diff options
72 files changed, 3098 insertions, 456 deletions
diff --git a/.gitignore b/.gitignore index 643e5d9b03..040df3eafd 100644 --- a/.gitignore +++ b/.gitignore @@ -1,4 +1,5 @@ /var/spack/stage +/var/spack/cache *.pyc /opt/ *~ diff --git a/lib/spack/docs/basic_usage.rst b/lib/spack/docs/basic_usage.rst index 65688dec46..8fad96010e 100644 --- a/lib/spack/docs/basic_usage.rst +++ b/lib/spack/docs/basic_usage.rst @@ -1135,6 +1135,79 @@ of module files: """Set up the compile and runtime environments for a package.""" pass + +Recursive Modules +`````````````````` + +In some cases, it is desirable to load not just a module, but also all +the modules it depends on. This is not required for most modules +because Spack builds binaries with RPATH support. However, not all +packages use RPATH to find their dependencies: this can be true in +particular for Python extensions, which are currently *not* built with +RPATH. + +Modules may be loaded recursively with the command: + +.. code-block:: sh + + $ module load `spack module tcl --dependencies <spec>... + +More than one spec may be placed on the command line here. + +Module Comamnds for Shell Scripts +`````````````````````````````````` + +Although Spack is flexbile, the ``module`` command is much faster. +This could become an issue when emitting a series of ``spack load`` +commands inside a shell script. By adding the ``--shell`` flag, +``spack module find`` may also be used to generate code that can be +cut-and-pasted into a shell script. For example: + +.. code-block:: sh + + $ spack module find tcl --dependencies --shell py-numpy git + # bzip2@1.0.6%gcc@4.9.3=linux-x86_64 + module load bzip2-1.0.6-gcc-4.9.3-ktnrhkrmbbtlvnagfatrarzjojmkvzsx + # ncurses@6.0%gcc@4.9.3=linux-x86_64 + module load ncurses-6.0-gcc-4.9.3-kaazyneh3bjkfnalunchyqtygoe2mncv + # zlib@1.2.8%gcc@4.9.3=linux-x86_64 + module load zlib-1.2.8-gcc-4.9.3-v3ufwaahjnviyvgjcelo36nywx2ufj7z + # sqlite@3.8.5%gcc@4.9.3=linux-x86_64 + module load sqlite-3.8.5-gcc-4.9.3-a3eediswgd5f3rmto7g3szoew5nhehbr + # readline@6.3%gcc@4.9.3=linux-x86_64 + module load readline-6.3-gcc-4.9.3-se6r3lsycrwxyhreg4lqirp6xixxejh3 + # python@3.5.1%gcc@4.9.3=linux-x86_64 + module load python-3.5.1-gcc-4.9.3-5q5rsrtjld4u6jiicuvtnx52m7tfhegi + # py-setuptools@20.5%gcc@4.9.3=linux-x86_64 + module load py-setuptools-20.5-gcc-4.9.3-4qr2suj6p6glepnedmwhl4f62x64wxw2 + # py-nose@1.3.7%gcc@4.9.3=linux-x86_64 + module load py-nose-1.3.7-gcc-4.9.3-pwhtjw2dvdvfzjwuuztkzr7b4l6zepli + # openblas@0.2.17%gcc@4.9.3+shared=linux-x86_64 + module load openblas-0.2.17-gcc-4.9.3-pw6rmlom7apfsnjtzfttyayzc7nx5e7y + # py-numpy@1.11.0%gcc@4.9.3+blas+lapack=linux-x86_64 + module load py-numpy-1.11.0-gcc-4.9.3-mulodttw5pcyjufva4htsktwty4qd52r + # curl@7.47.1%gcc@4.9.3=linux-x86_64 + module load curl-7.47.1-gcc-4.9.3-ohz3fwsepm3b462p5lnaquv7op7naqbi + # autoconf@2.69%gcc@4.9.3=linux-x86_64 + module load autoconf-2.69-gcc-4.9.3-bkibjqhgqm5e3o423ogfv2y3o6h2uoq4 + # cmake@3.5.0%gcc@4.9.3~doc+ncurses+openssl~qt=linux-x86_64 + module load cmake-3.5.0-gcc-4.9.3-x7xnsklmgwla3ubfgzppamtbqk5rwn7t + # expat@2.1.0%gcc@4.9.3=linux-x86_64 + module load expat-2.1.0-gcc-4.9.3-6pkz2ucnk2e62imwakejjvbv6egncppd + # git@2.8.0-rc2%gcc@4.9.3+curl+expat=linux-x86_64 + module load git-2.8.0-rc2-gcc-4.9.3-3bib4hqtnv5xjjoq5ugt3inblt4xrgkd + +The script may be further edited by removing unnecessary modules. +This script may be directly executed in bash via + +.. code-block :: sh + + source <( spack module find tcl --dependencies --shell py-numpy git ) + + +Regenerating Module files +~~~~~~~~~~~~~~~~~~~~~~~~~~~ + .. code-block:: python def setup_dependent_environment(self, spack_env, run_env, dependent_spec): @@ -1399,23 +1472,23 @@ files in the ``cmake`` package while retaining its dependencies. .. code-block:: sh - + $ spack view -v symlink myview cmake@3.5.2 ==> Linking package: "ncurses" ==> Linking package: "zlib" ==> Linking package: "openssl" ==> Linking package: "cmake" - + $ ls myview/ bin doc etc include lib share $ ls myview/bin/ captoinfo clear cpack ctest infotocap openssl tabs toe tset ccmake cmake c_rehash infocmp ncurses6-config reset tic tput - + $ spack view -v -d false rm myview cmake@3.5.2 ==> Removing package: "cmake" - + $ ls myview/bin/ captoinfo c_rehash infotocap openssl tabs toe tset clear infocmp ncurses6-config reset tic tput @@ -1425,7 +1498,7 @@ Limitations of Filesystem Views ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ This section describes some limitations that should be considered in -using filesystems views. +using filesystems views. Filesystem views are merely organizational. The binary executable programs, shared libraries and other build products found in a view diff --git a/lib/spack/docs/developer_guide.rst b/lib/spack/docs/developer_guide.rst index 0b618aa683..d28fe4b2a5 100644 --- a/lib/spack/docs/developer_guide.rst +++ b/lib/spack/docs/developer_guide.rst @@ -80,10 +80,11 @@ with a high level view of Spack's directory structure:: var/ spack/ <- build & stage directories - repos/ <- contains package repositories - builtin/ <- pkg repository that comes with Spack - repo.yaml <- descriptor for the builtin repository - packages/ <- directories under here contain packages + repos/ <- contains package repositories + builtin/ <- pkg repository that comes with Spack + repo.yaml <- descriptor for the builtin repository + packages/ <- directories under here contain packages + cache/ <- saves resources downloaded during installs opt/ spack/ <- packages are installed here diff --git a/lib/spack/docs/mirrors.rst b/lib/spack/docs/mirrors.rst index dad04d053b..583575a565 100644 --- a/lib/spack/docs/mirrors.rst +++ b/lib/spack/docs/mirrors.rst @@ -214,3 +214,21 @@ Adding a mirror really adds a line in ``~/.spack/mirrors.yaml``:: If you want to change the order in which mirrors are searched for packages, you can edit this file and reorder the sections. Spack will search the topmost mirror first and the bottom-most mirror last. + +.. _caching: + +Local Default Cache +---------------------------- + +Spack caches resources that are downloaded as part of installs. The cache is +a valid spack mirror: it uses the same directory structure and naming scheme +as other Spack mirrors (so it can be copied anywhere and referenced with a URL +like other mirrors). The mirror is maintained locally (within the Spack +installation directory) at :file:`var/spack/cache/`. It is always enabled (and +is always searched first when attempting to retrieve files for an installation) +but can be cleared with :ref:`purge <spack-purge>`; the cache directory can also +be deleted manually without issue. + +Caching includes retrieved tarball archives and source control repositories, but +only resources with an associated digest or commit ID (e.g. a revision number +for SVN) will be cached. diff --git a/lib/spack/docs/packaging_guide.rst b/lib/spack/docs/packaging_guide.rst index c09e8524b0..563ecd8185 100644 --- a/lib/spack/docs/packaging_guide.rst +++ b/lib/spack/docs/packaging_guide.rst @@ -377,6 +377,8 @@ add a line like this in the package class: version('8.2.1', '4136d7b4c04df68b686570afa26988ac') ... +Versions should be listed with the newest version first. + Version URLs ~~~~~~~~~~~~~~~~~ @@ -385,8 +387,21 @@ in the package. For example, Spack is smart enough to download version ``8.2.1.`` of the ``Foo`` package above from ``http://example.com/foo-8.2.1.tar.gz``. -If spack *cannot* extrapolate the URL from the ``url`` field, or if -the package doesn't have a ``url`` field, you can add a URL explicitly +If spack *cannot* extrapolate the URL from the ``url`` field by +default, you can write your own URL generation algorithm in place of +the ``url`` declaration. For example: + +.. code-block:: python + :linenos: + + class Foo(Package): + def url_for_version(self, version): + return 'http://example.com/version_%s/foo-%s.tar.gz' \ + % (version, version) + version('8.2.1', '4136d7b4c04df68b686570afa26988ac') + ... + +If a URL cannot be derived systematically, you can add an explicit URL for a particular version: .. code-block:: python @@ -703,6 +718,13 @@ Fetching a revision Subversion branches are handled as part of the directory structure, so you can check out a branch or tag by changing the ``url``. +Automatic caching of files fetched during installation +------------------------------------------------------ + +Spack maintains a cache (described :ref:`here <caching>`) which saves files +retrieved during package installations to avoid re-downloading in the case that +a package is installed with a different specification (but the same version) or +reinstalled on account of a change in the hashing scheme. .. _license: @@ -776,7 +798,7 @@ Spack will create a global license file located at file using the editor set in ``$EDITOR``, or vi if unset. It will look like this: -.. code-block:: +.. code-block:: sh # A license is required to use pgi. # @@ -807,7 +829,7 @@ You can add your license directly to this file, or tell FlexNet to use a license stored on a separate license server. Here is an example that points to a license server called licman1: -.. code-block:: +.. code-block:: sh SERVER licman1.mcs.anl.gov 00163eb7fba5 27200 USE_SERVER @@ -1339,6 +1361,19 @@ Now, the ``py-numpy`` package can be used as an argument to ``spack activate``. When it is activated, all the files in its prefix will be symbolically linked into the prefix of the python package. +Many packages produce Python extensions for *some* variants, but not +others: they should extend ``python`` only if the apropriate +variant(s) are selected. This may be accomplished with conditional +``extends()`` declarations: + +.. code-block:: python + + class FooLib(Package): + variant('python', default=True, description= \ + 'Build the Python extension Module') + extends('python', when='+python') + ... + Sometimes, certain files in one package will conflict with those in another, which means they cannot both be activated (symlinked) at the same time. In this case, you can tell Spack to ignore those files @@ -1844,7 +1879,7 @@ discover its dependencies. If you want to see the environment that a package will build with, or if you want to run commands in that environment to test them out, you -can use the :ref:```spack env`` <spack-env>` command, documented +can use the :ref:`spack env <spack-env>` command, documented below. .. _compiler-wrappers: @@ -2524,6 +2559,59 @@ File functions .. _package-lifecycle: +Coding Style Guidelines +--------------------------- + +The following guidelines are provided, in the interests of making +Spack packages work in a consistent manner: + + +Variant Names +~~~~~~~~~~~~~~ + +Spack packages with variants similar to already-existing Spack +packages should use the same name for their variants. Standard +variant names are: + +======= ======== ======================== +Name Default Description +------- -------- ------------------------ +shared True Build shared libraries +static Build static libraries +mpi Use MPI +python Build Python extension +------- -------- ------------------------ + +If specified in this table, the corresponding default should be used +when declaring a variant. + + +Version Lists +~~~~~~~~~~~~~~ + +Spack packges should list supported versions with the newest first. + +Special Versions +~~~~~~~~~~~~~~~~~ + +The following *special* version names may be used when building a package: + +* *@system*: Indicates a hook to the OS-installed version of the + package. This is useful, for example, to tell Spack to use the + OS-installed version in ``packages.yaml``:: + + openssl: + paths: + openssl@system: /usr + buildable: False + + Certain Spack internals look for the *@system* version and do + appropriate things in that case. + +* *@local*: Indicates the version was built manually from some source + tree of unknown provenance (see ``spack setup``). + + Packaging workflow commands --------------------------------- @@ -2618,11 +2706,16 @@ build process will start from scratch. ``spack purge`` ~~~~~~~~~~~~~~~~~ -Cleans up all of Spack's temporary files. Use this to recover disk -space if temporary files from interrupted or failed installs -accumulate in the staging area. This is equivalent to running ``spack -clean`` for every package you have fetched or staged. +Cleans up all of Spack's temporary and cached files. This can be used to +recover disk space if temporary files from interrupted or failed installs +accumulate in the staging area. + +When called with ``--stage`` or ``--all`` (or without arguments, in which case +the default is ``--all``) this removes all staged files; this is equivalent to +running ``spack clean`` for every package you have fetched or staged. +When called with ``--cache`` or ``--all`` this will clear all resources +:ref:`cached <caching>` during installs. Keeping the stage directory on success ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -2839,3 +2932,109 @@ might write: DWARF_PREFIX = $(spack location -i libdwarf) CXXFLAGS += -I$DWARF_PREFIX/include CXXFLAGS += -L$DWARF_PREFIX/lib + +Build System Configuration Support +---------------------------------- + +Imagine a developer creating a CMake-based (or Autotools) project in a local +directory, which depends on libraries A-Z. Once Spack has installed +those dependencies, one would like to run ``cmake`` with appropriate +command line and environment so CMake can find them. The ``spack +setup`` command does this conveniently, producing a CMake +configuration that is essentially the same as how Spack *would have* +configured the project. This can be demonstrated with a usage +example: + +.. code-block:: bash + + cd myproject + spack setup myproject@local + mkdir build; cd build + ../spconfig.py .. + make + make install + +Notes: + * Spack must have ``myproject/package.py`` in its repository for + this to work. + * ``spack setup`` produces the executable script ``spconfig.py`` in + the local directory, and also creates the module file for the + package. ``spconfig.py`` is normally run from the user's + out-of-source build directory. + * The version number given to ``spack setup`` is arbitrary, just + like ``spack diy``. ``myproject/package.py`` does not need to + have any valid downloadable versions listed (typical when a + project is new). + * spconfig.py produces a CMake configuration that *does not* use the + Spack wrappers. Any resulting binaries *will not* use RPATH, + unless the user has enabled it. This is recommended for + development purposes, not production. + * ``spconfig.py`` is human readable, and can serve as a developer + reference of what dependencies are being used. + * ``make install`` installs the package into the Spack repository, + where it may be used by other Spack packages. + * CMake-generated makefiles re-run CMake in some circumstances. Use + of ``spconfig.py`` breaks this behavior, requiring the developer + to manually re-run ``spconfig.py`` when a ``CMakeLists.txt`` file + has changed. + +CMakePackage +~~~~~~~~~~~~ + +In order ot enable ``spack setup`` functionality, the author of +``myproject/package.py`` must subclass from ``CMakePackage`` instead +of the standard ``Package`` superclass. Because CMake is +standardized, the packager does not need to tell Spack how to run +``cmake; make; make install``. Instead the packager only needs to +create (optional) methods ``configure_args()`` and ``configure_env()``, which +provide the arguments (as a list) and extra environment variables (as +a dict) to provide to the ``cmake`` command. Usually, these will +translate variant flags into CMake definitions. For example: + +.. code-block:: python + + def configure_args(self): + spec = self.spec + return [ + '-DUSE_EVERYTRACE=%s' % ('YES' if '+everytrace' in spec else 'NO'), + '-DBUILD_PYTHON=%s' % ('YES' if '+python' in spec else 'NO'), + '-DBUILD_GRIDGEN=%s' % ('YES' if '+gridgen' in spec else 'NO'), + '-DBUILD_COUPLER=%s' % ('YES' if '+coupler' in spec else 'NO'), + '-DUSE_PISM=%s' % ('YES' if '+pism' in spec else 'NO')] + +If needed, a packager may also override methods defined in +``StagedPackage`` (see below). + + +StagedPackage +~~~~~~~~~~~~~ + +``CMakePackage`` is implemented by subclassing the ``StagedPackage`` +superclass, which breaks down the standard ``Package.install()`` +method into several sub-stages: ``setup``, ``configure``, ``build`` +and ``install``. Details: + +* Instead of implementing the standard ``install()`` method, package + authors implement the methods for the sub-stages + ``install_setup()``, ``install_configure()``, + ``install_build()``, and ``install_install()``. + +* The ``spack install`` command runs the sub-stages ``configure``, + ``build`` and ``install`` in order. (The ``setup`` stage is + not run by default; see below). +* The ``spack setup`` command runs the sub-stages ``setup`` + and a dummy install (to create the module file). +* The sub-stage install methods take no arguments (other than + ``self``). The arguments ``spec`` and ``prefix`` to the standard + ``install()`` method may be accessed via ``self.spec`` and + ``self.prefix``. + +GNU Autotools +~~~~~~~~~~~~~ + +The ``setup`` functionality is currently only available for +CMake-based packages. Extending this functionality to GNU +Autotools-based packages would be easy (and should be done by a +developer who actively uses Autotools). Packages that use +non-standard build systems can gain ``setup`` functionality by +subclassing ``StagedPackage`` directly. diff --git a/lib/spack/spack/__init__.py b/lib/spack/spack/__init__.py index 75ddca1abc..20c9934704 100644 --- a/lib/spack/spack/__init__.py +++ b/lib/spack/spack/__init__.py @@ -48,6 +48,10 @@ var_path = join_path(spack_root, "var", "spack") stage_path = join_path(var_path, "stage") repos_path = join_path(var_path, "repos") share_path = join_path(spack_root, "share", "spack") +cache_path = join_path(var_path, "cache") + +import spack.fetch_strategy +cache = spack.fetch_strategy.FsCache(cache_path) prefix = spack_root opt_path = join_path(prefix, "opt") @@ -172,8 +176,10 @@ sys_type = None # TODO: it's not clear where all the stuff that needs to be included in packages # should live. This file is overloaded for spack core vs. for packages. # -__all__ = ['Package', 'Version', 'when', 'ver'] +__all__ = ['Package', 'StagedPackage', 'CMakePackage', \ + 'Version', 'when', 'ver'] from spack.package import Package, ExtensionConflictError +from spack.package import StagedPackage, CMakePackage from spack.version import Version, ver from spack.multimethod import when diff --git a/lib/spack/spack/build_environment.py b/lib/spack/spack/build_environment.py index 99c4cae020..fe5186a7d7 100644 --- a/lib/spack/spack/build_environment.py +++ b/lib/spack/spack/build_environment.py @@ -224,9 +224,12 @@ def set_compiler_environment_variables(pkg, env): return env -def set_build_environment_variables(pkg, env): +def set_build_environment_variables(pkg, env, dirty=False): """ - This ensures a clean install environment when we build packages + This ensures a clean install environment when we build packages. + + Arguments: + dirty -- skip unsetting the user's environment settings. """ # Add spack build environment path with compiler wrappers first in # the path. We add both spack.env_path, which includes default @@ -262,12 +265,26 @@ def set_build_environment_variables(pkg, env): # Install root prefix env.set(SPACK_INSTALL, spack.install_path) - # Remove these vars from the environment during build because they - # can affect how some packages find libraries. We want to make - # sure that builds never pull in unintended external dependencies. - env.unset('LD_LIBRARY_PATH') - env.unset('LD_RUN_PATH') - env.unset('DYLD_LIBRARY_PATH') + # Stuff in here sanitizes the build environemnt to eliminate + # anything the user has set that may interfere. + if not dirty: + # Remove these vars from the environment during build because they + # can affect how some packages find libraries. We want to make + # sure that builds never pull in unintended external dependencies. + env.unset('LD_LIBRARY_PATH') + env.unset('LIBRARY_PATH') + env.unset('CPATH') + env.unset('LD_RUN_PATH') + env.unset('DYLD_LIBRARY_PATH') + + # Remove any macports installs from the PATH. The macports ld can + # cause conflicts with the built-in linker on el capitan. Solves + # assembler issues, e.g.: + # suffix or operands invalid for `movq'" + path = get_path('PATH') + for p in path: + if '/macports/' in p: + env.remove_path('PATH', p) # Add bin directories from dependencies to the PATH for the build. bin_dirs = reversed( @@ -405,7 +422,7 @@ def load_external_modules(pkg): load_module(dep.external_module) -def setup_package(pkg): +def setup_package(pkg, dirty=False): """Execute all environment setup routines.""" spack_env = EnvironmentModifications() run_env = EnvironmentModifications() @@ -428,7 +445,7 @@ def setup_package(pkg): s.package.spec = s set_compiler_environment_variables(pkg, spack_env) - set_build_environment_variables(pkg, spack_env) + set_build_environment_variables(pkg, spack_env, dirty) load_external_modules(pkg) # traverse in postorder so package can use vars from its dependencies spec = pkg.spec @@ -457,7 +474,7 @@ def setup_package(pkg): spack_env.apply_modifications() -def fork(pkg, function): +def fork(pkg, function, dirty=False): """Fork a child process to do part of a spack build. Arguments: @@ -465,6 +482,7 @@ def fork(pkg, function): pkg -- pkg whose environemnt we should set up the forked process for. function -- arg-less function to run in the child process. + dirty -- If True, do NOT clean the environment before building. Usage: def child_fun(): @@ -488,7 +506,7 @@ def fork(pkg, function): if pid == 0: # Give the child process the package's build environment. - setup_package(pkg) + setup_package(pkg, dirty=dirty) try: # call the forked function. diff --git a/lib/spack/spack/cmd/create.py b/lib/spack/spack/cmd/create.py index 8cbb367f86..f5f234d7a7 100644 --- a/lib/spack/spack/cmd/create.py +++ b/lib/spack/spack/cmd/create.py @@ -95,9 +95,9 @@ class ${class_name}(Package): url = "${url}" ${versions} -${extends} - # FIXME: Add dependencies if this package requires them. - # depends_on("foo") + + # FIXME: Add additional dependencies if required. + ${dependencies} def install(self, spec, prefix): ${install} @@ -136,8 +136,18 @@ def setup_parser(subparser): class ConfigureGuesser(object): def __call__(self, stage): """Try to guess the type of build system used by the project. - Set the appropriate default installation instructions and any - necessary extensions for Python and R.""" + Set any necessary build dependencies or extensions. + Set the appropriate default installation instructions.""" + + # Build dependencies and extensions + dependenciesDict = { + 'autotools': "# depends_on('foo')", + 'cmake': "depends_on('cmake')", + 'scons': "depends_on('scons')", + 'python': "extends('python')", + 'R': "extends('R')", + 'unknown': "# depends_on('foo')" + } # Default installation instructions installDict = { @@ -214,16 +224,12 @@ class ConfigureGuesser(object): self.build_system = build_system + # Set any necessary build dependencies or extensions. + self.dependencies = dependenciesDict[build_system] + # Set the appropriate default installation instructions self.install = installDict[build_system] - # Set any necessary extensions for Python and R - extensions = '' - if build_system in ['python', 'R']: - extensions = "\n extends('{0}')\n".format(build_system) - - self.extends = extensions - def guess_name_and_version(url, args): # Try to deduce name and version of the new package from the URL @@ -361,7 +367,7 @@ def create(parser, args): class_name=mod_to_class(name), url=url, versions=make_version_calls(ver_hash_tuples), - extends=guesser.extends, + dependencies=guesser.dependencies, install=guesser.install)) # If everything checks out, go ahead and edit. diff --git a/lib/spack/spack/cmd/install.py b/lib/spack/spack/cmd/install.py index 9d3175786b..3133e080d7 100644 --- a/lib/spack/spack/cmd/install.py +++ b/lib/spack/spack/cmd/install.py @@ -54,6 +54,9 @@ def setup_parser(subparser): '--fake', action='store_true', dest='fake', help="Fake install. Just remove the prefix and touch a fake file in it.") subparser.add_argument( + '--dirty', action='store_true', dest='dirty', + help="Install a package *without* cleaning the environment.") + subparser.add_argument( 'packages', nargs=argparse.REMAINDER, help="specs of packages to install") @@ -79,4 +82,5 @@ def install(parser, args): make_jobs=args.jobs, verbose=args.verbose, fake=args.fake, + dirty=args.dirty, explicit=True) diff --git a/lib/spack/spack/cmd/load.py b/lib/spack/spack/cmd/load.py index 54cf01eb43..205abbb6b3 100644 --- a/lib/spack/spack/cmd/load.py +++ b/lib/spack/spack/cmd/load.py @@ -31,7 +31,7 @@ def setup_parser(subparser): """Parser is only constructed so that this prints a nice help message with -h. """ subparser.add_argument( - 'spec', nargs=argparse.REMAINDER, help='Spec of package to load with modules.') + 'spec', nargs=argparse.REMAINDER, help="Spec of package to load with modules. (If -, read specs from STDIN)") def load(parser, args): diff --git a/lib/spack/spack/cmd/module.py b/lib/spack/spack/cmd/module.py index 5292d42225..70da689b67 100644 --- a/lib/spack/spack/cmd/module.py +++ b/lib/spack/spack/cmd/module.py @@ -22,6 +22,7 @@ # 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 __future__ import print_function import os import shutil import sys @@ -41,46 +42,98 @@ def setup_parser(subparser): sp.add_parser('refresh', help='Regenerate all module files.') find_parser = sp.add_parser('find', help='Find module files for packages.') - find_parser.add_argument('module_type', - help="Type of module to find file for. [" + - '|'.join(module_types) + "]") - find_parser.add_argument('spec', - nargs='+', - help='spec to find a module file for.') + find_parser.add_argument( + 'module_type', + help="Type of module to find file for. [" + + '|'.join(module_types) + "]") -def module_find(mtype, spec_array): + find_parser.add_argument( + '-r', '--dependencies', action='store_true', + dest='recurse_dependencies', + help='Recursively traverse dependencies for modules to load.') + + find_parser.add_argument( + '-s', '--shell', action='store_true', dest='shell', + help='Generate shell script (instead of input for module command)') + + find_parser.add_argument( + '-p', '--prefix', dest='prefix', + help='Prepend to module names when issuing module load commands') + + find_parser.add_argument( + 'spec', nargs='+', + help='spec to find a module file for.') + + +def module_find(mtype, flags, spec_array): """Look at all installed packages and see if the spec provided matches any. If it does, check whether there is a module file of type <mtype> there, and print out the name that the user should type to use that package's module. + prefix: + Prepend this to module names when issuing "module load" commands. + Some systems seem to need it. """ if mtype not in module_types: tty.die("Invalid module type: '%s'. Options are %s" % (mtype, comma_or(module_types))) - specs = spack.cmd.parse_specs(spec_array) - if len(specs) > 1: - tty.die("You can only pass one spec.") - spec = specs[0] - - specs = spack.installed_db.query(spec) - if len(specs) == 0: - tty.die("No installed packages match spec %s" % spec) - - if len(specs) > 1: - tty.error("Multiple matches for spec %s. Choose one:" % spec) - for s in specs: - sys.stderr.write(s.tree(color=True)) - sys.exit(1) - - mt = module_types[mtype] - mod = mt(specs[0]) - if not os.path.isfile(mod.file_name): - tty.die("No %s module is installed for %s" % (mtype, spec)) - - print(mod.use_name) - + # -------------------------------------- + def _find_modules(spec, modules_list): + """Finds all modules and sub-modules for a spec""" + if str(spec.version) == 'system': + # No Spack module for system-installed packages + return + + if flags.recurse_dependencies: + for dep in spec.dependencies.values(): + _find_modules(dep, modules_list) + + mod = module_types[mtype](spec) + if not os.path.isfile(mod.file_name): + tty.die("No %s module is installed for %s" % (mtype, spec)) + modules_list.append((spec, mod)) + + + # -------------------------------------- + raw_specs = spack.cmd.parse_specs(spec_array) + modules = set() # Modules we will load + seen = set() + for raw_spec in raw_specs: + + # ----------- Make sure the spec only resolves to ONE thing + specs = spack.installed_db.query(raw_spec) + if len(specs) == 0: + tty.die("No installed packages match spec %s" % raw_spec) + + if len(specs) > 1: + tty.error("Multiple matches for spec %s. Choose one:" % raw_spec) + for s in specs: + sys.stderr.write(s.tree(color=True)) + sys.exit(1) + spec = specs[0] + + # ----------- Chase down modules for it and all its dependencies + modules_dups = list() + _find_modules(spec, modules_dups) + + # Remove duplicates while keeping order + modules_unique = list() + for spec,mod in modules_dups: + if mod.use_name not in seen: + modules_unique.append((spec,mod)) + seen.add(mod.use_name) + + # Output... + if flags.shell: + module_cmd = {'tcl': 'module load', 'dotkit': 'dotkit use'}[mtype] + for spec,mod in modules_unique: + if flags.shell: + print('# %s' % spec.format()) + print('%s %s%s' % (module_cmd, flags.prefix, mod.use_name)) + else: + print(mod.use_name) def module_refresh(): """Regenerate all module files for installed packages known to @@ -101,4 +154,4 @@ def module(parser, args): module_refresh() elif args.module_command == 'find': - module_find(args.module_type, args.spec) + module_find(args.module_type, args, args.spec) diff --git a/lib/spack/spack/cmd/purge.py b/lib/spack/spack/cmd/purge.py index 7b33ef7f69..f4e27a3969 100644 --- a/lib/spack/spack/cmd/purge.py +++ b/lib/spack/spack/cmd/purge.py @@ -22,9 +22,31 @@ # License along with this program; if not, write to the Free Software # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## +import spack import spack.stage as stage -description = "Remove all temporary build files and downloaded archives" +description = "Remove temporary build files and/or downloaded archives" + + +def setup_parser(subparser): + subparser.add_argument( + '-s', '--stage', action='store_true', default=True, + help="Remove all temporary build stages (default).") + subparser.add_argument( + '-c', '--cache', action='store_true', help="Remove cached downloads.") + subparser.add_argument( + '-a', '--all', action='store_true', + help="Remove all of the above.") + def purge(parser, args): - stage.purge() + # Special case: no flags. + if not any((args.stage, args.cache, args.all)): + stage.purge() + return + + # handle other flags with fall through. + if args.stage or args.all: + stage.purge() + if args.cache or args.all: + spack.cache.destroy() diff --git a/lib/spack/spack/cmd/setup.py b/lib/spack/spack/cmd/setup.py new file mode 100644 index 0000000000..02e9bfd281 --- /dev/null +++ b/lib/spack/spack/cmd/setup.py @@ -0,0 +1,91 @@ +############################################################################## +# Copyright (c) 2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Written by Elizabeth Fischer +# 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 +############################################################################## +import sys +import os +import argparse + +import llnl.util.tty as tty + +import spack +import spack.cmd +from spack.cmd.edit import edit_package +from spack.stage import DIYStage + +description = "Create a configuration script and module, but don't build." + +def setup_parser(subparser): + subparser.add_argument( + '-i', '--ignore-dependencies', action='store_true', dest='ignore_deps', + help="Do not try to install dependencies of requested packages.") + subparser.add_argument( + '-v', '--verbose', action='store_true', dest='verbose', + help="Display verbose build output while installing.") + subparser.add_argument( + 'spec', nargs=argparse.REMAINDER, + help="specs to use for install. Must contain package AND verison.") + + +def setup(self, args): + if not args.spec: + tty.die("spack setup requires a package spec argument.") + + specs = spack.cmd.parse_specs(args.spec) + if len(specs) > 1: + tty.die("spack setup only takes one spec.") + + # Take a write lock before checking for existence. + with spack.installed_db.write_transaction(): + spec = specs[0] + if not spack.repo.exists(spec.name): + tty.warn("No such package: %s" % spec.name) + create = tty.get_yes_or_no("Create this package?", default=False) + if not create: + tty.msg("Exiting without creating.") + sys.exit(1) + else: + tty.msg("Running 'spack edit -f %s'" % spec.name) + edit_package(spec.name, spack.repo.first_repo(), None, True) + return + + if not spec.versions.concrete: + tty.die("spack setup spec must have a single, concrete version. Did you forget a package version number?") + + spec.concretize() + package = spack.repo.get(spec) + + # It's OK if the package is already installed. + + # Forces the build to run out of the current directory. + package.stage = DIYStage(os.getcwd()) + + # TODO: make this an argument, not a global. + spack.do_checksum = False + + package.do_install( + keep_prefix=True, # Don't remove install directory, even if you think you should + ignore_deps=args.ignore_deps, + verbose=args.verbose, + keep_stage=True, # don't remove source dir for SETUP. + install_phases = set(['setup', 'provenance'])) diff --git a/lib/spack/spack/cmd/test.py b/lib/spack/spack/cmd/test.py index cb9dd26c71..36810321ef 100644 --- a/lib/spack/spack/cmd/test.py +++ b/lib/spack/spack/cmd/test.py @@ -31,6 +31,7 @@ from llnl.util.lang import list_modules import spack import spack.test +from spack.fetch_strategy import FetchError description ="Run unit tests" @@ -50,6 +51,24 @@ def setup_parser(subparser): help="verbose output") +class MockCache(object): + def store(self, copyCmd, relativeDst): + pass + + def fetcher(self, targetPath, digest): + return MockCacheFetcher() + + +class MockCacheFetcher(object): + def set_stage(self, stage): + pass + + def fetch(self): + raise FetchError("Mock cache always fails for tests") + + def __str__(self): + return "[mock fetcher]" + def test(parser, args): if args.list: print "Available tests:" @@ -66,4 +85,5 @@ def test(parser, args): if not os.path.exists(outputDir): mkdirp(outputDir) + spack.cache = MockCache() spack.test.run(args.names, outputDir, args.verbose) diff --git a/lib/spack/spack/fetch_strategy.py b/lib/spack/spack/fetch_strategy.py index 1953d7c1b3..38133ee0ca 100644 --- a/lib/spack/spack/fetch_strategy.py +++ b/lib/spack/spack/fetch_strategy.py @@ -307,10 +307,7 @@ class URLFetchStrategy(FetchStrategy): if not self.archive_file: raise NoArchiveFileError("Cannot call archive() before fetching.") - if not extension(destination) == extension(self.archive_file): - raise ValueError("Cannot archive without matching extensions.") - - shutil.move(self.archive_file, destination) + shutil.copy(self.archive_file, destination) @_needs_stage def check(self): @@ -348,7 +345,7 @@ class URLFetchStrategy(FetchStrategy): def __repr__(self): url = self.url if self.url else "no url" - return "URLFetchStrategy<%s>" % url + return "%s<%s>" % (self.__class__.__name__, url) def __str__(self): if self.url: @@ -357,6 +354,24 @@ class URLFetchStrategy(FetchStrategy): return "[no url]" +class CacheURLFetchStrategy(URLFetchStrategy): + """The resource associated with a cache URL may be out of date.""" + def __init__(self, *args, **kwargs): + super(CacheURLFetchStrategy, self).__init__(*args, **kwargs) + + @_needs_stage + def fetch(self): + super(CacheURLFetchStrategy, self).fetch() + if self.digest: + try: + self.check() + except ChecksumError: + # Future fetchers will assume they don't need to download if the + # file remains + os.remove(self.archive_file) + raise + + class VCSFetchStrategy(FetchStrategy): def __init__(self, name, *rev_types, **kwargs): @@ -815,6 +830,35 @@ def for_package_version(pkg, version): raise InvalidArgsError(pkg, version) +class FsCache(object): + def __init__(self, root): + self.root = os.path.abspath(root) + + def store(self, fetcher, relativeDst): + unique = False + uidGroups = [['tag', 'commit'], ['digest'], ['revision']] + for grp in uidGroups: + try: + unique |= any(getattr(fetcher, x) for x in grp) + except AttributeError: + pass + if unique: + break + if not unique: + return + + dst = join_path(self.root, relativeDst) + mkdirp(os.path.dirname(dst)) + fetcher.archive(dst) + + def fetcher(self, targetPath, digest): + url = "file://" + join_path(self.root, targetPath) + return CacheURLFetchStrategy(url, digest) + + def destroy(self): + shutil.rmtree(self.root, ignore_errors=True) + + class FetchError(spack.error.SpackError): def __init__(self, msg, long_msg=None): diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py index 6a61b3d52b..84bd99df54 100644 --- a/lib/spack/spack/package.py +++ b/lib/spack/spack/package.py @@ -37,6 +37,8 @@ import os import re import textwrap import time +import glob +import string import llnl.util.tty as tty import spack @@ -50,6 +52,8 @@ import spack.mirror import spack.repository import spack.url import spack.util.web + +from urlparse import urlparse from StringIO import StringIO from llnl.util.filesystem import * from llnl.util.lang import * @@ -58,9 +62,11 @@ from llnl.util.tty.log import log_output from spack.stage import Stage, ResourceStage, StageComposite from spack.util.compression import allowed_archive from spack.util.environment import dump_environment -from spack.util.executable import ProcessError +from spack.util.executable import ProcessError, Executable, which from spack.version import * +from spack import directory_layout from urlparse import urlparse + """Allowed URL schemes for spack packages.""" _ALLOWED_URL_SCHEMES = ["http", "https", "ftp", "file", "git"] @@ -748,6 +754,9 @@ class Package(object): if spack.do_checksum and self.version in self.versions: self.stage.check() + self.stage.cache_local() + + def do_stage(self, mirror_only=False): """Unpacks the fetched tarball, then changes into the expanded tarball directory.""" @@ -864,6 +873,7 @@ class Package(object): resource_stage_folder = '-'.join(pieces) return resource_stage_folder + install_phases = set(['configure', 'build', 'install', 'provenance']) def do_install(self, keep_prefix=False, keep_stage=False, @@ -872,7 +882,9 @@ class Package(object): verbose=False, make_jobs=None, fake=False, - explicit=False): + explicit=False, + dirty=False, + install_phases = install_phases): """Called by commands to install a package and its dependencies. Package implementations should override install() to describe @@ -888,6 +900,7 @@ class Package(object): fake -- Don't really build -- install fake stub files instead. skip_patch -- Skip patch stage of build if True. verbose -- Display verbose build output (by default, suppresses it) + dirty -- Don't clean the build environment before installing. make_jobs -- Number of make jobs to use for install. Default is ncpus """ if not self.spec.concrete: @@ -900,7 +913,7 @@ class Package(object): return # Ensure package is not already installed - if spack.install_layout.check_installed(self.spec): + if 'install' in install_phases and spack.install_layout.check_installed(self.spec): tty.msg("%s is already installed in %s" % (self.name, self.prefix)) rec = spack.installed_db.get_record(self.spec) if (not rec.explicit) and explicit: @@ -939,6 +952,10 @@ class Package(object): tty.msg("Building %s" % self.name) self.stage.keep = keep_stage + self.install_phases = install_phases + self.build_directory = join_path(self.stage.path, 'spack-build') + self.source_directory = self.stage.source_path + with self.stage: # Run the pre-install hook in the child process after # the directory is created. @@ -970,19 +987,29 @@ class Package(object): raise e # Ensure that something was actually installed. - self.sanity_check_prefix() + if 'install' in self.install_phases: + self.sanity_check_prefix() - # Copy provenance into the install directory on success - log_install_path = spack.install_layout.build_log_path( - self.spec) - env_install_path = spack.install_layout.build_env_path( - self.spec) - packages_dir = spack.install_layout.build_packages_path( - self.spec) - install(log_path, log_install_path) - install(env_path, env_install_path) - dump_packages(self.spec, packages_dir) + # Copy provenance into the install directory on success + if 'provenance' in self.install_phases: + log_install_path = spack.install_layout.build_log_path( + self.spec) + env_install_path = spack.install_layout.build_env_path( + self.spec) + packages_dir = spack.install_layout.build_packages_path( + self.spec) + + # Remove first if we're overwriting another build + # (can happen with spack setup) + try: + shutil.rmtree(packages_dir) # log_install_path and env_install_path are inside this + except: + pass + + install(log_path, log_install_path) + 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) @@ -1000,7 +1027,19 @@ class Package(object): try: # Create the install prefix and fork the build process. spack.install_layout.create_install_directory(self.spec) - spack.build_environment.fork(self, build_process) + except directory_layout.InstallDirectoryAlreadyExistsError: + if 'install' in install_phases: + # Abort install if install directory exists. + # But do NOT remove it (you'd be overwriting someon else's stuff) + tty.warn("Keeping existing install prefix in place.") + raise + else: + # We're not installing anyway, so don't worry if someone + # else has already written in the install directory + pass + + try: + spack.build_environment.fork(self, build_process, dirty=dirty) except: # remove the install prefix if anything went wrong during install. if not keep_prefix: @@ -1010,7 +1049,7 @@ class Package(object): "Spack will think this package is installed. " + "Manually remove this directory to fix:", self.prefix, - wrap=True) + wrap=False) raise # note: PARENT of the build process adds the new package to @@ -1482,6 +1521,152 @@ def _hms(seconds): parts.append("%.2fs" % s) return ' '.join(parts) +class StagedPackage(Package): + """A Package subclass where the install() is split up into stages.""" + + def install_setup(self): + """Creates an spack_setup.py script to configure the package later if we like.""" + raise InstallError("Package %s provides no install_setup() method!" % self.name) + + def install_configure(self): + """Runs the configure process.""" + raise InstallError("Package %s provides no install_configure() method!" % self.name) + + def install_build(self): + """Runs the build process.""" + raise InstallError("Package %s provides no install_build() method!" % self.name) + + def install_install(self): + """Runs the install process.""" + raise InstallError("Package %s provides no install_install() method!" % self.name) + + def install(self, spec, prefix): + if 'setup' in self.install_phases: + self.install_setup() + + if 'configure' in self.install_phases: + self.install_configure() + + if 'build' in self.install_phases: + self.install_build() + + if 'install' in self.install_phases: + self.install_install() + else: + # Create a dummy file so the build doesn't fail. + # That way, the module file will also be created. + with open(os.path.join(prefix, 'dummy'), 'w') as fout: + pass + +# stackoverflow.com/questions/12791997/how-do-you-do-a-simple-chmod-x-from-within-python +def make_executable(path): + mode = os.stat(path).st_mode + mode |= (mode & 0o444) >> 2 # copy R bits to X + os.chmod(path, mode) + + + +class CMakePackage(StagedPackage): + + def make_make(self): + import multiprocessing + # number of jobs spack will to build with. + jobs = multiprocessing.cpu_count() + if not self.parallel: + jobs = 1 + elif self.make_jobs: + jobs = self.make_jobs + + make = spack.build_environment.MakeExecutable('make', jobs) + return make + + def configure_args(self): + """Returns package-specific arguments to be provided to the configure command.""" + return list() + + def configure_env(self): + """Returns package-specific environment under which the configure command should be run.""" + return dict() + + def spack_transitive_include_path(self): + return ';'.join( + os.path.join(dep, 'include') + for dep in os.environ['SPACK_DEPENDENCIES'].split(os.pathsep) + ) + + def install_setup(self): + cmd = [str(which('cmake'))] + \ + spack.build_environment.get_std_cmake_args(self) + \ + ['-DCMAKE_INSTALL_PREFIX=%s' % os.environ['SPACK_PREFIX'], + '-DCMAKE_C_COMPILER=%s' % os.environ['SPACK_CC'], + '-DCMAKE_CXX_COMPILER=%s' % os.environ['SPACK_CXX'], + '-DCMAKE_Fortran_COMPILER=%s' % os.environ['SPACK_FC']] + \ + self.configure_args() + + env = dict() + env['PATH'] = os.environ['PATH'] + env['SPACK_TRANSITIVE_INCLUDE_PATH'] = self.spack_transitive_include_path() + env['CMAKE_PREFIX_PATH'] = os.environ['CMAKE_PREFIX_PATH'] + + setup_fname = 'spconfig.py' + with open(setup_fname, 'w') as fout: + fout.write(\ +r"""#!%s +# + +import sys +import os +import subprocess + +def cmdlist(str): + return list(x.strip().replace("'",'') for x in str.split('\n') if x) +env = dict(os.environ) +""" % sys.executable) + + env_vars = sorted(list(env.keys())) + for name in env_vars: + val = env[name] + if string.find(name, 'PATH') < 0: + fout.write('env[%s] = %s\n' % (repr(name),repr(val))) + else: + if name == 'SPACK_TRANSITIVE_INCLUDE_PATH': + sep = ';' + else: + sep = ':' + + fout.write('env[%s] = "%s".join(cmdlist("""\n' % (repr(name),sep)) + for part in string.split(val, sep): + fout.write(' %s\n' % part) + fout.write('"""))\n') + + fout.write("env['CMAKE_TRANSITIVE_INCLUDE_PATH'] = env['SPACK_TRANSITIVE_INCLUDE_PATH'] # Deprecated\n") + fout.write('\ncmd = cmdlist("""\n') + fout.write('%s\n' % cmd[0]) + for arg in cmd[1:]: + fout.write(' %s\n' % arg) + fout.write('""") + sys.argv[1:]\n') + fout.write('\nproc = subprocess.Popen(cmd, env=env)\nproc.wait()\n') + make_executable(setup_fname) + + + def install_configure(self): + cmake = which('cmake') + with working_dir(self.build_directory, create=True): + os.environ.update(self.configure_env()) + os.environ['SPACK_TRANSITIVE_INCLUDE_PATH'] = self.spack_transitive_include_path() + options = self.configure_args() + spack.build_environment.get_std_cmake_args(self) + cmake(self.source_directory, *options) + + def install_build(self): + make = self.make_make() + with working_dir(self.build_directory, create=False): + make() + + def install_install(self): + make = self.make_make() + with working_dir(self.build_directory, create=False): + make('install') + class FetchError(spack.error.SpackError): """Raised when something goes wrong during fetch.""" diff --git a/lib/spack/spack/platforms/linux.py b/lib/spack/spack/platforms/linux.py index 4d8adac384..4d3f59c320 100644 --- a/lib/spack/spack/platforms/linux.py +++ b/lib/spack/spack/platforms/linux.py @@ -1,16 +1,23 @@ import subprocess +import platform from spack.architecture import Platform, Target from spack.operating_systems.linux_distro import LinuxDistro class Linux(Platform): priority = 90 - front_end = 'x86_64' - back_end = 'x86_64' - default = 'x86_64' def __init__(self): super(Linux, self).__init__('linux') - self.add_target(self.default, Target(self.default)) + self.add_target('x86_64', Target('x86_64')) + self.add_target('ppc64le', Target('ppc64le')) + + self.default = platform.machine() + self.front_end = platform.machine() + self.back_end = platform.machine() + + if self.default not in self.targets: + self.add_target(self.default, Target(self.default)) + linux_dist = LinuxDistro() self.default_os = str(linux_dist) self.front_os = self.default_os diff --git a/lib/spack/spack/stage.py b/lib/spack/spack/stage.py index a76ec168ad..b08cce43b8 100644 --- a/lib/spack/spack/stage.py +++ b/lib/spack/spack/stage.py @@ -304,6 +304,7 @@ class Stage(object): # Add URL strategies for all the mirrors with the digest for url in urls: fetchers.insert(0, fs.URLFetchStrategy(url, digest)) + fetchers.insert(0, spack.cache.fetcher(self.mirror_path, digest)) for fetcher in fetchers: try: @@ -320,6 +321,7 @@ class Stage(object): self.fetcher = self.default_fetcher raise fs.FetchError(errMessage, None) + def check(self): """Check the downloaded archive against a checksum digest. No-op if this stage checks code out of a repository.""" @@ -333,6 +335,11 @@ class Stage(object): else: self.fetcher.check() + + def cache_local(self): + spack.cache.store(self.fetcher, self.mirror_path) + + def expand_archive(self): """Changes to the stage directory and attempt to expand the downloaded archive. Fail if the stage is not set up or if the archive is not yet @@ -436,7 +443,7 @@ class ResourceStage(Stage): shutil.move(source_path, destination_path) -@pattern.composite(method_list=['fetch', 'create', 'check', 'expand_archive', 'restage', 'destroy']) +@pattern.composite(method_list=['fetch', 'create', 'check', 'expand_archive', 'restage', 'destroy', 'cache_local']) class StageComposite: """ Composite for Stage type objects. The first item in this composite is considered to be the root package, and @@ -511,6 +518,9 @@ class DIYStage(object): # No need to destroy DIY stage. pass + def cache_local(self): + tty.msg("Sources for DIY stages are not cached") + def _get_mirrors(): """Get mirrors from spack configuration.""" diff --git a/lib/spack/spack/test/mock_packages_test.py b/lib/spack/spack/test/mock_packages_test.py index e1acc32cb7..c8b06cd7d7 100644 --- a/lib/spack/spack/test/mock_packages_test.py +++ b/lib/spack/spack/test/mock_packages_test.py @@ -84,15 +84,6 @@ compilers: modules: 'None' - compiler: spec: clang@3.3 - operating_system: redhat6 - paths: - cc: /path/to/clang - cxx: /path/to/clang++ - f77: None - fc: None - modules: 'None' -- compiler: - spec: clang@3.3 operating_system: yosemite paths: cc: /path/to/clang @@ -124,15 +115,6 @@ compilers: cxx: /path/to/g++ f77: /path/to/gfortran fc: /path/to/gfortran - operating_system: redhat6 - spec: gcc@4.5.0 - modules: 'None' -- compiler: - paths: - cc: /path/to/gcc - cxx: /path/to/g++ - f77: /path/to/gfortran - fc: /path/to/gfortran operating_system: yosemite spec: gcc@4.5.0 modules: 'None' diff --git a/lib/spack/spack/test/versions.py b/lib/spack/spack/test/versions.py index 4624f901c8..a3a328fb14 100644 --- a/lib/spack/spack/test/versions.py +++ b/lib/spack/spack/test/versions.py @@ -389,3 +389,39 @@ class VersionsTest(unittest.TestCase): self.assertEqual(v.dotted, '1.2.3') self.assertEqual(v.dashed, '1-2-3') self.assertEqual(v.underscored, '1_2_3') + + def test_repr_and_str(self): + + def check_repr_and_str(vrs): + a = Version(vrs) + self.assertEqual(repr(a), 'Version(\'' + vrs + '\')') + b = eval(repr(a)) + self.assertEqual(a, b) + self.assertEqual(str(a), vrs) + self.assertEqual(str(a), str(b)) + + check_repr_and_str('1.2.3') + check_repr_and_str('R2016a') + check_repr_and_str('R2016a.2-3_4') + + def test_get_item(self): + a = Version('0.1_2-3') + self.assertTrue(isinstance(a[1], int)) + # Test slicing + b = a[0:2] + self.assertTrue(isinstance(b, Version)) + self.assertEqual(b, Version('0.1')) + self.assertEqual(repr(b), 'Version(\'0.1\')') + self.assertEqual(str(b), '0.1') + b = a[0:3] + self.assertTrue(isinstance(b, Version)) + self.assertEqual(b, Version('0.1_2')) + self.assertEqual(repr(b), 'Version(\'0.1_2\')') + self.assertEqual(str(b), '0.1_2') + b = a[1:] + self.assertTrue(isinstance(b, Version)) + self.assertEqual(b, Version('1_2-3')) + self.assertEqual(repr(b), 'Version(\'1_2-3\')') + self.assertEqual(str(b), '1_2-3') + # Raise TypeError on tuples + self.assertRaises(TypeError, b.__getitem__, 1, 2) diff --git a/lib/spack/spack/version.py b/lib/spack/spack/version.py index 858d581472..6839643941 100644 --- a/lib/spack/spack/version.py +++ b/lib/spack/spack/version.py @@ -44,6 +44,7 @@ be called on any of the types:: concrete """ import re +import numbers from bisect import bisect_left from functools import wraps @@ -194,10 +195,24 @@ class Version(object): return iter(self.version) def __getitem__(self, idx): - return tuple(self.version[idx]) + cls = type(self) + if isinstance(idx, numbers.Integral): + return self.version[idx] + elif isinstance(idx, slice): + # Currently len(self.separators) == len(self.version) - 1 + extendend_separators = self.separators + ('',) + string_arg = [] + for token, sep in zip(self.version, extendend_separators)[idx]: + string_arg.append(str(token)) + string_arg.append(str(sep)) + string_arg.pop() # We don't need the last separator + string_arg = ''.join(string_arg) + return cls(string_arg) + message = '{cls.__name__} indices must be integers' + raise TypeError(message.format(cls=cls)) def __repr__(self): - return self.string + return 'Version(' + repr(self.string) + ')' def __str__(self): return self.string diff --git a/var/spack/repos/builtin/packages/arpack-ng/make_install.patch b/var/spack/repos/builtin/packages/arpack-ng/make_install.patch new file mode 100644 index 0000000000..ad5cffcc19 --- /dev/null +++ b/var/spack/repos/builtin/packages/arpack-ng/make_install.patch @@ -0,0 +1,24 @@ +diff --git a/CMakeLists.txt b/CMakeLists.txt +index 607d221..50426c3 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -389,3 +389,19 @@ target_link_libraries(bug_1323 arpack ${BLAS_LIBRARIES} ${LAPACK_LIBRARIES}) + add_test(bug_1323 Tests/bug_1323) + + add_dependencies(check dnsimp_test bug_1315_single bug_1315_double bug_1323) ++ ++############################ ++# install ++############################ ++# 'make install' to the correct location ++install(TARGETS arpack ++ ARCHIVE DESTINATION lib ++ LIBRARY DESTINATION lib ++ RUNTIME DESTINATION bin) ++ ++if (MPI) ++ install(TARGETS parpack ++ ARCHIVE DESTINATION lib ++ LIBRARY DESTINATION lib ++ RUNTIME DESTINATION bin) ++endif () diff --git a/var/spack/repos/builtin/packages/arpack-ng/package.py b/var/spack/repos/builtin/packages/arpack-ng/package.py index fcd5171a7d..d9021f8043 100644 --- a/var/spack/repos/builtin/packages/arpack-ng/package.py +++ b/var/spack/repos/builtin/packages/arpack-ng/package.py @@ -27,7 +27,8 @@ from spack import * class ArpackNg(Package): """ - ARPACK-NG is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems. + ARPACK-NG is a collection of Fortran77 subroutines designed to solve large + scale eigenvalue problems. Important Features: @@ -38,43 +39,76 @@ class ArpackNg(Package): Generalized Problems. * Routines for Banded Matrices - Standard or Generalized Problems. * Routines for The Singular Value Decomposition. - * Example driver routines that may be used as templates to implement numerous - Shift-Invert strategies for all problem types, data types and precision. + * Example driver routines that may be used as templates to implement + numerous Shift-Invert strategies for all problem types, data types and + precision. - This project is a joint project between Debian, Octave and Scilab in order to - provide a common and maintained version of arpack. + This project is a joint project between Debian, Octave and Scilab in order + to provide a common and maintained version of arpack. - Indeed, no single release has been published by Rice university for the last - few years and since many software (Octave, Scilab, R, Matlab...) forked it and - implemented their own modifications, arpack-ng aims to tackle this by providing - a common repository and maintained versions. + Indeed, no single release has been published by Rice university for the + last few years and since many software (Octave, Scilab, R, Matlab...) + forked it and implemented their own modifications, arpack-ng aims to tackle + this by providing a common repository and maintained versions. arpack-ng is replacing arpack almost everywhere. """ homepage = 'https://github.com/opencollab/arpack-ng' url = 'https://github.com/opencollab/arpack-ng/archive/3.3.0.tar.gz' + version('3.4.0', 'ae9ca13f2143a7ea280cb0e2fd4bfae4') version('3.3.0', 'ed3648a23f0a868a43ef44c97a21bad5') variant('shared', default=True, description='Enables the build of shared libraries') variant('mpi', default=False, description='Activates MPI support') - # The function pdlamch10 does not set the return variable. This is fixed upstream + # The function pdlamch10 does not set the return variable. + # This is fixed upstream # see https://github.com/opencollab/arpack-ng/issues/34 - patch('pdlamch10.patch', when='@3.3:') + patch('pdlamch10.patch', when='@3.3.0') + + patch('make_install.patch', when='@3.4.0') + patch('parpack_cmake.patch', when='@3.4.0') depends_on('blas') depends_on('lapack') - depends_on('automake') - depends_on('autoconf') - depends_on('libtool@2.4.2:') + depends_on('automake', when='@3.3.0') + depends_on('autoconf', when='@3.3.0') + depends_on('libtool@2.4.2:', when='@3.3.0') + depends_on('cmake@2.8.6:', when='@3.4.0:') depends_on('mpi', when='+mpi') + @when('@3.4.0:') + def install(self, spec, prefix): + + options = ['-DEXAMPLES=ON'] + options.extend(std_cmake_args) + options.append('-DCMAKE_INSTALL_NAME_DIR:PATH=%s/lib' % prefix) + + # TODO: + # Arpack calls directly find_package(BLAS REQUIRED) and + # find_package(LAPACK REQUIRED). Make sure correct Blas/Lapack are + # picked up. + + if '+mpi' in spec: + options.append('-DMPI=ON') + + # TODO: -DINTERFACE64=ON + + if '+shared' in spec: + options.append('-DBUILD_SHARED_LIBS=ON') + + cmake('.', *options) + make() + # TODO: make test does not work + # make('test') + + make('install') + + @when('@3.3.0') 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') @@ -83,7 +117,7 @@ class ArpackNg(Package): if '+mpi' in spec: options.extend([ '--enable-mpi', - 'F77=mpif77' #FIXME: avoid hardcoding MPI wrapper names + 'F77=%s' % spec['mpi'].mpif77 ]) if '~shared' in spec: diff --git a/var/spack/repos/builtin/packages/arpack-ng/parpack_cmake.patch b/var/spack/repos/builtin/packages/arpack-ng/parpack_cmake.patch new file mode 100644 index 0000000000..9b11bea6ac --- /dev/null +++ b/var/spack/repos/builtin/packages/arpack-ng/parpack_cmake.patch @@ -0,0 +1,18 @@ +diff --git a/CMakeLists.txt b/CMakeLists.txt +index 607d221..345b7fc 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -113,11 +113,12 @@ set_target_properties(arpack PROPERTIES OUTPUT_NAME arpack${LIBSUFFIX}) + + if (MPI) + # add_library(parpack SHARED +- add_library(parpack ++ add_library(parpack + ${parpacksrc_STAT_SRCS} + ${parpackutil_STAT_SRCS}) + + target_link_libraries(parpack ${MPI_Fortran_LIBRARIES}) ++ target_link_libraries(parpack arpack) + set_target_properties(parpack PROPERTIES OUTPUT_NAME parpack${LIBSUFFIX}) + endif () + diff --git a/var/spack/repos/builtin/packages/dealii/package.py b/var/spack/repos/builtin/packages/dealii/package.py index 23ec74abed..068dbec10a 100644 --- a/var/spack/repos/builtin/packages/dealii/package.py +++ b/var/spack/repos/builtin/packages/dealii/package.py @@ -245,7 +245,7 @@ class Dealii(Package): # change Linear Algebra to Trilinos # The below filter_file should be different for versions # before and after 8.4.0 - if spec.satisfies('@8.4.0:'): + if spec.satisfies('@8.4.0:') or spec.satisfies('@dev'): filter_file(r'(\/\/ #define FORCE_USE_OF_TRILINOS.*)', ('#define FORCE_USE_OF_TRILINOS'), 'step-40.cc') else: @@ -257,7 +257,7 @@ class Dealii(Package): # the rest of the tests on step 40 only works for # dealii version 8.4.0 and after - if spec.satisfies('@8.4.0:'): + if spec.satisfies('@8.4.0:') or spec.satisfies('@dev'): print('=====================================') print('=== Step-40 Trilinos SuperluDist ====') print('=====================================') diff --git a/var/spack/repos/builtin/packages/eigen/package.py b/var/spack/repos/builtin/packages/eigen/package.py index e20fcffdd7..9ff4107619 100644 --- a/var/spack/repos/builtin/packages/eigen/package.py +++ b/var/spack/repos/builtin/packages/eigen/package.py @@ -28,7 +28,9 @@ from spack import * class Eigen(Package): """ - Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms + Eigen is a C++ template library for linear algebra + + Matrices, vectors, numerical solvers, and related algorithms """ homepage = 'http://eigen.tuxfamily.org/' @@ -42,16 +44,16 @@ class Eigen(Package): variant('scotch', default=True, description='Enables scotch backend') variant('fftw', default=True, description='Enables FFTW backend') variant('suitesparse', default=True, description='Enables SuiteSparse support') + variant('mpfr', default=True, description='Enables support for multi-precisions floating points via mpfr') # TODO : dependency on googlehash, superlu, adolc missing - depends_on('cmake') depends_on('metis@5:', when='+metis') depends_on('scotch', when='+scotch') depends_on('fftw', when='+fftw') depends_on('suite-sparse', when='+suitesparse') - depends_on('mpfr@2.3.0:') # Eigen 3.2.7 requires at least 2.3.0 - depends_on('gmp') + depends_on('mpfr@2.3.0:', when="+mpfr") + depends_on('gmp', when="+mpfr") def install(self, spec, prefix): diff --git a/var/spack/repos/builtin/packages/fenics/package.py b/var/spack/repos/builtin/packages/fenics/package.py index 0845237656..465ab651be 100644 --- a/var/spack/repos/builtin/packages/fenics/package.py +++ b/var/spack/repos/builtin/packages/fenics/package.py @@ -57,6 +57,9 @@ class Fenics(Package): # variant('slepc4py', default=True, description='Uses SLEPc4py') # variant('pastix', default=True, description='Compile with Pastix') + patch('petsc-3.7.patch', when='^petsc@3.7:') + patch('petsc-version-detection.patch', when='@:1.6.1') + extends('python') depends_on('py-numpy') diff --git a/var/spack/repos/builtin/packages/fenics/petsc-3.7.patch b/var/spack/repos/builtin/packages/fenics/petsc-3.7.patch new file mode 100644 index 0000000000..c1ba5c4da6 --- /dev/null +++ b/var/spack/repos/builtin/packages/fenics/petsc-3.7.patch @@ -0,0 +1,394 @@ +diff -Naur dolfin-1.6.0/dolfin/common/SubSystemsManager.cpp dolfin-1.6.0.new/dolfin/common/SubSystemsManager.cpp +--- dolfin-1.6.0/dolfin/common/SubSystemsManager.cpp 2015-07-28 17:05:55.000000000 +0200 ++++ dolfin-1.6.0.new/dolfin/common/SubSystemsManager.cpp 2016-06-26 23:42:56.391929550 +0200 +@@ -179,7 +179,7 @@ + PetscInitialized(&is_initialized); + if (is_initialized) + { +- PetscOptionsInsert(&argc, &argv, PETSC_NULL); ++ PetscOptionsInsert(NULL, &argc, &argv, PETSC_NULL); + } + else + { +@@ -187,12 +187,12 @@ + PetscInitializeNoArguments(); + + // Set options to avoid common failures with some 3rd party solvers +- PetscOptionsSetValue("-mat_mumps_icntl_7", "0"); +- PetscOptionsSetValue("-mat_superlu_dist_colperm", "MMD_AT_PLUS_A"); ++ PetscOptionsSetValue(NULL, "-mat_mumps_icntl_7", "0"); ++ PetscOptionsSetValue(NULL, "-mat_superlu_dist_colperm", "MMD_AT_PLUS_A"); + + // Pass command line arguments to PETSc (will overwrite any + // default above) +- PetscOptionsInsert(&argc, &argv, PETSC_NULL); ++ PetscOptionsInsert(NULL, &argc, &argv, PETSC_NULL); + } + + // Set PETSc +diff -Naur dolfin-1.6.0/dolfin/la/PETScKrylovSolver.cpp dolfin-1.6.0.new/dolfin/la/PETScKrylovSolver.cpp +--- dolfin-1.6.0/dolfin/la/PETScKrylovSolver.cpp 2015-07-28 17:05:55.000000000 +0200 ++++ dolfin-1.6.0.new/dolfin/la/PETScKrylovSolver.cpp 2016-06-26 23:33:02.418351380 +0200 +@@ -564,6 +564,11 @@ + return solve(x, b); + } + //----------------------------------------------------------------------------- ++PetscErrorCode PETScKrylovSolver::ksp_monitor_norm(KSP ksp, PetscInt n, PetscReal rnorm, void *vf) ++{ ++ KSPMonitorTrueResidualNorm(ksp, n, rnorm, static_cast<PetscViewerAndFormat *>(vf)); ++} ++//----------------------------------------------------------------------------- + void PETScKrylovSolver::set_petsc_ksp_options() + { + PetscErrorCode ierr; +@@ -585,7 +590,8 @@ + const bool monitor_convergence = parameters["monitor_convergence"]; + if (monitor_convergence) + { +- ierr = KSPMonitorSet(_ksp, KSPMonitorTrueResidualNorm, 0, 0); ++ PetscViewerAndFormatCreate(PETSC_VIEWER_STDOUT_WORLD, PETSC_VIEWER_DEFAULT, &_vf); ++ ierr = KSPMonitorSet(_ksp, ksp_monitor_norm, _vf, 0); + if (ierr != 0) petsc_error(ierr, __FILE__, "KSPMonitorSet"); + } + +diff -Naur dolfin-1.6.0/dolfin/la/PETScKrylovSolver.h dolfin-1.6.0.new/dolfin/la/PETScKrylovSolver.h +--- dolfin-1.6.0/dolfin/la/PETScKrylovSolver.h 2015-07-28 17:05:55.000000000 +0200 ++++ dolfin-1.6.0.new/dolfin/la/PETScKrylovSolver.h 2016-06-26 23:19:40.767042975 +0200 +@@ -179,6 +179,12 @@ + // PETSc solver pointer + KSP _ksp; + ++ // viewer for monitoring ++ PetscViewerAndFormat* _vf; ++ ++ // monitoring function ++ static PetscErrorCode ksp_monitor_norm(KSP ksp, PetscInt n, PetscReal rnorm, void *ctx); ++ + // DOLFIN-defined PETScUserPreconditioner + PETScUserPreconditioner* pc_dolfin; + +diff -Naur dolfin-1.6.0/dolfin/la/PETScLUSolver.cpp dolfin-1.6.0.new/dolfin/la/PETScLUSolver.cpp +--- dolfin-1.6.0/dolfin/la/PETScLUSolver.cpp 2015-07-28 17:05:55.000000000 +0200 ++++ dolfin-1.6.0.new/dolfin/la/PETScLUSolver.cpp 2016-06-26 23:13:36.903732301 +0200 +@@ -246,14 +246,14 @@ + if (parameters["num_threads"].is_set()) + { + // Use number of threads specified for LU solver +- ierr = PetscOptionsSetValue("-mat_pastix_threadnbr", ++ ierr = PetscOptionsSetValue(NULL, "-mat_pastix_threadnbr", + parameters["num_threads"].value_str().c_str()); + if (ierr != 0) petsc_error(ierr, __FILE__, "PetscOptionsSetValue"); + } + else + { + // Use global number of threads +- ierr = PetscOptionsSetValue("-mat_pastix_threadnbr", ++ ierr = PetscOptionsSetValue(NULL, "-mat_pastix_threadnbr", + dolfin::parameters["num_threads"].value_str().c_str()); + if (ierr != 0) petsc_error(ierr, __FILE__, "PetscOptionsSetValue"); + } +diff -Naur dolfin-1.6.0/dolfin/la/PETScOptions.cpp dolfin-1.6.0.new/dolfin/la/PETScOptions.cpp +--- dolfin-1.6.0/dolfin/la/PETScOptions.cpp 2015-07-28 17:05:55.000000000 +0200 ++++ dolfin-1.6.0.new/dolfin/la/PETScOptions.cpp 2016-06-26 23:37:58.613121118 +0200 +@@ -54,7 +54,7 @@ + { + SubSystemsManager::init_petsc(); + PetscErrorCode ierr; +- ierr = PetscOptionsClearValue(option.c_str()); ++ ierr = PetscOptionsClearValue(NULL, option.c_str()); + if (ierr != 0) + { + dolfin_error("PETScOptions.cpp", +diff -Naur dolfin-1.6.0/dolfin/la/PETScOptions.h dolfin-1.6.0.new/dolfin/la/PETScOptions.h +--- dolfin-1.6.0/dolfin/la/PETScOptions.h 2015-07-28 17:05:55.000000000 +0200 ++++ dolfin-1.6.0.new/dolfin/la/PETScOptions.h 2016-06-26 23:37:54.352023709 +0200 +@@ -65,7 +65,7 @@ + + PetscErrorCode ierr; + std::string _option = "-" + option; +- ierr = PetscOptionsSetValue(_option.c_str(), ++ ierr = PetscOptionsSetValue(NULL, _option.c_str(), + boost::lexical_cast<std::string>(value).c_str()); + if (ierr != 0) + { +diff -Naur dolfin-1.6.0/dolfin/la/SLEPcEigenSolver.cpp dolfin-1.6.0.new/dolfin/la/SLEPcEigenSolver.cpp +--- dolfin-1.6.0/dolfin/la/SLEPcEigenSolver.cpp 2015-07-28 17:05:55.000000000 +0200 ++++ dolfin-1.6.0.new/dolfin/la/SLEPcEigenSolver.cpp 2016-06-26 23:35:25.930631132 +0200 +@@ -99,6 +99,19 @@ + solve(_matA->size(0)); + } + //----------------------------------------------------------------------------- ++PetscErrorCode SLEPcEigenSolver::eps_monitor(EPS eps, PetscInt its, PetscInt nconv, PetscScalar* eigr, ++ PetscScalar* eigi, PetscReal* errest, ++ PetscInt nest, void *vf) ++{ ++ EPSMonitorAll(eps, its, nconv, eigr, eigi, errest, nest, ++ static_cast<PetscViewerAndFormat *>(vf)); ++} ++//----------------------------------------------------------------------------- ++PetscErrorCode SLEPcEigenSolver::ksp_monitor(KSP ksp, PetscInt n, PetscReal rnorm, void *vf) ++{ ++ KSPMonitorDefault(ksp, n, rnorm, static_cast<PetscViewerAndFormat *>(vf)); ++} ++//----------------------------------------------------------------------------- + void SLEPcEigenSolver::solve(std::size_t n) + { + dolfin_assert(_matA); +@@ -139,10 +152,11 @@ + { + KSP ksp; + ST st; +- EPSMonitorSet(_eps, EPSMonitorAll, NULL, NULL); ++ PetscViewerAndFormatCreate(PETSC_VIEWER_STDOUT_WORLD, PETSC_VIEWER_DEFAULT, &_vf); ++ EPSMonitorSet(_eps, eps_monitor, _vf, NULL); + EPSGetST(_eps, &st); + STGetKSP(st, &ksp); +- KSPMonitorSet(ksp, KSPMonitorDefault, NULL, NULL); ++ KSPMonitorSet(ksp, ksp_monitor, _vf, NULL); + EPSView(_eps, PETSC_VIEWER_STDOUT_SELF); + } + +diff -Naur dolfin-1.6.0/dolfin/la/SLEPcEigenSolver.h dolfin-1.6.0.new/dolfin/la/SLEPcEigenSolver.h +--- dolfin-1.6.0/dolfin/la/SLEPcEigenSolver.h 2015-07-28 17:05:55.000000000 +0200 ++++ dolfin-1.6.0.new/dolfin/la/SLEPcEigenSolver.h 2016-06-26 23:36:08.784610612 +0200 +@@ -231,6 +231,11 @@ + // SLEPc solver pointer + EPS _eps; + ++ PetscViewerAndFormat* _vf; ++ static PetscErrorCode eps_monitor(EPS eps, int its, int nconv, PetscScalar *eigr, ++ PetscScalar *eigi, PetscReal* errest, ++ int nest, void *mctx); ++ static PetscErrorCode ksp_monitor(KSP ksp, PetscInt n, PetscReal rnorm, void *vf); + }; + + } +diff -Naur dolfin-1.6.0/dolfin/nls/PETScSNESSolver.cpp dolfin-1.6.0.new/dolfin/nls/PETScSNESSolver.cpp +--- dolfin-1.6.0/dolfin/nls/PETScSNESSolver.cpp 2015-07-28 17:05:55.000000000 +0200 ++++ dolfin-1.6.0.new/dolfin/nls/PETScSNESSolver.cpp 2016-06-26 23:19:40.166029256 +0200 +@@ -195,6 +195,15 @@ + return this->solve(nonlinear_problem, x); + } + //----------------------------------------------------------------------------- ++PetscErrorCode ++PETScSNESSolver::snes_monitor(SNES snes, PetscInt its, ++ PetscReal fgnorm, void *vf) ++{ ++ PetscViewerAndFormat * _vf = static_cast<PetscViewerAndFormat *>(vf); ++ SNESMonitorDefault(snes, its, fgnorm, _vf); ++ return(0); ++} ++//----------------------------------------------------------------------------- + void + PETScSNESSolver::init(NonlinearProblem& nonlinear_problem, + GenericVector& x) +@@ -237,9 +246,11 @@ + } + + // Set some options from the parameters +- if (report) +- SNESMonitorSet(_snes, SNESMonitorDefault, PETSC_NULL, PETSC_NULL); +- ++ if (report) { ++ PetscViewerAndFormatCreate(PETSC_VIEWER_STDOUT_WORLD, PETSC_VIEWER_DEFAULT, &_snes_ctx.vf); ++ SNESMonitorSet(_snes, PETScSNESSolver::snes_monitor, _snes_ctx.vf, PETSC_NULL); ++ } ++ + // Set the bounds, if any + set_bounds(x); + +@@ -293,8 +304,8 @@ + SNESGetLineSearch(_snes, &linesearch); + #endif + +- if (report) +- SNESLineSearchSetMonitor(linesearch, PETSC_TRUE); ++ // if (report) ++ // SNESLineSearchSetMonitor(linesearch, PETSC_TRUE); + const std::string line_search_type = std::string(parameters["line_search"]); + SNESLineSearchSetType(linesearch, line_search_type.c_str()); + +@@ -466,6 +477,24 @@ + } + #endif + //----------------------------------------------------------------------------- ++PetscErrorCode ++PETScSNESSolver::ksp_monitor(KSP ksp, PetscInt n, ++ PetscReal rnorm, void *vf) ++{ ++ PetscViewerAndFormat * _vf = static_cast<PetscViewerAndFormat *>(vf); ++ KSPMonitorDefault(ksp, n, rnorm, _vf); ++ return(0); ++} ++//----------------------------------------------------------------------------- ++PetscErrorCode ++PETScSNESSolver::ksp_monitor_norm(KSP ksp, PetscInt n, ++ PetscReal rnorm, void *vf) ++{ ++ PetscViewerAndFormat * _vf = static_cast<PetscViewerAndFormat *>(vf); ++ KSPMonitorTrueResidualNorm(ksp, n, rnorm, _vf); ++ return(0); ++} ++//----------------------------------------------------------------------------- + void PETScSNESSolver::set_linear_solver_parameters() + { + KSP ksp; +@@ -482,7 +511,7 @@ + PetscObjectGetComm((PetscObject)_snes, &comm); + + if (parameters["report"]) +- KSPMonitorSet(ksp, KSPMonitorDefault, PETSC_NULL, PETSC_NULL); ++ KSPMonitorSet(ksp, PETScSNESSolver::ksp_monitor, _snes_ctx.vf, PETSC_NULL); + + const std::string linear_solver = parameters["linear_solver"]; + const std::string preconditioner = parameters["preconditioner"]; +@@ -518,7 +547,7 @@ + KSPSetInitialGuessNonzero(ksp, PETSC_FALSE); + + if (krylov_parameters["monitor_convergence"]) +- KSPMonitorSet(ksp, KSPMonitorTrueResidualNorm, 0, 0); ++ KSPMonitorSet(ksp, PETScSNESSolver::ksp_monitor_norm, _snes_ctx.vf, 0); + + // Set tolerances + const int max_iters = krylov_parameters["maximum_iterations"]; +diff -Naur dolfin-1.6.0/dolfin/nls/PETScSNESSolver.h dolfin-1.6.0.new/dolfin/nls/PETScSNESSolver.h +--- dolfin-1.6.0/dolfin/nls/PETScSNESSolver.h 2015-07-28 17:05:55.000000000 +0200 ++++ dolfin-1.6.0.new/dolfin/nls/PETScSNESSolver.h 2016-06-26 22:31:21.554129282 +0200 +@@ -24,6 +24,7 @@ + + #include <map> + #include <petscsnes.h> ++#include <petscviewer.h> + #include <memory> + #include <dolfin/nls/NewtonSolver.h> + #include <dolfin/parameter/Parameters.h> +@@ -124,8 +125,15 @@ + Vec f_tmp; + const PETScVector* xl; + const PETScVector* xu; ++ PetscViewerAndFormat* vf; + }; + ++ ++ // monitoring functions ++ static PetscErrorCode snes_monitor(SNES snes, PetscInt its, PetscReal fgnorm, void* ctx); ++ static PetscErrorCode ksp_monitor(KSP ksp, PetscInt n, PetscReal rnorm, void *ctx); ++ static PetscErrorCode ksp_monitor_norm(KSP ksp, PetscInt n, PetscReal rnorm, void *ctx); ++ + // PETSc solver pointer + SNES _snes; + +diff -Naur dolfin-1.6.0/dolfin/nls/PETScTAOSolver.cpp dolfin-1.6.0.new/dolfin/nls/PETScTAOSolver.cpp +--- dolfin-1.6.0/dolfin/nls/PETScTAOSolver.cpp 2015-07-28 17:05:55.000000000 +0200 ++++ dolfin-1.6.0.new/dolfin/nls/PETScTAOSolver.cpp 2016-06-27 19:14:47.367885081 +0200 +@@ -186,6 +186,15 @@ + init(optimisation_problem, x.down_cast<PETScVector>(), lb, ub); + } + //----------------------------------------------------------------------------- ++PetscErrorCode ++PETScTAOSolver::ksp_monitor_norm(KSP ksp, PetscInt n, ++ PetscReal rnorm, void * vf) ++{ ++ PetscViewerAndFormat * _vf = static_cast<PetscViewerAndFormat *>(vf); ++ KSPMonitorTrueResidualNorm(ksp, n, rnorm, _vf); ++ return(0); ++} ++//----------------------------------------------------------------------------- + void PETScTAOSolver::init(OptimisationProblem& optimisation_problem, + PETScVector& x, + const PETScVector& lb, +@@ -365,9 +374,7 @@ + set_tao(parameters["method"]); + + // Set tolerances +- TaoSetTolerances(_tao, parameters["function_absolute_tol"], +- parameters["function_relative_tol"], +- parameters["gradient_absolute_tol"], ++ TaoSetTolerances(_tao, parameters["gradient_absolute_tol"], + parameters["gradient_relative_tol"], + parameters["gradient_t_tol"]); + +@@ -490,8 +497,10 @@ + KSPSetInitialGuessNonzero(ksp, PETSC_FALSE); + + // KSP monitor +- if (krylov_parameters["monitor_convergence"]) +- KSPMonitorSet(ksp, KSPMonitorTrueResidualNorm, 0, 0); ++ if (krylov_parameters["monitor_convergence"]) { ++ PetscViewerAndFormatCreate(PETSC_VIEWER_STDOUT_WORLD, PETSC_VIEWER_DEFAULT, &vf); ++ KSPMonitorSet(ksp, ksp_monitor_norm, vf, 0); ++ } + + // Get integer tolerances (to take care of casting to PetscInt) + const int max_iter = krylov_parameters["maximum_iterations"]; +diff -Naur dolfin-1.6.0/dolfin/nls/PETScTAOSolver.h dolfin-1.6.0.new/dolfin/nls/PETScTAOSolver.h +--- dolfin-1.6.0/dolfin/nls/PETScTAOSolver.h 2015-07-28 17:05:55.000000000 +0200 ++++ dolfin-1.6.0.new/dolfin/nls/PETScTAOSolver.h 2016-06-27 19:08:00.634361160 +0200 +@@ -146,6 +146,10 @@ + // TAO pointer + Tao _tao; + ++ // monitoring functions ++ PetscViewerAndFormat* vf; ++ static PetscErrorCode ksp_monitor_norm(KSP ksp, PetscInt n, PetscReal rnorm, void *ctx); ++ + // Update parameters when tao/ksp/pc_types are explictly given + void update_parameters(const std::string tao_type, + const std::string ksp_type, +diff -Naur dolfin-1.6.0/dolfin/nls/TAOLinearBoundSolver.cpp dolfin-1.6.0.new/dolfin/nls/TAOLinearBoundSolver.cpp +--- dolfin-1.6.0/dolfin/nls/TAOLinearBoundSolver.cpp 2015-07-28 17:05:55.000000000 +0200 ++++ dolfin-1.6.0.new/dolfin/nls/TAOLinearBoundSolver.cpp 2016-06-27 19:17:10.390216576 +0200 +@@ -313,9 +313,7 @@ + dolfin_assert(_tao); + + // Set tolerances +- TaoSetTolerances(_tao, parameters["function_absolute_tol"], +- parameters["function_relative_tol"], +- parameters["gradient_absolute_tol"], ++ TaoSetTolerances(_tao, parameters["gradient_absolute_tol"], + parameters["gradient_relative_tol"], + parameters["gradient_t_tol"]); + +@@ -340,6 +338,15 @@ + set_solver(method); + } + //----------------------------------------------------------------------------- ++PetscErrorCode ++TAOLinearBoundSolver::ksp_monitor_norm(KSP ksp, PetscInt n, ++ PetscReal rnorm, void * vf) ++{ ++ PetscViewerAndFormat * _vf = static_cast<PetscViewerAndFormat *>(vf); ++ KSPMonitorTrueResidualNorm(ksp, n, rnorm, _vf); ++ return(0); ++} ++//----------------------------------------------------------------------------- + void TAOLinearBoundSolver::set_ksp_options() + { + dolfin_assert(_tao); +@@ -360,8 +367,10 @@ + else + KSPSetInitialGuessNonzero(ksp, PETSC_FALSE); + +- if (krylov_parameters["monitor_convergence"]) +- KSPMonitorSet(ksp, KSPMonitorTrueResidualNorm, 0, 0); ++ if (krylov_parameters["monitor_convergence"]) { ++ PetscViewerAndFormatCreate(PETSC_VIEWER_STDOUT_WORLD, PETSC_VIEWER_DEFAULT, &vf); ++ KSPMonitorSet(ksp, ksp_monitor_norm, vf, 0); ++ } + + // Set tolerances + const int max_ksp_it = krylov_parameters["maximum_iterations"]; +diff -Naur dolfin-1.6.0/dolfin/nls/TAOLinearBoundSolver.h dolfin-1.6.0.new/dolfin/nls/TAOLinearBoundSolver.h +--- dolfin-1.6.0/dolfin/nls/TAOLinearBoundSolver.h 2015-07-28 17:05:55.000000000 +0200 ++++ dolfin-1.6.0.new/dolfin/nls/TAOLinearBoundSolver.h 2016-06-27 19:08:09.157561005 +0200 +@@ -174,6 +174,10 @@ + // Tao solver pointer + Tao _tao; + ++ // monitoring functions ++ PetscViewerAndFormat* vf; ++ static PetscErrorCode ksp_monitor_norm(KSP ksp, PetscInt n, PetscReal rnorm, void *ctx); ++ + // Petsc preconditioner + std::shared_ptr<PETScPreconditioner> preconditioner; + diff --git a/var/spack/repos/builtin/packages/fenics/petsc-version-detection.patch b/var/spack/repos/builtin/packages/fenics/petsc-version-detection.patch new file mode 100644 index 0000000000..1429cd7bc6 --- /dev/null +++ b/var/spack/repos/builtin/packages/fenics/petsc-version-detection.patch @@ -0,0 +1,39 @@ +--- dolfin-1.6.0.orig/cmake/modules/FindPETSc.cmake 2015-07-28 17:05:55.000000000 +0200 ++++ dolfin-1.6.0/cmake/modules/FindPETSc.cmake 2016-06-27 17:16:02.484402705 +0200 +@@ -207,13 +207,7 @@ + + endif() + +-# Build PETSc test program +-if (DOLFIN_SKIP_BUILD_TESTS) +- set(PETSC_TEST_RUNS TRUE) +- set(PETSC_VERSION "UNKNOWN") +- set(PETSC_VERSION_OK TRUE) +-elseif (FOUND_PETSC_CONF) +- ++if (FOUND_PETSC_CONF) + # Set flags for building test program + set(CMAKE_REQUIRED_INCLUDES ${PETSC_INCLUDE_DIRS}) + set(CMAKE_REQUIRED_LIBRARIES ${PETSC_LIBRARIES}) +@@ -271,7 +265,10 @@ + set(PETSC_VERSION_OK TRUE) + endif() + mark_as_advanced(PETSC_VERSION_OK) ++endif() + ++ # Build PETSc test program ++if (NOT DOLFIN_SKIP_BUILD_TESTS AND FOUND_PETSC_CONF) + # Run PETSc test program + set(PETSC_TEST_LIB_CPP + "${CMAKE_CURRENT_BINARY_DIR}/CMakeFiles/petsc_test_lib.cpp") +@@ -359,7 +356,9 @@ + else() + message(STATUS "PETSc configured without Cusp support") + endif() +- ++else() ++ set(PETSC_TEST_RUNS TRUE) ++ + endif() + + # Check sizeof(PetscInt) diff --git a/var/spack/repos/builtin/packages/gmsh/package.py b/var/spack/repos/builtin/packages/gmsh/package.py index e425d460c2..0951b86d57 100644 --- a/var/spack/repos/builtin/packages/gmsh/package.py +++ b/var/spack/repos/builtin/packages/gmsh/package.py @@ -27,39 +27,51 @@ from spack import * class Gmsh(Package): """ - Gmsh is a free 3D finite element grid generator with a built-in CAD engine and post-processor. Its design goal is - to provide a fast, light and user-friendly meshing tool with parametric input and advanced visualization - capabilities. Gmsh is built around four modules: geometry, mesh, solver and post-processing. The specification of - any input to these modules is done either interactively using the graphical user interface or in ASCII text files - using Gmsh's own scripting language. + Gmsh is a free 3D finite element grid generator with a built-in CAD engine + and post-processor. Its design goal is to provide a fast, light and + user-friendly meshing tool with parametric input and advanced visualization + capabilities. Gmsh is built around four modules: geometry, mesh, solver and + post-processing. The specification of any input to these modules is done + either interactively using the graphical user interface or in ASCII text + files using Gmsh's own scripting language. """ homepage = 'http://gmsh.info' url = 'http://gmsh.info/src/gmsh-2.11.0-source.tgz' + version('2.12.0', '7fbd2ec8071e79725266e72744d21e902d4fe6fa9e7c52340ad5f4be5c159d09') version('2.11.0', 'f15b6e7ac9ca649c9a74440e1259d0db') - # FIXME : Misses dependencies on gmm, PetsC, TetGen - - variant('shared', default=True, description='Enables the build of shared libraries') - variant('debug', default=False, description='Builds the library in debug mode') - variant('mpi', default=False, description='Builds MPI support for parser and solver') - variant('fltk', default=False, description='Enables the build of the FLTK GUI') - variant('hdf5', default=False, description='Enables HDF5 support') - variant('compression', default=True, description='Enables IO compression through zlib') + variant('shared', default=True, description='Enables the build of shared libraries') + variant('debug', default=False, description='Builds the library in debug mode') + variant('mpi', default=False, description='Builds MPI support for parser and solver') + variant('fltk', default=False, description='Enables the build of the FLTK GUI') + variant('hdf5', default=False, description='Enables HDF5 support') + variant('compression', default=True, description='Enables IO compression through zlib') + variant('oce', default=False, description='Build with OCE') + variant('petsc', default=False, description='Build with PETSc') + variant('slepc', default=False, description='Build with SLEPc (only when PETSc is enabled)') depends_on('blas') depends_on('lapack') + depends_on('cmake@2.8:') depends_on('gmp') - depends_on('mpi', when='+mpi') - depends_on('fltk', when='+fltk') # Assumes OpenGL with GLU is already provided by the system + depends_on('mpi', when='+mpi') + # Assumes OpenGL with GLU is already provided by the system: + depends_on('fltk', when='+fltk') depends_on('hdf5', when='+hdf5') - depends_on('zlib', when='+compression') + depends_on('oce', when='+oce') + depends_on('petsc+mpi', when='+petsc+mpi') + depends_on('petsc', when='+petsc~mpi') + depends_on('slepc', when='+slepc+petsc') + depends_on('zlib', when='+compression') def install(self, spec, prefix): - options = [] options.extend(std_cmake_args) + # Make sure native file dialogs are used + options.extend(['-DENABLE_NATIVE_FILE_CHOOSER=ON']) + build_directory = join_path(self.stage.path, 'spack-build') source_directory = self.stage.source_path @@ -68,11 +80,45 @@ class Gmsh(Package): # Prevent GMsh from using its own strange directory structure on OSX options.append('-DENABLE_OS_SPECIFIC_INSTALL=OFF') + # Make sure GMSH picks up correct BlasLapack by providing linker flags + options.append('-DBLAS_LAPACK_LIBRARIES=%s %s' % + (to_link_flags(spec['lapack'].lapack_shared_lib), + to_link_flags(spec['blas'].blas_shared_lib))) + + # Gmsh does not have an option to compile against external metis. + # Its own Metis, however, fails to build + options.append('-DENABLE_METIS=OFF') + + if '+fltk' in spec: + options.append('-DENABLE_FLTK=ON') + else: + options.append('-DENABLE_FLTK=OFF') + + if '+oce' in spec: + env['CASROOT'] = self.spec['oce'].prefix + options.extend(['-DENABLE_OCC=ON']) + else: + options.extend(['-DENABLE_OCC=OFF']) + + if '+petsc' in spec: + env['PETSC_DIR'] = self.spec['petsc'].prefix + options.extend(['-DENABLE_PETSC=ON']) + else: + options.extend(['-DENABLE_PETSC=OFF']) + + if '+slepc' in spec: + env['SLEPC_DIR'] = self.spec['slepc'].prefix + options.extend(['-DENABLE_SLEPC=ON']) + else: + options.extend(['-DENABLE_SLEPC=OFF']) + if '+shared' in spec: + # Builds dynamic executable and installs shared library options.extend(['-DENABLE_BUILD_SHARED:BOOL=ON', - '-DENABLE_BUILD_DYNAMIC:BOOL=ON']) # Builds dynamic executable and installs shared library + '-DENABLE_BUILD_DYNAMIC:BOOL=ON']) else: - options.append('-DENABLE_BUILD_LIB:BOOL=ON') # Builds and installs static library + # Builds and installs static library + options.append('-DENABLE_BUILD_LIB:BOOL=ON') if '+debug' in spec: options.append('-DCMAKE_BUILD_TYPE:STRING=Debug') diff --git a/var/spack/repos/builtin/packages/ibmisc/package.py b/var/spack/repos/builtin/packages/ibmisc/package.py new file mode 100644 index 0000000000..8e6cf429a7 --- /dev/null +++ b/var/spack/repos/builtin/packages/ibmisc/package.py @@ -0,0 +1,46 @@ +from spack import * + +class Ibmisc(CMakePackage): + """Misc. reusable utilities used by IceBin.""" + + homepage = "https://github.com/citibeth/ibmisc" + url = "https://github.com/citibeth/ibmisc/tarball/123" + + version('0.1.0', '12f2a32432a11db48e00217df18e59fa') + + variant('everytrace', default=False, description='Report errors through Everytrace') + variant('proj', default=True, description='Compile utilities for PROJ.4 library') + variant('blitz', default=True, description='Compile utilities for Blitz library') + variant('netcdf', default=True, description='Compile utilities for NetCDF library') + variant('boost', default=True, description='Compile utilities for Boost library') + variant('udunits2', default=True, description='Compile utilities for UDUNITS2 library') + variant('googletest', default=True, description='Compile utilities for Google Test library') + variant('python', default=True, description='Compile utilities for use with Python/Cython') + + extends('python') + + depends_on('eigen') + depends_on('everytrace', when='+everytrace') + depends_on('proj', when='+proj') + depends_on('blitz', when='+blitz') + depends_on('netcdf-cxx4', when='+netcdf') + depends_on('udunits2', when='+udunits2') + depends_on('googletest', when='+googletest') + depends_on('py-cython', when='+python') + depends_on('py-numpy', when='+python') + depends_on('boost', when='+boost') + + # Build dependencies + depends_on('cmake') + depends_on('doxygen') + + def configure_args(self): + spec = self.spec + return [ + '-DUSE_EVERYTRACE=%s' % ('YES' if '+everytrace' in spec else 'NO'), + '-DUSE_PROJ4=%s' % ('YES' if '+proj' in spec else 'NO'), + '-DUSE_BLITZ=%s' % ('YES' if '+blitz' in spec else 'NO'), + '-DUSE_NETCDF=%s' % ('YES' if '+netcdf' in spec else 'NO'), + '-DUSE_BOOST=%s' % ('YES' if '+boost' in spec else 'NO'), + '-DUSE_UDUNITS2=%s' % ('YES' if '+udunits2' in spec else 'NO'), + '-DUSE_GTEST=%s' % ('YES' if '+googletest' in spec else 'NO')] diff --git a/var/spack/repos/builtin/packages/intel/package.py b/var/spack/repos/builtin/packages/intel/package.py index ec3192380a..56d9fabddf 100644 --- a/var/spack/repos/builtin/packages/intel/package.py +++ b/var/spack/repos/builtin/packages/intel/package.py @@ -73,7 +73,7 @@ CONTINUE_WITH_OPTIONAL_ERROR=yes COMPONENTS=%s """ % (self.intel_prefix, self.global_license_file, self.intel_components)) - install_script = which("install.sh") + install_script = Executable("./install.sh") install_script('--silent', silent_config_filename) diff --git a/var/spack/repos/builtin/packages/lrzip/package.py b/var/spack/repos/builtin/packages/lrzip/package.py new file mode 100644 index 0000000000..42542acfdb --- /dev/null +++ b/var/spack/repos/builtin/packages/lrzip/package.py @@ -0,0 +1,61 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created 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 Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, 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 Lesser 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 Lrzip(Package): + """A compression utility that excels at compressing large files + (usually > 10-50 MB). Larger files and/or more free RAM means that the + utility will be able to more effectively compress your files (ie: faster / + smaller size), especially if the filesize(s) exceed 100 MB. You can either + choose to optimise for speed (fast compression / decompression) or size, + but not both.""" + + homepage = 'http://lrzip.kolivas.org' + url = 'https://github.com/ckolivas/lrzip/archive/v0.630.tar.gz' + + version('master', git='https://github.com/ckolivas/lrzip.git') + version('0.630', '3ca7f1d1365aa105089d1fbfc6b0924a') + version('0.621', '1f07227b39ae81a98934411e8611e341') + version('0.616', 'd40bdb046d0807ef602e36b1e9782cc0') + version('0.615', 'f1c01e7f3de07f54d916b61c989dfaf2') + + # depends_on('coreutils') + depends_on('lzo') + depends_on('zlib') + depends_on('bzip2') + + def install(self, spec, prefix): + set_executable('./autogen.sh') + autogen = Executable('./autogen.sh') + + configure_args = [ + '--prefix={0}'.format(prefix), + '--disable-dependency-tracking' + ] + autogen(*configure_args) + + make() + make('install') diff --git a/var/spack/repos/builtin/packages/lzo/package.py b/var/spack/repos/builtin/packages/lzo/package.py new file mode 100644 index 0000000000..0961bbb58c --- /dev/null +++ b/var/spack/repos/builtin/packages/lzo/package.py @@ -0,0 +1,49 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created 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 Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, 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 Lesser 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 Lzo(Package): + """Real-time data compression library""" + + homepage = 'https://www.oberhumer.com/opensource/lzo/' + url = 'https://www.oberhumer.com/opensource/lzo/download/lzo-2.09.tar.gz' + + version('2.09', 'c7ffc9a103afe2d1bba0b015e7aa887f') + version('2.08', 'fcec64c26a0f4f4901468f360029678f') + version('2.07', '4011935e95171e78ad4894f7335c982a') + version('2.06', '95380bd4081f85ef08c5209f4107e9f8') + version('2.05', 'c67cda5fa191bab761c7cb06fe091e36') + + def install(self, spec, prefix): + configure_args = [ + '--prefix={0}'.format(prefix), + '--disable-dependency-tracking', + '--enable-shared' + ] + configure(*configure_args) + make() + make('check') + make('install') diff --git a/var/spack/repos/builtin/packages/mfem/package.py b/var/spack/repos/builtin/packages/mfem/package.py index 504efb5e35..1b4456380b 100644 --- a/var/spack/repos/builtin/packages/mfem/package.py +++ b/var/spack/repos/builtin/packages/mfem/package.py @@ -31,11 +31,13 @@ class Mfem(Package): homepage = 'http://www.mfem.org' url = 'https://github.com/mfem/mfem' -# version('3.1', git='https://github.com/mfem/mfem.git', -# commit='dbae60fe32e071989b52efaaf59d7d0eb2a3b574') + version('3.2', '2938c3deed4ec4f7fd5b5f5cfe656845282e86e2dcd477d292390058b7b94340', + url='http://goo.gl/Y9T75B', expand=False, preferred=True) version('3.1', '841ea5cf58de6fae4de0f553b0e01ebaab9cd9c67fa821e8a715666ecf18fc57', url='http://goo.gl/xrScXn', expand=False) +# version('3.1', git='https://github.com/mfem/mfem.git', +# commit='dbae60fe32e071989b52efaaf59d7d0eb2a3b574') variant('metis', default=False, description='Activate support for metis') variant('hypre', default=False, description='Activate support for hypre') diff --git a/var/spack/repos/builtin/packages/mumps/mumps-shared.patch b/var/spack/repos/builtin/packages/mumps/mumps-shared.patch deleted file mode 100644 index 592f48037c..0000000000 --- a/var/spack/repos/builtin/packages/mumps/mumps-shared.patch +++ /dev/null @@ -1,119 +0,0 @@ -diff -Naur MUMPS_5.0.1/libseq/Makefile MUMPS_5.0.1.new/libseq/Makefile ---- MUMPS_5.0.1/libseq/Makefile 2015-07-23 19:08:32.000000000 +0200 -+++ MUMPS_5.0.1.new/libseq/Makefile 2016-06-07 10:41:16.585179151 +0200 -@@ -8,11 +8,15 @@ - - include ../Makefile.inc - --libmpiseq: libmpiseq$(PLAT)$(LIBEXT) -+libmpiseq: libmpiseq$(PLAT)$(LIBEXT) libmpiseq$(PLAT)$(SHLIBEXT) - - libmpiseq$(PLAT)$(LIBEXT): mpi.o mpic.o elapse.o - $(AR)$@ mpi.o mpic.o elapse.o - $(RANLIB) $@ -+ -+libmpiseq$(PLAT)$(SHLIBEXT): mpi.o mpic.o elapse.o -+ $(FC) $(LDFLAGS) $^ -o libmpiseq$(PLAT)$(SHLIBEXT) -+ - .f.o: - $(FC) $(OPTF) -c $*.f $(OUTF)$*.o - .c.o: -diff -Naur MUMPS_5.0.1/Makefile MUMPS_5.0.1.new/Makefile ---- MUMPS_5.0.1/Makefile 2015-07-23 19:08:29.000000000 +0200 -+++ MUMPS_5.0.1.new/Makefile 2016-06-07 10:50:21.863281217 +0200 -@@ -51,7 +51,7 @@ - dexamples: d - (cd examples ; $(MAKE) d) - --requiredobj: Makefile.inc $(LIBSEQNEEDED) $(libdir)/libpord$(PLAT)$(LIBEXT) -+requiredobj: Makefile.inc $(LIBSEQNEEDED) $(libdir)/libpord$(PLAT)$(LIBEXT) $(libdir)/libpord$(PLAT)$(SHLIBEXT) - - # dummy MPI library (sequential version) - -@@ -62,16 +62,25 @@ - $(libdir)/libpord$(PLAT)$(LIBEXT): - if [ "$(LPORDDIR)" != "" ] ; then \ - cd $(LPORDDIR); \ -- $(MAKE) CC="$(CC)" CFLAGS="$(OPTC)" AR="$(AR)" RANLIB="$(RANLIB)" OUTC="$(OUTC)" LIBEXT=$(LIBEXT); \ -+ $(MAKE) CC="$(CC)" CFLAGS="$(OPTC)" AR="$(AR)" RANLIB="$(RANLIB)" LDFLAGS="$(LDFLAGS)" OUTC="$(OUTC)" LIBEXT=$(LIBEXT) PLAT=$(PLAT) SHLIBEXT=$(SHLIBEXT); \ - fi; - if [ "$(LPORDDIR)" != "" ] ; then \ - cp $(LPORDDIR)/libpord$(LIBEXT) $@; \ - fi; - -+$(libdir)/libpord$(PLAT)$(SHLIBEXT): -+ if [ "$(LPORDDIR)" != "" ] ; then \ -+ cd $(LPORDDIR); \ -+ $(MAKE) CC="$(CC)" CFLAGS="$(OPTC)" AR="$(AR)" RANLIB="$(RANLIB)" LDFLAGS="$(LDFLAGS)" OUTC="$(OUTC)" LIBEXT=$(LIBEXT) PLAT=$(PLAT) SHLIBEXT=$(SHLIBEXT) libpord$(PLAT)$(SHLIBEXT); \ -+ fi; -+ if [ "$(LPORDDIR)" != "" ] ; then \ -+ cp $(LPORDDIR)/libpord$(PLAT)$(SHLIBEXT) $@; \ -+ fi; -+ - clean: - (cd src; $(MAKE) clean) - (cd examples; $(MAKE) clean) -- (cd $(libdir); $(RM) *$(PLAT)$(LIBEXT)) -+ (cd $(libdir); $(RM) *$(PLAT)$(LIBEXT) *$(PLAT)$(SHLIBEXT)) - (cd libseq; $(MAKE) clean) - if [ "$(LPORDDIR)" != "" ] ; then \ - cd $(LPORDDIR); $(MAKE) realclean; \ -diff -Naur MUMPS_5.0.1/PORD/lib/Makefile MUMPS_5.0.1.new/PORD/lib/Makefile ---- MUMPS_5.0.1/PORD/lib/Makefile 2015-07-23 19:08:29.000000000 +0200 -+++ MUMPS_5.0.1.new/PORD/lib/Makefile 2016-06-07 10:49:48.889000958 +0200 -@@ -13,7 +13,7 @@ - - OBJS = graph.o gbipart.o gbisect.o ddcreate.o ddbisect.o nestdiss.o \ - multisector.o gelim.o bucket.o tree.o \ -- symbfac.o interface.o sort.o minpriority.o -+ symbfac.o interface.o sort.o minpriority.o - - # Note: numfac.c read.c mapping.c triangular.c matrix.c kernel.c - # were not direcly used by MUMPS and have been removed from the -@@ -24,12 +24,15 @@ - .c.o: - $(CC) $(COPTIONS) -c $*.c $(OUTC)$*.o - --libpord$(LIBEXT):$(OBJS) -+libpord$(PLAT)$(LIBEXT):$(OBJS) - $(AR)$@ $(OBJS) - $(RANLIB) $@ - -+libpord$(PLAT)$(SHLIBEXT): $(OBJS) -+ $(CC) $(LDFLAGS) $(OBJS) -o libpord$(PLAT)$(SHLIBEXT) -+ - clean: - rm -f *.o - - realclean: -- rm -f *.o libpord.a -+ rm -f *.o libpord$(PLAT)$(SHLIBEXT) libpord$(PLAT)$(LIBEXT) -diff -Naur MUMPS_5.0.1/src/Makefile MUMPS_5.0.1.new/src/Makefile ---- MUMPS_5.0.1/src/Makefile 2015-07-23 19:08:29.000000000 +0200 -+++ MUMPS_5.0.1.new/src/Makefile 2016-06-07 10:40:52.534703722 +0200 -@@ -24,7 +24,10 @@ - include $(topdir)/Makefile.inc - - mumps_lib: $(libdir)/libmumps_common$(PLAT)$(LIBEXT) \ -- $(libdir)/lib$(ARITH)mumps$(PLAT)$(LIBEXT) -+ $(libdir)/libmumps_common$(PLAT)$(SHLIBEXT) \ -+ $(libdir)/lib$(ARITH)mumps$(PLAT)$(LIBEXT) \ -+ $(libdir)/lib$(ARITH)mumps$(PLAT)$(SHLIBEXT) -+ - - OBJS_COMMON_MOD = \ - ana_omp_m.o\ -@@ -162,6 +165,13 @@ - $(AR)$@ $? - $(RANLIB) $@ - -+$(libdir)/libmumps_common$(PLAT)$(SHLIBEXT): $(OBJS_COMMON_MOD) $(OBJS_COMMON_OTHER) -+ $(FC) $(LDFLAGS) $^ -L$(libdir) $(LORDERINGS) $(LIBS) $(LIBBLAS) $(LIBOTHERS) -o $(libdir)/libmumps_common$(PLAT)$(SHLIBEXT) -+ -+ -+$(libdir)/lib$(ARITH)mumps$(PLAT)$(SHLIBEXT): $(OBJS_MOD) $(OBJS_OTHER) -+ $(FC) $(LDFLAGS) $^ -L$(libdir) -lmumps_common$(PLAT) $(LORDERINGS) $(LIBS) $(LIBBLAS) $(LIBOTHERS) -o $(libdir)/lib$(ARITH)mumps$(PLAT)$(SHLIBEXT) -+ - # Dependencies between modules: - $(ARITH)mumps_load.o: $(ARITH)mumps_comm_buffer.o \ - $(ARITH)mumps_struc_def.o \ diff --git a/var/spack/repos/builtin/packages/mumps/package.py b/var/spack/repos/builtin/packages/mumps/package.py index 8a90ef72d0..92c45c9b95 100644 --- a/var/spack/repos/builtin/packages/mumps/package.py +++ b/var/spack/repos/builtin/packages/mumps/package.py @@ -23,10 +23,7 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## from spack import * -import os -import sys -import subprocess - +import os, sys, glob class Mumps(Package): """MUMPS: a MUltifrontal Massively Parallel sparse direct Solver""" @@ -47,6 +44,7 @@ class Mumps(Package): 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@5:', when='+metis') @@ -56,64 +54,49 @@ class Mumps(Package): depends_on('scalapack', when='+mpi') depends_on('mpi', when='+mpi') - patch('mumps-shared.patch', when='+shared') - # this function is not a patch function because in case scalapack # is needed it uses self.spec['scalapack'].fc_link set by the # setup_dependent_environment in scalapck. This happen after patch # end before install # def patch(self): def write_makefile_inc(self): - if (('+parmetis' in self.spec or - '+ptscotch' in self.spec)) and '+mpi' not in self.spec: - raise RuntimeError('You cannot use the variants parmetis or ptscotch without mpi') # NOQA: E501 + if ('+parmetis' in self.spec or '+ptscotch' in self.spec) and '+mpi' not in self.spec: + raise RuntimeError('You cannot use the variants parmetis or ptscotch without mpi') - makefile_conf = [ - "LIBBLAS = -L%s -lblas" % self.spec['blas'].prefix.lib - ] + makefile_conf = ["LIBBLAS = -L%s -lblas" % self.spec['blas'].prefix.lib] orderings = ['-Dpord'] if '+ptscotch' in self.spec or '+scotch' in self.spec: join_lib = ' -l%s' % ('pt' if '+ptscotch' in self.spec else '') - makefile_conf.extend([ - "ISCOTCH = -I%s" % self.spec['scotch'].prefix.include, - "LSCOTCH = -L%s %s%s" % (self.spec['scotch'].prefix.lib, - join_lib, - join_lib.join(['esmumps', - 'scotch', - 'scotcherr'])) - ]) + makefile_conf.extend( + ["ISCOTCH = -I%s" % self.spec['scotch'].prefix.include, + "LSCOTCH = -L%s %s%s" % (self.spec['scotch'].prefix.lib, + join_lib, + join_lib.join(['esmumps', 'scotch', 'scotcherr']))]) orderings.append('-Dscotch') if '+ptscotch' in self.spec: orderings.append('-Dptscotch') if '+parmetis' in self.spec and '+metis' in self.spec: - makefile_conf.extend([ - "IMETIS = -I%s" % self.spec['parmetis'].prefix.include, - "LMETIS = -L%s -l%s -L%s -l%s" % ( - self.spec['parmetis'].prefix.lib, 'parmetis', - self.spec['metis'].prefix.lib, 'metis') - ]) + libname = 'parmetis' if '+parmetis' in self.spec else 'metis' + makefile_conf.extend( + ["IMETIS = -I%s" % self.spec['parmetis'].prefix.include, + "LMETIS = -L%s -l%s -L%s -l%s" % (self.spec['parmetis'].prefix.lib, 'parmetis',self.spec['metis'].prefix.lib, 'metis')]) orderings.append('-Dparmetis') elif '+metis' in self.spec: - makefile_conf.extend([ - "IMETIS = -I%s" % self.spec['metis'].prefix.include, - "LMETIS = -L%s -l%s" % (self.spec['metis'].prefix.lib, - 'metis') - ]) + makefile_conf.extend( + ["IMETIS = -I%s" % self.spec['metis'].prefix.include, + "LMETIS = -L%s -l%s" % (self.spec['metis'].prefix.lib, 'metis')]) orderings.append('-Dmetis') 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 + # 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: @@ -121,7 +104,7 @@ class Mumps(Package): # the fortran compilation flags most probably are # working only for intel and gnu compilers this is # perhaps something the compiler should provide - ['OPTF = %s -O -DALLOW_NON_INIT %s' % (fpic, '-fdefault-integer-8' if self.compiler.name == "gcc" else '-i8'), # NOQA: E501 + ['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: @@ -130,47 +113,49 @@ class Mumps(Package): 'OPTL = %s -O ' % fpic, 'OPTC = %s -O ' % fpic]) + if '+mpi' in self.spec: makefile_conf.extend( - ["CC = %s" % self.spec['mpi'].mpicc, - "FC = %s" % self.spec['mpi'].mpifc, + ["CC = %s" % join_path(self.spec['mpi'].prefix.bin, 'mpicc'), + "FC = %s" % join_path(self.spec['mpi'].prefix.bin, 'mpif90'), + "FL = %s" % join_path(self.spec['mpi'].prefix.bin, 'mpif90'), "SCALAP = %s" % self.spec['scalapack'].fc_link, "MUMPS_TYPE = par"]) else: makefile_conf.extend( ["CC = cc", "FC = fc", + "FL = fc", "MUMPS_TYPE = seq"]) # TODO: change the value to the correct one according to the # compiler possible values are -DAdd_, -DAdd__ and/or -DUPPER - makefile_conf.extend([ - 'CDEFS = -DAdd_', - 'FL = $(FC)', - ]) + makefile_conf.append("CDEFS = -DAdd_") if '+shared' in self.spec: - makefile_conf.append('SHLIBEXT = .%s' % dso_suffix) if sys.platform == 'darwin': - makefile_conf.append( - 'LDFLAGS = -dynamiclib -Wl,-install_name -Wl,{0}/$(notdir $@) {1}{0} -undefined dynamic_lookup'.format(prefix.lib, self.compiler.fc_rpath_arg) # NOQA: E501 - ) + # Building dylibs with mpif90 causes segfaults on 10.8 and 10.10. Use gfortran. (Homebrew) + makefile_conf.extend([ + 'LIBEXT=.dylib', + 'AR=%s -dynamiclib -Wl,-install_name -Wl,%s/$(notdir $@) -undefined dynamic_lookup -o ' % (os.environ['FC'],prefix.lib), + 'RANLIB=echo' + ]) else: - makefile_conf.append( - 'LDFLAGS = -shared {0}{1}'.format( - self.compiler.fc_rpath_arg, - prefix.lib) - ) - - makefile_conf.extend([ - 'LIBEXT = .a', - 'AR = ar vr ', - 'RANLIB = ranlib' - ]) - - makefile_inc_template = \ - join_path(os.path.dirname(self.module.__file__), - 'Makefile.inc') + makefile_conf.extend([ + 'LIBEXT=.so', + 'AR=$(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') with open(makefile_inc_template, "r") as fh: makefile_conf.extend(fh.read().split('\n')) @@ -179,53 +164,46 @@ class Mumps(Package): makefile_inc = '\n'.join(makefile_conf) fh.write(makefile_inc) + + def install(self, spec, prefix): make_libs = [] # the choice to compile ?examples is to have kind of a sanity # check on the libraries generated. if '+float' in spec: - make_libs.append('s') + make_libs.append('sexamples') if '+complex' in spec: - make_libs.append('c') + make_libs.append('cexamples') if '+double' in spec: - make_libs.append('d') + make_libs.append('dexamples') if '+complex' in spec: - make_libs.append('z') + make_libs.append('zexamples') self.write_makefile_inc() - make('mumps_lib', parallel=False) - 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) - if '+shared' in spec: - install('libseq/libmpiseq.{0}'.format(dso_suffix), prefix.lib) - install('libseq/mpi.h', prefix.include) - install('libseq/mpif.h', 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 - # TODO: test the installed mumps and not the one in stage - if '~mpi' in spec: - for t in make_libs: - make('{0}examples'.format(t)) - - with working_dir('examples'): - for t in make_libs: - input_file = 'input_simpletest_{0}'.format( - 'real' if t in ['s', 'd'] else 'cmplx') - with open(input_file) as input: - test = './{0}simpletest'.format(t) - ret = subprocess.call(test, - stdin=input) - if ret is not 0: - raise RuntimeError( - 'The test {0} did not pass'.format(test)) + 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 + 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') diff --git a/var/spack/repos/builtin/packages/oce/package.py b/var/spack/repos/builtin/packages/oce/package.py index 0f0fcfb733..06b6b7cbb0 100644 --- a/var/spack/repos/builtin/packages/oce/package.py +++ b/var/spack/repos/builtin/packages/oce/package.py @@ -23,20 +23,22 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## from spack import * -import platform, sys +import platform + class Oce(Package): - """ - Open CASCADE Community Edition: - patches/improvements/experiments contributed by users over the official Open CASCADE library. + """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('0.17.2', 'bf2226be4cd192606af677cf178088e5') version('0.17.1', '36c67b87093c675698b483454258af91') - version('0.17' , 'f1a89395c4b0d199bea3db62b85f818d') + version('0.17', 'f1a89395c4b0d199bea3db62b85f818d') version('0.16.1', '4d591b240c9293e879f50d86a0cb2bb3') - version('0.16' , '7a4b4df5a104d75a537e25e7dd387eca') + version('0.16', '7a4b4df5a104d75a537e25e7dd387eca') variant('tbb', default=True, description='Build with Intel Threading Building Blocks') @@ -49,8 +51,7 @@ class Oce(Package): # 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') - + patch('null.patch', when='@0.16:0.17.1') def install(self, spec, prefix): options = [] @@ -63,7 +64,8 @@ class Oce(Package): '-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_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', @@ -77,15 +79,8 @@ class Oce(Package): '-DOCE_OSX_USE_COCOA:BOOL=ON', ]) - cmake('.', *options) + options.append('-DCMAKE_INSTALL_NAME_DIR:PATH=%s/lib' % prefix) + 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) + make("test") diff --git a/var/spack/repos/builtin/packages/octave-splines/package.py b/var/spack/repos/builtin/packages/octave-splines/package.py new file mode 100644 index 0000000000..11c9cc5ba7 --- /dev/null +++ b/var/spack/repos/builtin/packages/octave-splines/package.py @@ -0,0 +1,44 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created 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 Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, 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 Lesser 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 OctaveSplines(Package): + """Additional spline functions.""" + + homepage = "http://octave.sourceforge.net/splines/index.html" + url = "http://downloads.sourceforge.net/octave/splines-1.3.1.tar.gz" + + version('1.3.1', 'f9665d780c37aa6a6e17d1f424c49bdeedb89d1192319a4e39c08784122d18f9') + + extends('octave@3.6.0:') + + def install(self, spec, prefix): + octave('--quiet', + '--norc', + '--built-in-docstrings-file=/dev/null', + '--texi-macros-file=/dev/null', + '--eval', 'pkg prefix %s; pkg install %s' % + (prefix, self.stage.archive_file)) diff --git a/var/spack/repos/builtin/packages/octave/package.py b/var/spack/repos/builtin/packages/octave/package.py index 72ff0ee6fc..f97bfc7d12 100644 --- a/var/spack/repos/builtin/packages/octave/package.py +++ b/var/spack/repos/builtin/packages/octave/package.py @@ -36,6 +36,8 @@ class Octave(Package): homepage = "https://www.gnu.org/software/octave/" url = "ftp://ftp.gnu.org/gnu/octave/octave-4.0.0.tar.gz" + extendable = True + version('4.0.2', 'c2a5cacc6e4c52f924739cdf22c2c687') version('4.0.0', 'a69f8320a4f20a8480c1b278b1adb799') @@ -212,3 +214,16 @@ class Octave(Package): make() make("install") + + # ======================================================================== + # Set up environment to make install easy for Octave extensions. + # ======================================================================== + + def setup_dependent_package(self, module, ext_spec): + """Called before Octave modules' install() methods. + + In most cases, extensions will only need to have one line: + octave('--eval', 'pkg install %s' % self.stage.archive_file) + """ + # Octave extension builds can have a global Octave executable function + module.octave = Executable(join_path(self.spec.prefix.bin, 'octave')) diff --git a/var/spack/repos/builtin/packages/openssl/package.py b/var/spack/repos/builtin/packages/openssl/package.py index 377bffe723..e7c105d5f5 100644 --- a/var/spack/repos/builtin/packages/openssl/package.py +++ b/var/spack/repos/builtin/packages/openssl/package.py @@ -35,7 +35,7 @@ class Openssl(Package): Transport Layer Security (TLS v1) protocols as well as a full-strength general purpose cryptography library.""" homepage = "http://www.openssl.org" - url = "https://www.openssl.org/source/openssl-1.0.1h.tar.gz" + url = "https://www.openssl.org/source/openssl-1.0.1h.tar.gz" version('1.0.1h', '8d6d684a9430d5cc98a62a5d8fbda8cf') version('1.0.1r', '1abd905e079542ccae948af37e393d28') @@ -50,21 +50,25 @@ class Openssl(Package): parallel = False def url_for_version(self, version): - # This URL is computed pinging the place where the latest version is stored. To avoid slowdown - # due to repeated pinging, we store the URL in a private class attribute to do the job only once per version + # This URL is computed pinging the place where the latest version is + # stored. To avoid slowdown due to repeated pinging, we store the URL + # in a private class attribute to do the job only once per version openssl_urls = getattr(Openssl, '_openssl_url', {}) openssl_url = openssl_urls.get(version, None) # Same idea, but just to avoid issuing the same message multiple times warnings_given_to_user = getattr(Openssl, '_warnings_given', {}) if openssl_url is None: - if self.spec.satisfies('@external'): - # The version @external is reserved to system openssl. In that case return a fake url and exit - openssl_url = '@external (reserved version for system openssl)' + if self.spec.satisfies('@system'): + # The version @system is reserved to system openssl. In that + # case return a fake url and exit + openssl_url = '@system (reserved version for system openssl)' if not warnings_given_to_user.get(version, False): - tty.msg('Using openssl@external : the version @external is reserved for system openssl') + tty.msg('Using openssl@system: ' + 'the version @system is reserved for system openssl') warnings_given_to_user[version] = True else: - openssl_url = self.check_for_outdated_release(version, warnings_given_to_user) # Store the computed URL + openssl_url = self.check_for_outdated_release( + version, warnings_given_to_user) # Store the computed URL openssl_urls[version] = openssl_url # Store the updated dictionary of URLS Openssl._openssl_url = openssl_urls @@ -75,45 +79,55 @@ class Openssl(Package): def check_for_outdated_release(self, version, warnings_given_to_user): latest = 'ftp://ftp.openssl.org/source/openssl-{version}.tar.gz' - older = 'http://www.openssl.org/source/old/{version_number}/openssl-{version_full}.tar.gz' - # Try to use the url where the latest tarballs are stored. If the url does not exist (404), then - # return the url for older format + older = 'http://www.openssl.org/source/old/{version_number}/openssl-{version_full}.tar.gz' # NOQA: ignore=E501 + # Try to use the url where the latest tarballs are stored. + # If the url does not exist (404), then return the url for + # older format version_number = '.'.join([str(x) for x in version[:-1]]) try: openssl_url = latest.format(version=version) urllib.urlopen(openssl_url) except IOError: - openssl_url = older.format(version_number=version_number, version_full=version) - # Checks if we already warned the user for this particular version of OpenSSL. - # If not we display a warning message and mark this version + openssl_url = older.format( + version_number=version_number, version_full=version) + # Checks if we already warned the user for this particular + # version of OpenSSL. If not we display a warning message + # and mark this version if not warnings_given_to_user.get(version, False): tty.warn( - 'This installation depends on an old version of OpenSSL, which may have known security issues. ') - tty.warn('Consider updating to the latest version of this package.') - tty.warn('More details at {homepage}'.format(homepage=Openssl.homepage)) + 'This installation depends on an old version of OpenSSL, ' + 'which may have known security issues. ') + tty.warn( + 'Consider updating to the latest version of this package.') + tty.warn('More details at {homepage}'.format( + homepage=Openssl.homepage)) warnings_given_to_user[version] = True return openssl_url + def install(self, spec, prefix): # OpenSSL uses a variable APPS in its Makefile. If it happens to be set # in the environment, then this will override what is set in the # Makefile, leading to build errors. env.pop('APPS', None) - if spec.satisfies("target=x86_64") or spec.satisfies("target=ppc64"): + + if spec.satisfies('target=x86_64') or spec.satisfies('target=ppc64'): # This needs to be done for all 64-bit architectures (except Linux, # where it happens automatically?) env['KERNEL_BITS'] = '64' - config = Executable("./config") - config("--prefix=%s" % prefix, - "--openssldir=%s" % join_path(prefix, 'etc', 'openssl'), - "zlib", - "no-krb5", - "shared") + + options = ['zlib', 'no-krb5', 'shared'] + + config = Executable('./config') + config('--prefix=%s' % prefix, + '--openssldir=%s' % join_path(prefix, 'etc', 'openssl'), + *options) + # Remove non-standard compiler options if present. These options are # present e.g. on Darwin. They are non-standard, i.e. most compilers # (e.g. gcc) will not accept them. filter_file(r'-arch x86_64', '', 'Makefile') make() - make("install") + make('install') diff --git a/var/spack/repos/builtin/packages/petsc/package.py b/var/spack/repos/builtin/packages/petsc/package.py index 8dd1d8d2b9..6a7bee9788 100644 --- a/var/spack/repos/builtin/packages/petsc/package.py +++ b/var/spack/repos/builtin/packages/petsc/package.py @@ -148,6 +148,22 @@ class Petsc(Package): make('MAKE_NP=%s' % make_jobs, parallel=False) make("install") + # solve Poisson equation in 2D to make sure nothing is broken: + with working_dir('src/ksp/ksp/examples/tutorials'): + cc = os.environ['CC'] if '~mpi' in self.spec else self.spec['mpi'].mpicc # NOQA: ignore=E501 + os.system('%s ex50.c -I%s -L%s -lpetsc -o ex50' % ( + cc, prefix.include, prefix.lib)) + ex50 = Executable('./ex50') + ex50('-da_grid_x', '4', '-da_grid_y', '4') + if 'superlu-dist' in spec: + ex50('-da_grid_x', '4', '-da_grid_y', '4', '-pc_type', 'lu', '-pc_factor_mat_solver_package', 'superlu_dist') # NOQA: ignore=E501 + + if 'mumps' in spec: + ex50('-da_grid_x', '4', '-da_grid_y', '4', '-pc_type', 'lu', '-pc_factor_mat_solver_package', 'mumps') # NOQA: ignore=E501 + + if 'hypre' in spec: + ex50('-da_grid_x', '4', '-da_grid_y', '4', '-pc_type', 'hypre', '-pc_hypre_type', 'boomeramg') # NOQA: ignore=E501 + 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) diff --git a/var/spack/repos/builtin/packages/py-docutils/package.py b/var/spack/repos/builtin/packages/py-docutils/package.py new file mode 100644 index 0000000000..3a938d918b --- /dev/null +++ b/var/spack/repos/builtin/packages/py-docutils/package.py @@ -0,0 +1,43 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created 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 Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, 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 Lesser 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 PyDocutils(Package): + """Docutils is an open-source text processing system for processing + plaintext documentation into useful formats, such as HTML, LaTeX, + man-pages, open-document or XML. It includes reStructuredText, the + easy to read, easy to use, what-you-see-is-what-you-get plaintext + markup language.""" + + homepage = "http://docutils.sourceforge.net/" + url = "https://pypi.python.org/packages/source/d/docutils/docutils-0.12.tar.gz" + + version('0.12', '4622263b62c5c771c03502afa3157768') + + extends('python') + + def install(self, spec, prefix): + python('setup.py', 'install', '--prefix={0}'.format(prefix)) diff --git a/var/spack/repos/builtin/packages/py-h5py/package.py b/var/spack/repos/builtin/packages/py-h5py/package.py index 0180b658f5..67461babe7 100644 --- a/var/spack/repos/builtin/packages/py-h5py/package.py +++ b/var/spack/repos/builtin/packages/py-h5py/package.py @@ -43,8 +43,8 @@ class PyH5py(Package): # Build dependencies depends_on('py-cython@0.19:') depends_on('pkg-config') - depends_on('hdf5@1.8.4:+mpi', when='+mpi') - depends_on('hdf5@1.8.4:~mpi', when='~mpi') + depends_on('hdf5@1.8.4:') + depends_on('hdf5+mpi', when='+mpi') depends_on('mpi', when='+mpi') # Build and runtime dependencies diff --git a/var/spack/repos/builtin/packages/py-restview/package.py b/var/spack/repos/builtin/packages/py-restview/package.py new file mode 100644 index 0000000000..91b1db993e --- /dev/null +++ b/var/spack/repos/builtin/packages/py-restview/package.py @@ -0,0 +1,41 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created 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 Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, 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 Lesser 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 PyRestview(Package): + """A viewer for ReStructuredText documents that renders them on the fly.""" + + homepage = "https://mg.pov.lt/restview/" + url = "https://pypi.python.org/packages/source/r/restview/restview-2.6.1.tar.gz" + + version('2.6.1', 'ac8b70e15b8f1732d1733d674813666b') + + extends('python') + depends_on('py-docutils') + depends_on('py-pygments') + + def install(self, spec, prefix): + python('setup.py', 'install', '--prefix={0}'.format(prefix)) diff --git a/var/spack/repos/builtin/packages/python/package.py b/var/spack/repos/builtin/packages/python/package.py index 8033c52b91..d019133585 100644 --- a/var/spack/repos/builtin/packages/python/package.py +++ b/var/spack/repos/builtin/packages/python/package.py @@ -47,6 +47,8 @@ class Python(Package): extendable = True + variant('ucs4', default=False, description='Enable UCS4 unicode strings') + depends_on("openssl") depends_on("bzip2") depends_on("readline") @@ -82,6 +84,9 @@ class Python(Package): "LDFLAGS=-L{0}".format(ldflags) ] + if '+ucs4' in spec: + config_args.append('--enable-unicode=ucs4') + if spec.satisfies('@3:'): config_args.append('--without-ensurepip') diff --git a/var/spack/repos/builtin/packages/r-bh/package.py b/var/spack/repos/builtin/packages/r-bh/package.py new file mode 100644 index 0000000000..a0f30b779f --- /dev/null +++ b/var/spack/repos/builtin/packages/r-bh/package.py @@ -0,0 +1,54 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created 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 Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, 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 Lesser 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 RBh(Package): + """Boost provides free peer-reviewed portable C++ source libraries. A large + part of Boost is provided as C++ template code which is resolved entirely + at compile-time without linking. This package aims to provide the most + useful subset of Boost libraries for template use among CRAN package. By + placing these libraries in this package, we offer a more efficient + distribution system for CRAN as replication of this code in the sources of + other packages is avoided. As of release 1.60.0-2, the following Boost + libraries are included: 'algorithm' 'any' 'bimap' 'bind' 'circular_buffer' + 'concept' 'config' 'container' 'date'_'time' 'detail' 'dynamic_bitset' + 'exception' 'filesystem' 'flyweight' 'foreach' 'functional' 'fusion' + 'geometry' 'graph' 'heap' 'icl' 'integer' 'interprocess' 'intrusive' 'io' + 'iostreams' 'iterator' 'math' 'move' 'mpl' 'multiprcecision' 'numeric' + 'pending' 'phoenix' 'preprocessor' 'random' 'range' 'smart_ptr' 'spirit' + 'tuple' 'type_trains' 'typeof' 'unordered' 'utility' 'uuid'.""" + + homepage = "https://cran.r-project.org/web/packages/BH/index.html" + url = "https://cran.r-project.org/src/contrib/BH_1.60.0-2.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/BH" + + version('1.60.0-2', 'b50fdc85285da05add4e9da664a2d551') + + extends('R') + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-colorspace/package.py b/var/spack/repos/builtin/packages/r-colorspace/package.py new file mode 100644 index 0000000000..a7622cad95 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-colorspace/package.py @@ -0,0 +1,44 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created 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 Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, 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 Lesser 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 RColorspace(Package): + """Carries out mapping between assorted color spaces including RGB, HSV, + HLS, CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB and polar CIELAB. + Qualitative, sequential, and diverging color palettes based on HCL colors + are provided.""" + + homepage = "https://cran.r-project.org/web/packages/colorspace/index.html" + url = "https://cran.r-project.org/src/contrib/colorspace_1.2-6.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/colorspace" + + version('1.2-6', 'a30191e9caf66f77ff4e99c062e9dce1') + + extends('R') + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-dichromat/package.py b/var/spack/repos/builtin/packages/r-dichromat/package.py new file mode 100644 index 0000000000..663e5295af --- /dev/null +++ b/var/spack/repos/builtin/packages/r-dichromat/package.py @@ -0,0 +1,42 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created 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 Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, 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 Lesser 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 RDichromat(Package): + """Collapse red-green or green-blue distinctions to simulate the effects of + different types of color-blindness.""" + + homepage = "https://cran.r-project.org/web/packages/dichromat/index.html" + url = "https://cran.r-project.org/src/contrib/dichromat_2.0-0.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/dichromat" + + version('2.0-0', '84e194ac95a69763d740947a7ee346a6') + + extends('R') + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-ggplot2/package.py b/var/spack/repos/builtin/packages/r-ggplot2/package.py new file mode 100644 index 0000000000..2d1f53af26 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-ggplot2/package.py @@ -0,0 +1,54 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created 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 Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, 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 Lesser 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 RGgplot2(Package): + """An implementation of the grammar of graphics in R. It combines the + advantages of both base and lattice graphics: conditioning and shared axes + are handled automatically, and you can still build up a plot step by step + from multiple data sources. It also implements a sophisticated + multidimensional conditioning system and a consistent interface to map data + to aesthetic attributes. See http://ggplot2.org for more information, + documentation and examples.""" + + homepage = "http://ggplot2.org/" + url = "https://cran.r-project.org/src/contrib/ggplot2_2.1.0.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/ggplot2" + + version('2.1.0', '771928cfb97c649c720423deb3ec7fd3') + + extends('R') + + depends_on('r-digest') + depends_on('r-gtable') + depends_on('r-mass') + depends_on('r-plyr') + depends_on('r-reshape2') + depends_on('r-scales') + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-gridextra/package.py b/var/spack/repos/builtin/packages/r-gridextra/package.py new file mode 100644 index 0000000000..d215d10678 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-gridextra/package.py @@ -0,0 +1,44 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created 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 Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, 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 Lesser 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 RGridextra(Package): + """Provides a number of user-level functions to work with "grid" graphics, + notably to arrange multiple grid-based plots on a page, and draw tables.""" + + homepage = "https://github.com/baptiste/gridextra" + url = "https://cran.r-project.org/src/contrib/gridExtra_2.2.1.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/gridExtra" + + version('2.2.1', '7076c2122d387c7ef3add69a1c4fc1b2') + + extends('R') + + depends_on('r-gtable') + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-gtable/package.py b/var/spack/repos/builtin/packages/r-gtable/package.py new file mode 100644 index 0000000000..74dee0b3d5 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-gtable/package.py @@ -0,0 +1,41 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created 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 Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, 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 Lesser 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 RGtable(Package): + """Tools to make it easier to work with "tables" of 'grobs'.""" + + homepage = "https://cran.r-project.org/web/packages/gtable/index.html" + url = "https://cran.r-project.org/src/contrib/gtable_0.2.0.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/gtable" + + version('0.2.0', '124090ae40b2dd3170ae11180e0d4cab') + + extends('R') + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-inline/package.py b/var/spack/repos/builtin/packages/r-inline/package.py new file mode 100644 index 0000000000..35eb8ca76f --- /dev/null +++ b/var/spack/repos/builtin/packages/r-inline/package.py @@ -0,0 +1,43 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created 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 Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, 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 Lesser 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 RInline(Package): + """Functionality to dynamically define R functions and S4 methods with + inlined C, C++ or Fortran code supporting .C and .Call calling + conventions.""" + + homepage = "https://cran.r-project.org/web/packages/inline/index.html" + url = "https://cran.r-project.org/src/contrib/inline_0.3.14.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/inline" + + version('0.3.14', '9fe304a6ebf0e3889c4c6a7ad1c50bca') + + extends('R') + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-labeling/package.py b/var/spack/repos/builtin/packages/r-labeling/package.py new file mode 100644 index 0000000000..02e5da9d85 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-labeling/package.py @@ -0,0 +1,41 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created 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 Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, 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 Lesser 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 RLabeling(Package): + """Provides a range of axis labeling algorithms.""" + + homepage = "https://cran.r-project.org/web/packages/labeling/index.html" + url = "https://cran.r-project.org/src/contrib/labeling_0.3.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/labeling" + + version('0.3', 'ccd7082ec0b211aba8a89d85176bb534') + + extends('R') + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-lattice/package.py b/var/spack/repos/builtin/packages/r-lattice/package.py new file mode 100644 index 0000000000..ba29feefc4 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-lattice/package.py @@ -0,0 +1,44 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created 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 Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, 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 Lesser 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 RLattice(Package): + """A powerful and elegant high-level data visualization system inspired by + Trellis graphics, with an emphasis on multivariate data. Lattice is + sufficient for typical graphics needs, and is also flexible enough to + handle most nonstandard requirements. See ?Lattice for an introduction.""" + + homepage = "http://lattice.r-forge.r-project.org/" + url = "https://cran.r-project.org/src/contrib/lattice_0.20-33.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/lattice" + + version('0.20-33', 'd487c94db1bfe00a27270f4c71baf53e') + + extends('R') + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-magrittr/package.py b/var/spack/repos/builtin/packages/r-magrittr/package.py new file mode 100644 index 0000000000..11476c3d1e --- /dev/null +++ b/var/spack/repos/builtin/packages/r-magrittr/package.py @@ -0,0 +1,45 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created 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 Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, 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 Lesser 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 RMagrittr(Package): + """Provides a mechanism for chaining commands with a new forward-pipe + operator, %>%. This operator will forward a value, or the result of an + expression, into the next function call/expression. There is flexible + support for the type of right-hand side expressions. For more information, + see package vignette.""" + + homepage = "https://cran.r-project.org/web/packages/magrittr/index.html" + url = "https://cran.r-project.org/src/contrib/magrittr_1.5.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/magrittr" + + version('1.5', 'e74ab7329f2b9833f0c3c1216f86d65a') + + extends('R') + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-mass/package.py b/var/spack/repos/builtin/packages/r-mass/package.py new file mode 100644 index 0000000000..1ab01d2256 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-mass/package.py @@ -0,0 +1,42 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created 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 Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, 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 Lesser 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 RMass(Package): + """Functions and datasets to support Venables and Ripley, "Modern Applied + Statistics with S" (4th edition, 2002).""" + + homepage = "http://www.stats.ox.ac.uk/pub/MASS4/" + url = "https://cran.r-project.org/src/contrib/MASS_7.3-45.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/MASS" + + version('7.3-45', 'aba3d12fab30f1793bee168a1efea88b') + + extends('R') + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-matrix/package.py b/var/spack/repos/builtin/packages/r-matrix/package.py new file mode 100644 index 0000000000..fbd8a7b4df --- /dev/null +++ b/var/spack/repos/builtin/packages/r-matrix/package.py @@ -0,0 +1,44 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created 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 Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, 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 Lesser 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 RMatrix(Package): + """Classes and methods for dense and sparse matrices and operations on them + using 'LAPACK' and 'SuiteSparse'.""" + + homepage = "http://matrix.r-forge.r-project.org/" + url = "https://cran.r-project.org/src/contrib/Matrix_1.2-6.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/Matrix" + + version('1.2-6', 'f545307fb1284861e9266c4e9712c55e') + + extends('R') + + depends_on('r-lattice') + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-munsell/package.py b/var/spack/repos/builtin/packages/r-munsell/package.py new file mode 100644 index 0000000000..3216c95e00 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-munsell/package.py @@ -0,0 +1,47 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created 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 Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, 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 Lesser 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 RMunsell(Package): + """Provides easy access to, and manipulation of, the Munsell colours. + Provides a mapping between Munsell's original notation (e.g. "5R 5/10") and + hexadecimal strings suitable for use directly in R graphics. Also provides + utilities to explore slices through the Munsell colour tree, to transform + Munsell colours and display colour palettes.""" + + homepage = "https://cran.r-project.org/web/packages/munsell/index.html" + url = "https://cran.r-project.org/src/contrib/munsell_0.4.3.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/munsell" + + version('0.4.3', 'ebd205323dc37c948f499ee08be9c476') + + extends('R') + + depends_on('r-colorspace') + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-plyr/package.py b/var/spack/repos/builtin/packages/r-plyr/package.py new file mode 100644 index 0000000000..192e7e8b18 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-plyr/package.py @@ -0,0 +1,49 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created 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 Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, 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 Lesser 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 RPlyr(Package): + """A set of tools that solves a common set of problems: you need to break a + big problem down into manageable pieces, operate on each piece and then put + all the pieces back together. For example, you might want to fit a model to + each spatial location or time point in your study, summarise data by panels + or collapse high-dimensional arrays to simpler summary statistics. The + development of 'plyr' has been generously supported by 'Becton + Dickinson'.""" + + homepage = "http://had.co.nz/plyr" + url = "https://cran.r-project.org/src/contrib/plyr_1.8.4.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/plyr" + + version('1.8.4', 'ef455cf7fc06e34837692156b7b2587b') + + extends('R') + + depends_on('r-rcpp') + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-rcolorbrewer/package.py b/var/spack/repos/builtin/packages/r-rcolorbrewer/package.py new file mode 100644 index 0000000000..b81ec2561c --- /dev/null +++ b/var/spack/repos/builtin/packages/r-rcolorbrewer/package.py @@ -0,0 +1,42 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created 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 Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, 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 Lesser 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 RRcolorbrewer(Package): + """Provides color schemes for maps (and other graphics) designed by Cynthia + Brewer as described at http://colorbrewer2.org""" + + homepage = "http://colorbrewer2.org" + url = "https://cran.r-project.org/src/contrib/RColorBrewer_1.1-2.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/RColorBrewer" + + version('1.1-2', '66054d83eade4dff8a43ad4732691182') + + extends('R') + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-rcpp/package.py b/var/spack/repos/builtin/packages/r-rcpp/package.py new file mode 100644 index 0000000000..2428f4af3b --- /dev/null +++ b/var/spack/repos/builtin/packages/r-rcpp/package.py @@ -0,0 +1,49 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created 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 Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, 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 Lesser 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 RRcpp(Package): + """The 'Rcpp' package provides R functions as well as C++ classes which + offer a seamless integration of R and C++. Many R data types and objects + can be mapped back and forth to C++ equivalents which facilitates both + writing of new code as well as easier integration of third-party libraries. + Documentation about 'Rcpp' is provided by several vignettes included in + this package, via the 'Rcpp Gallery' site at <http://gallery.rcpp.org>, the + paper by Eddelbuettel and Francois (2011, JSS), and the book by + Eddelbuettel (2013, Springer); see 'citation("Rcpp")' for details on these + last two.""" + + homepage = "http://dirk.eddelbuettel.com/code/rcpp.html" + url = "https://cran.r-project.org/src/contrib/Rcpp_0.12.5.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/Rcpp" + + version('0.12.5', 'f03ec05b4e391cc46e7ce330e82ff5e2') + + extends('R') + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-rcppeigen/package.py b/var/spack/repos/builtin/packages/r-rcppeigen/package.py new file mode 100644 index 0000000000..3175628a73 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-rcppeigen/package.py @@ -0,0 +1,56 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created 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 Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, 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 Lesser 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 RRcppeigen(Package): + """R and 'Eigen' integration using 'Rcpp'. 'Eigen' is a C++ template + library for linear algebra: matrices, vectors, numerical solvers and + related algorithms. It supports dense and sparse matrices on integer, + floating point and complex numbers, decompositions of such matrices, and + solutions of linear systems. Its performance on many algorithms is + comparable with some of the best implementations based on 'Lapack' and + level-3 'BLAS'. The 'RcppEigen' package includes the header files from the + 'Eigen' C++ template library (currently version 3.2.8). Thus users do not + need to install 'Eigen' itself in order to use 'RcppEigen'. Since version + 3.1.1, 'Eigen' is licensed under the Mozilla Public License (version 2); + earlier version were licensed under the GNU LGPL version 3 or later. + 'RcppEigen' (the 'Rcpp' bindings/bridge to 'Eigen') is licensed under the + GNU GPL version 2 or later, as is the rest of 'Rcpp'.""" + + homepage = "http://eigen.tuxfamily.org/" + url = "https://cran.r-project.org/src/contrib/RcppEigen_0.3.2.8.1.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/RcppEigen" + + version('0.3.2.8.1', '4146e06e4fdf7f4d08db7839069d479f') + + extends('R') + + depends_on('r-matrix') + depends_on('r-rcpp') + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-reshape2/package.py b/var/spack/repos/builtin/packages/r-reshape2/package.py new file mode 100644 index 0000000000..a96a314008 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-reshape2/package.py @@ -0,0 +1,46 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created 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 Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, 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 Lesser 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 RReshape2(Package): + """Flexibly restructure and aggregate data using just two functions: melt + and dcast (or acast).""" + + homepage = "https://github.com/hadley/reshape" + url = "https://cran.r-project.org/src/contrib/reshape2_1.4.1.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/reshape2" + + version('1.4.1', '41e9dffdf5c6fa830321ac9c8ebffe00') + + extends('R') + + depends_on('r-plyr') + depends_on('r-stringr') + depends_on('r-rcpp') + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-rstan/package.py b/var/spack/repos/builtin/packages/r-rstan/package.py new file mode 100644 index 0000000000..00fd5116d9 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-rstan/package.py @@ -0,0 +1,57 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created 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 Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, 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 Lesser 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 RRstan(Package): + """User-facing R functions are provided to parse, compile, test, estimate, + and analyze Stan models by accessing the header-only Stan library provided + by the 'StanHeaders' package. The Stan project develops a probabilistic + programming language that implements full Bayesian statistical inference + via Markov Chain Monte Carlo, rough Bayesian inference via variational + approximation, and (optionally penalized) maximum likelihood estimation via + optimization. In all three cases, automatic differentiation is used to + quickly and accurately evaluate gradients without burdening the user with + the need to derive the partial derivatives.""" + + homepage = "http://mc-stan.org/" + url = "https://cran.r-project.org/src/contrib/rstan_2.10.1.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/rstan" + + version('2.10.1', 'f5d212f6f8551bdb91fe713d05d4052a') + + extends('R') + + depends_on('r-ggplot2') + depends_on('r-stanheaders') + depends_on('r-inline') + depends_on('r-gridextra') + depends_on('r-rcpp') + depends_on('r-rcppeigen') + depends_on('r-bh') + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-scales/package.py b/var/spack/repos/builtin/packages/r-scales/package.py new file mode 100644 index 0000000000..046a05d48e --- /dev/null +++ b/var/spack/repos/builtin/packages/r-scales/package.py @@ -0,0 +1,49 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created 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 Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, 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 Lesser 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 RScales(Package): + """Graphical scales map data to aesthetics, and provide methods for + automatically determining breaks and labels for axes and legends.""" + + homepage = "https://github.com/hadley/scales" + url = "https://cran.r-project.org/src/contrib/scales_0.4.0.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/scales" + + version('0.4.0', '7b5602d9c55595901192248bca25c099') + + extends('R') + + depends_on('r-rcolorbrewer') + depends_on('r-dichromat') + depends_on('r-plyr') + depends_on('r-munsell') + depends_on('r-labeling') + depends_on('r-rcpp') + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-stanheaders/package.py b/var/spack/repos/builtin/packages/r-stanheaders/package.py new file mode 100644 index 0000000000..c77b5aa8b6 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-stanheaders/package.py @@ -0,0 +1,55 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created 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 Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, 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 Lesser 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 RStanheaders(Package): + """The C++ header files of the Stan project are provided by this package, + but it contains no R code, vignettes, or function documentation. There is a + shared object containing part of the CVODES library, but it is not + accessible from R. StanHeaders is only useful for developers who want to + utilize the LinkingTo directive of their package's DESCRIPTION file to + build on the Stan library without incurring unnecessary dependencies. The + Stan project develops a probabilistic programming language that implements + full or approximate Bayesian statistical inference via Markov Chain Monte + Carlo or variational methods and implements (optionally penalized) maximum + likelihood estimation via optimization. The Stan library includes an + advanced automatic differentiation scheme, templated statistical and linear + algebra functions that can handle the automatically differentiable scalar + types (and doubles, ints, etc.), and a parser for the Stan language. The + 'rstan' package provides user-facing R functions to parse, compile, test, + estimate, and analyze Stan models.""" + + homepage = "http://mc-stan.org/" + url = "https://cran.r-project.org/src/contrib/StanHeaders_2.10.0-2.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/StanHeaders" + + version('2.10.0-2', '9d09b1e9278f08768f7a988ad9082d57') + + extends('R') + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-stringi/package.py b/var/spack/repos/builtin/packages/r-stringi/package.py new file mode 100644 index 0000000000..22774dedec --- /dev/null +++ b/var/spack/repos/builtin/packages/r-stringi/package.py @@ -0,0 +1,51 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created 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 Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, 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 Lesser 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 RStringi(Package): + """Allows for fast, correct, consistent, portable, as well as convenient + character string/text processing in every locale and any native encoding. + Owing to the use of the ICU library, the package provides R users with + platform-independent functions known to Java, Perl, Python, PHP, and Ruby + programmers. Among available features there are: pattern searching (e.g., + with ICU Java-like regular expressions or the Unicode Collation Algorithm), + random string generation, case mapping, string transliteration, + concatenation, Unicode normalization, date-time formatting and parsing, + etc.""" + + homepage = "http://www.gagolewski.com/software/stringi/" + url = "https://cran.r-project.org/src/contrib/stringi_1.1.1.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/stringi" + + version('1.1.1', '32b919ee3fa8474530c4942962a6d8d9') + + extends('R') + + depends_on('icu') + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-stringr/package.py b/var/spack/repos/builtin/packages/r-stringr/package.py new file mode 100644 index 0000000000..01fd969522 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-stringr/package.py @@ -0,0 +1,48 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created 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 Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, 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 Lesser 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 RStringr(Package): + """A consistent, simple and easy to use set of wrappers around the + fantastic 'stringi' package. All function and argument names (and + positions) are consistent, all functions deal with "NA"'s and zero length + vectors in the same way, and the output from one function is easy to feed + into the input of another.""" + + homepage = "https://cran.r-project.org/web/packages/stringr/index.html" + url = "https://cran.r-project.org/src/contrib/stringr_1.0.0.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/stringr" + + version('1.0.0', '5ca977c90351f78b1b888b379114a7b4') + + extends('R') + + depends_on('r-stringi') + depends_on('r-magrittr') + + def install(self, spec, prefix): + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/ruby/package.py b/var/spack/repos/builtin/packages/ruby/package.py index dd71913fc9..8dc314c171 100644 --- a/var/spack/repos/builtin/packages/ruby/package.py +++ b/var/spack/repos/builtin/packages/ruby/package.py @@ -35,9 +35,20 @@ class Ruby(Package): extendable = True version('2.2.0', 'cd03b28fd0b555970f5c4fd481700852') + depends_on('libffi') + depends_on('zlib') + variant('openssl', default=False, description="Enable OpenSSL support") + depends_on('openssl', when='+openssl') + variant('readline', default=False, description="Enable Readline support") + depends_on('readline', when='+readline') def install(self, spec, prefix): - configure("--prefix=%s" % prefix) + options = ["--prefix=%s" % prefix] + if '+openssl' in spec: + options.append("--with-openssl-dir=%s" % spec['openssl'].prefix) + if '+readline' in spec: + options.append("--with-readline-dir=%s" % spec['readline'].prefix) + configure(*options) make() make("install") diff --git a/var/spack/repos/builtin/packages/suite-sparse/package.py b/var/spack/repos/builtin/packages/suite-sparse/package.py index dd0dfa3e23..2cc89b843f 100644 --- a/var/spack/repos/builtin/packages/suite-sparse/package.py +++ b/var/spack/repos/builtin/packages/suite-sparse/package.py @@ -33,6 +33,7 @@ class SuiteSparse(Package): url = 'http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-4.5.1.tar.gz' version('4.5.1', 'f0ea9aad8d2d1ffec66a5b6bfeff5319') + version('4.5.3', '8ec57324585df3c6483ad7f556afccbd') # FIXME: (see below) # variant('tbb', default=True, description='Build with Intel TBB') @@ -40,34 +41,35 @@ class SuiteSparse(Package): depends_on('blas') depends_on('lapack') - depends_on('metis@5.1.0', when='@4.5.1') + 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. + # 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 - # It's basically a plain Makefile which include an header (SuiteSparse_config/SuiteSparse_config.mk) - # with a lot of convoluted logic in it. - # Any kind of customization will need to go through filtering of that file + # The build system of SuiteSparse is quite old-fashioned. + # It's basically a plain Makefile which include an header + # (SuiteSparse_config/SuiteSparse_config.mk)with a lot of convoluted + # logic in it. Any kind of customization will need to go through + # filtering of that file make_args = ['INSTALL=%s' % prefix] # inject Spack compiler wrappers make_args.extend([ - 'AUTOCC=no', - 'CC=cc', - 'CXX=c++', - 'F77=f77', + '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, + 'MY_METIS_LIB=-L%s -lmetis' % spec['metis'].prefix.lib, + 'MY_METIS_INC=%s' % spec['metis'].prefix.include, ]) # Intel TBB in SuiteSparseQR @@ -78,10 +80,13 @@ class SuiteSparse(Package): ]) # BLAS arguments require path to libraries - # FIXME : (blas / lapack always provide libblas and liblapack as aliases) - make_args.extend([ - 'BLAS=-lblas', - 'LAPACK=-llapack' - ]) + # FIXME: (blas/lapack always provide libblas and liblapack as aliases) + if '@4.5.1' in spec: + # adding -lstdc++ is clearly an ugly way to do this, but it follows + # with the TCOV path of SparseSuite 4.5.1's Suitesparse_config.mk + make_args.extend([ + 'BLAS=-lblas -lstdc++', + 'LAPACK=-llapack' + ]) make('install', *make_args) diff --git a/var/spack/repos/builtin/packages/swiftsim/package.py b/var/spack/repos/builtin/packages/swiftsim/package.py index e4607d9146..42e8fb466a 100644 --- a/var/spack/repos/builtin/packages/swiftsim/package.py +++ b/var/spack/repos/builtin/packages/swiftsim/package.py @@ -25,16 +25,8 @@ from spack import * -import spack.environment import llnl.util.tty as tty -# Needed to be able to download from the Durham gitlab repository -tty.warn('Setting "GIT_SSL_NO_VERIFY=1"') -tty.warn('This is needed to clone SWIFT repository') -gitlab_env = spack.environment.EnvironmentModifications() -gitlab_env.set('GIT_SSL_NO_VERIFY', 1) -gitlab_env.apply_modifications() - class Swiftsim(Package): """ @@ -46,7 +38,7 @@ class Swiftsim(Package): homepage = 'http://icc.dur.ac.uk/swift/' url = 'http://gitlab.cosma.dur.ac.uk/swift/swiftsim/repository/archive.tar.gz?ref=v0.3.0' - version('0.3.0', git='https://gitlab.cosma.dur.ac.uk/swift/swiftsim.git', tag='v0.3.0') + version('0.3.0', git='https://gitlab.cosma.dur.ac.uk/swift/swiftsim.git', commit='254cc1b563b2f88ddcf437b1f71da123bb9db733') variant('mpi', default=True, description='Enable distributed memory parallelism') @@ -61,6 +53,12 @@ class Swiftsim(Package): depends_on('hdf5~mpi', when='~mpi') depends_on('hdf5+mpi', when='+mpi') + def setup_environment(self, spack_env, run_env): + # Needed to be able to download from the Durham gitlab repository + tty.warn('Setting "GIT_SSL_NO_VERIFY=1"') + tty.warn('This is needed to clone SWIFT repository') + spack_env.set('GIT_SSL_NO_VERIFY', 1) + def install(self, spec, prefix): # Generate configure from configure.ac # and Makefile.am |