diff options
55 files changed, 1114 insertions, 317 deletions
diff --git a/lib/spack/docs/basic_usage.rst b/lib/spack/docs/basic_usage.rst index accf09cc2a..68f3d07b29 100644 --- a/lib/spack/docs/basic_usage.rst +++ b/lib/spack/docs/basic_usage.rst @@ -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. diff --git a/lib/spack/env/cc b/lib/spack/env/cc index 2eb6f46afe..18fd8f7bdb 100755 --- a/lib/spack/env/cc +++ b/lib/spack/env/cc @@ -39,7 +39,7 @@ # # This is the list of environment variables that need to be set before -# the script runs. They are set by routines in spack.build_environment +# the script runs. They are set by routines in spack.build_environment # as part of spack.package.Package.do_install(). parameters=" SPACK_PREFIX @@ -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 @@ -66,11 +66,10 @@ function die { for param in $parameters; do if [[ -z ${!param} ]]; then - die "Spack compiler must be run from spack! Input $param was missing!" + die "Spack compiler must be run from Spack! Input '$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. # @@ -78,19 +77,18 @@ done # 'command' is set based on the input command to $SPACK_[CC|CXX|F77|F90] # # 'mode' is set to one of: +# vcheck version check # cpp preprocess # cc compile # as assemble # ld link # ccld compile & link -# vcheck version check -# -# Depending on the mode, we may or may not add extra rpaths. -# This variable controls whether they are added. -add_rpaths=true command=$(basename "$0") case "$command" in + cpp) + mode=cpp + ;; cc|c89|c99|gcc|clang|icc|pgcc|xlc) command="$SPACK_CC" language="C" @@ -107,34 +105,20 @@ case "$command" in command="$SPACK_F77" language="Fortran 77" ;; - cpp) - mode=cpp - ;; ld) mode=ld - - # Darwin's linker has a -r argument that merges object files - # together. It doesn't work with -rpath. - if [[ $OSTYPE = darwin* ]]; then - for arg in "$@"; do - if [ "$arg" = -r ]; then - add_rpaths=false - break - fi - done - fi ;; *) die "Unkown compiler: $command" ;; esac -# If any of the arguments below is present then the mode is vcheck. In -# vcheck mode nothing is added in terms of extra search paths or -# libraries -if [ -z "$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 || $arg == -dumpversion ]]; then mode=vcheck break fi @@ -142,16 +126,16 @@ if [ -z "$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" = -S ]; then + elif [[ $arg == -S ]]; then mode=as break - elif [ "$arg" = -c ]; then + elif [[ $arg == -c ]]; then mode=cc break fi @@ -159,7 +143,7 @@ if [ -z "$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 @@ -170,10 +154,23 @@ if [[ -z $command ]]; then die "ERROR: Compiler '$SPACK_COMPILER_SPEC' does not support compiling $language programs." fi -if [ "$mode" == vcheck ] ; then +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 [[ $arg == -r ]]; then + add_rpaths=false + break + fi + done +fi + # Save original command for debug logging input_command="$@" args=("$@") @@ -183,17 +180,17 @@ IFS=':' read -ra deps <<< "$SPACK_DEPENDENCIES" for dep in "${deps[@]}"; do # Prepend include directories if [[ -d $dep/include ]]; then - if [[ $mode = cpp || $mode = cc || $mode = as || $mode = ccld ]]; then + if [[ $mode == cpp || $mode == cc || $mode == as || $mode == ccld ]]; then args=("-I$dep/include" "${args[@]}") fi fi # Prepend lib and RPATH directories if [[ -d $dep/lib ]]; then - if [[ $mode = ccld ]]; then + if [[ $mode == ccld ]]; then $add_rpaths && args=("-Wl,-rpath,$dep/lib" "${args[@]}") args=("-L$dep/lib" "${args[@]}") - elif [[ $mode = ld ]]; then + elif [[ $mode == ld ]]; then $add_rpaths && args=("-rpath" "$dep/lib" "${args[@]}") args=("-L$dep/lib" "${args[@]}") fi @@ -201,10 +198,10 @@ for dep in "${deps[@]}"; do # Prepend lib64 and RPATH directories if [[ -d $dep/lib64 ]]; then - if [[ $mode = ccld ]]; then + if [[ $mode == ccld ]]; then $add_rpaths && args=("-Wl,-rpath,$dep/lib64" "${args[@]}") args=("-L$dep/lib64" "${args[@]}") - elif [[ $mode = ld ]]; then + elif [[ $mode == ld ]]; then $add_rpaths && args=("-rpath" "$dep/lib64" "${args[@]}") args=("-L$dep/lib64" "${args[@]}") fi @@ -212,9 +209,9 @@ for dep in "${deps[@]}"; do done # Include all -L's and prefix/whatever dirs in rpath -if [[ $mode = ccld ]]; then +if [[ $mode == ccld ]]; then $add_rpaths && args=("-Wl,-rpath,$SPACK_PREFIX/lib" "-Wl,-rpath,$SPACK_PREFIX/lib64" "${args[@]}") -elif [[ $mode = ld ]]; then +elif [[ $mode == ld ]]; then $add_rpaths && args=("-rpath" "$SPACK_PREFIX/lib" "-rpath" "$SPACK_PREFIX/lib64" "${args[@]}") fi @@ -234,11 +231,14 @@ IFS=':' read -ra spack_env_dirs <<< "$SPACK_ENV_PATH" spack_env_dirs+=("" ".") PATH="" for dir in "${env_path[@]}"; do - remove="" - for rm_dir in "${spack_env_dirs[@]}"; do - if [[ $dir = $rm_dir ]]; then remove=True; fi + addpath=true + for env_dir in "${spack_env_dirs[@]}"; do + if [[ $dir == $env_dir ]]; then + addpath=false + break + fi done - if [[ -z $remove ]]; then + if $addpath; then PATH="${PATH:+$PATH:}$dir" fi done @@ -247,7 +247,7 @@ export PATH full_command=("$command" "${args[@]}") # In test command mode, write out full command for Spack tests. -if [[ $SPACK_TEST_COMMAND = dump-args ]]; then +if [[ $SPACK_TEST_COMMAND == dump-args ]]; then echo "${full_command[@]}" exit elif [[ -n $SPACK_TEST_COMMAND ]]; then @@ -257,7 +257,7 @@ 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-$SPACK_SHORT_SPEC.out.log" echo "[$mode] $command $input_command" >> $input_log diff --git a/lib/spack/spack/__init__.py b/lib/spack/spack/__init__.py index aee11f061f..9108e1d0e3 100644 --- a/lib/spack/spack/__init__.py +++ b/lib/spack/spack/__init__.py @@ -136,9 +136,7 @@ for path in _tmp_candidates: # 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 diff --git a/lib/spack/spack/build_environment.py b/lib/spack/spack/build_environment.py index 640db0c1d1..eb72f2a6b4 100644 --- a/lib/spack/spack/build_environment.py +++ b/lib/spack/spack/build_environment.py @@ -213,7 +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, @@ -278,21 +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() @@ -316,20 +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) - # Allow dependencies to modify the module + # traverse in postorder so package can use vars from its dependencies spec = pkg.spec - for dependency_spec in spec.traverse(root=False): - dpkg = dependency_spec.package - dpkg.setup_dependent_package(pkg.module, 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 set up environment as well - for dependency_spec in spec.traverse(root=False): - dpkg = dependency_spec.package + # Allow dependencies to modify the module + dpkg = dspec.package + dpkg.setup_dependent_package(pkg.module, spec) 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. diff --git a/lib/spack/spack/cmd/module.py b/lib/spack/spack/cmd/module.py index 315d9fc926..a67f5c0c13 100644 --- a/lib/spack/spack/cmd/module.py +++ b/lib/spack/spack/cmd/module.py @@ -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() diff --git a/lib/spack/spack/cmd/uninstall.py b/lib/spack/spack/cmd/uninstall.py index 350ef372cb..1ff3d8db5f 100644 --- a/lib/spack/spack/cmd/uninstall.py +++ b/lib/spack/spack/cmd/uninstall.py @@ -23,19 +23,33 @@ # 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" +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( @@ -44,10 +58,101 @@ def setup_parser(subparser): subparser.add_argument( '-a', '--all', action='store_true', dest='all', help="USE CAREFULLY. Remove ALL installed packages that match each " + - "supplied spec. i.e., if you say uninstall libelf, ALL versions of " + - "libelf are uninstalled. This is both useful and dangerous, like rm -r.") + "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) diff --git a/lib/spack/spack/modules.py b/lib/spack/spack/modules.py index f6a11c92e3..61624fbd70 100644 --- a/lib/spack/spack/modules.py +++ b/lib/spack/spack/modules.py @@ -163,9 +163,14 @@ class EnvModule(object): # package-specific modifications spack_env = EnvironmentModifications() for item in self.pkg.extendees: - package = self.spec[item].package - package.setup_dependent_package(self.pkg.module, self.spec) - package.setup_dependent_environment(spack_env, env, self.spec) + 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 self.spec.package.setup_environment(spack_env, env) @@ -206,7 +211,11 @@ class EnvModule(object): 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): diff --git a/lib/spack/spack/test/__init__.py b/lib/spack/spack/test/__init__.py index cd842561e6..175a49428c 100644 --- a/lib/spack/spack/test/__init__.py +++ b/lib/spack/spack/test/__init__.py @@ -67,7 +67,8 @@ test_names = ['versions', 'namespace_trie', 'yaml', 'sbang', - 'environment'] + 'environment', + 'cmd.uninstall'] def list_tests(): diff --git a/lib/spack/spack/test/cmd/__init__.py b/lib/spack/spack/test/cmd/__init__.py new file mode 100644 index 0000000000..e69de29bb2 --- /dev/null +++ b/lib/spack/spack/test/cmd/__init__.py diff --git a/lib/spack/spack/test/cmd/uninstall.py b/lib/spack/spack/test/cmd/uninstall.py new file mode 100644 index 0000000000..80efe06d36 --- /dev/null +++ b/lib/spack/spack/test/cmd/uninstall.py @@ -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) diff --git a/lib/spack/spack/test/database.py b/lib/spack/spack/test/database.py index ce6e8a0552..465263d057 100644 --- a/lib/spack/spack/test/database.py +++ b/lib/spack/spack/test/database.py @@ -28,16 +28,12 @@ both in memory and in its file """ 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 _print_ref_counts(): 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 @@ class DatabaseTest(MockPackagesTest): 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() diff --git a/lib/spack/spack/test/install.py b/lib/spack/spack/test/install.py index 8297893f01..fc5b7e67df 100644 --- a/lib/spack/spack/test/install.py +++ b/lib/spack/spack/test/install.py @@ -64,7 +64,14 @@ class InstallTest(MockPackagesTest): 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 @@ class InstallTest(MockPackagesTest): # 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 @@ class InstallTest(MockPackagesTest): 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 diff --git a/lib/spack/spack/test/mock_database.py b/lib/spack/spack/test/mock_database.py new file mode 100644 index 0000000000..82ba59fc48 --- /dev/null +++ b/lib/spack/spack/test/mock_database.py @@ -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 diff --git a/var/spack/repos/builtin.mock/packages/cmake-client/package.py b/var/spack/repos/builtin.mock/packages/cmake-client/package.py new file mode 100644 index 0000000000..a5d3ef156a --- /dev/null +++ b/var/spack/repos/builtin.mock/packages/cmake-client/package.py @@ -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')) diff --git a/var/spack/repos/builtin.mock/packages/cmake/package.py b/var/spack/repos/builtin.mock/packages/cmake/package.py new file mode 100644 index 0000000000..deb44c2bf7 --- /dev/null +++ b/var/spack/repos/builtin.mock/packages/cmake/package.py @@ -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) diff --git a/var/spack/repos/builtin/packages/bash/package.py b/var/spack/repos/builtin/packages/bash/package.py new file mode 100644 index 0000000000..9c9fbeedcf --- /dev/null +++ b/var/spack/repos/builtin/packages/bash/package.py @@ -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") diff --git a/var/spack/repos/builtin/packages/boost/package.py b/var/spack/repos/builtin/packages/boost/package.py index f889da21f2..12bc9508c3 100644 --- a/var/spack/repos/builtin/packages/boost/package.py +++ b/var/spack/repos/builtin/packages/boost/package.py @@ -199,6 +199,18 @@ class Boost(Package): 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'] = './' diff --git a/var/spack/repos/builtin/packages/dbus/package.py b/var/spack/repos/builtin/packages/dbus/package.py index 422f5a19eb..74ce8ef502 100644 --- a/var/spack/repos/builtin/packages/dbus/package.py +++ b/var/spack/repos/builtin/packages/dbus/package.py @@ -20,6 +20,8 @@ class Dbus(Package): version('1.8.4', '4717cb8ab5b80978fcadf2b4f2f72e1b') version('1.8.2', 'd6f709bbec0a022a1847c7caec9d6068') + depends_on('expat') + def install(self, spec, prefix): configure( "--prefix=%s" % prefix, diff --git a/var/spack/repos/builtin/packages/dealii/package.py b/var/spack/repos/builtin/packages/dealii/package.py index 0b76db3827..b251d50ca1 100644 --- a/var/spack/repos/builtin/packages/dealii/package.py +++ b/var/spack/repos/builtin/packages/dealii/package.py @@ -23,8 +23,10 @@ class Dealii(Package): # required dependencies, light version depends_on ("blas") - depends_on ("boost", when='~mpi') - depends_on ("boost+mpi", when='+mpi') + # 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") @@ -38,7 +40,7 @@ class Dealii(Package): depends_on ("arpack-ng+mpi", when='+arpack+mpi') depends_on ("doxygen", when='+doc') depends_on ("hdf5+mpi~cxx", when='+hdf5+mpi') #FIXME NetCDF declares dependency with ~cxx, why? - depends_on ("metis", when='+metis') + depends_on ("metis@5:", when='+metis') depends_on ("netcdf+mpi", when="+netcdf+mpi") depends_on ("netcdf-cxx", when='+netcdf+mpi') depends_on ("oce", when='+oce') @@ -174,6 +176,19 @@ class Dealii(Package): 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'): diff --git a/var/spack/repos/builtin/packages/dia/package.py b/var/spack/repos/builtin/packages/dia/package.py new file mode 100644 index 0000000000..1cb5910e46 --- /dev/null +++ b/var/spack/repos/builtin/packages/dia/package.py @@ -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') diff --git a/var/spack/repos/builtin/packages/dyninst/package.py b/var/spack/repos/builtin/packages/dyninst/package.py index 0111dcbe08..b28e897a0f 100644 --- a/var/spack/repos/builtin/packages/dyninst/package.py +++ b/var/spack/repos/builtin/packages/dyninst/package.py @@ -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', diff --git a/var/spack/repos/builtin/packages/eigen/package.py b/var/spack/repos/builtin/packages/eigen/package.py index 8d6e672f86..1501989812 100644 --- a/var/spack/repos/builtin/packages/eigen/package.py +++ b/var/spack/repos/builtin/packages/eigen/package.py @@ -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') diff --git a/var/spack/repos/builtin/packages/environment-modules/package.py b/var/spack/repos/builtin/packages/environment-modules/package.py new file mode 100644 index 0000000000..45181da41b --- /dev/null +++ b/var/spack/repos/builtin/packages/environment-modules/package.py @@ -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') diff --git a/var/spack/repos/builtin/packages/git/package.py b/var/spack/repos/builtin/packages/git/package.py index 586b6ce3c3..388f84aefd 100644 --- a/var/spack/repos/builtin/packages/git/package.py +++ b/var/spack/repos/builtin/packages/git/package.py @@ -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") diff --git a/var/spack/repos/builtin/packages/global/package.py b/var/spack/repos/builtin/packages/global/package.py index e8f06516d9..aac1cede30 100644 --- a/var/spack/repos/builtin/packages/global/package.py +++ b/var/spack/repos/builtin/packages/global/package.py @@ -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)] diff --git a/var/spack/repos/builtin/packages/hdf5/package.py b/var/spack/repos/builtin/packages/hdf5/package.py index 513a38ee8a..f26e225b83 100644 --- a/var/spack/repos/builtin/packages/hdf5/package.py +++ b/var/spack/repos/builtin/packages/hdf5/package.py @@ -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') @@ -80,10 +81,16 @@ class Hdf5(Package): # sanity check in configure, so this doesn't merit a variant. extra_args.append("--enable-unsupported") - if '+debug' in spec: - extra_args.append('--enable-debug=all') + 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: - extra_args.append('--enable-production') + if '+debug' in spec: + extra_args.append('--enable-debug=all') + else: + extra_args.append('--enable-production') if '+shared' in spec: extra_args.append('--enable-shared') @@ -139,5 +146,7 @@ class Hdf5(Package): 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" diff --git a/var/spack/repos/builtin/packages/ipopt/package.py b/var/spack/repos/builtin/packages/ipopt/package.py new file mode 100644 index 0000000000..13c37bf79c --- /dev/null +++ b/var/spack/repos/builtin/packages/ipopt/package.py @@ -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) diff --git a/var/spack/repos/builtin/packages/libxcb/package.py b/var/spack/repos/builtin/packages/libxcb/package.py index 1dd5954c99..d7d94c4546 100644 --- a/var/spack/repos/builtin/packages/libxcb/package.py +++ b/var/spack/repos/builtin/packages/libxcb/package.py @@ -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') diff --git a/var/spack/repos/builtin/packages/metis/package.py b/var/spack/repos/builtin/packages/metis/package.py index 9301135f9f..41e3ebb429 100644 --- a/var/spack/repos/builtin/packages/metis/package.py +++ b/var/spack/repos/builtin/packages/metis/package.py @@ -24,7 +24,7 @@ ############################################################################## from spack import * -import glob,sys +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') @@ -45,12 +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') + 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 = [] @@ -79,10 +155,28 @@ class Metis(Package): 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') diff --git a/var/spack/repos/builtin/packages/modules/package.py b/var/spack/repos/builtin/packages/modules/package.py deleted file mode 100644 index b014ee460c..0000000000 --- a/var/spack/repos/builtin/packages/modules/package.py +++ /dev/null @@ -1,25 +0,0 @@ -from spack import * - -class Modules(Package): - """ The Environment Modules package provides for the dynamic modification of a user's environment via modulefiles. """ - - homepage = "http://modules.sf.net" - url = "http://downloads.sourceforge.net/project/modules/Modules/modules-3.2.10/modules-3.2.10.tar.gz" - - version('3.2.10', '8b097fdcb90c514d7540bb55a3cb90fb') - - depends_on("tcl") - - def install(self, spec, prefix): - - options = ['--prefix=%s' % prefix, - '--disable-debug', - '--disable-dependency-tracking', - '--disable-silent-rules', - '--disable-versioning', - '--datarootdir=%s' % prefix.share, - 'CPPFLAGS=-DUSE_INTERP_ERRORLINE'] - - configure(*options) - make() - make("install") diff --git a/var/spack/repos/builtin/packages/mpich/package.py b/var/spack/repos/builtin/packages/mpich/package.py index 2d7955e08d..b317ec6651 100644 --- a/var/spack/repos/builtin/packages/mpich/package.py +++ b/var/spack/repos/builtin/packages/mpich/package.py @@ -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.""" diff --git a/var/spack/repos/builtin/packages/mumps/package.py b/var/spack/repos/builtin/packages/mumps/package.py index 26440ab7c8..58f790ec32 100644 --- a/var/spack/repos/builtin/packages/mumps/package.py +++ b/var/spack/repos/builtin/packages/mumps/package.py @@ -1,5 +1,5 @@ from spack import * -import os, sys +import os, sys, glob class Mumps(Package): """MUMPS: a MUltifrontal Massively Parallel sparse direct Solver""" @@ -23,7 +23,7 @@ class Mumps(Package): 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') @@ -164,10 +164,13 @@ class Mumps(Package): install_tree('lib', prefix.lib) install_tree('include', prefix.include) - if '~mpi' in spec: + + if '~mpi' in spec: 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 diff --git a/var/spack/repos/builtin/packages/mvapich2/package.py b/var/spack/repos/builtin/packages/mvapich2/package.py index e4e95f92af..3e60b517db 100644 --- a/var/spack/repos/builtin/packages/mvapich2/package.py +++ b/var/spack/repos/builtin/packages/mvapich2/package.py @@ -140,6 +140,13 @@ class Mvapich2(Package): 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 = [ diff --git a/var/spack/repos/builtin/packages/ncurses/package.py b/var/spack/repos/builtin/packages/ncurses/package.py index 8dc808caac..219fbce226 100644 --- a/var/spack/repos/builtin/packages/ncurses/package.py +++ b/var/spack/repos/builtin/packages/ncurses/package.py @@ -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:') diff --git a/var/spack/repos/builtin/packages/netcdf-cxx/package.py b/var/spack/repos/builtin/packages/netcdf-cxx/package.py index 5334dfb853..8aa1d8b236 100644 --- a/var/spack/repos/builtin/packages/netcdf-cxx/package.py +++ b/var/spack/repos/builtin/packages/netcdf-cxx/package.py @@ -1,7 +1,11 @@ from spack import * class NetcdfCxx(Package): - """C++ compatibility bindings for NetCDF""" + """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" diff --git a/var/spack/repos/builtin/packages/netlib-lapack/package.py b/var/spack/repos/builtin/packages/netlib-lapack/package.py index 05436332ac..f70e634347 100644 --- a/var/spack/repos/builtin/packages/netlib-lapack/package.py +++ b/var/spack/repos/builtin/packages/netlib-lapack/package.py @@ -34,15 +34,17 @@ class NetlibLapack(Package): def patch(self): # Fix cblas CMakeLists.txt -- has wrong case for subdirectory name. - filter_file('${CMAKE_CURRENT_SOURCE_DIR}/CMAKE/', - '${CMAKE_CURRENT_SOURCE_DIR}/cmake/', 'CBLAS/CMakeLists.txt', string=True) - + if self.spec.satisfies('@3.6.0:'): + filter_file('${CMAKE_CURRENT_SOURCE_DIR}/CMAKE/', + '${CMAKE_CURRENT_SOURCE_DIR}/cmake/', 'CBLAS/CMakeLists.txt', string=True) def install_one(self, spec, prefix, shared): cmake_args = ['-DBUILD_SHARED_LIBS:BOOL=%s' % ('ON' if shared else 'OFF'), - '-DCBLAS=ON', # always build CBLAS '-DCMAKE_BUILD_TYPE:STRING=%s' % ('Debug' if '+debug' in spec else 'Release'), '-DLAPACKE:BOOL=%s' % ('ON' if '+lapacke' in spec else 'OFF')] + if spec.satisfies('@3.6.0:'): + cmake_args.extend(['-DCBLAS=ON']) # always build CBLAS + 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 @@ -80,6 +82,3 @@ class NetlibLapack(Package): if '+shared' in self.spec: self.spec.blas_shared_lib = join_path(libdir, 'libblas.%s' % dso_suffix) self.spec.lapack_shared_lib = join_path(libdir, 'liblapack.%s' % dso_suffix) - - - diff --git a/var/spack/repos/builtin/packages/netlib-scalapack/package.py b/var/spack/repos/builtin/packages/netlib-scalapack/package.py index d59f8e41fe..276876d197 100644 --- a/var/spack/repos/builtin/packages/netlib-scalapack/package.py +++ b/var/spack/repos/builtin/packages/netlib-scalapack/package.py @@ -18,6 +18,7 @@ class NetlibScalapack(Package): provides('scalapack') + depends_on('cmake') depends_on('mpi') depends_on('lapack') diff --git a/var/spack/repos/builtin/packages/openblas/package.py b/var/spack/repos/builtin/packages/openblas/package.py index 4ec829a85b..9f13d0690b 100644 --- a/var/spack/repos/builtin/packages/openblas/package.py +++ b/var/spack/repos/builtin/packages/openblas/package.py @@ -19,8 +19,11 @@ class Openblas(Package): def install(self, spec, prefix): - make_defs = ['CC=%s' % spack_cc, - 'FC=%s' % spack_fc] + # 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'] @@ -67,4 +70,3 @@ class Openblas(Package): if '+shared' in self.spec: self.spec.blas_shared_lib = join_path(libdir, 'libopenblas.%s' % dso_suffix) self.spec.lapack_shared_lib = self.spec.blas_shared_lib - diff --git a/var/spack/repos/builtin/packages/parmetis/package.py b/var/spack/repos/builtin/packages/parmetis/package.py index ff4370aa4b..b49f8dae00 100644 --- a/var/spack/repos/builtin/packages/parmetis/package.py +++ b/var/spack/repos/builtin/packages/parmetis/package.py @@ -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/ diff --git a/var/spack/repos/builtin/packages/petsc/package.py b/var/spack/repos/builtin/packages/petsc/package.py index 5c1fc6cc92..1161dd7d67 100644 --- a/var/spack/repos/builtin/packages/petsc/package.py +++ b/var/spack/repos/builtin/packages/petsc/package.py @@ -40,7 +40,7 @@ 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') diff --git a/var/spack/repos/builtin/packages/py-dask/package.py b/var/spack/repos/builtin/packages/py-dask/package.py new file mode 100644 index 0000000000..cf0a16f21e --- /dev/null +++ b/var/spack/repos/builtin/packages/py-dask/package.py @@ -0,0 +1,15 @@ +from spack import * + +class PyDask(Package): + """Minimal task scheduling abstraction""" + homepage = "https://github.com/dask/dask/" + url = "https://pypi.python.org/packages/source/d/dask/dask-0.8.1.tar.gz" + + version('0.8.1', '5dd8e3a3823b3bc62c9a6d192e2cb5b4') + + extends('python') + + depends_on('py-setuptools') + + def install(self, spec, prefix): + python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-decorator/package.py b/var/spack/repos/builtin/packages/py-decorator/package.py new file mode 100644 index 0000000000..abbd9f43d1 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-decorator/package.py @@ -0,0 +1,15 @@ +from spack import * + +class PyDecorator(Package): + """The aim of the decorator module it to simplify the usage of decorators for the average programmer, and to popularize decorators by showing various non-trivial examples.""" + homepage = "https://github.com/micheles/decorator" + url = "https://pypi.python.org/packages/source/d/decorator/decorator-4.0.9.tar.gz" + + version('4.0.9', 'f12c5651ccd707e12a0abaa4f76cd69a') + + extends('python') + + depends_on('py-setuptools') + + def install(self, spec, prefix): + python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-mpmath/package.py b/var/spack/repos/builtin/packages/py-mpmath/package.py new file mode 100644 index 0000000000..4d3261ae8f --- /dev/null +++ b/var/spack/repos/builtin/packages/py-mpmath/package.py @@ -0,0 +1,13 @@ +from spack import * + +class PyMpmath(Package): + """A Python library for arbitrary-precision floating-point arithmetic.""" + homepage = "http://mpmath.org" + url = "https://pypi.python.org/packages/source/m/mpmath/mpmath-all-0.19.tar.gz" + + version('0.19', 'd1b7e19dd6830d0d7b5e1bc93d46c02c') + + extends('python') + + def install(self, spec, prefix): + python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-networkx/package.py b/var/spack/repos/builtin/packages/py-networkx/package.py new file mode 100644 index 0000000000..893146ec3e --- /dev/null +++ b/var/spack/repos/builtin/packages/py-networkx/package.py @@ -0,0 +1,15 @@ +from spack import * + +class PyNetworkx(Package): + """NetworkX is a Python package for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks.""" + homepage = "http://networkx.github.io/" + url = "https://pypi.python.org/packages/source/n/networkx/networkx-1.11.tar.gz" + + version('1.11', '6ef584a879e9163013e9a762e1cf7cd1') + + extends('python') + + depends_on('py-decorator') + + def install(self, spec, prefix): + python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-pillow/package.py b/var/spack/repos/builtin/packages/py-pillow/package.py index adc8507bd5..66d9bb4382 100644 --- a/var/spack/repos/builtin/packages/py-pillow/package.py +++ b/var/spack/repos/builtin/packages/py-pillow/package.py @@ -1,4 +1,5 @@ from spack import * +import os class PyPillow(Package): """Pillow is the friendly PIL fork by Alex Clark and Contributors. PIL is the Python Imaging Library by Fredrik Lundh and Contributors. The Python Imaging Library (PIL) adds image processing capabilities to your Python interpreter. This library supports many file formats, and provides powerful image processing and graphics capabilities.""" @@ -7,8 +8,68 @@ class PyPillow(Package): url = "https://pypi.python.org/packages/source/P/Pillow/Pillow-3.0.0.tar.gz" version('3.0.0', 'fc8ac44e93da09678eac7e30c9b7377d') + provides('PIL') + + # These defaults correspond to Pillow defaults + variant('jpeg', default=True, description='Provide JPEG functionality') + variant('zlib', default=True, description='Access to compressed PNGs') + variant('tiff', default=False, description='Access to TIFF files') + variant('freetype', default=False, description='Font related services') + variant('tk', default=False, description='Support for tkinter bitmap and photo images') + variant('lcms', default=False, description='Color management') + + # Spack does not (yet) support these modes of building + # variant('webp', default=False, description='') + # variant('webpmux', default=False, description='') + # variant('jpeg2000', default=False, description='') + extends('python') + depends_on('binutils') depends_on('py-setuptools') + depends_on('jpeg', when='+jpeg') # BUG: It will use the system libjpeg anyway + depends_on('zlib', when='+zlib') + depends_on('tiff', when='+tiff') + depends_on('freetype', when='+freetype') + depends_on('lcms', when='+lcms') + depends_on('tcl', when='+tk') + depends_on('tk', when='+tk') + def install(self, spec, prefix): - python('setup.py', 'install', '--prefix=%s' % prefix) + libpath=[] + + if '+jpeg' in spec: + libpath.append(join_path(spec['jpeg'].prefix, 'lib')) + if '+zlib' in spec: + libpath.append(join_path(spec['zlib'].prefix, 'lib')) + if '+tiff' in spec: + libpath.append(join_path(spec['tiff'].prefix, 'lib')) + if '+freetype' in spec: + libpath.append(join_path(spec['freetype'].prefix, 'lib')) + if '+lcms' in spec: + libpath.append(join_path(spec['lcms'].prefix, 'lib')) + + # This has not been tested, and likely needs some other treatment. + #if '+tk' in spec: + # libpath.append(join_path(spec['tcl'].prefix, 'lib')) + # libpath.append(join_path(spec['tk'].prefix, 'lib')) + + # -------- Building + cmd = ['build_ext', + '--%s-jpeg' % ('enable' if '+jpeg' in spec else 'disable'), + '--%s-zlib' % ('enable' if '+zlib' in spec else 'disable'), + '--%s-tiff' % ('enable' if '+tiff' in spec else 'disable'), + '--%s-freetype' % ('enable' if '+freetype' in spec else 'disable'), + '--%s-lcms' % ('enable' if '+lcms' in spec else 'disable'), + '-L'+':'.join(libpath) # NOTE: This does not make it find libjpeg + ] + + #if '+tk' in spec: + # cmd.extend(['--enable-tcl', '--enable-tk']) + #else: + # cmd.extend(['--disable-tcl', '--disable-tk']) + + # --------- Installation + cmd.extend(['install', '--prefix=%s' % prefix]) + + python('setup.py', *cmd) diff --git a/var/spack/repos/builtin/packages/py-scikit-image/package.py b/var/spack/repos/builtin/packages/py-scikit-image/package.py new file mode 100644 index 0000000000..22ce1f8374 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-scikit-image/package.py @@ -0,0 +1,20 @@ +from spack import * + +class PyScikitImage(Package): + """Image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.""" + homepage = "http://scikit-image.org/" + url = "https://pypi.python.org/packages/source/s/scikit-image/scikit-image-0.12.3.tar.gz" + + version('0.12.3', '04ea833383e0b6ad5f65da21292c25e1') + + extends('python', ignore=r'bin/.*\.py$|bin/f2py$') + + depends_on('py-dask') + depends_on('py-pillow') + depends_on('py-networkx') + depends_on('py-six') + depends_on('py-scipy') + depends_on('py-matplotlib') + + def install(self, spec, prefix): + python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-scikit-learn/package.py b/var/spack/repos/builtin/packages/py-scikit-learn/package.py index 5b078ce901..2d7985b98c 100644 --- a/var/spack/repos/builtin/packages/py-scikit-learn/package.py +++ b/var/spack/repos/builtin/packages/py-scikit-learn/package.py @@ -7,8 +7,13 @@ class PyScikitLearn(Package): version('0.15.2', 'd9822ad0238e17b382a3c756ea94fe0d') version('0.16.1', '363ddda501e3b6b61726aa40b8dbdb7e') + version('0.17.1', 'a2f8b877e6d99b1ed737144f5a478dfc') extends('python') + depends_on('py-setuptools') + depends_on('py-numpy') + depends_on('py-scipy') + def install(self, spec, prefix): python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-sympy/package.py b/var/spack/repos/builtin/packages/py-sympy/package.py index c17e35b95f..bbce8c74e3 100644 --- a/var/spack/repos/builtin/packages/py-sympy/package.py +++ b/var/spack/repos/builtin/packages/py-sympy/package.py @@ -6,8 +6,10 @@ class PySympy(Package): url = "https://pypi.python.org/packages/source/s/sympy/sympy-0.7.6.tar.gz" version('0.7.6', '3d04753974306d8a13830008e17babca') + version('1.0', '43e797de799f00f9e8fd2307dba9fab1') extends('python') + depends_on('py-mpmath', when='@1.0:') def install(self, spec, prefix): python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/qt/package.py b/var/spack/repos/builtin/packages/qt/package.py index ab09469042..8cb88e6c85 100644 --- a/var/spack/repos/builtin/packages/qt/package.py +++ b/var/spack/repos/builtin/packages/qt/package.py @@ -4,7 +4,6 @@ import os class Qt(Package): """Qt is a comprehensive cross-platform C++ application framework.""" homepage = 'http://qt.io' - url = 'http://download.qt.io/archive/qt/5.5/5.5.1/single/qt-everywhere-opensource-src-5.5.1.tar.gz' version('5.5.1', '59f0216819152b77536cf660b015d784') version('5.4.2', 'fa1c4d819b401b267eb246a543a63ea5') diff --git a/var/spack/repos/builtin/packages/readline/package.py b/var/spack/repos/builtin/packages/readline/package.py index 1b870e0e7f..0c429ea756 100644 --- a/var/spack/repos/builtin/packages/readline/package.py +++ b/var/spack/repos/builtin/packages/readline/package.py @@ -2,12 +2,12 @@ from spack import * class Readline(Package): """The GNU Readline library provides a set of functions for use by - applications that allow users to edit command li nes as they + applications that allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. The Readline library includes additional functions to maintain a list of previously-entered command lines, to recall and perhaps reedit those lines, and perform csh-like - history expansion on previous commands. """ + history expansion on previous commands.""" homepage = "http://cnswww.cns.cwru.edu/php/chet/readline/rltop.html" url = "ftp://ftp.cwru.edu/pub/bash/readline-6.3.tar.gz" diff --git a/var/spack/repos/builtin/packages/suite-sparse/package.py b/var/spack/repos/builtin/packages/suite-sparse/package.py index c2196dcec4..a4b3979a15 100644 --- a/var/spack/repos/builtin/packages/suite-sparse/package.py +++ b/var/spack/repos/builtin/packages/suite-sparse/package.py @@ -10,10 +10,18 @@ class SuiteSparse(Package): version('4.5.1', 'f0ea9aad8d2d1ffec66a5b6bfeff5319') + # FIXME: (see below) + # variant('tbb', default=True, description='Build with Intel TBB') + depends_on('blas') depends_on('lapack') depends_on('metis@5.1.0', when='@4.5.1') + # FIXME: + # in @4.5.1. TBB support in SPQR seems to be broken as TBB-related linkng flags + # does not seem to be used, which leads to linking errors on Linux. + # Try re-enabling in future versions. + # depends_on('tbb', when='+tbb') def install(self, spec, prefix): # The build system of SuiteSparse is quite old-fashioned @@ -21,16 +29,35 @@ class SuiteSparse(Package): # with a lot of convoluted logic in it. # Any kind of customization will need to go through filtering of that file - # FIXME : this actually uses the current workaround - # FIXME : (blas / lapack always provide libblas and liblapack as aliases) - make('install', 'INSTALL=%s' % prefix, + make_args = ['INSTALL=%s' % prefix] - # inject Spack compiler wrappers + # inject Spack compiler wrappers + make_args.extend([ 'AUTOCC=no', 'CC=cc', 'CXX=c++', 'F77=f77', + ]) + + # use Spack's metis in CHOLMOD/Partition module, + # otherwise internal Metis will be compiled + make_args.extend([ + 'MY_METIS_LIB=-L%s -lmetis' % spec['metis'].prefix.lib, + 'MY_METIS_INC=%s' % spec['metis'].prefix.include, + ]) + + # Intel TBB in SuiteSparseQR + if '+tbb' in spec: + make_args.extend([ + 'SPQR_CONFIG=-DHAVE_TBB', + 'TBB=-L%s -ltbb' % spec['tbb'].prefix.lib, + ]) + + # BLAS arguments require path to libraries + # FIXME : (blas / lapack always provide libblas and liblapack as aliases) + make_args.extend([ + 'BLAS=-lblas', + 'LAPACK=-llapack' + ]) - # BLAS arguments require path to libraries - 'BLAS=-lblas', - 'LAPACK=-llapack') + make('install', *make_args) diff --git a/var/spack/repos/builtin/packages/superlu-dist/package.py b/var/spack/repos/builtin/packages/superlu-dist/package.py index ddcb7f9225..5cf5e129b4 100644 --- a/var/spack/repos/builtin/packages/superlu-dist/package.py +++ b/var/spack/repos/builtin/packages/superlu-dist/package.py @@ -15,7 +15,7 @@ class SuperluDist(Package): depends_on ('blas') depends_on ('lapack') depends_on ('parmetis') - depends_on ('metis') + depends_on ('metis@5:') def install(self, spec, prefix): makefile_inc = [] diff --git a/var/spack/repos/builtin/packages/tcl/package.py b/var/spack/repos/builtin/packages/tcl/package.py index 529adf7788..db8bee88d0 100644 --- a/var/spack/repos/builtin/packages/tcl/package.py +++ b/var/spack/repos/builtin/packages/tcl/package.py @@ -10,8 +10,13 @@ class Tcl(Package): extensible.""" homepage = "http://www.tcl.tk" - version('8.6.3', 'db382feca91754b7f93da16dc4cdad1f', - url="http://prdownloads.sourceforge.net/tcl/tcl8.6.3-src.tar.gz") + def url_for_version(self, version): + return 'http://prdownloads.sourceforge.net/tcl/tcl%s-src.tar.gz' % version + + version('8.6.5', '0e6426a4ca9401825fbc6ecf3d89a326') + version('8.6.4', 'd7cbb91f1ded1919370a30edd1534304') + version('8.6.3', 'db382feca91754b7f93da16dc4cdad1f') + version('8.5.19', '0e6426a4ca9401825fbc6ecf3d89a326') depends_on('zlib') diff --git a/var/spack/repos/builtin/packages/tk/package.py b/var/spack/repos/builtin/packages/tk/package.py index 96736f6f95..839d217f34 100644 --- a/var/spack/repos/builtin/packages/tk/package.py +++ b/var/spack/repos/builtin/packages/tk/package.py @@ -8,9 +8,11 @@ class Tk(Package): applications that run unchanged across Windows, Mac OS X, Linux and more.""" homepage = "http://www.tcl.tk" - url = "http://prdownloads.sourceforge.net/tcl/tk8.6.3-src.tar.gz" - version('src', '85ca4dbf4dcc19777fd456f6ee5d0221') + def url_for_version(self, version): + return "http://prdownloads.sourceforge.net/tcl/tk%s-src.tar.gz" % version + + version('8.6.3', '85ca4dbf4dcc19777fd456f6ee5d0221') depends_on("tcl") diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py index 6223848c68..0f72055fa7 100644 --- a/var/spack/repos/builtin/packages/trilinos/package.py +++ b/var/spack/repos/builtin/packages/trilinos/package.py @@ -42,7 +42,7 @@ class Trilinos(Package): depends_on('matio') depends_on('glm') depends_on('swig') - depends_on('metis',when='+metis') + depends_on('metis@5:',when='+metis') depends_on('suite-sparse',when='+suite-sparse') # MPI related dependencies |