diff options
52 files changed, 1921 insertions, 416 deletions
diff --git a/etc/spack/modules.yaml b/etc/spack/modules.yaml index 99be5e7b6d..5f31cdd5c0 100644 --- a/etc/spack/modules.yaml +++ b/etc/spack/modules.yaml @@ -22,8 +22,8 @@ modules: include: - CPATH lib/pkgconfig: - - PKGCONFIG + - PKG_CONFIG_PATH lib64/pkgconfig: - - PKGCONFIG + - PKG_CONFIG_PATH '': - CMAKE_PREFIX_PATH diff --git a/lib/spack/docs/basic_usage.rst b/lib/spack/docs/basic_usage.rst index 50c48b802b..ec193e767d 100644 --- a/lib/spack/docs/basic_usage.rst +++ b/lib/spack/docs/basic_usage.rst @@ -24,12 +24,29 @@ Spack can install: .. command-output:: spack list -The packages are listed by name in alphabetical order. You can also -do wildcats searches using ``*``: +The packages are listed by name in alphabetical order. If you specify a +pattern to match, it will follow this set of rules. A pattern with no +wildcards, ``*`` or ``?``, will be treated as though it started and ended with +``*``, so ``util`` is equivalent to ``*util*``. A pattern with no capital +letters will be treated as case-insensitive. You can also add the ``-i`` flag +to specify a case insensitive search, or ``-d`` to search the description of +the package in addition to the name. Some examples: -.. command-output:: spack list m* +All packages whose names contain "sql" case insensitive: -.. command-output:: spack list *util* +.. command-output:: spack list sql + +All packages whose names start with a capital M: + +.. command-output:: spack list 'M*' + +All packages whose names or descriptions contain Documentation: + +.. command-output:: spack list -d Documentation + +All packages whose names contain documentation case insensitive: + +.. command-output:: spack list -d documentation .. _spack-info: diff --git a/lib/spack/docs/packaging_guide.rst b/lib/spack/docs/packaging_guide.rst index 1f83f611b0..54b886310a 100644 --- a/lib/spack/docs/packaging_guide.rst +++ b/lib/spack/docs/packaging_guide.rst @@ -1950,6 +1950,19 @@ instead of hard-coding ``join_path(self.spec['mpi'].prefix.bin, 'mpicc')`` for the reasons outlined above. +Blas and Lapack libraries +~~~~~~~~~~~~~~~~~~~~~~~~~ +Different packages provide implementation of ``Blas`` and ``Lapack`` routines. +The names of the resulting static and/or shared libraries differ from package +to package. In order to make ``install()`` method indifferent to the +choice of ``Blas`` implementation, each package which provides it +sets up ``self.spec.blas_shared_lib`` and ``self.spec.blas_static_lib `` to +point to the shared and static ``Blas`` libraries, respectively. The same +applies to packages which provide ``Lapack``. Package developers are advised to +use these variables, for example ``spec['blas'].blas_shared_lib`` instead of +hard-coding ``join_path(spec['blas'].prefix.lib, 'libopenblas.so')``. + + Forking ``install()`` ~~~~~~~~~~~~~~~~~~~~~ diff --git a/lib/spack/llnl/util/filesystem.py b/lib/spack/llnl/util/filesystem.py index 6661a80f27..d72e8bae92 100644 --- a/lib/spack/llnl/util/filesystem.py +++ b/lib/spack/llnl/util/filesystem.py @@ -22,28 +22,28 @@ # License along with this program; if not, write to the Free Software # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## -__all__ = ['set_install_permissions', 'install', 'install_tree', 'traverse_tree', - 'expand_user', 'working_dir', 'touch', 'touchp', 'mkdirp', - 'force_remove', 'join_path', 'ancestor', 'can_access', 'filter_file', - 'FileFilter', 'change_sed_delimiter', 'is_exe', 'force_symlink', - 'set_executable', 'copy_mode', 'unset_executable_mode', - 'remove_dead_links', 'remove_linked_tree', 'find_library_path', - 'fix_darwin_install_name'] - import os import glob -import sys import re import shutil import stat import errno import getpass from contextlib import contextmanager, closing -from tempfile import NamedTemporaryFile import subprocess import llnl.util.tty as tty -from spack.util.compression import ALLOWED_ARCHIVE_TYPES + +__all__ = ['set_install_permissions', 'install', 'install_tree', + 'traverse_tree', + 'expand_user', 'working_dir', 'touch', 'touchp', 'mkdirp', + 'force_remove', 'join_path', 'ancestor', 'can_access', + 'filter_file', + 'FileFilter', 'change_sed_delimiter', 'is_exe', 'force_symlink', + 'set_executable', 'copy_mode', 'unset_executable_mode', + 'remove_dead_links', 'remove_linked_tree', 'find_library_path', + 'fix_darwin_install_name', 'to_link_flags'] + def filter_file(regex, repl, *filenames, **kwargs): """Like sed, but uses python regular expressions. @@ -69,6 +69,7 @@ def filter_file(regex, repl, *filenames, **kwargs): # Allow strings to use \1, \2, etc. for replacement, like sed if not callable(repl): unescaped = repl.replace(r'\\', '\\') + def replace_groups_with_groupid(m): def groupid_to_group(x): return m.group(int(x.group(1))) @@ -157,9 +158,12 @@ def set_install_permissions(path): def copy_mode(src, dest): src_mode = os.stat(src).st_mode dest_mode = os.stat(dest).st_mode - if src_mode & stat.S_IXUSR: dest_mode |= stat.S_IXUSR - if src_mode & stat.S_IXGRP: dest_mode |= stat.S_IXGRP - if src_mode & stat.S_IXOTH: dest_mode |= stat.S_IXOTH + if src_mode & stat.S_IXUSR: + dest_mode |= stat.S_IXUSR + if src_mode & stat.S_IXGRP: + dest_mode |= stat.S_IXGRP + if src_mode & stat.S_IXOTH: + dest_mode |= stat.S_IXOTH os.chmod(dest, dest_mode) @@ -224,9 +228,10 @@ def force_remove(*paths): for path in paths: try: os.remove(path) - except OSError, e: + except OSError: pass + @contextmanager def working_dir(dirname, **kwargs): if kwargs.get('create', False): @@ -240,7 +245,7 @@ def working_dir(dirname, **kwargs): def touch(path): """Creates an empty file at the specified path.""" - with open(path, 'a') as file: + with open(path, 'a'): os.utime(path, None) @@ -253,7 +258,7 @@ def touchp(path): def force_symlink(src, dest): try: os.symlink(src, dest) - except OSError as e: + except OSError: os.remove(dest) os.symlink(src, dest) @@ -275,7 +280,7 @@ def ancestor(dir, n=1): def can_access(file_name): """True if we have read/write access to the file.""" - return os.access(file_name, os.R_OK|os.W_OK) + return os.access(file_name, os.R_OK | os.W_OK) def traverse_tree(source_root, dest_root, rel_path='', **kwargs): @@ -343,13 +348,14 @@ def traverse_tree(source_root, dest_root, rel_path='', **kwargs): # Treat as a directory if os.path.isdir(source_child) and ( - follow_links or not os.path.islink(source_child)): + follow_links or not os.path.islink(source_child)): # When follow_nonexisting isn't set, don't descend into dirs # in source that do not exist in dest if follow_nonexisting or os.path.exists(dest_child): - tuples = traverse_tree(source_root, dest_root, rel_child, **kwargs) - for t in tuples: yield t + tuples = traverse_tree(source_root, dest_root, rel_child, **kwargs) # NOQA: ignore=E501 + for t in tuples: + yield t # Treat as a file. elif not ignore(os.path.join(rel_path, f)): @@ -379,6 +385,7 @@ def remove_dead_links(root): if not os.path.exists(real_path): os.unlink(path) + def remove_linked_tree(path): """ Removes a directory and its contents. If the directory is a @@ -402,28 +409,41 @@ def fix_darwin_install_name(path): Fix install name of dynamic libraries on Darwin to have full path. There are two parts of this task: (i) use install_name('-id',...) to change install name of a single lib; - (ii) use install_name('-change',...) to change the cross linking between libs. - The function assumes that all libraries are in one folder and currently won't - follow subfolders. + (ii) use install_name('-change',...) to change the cross linking between + libs. The function assumes that all libraries are in one folder and + currently won't follow subfolders. Args: path: directory in which .dylib files are alocated """ - libs = glob.glob(join_path(path,"*.dylib")) + libs = glob.glob(join_path(path, "*.dylib")) for lib in libs: # fix install name first: - subprocess.Popen(["install_name_tool", "-id",lib,lib], stdout=subprocess.PIPE).communicate()[0] - long_deps = subprocess.Popen(["otool", "-L",lib], stdout=subprocess.PIPE).communicate()[0].split('\n') + subprocess.Popen(["install_name_tool", "-id", lib, lib], stdout=subprocess.PIPE).communicate()[0] # NOQA: ignore=E501 + long_deps = subprocess.Popen(["otool", "-L", lib], stdout=subprocess.PIPE).communicate()[0].split('\n') # NOQA: ignore=E501 deps = [dep.partition(' ')[0][1::] for dep in long_deps[2:-1]] # fix all dependencies: for dep in deps: for loc in libs: if dep == os.path.basename(loc): - subprocess.Popen(["install_name_tool", "-change",dep,loc,lib], stdout=subprocess.PIPE).communicate()[0] + subprocess.Popen(["install_name_tool", "-change", dep, loc, lib], stdout=subprocess.PIPE).communicate()[0] # NOQA: ignore=E501 break +def to_link_flags(library): + """Transforms a path to a <library> into linking flags -L<dir> -l<name>. + + Return: + A string of linking flags. + """ + dir = os.path.dirname(library) + # Asume libXYZ.suffix + name = os.path.basename(library)[3:].split(".")[0] + res = '-L%s -l%s' % (dir, name) + return res + + def find_library_path(libname, *paths): """Searches for a file called <libname> in each path. diff --git a/lib/spack/spack/build_environment.py b/lib/spack/spack/build_environment.py index c5efa97c7b..83468be8e6 100644 --- a/lib/spack/spack/build_environment.py +++ b/lib/spack/spack/build_environment.py @@ -75,13 +75,13 @@ SPACK_NO_PARALLEL_MAKE = 'SPACK_NO_PARALLEL_MAKE' # set_build_environment_variables and used to pass parameters to # Spack's compiler wrappers. # -SPACK_ENV_PATH = 'SPACK_ENV_PATH' -SPACK_DEPENDENCIES = 'SPACK_DEPENDENCIES' -SPACK_PREFIX = 'SPACK_PREFIX' -SPACK_INSTALL = 'SPACK_INSTALL' -SPACK_DEBUG = 'SPACK_DEBUG' -SPACK_SHORT_SPEC = 'SPACK_SHORT_SPEC' -SPACK_DEBUG_LOG_DIR = 'SPACK_DEBUG_LOG_DIR' +SPACK_ENV_PATH = 'SPACK_ENV_PATH' +SPACK_DEPENDENCIES = 'SPACK_DEPENDENCIES' +SPACK_PREFIX = 'SPACK_PREFIX' +SPACK_INSTALL = 'SPACK_INSTALL' +SPACK_DEBUG = 'SPACK_DEBUG' +SPACK_SHORT_SPEC = 'SPACK_SHORT_SPEC' +SPACK_DEBUG_LOG_DIR = 'SPACK_DEBUG_LOG_DIR' # Platform-specific library suffix. @@ -98,6 +98,7 @@ class MakeExecutable(Executable): Note that if the SPACK_NO_PARALLEL_MAKE env var is set it overrides everything. """ + def __init__(self, name, jobs): super(MakeExecutable, self).__init__(name) self.jobs = jobs @@ -129,8 +130,13 @@ def load_module(mod): text = modulecmd('show', mod, output=str, error=str).split() for i, word in enumerate(text): if word == 'conflict': +<<<<<<< HEAD + exec(compile(modulecmd('unload', text[ + i + 1], output=str, error=str), '<string>', 'exec')) +======= exec(compile(modulecmd('unload', text[i + 1], output=str, error=str), '<string>', 'exec')) +>>>>>>> aa86488fd9809ced16704e4bd4d607c89d6dda75 # Load the module now that there are no conflicts load = modulecmd('load', mod, output=str, error=str) exec(compile(load, '<string>', 'exec')) @@ -188,20 +194,20 @@ def set_compiler_environment_variables(pkg, env): # TODO : add additional kwargs for better diagnostics, like requestor, # ttyout, ttyerr, etc. link_dir = spack.build_env_path - env.set('CC', join_path(link_dir, compiler.link_paths['cc'])) - env.set('CXX', join_path(link_dir, compiler.link_paths['cxx'])) - env.set('F77', join_path(link_dir, compiler.link_paths['f77'])) - env.set('FC', join_path(link_dir, compiler.link_paths['fc'])) # Set SPACK compiler variables so that our wrapper knows what to call if compiler.cc: env.set('SPACK_CC', compiler.cc) + env.set('CC', join_path(link_dir, compiler.link_paths['cc'])) if compiler.cxx: env.set('SPACK_CXX', compiler.cxx) + env.set('CXX', join_path(link_dir, compiler.link_paths['cxx'])) if compiler.f77: env.set('SPACK_F77', compiler.f77) + env.set('F77', join_path(link_dir, compiler.link_paths['f77'])) if compiler.fc: env.set('SPACK_FC', compiler.fc) + env.set('FC', join_path(link_dir, compiler.link_paths['fc'])) # Set SPACK compiler rpath flags so that our wrapper knows what to use env.set('SPACK_CC_RPATH_ARG', compiler.cc_rpath_arg) @@ -238,8 +244,13 @@ def set_build_environment_variables(pkg, env): # handled by putting one in the <build_env_path>/case-insensitive # directory. Add that to the path too. env_paths = [] +<<<<<<< HEAD + compiler_specific = join_path(spack.build_env_path, pkg.compiler.name) + for item in [spack.build_env_path, compiler_specific]: +======= for item in [spack.build_env_path, join_path(spack.build_env_path, pkg.compiler.name)]: +>>>>>>> aa86488fd9809ced16704e4bd4d607c89d6dda75 env_paths.append(item) ci = join_path(item, 'case-insensitive') if os.path.isdir(ci): @@ -269,8 +280,13 @@ def set_build_environment_variables(pkg, env): env.unset('DYLD_LIBRARY_PATH') # Add bin directories from dependencies to the PATH for the build. +<<<<<<< HEAD + bin_dirs = reversed( + filter(os.path.isdir, ['%s/bin' % prefix for prefix in dep_prefixes])) +======= bin_dirs = reversed(filter(os.path.isdir, ['%s/bin' % prefix for prefix in dep_prefixes])) +>>>>>>> aa86488fd9809ced16704e4bd4d607c89d6dda75 for item in bin_dirs: env.prepend_path('PATH', item) @@ -285,6 +301,10 @@ def set_build_environment_variables(pkg, env): for directory in ('lib', 'lib64', 'share'): pcdir = join_path(pre, directory, 'pkgconfig') if os.path.isdir(pcdir): +<<<<<<< HEAD + # pkg_config_dirs.append(pcdir) +======= +>>>>>>> aa86488fd9809ced16704e4bd4d607c89d6dda75 env.prepend_path('PKG_CONFIG_PATH', pcdir) if pkg.spec.architecture.target.module_name: @@ -308,7 +328,7 @@ def set_module_variables_for_package(pkg, module): m.make_jobs = jobs # TODO: make these build deps that can be installed if not found. - m.make = MakeExecutable('make', jobs) + m.make = MakeExecutable('make', jobs) m.gmake = MakeExecutable('gmake', jobs) m.scons = MakeExecutable('scons', jobs) @@ -339,29 +359,29 @@ def set_module_variables_for_package(pkg, module): # Put spack compiler paths in module scope. link_dir = spack.build_env_path - m.spack_cc = join_path(link_dir, pkg.compiler.link_paths['cc']) + m.spack_cc = join_path(link_dir, pkg.compiler.link_paths['cc']) m.spack_cxx = join_path(link_dir, pkg.compiler.link_paths['cxx']) m.spack_f77 = join_path(link_dir, pkg.compiler.link_paths['f77']) - m.spack_fc = join_path(link_dir, pkg.compiler.link_paths['fc']) + m.spack_fc = join_path(link_dir, pkg.compiler.link_paths['fc']) # Emulate some shell commands for convenience - m.pwd = os.getcwd - m.cd = os.chdir - m.mkdir = os.mkdir - m.makedirs = os.makedirs - m.remove = os.remove - m.removedirs = os.removedirs - m.symlink = os.symlink - - m.mkdirp = mkdirp - m.install = install + m.pwd = os.getcwd + m.cd = os.chdir + m.mkdir = os.mkdir + m.makedirs = os.makedirs + m.remove = os.remove + m.removedirs = os.removedirs + m.symlink = os.symlink + + m.mkdirp = mkdirp + m.install = install m.install_tree = install_tree - m.rmtree = shutil.rmtree - m.move = shutil.move + m.rmtree = shutil.rmtree + m.move = shutil.move # Useful directories within the prefix are encapsulated in # a Prefix object. - m.prefix = pkg.prefix + m.prefix = pkg.prefix # Platform-specific library suffix. m.dso_suffix = dso_suffix @@ -382,7 +402,13 @@ def get_rpaths(pkg): def parent_class_modules(cls): +<<<<<<< HEAD + """ + Get list of super class modules that are all descend from spack.Package + """ +======= """Get list of super class modules that all descend from spack.Package""" +>>>>>>> aa86488fd9809ced16704e4bd4d607c89d6dda75 if not issubclass(cls, spack.Package) or issubclass(spack.Package, cls): return [] result = [] @@ -405,7 +431,7 @@ def load_external_modules(pkg): def setup_package(pkg): """Execute all environment setup routines.""" spack_env = EnvironmentModifications() - run_env = EnvironmentModifications() + run_env = EnvironmentModifications() # Before proceeding, ensure that specs and packages are consistent # @@ -510,7 +536,9 @@ def fork(pkg, function): # message. Just make the parent exit with an error code. pid, returncode = os.waitpid(pid, 0) if returncode != 0: - raise InstallError("Installation process had nonzero exit code.") + message = "Installation process had nonzero exit code : {code}" + strcode = str(returncode) + raise InstallError(message.format(code=strcode)) class InstallError(spack.error.SpackError): diff --git a/lib/spack/spack/cmd/compiler.py b/lib/spack/spack/cmd/compiler.py index c95045ef85..c325628ebf 100644 --- a/lib/spack/spack/cmd/compiler.py +++ b/lib/spack/spack/cmd/compiler.py @@ -76,10 +76,16 @@ def compiler_find(args): if not paths: paths = get_path('PATH') - compilers = [c for c in spack.compilers.find_compilers(*args.add_paths) - if c.spec not in spack.compilers.all_compilers(scope=args.scope)] + # Don't initialize compilers config via compilers.get_compiler_config. + # Just let compiler_find do the + # entire process and return an empty config from all_compilers + # Default for any other process is init_config=True + compilers = [c for c in spack.compilers.find_compilers(*paths) + if c.spec not in spack.compilers.all_compilers( + scope=args.scope, init_config=False)] if compilers: - spack.compilers.add_compilers_to_config(compilers, scope=args.scope) + spack.compilers.add_compilers_to_config(compilers, scope=args.scope, + init_config=False) n = len(compilers) s = 's' if n > 1 else '' filename = spack.config.get_config_filename(args.scope, 'compilers') diff --git a/lib/spack/spack/cmd/list.py b/lib/spack/spack/cmd/list.py index 1e3699cee0..c921efd1bd 100644 --- a/lib/spack/spack/cmd/list.py +++ b/lib/spack/spack/cmd/list.py @@ -29,36 +29,62 @@ from llnl.util.tty.colify import colify import spack import fnmatch +import re + +description = "List available spack packages" -description ="List available spack packages" def setup_parser(subparser): subparser.add_argument( 'filter', nargs=argparse.REMAINDER, help='Optional glob patterns to filter results.') subparser.add_argument( - '-i', '--insensitive', action='store_true', default=False, - help='Filtering will be case insensitive.') + '-s', '--sensitive', action='store_true', default=False, + help='Use case-sensitive filtering. Default is case sensitive, ' + 'unless the query contains a capital letter.') + subparser.add_argument( + '-d', '--search-description', action='store_true', default=False, + help='Filtering will also search the description for a match.') def list(parser, args): # Start with all package names. - pkgs = spack.repo.all_package_names() + pkgs = set(spack.repo.all_package_names()) # filter if a filter arg was provided if args.filter: - def match(p, f): - if args.insensitive: - p = p.lower() - f = f.lower() - return fnmatch.fnmatchcase(p, f) - pkgs = [p for p in pkgs if any(match(p, f) for f in args.filter)] + res = [] + for f in args.filter: + if '*' not in f and '?' not in f: + r = fnmatch.translate('*' + f + '*') + else: + r = fnmatch.translate(f) + + re_flags = re.I + if any(l.isupper for l in f) or args.sensitive: + re_flags = 0 + rc = re.compile(r, flags=re_flags) + res.append(rc) + + if args.search_description: + def match(p, f): + if f.match(p): + return True + + pkg = spack.repo.get(p) + if pkg.__doc__: + return f.match(pkg.__doc__) + return False + else: + def match(p, f): + return f.match(p) + pkgs = [p for p in pkgs if any(match(p, f) for f in res)] # sort before displaying. - sorted_packages = sorted(pkgs, key=lambda s:s.lower()) + sorted_packages = sorted(pkgs, key=lambda s: s.lower()) # Print all the package names in columns - indent=0 + indent = 0 if sys.stdout.isatty(): tty.msg("%d packages." % len(sorted_packages)) colify(sorted_packages, indent=indent) diff --git a/lib/spack/spack/compilers/__init__.py b/lib/spack/spack/compilers/__init__.py index ae72b743b2..a70d42982f 100644 --- a/lib/spack/spack/compilers/__init__.py +++ b/lib/spack/spack/compilers/__init__.py @@ -83,7 +83,7 @@ def _to_dict(compiler): return {'compiler': d} -def get_compiler_config(scope=None): +def get_compiler_config(scope=None, init_config=True): """Return the compiler configuration for the specified architecture. """ def init_compiler_config(): @@ -93,12 +93,12 @@ def get_compiler_config(scope=None): for compiler in compilers: compilers_dict.append(_to_dict(compiler)) spack.config.update_config('compilers', compilers_dict, scope=scope) - + config = spack.config.get_config('compilers', scope=scope) # Update the configuration if there are currently no compilers # configured. Avoid updating automatically if there ARE site # compilers configured but no user ones. - if not config: + if not config and init_config: if scope is None: # We know no compilers were configured in any scope. init_compiler_config() @@ -117,14 +117,14 @@ def get_compiler_config(scope=None): return [] # Return empty list which we will later append to. -def add_compilers_to_config(compilers, scope=None): +def add_compilers_to_config(compilers, scope=None, init_config=True): """Add compilers to the config for the specified architecture. Arguments: - compilers: a list of Compiler objects. - scope: configuration scope to modify. """ - compiler_config = get_compiler_config(scope) + compiler_config = get_compiler_config(scope, init_config) for compiler in compilers: compiler_config.append(_to_dict(compiler)) global _cache_config_file @@ -153,23 +153,23 @@ def remove_compiler_from_config(compiler_spec, scope=None): spack.config.update_config('compilers', filtered_compiler_config, scope) -def all_compilers_config(scope=None): +def all_compilers_config(scope=None, init_config=True): """Return a set of specs for all the compiler versions currently available to build with. These are instances of CompilerSpec. """ # Get compilers for this architecture. global _cache_config_file #Create a cache of the config file so we don't load all the time. if not _cache_config_file: - _cache_config_file = get_compiler_config(scope) + _cache_config_file = get_compiler_config(scope, init_config) return _cache_config_file else: return _cache_config_file -def all_compilers(scope=None): +def all_compilers(scope=None, init_config=True): # Return compiler specs from the merged config. return [spack.spec.CompilerSpec(s['compiler']['spec']) - for s in all_compilers_config(scope)] + for s in all_compilers_config(scope, init_config)] def default_compiler(): diff --git a/lib/spack/spack/compilers/gcc.py b/lib/spack/spack/compilers/gcc.py index 3f552eaece..2fae6688db 100644 --- a/lib/spack/spack/compilers/gcc.py +++ b/lib/spack/spack/compilers/gcc.py @@ -77,9 +77,9 @@ class Gcc(Compiler): return get_compiler_version( fc, '-dumpversion', # older gfortran versions don't have simple dumpversion output. - r'(?:GNU Fortran \(GCC\))?(\d+\.\d+(?:\.\d+)?)', module) + r'(?:GNU Fortran \(GCC\))?(\d+\.\d+(?:\.\d+)?)') @classmethod def f77_version(cls, f77): - return cls.fc_version(f77, module) + return cls.fc_version(f77) diff --git a/lib/spack/spack/environment.py b/lib/spack/spack/environment.py index af642dcc9b..30c6228ca4 100644 --- a/lib/spack/spack/environment.py +++ b/lib/spack/spack/environment.py @@ -1,4 +1,4 @@ -############################################################################## +# # Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. # Produced at the Lawrence Livermore National Laboratory. # @@ -21,14 +21,17 @@ # 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 collections import inspect +import json import os import os.path +import subprocess class NameModifier(object): + def __init__(self, name, **kwargs): self.name = name self.args = {'name': name} @@ -36,6 +39,7 @@ class NameModifier(object): class NameValueModifier(object): + def __init__(self, name, value, **kwargs): self.name = name self.value = value @@ -45,23 +49,27 @@ class NameValueModifier(object): class SetEnv(NameValueModifier): + def execute(self): os.environ[self.name] = str(self.value) class UnsetEnv(NameModifier): + def execute(self): # Avoid throwing if the variable was not set os.environ.pop(self.name, None) class SetPath(NameValueModifier): + def execute(self): string_path = concatenate_paths(self.value, separator=self.separator) os.environ[self.name] = string_path class AppendPath(NameValueModifier): + def execute(self): environment_value = os.environ.get(self.name, '') directories = environment_value.split( @@ -71,6 +79,7 @@ class AppendPath(NameValueModifier): class PrependPath(NameValueModifier): + def execute(self): environment_value = os.environ.get(self.name, '') directories = environment_value.split( @@ -80,6 +89,7 @@ class PrependPath(NameValueModifier): class RemovePath(NameValueModifier): + def execute(self): environment_value = os.environ.get(self.name, '') directories = environment_value.split( @@ -90,6 +100,7 @@ class RemovePath(NameValueModifier): class EnvironmentModifications(object): + """ Keeps track of requests to modify the current environment. @@ -240,6 +251,126 @@ class EnvironmentModifications(object): for x in actions: x.execute() + @staticmethod + def from_sourcing_files(*args, **kwargs): + """ + Creates an instance of EnvironmentModifications that, if executed, + has the same effect on the environment as sourcing the files passed as + parameters + + Args: + *args: list of files to be sourced + + Returns: + instance of EnvironmentModifications + """ + env = EnvironmentModifications() + # Check if the files are actually there + if not all(os.path.isfile(file) for file in args): + raise RuntimeError('trying to source non-existing files') + # Relevant kwd parameters and formats + info = dict(kwargs) + info.setdefault('shell', '/bin/bash') + info.setdefault('shell_options', '-c') + info.setdefault('source_command', 'source') + info.setdefault('suppress_output', '&> /dev/null') + info.setdefault('concatenate_on_success', '&&') + + shell = '{shell}'.format(**info) + shell_options = '{shell_options}'.format(**info) + source_file = '{source_command} {file} {concatenate_on_success}' + dump_environment = 'python -c "import os, json; print json.dumps(dict(os.environ))"' # NOQA: ignore=E501 + # Construct the command that will be executed + command = [source_file.format(file=file, **info) for file in args] + command.append(dump_environment) + command = ' '.join(command) + command = [ + shell, + shell_options, + command + ] + + # Try to source all the files, + proc = subprocess.Popen( + command, stdout=subprocess.PIPE, env=os.environ) + proc.wait() + if proc.returncode != 0: + raise RuntimeError('sourcing files returned a non-zero exit code') + output = ''.join([line for line in proc.stdout]) + # Construct a dictionary with all the variables in the new environment + after_source_env = dict(json.loads(output)) + this_environment = dict(os.environ) + + # Filter variables that are not related to sourcing a file + to_be_filtered = 'SHLVL', '_', 'PWD', 'OLDPWD' + for d in after_source_env, this_environment: + for name in to_be_filtered: + d.pop(name, None) + + # Fill the EnvironmentModifications instance + + # New variables + new_variables = set(after_source_env) - set(this_environment) + for x in new_variables: + env.set(x, after_source_env[x]) + # Variables that have been unset + unset_variables = set(this_environment) - set(after_source_env) + for x in unset_variables: + env.unset(x) + # Variables that have been modified + common_variables = set(this_environment).intersection(set(after_source_env)) # NOQA: ignore=E501 + modified_variables = [x for x in common_variables if this_environment[x] != after_source_env[x]] # NOQA: ignore=E501 + + def return_separator_if_any(first_value, second_value): + separators = ':', ';' + for separator in separators: + if separator in first_value and separator in second_value: + return separator + return None + + for x in modified_variables: + current = this_environment[x] + modified = after_source_env[x] + sep = return_separator_if_any(current, modified) + if sep is None: + # We just need to set the variable to the new value + env.set(x, after_source_env[x]) + else: + current_list = current.split(sep) + modified_list = modified.split(sep) + # Paths that have been removed + remove_list = [ + ii for ii in current_list if ii not in modified_list] + # Check that nothing has been added in the middle of vurrent + # list + remaining_list = [ + ii for ii in current_list if ii in modified_list] + start = modified_list.index(remaining_list[0]) + end = modified_list.index(remaining_list[-1]) + search = sep.join(modified_list[start:end + 1]) + if search not in current: + # We just need to set the variable to the new value + env.set(x, after_source_env[x]) + break + else: + try: + prepend_list = modified_list[:start] + except KeyError: + prepend_list = [] + try: + append_list = modified_list[end + 1:] + except KeyError: + append_list = [] + + for item in remove_list: + env.remove_path(x, item) + for item in append_list: + env.append_path(x, item) + for item in prepend_list: + env.prepend_path(x, item) + + return env + def concatenate_paths(paths, separator=':'): """ diff --git a/lib/spack/spack/hooks/sbang.py b/lib/spack/spack/hooks/sbang.py index 83d67ea225..cb0ad42b14 100644 --- a/lib/spack/spack/hooks/sbang.py +++ b/lib/spack/spack/hooks/sbang.py @@ -24,7 +24,6 @@ ############################################################################## import os -from llnl.util.filesystem import * import llnl.util.tty as tty import spack @@ -34,6 +33,7 @@ import spack.modules # here, as it is the shortest I could find on a modern OS. shebang_limit = 127 + def shebang_too_long(path): """Detects whether a file has a shebang line that is too long.""" with open(path, 'r') as script: @@ -57,16 +57,10 @@ def filter_shebang(path): if original.startswith(new_sbang_line): return - backup = path + ".shebang.bak" - os.rename(path, backup) - with open(path, 'w') as new_file: new_file.write(new_sbang_line) new_file.write(original) - copy_mode(backup, path) - unset_executable_mode(backup) - tty.warn("Patched overly long shebang in %s" % path) diff --git a/lib/spack/spack/test/data/sourceme_first.sh b/lib/spack/spack/test/data/sourceme_first.sh new file mode 100644 index 0000000000..800f639ac8 --- /dev/null +++ b/lib/spack/spack/test/data/sourceme_first.sh @@ -0,0 +1,3 @@ +#!/usr/bin/env bash +export NEW_VAR='new' +export UNSET_ME='overridden' diff --git a/lib/spack/spack/test/data/sourceme_second.sh b/lib/spack/spack/test/data/sourceme_second.sh new file mode 100644 index 0000000000..9955a0e6d6 --- /dev/null +++ b/lib/spack/spack/test/data/sourceme_second.sh @@ -0,0 +1,3 @@ +#!/usr/bin/env bash +export PATH_LIST='/path/first:/path/second:/path/fourth' +unset EMPTY_PATH_LIST
\ No newline at end of file diff --git a/lib/spack/spack/test/environment.py b/lib/spack/spack/test/environment.py index a0d959db2f..f3644cb0b7 100644 --- a/lib/spack/spack/test/environment.py +++ b/lib/spack/spack/test/environment.py @@ -24,16 +24,21 @@ ############################################################################## import unittest import os -import copy + +from spack import spack_root +from llnl.util.filesystem import join_path from spack.environment import EnvironmentModifications +from spack.environment import SetEnv, UnsetEnv +from spack.environment import RemovePath, PrependPath, AppendPath class EnvironmentTest(unittest.TestCase): + def setUp(self): os.environ['UNSET_ME'] = 'foo' os.environ['EMPTY_PATH_LIST'] = '' os.environ['PATH_LIST'] = '/path/second:/path/third' - os.environ['REMOVE_PATH_LIST'] = '/a/b:/duplicate:/a/c:/remove/this:/a/d:/duplicate/:/f/g' + os.environ['REMOVE_PATH_LIST'] = '/a/b:/duplicate:/a/c:/remove/this:/a/d:/duplicate/:/f/g' # NOQA: ignore=E501 def tearDown(self): pass @@ -77,9 +82,18 @@ class EnvironmentTest(unittest.TestCase): env.remove_path('REMOVE_PATH_LIST', '/duplicate/') env.apply_modifications() - self.assertEqual('/path/first:/path/second:/path/third:/path/last', os.environ['PATH_LIST']) - self.assertEqual('/path/first:/path/middle:/path/last', os.environ['EMPTY_PATH_LIST']) - self.assertEqual('/path/first:/path/middle:/path/last', os.environ['NEWLY_CREATED_PATH_LIST']) + self.assertEqual( + '/path/first:/path/second:/path/third:/path/last', + os.environ['PATH_LIST'] + ) + self.assertEqual( + '/path/first:/path/middle:/path/last', + os.environ['EMPTY_PATH_LIST'] + ) + self.assertEqual( + '/path/first:/path/middle:/path/last', + os.environ['NEWLY_CREATED_PATH_LIST'] + ) self.assertEqual('/a/b:/a/c:/a/d:/f/g', os.environ['REMOVE_PATH_LIST']) def test_extra_arguments(self): @@ -98,3 +112,41 @@ class EnvironmentTest(unittest.TestCase): self.assertEqual(len(copy_construct), 2) for x, y in zip(env, copy_construct): assert x is y + + def test_source_files(self): + datadir = join_path(spack_root, 'lib', 'spack', + 'spack', 'test', 'data') + files = [ + join_path(datadir, 'sourceme_first.sh'), + join_path(datadir, 'sourceme_second.sh') + ] + env = EnvironmentModifications.from_sourcing_files(*files) + modifications = env.group_by_name() + + self.assertEqual(len(modifications), 4) + # Set new variables + self.assertEqual(len(modifications['NEW_VAR']), 1) + self.assertTrue(isinstance(modifications['NEW_VAR'][0], SetEnv)) + self.assertEqual(modifications['NEW_VAR'][0].value, 'new') + # Unset variables + self.assertEqual(len(modifications['EMPTY_PATH_LIST']), 1) + self.assertTrue(isinstance( + modifications['EMPTY_PATH_LIST'][0], UnsetEnv)) + # Modified variables + self.assertEqual(len(modifications['UNSET_ME']), 1) + self.assertTrue(isinstance(modifications['UNSET_ME'][0], SetEnv)) + self.assertEqual(modifications['UNSET_ME'][0].value, 'overridden') + + self.assertEqual(len(modifications['PATH_LIST']), 3) + self.assertTrue( + isinstance(modifications['PATH_LIST'][0], RemovePath) + ) + self.assertEqual(modifications['PATH_LIST'][0].value, '/path/third') + self.assertTrue( + isinstance(modifications['PATH_LIST'][1], AppendPath) + ) + self.assertEqual(modifications['PATH_LIST'][1].value, '/path/fourth') + self.assertTrue( + isinstance(modifications['PATH_LIST'][2], PrependPath) + ) + self.assertEqual(modifications['PATH_LIST'][2].value, '/path/first') diff --git a/share/spack/qa/run-flake8 b/share/spack/qa/run-flake8 index 44eb0167fb..57534eb6e2 100755 --- a/share/spack/qa/run-flake8 +++ b/share/spack/qa/run-flake8 @@ -29,6 +29,8 @@ for file in $changed; do perl -i -pe 's/^(\s*url\s*=.*)$/\1 # NOQA: ignore=E501/' $file perl -i -pe 's/^(\s*version\(.*\).*)$/\1 # NOQA: ignore=E501/' $file perl -i -pe 's/^(\s*variant\(.*\).*)$/\1 # NOQA: ignore=E501/' $file + perl -i -pe 's/^(\s*depends_on\(.*\).*)$/\1 # NOQA: ignore=E501/' $file + perl -i -pe 's/^(\s*extends\(.*\).*)$/\1 # NOQA: ignore=E501/' $file # Exempt '@when' decorated functions from redefinition errors. perl -i -pe 's/^(\s*\@when\(.*\).*)$/\1 # NOQA: ignore=F811/' $file diff --git a/var/spack/repos/builtin/packages/R/package.py b/var/spack/repos/builtin/packages/R/package.py index 0177fe1a2b..001dde5329 100644 --- a/var/spack/repos/builtin/packages/R/package.py +++ b/var/spack/repos/builtin/packages/R/package.py @@ -22,30 +22,25 @@ # 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 functools -import glob -import inspect import os -import re -from contextlib import closing -import spack -from llnl.util.lang import match_predicate from spack import * from spack.util.environment import * class R(Package): - """ - R is 'GNU S', a freely available language and environment for statistical computing and graphics which provides a - wide variety of statistical and graphical techniques: linear and nonlinear modelling, statistical tests, time series - analysis, classification, clustering, etc. Please consult the R project homepage for further information. - """ + """R is 'GNU S', a freely available language and environment for + statistical computing and graphics which provides a wide variety of + statistical and graphical techniques: linear and nonlinear modelling, + statistical tests, time series analysis, classification, clustering, etc. + Please consult the R project homepage for further information.""" + homepage = "https://www.r-project.org" url = "http://cran.cnr.berkeley.edu/src/base/R-3/R-3.1.2.tar.gz" - + extendable = True + version('3.3.0', '5a7506c8813432d1621c9725e86baf7a') version('3.2.3', '1ba3dac113efab69e706902810cc2970') version('3.2.2', '57cef5c2e210a5454da1979562a10e5b') version('3.2.1', 'c2aac8b40f84e08e7f8c9068de9239a3') @@ -53,7 +48,8 @@ class R(Package): version('3.1.3', '53a85b884925aa6b5811dfc361d73fc4') version('3.1.2', '3af29ec06704cbd08d4ba8d69250ae74') - variant('external-lapack', default=False, description='Links to externally installed BLAS/LAPACK') + variant('external-lapack', default=False, + description='Links to externally installed BLAS/LAPACK') # Virtual dependencies depends_on('blas', when='+external-lapack') @@ -65,6 +61,7 @@ class R(Package): depends_on('icu') depends_on('glib') depends_on('zlib') + depends_on('bzip2') depends_on('libtiff') depends_on('jpeg') depends_on('cairo') @@ -72,18 +69,21 @@ class R(Package): depends_on('freetype') depends_on('tcl') depends_on('tk') + depends_on('curl') + depends_on('pcre') + depends_on('jdk') def install(self, spec, prefix): rlibdir = join_path(prefix, 'rlib') - options = ['--prefix=%s' % prefix, - '--libdir=%s' % rlibdir, - '--enable-R-shlib', - '--enable-BLAS-shlib', - '--enable-R-framework=no'] + configure_args = ['--prefix=%s' % prefix, + '--libdir=%s' % rlibdir, + '--enable-R-shlib', + '--enable-BLAS-shlib', + '--enable-R-framework=no'] if '+external-lapack' in spec: - options.extend(['--with-blas', '--with-lapack']) + configure_args.extend(['--with-blas', '--with-lapack']) - configure(*options) + configure(*configure_args) make() make('install') @@ -106,25 +106,24 @@ class R(Package): r_libs_path = ':'.join(r_libs_path) spack_env.set('R_LIBS', r_libs_path) - # For run time environment set only the path for extension_spec and prepend it to R_LIBS + # For run time environment set only the path for extension_spec and + # prepend it to R_LIBS if extension_spec.package.extends(self.spec): - run_env.prepend_path('R_LIBS', os.path.join(extension_spec.prefix, self.r_lib_dir)) - + run_env.prepend_path('R_LIBS', os.path.join( + extension_spec.prefix, self.r_lib_dir)) def setup_dependent_package(self, module, ext_spec): - """ - Called before R modules' install() methods. - - In most cases, extensions will only need to have one line:: - - R('CMD', 'INSTALL', '--library=%s' % self.module.r_lib_dir, '%s' % self.stage.archive_file) - """ + """Called before R modules' install() methods. In most cases, + extensions will only need to have one line: + R('CMD', 'INSTALL', '--library=%s' % self.module.r_lib_dir, '%s' % + self.stage.source_path)""" # R extension builds can have a global R executable function module.R = Executable(join_path(self.spec.prefix.bin, 'R')) # Add variable for library directry module.r_lib_dir = os.path.join(ext_spec.prefix, self.r_lib_dir) - # Make the site packages directory for extensions, if it does not exist already. + # Make the site packages directory for extensions, if it does not exist + # already. if ext_spec.package.is_extension: mkdirp(module.r_lib_dir) diff --git a/var/spack/repos/builtin/packages/armadillo/package.py b/var/spack/repos/builtin/packages/armadillo/package.py new file mode 100644 index 0000000000..b3e5994e30 --- /dev/null +++ b/var/spack/repos/builtin/packages/armadillo/package.py @@ -0,0 +1,67 @@ +############################################################################## +# 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 Armadillo(Package): + """Armadillo is a high quality linear algebra library (matrix maths) + for the C++ language, aiming towards a good balance between speed and + ease of use.""" + + homepage = "http://arma.sourceforge.net/" + url = "http://sourceforge.net/projects/arma/files/armadillo-7.200.1.tar.xz" + + version('7.200.1', 'ed86d6df0058979e107502e1fe3e469e') + + variant('hdf5', default=False, description='Include HDF5 support') + + depends_on('arpack') + depends_on('blas') + depends_on('lapack') + depends_on('superlu@5.2:') + depends_on('hdf5', when='+hdf5') + + def install(self, spec, prefix): + cmake_args = [ + # ARPACK support + '-DARPACK_LIBRARY={0}/libarpack.a'.format( + spec['arpack'].prefix.lib), + # BLAS support + '-DBLAS_LIBRARY={0}'.format(spec['blas'].blas_shared_lib), + # LAPACK support + '-DLAPACK_LIBRARY={0}'.format(spec['lapack'].lapack_shared_lib), + # SuperLU support + '-DSuperLU_INCLUDE_DIR={0}'.format(spec['superlu'].prefix.include), + '-DSuperLU_LIBRARY={0}/libsuperlu.a'.format( + spec['superlu'].prefix.lib64), + # HDF5 support + '-DDETECT_HDF5={0}'.format('ON' if '+hdf5' in spec else 'OFF') + ] + + cmake_args.extend(std_cmake_args) + cmake('.', *cmake_args) + + make() + make('install') diff --git a/var/spack/repos/builtin/packages/arpack/package.py b/var/spack/repos/builtin/packages/arpack/package.py index 75158776fe..91b5f06a4a 100644 --- a/var/spack/repos/builtin/packages/arpack/package.py +++ b/var/spack/repos/builtin/packages/arpack/package.py @@ -24,12 +24,12 @@ ############################################################################## from spack import * import os -import shutil + class Arpack(Package): """A collection of Fortran77 subroutines designed to solve large scale - eigenvalue problems. - """ + eigenvalue problems.""" + homepage = "http://www.caam.rice.edu/software/ARPACK/" url = "http://www.caam.rice.edu/software/ARPACK/SRC/arpack96.tar.gz" @@ -39,27 +39,35 @@ class Arpack(Package): depends_on('lapack') def patch(self): - # Filter the cray makefile to make a spack one. - shutil.move('ARMAKES/ARmake.CRAY', 'ARmake.inc') makefile = FileFilter('ARmake.inc') - # Be sure to use Spack F77 wrapper - makefile.filter('^FC.*', 'FC = f77') - makefile.filter('^FFLAGS.*', 'FFLAGS = -O2 -g') + # Section 1: Paths and Libraries + + # Change the build directory + makefile.filter('^home.*', 'home = %s' % os.getcwd()) + + # Use external BLAS/LAPACK + makefile.filter('^BLASdir.*', + 'BLASdir = %s' % self.spec['blas'].prefix) + makefile.filter('^LAPACKdir.*', + 'LAPACKdir = %s' % self.spec['lapack'].prefix) + + # Do not include the platform in the library name + makefile.filter('^PLAT.*', 'PLAT = ') + makefile.filter('^ARPACKLIB.*', 'ARPACKLIB = $(home)/libarpack.a') - # Set up some variables. - makefile.filter('^PLAT.*', 'PLAT = ') - makefile.filter('^home.*', 'home = %s' % os.getcwd()) - makefile.filter('^BLASdir.*', 'BLASdir = %s' % self.spec['blas'].prefix) - makefile.filter('^LAPACKdir.*', 'LAPACKdir = %s' % self.spec['lapack'].prefix) + # Section 2: Compilers - # build the library in our own prefix. - makefile.filter('^ARPACKLIB.*', 'ARPACKLIB = %s/libarpack.a' % os.getcwd()) + # Be sure to use the Spack compiler wrapper + makefile.filter('^FC.*', 'FC = {0}'.format(os.environ['F77'])) + makefile.filter('^FFLAGS.*', 'FFLAGS = -O2 -g -fPIC') + if not which('ranlib'): + makefile.filter('^RANLIB.*', 'RANLIB = touch') def install(self, spec, prefix): with working_dir('SRC'): make('all') - mkdirp(prefix.lib) + mkdir(prefix.lib) install('libarpack.a', prefix.lib) diff --git a/var/spack/repos/builtin/packages/boost/package.py b/var/spack/repos/builtin/packages/boost/package.py index cde76c590a..67294fb9a1 100644 --- a/var/spack/repos/builtin/packages/boost/package.py +++ b/var/spack/repos/builtin/packages/boost/package.py @@ -25,7 +25,6 @@ from spack import * import spack import sys - import os @@ -91,6 +90,7 @@ class Boost(Package): 'system', 'test', 'thread', + 'timer', 'wave']) # mpi/python are not installed by default because they pull in many diff --git a/var/spack/repos/builtin/packages/dealii/package.py b/var/spack/repos/builtin/packages/dealii/package.py index 54b6426d36..23ec74abed 100644 --- a/var/spack/repos/builtin/packages/dealii/package.py +++ b/var/spack/repos/builtin/packages/dealii/package.py @@ -80,8 +80,8 @@ class Dealii(Package): depends_on("netcdf-cxx", when='+netcdf+mpi') depends_on("oce", when='+oce') depends_on("p4est", when='+p4est+mpi') - depends_on("petsc+mpi", when='+petsc+mpi') - depends_on("slepc", when='+slepc+petsc+mpi') + depends_on("petsc@:3.6.4+mpi", when='+petsc+mpi') # FIXME: update after 3.7 is supported upstream. # NOQA: ignore=E501 + depends_on("slepc@:3.6.3", when='+slepc+petsc+mpi') depends_on("trilinos", when='+trilinos+mpi') # developer dependnecies @@ -108,12 +108,11 @@ class Dealii(Package): # of Spack's. Be more specific to avoid this. # Note that both lapack and blas are provided in -DLAPACK_XYZ. '-DLAPACK_FOUND=true', - '-DLAPACK_INCLUDE_DIRS=%s;%s' % - (spec['lapack'].prefix.include, - spec['blas'].prefix.include), - '-DLAPACK_LIBRARIES=%s;%s' % - (spec['lapack'].lapack_shared_lib, - spec['blas'].blas_shared_lib), + '-DLAPACK_INCLUDE_DIRS=%s;%s' % ( + spec['lapack'].prefix.include, spec['blas'].prefix.include), + '-DLAPACK_LIBRARIES=%s;%s' % ( + spec['lapack'].lapack_shared_lib, + spec['blas'].blas_shared_lib), '-DMUPARSER_DIR=%s' % spec['muparser'].prefix, '-DUMFPACK_DIR=%s' % spec['suite-sparse'].prefix, '-DTBB_DIR=%s' % spec['tbb'].prefix, @@ -168,14 +167,14 @@ class Dealii(Package): if '+netcdf' in spec: options.extend([ '-DNETCDF_FOUND=true', - '-DNETCDF_LIBRARIES=%s;%s' % - (join_path(spec['netcdf-cxx'].prefix.lib, - 'libnetcdf_c++.%s' % dsuf), - join_path(spec['netcdf'].prefix.lib, - 'libnetcdf.%s' % dsuf)), - '-DNETCDF_INCLUDE_DIRS=%s;%s' % - (spec['netcdf-cxx'].prefix.include, - spec['netcdf'].prefix.include), + '-DNETCDF_LIBRARIES=%s;%s' % ( + join_path(spec['netcdf-cxx'].prefix.lib, + 'libnetcdf_c++.%s' % dsuf), + join_path(spec['netcdf'].prefix.lib, + 'libnetcdf.%s' % dsuf)), + '-DNETCDF_INCLUDE_DIRS=%s;%s' % ( + spec['netcdf-cxx'].prefix.include, + spec['netcdf'].prefix.include), ]) else: options.extend([ @@ -266,9 +265,9 @@ class Dealii(Package): filter_file(r'(LA::SolverCG solver\(solver_control\);)', ('TrilinosWrappers::SolverDirect::AdditionalData data(false,"Amesos_Superludist"); TrilinosWrappers::SolverDirect solver(solver_control,data);'), 'step-40.cc') # NOQA: ignore=E501 filter_file(r'(LA::MPI::PreconditionAMG preconditioner;)', (''), 'step-40.cc') - filter_file(r'(LA::MPI::PreconditionAMG::AdditionalData data;)', + filter_file(r'(LA::MPI::PreconditionAMG::AdditionalData data;)', # NOQA: ignore=E501 (''), 'step-40.cc') - filter_file(r'(preconditioner.initialize\(system_matrix, data\);)', + filter_file(r'(preconditioner.initialize\(system_matrix, data\);)', # NOQA: ignore=E501 (''), 'step-40.cc') filter_file(r'(solver\.solve \(system_matrix, completely_distributed_solution, system_rhs,)', ('solver.solve (system_matrix, completely_distributed_solution, system_rhs);'), 'step-40.cc') # NOQA: ignore=E501 filter_file(r'(preconditioner\);)', (''), 'step-40.cc') diff --git a/var/spack/repos/builtin/packages/ferret/package.py b/var/spack/repos/builtin/packages/ferret/package.py new file mode 100644 index 0000000000..15ddfcee16 --- /dev/null +++ b/var/spack/repos/builtin/packages/ferret/package.py @@ -0,0 +1,103 @@ +############################################################################## +# 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 * +import os + + +class Ferret(Package): + """Ferret is an interactive computer visualization and analysis environment + designed to meet the needs of oceanographers and meteorologists + analyzing large and complex gridded data sets.""" + homepage = "http://ferret.noaa.gov/Ferret/" + url = "ftp://ftp.pmel.noaa.gov/ferret/pub/source/fer_source.tar.gz" + + version('6.96', '51722027c864369f41bab5751dfff8cc', + url="ftp://ftp.pmel.noaa.gov/ferret/pub/source/fer_source.tar.gz") + + depends_on("hdf5~mpi~fortran") + depends_on("netcdf~mpi") + depends_on("netcdf-fortran") + depends_on("readline") + depends_on("zlib") + + def patch(self): + hdf5_prefix = self.spec['hdf5'].prefix + netcdff_prefix = self.spec['netcdf-fortran'].prefix + readline_prefix = self.spec['readline'].prefix + libz_prefix = self.spec['zlib'].prefix + + filter_file(r'^BUILDTYPE.+', + 'BUILDTYPE = x86_64-linux', + 'FERRET/site_specific.mk') + filter_file(r'^INSTALL_FER_DIR.+', + 'INSTALL_FER_DIR = %s' % self.spec.prefix, + 'FERRET/site_specific.mk') + filter_file(r'^HDF5_DIR.+', + 'HDF5_DIR = %s' % hdf5_prefix, + 'FERRET/site_specific.mk') + filter_file(r'^NETCDF4_DIR.+', + 'NETCDF4_DIR = %s' % netcdff_prefix, + 'FERRET/site_specific.mk') + filter_file(r'^READLINE_DIR.+', + 'READLINE_DIR = %s' % readline_prefix, + 'FERRET/site_specific.mk') + filter_file(r'^LIBZ_DIR.+', + 'LIBZ_DIR = %s' % libz_prefix, + 'FERRET/site_specific.mk') + filter_file(r'^JAVA_HOME.+', + ' ', + 'FERRET/site_specific.mk') + filter_file(r'-lm', + '-lgfortran -lm', + 'FERRET/platform_specific.mk.x86_64-linux') + + def install(self, spec, prefix): + hdf5_prefix = spec['hdf5'].prefix + netcdff_prefix = spec['netcdf-fortran'].prefix + netcdf_prefix = spec['netcdf'].prefix + libz_prefix = spec['zlib'].prefix + ln = which('ln') + ln('-sf', + hdf5_prefix + '/lib', + hdf5_prefix + '/lib64') + ln('-sf', + netcdff_prefix + '/lib', + netcdff_prefix + '/lib64') + ln('-sf', + netcdf_prefix + '/lib/libnetcdf.a', + netcdff_prefix + '/lib/libnetcdf.a') + ln('-sf', + netcdf_prefix + '/lib/libnetcdf.la', + netcdff_prefix + '/lib/libnetcdf.la') + ln('-sf', + libz_prefix + '/lib', + libz_prefix + '/lib64') + os.environ['LDFLAGS'] = '-lquadmath' + with working_dir('FERRET', create=False): + os.environ['LD_X11'] = '-L/usr/lib/X11 -lX11' + os.environ['HOSTTYPE'] = 'x86_64-linux' + make(parallel=False) + make("install") diff --git a/var/spack/repos/builtin/packages/mpich/package.py b/var/spack/repos/builtin/packages/mpich/package.py index 164d9db541..ea1844aea0 100644 --- a/var/spack/repos/builtin/packages/mpich/package.py +++ b/var/spack/repos/builtin/packages/mpich/package.py @@ -23,15 +23,14 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## from spack import * -import os class Mpich(Package): """MPICH is a high performance and widely portable implementation of the Message Passing Interface (MPI) standard.""" homepage = "http://www.mpich.org" - url = "http://www.mpich.org/static/downloads/3.0.4/mpich-3.0.4.tar.gz" - list_url = "http://www.mpich.org/static/downloads/" + url = "http://www.mpich.org/static/downloads/3.0.4/mpich-3.0.4.tar.gz" + list_url = "http://www.mpich.org/static/downloads/" list_depth = 2 version('3.2', 'f414cfa77099cd1fa1a5ae4e22db508a') @@ -42,7 +41,8 @@ class Mpich(Package): version('3.1', '5643dd176499bfb7d25079aaff25f2ec') version('3.0.4', '9c5d5d4fe1e17dd12153f40bc5b6dbc0') - variant('verbs', default=False, description='Build support for OpenFabrics verbs.') + variant('verbs', default=False, + description='Build support for OpenFabrics verbs.') variant('pmi', default=True, description='Build with PMI support') variant('hydra', default=True, description='Build the hydra process manager') @@ -57,9 +57,9 @@ class Mpich(Package): spack_env.set('MPICH_FC', spack_fc) def setup_dependent_package(self, module, dep_spec): - self.spec.mpicc = join_path(self.prefix.bin, 'mpicc') + self.spec.mpicc = join_path(self.prefix.bin, 'mpicc') self.spec.mpicxx = join_path(self.prefix.bin, 'mpic++') - self.spec.mpifc = join_path(self.prefix.bin, 'mpif90') + self.spec.mpifc = join_path(self.prefix.bin, 'mpif90') self.spec.mpif77 = join_path(self.prefix.bin, 'mpif77') def install(self, spec, prefix): @@ -92,7 +92,6 @@ class Mpich(Package): self.filter_compilers() - def filter_compilers(self): """Run after install to make the MPI compilers use the compilers that Spack built the package with. @@ -102,18 +101,20 @@ class Mpich(Package): be bound to whatever compiler they were built with. """ bin = self.prefix.bin - mpicc = os.path.join(bin, 'mpicc') - mpicxx = os.path.join(bin, 'mpicxx') - mpif77 = os.path.join(bin, 'mpif77') - mpif90 = os.path.join(bin, 'mpif90') - - spack_cc = os.environ['CC'] - spack_cxx = os.environ['CXX'] - spack_f77 = os.environ['F77'] - spack_fc = os.environ['FC'] - - kwargs = { 'ignore_absent' : True, 'backup' : False, 'string' : True } - filter_file('CC="%s"' % spack_cc , 'CC="%s"' % self.compiler.cc, mpicc, **kwargs) - filter_file('CXX="%s"'% spack_cxx, 'CXX="%s"' % self.compiler.cxx, mpicxx, **kwargs) - filter_file('F77="%s"'% spack_f77, 'F77="%s"' % self.compiler.f77, mpif77, **kwargs) - filter_file('FC="%s"' % spack_fc , 'FC="%s"' % self.compiler.fc, mpif90, **kwargs) + mpicc = join_path(bin, 'mpicc') + mpicxx = join_path(bin, 'mpicxx') + mpif77 = join_path(bin, 'mpif77') + mpif90 = join_path(bin, 'mpif90') + + # Substitute Spack compile wrappers for the real + # underlying compiler + kwargs = {'ignore_absent': True, 'backup': False, 'string': True} + filter_file(env['CC'], self.compiler.cc, mpicc, **kwargs) + filter_file(env['CXX'], self.compiler.cxx, mpicxx, **kwargs) + filter_file(env['F77'], self.compiler.f77, mpif77, **kwargs) + filter_file(env['FC'], self.compiler.fc, mpif90, **kwargs) + + # Remove this linking flag if present + # (it turns RPATH into RUNPATH) + for wrapper in (mpicc, mpicxx, mpif77, mpif90): + filter_file('-Wl,--enable-new-dtags', '', wrapper, **kwargs) diff --git a/var/spack/repos/builtin/packages/mumps/mumps-shared.patch b/var/spack/repos/builtin/packages/mumps/mumps-shared.patch new file mode 100644 index 0000000000..592f48037c --- /dev/null +++ b/var/spack/repos/builtin/packages/mumps/mumps-shared.patch @@ -0,0 +1,119 @@ +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 92c45c9b95..8a90ef72d0 100644 --- a/var/spack/repos/builtin/packages/mumps/package.py +++ b/var/spack/repos/builtin/packages/mumps/package.py @@ -23,7 +23,10 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## from spack import * -import os, sys, glob +import os +import sys +import subprocess + class Mumps(Package): """MUMPS: a MUltifrontal Massively Parallel sparse direct Solver""" @@ -44,7 +47,6 @@ 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') @@ -54,49 +56,64 @@ 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') + 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 - 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: - 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')]) + 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: @@ -104,7 +121,7 @@ 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'), + ['OPTF = %s -O -DALLOW_NON_INIT %s' % (fpic, '-fdefault-integer-8' if self.compiler.name == "gcc" else '-i8'), # NOQA: E501 'OPTL = %s -O ' % fpic, 'OPTC = %s -O -DINTSIZE64' % fpic]) else: @@ -113,49 +130,47 @@ class Mumps(Package): 'OPTL = %s -O ' % fpic, 'OPTC = %s -O ' % fpic]) - if '+mpi' in self.spec: makefile_conf.extend( - ["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'), + ["CC = %s" % self.spec['mpi'].mpicc, + "FC = %s" % self.spec['mpi'].mpifc, "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.append("CDEFS = -DAdd_") + makefile_conf.extend([ + 'CDEFS = -DAdd_', + 'FL = $(FC)', + ]) if '+shared' in self.spec: + makefile_conf.append('SHLIBEXT = .%s' % dso_suffix) if sys.platform == 'darwin': - # Building dylibs with mpif90 causes segfaults on 10.8 and 10.10. Use gfortran. (Homebrew) - makefile_conf.extend([ - 'LIBEXT=.dylib', - 'AR=%s -dynamiclib -Wl,-install_name -Wl,%s/$(notdir $@) -undefined dynamic_lookup -o ' % (os.environ['FC'],prefix.lib), - 'RANLIB=echo' - ]) + makefile_conf.append( + 'LDFLAGS = -dynamiclib -Wl,-install_name -Wl,{0}/$(notdir $@) {1}{0} -undefined dynamic_lookup'.format(prefix.lib, self.compiler.fc_rpath_arg) # NOQA: E501 + ) else: - makefile_conf.extend([ - 'LIBEXT=.so', - 'AR=$(FL) -shared -Wl,-soname -Wl,%s/$(notdir $@) -o' % prefix.lib, - 'RANLIB=echo' - ]) - else: - makefile_conf.extend([ - 'LIBEXT = .a', - 'AR = ar vr', - 'RANLIB = ranlib' - ]) - - - makefile_inc_template = join_path(os.path.dirname(self.module.__file__), - 'Makefile.inc') + 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') with open(makefile_inc_template, "r") as fh: makefile_conf.extend(fh.read().split('\n')) @@ -164,46 +179,53 @@ 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('sexamples') + make_libs.append('s') if '+complex' in spec: - make_libs.append('cexamples') + make_libs.append('c') if '+double' in spec: - make_libs.append('dexamples') + make_libs.append('d') if '+complex' in spec: - make_libs.append('zexamples') + make_libs.append('z') self.write_makefile_inc() - # Build fails in parallel - make(*make_libs, parallel=False) + make('mumps_lib', parallel=False) + make(*make_libs) install_tree('lib', prefix.lib) install_tree('include', prefix.include) - 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') + 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)) diff --git a/var/spack/repos/builtin/packages/mvapich2/package.py b/var/spack/repos/builtin/packages/mvapich2/package.py index d1944023d1..34bace10d6 100644 --- a/var/spack/repos/builtin/packages/mvapich2/package.py +++ b/var/spack/repos/builtin/packages/mvapich2/package.py @@ -23,7 +23,6 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## from spack import * -import os class Mvapich2(Package): @@ -245,27 +244,20 @@ class Mvapich2(Package): be bound to whatever compiler they were built with. """ bin = self.prefix.bin - mpicc = os.path.join(bin, 'mpicc') - mpicxx = os.path.join(bin, 'mpicxx') - mpif77 = os.path.join(bin, 'mpif77') - mpif90 = os.path.join(bin, 'mpif90') - - spack_cc = os.environ['CC'] - spack_cxx = os.environ['CXX'] - spack_f77 = os.environ['F77'] - spack_fc = os.environ['FC'] - - kwargs = { - 'ignore_absent': True, - 'backup': False, - 'string': True - } - - filter_file('CC="%s"' % spack_cc, - 'CC="%s"' % self.compiler.cc, mpicc, **kwargs) - filter_file('CXX="%s"' % spack_cxx, - 'CXX="%s"' % self.compiler.cxx, mpicxx, **kwargs) - filter_file('F77="%s"' % spack_f77, - 'F77="%s"' % self.compiler.f77, mpif77, **kwargs) - filter_file('FC="%s"' % spack_fc, - 'FC="%s"' % self.compiler.fc, mpif90, **kwargs) + mpicc = join_path(bin, 'mpicc') + mpicxx = join_path(bin, 'mpicxx') + mpif77 = join_path(bin, 'mpif77') + mpif90 = join_path(bin, 'mpif90') + + # Substitute Spack compile wrappers for the real + # underlying compiler + kwargs = {'ignore_absent': True, 'backup': False, 'string': True} + filter_file(env['CC'], self.compiler.cc, mpicc, **kwargs) + filter_file(env['CXX'], self.compiler.cxx, mpicxx, **kwargs) + filter_file(env['F77'], self.compiler.f77, mpif77, **kwargs) + filter_file(env['FC'], self.compiler.fc, mpif90, **kwargs) + + # Remove this linking flag if present + # (it turns RPATH into RUNPATH) + for wrapper in (mpicc, mpicxx, mpif77, mpif90): + filter_file('-Wl,--enable-new-dtags', '', wrapper, **kwargs) diff --git a/var/spack/repos/builtin/packages/openmpi/package.py b/var/spack/repos/builtin/packages/openmpi/package.py index be3d1342fc..588d862d96 100644 --- a/var/spack/repos/builtin/packages/openmpi/package.py +++ b/var/spack/repos/builtin/packages/openmpi/package.py @@ -24,6 +24,8 @@ ############################################################################## import os +import llnl.util.tty as tty + from spack import * @@ -61,6 +63,7 @@ class Openmpi(Package): list_url = "http://www.open-mpi.org/software/ompi/" list_depth = 3 + version('1.10.3', 'e2fe4513200e2aaa1500b762342c674b') version('1.10.2', 'b2f43d9635d2d52826e5ef9feb97fd4c') version('1.10.1', 'f0fcd77ed345b7eafb431968124ba16e') version('1.10.0', '280cf952de68369cebaca886c5ce0304') @@ -72,20 +75,27 @@ class Openmpi(Package): patch('configure.patch', when="@1.10.0:1.10.1") variant('psm', default=False, description='Build support for the PSM library.') - variant('psm2', default=False, description='Build support for the Intel PSM2 library.') - variant('pmi', default=False, description='Build support for PMI-based launchers') - variant('verbs', default=_verbs_dir() is not None, description='Build support for OpenFabrics verbs.') + variant('psm2', default=False, + description='Build support for the Intel PSM2 library.') + variant('pmi', default=False, + description='Build support for PMI-based launchers') + variant('verbs', default=_verbs_dir() is not None, + description='Build support for OpenFabrics verbs.') variant('mxm', default=False, description='Build Mellanox Messaging support') - variant('thread_multiple', default=False, description='Enable MPI_THREAD_MULTIPLE support') + variant('thread_multiple', default=False, + description='Enable MPI_THREAD_MULTIPLE support') # TODO : variant support for alps, loadleveler is missing - variant('tm', default=False, description='Build TM (Torque, PBSPro, and compatible) support') - variant('slurm', default=False, description='Build SLURM scheduler component') + variant('tm', default=False, + description='Build TM (Torque, PBSPro, and compatible) support') + variant('slurm', default=False, + description='Build SLURM scheduler component') variant('sqlite3', default=False, description='Build sqlite3 support') - variant('vt', default=True, description='Build support for contributed package vt') + variant('vt', default=True, + description='Build support for contributed package vt') # TODO : support for CUDA is missing @@ -96,8 +106,7 @@ class Openmpi(Package): depends_on('sqlite', when='+sqlite3') def url_for_version(self, version): - return "http://www.open-mpi.org/software/ompi/v%s/downloads/openmpi-%s.tar.bz2" % (version.up_to(2), version) - + return "http://www.open-mpi.org/software/ompi/v%s/downloads/openmpi-%s.tar.bz2" % (version.up_to(2), version) # NOQA: ignore=E501 def setup_dependent_environment(self, spack_env, run_env, dependent_spec): spack_env.set('OMPI_CC', spack_cc) @@ -106,14 +115,30 @@ class Openmpi(Package): spack_env.set('OMPI_F77', spack_f77) def setup_dependent_package(self, module, dep_spec): - self.spec.mpicc = join_path(self.prefix.bin, 'mpicc') + self.spec.mpicc = join_path(self.prefix.bin, 'mpicc') self.spec.mpicxx = join_path(self.prefix.bin, 'mpic++') - self.spec.mpifc = join_path(self.prefix.bin, 'mpif90') + self.spec.mpifc = join_path(self.prefix.bin, 'mpif90') self.spec.mpif77 = join_path(self.prefix.bin, 'mpif77') + def setup_environment(self, spack_env, run_env): + # As of 06/2016 there is no mechanism to specify that packages which + # depends on MPI need C or/and Fortran implementation. For now + # require both. + if (self.compiler.f77 is None) or (self.compiler.fc is None): + tty.warn('OpenMPI : FORTRAN compiler not found') + tty.warn('OpenMPI : FORTRAN bindings will be disabled') + spack_env.unset('FC') + spack_env.unset('F77') + # Setting an attribute here and using it in the 'install' + # method is needed to ensure tty.warn is actually displayed + # to user and not redirected to spack-build.out + self.config_extra = ['--enable-mpi-fortran=none', + '--disable-oshmem-fortran'] + @property def verbs(self): - # Up through version 1.6, this option was previously named --with-openib + # Up through version 1.6, this option was previously named + # --with-openib if self.spec.satisfies('@:1.6'): return 'openib' # In version 1.7, it was renamed to be --with-verbs @@ -121,17 +146,14 @@ class Openmpi(Package): return 'verbs' def install(self, spec, prefix): - # As of 06/2016 there is no mechanism to specify that packages which - # depends on MPI need C or/and Fortran implementation. For now - # require both. - if (self.compiler.f77 is None) or (self.compiler.fc is None): - raise InstallError('OpenMPI requires both C and Fortran ', - 'compilers!') - config_args = ["--prefix=%s" % prefix, "--with-hwloc=%s" % spec['hwloc'].prefix, "--enable-shared", "--enable-static"] + + if getattr(self, 'config_extra', None) is not None: + config_args.extend(self.config_extra) + # Variant based arguments config_args.extend([ # Schedulers @@ -142,7 +164,7 @@ class Openmpi(Package): '--with-psm2' if '+psm2' in spec else '--without-psm2', '--with-mxm' if '+mxm' in spec else '--without-mxm', # Other options - '--enable-mpi-thread-multiple' if '+thread_multiple' in spec else '--disable-mpi-thread-multiple', + '--enable-mpi-thread-multiple' if '+thread_multiple' in spec else '--disable-mpi-thread-multiple', # NOQA: ignore=E501 '--with-pmi' if '+pmi' in spec else '--without-pmi', '--with-sqlite3' if '+sqlite3' in spec else '--without-sqlite3', '--enable-vt' if '+vt' in spec else '--disable-vt' @@ -160,10 +182,7 @@ class Openmpi(Package): # use this for LANL builds, but for LLNL builds, we need: # "--with-platform=contrib/platform/llnl/optimized" if self.version == ver("1.6.5") and '+lanl' in spec: - config_args.append("--with-platform=contrib/platform/lanl/tlcc2/optimized-nopanasas") - - if not self.compiler.f77 and not self.compiler.fc: - config_args.append("--enable-mpi-fortran=no") + config_args.append("--with-platform=contrib/platform/lanl/tlcc2/optimized-nopanasas") # NOQA: ignore=E501 configure(*config_args) make() @@ -180,40 +199,33 @@ class Openmpi(Package): be bound to whatever compiler they were built with. """ kwargs = {'ignore_absent': True, 'backup': False, 'string': False} - dir = os.path.join(self.prefix, 'share/openmpi/') - - cc_wrappers = ['mpicc-vt-wrapper-data.txt', 'mpicc-wrapper-data.txt', - 'ortecc-wrapper-data.txt', 'shmemcc-wrapper-data.txt'] - - cxx_wrappers = ['mpic++-vt-wrapper-data.txt', 'mpic++-wrapper-data.txt', - 'ortec++-wrapper-data.txt'] - - fc_wrappers = ['mpifort-vt-wrapper-data.txt', - 'mpifort-wrapper-data.txt', 'shmemfort-wrapper-data.txt'] - - for wrapper in cc_wrappers: - filter_file('compiler=.*', 'compiler=%s' % self.compiler.cc, - os.path.join(dir, wrapper), **kwargs) - - for wrapper in cxx_wrappers: - filter_file('compiler=.*', 'compiler=%s' % self.compiler.cxx, - os.path.join(dir, wrapper), **kwargs) - - for wrapper in fc_wrappers: - filter_file('compiler=.*', 'compiler=%s' % self.compiler.fc, - os.path.join(dir, wrapper), **kwargs) - - # These are symlinks in newer versions, so check that here - f77_wrappers = ['mpif77-vt-wrapper-data.txt', 'mpif77-wrapper-data.txt'] - f90_wrappers = ['mpif90-vt-wrapper-data.txt', 'mpif90-wrapper-data.txt'] - - for wrapper in f77_wrappers: - path = os.path.join(dir, wrapper) - if not os.path.islink(path): - filter_file('compiler=.*', 'compiler=%s' % self.compiler.f77, - path, **kwargs) - for wrapper in f90_wrappers: - path = os.path.join(dir, wrapper) - if not os.path.islink(path): - filter_file('compiler=.*', 'compiler=%s' % self.compiler.fc, - path, **kwargs) + wrapper_basepath = join_path(self.prefix, 'share', 'openmpi') + + wrappers = [ + ('mpicc-vt-wrapper-data.txt', self.compiler.cc), + ('mpicc-wrapper-data.txt', self.compiler.cc), + ('ortecc-wrapper-data.txt', self.compiler.cc), + ('shmemcc-wrapper-data.txt', self.compiler.cc), + ('mpic++-vt-wrapper-data.txt', self.compiler.cxx), + ('mpic++-wrapper-data.txt', self.compiler.cxx), + ('ortec++-wrapper-data.txt', self.compiler.cxx), + ('mpifort-vt-wrapper-data.txt', self.compiler.fc), + ('mpifort-wrapper-data.txt', self.compiler.fc), + ('shmemfort-wrapper-data.txt', self.compiler.fc), + ('mpif90-vt-wrapper-data.txt', self.compiler.fc), + ('mpif90-wrapper-data.txt', self.compiler.fc), + ('mpif77-vt-wrapper-data.txt', self.compiler.f77), + ('mpif77-wrapper-data.txt', self.compiler.f77) + ] + + for wrapper_name, compiler in wrappers: + wrapper = join_path(wrapper_basepath, wrapper_name) + if not os.path.islink(wrapper): + # Substitute Spack compile wrappers for the real + # underlying compiler + match = 'compiler=.*' + substitute = 'compiler={compiler}'.format(compiler=compiler) + filter_file(match, substitute, wrapper, **kwargs) + # Remove this linking flag if present + # (it turns RPATH into RUNPATH) + filter_file('-Wl,--enable-new-dtags', '', wrapper, **kwargs) diff --git a/var/spack/repos/builtin/packages/pcre/package.py b/var/spack/repos/builtin/packages/pcre/package.py index 8e0f83110e..a43729a1ac 100644 --- a/var/spack/repos/builtin/packages/pcre/package.py +++ b/var/spack/repos/builtin/packages/pcre/package.py @@ -29,6 +29,7 @@ class Pcre(Package): """The PCRE package contains Perl Compatible Regular Expression libraries. These are useful for implementing regular expression pattern matching using the same syntax and semantics as Perl 5.""" + homepage = "http://www.pcre.org""" url = "ftp://ftp.csx.cam.ac.uk/pub/software/programming/pcre/pcre-8.36.tar.bz2" @@ -37,7 +38,15 @@ class Pcre(Package): patch("intel.patch") + variant('utf', default=True, + description='Enable support for UTF-8/16/32, ' + 'incompatible with EBCDIC.') + def install(self, spec, prefix): - configure("--prefix=%s" % prefix) + configure_args = ['--prefix=%s' % prefix] + if '+utf' in spec: + configure_args.append('--enable-utf') + + configure(*configure_args) make() make("install") diff --git a/var/spack/repos/builtin/packages/petsc/package.py b/var/spack/repos/builtin/packages/petsc/package.py index 6456a1aabf..8dd1d8d2b9 100644 --- a/var/spack/repos/builtin/packages/petsc/package.py +++ b/var/spack/repos/builtin/packages/petsc/package.py @@ -28,13 +28,16 @@ from spack import * class Petsc(Package): """ - PETSc is a suite of data structures and routines for the scalable (parallel) solution of scientific applications - modeled by partial differential equations. + PETSc is a suite of data structures and routines for the scalable + (parallel) solution of scientific applications modeled by partial + differential equations. """ homepage = "http://www.mcs.anl.gov/petsc/index.html" url = "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-3.5.3.tar.gz" + version('3.7.2', '50da49867ce7a49e7a0c1b37f4ec7b34') + version('3.6.4', '7632da2375a3df35b8891c9526dbdde7') version('3.6.3', '91dd3522de5a5ef039ff8f50800db606') version('3.5.3', 'd4fd2734661e89f18ac6014b5dd1ef2f') version('3.5.2', 'ad170802b3b058b5deb9cd1f968e7e13') @@ -69,10 +72,12 @@ class Petsc(Package): depends_on('hdf5+mpi', when='+hdf5+mpi') depends_on('parmetis', when='+metis+mpi') # Hypre does not support complex numbers. - # Also PETSc prefer to build it without internal superlu, likely due to conflict in headers - # see https://bitbucket.org/petsc/petsc/src/90564b43f6b05485163c147b464b5d6d28cde3ef/config/BuildSystem/config/packages/hypre.py + # Also PETSc prefer to build it without internal superlu, likely due to + # conflict in headers see + # https://bitbucket.org/petsc/petsc/src/90564b43f6b05485163c147b464b5d6d28cde3ef/config/BuildSystem/config/packages/hypre.py # NOQA: ignore=E501 depends_on('hypre~internal-superlu', when='+hypre+mpi~complex') - depends_on('superlu-dist', when='+superlu-dist+mpi') + depends_on('superlu-dist@:4.3', when='@:3.6.4+superlu-dist+mpi') + depends_on('superlu-dist@5.0.0:', when='@3.7:+superlu-dist+mpi') depends_on('mumps+mpi', when='+mumps+mpi') depends_on('scalapack', when='+mumps+mpi') @@ -80,17 +85,17 @@ class Petsc(Package): if '~mpi' in self.spec: compiler_opts = [ '--with-cc=%s' % os.environ['CC'], - '--with-cxx=%s' % (os.environ['CXX'] if self.compiler.cxx is not None else '0'), - '--with-fc=%s' % (os.environ['FC'] if self.compiler.fc is not None else '0'), + '--with-cxx=%s' % (os.environ['CXX'] if self.compiler.cxx is not None else '0'), # NOQA: ignore=E501 + '--with-fc=%s' % (os.environ['FC'] if self.compiler.fc is not None else '0'), # NOQA: ignore=E501 '--with-mpi=0' ] - error_message_fmt = '\t{library} support requires "+mpi" to be activated' + error_message_fmt = '\t{library} support requires "+mpi" to be activated' # NOQA: ignore=E501 - # If mpi is disabled (~mpi), it's an error to have any of these enabled. - # This generates a list of any such errors. + # If mpi is disabled (~mpi), it's an error to have any of these + # enabled. This generates a list of any such errors. errors = [error_message_fmt.format(library=x) - for x in ('hdf5', 'hypre', 'parmetis','mumps','superlu-dist') - if ('+'+x) in self.spec] + for x in ('hdf5', 'hypre', 'parmetis', 'mumps', 'superlu-dist') # NOQA: ignore=E501 + if ('+' + x) in self.spec] if errors: errors = ['incompatible variants given'] + errors raise RuntimeError('\n'.join(errors)) @@ -105,26 +110,31 @@ class Petsc(Package): options = ['--with-ssl=0'] options.extend(self.mpi_dependent_options()) options.extend([ - '--with-precision=%s' % ('double' if '+double' in spec else 'single'), - '--with-scalar-type=%s' % ('complex' if '+complex' in spec else 'real'), + '--with-precision=%s' % ('double' if '+double' in spec else 'single'), # NOQA: ignore=E501 + '--with-scalar-type=%s' % ('complex' if '+complex' in spec else 'real'), # NOQA: ignore=E501 '--with-shared-libraries=%s' % ('1' if '+shared' in spec else '0'), '--with-debugging=%s' % ('1' if '+debug' in spec else '0'), '--with-blas-lapack-dir=%s' % spec['lapack'].prefix ]) # Activates library support if needed - for library in ('metis', 'boost', 'hdf5', 'hypre', 'parmetis','mumps','scalapack'): + for library in ('metis', 'boost', 'hdf5', 'hypre', 'parmetis', + 'mumps', 'scalapack'): options.append( - '--with-{library}={value}'.format(library=library, value=('1' if library in spec else '0')) + '--with-{library}={value}'.format(library=library, value=('1' if library in spec else '0')) # NOQA: ignore=E501 ) if library in spec: options.append( - '--with-{library}-dir={path}'.format(library=library, path=spec[library].prefix) + '--with-{library}-dir={path}'.format(library=library, path=spec[library].prefix) # NOQA: ignore=E501 ) - # PETSc does not pick up SuperluDist from the dir as they look for superlu_dist_4.1.a + # PETSc does not pick up SuperluDist from the dir as they look for + # superlu_dist_4.1.a if 'superlu-dist' in spec: options.extend([ - '--with-superlu_dist-include=%s' % spec['superlu-dist'].prefix.include, - '--with-superlu_dist-lib=%s' % join_path(spec['superlu-dist'].prefix.lib, 'libsuperlu_dist.a'), + '--with-superlu_dist-include=%s' % + spec['superlu-dist'].prefix.include, + '--with-superlu_dist-lib=%s' % + join_path(spec['superlu-dist'].prefix.lib, + 'libsuperlu_dist.a'), '--with-superlu_dist=1' ]) else: diff --git a/var/spack/repos/builtin/packages/psi4/package.py b/var/spack/repos/builtin/packages/psi4/package.py new file mode 100644 index 0000000000..fc77ba7412 --- /dev/null +++ b/var/spack/repos/builtin/packages/psi4/package.py @@ -0,0 +1,115 @@ +############################################################################## +# 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 * +import os + + +class Psi4(Package): + """Psi4 is an open-source suite of ab initio quantum chemistry + programs designed for efficient, high-accuracy simulations of + a variety of molecular properties.""" + + homepage = "http://www.psicode.org/" + url = "https://github.com/psi4/psi4/archive/0.5.tar.gz" + + version('0.5', '53041b8a9be3958384171d0d22f9fdd0') + + # Required dependencies + depends_on('blas') + depends_on('lapack') + depends_on('boost+chrono+filesystem+python+regex+serialization+system+timer+thread') + depends_on('python') + depends_on('cmake') + depends_on('py-numpy') + + # Optional dependencies + # TODO: add packages for these + # depends_on('perl') + # depends_on('erd') + # depends_on('pcm-solver') + # depends_on('chemps2') + + def install(self, spec, prefix): + cmake_args = [ + '-DBLAS_TYPE={0}'.format(spec['blas'].name.upper()), + '-DBLAS_LIBRARIES={0}'.format(spec['blas'].blas_shared_lib), + '-DLAPACK_TYPE={0}'.format(spec['lapack'].name.upper()), + '-DLAPACK_LIBRARIES={0}'.format(spec['lapack'].lapack_shared_lib), + '-DBOOST_INCLUDEDIR={0}'.format(spec['boost'].prefix.include), + '-DBOOST_LIBRARYDIR={0}'.format(spec['boost'].prefix.lib), + '-DENABLE_CHEMPS2=OFF' + ] + + cmake_args.extend(std_cmake_args) + + with working_dir('spack-build', create=True): + cmake('..', *cmake_args) + + make() + make('install') + + self.filter_compilers(spec, prefix) + + def filter_compilers(self, spec, prefix): + """Run after install to tell the configuration files to + use the compilers that Spack built the package with. + + If this isn't done, they'll have PLUGIN_CXX set to + Spack's generic cxx. We want it to be bound to + whatever compiler it was built with.""" + + kwargs = {'ignore_absent': True, 'backup': False, 'string': True} + + cc_files = ['bin/psi4-config'] + cxx_files = ['bin/psi4-config', 'include/psi4/psiconfig.h'] + template = 'share/psi4/plugin/Makefile.template' + + for filename in cc_files: + filter_file(os.environ['CC'], self.compiler.cc, + os.path.join(prefix, filename), **kwargs) + + for filename in cxx_files: + filter_file(os.environ['CXX'], self.compiler.cxx, + os.path.join(prefix, filename), **kwargs) + + # The binary still keeps track of the compiler used to install Psi4 + # and uses it when creating a plugin template + filter_file('@PLUGIN_CXX@', self.compiler.cxx, + os.path.join(prefix, template), **kwargs) + + # The binary links to the build include directory instead of the + # installation include directory: + # https://github.com/psi4/psi4/issues/410 + filter_file('@PLUGIN_INCLUDES@', '-I{0}'.format( + ' -I'.join([ + os.path.join(spec['psi4'].prefix.include, 'psi4'), + os.path.join(spec['boost'].prefix.include, 'boost'), + os.path.join(spec['python'].prefix.include, 'python{0}'.format( + spec['python'].version.up_to(2))), + spec['lapack'].prefix.include, + spec['blas'].prefix.include, + '/usr/include' + ]) + ), os.path.join(prefix, template), **kwargs) diff --git a/var/spack/repos/builtin/packages/r-BiocGenerics/package.py b/var/spack/repos/builtin/packages/r-BiocGenerics/package.py index 0d3b6a3e57..5a6ce72a4b 100644 --- a/var/spack/repos/builtin/packages/r-BiocGenerics/package.py +++ b/var/spack/repos/builtin/packages/r-BiocGenerics/package.py @@ -24,15 +24,33 @@ ############################################################################## from spack import * + class RBiocgenerics(Package): """S4 generic functions needed by many Bioconductor packages.""" - homepage = 'https://www.bioconductor.org/packages/release/bioc/html/BiocGenerics.html' - url = "https://www.bioconductor.org/packages/release/bioc/src/contrib/BiocGenerics_0.16.1.tar.gz" - - version('0.16.1', 'c2148ffd86fc6f1f819c7f68eb2c744f', expand=False) + homepage = 'https://bioconductor.org/packages/BiocGenerics/' + version('bioc-3.3', + git='https://github.com/Bioconductor-mirror/BiocGenerics.git', + branch='release-3.3') + version('bioc-3.2', + git='https://github.com/Bioconductor-mirror/BiocGenerics.git', + branch='release-3.2') extends('R') + def validate(self, spec): + """ + Checks that the version of R is appropriate for the Bioconductor + version. + """ + if spec.satisfies('@bioc-3.3'): + if not spec.satisfies('^R@3.3.0:3.3.9'): + raise InstallError('Must use R-3.3 for Bioconductor-3.3') + elif spec.satisfies('@bioc-3.2'): + if not spec.satisfies('^R@3.2.0:3.2.9'): + raise InstallError('Must use R-3.2 for Bioconductor-3.2') + def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library=%s' % self.module.r_lib_dir, '%s' % self.stage.archive_file) + self.validate(spec) + R('CMD', 'INSTALL', '--library=%s' % + self.module.r_lib_dir, '%s' % self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-R6/package.py b/var/spack/repos/builtin/packages/r-R6/package.py new file mode 100644 index 0000000000..0b75888e79 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-R6/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 RR6(Package): + """The R6 package allows the creation of classes with reference semantics, + similar to R's built-in reference classes. Compared to reference classes, + R6 classes are simpler and lighter-weight, and they are not built on S4 + classes so they do not require the methods package. These classes allow + public and private members, and they support inheritance, even when the + classes are defined in different packages.""" + + homepage = "https://github.com/wch/R6/" + url = "https://cran.r-project.org/src/contrib/R6_2.1.2.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/R6" + + version('2.1.2', 'b6afb9430e48707be87638675390e457') + + 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-abind/package.py b/var/spack/repos/builtin/packages/r-abind/package.py index 34a1eee79f..96f623a096 100644 --- a/var/spack/repos/builtin/packages/r-abind/package.py +++ b/var/spack/repos/builtin/packages/r-abind/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class RAbind(Package): """Combine multidimensional arrays into a single array. This is a generalization of 'cbind' and 'rbind'. Works with vectors, matrices, and @@ -32,11 +33,12 @@ class RAbind(Package): homepage = "https://cran.r-project.org/" url = "https://cran.r-project.org/src/contrib/abind_1.4-3.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/abind" - version('1.4-3', '10fcf80c677b991bf263d38be35a1fc5', expand=False) + version('1.4-3', '10fcf80c677b991bf263d38be35a1fc5') extends('R') def install(self, spec, prefix): - - R('CMD', 'INSTALL', '--library=%s' % self.module.r_lib_dir, '%s' % self.stage.archive_file) + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-curl/package.py b/var/spack/repos/builtin/packages/r-curl/package.py new file mode 100644 index 0000000000..c6e8f22a94 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-curl/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 RCurl(Package): + """The curl() and curl_download() functions provide highly configurable + drop-in replacements for base url() and download.file() with better + performance, support for encryption (https, ftps), gzip compression, + authentication, and other libcurl goodies. The core of the package + implements a framework for performing fully customized requests where data + can be processed either in memory, on disk, or streaming via the callback + or connection interfaces. Some knowledge of libcurl is recommended; for a + more-user-friendly web client see the 'httr' package which builds on this + package with http specific tools and logic.""" + + homepage = "https://github.com/jeroenooms/curl" + url = "https://cran.r-project.org/src/contrib/curl_0.9.7.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/RCurl" + + version('0.9.7', 'a101f7de948cb828fef571c730f39217') + + extends('R') + + depends_on('curl') + + 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-devtools/package.py b/var/spack/repos/builtin/packages/r-devtools/package.py new file mode 100644 index 0000000000..5f0b7b8779 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-devtools/package.py @@ -0,0 +1,50 @@ +############################################################################## +# 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 RDevtools(Package): + """Collection of package development tools.""" + + homepage = "https://github.com/hadley/devtools" + url = "https://cran.r-project.org/src/contrib/devtools_1.11.1.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/devtools" + + version('1.11.1', '242672ee27d24dddcbdaac88c586b6c2') + + extends('R') + + depends_on('r-httr') + depends_on('r-memoise') + depends_on('r-whisker') + depends_on('r-digest') + depends_on('r-rstudioapi') + depends_on('r-jsonlite') + depends_on('r-git2r') + depends_on('r-withr') + + 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-digest/package.py b/var/spack/repos/builtin/packages/r-digest/package.py new file mode 100644 index 0000000000..1d11afb139 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-digest/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 RDigest(Package): + """Implementation of a function 'digest()' for the creation of hash digests + of arbitrary R objects (using the md5, sha-1, sha-256, crc32, xxhash and + murmurhash algorithms) permitting easy comparison of R language objects, as + well as a function 'hmac()' to create hash-based message authentication + code. The md5 algorithm by Ron Rivest is specified in RFC 1321, the sha-1 + and sha-256 algorithms are specified in FIPS-180-1 and FIPS-180-2, and the + crc32 algorithm is described in + ftp://ftp.rocksoft.com/cliens/rocksoft/papers/crc_v3.txt. For md5, sha-1, + sha-256 and aes, this package uses small standalone implementations that + were provided by Christophe Devine. For crc32, code from the zlib library + is used. For sha-512, an implementation by Aaron D. Gifford is used. For + xxhash, the implementation by Yann Collet is used. For murmurhash, an + implementation by Shane Day is used. Please note that this package is not + meant to be deployed for cryptographic purposes for which more + comprehensive (and widely tested) libraries such as OpenSSL should be + used.""" + + homepage = "http://dirk.eddelbuettel.com/code/digest.html" + url = "https://cran.r-project.org/src/contrib/digest_0.6.9.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/digest" + + version('0.6.9', '48048ce6c466bdb124716e45ba4a0e83') + + 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-filehash/package.py b/var/spack/repos/builtin/packages/r-filehash/package.py index fffae68019..a09b458eaf 100644 --- a/var/spack/repos/builtin/packages/r-filehash/package.py +++ b/var/spack/repos/builtin/packages/r-filehash/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class RFilehash(Package): """Implements a simple key-value style database where character string keys are associated with data values that are stored on the disk. A simple @@ -37,10 +38,12 @@ class RFilehash(Package): homepage = 'https://cran.r-project.org/' url = "https://cran.r-project.org/src/contrib/filehash_2.3.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/filehash" - version('2.3', '01fffafe09b148ccadc9814c103bdc2f', expand=False) + version('2.3', '01fffafe09b148ccadc9814c103bdc2f') extends('R') def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library=%s' % self.module.r_lib_dir, '%s' % self.stage.archive_file) + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-git2r/package.py b/var/spack/repos/builtin/packages/r-git2r/package.py new file mode 100644 index 0000000000..1f08379d6e --- /dev/null +++ b/var/spack/repos/builtin/packages/r-git2r/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 RGit2r(Package): + """Interface to the 'libgit2' library, which is a pure C implementation of + the 'Git' core methods. Provides access to 'Git' repositories to extract + data and running some basic 'Git' commands.""" + + homepage = "https://github.com/ropensci/git2r" + url = "https://cran.r-project.org/src/contrib/git2r_0.15.0.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/git2r" + + version('0.15.0', '57658b3298f9b9aadc0dd77b4ef6a1e1') + + extends('R') + + depends_on('zlib') + depends_on('openssl') + + 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-httr/package.py b/var/spack/repos/builtin/packages/r-httr/package.py new file mode 100644 index 0000000000..77ec34ab03 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-httr/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 RHttr(Package): + """Useful tools for working with HTTP organised by HTTP verbs (GET(), + POST(), etc). Configuration functions make it easy to control additional + request components (authenticate(), add_headers() and so on).""" + + homepage = "https://github.com/hadley/httr" + url = "https://cran.r-project.org/src/contrib/httr_1.1.0.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/httr" + + version('1.1.0', '5ffbbc5c2529e49f00aaa521a2b35600') + + extends('R') + + depends_on('r-jsonlite') + depends_on('r-mime') + depends_on('r-curl') + depends_on('r-openssl') + depends_on('r-R6') + + 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-jsonlite/package.py b/var/spack/repos/builtin/packages/r-jsonlite/package.py new file mode 100644 index 0000000000..6e231ed345 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-jsonlite/package.py @@ -0,0 +1,50 @@ +############################################################################## +# 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 RJsonlite(Package): + """A fast JSON parser and generator optimized for statistical data and the + web. Started out as a fork of 'RJSONIO', but has been completely rewritten + in recent versions. The package offers flexible, robust, high performance + tools for working with JSON in R and is particularly powerful for building + pipelines and interacting with a web API. The implementation is based on + the mapping described in the vignette (Ooms, 2014). In addition to + converting JSON data from/to R objects, 'jsonlite' contains functions to + stream, validate, and prettify JSON data. The unit tests included with the + package verify that all edge cases are encoded and decoded consistently for + use with dynamic data in systems and applications.""" + + homepage = "https://github.com/jeroenooms/jsonlite" + url = "https://cran.r-project.org/src/contrib/jsonlite_0.9.21.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/jsonlite" + + version('0.9.21', '4fc382747f88a79ff0718a0d06bed45d') + + 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-magic/package.py b/var/spack/repos/builtin/packages/r-magic/package.py index f86917ec0c..f6ba97740b 100644 --- a/var/spack/repos/builtin/packages/r-magic/package.py +++ b/var/spack/repos/builtin/packages/r-magic/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class RMagic(Package): """A collection of efficient, vectorized algorithms for the creation and investigation of magic squares and hypercubes, including a variety of @@ -32,12 +33,14 @@ class RMagic(Package): homepage = "https://cran.r-project.org/" url = "https://cran.r-project.org/src/contrib/magic_1.5-6.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/magic" - version('1.5-6', 'a68e5ced253b2196af842e1fc84fd029', expand=False) + version('1.5-6', 'a68e5ced253b2196af842e1fc84fd029') extends('R') depends_on('r-abind') def install(self, spec, prefix): - R('CMD', 'INSTALL', '--library=%s' % self.module.r_lib_dir, '%s' % self.stage.archive_file) + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path) diff --git a/var/spack/repos/builtin/packages/r-memoise/package.py b/var/spack/repos/builtin/packages/r-memoise/package.py new file mode 100644 index 0000000000..6a0fb78650 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-memoise/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 RMemoise(Package): + """Cache the results of a function so that when you call it again with the + same arguments it returns the pre-computed value.""" + + homepage = "https://github.com/hadley/memoise" + url = "https://cran.r-project.org/src/contrib/memoise_1.0.0.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/memoise" + + version('1.0.0', 'd31145292e2a88ae9a504cab1602e4ac') + + extends('R') + + depends_on('r-digest') + + 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-mime/package.py b/var/spack/repos/builtin/packages/r-mime/package.py new file mode 100644 index 0000000000..fb079f44c5 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-mime/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 RMime(Package): + """Guesses the MIME type from a filename extension using the data derived + from /etc/mime.types in UNIX-type systems.""" + + homepage = "https://github.com/yihui/mime" + url = "https://cran.r-project.org/src/contrib/mime_0.4.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/mime" + + version('0.4', '789cb33e41db2206c6fc7c3e9fbc2c02') + + 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-openssl/package.py b/var/spack/repos/builtin/packages/r-openssl/package.py new file mode 100644 index 0000000000..3e77923d76 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-openssl/package.py @@ -0,0 +1,52 @@ +############################################################################## +# 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 ROpenssl(Package): + """Bindings to OpenSSL libssl and libcrypto, plus custom SSH pubkey + parsers. Supports RSA, DSA and EC curves P-256, P-384 and P-521. + Cryptographic signatures can either be created and verified manually or via + x509 certificates. AES can be used in cbc, ctr or gcm mode for symmetric + encryption; RSA for asymmetric (public key) encryption or EC for Diffie + Hellman. High-level envelope functions combine RSA and AES for encrypting + arbitrary sized data. Other utilities include key generators, hash + functions (md5, sha1, sha256, etc), base64 encoder, a secure random number + generator, and 'bignum' math methods for manually performing crypto + calculations on large multibyte integers.""" + + homepage = "https://github.com/jeroenooms/openssl#readme" + url = "https://cran.r-project.org/src/contrib/openssl_0.9.4.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/openssl" + + version('0.9.4', '82a890e71ed0e74499878bedacfb8ccb') + + extends('R') + + depends_on('openssl') + + 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-packrat/package.py b/var/spack/repos/builtin/packages/r-packrat/package.py new file mode 100644 index 0000000000..9520952bd7 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-packrat/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 RPackrat(Package): + """Manage the R packages your project depends on in an isolated, portable, + and reproducible way.""" + + homepage = "https://github.com/rstudio/packrat/" + url = "https://cran.r-project.org/src/contrib/packrat_0.4.7-1.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/packrat" + + version('0.4.7-1', '80c2413269b292ade163a70ba5053e84') + + 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-rstudioapi/package.py b/var/spack/repos/builtin/packages/r-rstudioapi/package.py new file mode 100644 index 0000000000..0ef2d9b987 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-rstudioapi/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 RRstudioapi(Package): + """Access the RStudio API (if available) and provide informative error + messages when it's not.""" + + homepage = "https://cran.r-project.org/web/packages/rstudioapi/index.html" + url = "https://cran.r-project.org/src/contrib/rstudioapi_0.5.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/rstudioapi" + + version('0.5', '6ce1191da74e7bcbf06b61339486b3ba') + + 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-whisker/package.py b/var/spack/repos/builtin/packages/r-whisker/package.py new file mode 100644 index 0000000000..f338d150f1 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-whisker/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 RWhisker(Package): + """logicless templating, reuse templates in many programming languages + including R""" + + homepage = "http://github.com/edwindj/whisker" + url = "https://cran.r-project.org/src/contrib/whisker_0.3-2.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/whisker" + + version('0.3-2', 'c4b9bf9a22e69ce003fe68663ab5e8e6') + + 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-withr/package.py b/var/spack/repos/builtin/packages/r-withr/package.py new file mode 100644 index 0000000000..5ce7437c84 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-withr/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 RWithr(Package): + """A set of functions to run code 'with' safely and temporarily modified + global state. Many of these functions were originally a part of the + 'devtools' package, this provides a simple package with limited + dependencies to provide access to these functions.""" + + homepage = "http://github.com/jimhester/withr" + url = "https://cran.r-project.org/src/contrib/withr_1.0.1.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/withr" + + version('1.0.1', 'ac38af2c6f74027c9592dd8f0acb7598') + + 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/slepc/package.py b/var/spack/repos/builtin/packages/slepc/package.py index c148a579ec..d3739bf6a6 100644 --- a/var/spack/repos/builtin/packages/slepc/package.py +++ b/var/spack/repos/builtin/packages/slepc/package.py @@ -34,13 +34,16 @@ class Slepc(Package): homepage = "http://www.grycap.upv.es/slepc" url = "http://slepc.upv.es/download/download.php?filename=slepc-3.6.2.tar.gz" + version('3.7.1', '670216f263e3074b21e0623c01bc0f562fdc0bffcd7bd42dd5d8edbe73a532c2') + version('3.6.3', '384939d009546db37bc05ed81260c8b5ba451093bf891391d32eb7109ccff876') version('3.6.2', '2ab4311bed26ccf7771818665991b2ea3a9b15f97e29fd13911ab1293e8e65df') - variant('arpack', default=False, description='Enables Arpack wrappers') + variant('arpack', default=True, description='Enables Arpack wrappers') - depends_on('petsc') - depends_on('arpack-ng~mpi',when='+arpack^petsc~mpi') - depends_on('arpack-ng+mpi',when='+arpack^petsc+mpi') + depends_on('petsc@3.7:', when='@3.7.1:') + depends_on('petsc@3.6.3:3.6.4', when='@3.6.2:3.6.3') + depends_on('arpack-ng~mpi', when='+arpack^petsc~mpi') + depends_on('arpack-ng+mpi', when='+arpack^petsc+mpi') def install(self, spec, prefix): # set SLEPC_DIR for installation @@ -64,7 +67,7 @@ class Slepc(Package): configure('--prefix=%s' % prefix, *options) make('MAKE_NP=%s' % make_jobs, parallel=False) - #FIXME: + # FIXME: # make('test') make('install') diff --git a/var/spack/repos/builtin/packages/superlu-dist/package.py b/var/spack/repos/builtin/packages/superlu-dist/package.py index 6c06b5497c..e51d7224d9 100644 --- a/var/spack/repos/builtin/packages/superlu-dist/package.py +++ b/var/spack/repos/builtin/packages/superlu-dist/package.py @@ -25,50 +25,54 @@ from spack import * import glob + class SuperluDist(Package): - """A general purpose library for the direct solution of large, sparse, nonsymmetric systems of linear equations on high performance machines.""" + """A general purpose library for the direct solution of large, sparse, + nonsymmetric systems of linear equations on high performance machines.""" homepage = "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/" url = "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/superlu_dist_4.1.tar.gz" version('5.0.0', '2b53baf1b0ddbd9fcf724992577f0670') - # default to version 4.3 since petsc and trilinos are not tested with 5.0. - version('4.3', 'ee66c84e37b4f7cc557771ccc3dc43ae', preferred=True) + version('4.3', 'ee66c84e37b4f7cc557771ccc3dc43ae') version('4.2', 'ae9fafae161f775fbac6eba11e530a65') version('4.1', '4edee38cc29f687bd0c8eb361096a455') version('4.0', 'c0b98b611df227ae050bc1635c6940e0') - depends_on ('mpi') - depends_on ('blas') - depends_on ('lapack') - depends_on ('parmetis') - depends_on ('metis@5:') + depends_on('mpi') + depends_on('blas') + depends_on('lapack') + depends_on('parmetis') + depends_on('metis@5:') def install(self, spec, prefix): makefile_inc = [] makefile_inc.extend([ 'PLAT = _mac_x', - 'DSuperLUroot = %s' % self.stage.source_path, #self.stage.path, prefix + 'DSuperLUroot = %s' % self.stage.source_path, 'DSUPERLULIB = $(DSuperLUroot)/lib/libsuperlu_dist.a', 'BLASDEF = -DUSE_VENDOR_BLAS', - 'BLASLIB = -L%s -llapack %s -lblas' % (spec['lapack'].prefix.lib, spec['blas'].prefix.lib), # FIXME: avoid hardcoding blas/lapack lib names + 'BLASLIB = %s %s' % + (to_link_flags(spec['lapack'].lapack_shared_lib), + to_link_flags(spec['blas'].blas_shared_lib)), 'METISLIB = -L%s -lmetis' % spec['metis'].prefix.lib, 'PARMETISLIB = -L%s -lparmetis' % spec['parmetis'].prefix.lib, 'FLIBS =', - 'LIBS = $(DSUPERLULIB) $(BLASLIB) $(PARMETISLIB) $(METISLIB)', + 'LIBS = $(DSUPERLULIB) $(BLASLIB) $(PARMETISLIB) $(METISLIB)', # NOQA: ignore=E501 'ARCH = ar', 'ARCHFLAGS = cr', 'RANLIB = true', - 'CC = mpicc', # FIXME avoid hardcoding MPI compiler names - 'CFLAGS = -fPIC -std=c99 -O2 -I%s -I%s' %(spec['parmetis'].prefix.include, spec['metis'].prefix.include), + 'CC = %s' % spec['mpi'].mpicc, + 'CFLAGS = -fPIC -std=c99 -O2 -I%s -I%s' % + (spec['parmetis'].prefix.include, + spec['metis'].prefix.include), 'NOOPTS = -fPIC -std=c99', - 'FORTRAN = mpif77', + 'FORTRAN = %s' % spec['mpi'].mpif77, 'F90FLAGS = -O2', - 'LOADER = mpif77', + 'LOADER = %s' % spec['mpi'].mpif77, 'LOADOPTS =', 'CDEFS = -DAdd_' - ]) + ]) - #with working_dir('src'): with open('make.inc', 'w') as fh: fh.write('\n'.join(makefile_inc)) @@ -83,9 +87,10 @@ class SuperluDist(Package): mkdirp(headers_location) mkdirp(prefix.lib) - headers = glob.glob(join_path(self.stage.source_path, 'SRC','*.h')) + headers = glob.glob(join_path(self.stage.source_path, 'SRC', '*.h')) for h in headers: - install(h,headers_location) + install(h, headers_location) - superludist_lib = join_path(self.stage.source_path, 'lib/libsuperlu_dist.a') - install(superludist_lib,self.prefix.lib) + superludist_lib = join_path(self.stage.source_path, + 'lib/libsuperlu_dist.a') + install(superludist_lib, self.prefix.lib) diff --git a/var/spack/repos/builtin/packages/superlu/package.py b/var/spack/repos/builtin/packages/superlu/package.py new file mode 100644 index 0000000000..c634c1d1ba --- /dev/null +++ b/var/spack/repos/builtin/packages/superlu/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 Superlu(Package): + """SuperLU is a general purpose library for the direct solution of large, + sparse, nonsymmetric systems of linear equations on high performance + machines. SuperLU is designed for sequential machines.""" + + homepage = "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/#superlu" + url = "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/superlu_5.2.1.tar.gz" + + version('5.2.1', '3a1a9bff20cb06b7d97c46d337504447') + + depends_on('blas') + + def install(self, spec, prefix): + cmake_args = [ + '-DCMAKE_POSITION_INDEPENDENT_CODE=ON', + # BLAS support + '-Denable_blaslib=OFF', + '-DBLAS_blas_LIBRARY={0}'.format(spec['blas'].blas_shared_lib) + ] + + cmake_args.extend(std_cmake_args) + + with working_dir('spack-build', create=True): + cmake('..', *cmake_args) + + make() + make('install') diff --git a/var/spack/repos/builtin/packages/tmux/package.py b/var/spack/repos/builtin/packages/tmux/package.py index c46425c0d3..573ee38a79 100644 --- a/var/spack/repos/builtin/packages/tmux/package.py +++ b/var/spack/repos/builtin/packages/tmux/package.py @@ -24,26 +24,33 @@ ############################################################################## from spack import * + class Tmux(Package): """tmux is a terminal multiplexer. What is a terminal multiplexer? It lets - you switch easily between several programs in one terminal, detach them (they - keep running in the background) and reattach them to a different terminal. And - do a lot more. + you switch easily between several programs in one terminal, detach them + (they keep running in the background) and reattach them to a different + terminal. And do a lot more. """ homepage = "http://tmux.github.io" - url = "https://github.com/tmux/tmux/releases/download/2.1/tmux-2.1.tar.gz" + url = "https://github.com/tmux/tmux/releases/download/2.2/tmux-2.2.tar.gz" version('1.9a', 'b07601711f96f1d260b390513b509a2d') version('2.1', '74a2855695bccb51b6e301383ad4818c') + version('2.2', 'bd95ee7205e489c62c616bb7af040099') depends_on('libevent') depends_on('ncurses') def install(self, spec, prefix): + pkg_config_path = ':'.join([ + spec['libevent'].prefix, + spec['ncurses'].prefix + ]) + configure( "--prefix=%s" % prefix, - "PKG_CONFIG_PATH=%s:%s" % (spec['libevent'].prefix, spec['ncurses'].prefix)) + "PKG_CONFIG_PATH=%s" % pkg_config_path) make() make("install") diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py index 6913d79dcc..3a53ac5c01 100644 --- a/var/spack/repos/builtin/packages/trilinos/package.py +++ b/var/spack/repos/builtin/packages/trilinos/package.py @@ -45,6 +45,8 @@ class Trilinos(Package): homepage = "https://trilinos.org/" url = "http://trilinos.csbsju.edu/download/files/trilinos-12.2.1-Source.tar.gz" + version('12.6.3', '960f5f4d3f7c3da818e5a5fb4684559eff7e0c25f959ef576561b8a52f0e4d1e') + version('12.6.2', '0c076090508170ddee5efeed317745027f9418319720dc40a072e478775279f9') version('12.6.1', 'adcf2d3aab74cdda98f88fee19cd1442604199b0515ee3da4d80cbe8f37d00e4') version('12.4.2', '7c830f7f0f68b8ad324690603baf404e') version('12.2.1', '6161926ea247863c690e927687f83be9') @@ -89,7 +91,8 @@ class Trilinos(Package): # work at the end. But let's avoid all this by simply using shared libs depends_on('mumps@5.0:+mpi+shared', when='+mumps') depends_on('scalapack', when='+mumps') - depends_on('superlu-dist', when='+superlu-dist') + depends_on('superlu-dist@:4.3', when='@:12.6.1+superlu-dist') + depends_on('superlu-dist', when='@12.6.2:+superlu-dist') depends_on('hypre~internal-superlu', when='+hypre') depends_on('hdf5+mpi', when='+hdf5') depends_on('python', when='+python') |