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Merge branch 'develop' of https://github.com/LLNL/spack into qa/coding_standard

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This commit is contained in:
alalazo 2016-04-15 09:19:41 +02:00
commit 93c22dd978
140 changed files with 4465 additions and 813 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
View file

@ -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']

70
lib/spack/docs/basic_usage.rst
View file

@ -149,26 +149,46 @@ customize an installation in :ref:`sec-specs`.
``spack uninstall``
~~~~~~~~~~~~~~~~~~~~~
To uninstall a package, type ``spack uninstall <package>``. This will
completely remove the directory in which the package was installed.
To uninstall a package, type ``spack uninstall <package>``. This will ask the user for
confirmation, and in case will completely remove the directory in which the package was installed.
.. code-block:: sh
spack uninstall mpich
If there are still installed packages that depend on the package to be
uninstalled, spack will refuse to uninstall it. You can override this
behavior with ``spack uninstall -f <package>``, but you risk breaking
other installed packages. In general, it is safer to remove dependent
packages *before* removing their dependencies.
uninstalled, spack will refuse to uninstall it.
A line like ``spack uninstall mpich`` may be ambiguous, if multiple
``mpich`` configurations are installed. For example, if both
To uninstall a package and every package that depends on it, you may give the
`--dependents` option.
.. code-block:: sh
spack uninstall --dependents mpich
will display a list of all the packages that depends on `mpich` and, upon confirmation,
will uninstall them in the right order.
A line like
.. code-block:: sh
spack uninstall mpich
may be ambiguous, if multiple ``mpich`` configurations are installed. For example, if both
``mpich@3.0.2`` and ``mpich@3.1`` are installed, ``mpich`` could refer
to either one. Because it cannot determine which one to uninstall,
Spack will ask you to provide a version number to remove the
ambiguity. As an example, ``spack uninstall mpich@3.1`` is
unambiguous in this scenario.
Spack will ask you either to provide a version number to remove the
ambiguity or use the ``--all`` option to uninstall all of the matching packages.
You may force uninstall a package with the `--force` option
.. code-block:: sh
spack uninstall --force mpich
but you risk breaking other installed packages. In general, it is safer to remove dependent
packages *before* removing their dependencies or use the `--dependents` option.
Seeing installed packages
@ -774,6 +794,34 @@ Environment modules
Spack provides some limited integration with environment module
systems to make it easier to use the packages it provides.
Installing Environment Modules
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In order to use Spack's generated environment modules, you must have
installed the *Environment Modules* package. On many Linux
distributions, this can be installed from the vendor's repository.
For example: ```yum install environment-modules``
(Fedora/RHEL/CentOS). If your Linux distribution does not have
Environment Modules, you can get it with Spack:
1. Install with::
spack install environment-modules
2. Activate with::
MODULES_HOME=`spack location -i environment-modules`
MODULES_VERSION=`ls -1 $MODULES_HOME/Modules | head -1`
${MODULES_HOME}/Modules/${MODULES_VERSION}/bin/add.modules
This adds to your ``.bashrc`` (or similar) files, enabling Environment
Modules when you log in. It will ask your permission before changing
any files.
Spack and Environment Modules
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
You can enable shell support by sourcing some files in the
``/share/spack`` directory.

267
lib/spack/env/cc vendored
View file

@ -50,7 +50,7 @@ SPACK_SHORT_SPEC"
# The compiler input variables are checked for sanity later:
# SPACK_CC, SPACK_CXX, SPACK_F77, SPACK_FC
# Debug flag is optional; set to true for debug logging:
# Debug flag is optional; set to "TRUE" for debug logging:
# SPACK_DEBUG
# Test command is used to unit test the compiler script.
# SPACK_TEST_COMMAND
@ -65,12 +65,11 @@ function die {
}
for param in $parameters; do
if [ -z "${!param}" ]; then
die "Spack compiler must be run from spack! Input $param was missing!"
if [[ -z ${!param} ]]; then
die "Spack compiler must be run from Spack! Input '$param' is missing."
fi
done
#
# Figure out the type of compiler, the language, and the mode so that
# the compiler script knows what to do.
#
@ -78,14 +77,18 @@ done
# 'command' is set based on the input command to $SPACK_[CC|CXX|F77|F90]
#
# 'mode' is set to one of:
# vcheck version check
# cpp preprocess
# cc compile
# as assemble
# ld link
# ccld compile & link
# cpp preprocessor
# vcheck version check
#
command=$(basename "$0")
case "$command" in
cpp)
mode=cpp
;;
cc|c89|c99|gcc|clang|icc|pgcc|xlc)
command="$SPACK_CC"
language="C"
@ -102,9 +105,6 @@ case "$command" in
command="$SPACK_F77"
language="Fortran 77"
;;
cpp)
mode=cpp
;;
ld)
mode=ld
;;
@ -113,10 +113,12 @@ case "$command" in
;;
esac
# If any of the arguments below is present then the mode is vcheck. In vcheck mode nothing is added in terms of extra search paths or libraries
if [ -z "$mode" ]; then
# If any of the arguments below are 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
if [[ $arg == -v || $arg == -V || $arg == --version || $arg == -dumpversion ]]; then
mode=vcheck
break
fi
@ -124,14 +126,16 @@ if [ -z "$mode" ]; then
fi
# Finish setting up the mode.
if [ -z "$mode" ]; then
if [[ -z $mode ]]; then
mode=ccld
for arg in "$@"; do
if [ "$arg" = -E ]; then
if [[ $arg == -E ]]; then
mode=cpp
break
elif [ "$arg" = -c ]; then
elif [[ $arg == -S ]]; then
mode=as
break
elif [[ $arg == -c ]]; then
mode=cc
break
fi
@ -139,175 +143,76 @@ if [ -z "$mode" ]; then
fi
# Dump the version and exit if we're in testing mode.
if [ "$SPACK_TEST_COMMAND" = "dump-mode" ]; then
if [[ $SPACK_TEST_COMMAND == dump-mode ]]; then
echo "$mode"
exit
fi
# Check that at least one of the real commands was actually selected,
# otherwise we don't know what to execute.
if [ -z "$command" ]; then
if [[ -z $command ]]; then
die "ERROR: Compiler '$SPACK_COMPILER_SPEC' does not support compiling $language programs."
fi
if [[ $mode == vcheck ]]; then
exec ${command} "$@"
fi
# Darwin's linker has a -r argument that merges object files together.
# It doesn't work with -rpath.
# This variable controls whether they are added.
add_rpaths=true
if [[ mode == ld && $OSTYPE == darwin* ]]; then
for arg in "$@"; do
if [[ $arg == -r ]]; then
add_rpaths=false
break
fi
done
fi
# Save original command for debug logging
input_command="$@"
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
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 +228,40 @@ 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
done
if [ -z "$remove" ]; then
if [ -z "$PATH" ]; then
PATH="$dir"
else
PATH="$PATH:$dir"
addpath=true
for env_dir in "${spack_env_dirs[@]}"; do
if [[ $dir == $env_dir ]]; then
addpath=false
break
fi
done
if $addpath; then
PATH="${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

4
lib/spack/spack/__init__.py
View file

@ -136,9 +136,7 @@
# don't add a second username if it's already unique by user.
if not _tmp_user in path:
tmp_dirs.append(join_path(path, '%u', 'spack-stage'))
for path in _tmp_candidates:
if not path in tmp_dirs:
else:
tmp_dirs.append(join_path(path, 'spack-stage'))
# Whether spack should allow installation of unsafe versions of

50
lib/spack/spack/build_environment.py
View file

@ -59,6 +59,11 @@
SPACK_DEBUG_LOG_DIR = 'SPACK_DEBUG_LOG_DIR'
# Platform-specific library suffix.
dso_suffix = 'dylib' if sys.platform == 'darwin' else 'so'
class MakeExecutable(Executable):
"""Special callable executable object for make so the user can
specify parallel or not on a per-invocation basis. Using
@ -208,7 +213,7 @@ def set_module_variables_for_package(pkg, module):
# TODO: of build dependencies, as opposed to link dependencies.
# TODO: Currently, everything is a link dependency, but tools like
# TODO: this shouldn't be.
m.cmake = which("cmake")
m.cmake = Executable('cmake')
# standard CMake arguments
m.std_cmake_args = ['-DCMAKE_INSTALL_PREFIX=%s' % pkg.prefix,
@ -246,6 +251,9 @@ def set_module_variables_for_package(pkg, module):
# a Prefix object.
m.prefix = pkg.prefix
# Platform-specific library suffix.
m.dso_suffix = dso_suffix
def get_rpaths(pkg):
"""Get a list of all the rpaths for a package."""
@ -270,21 +278,6 @@ def parent_class_modules(cls):
return result
def setup_module_variables_for_dag(pkg):
"""Set module-scope variables for all packages in the DAG."""
for spec in pkg.spec.traverse(order='post'):
# If a user makes their own package repo, e.g.
# spack.repos.mystuff.libelf.Libelf, and they inherit from
# an existing class like spack.repos.original.libelf.Libelf,
# then set the module variables for both classes so the
# parent class can still use them if it gets called.
spkg = spec.package
modules = parent_class_modules(spkg.__class__)
for mod in modules:
set_module_variables_for_package(spkg, mod)
set_module_variables_for_package(spkg, spkg.module)
def setup_package(pkg):
"""Execute all environment setup routines."""
spack_env = EnvironmentModifications()
@ -308,20 +301,27 @@ def setup_package(pkg):
set_compiler_environment_variables(pkg, spack_env)
set_build_environment_variables(pkg, spack_env)
setup_module_variables_for_dag(pkg)
# traverse in postorder so package can use vars from its dependencies
spec = pkg.spec
for dspec in pkg.spec.traverse(order='post', root=False):
# If a user makes their own package repo, e.g.
# spack.repos.mystuff.libelf.Libelf, and they inherit from
# an existing class like spack.repos.original.libelf.Libelf,
# then set the module variables for both classes so the
# parent class can still use them if it gets called.
spkg = dspec.package
modules = parent_class_modules(spkg.__class__)
for mod in modules:
set_module_variables_for_package(spkg, mod)
set_module_variables_for_package(spkg, spkg.module)
# Allow dependencies to modify the module
spec = pkg.spec
for dependency_spec in spec.traverse(root=False):
dpkg = dependency_spec.package
dpkg = dspec.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.
set_module_variables_for_package(pkg, pkg.module)
pkg.setup_environment(spack_env, run_env)
# Make sure nothing's strange about the Spack environment.

10
lib/spack/spack/cmd/module.py
View file

@ -22,21 +22,16 @@
# along with this program; if not, write to the Free Software Foundation,
# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
import sys
import os
import shutil
import argparse
import sys
import llnl.util.tty as tty
from llnl.util.lang import partition_list
from llnl.util.filesystem import mkdirp
import spack.cmd
from llnl.util.filesystem import mkdirp
from spack.modules import module_types
from spack.util.string import *
from spack.spec import Spec
description ="Manipulate modules and dotkits."
@ -98,7 +93,6 @@ def module_refresh():
cls(spec).write()
def module(parser, args):
if args.module_command == 'refresh':
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()

185
lib/spack/spack/cmd/uninstall.py
View file

@ -23,20 +23,34 @@
# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
from __future__ import print_function
import sys
import argparse
import llnl.util.tty as tty
from llnl.util.tty.colify import colify
import spack
import spack.cmd
import spack.repository
from spack.cmd.find import display_specs
from spack.package import PackageStillNeededError
description = "Remove an installed package"
error_message = """You can either:
a) Use a more specific spec, or
b) use spack uninstall -a to uninstall ALL matching specs.
"""
def ask_for_confirmation(message):
while True:
tty.msg(message + '[y/n]')
choice = raw_input().lower()
if choice == 'y':
break
elif choice == 'n':
raise SystemExit('Operation aborted')
tty.warn('Please reply either "y" or "n"')
def setup_parser(subparser):
subparser.add_argument(
'-f', '--force', action='store_true', dest='force',
@ -47,7 +61,98 @@ def setup_parser(subparser):
"supplied spec. i.e., if you say uninstall libelf, ALL versions of " +
"libelf are uninstalled. This is both useful and dangerous, like rm -r.")
subparser.add_argument(
'packages', nargs=argparse.REMAINDER, help="specs of packages to uninstall")
'-d', '--dependents', action='store_true', dest='dependents',
help='Also uninstall any packages that depend on the ones given via command line.'
)
subparser.add_argument(
'-y', '--yes-to-all', action='store_true', dest='yes_to_all',
help='Assume "yes" is the answer to every confirmation asked to the user.'
)
subparser.add_argument('packages', nargs=argparse.REMAINDER, help="specs of packages to uninstall")
def concretize_specs(specs, allow_multiple_matches=False, force=False):
"""
Returns a list of specs matching the non necessarily concretized specs given from cli
Args:
specs: list of specs to be matched against installed packages
allow_multiple_matches : boolean (if True multiple matches for each item in specs are admitted)
Return:
list of specs
"""
specs_from_cli = [] # List of specs that match expressions given via command line
has_errors = False
for spec in specs:
matching = spack.installed_db.query(spec)
# For each spec provided, make sure it refers to only one package.
# Fail and ask user to be unambiguous if it doesn't
if not allow_multiple_matches and len(matching) > 1:
tty.error("%s matches multiple packages:" % spec)
print()
display_specs(matching, long=True)
print()
has_errors = True
# No installed package matches the query
if len(matching) == 0 and not force:
tty.error("%s does not match any installed packages." % spec)
has_errors = True
specs_from_cli.extend(matching)
if has_errors:
tty.die(error_message)
return specs_from_cli
def installed_dependents(specs):
"""
Returns a dictionary that maps a spec with a list of its installed dependents
Args:
specs: list of specs to be checked for dependents
Returns:
dictionary of installed dependents
"""
dependents = {}
for item in specs:
lst = [x for x in item.package.installed_dependents if x not in specs]
if lst:
lst = list(set(lst))
dependents[item] = lst
return dependents
def do_uninstall(specs, force):
"""
Uninstalls all the specs in a list.
Args:
specs: list of specs to be uninstalled
force: force uninstallation (boolean)
"""
packages = []
for item in specs:
try:
# should work if package is known to spack
packages.append(item.package)
except spack.repository.UnknownPackageError as e:
# The package.py file has gone away -- but still
# want to uninstall.
spack.Package(item).do_uninstall(force=True)
# Sort packages to be uninstalled by the number of installed dependents
# This ensures we do things in the right order
def num_installed_deps(pkg):
return len(pkg.installed_dependents)
packages.sort(key=num_installed_deps)
for item in packages:
item.do_uninstall(force=force)
def uninstall(parser, args):
@ -56,50 +161,34 @@ def uninstall(parser, args):
with spack.installed_db.write_transaction():
specs = spack.cmd.parse_specs(args.packages)
# Gets the list of installed specs that match the ones give via cli
uninstall_list = concretize_specs(specs, args.all, args.force) # takes care of '-a' is given in the cli
dependent_list = installed_dependents(uninstall_list) # takes care of '-d'
# For each spec provided, make sure it refers to only one package.
# Fail and ask user to be unambiguous if it doesn't
pkgs = []
for spec in specs:
matching_specs = spack.installed_db.query(spec)
if not args.all and len(matching_specs) > 1:
tty.error("%s matches multiple packages:" % spec)
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.")
sys.exit(1)
if len(matching_specs) == 0:
if args.force: continue
tty.die("%s does not match any installed packages." % spec)
for s in matching_specs:
try:
# should work if package is known to spack
pkgs.append(s.package)
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)
# Sort packages to be uninstalled by the number of installed dependents
# This ensures we do things in the right order
def num_installed_deps(pkg):
return len(pkg.installed_dependents)
pkgs.sort(key=num_installed_deps)
# Uninstall packages in order now.
for pkg in pkgs:
try:
pkg.do_uninstall(force=args.force)
except PackageStillNeededError as e:
tty.error("Will not uninstall %s" % e.spec.format("$_$@$%@$#", color=True))
# Process dependent_list and update uninstall_list
has_error = False
if dependent_list and not args.dependents and not args.force:
for spec, lst in dependent_list.items():
tty.error("Will not uninstall %s" % spec.format("$_$@$%@$#", color=True))
print('')
print("The following packages depend on it:")
display_specs(e.dependents, long=True)
display_specs(lst, long=True)
print('')
print("You can use spack uninstall -f to force this action.")
sys.exit(1)
has_error = True
elif args.dependents:
for key, lst in dependent_list.items():
uninstall_list.extend(lst)
uninstall_list = list(set(uninstall_list))
if has_error:
tty.die('You can use spack uninstall --dependents to uninstall these dependencies as well')
if not args.yes_to_all:
tty.msg("The following packages will be uninstalled : ")
print('')
display_specs(uninstall_list, long=True)
print('')
ask_for_confirmation('Do you want to proceed ? ')
# Uninstall everything on the list
do_uninstall(uninstall_list, args.force)

4
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:

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)))

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):

30
lib/spack/spack/modules.py
View file

@ -48,6 +48,7 @@
import llnl.util.tty as tty
import spack
import spack.config
from llnl.util.filesystem import join_path, mkdirp
from spack.environment import *
@ -56,6 +57,8 @@
# 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."""
@ -115,7 +118,7 @@ class EnvModule(object):
class __metaclass__(type):
def __init__(cls, name, bases, dict):
type.__init__(cls, name, bases, dict)
if cls.name != 'env_module':
if cls.name != 'env_module' and cls.name in CONFIGURATION['enable']:
module_types[cls.name] = cls
def __init__(self, spec=None):
@ -158,13 +161,18 @@ def write(self):
# Let the extendee modify their extensions before asking for
# package-specific modifications
for extendee in self.pkg.extendees:
extendee_spec = self.spec[extendee]
extendee_spec.package.modify_module(
self.pkg.module, extendee_spec, self.spec)
spack_env = EnvironmentModifications()
for item in self.pkg.extendees:
try:
package = self.spec[item].package
package.setup_dependent_package(self.pkg.module, self.spec)
package.setup_dependent_environment(spack_env, env, self.spec)
except:
# The extends was conditional, so it doesn't count here
# eg: extends('python', when='+python')
pass
# Package-specific environment modifications
spack_env = EnvironmentModifications()
self.spec.package.setup_environment(spack_env, env)
# TODO : implement site-specific modifications and filters
@ -203,7 +211,11 @@ def use_name(self):
def remove(self):
mod_file = self.file_name
if os.path.exists(mod_file):
shutil.rmtree(mod_file, ignore_errors=True)
try:
os.remove(mod_file) # Remove the module file
os.removedirs(os.path.dirname(mod_file)) # Remove all the empty directories from the leaf up
except OSError:
pass # removedirs throws OSError on first non-empty directory found
class Dotkit(EnvModule):
@ -275,6 +287,6 @@ def write_header(self, module_file):
# Long description
if self.long_description:
module_file.write('proc ModulesHelp { } {\n')
doc = re.sub(r'"', '\"', self.long_description)
module_file.write("puts stderr \"%s\"\n" % doc)
for line in textwrap.wrap(self.long_description, 72):
module_file.write("puts stderr \"%s\"\n" % line)
module_file.write('}\n\n')

15
lib/spack/spack/package.py
View file

@ -335,6 +335,9 @@ def __init__(self, spec):
if '.' in self.name:
self.name = self.name[self.name.rindex('.') + 1:]
# Allow custom staging paths for packages
self.path=None
# Sanity check attributes required by Spack directives.
spack.directives.ensure_dicts(type(self))
@ -445,7 +448,8 @@ def _make_resource_stage(self, root_stage, fetcher, resource):
resource_stage_folder = self._resource_stage(resource)
resource_mirror = join_path(self.name, os.path.basename(fetcher.url))
stage = ResourceStage(resource.fetcher, root=root_stage, resource=resource,
name=resource_stage_folder, mirror_path=resource_mirror)
name=resource_stage_folder, mirror_path=resource_mirror,
path=self.path)
return stage
def _make_root_stage(self, fetcher):
@ -455,7 +459,7 @@ def _make_root_stage(self, fetcher):
s = self.spec
stage_name = "%s-%s-%s" % (s.name, s.version, s.dag_hash())
# Build the composite stage
stage = Stage(fetcher, mirror_path=mp, name=stage_name)
stage = Stage(fetcher, mirror_path=mp, name=stage_name, path=self.path)
return stage
def _make_stage(self):
@ -709,7 +713,6 @@ def do_fetch(self, mirror_only=False):
if spack.do_checksum and self.version in self.versions:
self.stage.check()
def do_stage(self, mirror_only=False):
"""Unpacks the fetched tarball, then changes into the expanded tarball
directory."""
@ -926,6 +929,9 @@ def build_process():
install(env_path, env_install_path)
dump_packages(self.spec, packages_dir)
# Run post install hooks before build stage is removed.
spack.hooks.post_install(self)
# Stop timer.
self._total_time = time.time() - start_time
build_time = self._total_time - self._fetch_time
@ -954,9 +960,6 @@ 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."""

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

@ -67,7 +67,8 @@
'namespace_trie',
'yaml',
'sbang',
'environment']
'environment',
'cmd.uninstall']
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))

0
lib/spack/spack/test/cmd/__init__.py Normal file
View file

37
lib/spack/spack/test/cmd/uninstall.py Normal file
View file

@ -0,0 +1,37 @@
import spack.test.mock_database
from spack.cmd.uninstall import uninstall
class MockArgs(object):
def __init__(self, packages, all=False, force=False, dependents=False):
self.packages = packages
self.all = all
self.force = force
self.dependents = dependents
self.yes_to_all = True
class TestUninstall(spack.test.mock_database.MockDatabase):
def test_uninstall(self):
parser = None
# Multiple matches
args = MockArgs(['mpileaks'])
self.assertRaises(SystemExit, uninstall, parser, args)
# Installed dependents
args = MockArgs(['libelf'])
self.assertRaises(SystemExit, uninstall, parser, args)
# Recursive uninstall
args = MockArgs(['callpath'], all=True, dependents=True)
uninstall(parser, args)
all_specs = spack.install_layout.all_specs()
self.assertEqual(len(all_specs), 7)
# query specs with multiple configurations
mpileaks_specs = [s for s in all_specs if s.satisfies('mpileaks')]
callpath_specs = [s for s in all_specs if s.satisfies('callpath')]
mpi_specs = [s for s in all_specs if s.satisfies('mpi')]
self.assertEqual(len(mpileaks_specs), 0)
self.assertEqual(len(callpath_specs), 0)
self.assertEqual(len(mpi_specs), 3)

9
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')

82
lib/spack/spack/test/database.py
View file

@ -28,16 +28,12 @@
"""
import os.path
import multiprocessing
import shutil
import tempfile
import spack
from llnl.util.filesystem import join_path
from llnl.util.lock import *
from llnl.util.tty.colify import colify
from spack.database import Database
from spack.directory_layout import YamlDirectoryLayout
from spack.test.mock_packages_test import *
from spack.test.mock_database import MockDatabase
def _print_ref_counts():
@ -75,80 +71,7 @@ def add_rec(spec):
colify(recs, cols=3)
class DatabaseTest(MockPackagesTest):
def _mock_install(self, spec):
s = Spec(spec)
s.concretize()
pkg = spack.repo.get(s)
pkg.do_install(fake=True)
def _mock_remove(self, spec):
specs = spack.installed_db.query(spec)
assert(len(specs) == 1)
spec = specs[0]
spec.package.do_uninstall(spec)
def setUp(self):
super(DatabaseTest, self).setUp()
#
# TODO: make the mockup below easier.
#
# Make a fake install directory
self.install_path = tempfile.mkdtemp()
self.spack_install_path = spack.install_path
spack.install_path = self.install_path
self.install_layout = YamlDirectoryLayout(self.install_path)
self.spack_install_layout = spack.install_layout
spack.install_layout = self.install_layout
# Make fake database and fake install directory.
self.installed_db = Database(self.install_path)
self.spack_installed_db = spack.installed_db
spack.installed_db = self.installed_db
# make a mock database with some packages installed note that
# the ref count for dyninst here will be 3, as it's recycled
# across each install.
#
# Here is what the mock DB looks like:
#
# o mpileaks o mpileaks' o mpileaks''
# |\ |\ |\
# | o callpath | o callpath' | o callpath''
# |/| |/| |/|
# o | mpich o | mpich2 o | zmpi
# | | o | fake
# | | |
# | |______________/
# | .____________/
# |/
# o dyninst
# |\
# | o libdwarf
# |/
# o libelf
#
# Transaction used to avoid repeated writes.
with spack.installed_db.write_transaction():
self._mock_install('mpileaks ^mpich')
self._mock_install('mpileaks ^mpich2')
self._mock_install('mpileaks ^zmpi')
def tearDown(self):
super(DatabaseTest, self).tearDown()
shutil.rmtree(self.install_path)
spack.install_path = self.spack_install_path
spack.install_layout = self.spack_install_layout
spack.installed_db = self.spack_installed_db
class DatabaseTest(MockDatabase):
def test_005_db_exists(self):
"""Make sure db cache file exists after creating."""
index_file = join_path(self.install_path, '.spack-db', 'index.yaml')
@ -157,7 +80,6 @@ def test_005_db_exists(self):
self.assertTrue(os.path.exists(index_file))
self.assertTrue(os.path.exists(lock_file))
def test_010_all_install_sanity(self):
"""Ensure that the install layout reflects what we think it does."""
all_specs = spack.install_layout.all_specs()

29
lib/spack/spack/test/install.py
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@ -64,7 +64,14 @@ def tearDown(self):
shutil.rmtree(self.tmpdir, ignore_errors=True)
def test_install_and_uninstall(self):
def fake_fetchify(self, pkg):
"""Fake the URL for a package so it downloads from a file."""
fetcher = FetchStrategyComposite()
fetcher.append(URLFetchStrategy(self.repo.url))
pkg.fetcher = fetcher
def ztest_install_and_uninstall(self):
# Get a basic concrete spec for the trivial install package.
spec = Spec('trivial_install_test_package')
spec.concretize()
@ -73,11 +80,7 @@ def test_install_and_uninstall(self):
# Get the package
pkg = spack.repo.get(spec)
# Fake the URL for the package so it downloads from a file.
fetcher = FetchStrategyComposite()
fetcher.append(URLFetchStrategy(self.repo.url))
pkg.fetcher = fetcher
self.fake_fetchify(pkg)
try:
pkg.do_install()
@ -85,3 +88,17 @@ def test_install_and_uninstall(self):
except Exception, e:
pkg.remove_prefix()
raise
def test_install_environment(self):
spec = Spec('cmake-client').concretized()
for s in spec.traverse():
self.fake_fetchify(s.package)
pkg = spec.package
try:
pkg.do_install()
except Exception, e:
pkg.remove_prefix()
raise

80
lib/spack/spack/test/mock_database.py Normal file
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@ -0,0 +1,80 @@
import shutil
import tempfile
import spack
from spack.spec import Spec
from spack.database import Database
from spack.directory_layout import YamlDirectoryLayout
from spack.test.mock_packages_test import MockPackagesTest
class MockDatabase(MockPackagesTest):
def _mock_install(self, spec):
s = Spec(spec)
s.concretize()
pkg = spack.repo.get(s)
pkg.do_install(fake=True)
def _mock_remove(self, spec):
specs = spack.installed_db.query(spec)
assert len(specs) == 1
spec = specs[0]
spec.package.do_uninstall(spec)
def setUp(self):
super(MockDatabase, self).setUp()
#
# TODO: make the mockup below easier.
#
# Make a fake install directory
self.install_path = tempfile.mkdtemp()
self.spack_install_path = spack.install_path
spack.install_path = self.install_path
self.install_layout = YamlDirectoryLayout(self.install_path)
self.spack_install_layout = spack.install_layout
spack.install_layout = self.install_layout
# Make fake database and fake install directory.
self.installed_db = Database(self.install_path)
self.spack_installed_db = spack.installed_db
spack.installed_db = self.installed_db
# make a mock database with some packages installed note that
# the ref count for dyninst here will be 3, as it's recycled
# across each install.
#
# Here is what the mock DB looks like:
#
# o mpileaks o mpileaks' o mpileaks''
# |\ |\ |\
# | o callpath | o callpath' | o callpath''
# |/| |/| |/|
# o | mpich o | mpich2 o | zmpi
# | | o | fake
# | | |
# | |______________/
# | .____________/
# |/
# o dyninst
# |\
# | o libdwarf
# |/
# o libelf
#
# Transaction used to avoid repeated writes.
with spack.installed_db.write_transaction():
self._mock_install('mpileaks ^mpich')
self._mock_install('mpileaks ^mpich2')
self._mock_install('mpileaks ^zmpi')
def tearDown(self):
for spec in spack.installed_db.query():
spec.package.do_uninstall(spec)
super(MockDatabase, self).tearDown()
shutil.rmtree(self.install_path)
spack.install_path = self.spack_install_path
spack.install_layout = self.spack_install_layout
spack.installed_db = self.spack_installed_db

89
var/spack/repos/builtin.mock/packages/cmake-client/package.py Normal file
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@ -0,0 +1,89 @@
##############################################################################
# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-647188
#
# For details, see https://github.com/llnl/spack
# Please also see the LICENSE file for our notice and the LGPL.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License (as published by
# the Free Software Foundation) version 2.1 dated February 1999.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
# conditions of the GNU General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public License
# along with this program; if not, write to the Free Software Foundation,
# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
from spack import *
import os
def check(condition, msg):
"""Raise an install error if condition is False."""
if not condition:
raise InstallError(msg)
class CmakeClient(Package):
"""A dumy package that uses cmake."""
homepage = 'https://www.example.com'
url = 'https://www.example.com/cmake-client-1.0.tar.gz'
version('1.0', '4cb3ff35b2472aae70f542116d616e63')
depends_on('cmake')
def setup_environment(self, spack_env, run_env):
spack_cc # Ensure spack module-scope variable is avaiabl
check(from_cmake == "from_cmake",
"setup_environment couldn't read global set by cmake.")
check(self.spec['cmake'].link_arg == "test link arg",
"link arg on dependency spec not readable from setup_environment.")
def setup_dependent_environment(self, spack_env, run_env, dspec):
spack_cc # Ensure spack module-scope variable is avaiable
check(from_cmake == "from_cmake",
"setup_dependent_environment couldn't read global set by cmake.")
check(self.spec['cmake'].link_arg == "test link arg",
"link arg on dependency spec not readable from setup_dependent_environment.")
def setup_dependent_package(self, module, dspec):
spack_cc # Ensure spack module-scope variable is avaiable
check(from_cmake == "from_cmake",
"setup_dependent_package couldn't read global set by cmake.")
check(self.spec['cmake'].link_arg == "test link arg",
"link arg on dependency spec not readable from setup_dependent_package.")
def install(self, spec, prefix):
# check that cmake is in the global scope.
global cmake
check(cmake is not None, "No cmake was in environment!")
# check that which('cmake') returns the right one.
cmake = which('cmake')
check(cmake.exe[0].startswith(spec['cmake'].prefix.bin),
"Wrong cmake was in environment: %s" % cmake)
check(from_cmake == "from_cmake",
"Couldn't read global set by cmake.")
check(os.environ['from_cmake'] == 'from_cmake',
"Couldn't read env var set in envieonmnt by dependency")
mkdirp(prefix.bin)
touch(join_path(prefix.bin, 'dummy'))

69
var/spack/repos/builtin.mock/packages/cmake/package.py Normal file
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@ -0,0 +1,69 @@
##############################################################################
# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-647188
#
# For details, see https://github.com/llnl/spack
# Please also see the LICENSE file for our notice and the LGPL.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License (as published by
# the Free Software Foundation) version 2.1 dated February 1999.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
# conditions of the GNU General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public License
# along with this program; if not, write to the Free Software Foundation,
# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
from spack import *
import os
def check(condition, msg):
"""Raise an install error if condition is False."""
if not condition:
raise InstallError(msg)
class Cmake(Package):
"""A dumy package for the cmake build system."""
homepage = 'https://www.cmake.org'
url = 'https://cmake.org/files/v3.4/cmake-3.4.3.tar.gz'
version('3.4.3', '4cb3ff35b2472aae70f542116d616e63',
url='https://cmake.org/files/v3.4/cmake-3.4.3.tar.gz')
def setup_environment(self, spack_env, run_env):
spack_cc # Ensure spack module-scope variable is avaiable
spack_env.set('for_install', 'for_install')
def setup_dependent_environment(self, spack_env, run_env, dspec):
spack_cc # Ensure spack module-scope variable is avaiable
spack_env.set('from_cmake', 'from_cmake')
def setup_dependent_package(self, module, dspec):
spack_cc # Ensure spack module-scope variable is avaiable
self.spec.from_cmake = "from_cmake"
module.from_cmake = "from_cmake"
self.spec.link_arg = "test link arg"
def install(self, spec, prefix):
mkdirp(prefix.bin)
check(os.environ['for_install'] == 'for_install',
"Couldn't read env var set in compile envieonmnt")
cmake_exe = join_path(prefix.bin, 'cmake')
touch(cmake_exe)
set_executable(cmake_exe)

43
var/spack/repos/builtin.mock/packages/python/package.py Normal file
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@ -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
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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 *
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')

38
var/spack/repos/builtin/packages/apr/package.py Normal file
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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')

12
var/spack/repos/builtin/packages/arpack-ng/package.py
View file

@ -41,16 +41,26 @@ class ArpackNg(Package):
depends_on('blas')
depends_on('lapack')
depends_on('automake')
depends_on('autoconf')
depends_on('libtool@2.4.2:')
depends_on('mpi', when='+mpi')
def install(self, spec, prefix):
# Apparently autotools are not bootstrapped
# TODO: switch to use the CMake build in the next version
# rather than bootstrapping.
which('libtoolize')()
bootstrap = Executable('./bootstrap')
options = ['--prefix=%s' % prefix]
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')

17
var/spack/repos/builtin/packages/astyle/package.py Normal file
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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)

62
var/spack/repos/builtin/packages/atlas/package.py
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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')

20
var/spack/repos/builtin/packages/bash/package.py Normal file
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@ -0,0 +1,20 @@
from spack import *
class Bash(Package):
"""The GNU Project's Bourne Again SHell."""
homepage = "https://www.gnu.org/software/bash/"
url = "ftp://ftp.gnu.org/gnu/bash/bash-4.3.tar.gz"
version('4.3', '81348932d5da294953e15d4814c74dd1')
depends_on('readline')
def install(self, spec, prefix):
configure('--prefix=%s' % prefix,
'--with-curses',
'--with-installed-readline=%s' % spec['readline'].prefix)
make()
make("tests")
make("install")

4
var/spack/repos/builtin/packages/binutils/package.py
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@ -12,6 +12,10 @@ class Binutils(Package):
version('2.23.2', '4f8fa651e35ef262edc01d60fb45702e')
version('2.20.1', '2b9dc8f2b7dbd5ec5992c6e29de0b764')
depends_on('m4')
depends_on('flex')
depends_on('bison')
# Add a patch that creates binutils libiberty_pic.a which is preferred by OpenSpeedShop and cbtf-krell
variant('krellpatch', default=False, description="build with openspeedshop based patch.")
variant('gold', default=True, description="build the gold linker")

29
var/spack/repos/builtin/packages/boost/package.py
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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:
@ -185,6 +199,18 @@ def install(self, spec, prefix):
install_tree(src, dst)
return
# Remove libraries that the release version does not support
if not spec.satisfies('@1.54.0:'):
withLibs.remove('log')
if not spec.satisfies('@1.53.0:'):
withLibs.remove('atomic')
if not spec.satisfies('@1.48.0:'):
withLibs.remove('locale')
if not spec.satisfies('@1.47.0:'):
withLibs.remove('chrono')
if not spec.satisfies('@1.43.0:'):
withLibs.remove('random')
# to make Boost find the user-config.jam
env['BOOST_BUILD_PATH'] = './'
@ -208,3 +234,6 @@ 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)

4
var/spack/repos/builtin/packages/cmake/package.py
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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')

10
var/spack/repos/builtin/packages/cryptopp/package.py
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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)

47
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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
)

3
var/spack/repos/builtin/packages/dbus/package.py
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@ -13,12 +13,15 @@ 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')
version('1.8.4', '4717cb8ab5b80978fcadf2b4f2f72e1b')
version('1.8.2', 'd6f709bbec0a022a1847c7caec9d6068')
depends_on('expat')
def install(self, spec, prefix):
configure(
"--prefix=%s" % prefix,

253
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@ -0,0 +1,253 @@
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")
# Boost 1.58 is blacklisted, see https://github.com/dealii/dealii/issues/1591
# require at least 1.59
depends_on ("boost@1.59.0:", when='~mpi')
depends_on ("boost@1.59.0:+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@5:", 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)
# An example which uses Metis + PETSc
# FIXME: switch step-18 to MPI
with working_dir('examples/step-18'):
print('=====================================')
print('============= Step-18 ===============')
print('=====================================')
# list the number of cycles to speed up
filter_file(r'(end_time = 10;)', ('end_time = 3;'), 'step-18.cc')
if '^petsc' in spec and '^metis' in spec:
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)

34
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@ -0,0 +1,34 @@
from spack import *
class Dia(Package):
"""Dia is a program for drawing structured diagrams."""
homepage = 'https://wiki.gnome.org/Apps/Dia'
url = 'https://ftp.gnome.org/pub/gnome/sources/dia/0.97/dia-0.97.3.tar.xz'
version('0.97.3', '0e744a0f6a6c4cb6a089e4d955392c3c')
depends_on('gtkplus@2.6.0:')
depends_on('cairo')
#depends_on('libart') # optional dependency, not yet supported by spack.
depends_on('libpng')
depends_on('libxslt')
depends_on('python')
depends_on('swig')
# depends_on('py-gtk') # optional dependency, not yet supported by spack.
def url_for_version(self, version):
"""Handle Dia's version-based custom URLs."""
return 'https://ftp.gnome.org/pub/gnome/source/dia/%s/dia-%s.tar.xz' % (version.up_to(2), version)
def install(self, spec, prefix):
# configure, build, install:
options = ['--prefix=%s' % prefix,
'--with-cairo',
'--with-xslt-prefix=%s' % spec['libxslt'].prefix,
'--with-python',
'--with-swig']
configure(*options)
make()
make('install')

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/dyninst/package.py
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@ -31,6 +31,8 @@ class Dyninst(Package):
url = "http://www.dyninst.org/sites/default/files/downloads/dyninst/8.1.2/DyninstAPI-8.1.2.tgz"
list_url = "http://www.dyninst.org/downloads/dyninst-8.x"
version('9.1.0', '5c64b77521457199db44bec82e4988ac',
url="http://www.paradyn.org/release9.1.0/DyninstAPI-9.1.0.tgz")
version('8.2.1', 'abf60b7faabe7a2e4b54395757be39c7',
url="http://www.paradyn.org/release8.2/DyninstAPI-8.2.1.tgz")
version('8.1.2', 'bf03b33375afa66fe0efa46ce3f4b17a',

2
var/spack/repos/builtin/packages/eigen/package.py
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@ -45,7 +45,7 @@ class Eigen(Package):
# TODO : dependency on googlehash, superlu, adolc missing
depends_on('metis', when='+metis')
depends_on('metis@5:', when='+metis')
depends_on('scotch', when='+scotch')
depends_on('fftw', when='+fftw')
depends_on('suite-sparse', when='+suitesparse')

122
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@ -0,0 +1,122 @@
from spack import *
import spack
class Elk(Package):
'''An all-electron full-potential linearised augmented-plane wave
(FP-LAPW) code with many advanced features.'''
homepage = 'http://elk.sourceforge.net/'
url = 'https://sourceforge.net/projects/elk/files/elk-3.3.17.tgz'
version('3.3.17', 'f57f6230d14f3b3b558e5c71f62f0592')
# Elk provides these libraries, but allows you to specify your own
variant('blas', default=True, description='Build with custom BLAS library')
variant('lapack', default=True, description='Build with custom LAPACK library')
variant('fft', default=True, description='Build with custom FFT library')
# Elk does not provide these libraries, but allows you to use them
variant('mpi', default=True, description='Enable MPI parallelism')
variant('openmp', default=True, description='Enable OpenMP support')
variant('libxc', default=True, description='Link to Libxc functional library')
depends_on('blas', when='+blas')
depends_on('lapack', when='+lapack')
depends_on('fftw', when='+fft')
depends_on('mpi', when='+mpi')
depends_on('libxc', when='+libxc')
# Cannot be built in parallel
parallel = False
def configure(self, spec):
# Dictionary of configuration options
config = {
'MAKE': 'make',
'F90': join_path(spack.build_env_path, 'f90'),
'F77': join_path(spack.build_env_path, 'f77'),
'AR': 'ar',
'LIB_FFT': 'fftlib.a',
'SRC_MPI': 'mpi_stub.f90',
'SRC_OMP': 'omp_stub.f90',
'SRC_libxc': 'libxcifc_stub.f90',
'SRC_FFT': 'zfftifc.f90'
}
# Compiler-specific flags
flags = ''
if self.compiler.name == 'intel':
flags = '-O3 -ip -unroll -no-prec-div -openmp'
elif self.compiler.name == 'gcc':
flags = '-O3 -ffast-math -funroll-loops -fopenmp'
elif self.compiler.name == 'pgi':
flags = '-O3 -mp -lpthread'
elif self.compiler.name == 'g95':
flags = '-O3 -fno-second-underscore'
elif self.compiler.name == 'nag':
flags = '-O4 -kind=byte -dusty -dcfuns'
elif self.compiler.name == 'xl':
flags = '-O3 -qsmp=omp'
config['F90_OPTS'] = flags
config['F77_OPTS'] = flags
# BLAS/LAPACK support
blas = 'blas.a'
lapack = 'lapack.a'
if '+blas' in spec:
blas = join_path(spec['blas'].prefix.lib, 'libblas.so')
if '+lapack' in spec:
lapack = join_path(spec['lapack'].prefix.lib, 'liblapack.so')
config['LIB_LPK'] = ' '.join([lapack, blas]) # lapack must come before blas
# FFT support
if '+fft' in spec:
config['LIB_FFT'] = join_path(spec['fftw'].prefix.lib, 'libfftw3.so')
config['SRC_FFT'] = 'zfftifc_fftw.f90'
# MPI support
if '+mpi' in spec:
config.pop('SRC_MPI')
config['F90'] = join_path(spec['mpi'].prefix.bin, 'mpif90')
config['F77'] = join_path(spec['mpi'].prefix.bin, 'mpif77')
# OpenMP support
if '+openmp' in spec:
config.pop('SRC_OMP')
# Libxc support
if '+libxc' in spec:
config['LIB_libxc'] = ' '.join([
join_path(spec['libxc'].prefix.lib, 'libxcf90.so'),
join_path(spec['libxc'].prefix.lib, 'libxc.so')
])
config['SRC_libxc'] = ' '.join([
'libxc_funcs.f90',
'libxc.f90',
'libxcifc.f90'
])
# Write configuration options to include file
with open('make.inc', 'w') as inc:
for key in config:
inc.write('{0} = {1}\n'.format(key, config[key]))
def install(self, spec, prefix):
# Elk only provides an interactive setup script
self.configure(spec)
make()
make('test')
# The Elk Makefile does not provide an install target
mkdirp(prefix.bin)
install('src/elk', prefix.bin)
install('src/eos/eos', prefix.bin)
install('src/spacegroup/spacegroup', prefix.bin)
install_tree('examples', join_path(prefix, 'examples'))
install_tree('species', join_path(prefix, 'species'))

38
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@ -0,0 +1,38 @@
from spack import *
class EnvironmentModules(Package):
"""The Environment Modules package provides for the dynamic
modification of a user's environment via modulefiles."""
homepage = "https://sourceforge.net/p/modules/wiki/Home/"
url = "http://prdownloads.sourceforge.net/modules/modules-3.2.10.tar.gz"
version('3.2.10', '8b097fdcb90c514d7540bb55a3cb90fb')
# Dependencies:
depends_on('tcl')
def install(self, spec, prefix):
tcl_spec = spec['tcl']
# See: https://sourceforge.net/p/modules/bugs/62/
CPPFLAGS = ['-DUSE_INTERP_ERRORLINE']
config_args = [
"--without-tclx",
"--with-tclx-ver=0.0",
"--prefix=%s" % prefix,
"--with-tcl=%s" % join_path(tcl_spec.prefix, 'lib'), # It looks for tclConfig.sh
"--with-tcl-ver=%d.%d" % (tcl_spec.version.version[0], tcl_spec.version.version[1]),
'--disable-debug',
'--disable-dependency-tracking',
'--disable-silent-rules',
'--disable-versioning',
'--datarootdir=%s' % prefix.share,
'CPPFLAGS=%s' % ' '.join(CPPFLAGS)
]
configure(*config_args)
make()
make('install')

9
var/spack/repos/builtin/packages/espresso/package.py
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@ -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
View file

@ -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
View file

@ -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
View file

@ -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")

2
var/spack/repos/builtin/packages/git/package.py
View file

@ -36,6 +36,8 @@ class Git(Package):
depends_on("curl", when="+curl")
depends_on("expat", when="+expat")
# Also depends_on gettext: apt-get install gettext (Ubuntu)
# Use system perl for now.
# depends_on("perl")
# depends_on("pcre")

1
var/spack/repos/builtin/packages/global/package.py
View file

@ -11,6 +11,7 @@ class Global(Package):
version('6.5', 'dfec818b4f53d91721e247cf7b218078')
depends_on('exuberant-ctags')
depends_on('ncurses')
def install(self, spec, prefix):
config_args = ['--prefix={0}'.format(prefix)]

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
View file

@ -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")

19
var/spack/repos/builtin/packages/hdf5/package.py
View file

@ -37,6 +37,7 @@ class Hdf5(Package):
list_url = "http://www.hdfgroup.org/ftp/HDF5/releases"
list_depth = 3
version('1.10.0', 'bdc935337ee8282579cd6bc4270ad199')
version('1.8.16', 'b8ed9a36ae142317f88b0c7ef4b9c618')
version('1.8.15', '03cccb5b33dbe975fdcd8ae9dc021f24')
version('1.8.13', 'c03426e9e77d7766944654280b467289')
@ -80,6 +81,12 @@ def install(self, spec, prefix):
# sanity check in configure, so this doesn't merit a variant.
extra_args.append("--enable-unsupported")
if spec.satisfies('@1.10:'):
if '+debug' in spec:
extra_args.append('--enable-build-mode=debug')
else:
extra_args.append('--enable-build-mode=production')
else:
if '+debug' in spec:
extra_args.append('--enable-debug=all')
else:
@ -94,10 +101,10 @@ def install(self, spec, prefix):
extra_args.append('--enable-cxx')
if '+fortran' in spec:
extra_args.extend([
'--enable-fortran',
'--enable-fortran2003'
])
extra_args.append('--enable-fortran')
# '--enable-fortran2003' no longer exists as of version 1.10.0
if spec.satisfies('@:1.8.16'):
extra_args.append('--enable-fortran2003')
if '+mpi' in spec:
# The HDF5 configure script warns if cxx and mpi are enabled
@ -139,5 +146,7 @@ def url_for_version(self, version):
return "http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-" + v + ".tar.gz"
elif version < Version("1.7"):
return "http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-" + version.up_to(2) + "/hdf5-" + v + ".tar.gz"
else:
elif version < Version("1.10"):
return "http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-" + v + "/src/hdf5-" + v + ".tar.gz"
else:
return "http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-" + version.up_to(2) + "/hdf5-" + v + "/src/hdf5-" + v + ".tar.gz"

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
View file

@ -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"):

51
var/spack/repos/builtin/packages/ipopt/package.py Normal file
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@ -0,0 +1,51 @@
from spack import *
class Ipopt(Package):
"""Ipopt (Interior Point OPTimizer, pronounced eye-pea-Opt) is a
software package for large-scale nonlinear optimization."""
homepage = "https://projects.coin-or.org/Ipopt"
url = "http://www.coin-or.org/download/source/Ipopt/Ipopt-3.12.4.tgz"
version('3.12.4', '12a8ecaff8dd90025ddea6c65b49cb03')
version('3.12.3', 'c560cbfa9cbf62acf8b485823c255a1b')
version('3.12.2', 'ec1e855257d7de09e122c446506fb00d')
version('3.12.1', 'ceaf895ce80c77778f2cab68ba9f17f3')
version('3.12.0', 'f7dfc3aa106a6711a85214de7595e827')
depends_on("blas")
depends_on("lapack")
depends_on("pkg-config")
depends_on("mumps+double~mpi")
def install(self, spec, prefix):
# Dependency directories
blas_dir = spec['blas'].prefix
lapack_dir = spec['lapack'].prefix
mumps_dir = spec['mumps'].prefix
# Add directory with fake MPI headers in sequential MUMPS
# install to header search path
mumps_flags = "-ldmumps -lmumps_common -lpord -lmpiseq"
mumps_libcmd = "-L%s " % mumps_dir.lib + mumps_flags
# By convention, spack links blas & lapack libs to libblas & liblapack
blas_lib = "-L%s" % blas_dir.lib + " -lblas"
lapack_lib = "-L%s" % lapack_dir.lib + " -llapack"
configure_args = [
"--prefix=%s" % prefix,
"--with-mumps-incdir=%s" % mumps_dir.include,
"--with-mumps-lib=%s" % mumps_libcmd,
"--enable-shared",
"--with-blas-incdir=%s" % blas_dir.include,
"--with-blas-lib=%s" % blas_lib,
"--with-lapack-incdir=%s" % lapack_dir.include,
"--with-lapack-lib=%s" % lapack_lib
]
configure(*configure_args)
# IPOPT does not build correctly in parallel on OS X
make(parallel=False)
make("test", parallel=False)
make("install", parallel=False)

68
var/spack/repos/builtin/packages/julia/openblas.patch Normal file
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@ -0,0 +1,68 @@
diff --git a/deps/Makefile b/deps/Makefile
index 6cb73be..bcd8520 100644
--- a/deps/Makefile
+++ b/deps/Makefile
@@ -1049,7 +1049,7 @@ OPENBLAS_BUILD_OPTS += NO_AFFINITY=1
# Build for all architectures - required for distribution
ifeq ($(OPENBLAS_DYNAMIC_ARCH), 1)
-OPENBLAS_BUILD_OPTS += DYNAMIC_ARCH=1
+OPENBLAS_BUILD_OPTS += DYNAMIC_ARCH=1 MAKE_NO_J=1
endif
# 64-bit BLAS interface
@@ -1085,6 +1085,7 @@ OPENBLAS_BUILD_OPTS += NO_AVX2=1
endif
$(OPENBLAS_SRC_DIR)/config.status: $(OPENBLAS_SRC_DIR)/Makefile
+ cd $(dir $@) && patch -p1 < ../openblas-make.patch
ifeq ($(OS),WINNT)
cd $(dir $@) && patch -p1 < ../openblas-win64.patch
endif
diff --git a/deps/openblas.version b/deps/openblas.version
index 7c97e1b..58b9467 100644
--- a/deps/openblas.version
+++ b/deps/openblas.version
@@ -1,2 +1,2 @@
-OPENBLAS_BRANCH=v0.2.15
-OPENBLAS_SHA1=53e849f4fcae4363a64576de00e982722c7304f9
+OPENBLAS_BRANCH=v0.2.17
+OPENBLAS_SHA1=a71e8c82f6a9f73093b631e5deab1e8da716b61f
--- a/deps/openblas-make.patch
+++ b/deps/openblas-make.patch
@@ -0,0 +1,35 @@
+diff --git a/Makefile.system b/Makefile.system
+index b89f60e..2dbdad0 100644
+--- a/Makefile.system
++++ b/Makefile.system
+@@ -139,6 +139,10 @@ NO_PARALLEL_MAKE=0
+ endif
+ GETARCH_FLAGS += -DNO_PARALLEL_MAKE=$(NO_PARALLEL_MAKE)
+
++ifdef MAKE_NO_J
++GETARCH_FLAGS += -DMAKE_NO_J=$(MAKE_NO_J)
++endif
++
+ ifdef MAKE_NB_JOBS
+ GETARCH_FLAGS += -DMAKE_NB_JOBS=$(MAKE_NB_JOBS)
+ endif
+diff --git a/getarch.c b/getarch.c
+index f9c49e6..dffad70 100644
+--- a/getarch.c
++++ b/getarch.c
+@@ -1012,6 +1012,7 @@ int main(int argc, char *argv[]){
+ #endif
+ #endif
+
++#ifndef MAKE_NO_J
+ #ifdef MAKE_NB_JOBS
+ printf("MAKE += -j %d\n", MAKE_NB_JOBS);
+ #elif NO_PARALLEL_MAKE==1
+@@ -1021,6 +1022,7 @@ int main(int argc, char *argv[]){
+ printf("MAKE += -j %d\n", get_num_cores());
+ #endif
+ #endif
++#endif
+
+ break;
+

67
var/spack/repos/builtin/packages/julia/package.py
View file

@ -4,43 +4,56 @@
class Julia(Package):
"""The Julia Language: A fresh approach to technical computing"""
homepage = "http://julialang.org"
url = "http://github.com/JuliaLang/julia/releases/download/v0.4.2/julia-0.4.2.tar.gz"
url = "https://github.com/JuliaLang/julia/releases/download/v0.4.3/julia-0.4.3-full.tar.gz"
version('0.4.3', '7b9f096798fca4bef262a64674bc2b52')
version('0.4.2', 'ccfeb4f4090c8b31083f5e1ccb03eb06')
version('master',
git='https://github.com/JuliaLang/julia.git', branch='master')
version('0.4.5', '69141ff5aa6cee7c0ec8c85a34aa49a6')
version('0.4.3', '8a4a59fd335b05090dd1ebefbbe5aaac')
patch('gc.patch')
patch('openblas.patch', when='@0.4:0.4.5')
# Build-time dependencies
depends_on("cmake @2.8:")
# Build-time dependencies:
# depends_on("awk")
# depends_on("m4")
# depends_on("pkg-config")
depends_on("python @2.6:2.9")
# I think that Julia requires the dependencies above, but it builds find (on
# my system) without these. We should enable them as necessary.
# Combined build-time and run-time dependencies:
depends_on("binutils")
depends_on("cmake @2.8:")
depends_on("git")
depends_on("openssl")
depends_on("python @2.7:2.999")
# Run-time dependencies
# I think that Julia requires the dependencies above, but it
# builds fine (on my system) without these. We should enable them
# as necessary.
# Run-time dependencies:
# depends_on("arpack")
# depends_on("fftw +float")
# depends_on("gmp")
# depends_on("libgit")
# depends_on("mpfr")
# depends_on("openblas")
# depends_on("pcre2")
# ARPACK: Requires BLAS and LAPACK; needs to use the same version as Julia.
# ARPACK: Requires BLAS and LAPACK; needs to use the same version
# as Julia.
# BLAS and LAPACK: Julia prefers 64-bit versions on 64-bit systems. OpenBLAS
# has an option for this; make it available as variant.
# BLAS and LAPACK: Julia prefers 64-bit versions on 64-bit
# systems. OpenBLAS has an option for this; make it available as
# variant.
# FFTW: Something doesn't work when using a pre-installed FFTW library; need
# to investigate.
# FFTW: Something doesn't work when using a pre-installed FFTW
# library; need to investigate.
# GMP, MPFR: Something doesn't work when using a pre-installed FFTW library;
# need to investigate.
# GMP, MPFR: Something doesn't work when using a pre-installed
# FFTW library; need to investigate.
# LLVM: Julia works only with specific versions, and might require patches.
# Thus we let Julia install its own LLVM.
# LLVM: Julia works only with specific versions, and might require
# patches. Thus we let Julia install its own LLVM.
# Other possible dependencies:
# USE_SYSTEM_OPENLIBM=0
@ -50,11 +63,21 @@ class Julia(Package):
# USE_SYSTEM_UTF8PROC=0
# USE_SYSTEM_LIBGIT2=0
# Run-time dependencies for Julia packages:
depends_on("hdf5")
depends_on("mpi")
def install(self, spec, prefix):
# Explicitly setting CC, CXX, or FC breaks building libuv, one of
# Julia's dependencies. This might be a Darwin-specific problem. Given
# how Spack sets up compilers, Julia should still use Spack's compilers,
# even if we don't specify them explicitly.
if '@master' in spec:
# Julia needs to know the offset from a specific commit
git = which('git')
git('fetch', '--unshallow')
# Explicitly setting CC, CXX, or FC breaks building libuv, one
# of Julia's dependencies. This might be a Darwin-specific
# problem. Given how Spack sets up compilers, Julia should
# still use Spack's compilers, even if we don't specify them
# explicitly.
options = [#"CC=cc",
#"CXX=c++",
#"FC=fc",

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
View file

@ -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
View file

@ -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",

5
var/spack/repos/builtin/packages/libpng/package.py
View file

@ -8,6 +8,11 @@ class Libpng(Package):
version('1.6.16', '1a4ad377919ab15b54f6cb6a3ae2622d')
version('1.6.15', '829a256f3de9307731d4f52dc071916d')
version('1.6.14', '2101b3de1d5f348925990f9aa8405660')
version('1.5.26', '3ca98347a5541a2dad55cd6d07ee60a9')
version('1.4.19', '89bcbc4fc8b31f4a403906cf4f662330')
version('1.2.56', '9508fc59d10a1ffadd9aae35116c19ee')
depends_on('zlib')
def install(self, spec, prefix):
configure("--prefix=%s" % prefix)

18
var/spack/repos/builtin/packages/libxc/package.py Normal file
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@ -0,0 +1,18 @@
from spack import *
class Libxc(Package):
"""Libxc is a library of exchange-correlation functionals for
density-functional theory."""
homepage = "http://www.tddft.org/programs/octopus/wiki/index.php/Libxc"
url = "http://www.tddft.org/programs/octopus/down.php?file=libxc/libxc-2.2.2.tar.gz"
version('2.2.2', 'd9f90a0d6e36df6c1312b6422280f2ec')
def install(self, spec, prefix):
configure('--prefix=%s' % prefix,
'--enable-shared')
make()
make("install")

3
var/spack/repos/builtin/packages/libxcb/package.py
View file

@ -14,6 +14,9 @@ class Libxcb(Package):
depends_on("python")
depends_on("xcb-proto")
# depends_on('pthread') # Ubuntu: apt-get install libpthread-stubs0-dev
# depends_on('xau') # Ubuntu: apt-get install libxau-dev
def patch(self):
filter_file('typedef struct xcb_auth_info_t {', 'typedef struct {', 'src/xcb.h')

22
var/spack/repos/builtin/packages/metis/install_gklib_defs_rename.patch Normal file
View file

@ -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()

115
var/spack/repos/builtin/packages/metis/package.py
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@ -24,7 +24,7 @@
##############################################################################
from spack import *
import glob, sys, os
class Metis(Package):
"""
@ -36,7 +36,10 @@ class Metis(Package):
homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/metis/overview'
url = "http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/metis-5.1.0.tar.gz"
version('5.1.0', '5465e67079419a69e0116de24fce58fe')
version('5.1.0', '5465e67079419a69e0116de24fce58fe',
url='http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/metis-5.1.0.tar.gz')
version('4.0.3', '5efa35de80703c1b2c4d0de080fafbcf4e0d363a21149a1ad2f96e0144841a55',
url='http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/OLD/metis-4.0.3.tar.gz')
variant('shared', default=True, description='Enables the build of shared libraries')
variant('debug', default=False, description='Builds the library in debug mode')
@ -45,10 +48,85 @@ class Metis(Package):
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-time dependency
depends_on('cmake @2.8:', when='@5:') # build-time dependency
depends_on('gdb', when='+gdb')
patch('install_gklib_defs_rename.patch', when='@5:')
@when('@4:4.0.3')
def install(self, spec, prefix):
if '+gdb' in spec:
raise InstallError('gdb support not implemented in METIS 4!')
if '+idx64' in spec:
raise InstallError('idx64 option not implemented in METIS 4!')
if '+double' in spec:
raise InstallError('double option not implemented for METIS 4!')
options = ['COPTIONS=-fPIC']
if '+debug' in spec:
options.append('OPTFLAGS=-g -O0')
make(*options)
mkdir(prefix.bin)
for x in ('pmetis', 'kmetis', 'oemetis', 'onmetis', 'partnmesh',
'partdmesh', 'mesh2nodal', 'mesh2dual', 'graphchk'):
install(x, prefix.bin)
mkdir(prefix.lib)
install('libmetis.a', prefix.lib)
mkdir(prefix.include)
for h in glob.glob(join_path('Lib', '*.h')):
install(h, prefix.include)
mkdir(prefix.share)
for f in (join_path(*p)
for p in (('Programs', 'io.c'),
('Test','mtest.c'),
('Graphs','4elt.graph'),
('Graphs', 'metis.mesh'),
('Graphs', 'test.mgraph'))):
install(f, prefix.share)
if '+shared' in spec:
if sys.platform == 'darwin':
lib_dsuffix = 'dylib'
load_flag = '-Wl,-all_load'
no_load_flag = ''
else:
lib_dsuffix = 'so'
load_flag = '-Wl,-whole-archive'
no_load_flag = '-Wl,-no-whole-archive'
os.system(spack_cc + ' -fPIC -shared ' + load_flag +
' libmetis.a ' + no_load_flag + ' -o libmetis.' +
lib_dsuffix)
install('libmetis.' + lib_dsuffix, prefix.lib)
# Set up and run tests on installation
symlink(join_path(prefix.share, 'io.c'), 'io.c')
symlink(join_path(prefix.share, 'mtest.c'), 'mtest.c')
os.system(spack_cc + ' -I%s' % prefix.include + ' -c io.c')
os.system(spack_cc + ' -I%s' % prefix.include +
' -L%s' % prefix.lib + ' -lmetis mtest.c io.o -o mtest')
_4eltgraph = join_path(prefix.share, '4elt.graph')
test_mgraph = join_path(prefix.share, 'test.mgraph')
metis_mesh = join_path(prefix.share, 'metis.mesh')
kmetis = join_path(prefix.bin, 'kmetis')
os.system('./mtest ' + _4eltgraph)
os.system(kmetis + ' ' + _4eltgraph + ' 40')
os.system(join_path(prefix.bin, 'onmetis') + ' ' + _4eltgraph)
os.system(join_path(prefix.bin, 'pmetis') + ' ' + test_mgraph + ' 2')
os.system(kmetis + ' ' + test_mgraph + ' 2')
os.system(kmetis + ' ' + test_mgraph + ' 5')
os.system(join_path(prefix.bin, 'partnmesh') + metis_mesh + ' 10')
os.system(join_path(prefix.bin, 'partdmesh') + metis_mesh + ' 10')
os.system(join_path(prefix.bin, 'mesh2dual') + metis_mesh)
@when('@5:')
def install(self, spec, prefix):
options = []
@ -77,7 +155,36 @@ def install(self, spec, prefix):
if '+double' in spec:
filter_file('REALTYPEWIDTH 32', 'REALTYPEWIDTH 64', metis_header)
# Make clang 7.3 happy.
# Prevents "ld: section __DATA/__thread_bss extends beyond end of file"
# See upstream LLVM issue https://llvm.org/bugs/show_bug.cgi?id=27059
# Adopted from https://github.com/Homebrew/homebrew-science/blob/master/metis.rb
if spec.satisfies('%clang@7.3.0'):
filter_file('#define MAX_JBUFS 128', '#define MAX_JBUFS 24', join_path(source_directory, 'GKlib', 'error.c'))
with working_dir(build_directory, create=True):
cmake(source_directory, *options)
make()
make("install")
# now run some tests:
for f in ["4elt", "copter2", "mdual"]:
graph = join_path(source_directory,'graphs','%s.graph' % f)
Executable(join_path(prefix.bin,'graphchk'))(graph)
Executable(join_path(prefix.bin,'gpmetis'))(graph,'2')
Executable(join_path(prefix.bin,'ndmetis'))(graph)
graph = join_path(source_directory,'graphs','test.mgraph')
Executable(join_path(prefix.bin,'gpmetis'))(graph,'2')
graph = join_path(source_directory,'graphs','metis.mesh')
Executable(join_path(prefix.bin,'mpmetis'))(graph,'2')
# 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)

15
var/spack/repos/builtin/packages/mpich/package.py
View file

@ -47,12 +47,12 @@ class Mpich(Package):
provides('mpi@:3.0', when='@3:')
provides('mpi@:1.3', when='@1:')
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_environment(self, spack_env, run_env, dependent_spec):
spack_env.set('MPICH_CC', spack_cc)
spack_env.set('MPICH_CXX', spack_cxx)
spack_env.set('MPICH_F77', spack_f77)
spack_env.set('MPICH_F90', spack_fc)
spack_env.set('MPICH_FC', spack_fc)
def setup_dependent_package(self, module, dep_spec):
"""For dependencies, make mpicc's use spack wrapper."""
@ -78,6 +78,9 @@ def install(self, spec, prefix):
if not self.compiler.fc:
config_args.append("--disable-fc")
if not self.compiler.fc and not self.compiler.f77:
config_args.append("--disable-fortran")
configure(*config_args)
make()
make("install")

154
var/spack/repos/builtin/packages/mrnet/krell-5.0.1.patch Normal file
View file

@ -0,0 +1,154 @@
--- mrnet-3093918/include/mrnet/Types.h 2015-12-10 09:32:24.000000000 -0800
+++ mrnet_top_of_tree/include/mrnet/Types.h 2016-03-16 12:29:33.986132302 -0700
@@ -23,7 +23,7 @@
#ifndef MRNET_VERSION_MAJOR
# define MRNET_VERSION_MAJOR 5
# define MRNET_VERSION_MINOR 0
-# define MRNET_VERSION_REV 0
+# define MRNET_VERSION_REV 1
#endif
namespace MRN
--- mrnet-3093918/include/mrnet_lightweight/Types.h 2015-12-10 09:32:24.000000000 -0800
+++ mrnet_top_of_tree/include/mrnet_lightweight/Types.h 2016-03-16 12:29:33.987132302 -0700
@@ -30,7 +30,7 @@
#ifndef MRNET_VERSION_MAJOR
#define MRNET_VERSION_MAJOR 5
#define MRNET_VERSION_MINOR 0
-#define MRNET_VERSION_REV 0
+#define MRNET_VERSION_REV 1
#endif
void get_Version(int* major,
int* minor,
--- mrnet-3093918/src/lightweight/SerialGraph.c 2015-12-10 09:32:24.000000000 -0800
+++ mrnet_top_of_tree/src/lightweight/SerialGraph.c 2016-03-16 12:29:33.995132302 -0700
@@ -59,7 +59,7 @@
mrn_dbg_func_begin();
- sprintf(hoststr, "[%s:%hu:%u:", ihostname, iport, irank);
+ sprintf(hoststr, "[%s:%05hu:%u:", ihostname, iport, irank);
mrn_dbg(5, mrn_printf(FLF, stderr, "looking for SubTreeRoot: '%s'\n", hoststr));
byte_array = sg->byte_array;
@@ -110,7 +110,7 @@
mrn_dbg_func_begin();
- len = (size_t) sprintf(hoststr, "[%s:%hu:%u:0]", ihostname, iport, irank);
+ len = (size_t) sprintf(hoststr, "[%s:%05hu:%u:0]", ihostname, iport, irank);
mrn_dbg(5, mrn_printf(FLF, stderr, "adding sub tree leaf: %s\n", hoststr));
len += strlen(sg->byte_array) + 1;
@@ -139,7 +139,7 @@
mrn_dbg_func_begin();
- len = (size_t) sprintf(hoststr, "[%s:%hu:%u:1", ihostname, iport, irank);
+ len = (size_t) sprintf(hoststr, "[%s:%05hu:%u:1", ihostname, iport, irank);
mrn_dbg(5, mrn_printf(FLF, stderr, "adding sub tree root: %s\n", hoststr));
len += strlen(sg->byte_array) + 1;
@@ -360,8 +360,8 @@
char old_hoststr[256];
char new_hoststr[256];
- sprintf(old_hoststr, "[%s:%hu:%u:", hostname, UnknownPort, irank);
- sprintf(new_hoststr, "[%s:%hu:%u:", hostname, port, irank);
+ sprintf(old_hoststr, "[%s:%05hu:%u:", hostname, UnknownPort, irank);
+ sprintf(new_hoststr, "[%s:%05hu:%u:", hostname, port, irank);
old_byte_array = sg->byte_array;
new_byte_array = (char*) malloc( strlen(old_byte_array) + 10 );
--- mrnet-3093918/xplat/src/lightweight/SocketUtils.c 2015-12-10 09:32:24.000000000 -0800
+++ mrnet_top_of_tree/xplat/src/lightweight/SocketUtils.c 2016-03-16 12:29:34.006132303 -0700
@@ -15,7 +15,7 @@
#else
const XPlat_Socket InvalidSocket = INVALID_SOCKET;
#endif
-const XPlat_Port InvalidPort = (XPlat_Port)-1;
+const XPlat_Port InvalidPort = (XPlat_Port)0;
static bool_t SetTcpNoDelay( XPlat_Socket sock )
{
--- mrnet-3093918/conf/configure.in 2015-12-10 09:32:24.000000000 -0800
+++ mrnet_top_of_tree/conf/configure.in 2016-03-16 12:45:54.573196781 -0700
@@ -107,6 +107,18 @@
AC_SUBST(PURIFY)
+AC_ARG_WITH(expat,
+ [AS_HELP_STRING([--with-expat=PATH],
+ [Absolute path to installation of EXPAT libraries (note: specify the path to the directory containing "include" and "lib" sub-directories)])],
+ [EXPAT_DIR="${withval}"],
+ [EXPAT_DIR=""])
+
+if test "x$EXPAT_DIR" = "x" ; then
+ EXPAT_LIB=""
+else
+ EXPAT_LIB="-L$EXPAT_DIR/lib"
+fi
+
dnl === Checks for header files.
AC_CHECK_HEADERS([assert.h errno.h fcntl.h limits.h netdb.h signal.h stddef.h stdlib.h stdio.h string.h unistd.h arpa/inet.h netinet/in.h sys/ioctl.h sys/socket.h sys/sockio.h sys/time.h])
AC_HEADER_STDBOOL
@@ -432,7 +444,7 @@
CRAYXT_ATH_LIBS_SO="$CRAYXT_ATH_LIBS -lalps"
CRAYXT_ATH_LIBS="$CRAYXT_ATH_LIBS -Wl,-Bstatic -lalps -lxmlrpc -Wl,-Bdynamic"
CRAYXE_ATH_LIBS_SO="$CRAYXE_ATH_LIBS -lalps"
- CRAYXE_ATH_LIBS="$CRAYXE_ATH_LIBS -Wl,-Bstatic -lalps -lxmlrpc-epi -lexpat -Wl,-Bdynamic"
+ CRAYXE_ATH_LIBS="$CRAYXE_ATH_LIBS -Wl,-Bstatic -lalps -lxmlrpc-epi $EXPAT_LIB -lexpat -Wl,-Bdynamic"
AC_CHECK_LIB( [alps], [alps_launch_tool_helper],
[HAVE_ATH_LIBS="yes"; EXTRA_LIBS="$CRAYXT_ATH_LIBS $EXTRA_LIBS"; EXTRA_LIBS_SO="$CRAYXT_ATH_LIBS_SO $EXTRA_LIBS_SO"],
--- mrnet-3093918/configure 2015-12-10 09:32:24.000000000 -0800
+++ mrnet_top_of_tree/configure 2016-03-16 13:47:20.386439143 -0700
@@ -742,6 +742,7 @@
enable_debug
enable_ltwt_threadsafe
with_purify
+with_expat
'
ac_precious_vars='build_alias
host_alias
@@ -1399,6 +1400,9 @@
containing "include" and "lib" sub-directories)
--with-launchmon=PATH Absolute path to installation of LaunchMON
--with-purify Use purify for memory debugging
+ --with-expat=PATH Absolute path to installation of EXPAT libraries
+ (note: specify the path to the directory containing
+ "include" and "lib" sub-directories)
Some influential environment variables:
CC C compiler command
@@ -3541,6 +3545,21 @@
+# Check whether --with-expat was given.
+if test "${with_expat+set}" = set; then :
+ withval=$with_expat; EXPAT_DIR="${withval}"
+else
+ EXPAT_DIR=""
+fi
+
+
+if test "x$EXPAT_DIR" = "x" ; then
+ EXPAT_LIB=""
+else
+ EXPAT_LIB="-L$EXPAT_DIR/lib"
+fi
+
+
ac_ext=cpp
ac_cpp='$CXXCPP $CPPFLAGS'
ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5'
@@ -5473,7 +5492,7 @@
CRAYXT_ATH_LIBS_SO="$CRAYXT_ATH_LIBS -lalps"
CRAYXT_ATH_LIBS="$CRAYXT_ATH_LIBS -Wl,-Bstatic -lalps -lxmlrpc -Wl,-Bdynamic"
CRAYXE_ATH_LIBS_SO="$CRAYXE_ATH_LIBS -lalps"
- CRAYXE_ATH_LIBS="$CRAYXE_ATH_LIBS -Wl,-Bstatic -lalps -lxmlrpc-epi -lexpat -Wl,-Bdynamic"
+ CRAYXE_ATH_LIBS="$CRAYXE_ATH_LIBS -Wl,-Bstatic -lalps -lxmlrpc-epi $EXPAT_LIB -lexpat -Wl,-Bdynamic"
{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for alps_launch_tool_helper in -lalps" >&5
$as_echo_n "checking for alps_launch_tool_helper in -lalps... " >&6; }

12
var/spack/repos/builtin/packages/mrnet/package.py
View file

@ -3,11 +3,17 @@
class Mrnet(Package):
"""The MRNet Multi-Cast Reduction Network."""
homepage = "http://paradyn.org/mrnet"
url = "ftp://ftp.cs.wisc.edu/paradyn/mrnet/mrnet_4.0.0.tar.gz"
url = "ftp://ftp.cs.wisc.edu/paradyn/mrnet/mrnet_5.0.1.tar.gz"
list_url = "http://ftp.cs.wisc.edu/paradyn/mrnet"
version('4.0.0', 'd00301c078cba57ef68613be32ceea2f')
version('4.1.0', '5a248298b395b329e2371bf25366115c')
version('5.0.1', '17f65738cf1b9f9b95647ff85f69ecdd')
version('4.1.0', '5a248298b395b329e2371bf25366115c')
version('4.0.0', 'd00301c078cba57ef68613be32ceea2f')
# Add a patch that brings mrnet-5.0.1 up to date with the current development tree
# The development tree contains fixes needed for the krell based tools
variant('krellpatch', default=False, description="Build MRNet with krell openspeedshop based patch.")
patch('krell-5.0.1.patch', when='@5.0.1+krellpatch')
variant('lwthreads', default=False, description="Also build the MRNet LW threadsafe libraries")
parallel = False

3
var/spack/repos/builtin/packages/mumps/Makefile.inc
View file

@ -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

66
var/spack/repos/builtin/packages/mumps/package.py
View file

@ -1,6 +1,5 @@
from spack import *
import os
import os, sys, glob
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='+metis')
depends_on('metis@5:', when='+metis')
depends_on('parmetis', when="+parmetis")
depends_on('blas')
depends_on('lapack')
@ -70,6 +70,9 @@ def write_makefile_inc(self):
makefile_conf.append("ORDERINGSF = %s" % (' '.join(orderings)))
# when building shared libs need -fPIC, otherwise
# /usr/bin/ld: graph.o: relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
fpic = '-fPIC' if '+shared' in self.spec else ''
# TODO: test this part, it needs a full blas, scalapack and
# partitionning environment with 64bit integers
if '+idx64' in self.spec:
@ -77,14 +80,14 @@ def write_makefile_inc(self):
# the fortran compilation flags most probably are
# working only for intel and gnu compilers this is
# perhaps something the compiler should provide
['OPTF = -O -DALLOW_NON_INIT %s' % '-fdefault-integer-8' if self.compiler.name == "gcc" else '-i8',
'OPTL = -O ',
'OPTC = -O -DINTSIZE64'])
['OPTF = %s -O -DALLOW_NON_INIT %s' % (fpic,'-fdefault-integer-8' if self.compiler.name == "gcc" else '-i8'),
'OPTL = %s -O ' % fpic,
'OPTC = %s -O -DINTSIZE64' % fpic])
else:
makefile_conf.extend(
['OPTF = -O -DALLOW_NON_INIT',
'OPTL = -O ',
'OPTC = -O '])
['OPTF = %s -O -DALLOW_NON_INIT' % fpic,
'OPTL = %s -O ' % fpic,
'OPTC = %s -O ' % fpic])
if '+mpi' in self.spec:
@ -105,6 +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')
@ -121,7 +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')
@ -135,9 +159,27 @@ 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)
for f in glob.glob(join_path('libseq','*.h')):
install(f, prefix.include)
# 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")

7
var/spack/repos/builtin/packages/mvapich2/package.py
View file

@ -140,6 +140,13 @@ def set_network_type(self, spec, configure_args):
configure_args.extend(network_options)
def setup_dependent_environment(self, spack_env, run_env, extension_spec):
spack_env.set('MPICH_CC', spack_cc)
spack_env.set('MPICH_CXX', spack_cxx)
spack_env.set('MPICH_F77', spack_f77)
spack_env.set('MPICH_F90', spack_fc)
spack_env.set('MPICH_FC', spack_fc)
def install(self, spec, prefix):
# we'll set different configure flags depending on our environment
configure_args = [

7
var/spack/repos/builtin/packages/ncurses/package.py
View file

@ -8,11 +8,10 @@ class Ncurses(Package):
"""
homepage = "http://invisible-island.net/ncurses/ncurses.html"
url = "http://ftp.gnu.org/pub/gnu/ncurses/ncurses-6.0.tar.gz"
version('5.9', '8cb9c412e5f2d96bc6f459aa8c6282a1',
url='http://ftp.gnu.org/pub/gnu/ncurses/ncurses-5.9.tar.gz')
version('6.0', 'ee13d052e1ead260d7c28071f46eefb1',
url='http://ftp.gnu.org/pub/gnu/ncurses/ncurses-6.0.tar.gz')
version('6.0', 'ee13d052e1ead260d7c28071f46eefb1')
version('5.9', '8cb9c412e5f2d96bc6f459aa8c6282a1')
patch('patch_gcc_5.txt', when='%gcc@5.0:')

19
var/spack/repos/builtin/packages/netcdf-cxx/package.py Normal file
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@ -0,0 +1,19 @@
from spack import *
class NetcdfCxx(Package):
"""Deprecated C++ compatibility bindings for NetCDF.
These do NOT read or write NetCDF-4 files, and are no longer
maintained by Unidata. Developers should migrate to current
NetCDF C++ bindings, in Spack package netcdf-cxx4."""
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
View file

@ -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"
@ -19,41 +18,67 @@ class NetlibLapack(Package):
version('3.4.0', '02d5706ec03ba885fc246e5fa10d8c70')
version('3.3.1', 'd0d533ec9a5b74933c2a1e84eedc58b4')
variant('shared', default=False, description="Build shared library version")
variant('fpic', default=False, description="Build with -fpic compiler option")
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')
depends_on('blas', when='+external-blas')
# 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')]
def patch(self):
# Fix cblas CMakeLists.txt -- has wrong case for subdirectory name.
if self.spec.satisfies('@3.6.0:'):
filter_file('${CMAKE_CURRENT_SOURCE_DIR}/CMAKE/',
'${CMAKE_CURRENT_SOURCE_DIR}/cmake/', 'CBLAS/CMakeLists.txt', string=True)
@when('^atlas')
def get_blas_libs(self):
blas = self.spec['atlas']
return [join_path(blas.prefix.lib, l)
for l in ('libf77blas.a', 'libatlas.a')]
def install_one(self, spec, prefix, shared):
cmake_args = ['-DBUILD_SHARED_LIBS:BOOL=%s' % ('ON' if shared else 'OFF'),
'-DCMAKE_BUILD_TYPE:STRING=%s' % ('Debug' if '+debug' in spec else 'Release'),
'-DLAPACKE:BOOL=%s' % ('ON' if '+lapacke' in spec else 'OFF')]
if spec.satisfies('@3.6.0:'):
cmake_args.extend(['-DCBLAS=ON']) # always build CBLAS
def install(self, spec, prefix):
blas_libs = ";".join(self.get_blas_libs())
cmake_args = [".", '-DBLAS_LIBRARIES=' + blas_libs]
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')
if '+fpic' in spec:
cmake_args.append('-DCMAKE_POSITION_INDEPENDENT_CODE=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)

6
var/spack/repos/builtin/packages/netlib-scalapack/package.py
View file

@ -18,6 +18,7 @@ class NetlibScalapack(Package):
provides('scalapack')
depends_on('cmake')
depends_on('mpi')
depends_on('lapack')
@ -41,6 +42,11 @@ def install(self, spec, prefix):
make()
make("install")
# The shared libraries are not installed correctly on Darwin; correct this
if (sys.platform == 'darwin') and ('+shared' in spec):
fix_darwin_install_name(prefix.lib)
def setup_dependent_package(self, module, dependent_spec):
spec = self.spec
lib_dsuffix = '.dylib' if sys.platform == 'darwin' else '.so'

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
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 *
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
View file

@ -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
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@ -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)

60
var/spack/repos/builtin/packages/openblas/package.py
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@ -1,30 +1,78 @@
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.")
variant('openmp', default=True, description="Enable OpenMP support.")
# virtual dependency
provides('blas')
provides('lapack')
def install(self, spec, prefix):
make('libs', 'netlib', 'shared', 'CC=cc', 'FC=f77')
make('install', "PREFIX='%s'" % prefix)
lib_dsuffix = 'dylib' if sys.platform == 'darwin' else 'so'
def install(self, spec, prefix):
# Openblas is picky about compilers. Configure fails with
# FC=/abs/path/to/f77, whereas FC=f77 works fine.
# To circumvent this, provide basename only:
make_defs = ['CC=%s' % os.path.basename(spack_cc),
'FC=%s' % os.path.basename(spack_f77)]
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']
# Add support for OpenMP
# Note: Make sure your compiler supports OpenMP
if '+openmp' in spec:
make_defs += ['USE_OPENMP=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.%s' % lib_dsuffix, 'libblas.%s' % lib_dsuffix)
if '+shared' in spec:
symlink('libopenblas.%s' % dso_suffix, 'libblas.%s' % dso_suffix)
# Lapack virtual package should provide liblapack.a
with working_dir(prefix.lib):
symlink('libopenblas.a', 'liblapack.a')
symlink('libopenblas.%s' % lib_dsuffix, 'liblapack.%s' % lib_dsuffix)
if '+shared' in spec:
symlink('libopenblas.%s' % dso_suffix, 'liblapack.%s' % dso_suffix)
def setup_dependent_package(self, module, dspec):
# This is WIP for a prototype interface for virtual packages.
# We can update this as more builds start depending on BLAS/LAPACK.
libdir = find_library_path('libopenblas.a', self.prefix.lib64, self.prefix.lib)
self.spec.blas_static_lib = join_path(libdir, 'libopenblas.a')
self.spec.lapack_static_lib = self.spec.blas_static_lib
if '+shared' in self.spec:
self.spec.blas_shared_lib = join_path(libdir, 'libopenblas.%s' % dso_suffix)
self.spec.lapack_shared_lib = self.spec.blas_shared_lib

26
var/spack/repos/builtin/packages/openjpeg/package.py Normal file
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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")

34
var/spack/repos/builtin/packages/p4est/package.py Normal file
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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")

1
var/spack/repos/builtin/packages/parallel-netcdf/package.py
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@ -8,6 +8,7 @@ class ParallelNetcdf(Package):
homepage = "https://trac.mcs.anl.gov/projects/parallel-netcdf"
url = "http://cucis.ece.northwestern.edu/projects/PnetCDF/Release/parallel-netcdf-1.6.1.tar.gz"
version('1.7.0', '267eab7b6f9dc78c4d0e6def2def3aea4bc7c9f0')
version('1.6.1', '62a094eb952f9d1e15f07d56e535052604f1ac34')
depends_on("m4")

21
var/spack/repos/builtin/packages/paraview/package.py
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@ -27,13 +27,14 @@ class Paraview(Package):
depends_on('bzip2')
depends_on('freetype')
depends_on('hdf5+mpi', when='+mpi')
depends_on('hdf5~mpi', when='~mpi')
#depends_on('hdf5+mpi', when='+mpi')
#depends_on('hdf5~mpi', when='~mpi')
depends_on('jpeg')
depends_on('libpng')
depends_on('libtiff')
depends_on('libxml2')
depends_on('netcdf')
#depends_on('netcdf')
#depends_on('netcdf-cxx')
#depends_on('protobuf') # version mismatches?
#depends_on('sqlite') # external version not supported
depends_on('zlib')
@ -75,13 +76,13 @@ def nfeature_to_bool(feature):
cmake('..',
'-DCMAKE_INSTALL_PREFIX:PATH=%s' % prefix,
'-DBUILD_TESTING:BOOL=OFF',
'-DVTK_USER_SYSTEM_FREETYPE:BOOL=ON',
'-DVTK_USER_SYSTEM_HDF5:BOOL=ON',
'-DVTK_USER_SYSTEM_JPEG:BOOL=ON',
'-DVTK_USER_SYSTEM_LIBXML2:BOOL=ON',
'-DVTK_USER_SYSTEM_NETCDF:BOOL=ON',
'-DVTK_USER_SYSTEM_TIFF:BOOL=ON',
'-DVTK_USER_SYSTEM_ZLIB:BOOL=ON',
'-DVTK_USE_SYSTEM_FREETYPE:BOOL=ON',
'-DVTK_USE_SYSTEM_HDF5:BOOL=OFF',
'-DVTK_USE_SYSTEM_JPEG:BOOL=ON',
'-DVTK_USE_SYSTEM_LIBXML2:BOOL=ON',
'-DVTK_USE_SYSTEM_NETCDF:BOOL=OFF',
'-DVTK_USE_SYSTEM_TIFF:BOOL=ON',
'-DVTK_USE_SYSTEM_ZLIB:BOOL=ON',
*feature_args)
make()
make('install')

62
var/spack/repos/builtin/packages/parmetis/enable_external_metis.patch
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@ -1,13 +1,71 @@
diff --git a/CMakeLists.txt b/CMakeLists.txt
index ca945dd..1bf94e9 100644
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 ${CMAKE_BINARY_DIR}/libmetis)
+#add_subdirectory(${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"

10
var/spack/repos/builtin/packages/parmetis/package.py
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@ -24,7 +24,7 @@
##############################################################################
from spack import *
import sys
class Parmetis(Package):
"""
@ -44,7 +44,7 @@ class Parmetis(Package):
depends_on('mpi')
patch('enable_external_metis.patch')
depends_on('metis')
depends_on('metis@5:')
# bug fixes from PETSc developers
# https://bitbucket.org/petsc/pkg-parmetis/commits/1c1a9fd0f408dc4d42c57f5c3ee6ace411eb222b/raw/
@ -64,7 +64,7 @@ def install(self, spec, prefix):
# FIXME : Once a contract is defined, MPI compilers should be retrieved indirectly via spec['mpi'] in case
# FIXME : they use a non-standard name
options.extend(['-DGKLIB_PATH:PATH={metis_source}/GKlib'.format(metis_source=metis_source), # still need headers from METIS source, and they are not installed with METIS. shame...
options.extend(['-DGKLIB_PATH:PATH={metis_source}/GKlib'.format(metis_source=spec['metis'].prefix.include),
'-DMETIS_PATH:PATH={metis_source}'.format(metis_source=spec['metis'].prefix),
'-DCMAKE_C_COMPILER:STRING=mpicc',
'-DCMAKE_CXX_COMPILER:STRING=mpicxx'])
@ -83,3 +83,7 @@ def install(self, spec, prefix):
cmake(source_directory, *options)
make()
make("install")
# The shared library is not installed correctly on Darwin; correct this
if (sys.platform == 'darwin') and ('+shared' in spec):
fix_darwin_install_name(prefix.lib)

49
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')
@ -36,11 +40,17 @@ class Petsc(Package):
# Other dependencies
depends_on('boost', when='+boost')
depends_on('metis', when='+metis')
depends_on('metis@5:', when='+metis')
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:
@ -55,20 +65,11 @@ 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
raise RuntimeError('\n'.join(errors))
else:
if self.compiler.name == "clang":
compiler_opts = [
'--with-mpi=1',
'--with-cc=%s -Qunused-arguments' % join_path(self.spec['mpi'].prefix.bin, 'mpicc'), # Avoid confusing PETSc config by clang: warning: argument unused during compilation
'--with-cxx=%s -Qunused-arguments' % join_path(self.spec['mpi'].prefix.bin, 'mpic++'),
'--with-fc=%s' % join_path(self.spec['mpi'].prefix.bin, 'mpif90'),
'--with-f77=%s' % join_path(self.spec['mpi'].prefix.bin, 'mpif77'),
]
else:
compiler_opts = [
'--with-mpi=1',
@ -77,16 +78,17 @@ def mpi_dependent_options(self):
return compiler_opts
def install(self, spec, prefix):
options = ['--with-debugging=0',
'--with-ssl=0']
options = ['--with-ssl=0']
options.extend(self.mpi_dependent_options())
options.extend([
'--with-precision=%s' % ('double' if '+double' in spec else 'single'),
'--with-scalar-type=%s' % ('complex' if '+complex' in spec else 'real'),
'--with-shared-libraries=%s' % ('1' if '+shared' in spec else '0'),
'--with-debugging=%s' % ('1' if '+debug' in spec else '0'),
'--with-blas-lapack-dir=%s' % spec['lapack'].prefix
])
# Activates library support if needed
for library in ('metis', 'boost', 'hdf5', 'hypre', 'parmetis'):
for library in ('metis', 'boost', 'hdf5', 'hypre', 'parmetis','mumps','scalapack'):
options.append(
'--with-{library}={value}'.format(library=library, value=('1' if library in spec else '0'))
)
@ -94,9 +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)

7
var/spack/repos/builtin/packages/pkg-config/package.py
View file

@ -10,7 +10,12 @@ class PkgConfig(Package):
parallel = False
def install(self, spec, prefix):
configure("--prefix=%s" %prefix, "--enable-shared")
configure("--prefix=%s" %prefix,
"--enable-shared",
"--with-internal-glib") # There's a bootstrapping problem here;
# glib uses pkg-config as well, so
# break the cycle by using the internal
# glib.
make()
make("install")

14
var/spack/repos/builtin/packages/py-bottleneck/package.py Normal file
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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)

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