):
depends_on("ghostscript")
def install(self, spec, prefix):
configure("--prefix=%s" %prefix)
options = ['--prefix=%s' % prefix]
if not '+perl' in spec:
options.append('--disable-perl')
configure(*options)
make()
make("install")

73
var/spack/repos/builtin/packages/hoomd-blue/package.py Normal file
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@ -0,0 +1,73 @@
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=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')
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')
# 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
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("test")
make("install")

13
var/spack/repos/builtin/packages/hypre/package.py
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@ -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 +12,10 @@ 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)")
# SuperluDist have conflicting headers with those in Hypre
variant('internal-superlu', default=True, description="Use internal Superlu routines")
depends_on("mpi")
depends_on("blas")
@ -37,6 +40,12 @@ 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")
# 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.
with working_dir("src"):

35
var/spack/repos/builtin/packages/kealib/package.py Normal file
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@ -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")

2
var/spack/repos/builtin/packages/libdrm/package.py
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@ -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)

2
var/spack/repos/builtin/packages/libelf/package.py
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@ -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",

2
var/spack/repos/builtin/packages/libpng/package.py
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@ -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()

17
var/spack/repos/builtin/packages/llvm/package.py
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@ -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')
@ -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',

22
var/spack/repos/builtin/packages/metis/install_gklib_defs_rename.patch Normal file
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@ -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()

15
var/spack/repos/builtin/packages/metis/package.py
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@ -24,7 +24,7 @@
##############################################################################
from spack import *
import glob,sys
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 = []
@ -81,3 +83,14 @@ def install(self, spec, prefix):
cmake(source_directory, *options)
make()
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)
# 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)

25
var/spack/repos/builtin/packages/modules/package.py Normal file
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@ -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")

20
var/spack/repos/builtin/packages/mpich/package.py
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@ -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."""
@ -46,14 +47,16 @@ class Mpich(Package):
provides('mpi@:3.0', when='@3:')
provides('mpi@:1.3', when='@1:')
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']
def setup_dependent_environment(self, env, dependent_spec):
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_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')
def install(self, spec, prefix):
@ -75,6 +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")

3
var/spack/repos/builtin/packages/mumps/Makefile.inc
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@ -8,12 +8,9 @@ IORDERINGSF = $(ISCOTCH)
IORDERINGSC = $(IMETIS) $(IPORD) $(ISCOTCH)
PLAT =
LIBEXT = .a
OUTC = -o
OUTF = -o
RM = /bin/rm -f
AR = ar vr
RANLIB = ranlib
INCSEQ = -I$(topdir)/libseq
LIBSEQ = -L$(topdir)/libseq -lmpiseq

77
var/spack/repos/builtin/packages/mumps/package.py
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@ -1,6 +1,5 @@
from spack import *
import os
import os, sys
class Mumps(Package):
"""MUMPS: a MUltifrontal Massively Parallel sparse direct Solver"""
@ -19,11 +18,12 @@ 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')
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')
@ -54,18 +54,25 @@ 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)))
# 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:
@ -73,14 +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:
@ -101,6 +108,27 @@ 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 -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 -Wl,-soname -Wl,%s/$(notdir $@) -o' % prefix.lib,
'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')
@ -117,7 +145,7 @@ 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')
@ -131,9 +159,24 @@ def install(self, spec, prefix):
self.write_makefile_inc()
make(*make_libs)
# 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')

18
var/spack/repos/builtin/packages/muparser/package.py Normal file
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@ -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(parallel=False)
make("install")

2
var/spack/repos/builtin/packages/mvapich2/package.py
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@ -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"]

15
var/spack/repos/builtin/packages/netcdf-cxx/package.py Normal file
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@ -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")

7
var/spack/repos/builtin/packages/netcdf/package.py
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@ -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')

46
var/spack/repos/builtin/packages/netlib-blas/package.py
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@ -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')

87
var/spack/repos/builtin/packages/netlib-lapack/package.py
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@ -1,13 +1,12 @@
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"
@ -19,42 +18,68 @@ 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('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', when='~external-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')]
depends_on('blas', when='+external-blas')
@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 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(self, spec, prefix):
blas_libs = ";".join(self.get_blas_libs())
cmake_args = [".", '-DBLAS_LIBRARIES=' + blas_libs]
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:
# 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')
])
if '+shared' in spec:
cmake_args.append('-DBUILD_SHARED_LIBS=ON')
cmake_args.extend(std_cmake_args)
cmake_args += std_cmake_args
cmake(*cmake_args)
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)

20
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@ -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"""
@ -40,11 +41,16 @@ def install(self, spec, prefix):
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'
# 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)
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)]
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 else '.a'
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)]

6
var/spack/repos/builtin/packages/ninja/package.py
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@ -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)

44
var/spack/repos/builtin/packages/numdiff/package.py Normal file
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@ -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 *
import sys
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')
depends_on('gettext', sys.platform=='darwin')
def install(self, spec, prefix):
options = ['--prefix=%s' % prefix]
configure(*options)
make()
make('install')

482
var/spack/repos/builtin/packages/oce/null.patch Normal file
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@ -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();

67
var/spack/repos/builtin/packages/oce/package.py Normal file
View File

@ -0,0 +1,67 @@
from spack import *
import platform, sys
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')
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 = []
options.extend(std_cmake_args)
options.extend([
'-DOCE_INSTALL_PREFIX=%s' % prefix,
'-DOCE_BUILD_SHARED_LIB:BOOL=ON',
'-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=%s' % ('TBB' if '+tbb' in spec else 'NONE'),
'-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")
# 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)

2
var/spack/repos/builtin/packages/octave/package.py
View File

@ -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')

50
var/spack/repos/builtin/packages/openblas/package.py
View File

@ -1,28 +1,70 @@
from spack import *
import sys
import os
class Openblas(Package):
"""OpenBLAS: An optimized BLAS library"""
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')
variant('shared', default=True, description="Build shared libraries as well as static libs.")
# virtual dependency
provides('blas')
provides('lapack')
def install(self, spec, prefix):
make('libs', 'netlib', 'shared', 'CC=cc', 'FC=f77')
make('install', "PREFIX='%s'" % prefix)
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'):
make_defs += ['BUILD_LAPACK_DEPRECATED=1']
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)
# 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')
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.so', 'liblapack.so')
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

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@ -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")

13
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@ -41,12 +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_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 setup_dependent_environment(self, spack_env, run_env, dependent_spec):
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):
config_args = ["--prefix=%s" % prefix,

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@ -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")

4
var/spack/repos/builtin/packages/paraview/package.py
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@ -16,9 +16,9 @@ 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('python@2:2.7', when='+python')
depends_on('py-numpy', when='+python')
depends_on('py-matplotlib', when='+python')
depends_on('tcl', when='+tcl')

71
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@ -0,0 +1,71 @@
diff --git a/CMakeLists.txt b/CMakeLists.txt
index ca945dd..aff8b5f 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)
+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
+++ 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"

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var/spack/repos/builtin/packages/parmetis/package.py
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@ -24,10 +24,7 @@
##############################################################################
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
import sys
class Parmetis(Package):
"""
@ -43,13 +40,17 @@ 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')
# 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')
@ -63,8 +64,8 @@ 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=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'])
@ -78,18 +79,11 @@ 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)
# 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)

77
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@ -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

35
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@ -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

37
var/spack/repos/builtin/packages/petsc/package.py
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@ -20,11 +20,15 @@ class Petsc(Package):
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('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')
@ -40,7 +44,13 @@ class Petsc(Package):
depends_on('hdf5+mpi', when='+hdf5+mpi')
depends_on('parmetis', when='+metis+mpi')
depends_on('hypre', when='+hypre+mpi')
# 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')
def mpi_dependent_options(self):
if '~mpi' in self.spec:
@ -55,7 +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')
for x in ('hdf5', 'hypre', 'parmetis','mumps','superlu-dist')
if ('+'+x) in self.spec]
if errors:
errors = ['incompatible variants given'] + errors
@ -68,15 +78,17 @@ def mpi_dependent_options(self):
return compiler_opts
def install(self, spec, prefix):
options = []
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'))
)
@ -84,9 +96,24 @@ 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)
# 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)

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@ -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)

8
var/spack/repos/builtin/packages/py-cython/package.py
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@ -3,10 +3,14 @@
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('0.23.5', '66b62989a67c55af016c916da36e7514')
version('0.23.4', '157df1f69bcec6b56fd97e0f2e057f6e')
# These versions contain illegal Python3 code...
version('0.22', '1ae25add4ef7b63ee9b4af697300d6b6')
version('0.21.2', 'd21adb870c75680dc857cd05d41046a4')
extends('python')

1
var/spack/repos/builtin/packages/py-dateutil/package.py
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@ -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')

15
var/spack/repos/builtin/packages/py-libxml2/package.py
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@ -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)

2
var/spack/repos/builtin/packages/py-matplotlib/package.py
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@ -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')

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@ -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)

2
var/spack/repos/builtin/packages/py-nose/package.py
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@ -1,5 +1,6 @@
from spack import *
class PyNose(Package):
"""nose extends the test loading and running features of unittest,
making it easier to write, find and run tests."""
@ -9,6 +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')

3
var/spack/repos/builtin/packages/py-numexpr/package.py
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@ -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):

34
var/spack/repos/builtin/packages/py-numpy/package.py
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@ -1,24 +1,44 @@
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('1.11.0', 'bc56fb9fc2895aa4961802ffbdb31d0b')
version('1.10.4', 'aed294de0aa1ac7bd3f9745f4f1968ad')
version('1.9.2', 'a1ed53432dbcd256398898d35bc8e645')
version('1.9.1', '78842b73560ec378142665e712ae4ad9')
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)

11
var/spack/repos/builtin/packages/py-pandas/package.py
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@ -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)

1
var/spack/repos/builtin/packages/py-pytz/package.py
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@ -7,6 +7,7 @@ class PyPytz(Package):
version('2014.10', 'eb1cb941a20c5b751352c52486aa1dd7')
version('2015.4', '417a47b1c432d90333e42084a605d3d8')
version('2016.3', 'abae92c3301b27bd8a9f56b14f52cb29')
extends('python')

17
var/spack/repos/builtin/packages/py-scipy/package.py
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@ -2,17 +2,24 @@
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')
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)

1
var/spack/repos/builtin/packages/py-setuptools/package.py
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@ -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')

1
var/spack/repos/builtin/packages/py-six/package.py
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@ -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')

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