diff options
137 files changed, 5268 insertions, 790 deletions
@@ -79,6 +79,15 @@ # Obviously, for this to work, `sbang` needs to have a short enough # path that *it* will run without hitting OS limits. # +# For Lua, scripts the second line can't start with #!, as # is not +# the comment character in lua (even though lua ignores #! on the +# *first* line of a script). So, instrument a lua script like this, +# using -- instead of # on the second line: +# +# 1 #!/bin/bash /path/to/sbang +# 2 --!/long/path/to/lua with arguments +# 3 +# 4 print "success!" # # How it works # ----------------------------- @@ -95,6 +104,8 @@ lines=0 while read line && ((lines < 2)) ; do if [[ "$line" = '#!'* ]]; then interpreter="${line#\#!}" + elif [[ "$line" = '--!'*lua* ]]; then + interpreter="${line#--!}" fi lines=$((lines+1)) done < "$script" @@ -77,7 +77,7 @@ import llnl.util.tty as tty from llnl.util.tty.color import * import spack from spack.error import SpackError -from external import argparse +import argparse # Command parsing parser = argparse.ArgumentParser( 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/configuration.rst b/lib/spack/docs/configuration.rst index c613071c65..a6f876b2aa 100644 --- a/lib/spack/docs/configuration.rst +++ b/lib/spack/docs/configuration.rst @@ -140,7 +140,6 @@ Here's an example packages.yaml file that sets preferred packages: packages: dyninst: compiler: [gcc@4.9] - variants: +debug gperftools: version: [2.2, 2.4, 2.3] all: @@ -150,8 +149,8 @@ Here's an example packages.yaml file that sets preferred packages: At a high level, this example is specifying how packages should be -concretized. The dyninst package should prefer using gcc 4.9 and -be built with debug options. The gperftools package should prefer version +concretized. The dyninst package should prefer using gcc 4.9. +The gperftools package should prefer version 2.2 over 2.4. Every package on the system should prefer mvapich for its MPI and gcc 4.4.7 (except for Dyninst, which overrides this by preferring gcc 4.9). These options are used to fill in implicit defaults. Any of them can be overwritten @@ -160,7 +159,7 @@ on the command line if explicitly requested. Each packages.yaml file begins with the string ``packages:`` and package names are specified on the next level. The special string ``all`` applies settings to each package. Underneath each package name is -one or more components: ``compiler``, ``variants``, ``version``, +one or more components: ``compiler``, ``version``, or ``providers``. Each component has an ordered list of spec ``constraints``, with earlier entries in the list being preferred over later entries. 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..e800c6717a 100644 --- a/lib/spack/llnl/util/filesystem.py +++ b/lib/spack/llnl/util/filesystem.py @@ -22,33 +22,33 @@ # 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. - Filters every line of file through regex and replaces the file + Filters every line of each file through regex and replaces the file with a filtered version. Preserves mode of filtered files. As with re.sub, ``repl`` can be either a string or a callable. @@ -59,7 +59,7 @@ def filter_file(regex, repl, *filenames, **kwargs): Keyword Options: string[=False] If True, treat regex as a plain string. - backup[=True] Make a backup files suffixed with ~ + backup[=True] Make backup file(s) suffixed with ~ ignore_absent[=False] Ignore any files that don't exist. """ string = kwargs.get('string', False) @@ -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))) @@ -79,26 +80,26 @@ def filter_file(regex, repl, *filenames, **kwargs): regex = re.escape(regex) for filename in filenames: - backup = filename + "~" + backup_filename = filename + "~" if ignore_absent and not os.path.exists(filename): continue - shutil.copy(filename, backup) + shutil.copy(filename, backup_filename) try: - with closing(open(backup)) as infile: + with closing(open(backup_filename)) as infile: with closing(open(filename, 'w')) as outfile: for line in infile: foo = re.sub(regex, repl, line) outfile.write(foo) except: # clean up the original file on failure. - shutil.move(backup, filename) + shutil.move(backup_filename, filename) raise finally: if not backup: - shutil.rmtree(backup, ignore_errors=True) + os.remove(backup_filename) class FileFilter(object): @@ -113,7 +114,7 @@ class FileFilter(object): def change_sed_delimiter(old_delim, new_delim, *filenames): """Find all sed search/replace commands and change the delimiter. e.g., if the file contains seds that look like 's///', you can - call change_sed_delimeter('/', '@', file) to change the + call change_sed_delimiter('/', '@', file) to change the delimiter to '@'. NOTE that this routine will fail if the delimiter is ' or ". @@ -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) @@ -175,7 +179,7 @@ def install(src, dest): """Manually install a file to a particular location.""" tty.debug("Installing %s to %s" % (src, dest)) - # Expand dsst to its eventual full path if it is a directory. + # Expand dest to its eventual full path if it is a directory. if os.path.isdir(dest): dest = join_path(dest, os.path.basename(src)) @@ -215,7 +219,7 @@ def mkdirp(*paths): if not os.path.exists(path): os.makedirs(path) elif not os.path.isdir(path): - raise OSError(errno.EEXIST, "File alredy exists", path) + raise OSError(errno.EEXIST, "File already exists", path) def force_remove(*paths): @@ -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): @@ -304,7 +309,7 @@ def traverse_tree(source_root, dest_root, rel_path='', **kwargs): Optional args: - order=[pre|post] -- Whether to do pre- or post-order traveral. + order=[pre|post] -- Whether to do pre- or post-order traversal. ignore=<predicate> -- Predicate indicating which files to ignore. @@ -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 + path: directory in which .dylib files are located """ - 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) + # Assume 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/architecture.py b/lib/spack/spack/architecture.py index cbac7b41d6..a7cda2bf68 100644 --- a/lib/spack/spack/architecture.py +++ b/lib/spack/spack/architecture.py @@ -91,16 +91,10 @@ from spack.util.multiproc import parmap import spack.error as serr -class InvalidSysTypeError(serr.SpackError): - def __init__(self, sys_type): - super(InvalidSysTypeError, self).__init__( - "Invalid sys_type value for Spack: " + sys_type) - - -class NoSysTypeError(serr.SpackError): +class NoPlatformError(serr.SpackError): def __init__(self): - super(NoSysTypeError, self).__init__( - "Could not determine sys_type for this machine.") + super(NoPlatformError, self).__init__( + "Could not determine a platform for this machine.") @key_ordering @@ -345,14 +339,17 @@ class OperatingSystem(object): @key_ordering class Arch(object): - "Architecture is now a class to help with setting attributes" - - def __init__(self, platform=None, platform_os=None, target=None): - self.platform = platform - if platform and platform_os: - platform_os = self.platform.operating_system(platform_os) - self.platform_os = platform_os - if platform and target: + """Architecture is now a class to help with setting attributes. + + TODO: refactor so that we don't need this class. + """ + + def __init__(self, plat=None, os=None, target=None): + self.platform = plat + if plat and os: + os = self.platform.operating_system(os) + self.platform_os = os + if plat and target: target = self.platform.target(target) self.target = target @@ -409,27 +406,27 @@ class Arch(object): return d -def _target_from_dict(target_name, platform=None): +def _target_from_dict(target_name, plat=None): """ Creates new instance of target and assigns all the attributes of that target from the dictionary """ - if not platform: - platform = sys_type() - return platform.target(target_name) + if not plat: + plat = platform() + return plat.target(target_name) -def _operating_system_from_dict(os_name, platform=None): +def _operating_system_from_dict(os_name, plat=None): """ uses platform's operating system method to grab the constructed operating systems that are valid on the platform. """ - if not platform: - platform = sys_type() + if not plat: + plat = platform() if isinstance(os_name, dict): name = os_name['name'] version = os_name['version'] - return platform.operating_system(name+version) + return plat.operating_system(name+version) else: - return platform.operating_system(os_name) + return plat.operating_system(os_name) def _platform_from_dict(platform_name): @@ -504,16 +501,35 @@ def all_platforms(): @memoized -def sys_type(): - """ Gather a list of all available subclasses of platforms. - Sorts the list according to their priority looking. Priority is - an arbitrarily set number. Detects platform either using uname or - a file path (/opt/cray...) +def platform(): + """Detects the platform for this machine. + + Gather a list of all available subclasses of platforms. + Sorts the list according to their priority looking. Priority is + an arbitrarily set number. Detects platform either using uname or + a file path (/opt/cray...) """ # Try to create a Platform object using the config file FIRST platform_list = all_platforms() platform_list.sort(key=lambda a: a.priority) - for platform in platform_list: - if platform.detect(): - return platform() + for platform_cls in platform_list: + if platform_cls.detect(): + return platform_cls() + + +@memoized +def sys_type(): + """Print out the "default" platform-os-target tuple for this machine. + + On machines with only one target OS/target, prints out the + platform-os-target for the frontend. For machines with a frontend + and a backend, prints the default backend. + + TODO: replace with use of more explicit methods to get *all* the + backends, as client code should really be aware of cross-compiled + architectures. + + """ + arch = Arch(platform(), 'default_os', 'default_target') + return str(arch) diff --git a/lib/spack/spack/build_environment.py b/lib/spack/spack/build_environment.py index 7c65091d49..99c4cae020 100644 --- a/lib/spack/spack/build_environment.py +++ b/lib/spack/spack/build_environment.py @@ -75,20 +75,19 @@ 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. dso_suffix = 'dylib' if sys.platform == 'darwin' else 'so' - class MakeExecutable(Executable): """Special callable executable object for make so the user can specify parallel or not on a per-invocation basis. Using @@ -99,6 +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 @@ -113,12 +113,13 @@ class MakeExecutable(Executable): return super(MakeExecutable, self).__call__(*args, **kwargs) + def load_module(mod): """Takes a module name and removes modules until it is possible to load that module. It then loads the provided module. Depends on the modulecmd implementation of modules used in cray and lmod. """ - #Create an executable of the module command that will output python code + # Create an executable of the module command that will output python code modulecmd = which('modulecmd') modulecmd.add_default_arg('python') @@ -129,11 +130,13 @@ def load_module(mod): text = modulecmd('show', mod, output=str, error=str).split() for i, word in enumerate(text): if word == 'conflict': - 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')) # Load the module now that there are no conflicts load = modulecmd('load', mod, output=str, error=str) exec(compile(load, '<string>', 'exec')) + def get_path_from_module(mod): """Inspects a TCL module for entries that indicate the absolute path at which the library supported by said module can be found. @@ -146,7 +149,7 @@ def get_path_from_module(mod): text = modulecmd('show', mod, output=str, error=str).split('\n') # If it lists its package directory, return that for line in text: - if line.find(mod.upper()+'_DIR') >= 0: + if line.find(mod.upper() + '_DIR') >= 0: words = line.split() return words[2] @@ -154,49 +157,52 @@ def get_path_from_module(mod): for line in text: rpath = line.find('-rpath/') if rpath >= 0: - return line[rpath+6:line.find('/lib')] + return line[rpath + 6:line.find('/lib')] # If it lists a -L instruction, use that for line in text: L = line.find('-L/') if L >= 0: - return line[L+2:line.find('/lib')] + return line[L + 2:line.find('/lib')] # If it sets the LD_LIBRARY_PATH or CRAY_LD_LIBRARY_PATH, use that for line in text: - if line.find('LD_LIBRARY_PATH') >= 0: + if line.find('LD_LIBRARY_PATH') >= 0: words = line.split() path = words[2] return path[:path.find('/lib')] # Unable to find module path return None + def set_compiler_environment_variables(pkg, env): assert(pkg.spec.concrete) compiler = pkg.compiler flags = pkg.spec.compiler_flags # Set compiler variables used by CMake and autotools - assert all(key in compiler.link_paths for key in ('cc', 'cxx', 'f77', 'fc')) + assert all(key in compiler.link_paths for key in ( + 'cc', 'cxx', 'f77', 'fc')) # Populate an object with the list of environment modifications # and return it - # TODO : add additional kwargs for better diagnostics, like requestor, ttyout, ttyerr, etc. + # 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) @@ -233,7 +239,8 @@ 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 = [] - for item in [spack.build_env_path, join_path(spack.build_env_path, pkg.compiler.name)]: + compiler_specific = join_path(spack.build_env_path, pkg.compiler.name) + for item in [spack.build_env_path, compiler_specific]: env_paths.append(item) ci = join_path(item, 'case-insensitive') if os.path.isdir(ci): @@ -246,7 +253,8 @@ def set_build_environment_variables(pkg, env): # Prefixes of all of the package's dependencies go in SPACK_DEPENDENCIES dep_prefixes = [d.prefix for d in pkg.spec.traverse(root=False)] env.set_path(SPACK_DEPENDENCIES, dep_prefixes) - env.set_path('CMAKE_PREFIX_PATH', dep_prefixes) # Add dependencies to CMAKE_PREFIX_PATH + # Add dependencies to CMAKE_PREFIX_PATH + env.set_path('CMAKE_PREFIX_PATH', dep_prefixes) # Install prefix env.set(SPACK_PREFIX, pkg.prefix) @@ -262,7 +270,8 @@ def set_build_environment_variables(pkg, env): env.unset('DYLD_LIBRARY_PATH') # Add bin directories from dependencies to the PATH for the build. - 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])) for item in bin_dirs: env.prepend_path('PATH', item) @@ -277,8 +286,7 @@ def set_build_environment_variables(pkg, env): for directory in ('lib', 'lib64', 'share'): pcdir = join_path(pre, directory, 'pkgconfig') if os.path.isdir(pcdir): - #pkg_config_dirs.append(pcdir) - env.prepend_path('PKG_CONFIG_PATH',pcdir) + env.prepend_path('PKG_CONFIG_PATH', pcdir) if pkg.spec.architecture.target.module_name: load_module(pkg.spec.architecture.target.module_name) @@ -290,7 +298,7 @@ def set_module_variables_for_package(pkg, module): """Populate the module scope of install() with some useful functions. This makes things easier for package writers. """ - # number of jobs spack will to build with. + # number of jobs spack will build with. jobs = multiprocessing.cpu_count() if not pkg.parallel: jobs = 1 @@ -301,8 +309,9 @@ 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) # easy shortcut to os.environ m.env = os.environ @@ -316,6 +325,7 @@ def set_module_variables_for_package(pkg, module): # TODO: Currently, everything is a link dependency, but tools like # TODO: this shouldn't be. m.cmake = Executable('cmake') + m.ctest = Executable('ctest') # standard CMake arguments m.std_cmake_args = ['-DCMAKE_INSTALL_PREFIX=%s' % pkg.prefix, @@ -325,33 +335,34 @@ def set_module_variables_for_package(pkg, module): # Set up CMake rpath m.std_cmake_args.append('-DCMAKE_INSTALL_RPATH_USE_LINK_PATH=FALSE') - m.std_cmake_args.append('-DCMAKE_INSTALL_RPATH=%s' % ":".join(get_rpaths(pkg))) + m.std_cmake_args.append('-DCMAKE_INSTALL_RPATH=%s' % + ":".join(get_rpaths(pkg))) # 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 @@ -365,20 +376,22 @@ def get_rpaths(pkg): rpaths.extend(d.prefix.lib64 for d in pkg.spec.dependencies.values() if os.path.isdir(d.prefix.lib64)) # Second module is our compiler mod name. We use that to get rpaths from - # module show output. + # module show output. if pkg.compiler.modules and len(pkg.compiler.modules) > 1: rpaths.append(get_path_from_module(pkg.compiler.modules[1])) return rpaths def parent_class_modules(cls): - """Get list of super class modules that are all descend from spack.Package""" + """ + Get list of super class modules that are all descend from spack.Package + """ if not issubclass(cls, spack.Package) or issubclass(spack.Package, cls): return [] result = [] module = sys.modules.get(cls.__module__) if module: - result = [ module ] + result = [module] for c in cls.__bases__: result.extend(parent_class_modules(c)) return result @@ -390,11 +403,12 @@ def load_external_modules(pkg): for dep in list(pkg.spec.traverse()): if dep.external_module: load_module(dep.external_module) - + + 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 # @@ -410,7 +424,8 @@ def setup_package(pkg): # throwaway environment, but it is kind of dirty. # # TODO: Think about how to avoid this fix and do something cleaner. - for s in pkg.spec.traverse(): s.package.spec = s + for s in pkg.spec.traverse(): + s.package.spec = s set_compiler_environment_variables(pkg, spack_env) set_build_environment_variables(pkg, spack_env) @@ -498,7 +513,9 @@ 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.".format(str(returncode))) + 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/create.py b/lib/spack/spack/cmd/create.py index 41bfa741f6..8cbb367f86 100644 --- a/lib/spack/spack/cmd/create.py +++ b/lib/spack/spack/cmd/create.py @@ -1,4 +1,3 @@ -_copyright = """\ ############################################################################## # Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. # Produced at the Lawrence Livermore National Laboratory. @@ -23,10 +22,8 @@ _copyright = """\ # 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 string import os -import hashlib import re from ordereddict_backport import OrderedDict @@ -41,16 +38,37 @@ import spack.util.web from spack.spec import Spec from spack.util.naming import * from spack.repository import Repo, RepoError -import spack.util.crypto as crypto from spack.util.executable import which -from spack.stage import Stage description = "Create a new package file from an archive URL" -package_template = string.Template( - _copyright + """ +package_template = string.Template("""\ +############################################################################## +# 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 +############################################################################## # # This is a template package file for Spack. We've put "FIXME" # next to all the things you'll want to change. Once you've handled @@ -68,24 +86,21 @@ package_template = string.Template( # from spack import * + class ${class_name}(Package): - ""\"FIXME: put a proper description of your package here.""\" - # FIXME: add a proper url for your package's homepage here. + ""\"FIXME: Put a proper description of your package here.""\" + + # FIXME: Add a proper url for your package's homepage here. homepage = "http://www.example.com" url = "${url}" ${versions} - +${extends} # FIXME: Add dependencies if this package requires them. # depends_on("foo") def install(self, spec, prefix): - # FIXME: Modify the configure line to suit your build system here. - ${configure} - - # FIXME: Add logic to build and install here - make() - make("install") +${install} """) @@ -120,41 +135,95 @@ def setup_parser(subparser): class ConfigureGuesser(object): def __call__(self, stage): - """Try to guess the type of build system used by the project, and return - an appropriate configure line. - """ - autotools = "configure('--prefix=%s' % prefix)" - cmake = "cmake('.', *std_cmake_args)" - python = "python('setup.py', 'install', '--prefix=%s' % prefix)" - r = "R('CMD', 'INSTALL', '--library=%s' % self.module.r_lib_dir, '%s' % self.stage.archive_file)" - - config_lines = ((r'/configure$', 'autotools', autotools), - (r'/CMakeLists.txt$', 'cmake', cmake), - (r'/setup.py$', 'python', python), - (r'/NAMESPACE$', 'r', r)) - - # Peek inside the tarball. - tar = which('tar') - output = tar( - "--exclude=*/*/*", "-tf", stage.archive_file, output=str) - lines = output.split("\n") - - # Set the configure line to the one that matched. - for pattern, bs, cl in config_lines: + """Try to guess the type of build system used by the project. + Set the appropriate default installation instructions and any + necessary extensions for Python and R.""" + + # Default installation instructions + installDict = { + 'autotools': """\ + # FIXME: Modify the configure line to suit your build system here. + configure('--prefix={0}'.format(prefix)) + + # FIXME: Add logic to build and install here. + make() + make('install')""", + + 'cmake': """\ + with working_dir('spack-build', create=True): + # FIXME: Modify the cmake line to suit your build system here. + cmake('..', *std_cmake_args) + + # FIXME: Add logic to build and install here. + make() + make('install')""", + + 'scons': """\ + # FIXME: Add logic to build and install here. + scons('prefix={0}'.format(prefix)) + scons('install')""", + + 'python': """\ + # FIXME: Add logic to build and install here. + python('setup.py', 'install', '--prefix={0}'.format(prefix))""", + + 'R': """\ + # FIXME: Add logic to build and install here. + R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir), + self.stage.source_path)""", + + 'unknown': """\ + # FIXME: Unknown build system + make() + make('install')""" + } + + # A list of clues that give us an idea of the build system a package + # uses. If the regular expression matches a file contained in the + # archive, the corresponding build system is assumed. + clues = [ + (r'/configure$', 'autotools'), + (r'/CMakeLists.txt$', 'cmake'), + (r'/SConstruct$', 'scons'), + (r'/setup.py$', 'python'), + (r'/NAMESPACE$', 'R') + ] + + # Peek inside the compressed file. + if stage.archive_file.endswith('.zip'): + try: + unzip = which('unzip') + output = unzip('-l', stage.archive_file, output=str) + except: + output = '' + else: + try: + tar = which('tar') + output = tar('--exclude=*/*/*', '-tf', + stage.archive_file, output=str) + except: + output = '' + lines = output.split('\n') + + # Determine the build system based on the files contained + # in the archive. + build_system = 'unknown' + for pattern, bs in clues: if any(re.search(pattern, l) for l in lines): - config_line = cl build_system = bs - break - else: - # None matched -- just put both, with cmake commented out - config_line = "# FIXME: Spack couldn't guess one, so here are some options:\n" - config_line += " # " + autotools + "\n" - config_line += " # " + cmake - build_system = 'unknown' - self.configure = config_line self.build_system = build_system + # Set the appropriate default installation instructions + self.install = installDict[build_system] + + # Set any necessary extensions for Python and R + extensions = '' + if build_system in ['python', 'R']: + extensions = "\n extends('{0}')\n".format(build_system) + + self.extends = extensions + def guess_name_and_version(url, args): # Try to deduce name and version of the new package from the URL @@ -168,7 +237,7 @@ def guess_name_and_version(url, args): else: try: name = spack.url.parse_name(url, version) - except spack.url.UndetectableNameError, e: + except spack.url.UndetectableNameError: # Use a user-supplied name if one is present tty.die("Couldn't guess a name for this package. Try running:", "", "spack create --name <name> <url>") @@ -182,7 +251,8 @@ def guess_name_and_version(url, args): def find_repository(spec, args): # figure out namespace for spec if spec.namespace and args.namespace and spec.namespace != args.namespace: - tty.die("Namespaces '%s' and '%s' do not match." % (spec.namespace, args.namespace)) + tty.die("Namespaces '%s' and '%s' do not match." % (spec.namespace, + args.namespace)) if not spec.namespace and args.namespace: spec.namespace = args.namespace @@ -193,8 +263,8 @@ def find_repository(spec, args): try: repo = Repo(repo_path) if spec.namespace and spec.namespace != repo.namespace: - tty.die("Can't create package with namespace %s in repo with namespace %s" - % (spec.namespace, repo.namespace)) + tty.die("Can't create package with namespace %s in repo with " + "namespace %s" % (spec.namespace, repo.namespace)) except RepoError as e: tty.die(str(e)) else: @@ -214,11 +284,7 @@ def find_repository(spec, args): def fetch_tarballs(url, name, version): """Try to find versions of the supplied archive by scraping the web. - - Prompts the user to select how many to download if many are found. - - - """ + Prompts the user to select how many to download if many are found.""" versions = spack.util.web.find_versions_of_archive(url) rkeys = sorted(versions.keys(), reverse=True) versions = OrderedDict(zip(rkeys, (versions[v] for v in rkeys))) @@ -226,11 +292,11 @@ def fetch_tarballs(url, name, version): archives_to_fetch = 1 if not versions: # If the fetch failed for some reason, revert to what the user provided - versions = { version : url } + versions = {version: url} elif len(versions) > 1: tty.msg("Found %s versions of %s:" % (len(versions), name), *spack.cmd.elide_list( - ["%-10s%s" % (v,u) for v, u in versions.iteritems()])) + ["%-10s%s" % (v, u) for v, u in versions.iteritems()])) print archives_to_fetch = tty.get_number( "Include how many checksums in the package file?", @@ -277,7 +343,7 @@ def create(parser, args): name = 'py-%s' % name # Prepend 'r-' to R package names, by convention. - if guesser.build_system == 'r': + if guesser.build_system == 'R': name = 'r-%s' % name # Create a directory for the new package. @@ -292,10 +358,11 @@ def create(parser, args): pkg_file.write( package_template.substitute( name=name, - configure=guesser.configure, class_name=mod_to_class(name), url=url, - versions=make_version_calls(ver_hash_tuples))) + versions=make_version_calls(ver_hash_tuples), + extends=guesser.extends, + install=guesser.install)) # If everything checks out, go ahead and edit. spack.editor(pkg_path) 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/cmd/repo.py b/lib/spack/spack/cmd/repo.py index 399237b169..cbd8f4784e 100644 --- a/lib/spack/spack/cmd/repo.py +++ b/lib/spack/spack/cmd/repo.py @@ -26,7 +26,7 @@ import os import re import shutil -from external import argparse +import argparse import llnl.util.tty as tty from llnl.util.filesystem import join_path, mkdirp diff --git a/lib/spack/spack/compilers/__init__.py b/lib/spack/spack/compilers/__init__.py index ae72b743b2..0ba94741da 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(): @@ -98,7 +98,7 @@ def get_compiler_config(scope=None): # 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 @@ -142,8 +142,8 @@ def remove_compiler_from_config(compiler_spec, scope=None): """ compiler_config = get_compiler_config(scope) config_length = len(compiler_config) - - filtered_compiler_config = [comp for comp in compiler_config + + filtered_compiler_config = [comp for comp in compiler_config if spack.spec.CompilerSpec(comp['compiler']['spec']) != compiler_spec] # Need a better way for this 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(): @@ -315,7 +315,7 @@ def all_os_classes(): """ classes = [] - platform = spack.architecture.sys_type() + platform = spack.architecture.platform() for os_class in platform.operating_sys.values(): classes.append(os_class) 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/concretize.py b/lib/spack/spack/concretize.py index 1f37455c77..f792008c49 100644 --- a/lib/spack/spack/concretize.py +++ b/lib/spack/spack/concretize.py @@ -221,7 +221,7 @@ class DefaultConcretizer(object): if isinstance(spec.root.architecture.platform,spack.architecture.Platform): spec.architecture.platform = spec.root.architecture.platform else: - spec.architecture.platform = spack.architecture.sys_type() + spec.architecture.platform = spack.architecture.platform() return True #changed? def concretize_architecture(self, spec): @@ -334,7 +334,7 @@ class DefaultConcretizer(object): Default specs set at the compiler level will still be added later. """ - + if not spec.architecture.platform_os: #Although this usually means changed, this means awaiting other changes return True @@ -347,7 +347,7 @@ class DefaultConcretizer(object): and flag in p.compiler_flags)) if not flag in spec.compiler_flags or \ not (sorted(spec.compiler_flags[flag]) >= sorted(nearest.compiler_flags[flag])): - if flag in spec.compiler_flags: + if flag in spec.compiler_flags: spec.compiler_flags[flag] = list(set(spec.compiler_flags[flag]) | set(nearest.compiler_flags[flag])) else: diff --git a/lib/spack/spack/config.py b/lib/spack/spack/config.py index db0787edc6..84179e1469 100644 --- a/lib/spack/spack/config.py +++ b/lib/spack/spack/config.py @@ -307,6 +307,8 @@ section_schemas = { 'autoload': {'$ref': '#/definitions/dependency_selection'}, 'prerequisites': {'$ref': '#/definitions/dependency_selection'}, 'conflict': {'$ref': '#/definitions/array_of_strings'}, + 'load': {'$ref': '#/definitions/array_of_strings'}, + 'suffixes': {'$ref': '#/definitions/dictionary_of_strings'}, 'environment': { 'type': 'object', 'default': {}, diff --git a/lib/spack/spack/database.py b/lib/spack/spack/database.py index f941346bb1..a4bbff3d5a 100644 --- a/lib/spack/spack/database.py +++ b/lib/spack/spack/database.py @@ -631,11 +631,13 @@ class WriteTransaction(_Transaction): class CorruptDatabaseError(SpackError): def __init__(self, path, msg=''): super(CorruptDatabaseError, self).__init__( - "Spack database is corrupt: %s. %s" % (path, msg)) + "Spack database is corrupt: %s. %s." + \ + "Try running `spack reindex` to fix." % (path, msg)) class InvalidDatabaseVersionError(SpackError): def __init__(self, expected, found): super(InvalidDatabaseVersionError, self).__init__( - "Expected database version %s but found version %s" % + "Expected database version %s but found version %s." + \ + "Try running `spack reindex` to fix." % (expected, found)) diff --git a/lib/spack/spack/directory_layout.py b/lib/spack/spack/directory_layout.py index 7e20365b0f..ee13e2dcbc 100644 --- a/lib/spack/spack/directory_layout.py +++ b/lib/spack/spack/directory_layout.py @@ -165,7 +165,7 @@ class DirectoryLayout(object): class YamlDirectoryLayout(DirectoryLayout): """Lays out installation directories like this:: <install root>/ - <target>/ + <platform-os-target>/ <compiler>-<compiler version>/ <name>-<version>-<variants>-<hash> 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..3a957c6e0e 100644 --- a/lib/spack/spack/hooks/sbang.py +++ b/lib/spack/spack/hooks/sbang.py @@ -23,8 +23,8 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## import os +import re -from llnl.util.filesystem import * import llnl.util.tty as tty import spack @@ -34,6 +34,7 @@ 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: @@ -57,17 +58,15 @@ def filter_shebang(path): if original.startswith(new_sbang_line): return - backup = path + ".shebang.bak" - os.rename(path, backup) + # Use --! instead of #! on second line for lua. + if re.search(r'^#!(/[^/]*)*lua\b', original): + original = re.sub(r'^#', '--', original) 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) + tty.warn("Patched overlong shebang in %s" % path) def filter_shebangs_in_directory(directory): diff --git a/lib/spack/spack/modules.py b/lib/spack/spack/modules.py index d2b819e80a..ce46047fa3 100644 --- a/lib/spack/spack/modules.py +++ b/lib/spack/spack/modules.py @@ -285,11 +285,18 @@ class EnvModule(object): naming_tokens = self.tokens naming_scheme = self.naming_scheme name = naming_scheme.format(**naming_tokens) - name += '-' + self.spec.dag_hash( - ) # Always append the hash to make the module file unique # Not everybody is working on linux... parts = name.split('/') name = join_path(*parts) + # Add optional suffixes based on constraints + configuration, _ = parse_config_options(self) + suffixes = [name] + for constraint, suffix in configuration.get('suffixes', {}).items(): + if constraint in self.spec: + suffixes.append(suffix) + # Always append the hash to make the module file unique + suffixes.append(self.spec.dag_hash()) + name = '-'.join(suffixes) return name @property @@ -381,6 +388,8 @@ class EnvModule(object): for x in filter_blacklisted( module_configuration.pop('autoload', []), self.name): module_file_content += self.autoload(x) + for x in module_configuration.pop('load', []): + module_file_content += self.autoload(x) for x in filter_blacklisted( module_configuration.pop('prerequisites', []), self.name): module_file_content += self.prerequisite(x) @@ -402,8 +411,12 @@ class EnvModule(object): return tuple() def autoload(self, spec): - m = type(self)(spec) - return self.autoload_format.format(module_file=m.use_name) + if not isinstance(spec, str): + m = type(self)(spec) + module_file = m.use_name + else: + module_file = spec + return self.autoload_format.format(module_file=module_file) def prerequisite(self, spec): m = type(self)(spec) @@ -441,7 +454,6 @@ class EnvModule(object): class Dotkit(EnvModule): name = 'dotkit' - path = join_path(spack.share_path, "dotkit") environment_modifications_formats = { PrependPath: 'dk_alter {name} {value}\n', @@ -454,7 +466,7 @@ class Dotkit(EnvModule): @property def file_name(self): - return join_path(Dotkit.path, self.spec.architecture, + return join_path(spack.share_path, "dotkit", self.spec.architecture, '%s.dk' % self.use_name) @property @@ -482,7 +494,6 @@ class Dotkit(EnvModule): class TclModule(EnvModule): name = 'tcl' - path = join_path(spack.share_path, "modules") environment_modifications_formats = { PrependPath: 'prepend-path --delim "{delim}" {name} \"{value}\"\n', @@ -503,7 +514,7 @@ class TclModule(EnvModule): @property def file_name(self): - return join_path(TclModule.path, self.spec.architecture, self.use_name) + return join_path(spack.share_path, "modules", self.spec.architecture, self.use_name) @property def header(self): diff --git a/lib/spack/spack/multimethod.py b/lib/spack/spack/multimethod.py index 170ef3cea2..0818f9092f 100644 --- a/lib/spack/spack/multimethod.py +++ b/lib/spack/spack/multimethod.py @@ -149,7 +149,7 @@ class when(object): @when('arch=chaos_5_x86_64_ib') def install(self, prefix): # This will be executed instead of the default install if - # the package's sys_type() is chaos_5_x86_64_ib. + # the package's platform() is chaos_5_x86_64_ib. @when('arch=bgqos_0") def install(self, prefix): diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py index c5250d17c0..b73056fd30 100644 --- a/lib/spack/spack/package.py +++ b/lib/spack/spack/package.py @@ -398,6 +398,12 @@ class Package(object): spack.repo.get(self.extendee_spec)._check_extendable() @property + def package_dir(self): + """Return the directory where the package.py file lives.""" + return os.path.dirname(self.module.__file__) + + + @property def global_license_dir(self): """Returns the directory where global license files for all packages are stored.""" @@ -687,7 +693,7 @@ class Package(object): """Get the spack.compiler.Compiler object used to build this package""" if not self.spec.concrete: raise ValueError("Can only get a compiler for a concrete package.") - return spack.compilers.compiler_for_spec(self.spec.compiler, + return spack.compilers.compiler_for_spec(self.spec.compiler, self.spec.architecture) def url_version(self, version): diff --git a/lib/spack/spack/repository.py b/lib/spack/spack/repository.py index 70134964ad..2c160a5f45 100644 --- a/lib/spack/spack/repository.py +++ b/lib/spack/spack/repository.py @@ -30,7 +30,7 @@ import imp import re import traceback from bisect import bisect_left -from external import yaml +import yaml import llnl.util.tty as tty from llnl.util.filesystem import * diff --git a/lib/spack/spack/spec.py b/lib/spack/spack/spec.py index 54219ec1b4..77bc57147d 100644 --- a/lib/spack/spack/spec.py +++ b/lib/spack/spack/spec.py @@ -2216,7 +2216,7 @@ class SpecParser(spack.parse.Parser): for spec in specs: for s in spec.traverse(): if s.architecture.os_string or s.architecture.target_string: - s._set_platform(spack.architecture.sys_type()) + s._set_platform(spack.architecture.platform()) return specs def parse_compiler(self, text): diff --git a/lib/spack/spack/test/architecture.py b/lib/spack/spack/test/architecture.py index a6847c5744..ae3f08deed 100644 --- a/lib/spack/spack/test/architecture.py +++ b/lib/spack/spack/test/architecture.py @@ -5,7 +5,7 @@ import unittest import os import platform as py_platform import spack -from spack.architecture import * +import spack.architecture from spack.spec import * from spack.platforms.cray_xc import CrayXc from spack.platforms.linux import Linux @@ -19,14 +19,14 @@ class ArchitectureTest(MockPackagesTest): def setUp(self): super(ArchitectureTest, self).setUp() - self.platform = sys_type() + self.platform = spack.architecture.platform() def tearDown(self): super(ArchitectureTest, self).tearDown() def test_dict_functions_for_architecture(self): - arch = Arch() - arch.platform = spack.architecture.sys_type() + arch = spack.architecture.Arch() + arch.platform = spack.architecture.platform() arch.platform_os = arch.platform.operating_system('default_os') arch.target = arch.platform.target('default_target') @@ -36,18 +36,23 @@ class ArchitectureTest(MockPackagesTest): self.assertEqual(arch, new_arch) - self.assertTrue( isinstance(arch, Arch) ) - self.assertTrue( isinstance(arch.platform, Platform) ) - self.assertTrue( isinstance(arch.platform_os, OperatingSystem) ) - self.assertTrue( isinstance(arch.target, Target) ) - self.assertTrue( isinstance(new_arch, Arch) ) - self.assertTrue( isinstance(new_arch.platform, Platform) ) - self.assertTrue( isinstance(new_arch.platform_os, OperatingSystem) ) - self.assertTrue( isinstance(new_arch.target, Target) ) - - - def test_sys_type(self): - output_platform_class = sys_type() + self.assertTrue( isinstance(arch, spack.architecture.Arch) ) + self.assertTrue( isinstance(arch.platform, spack.architecture.Platform) ) + self.assertTrue( isinstance(arch.platform_os, + spack.architecture.OperatingSystem) ) + self.assertTrue( isinstance(arch.target, + spack.architecture.Target) ) + self.assertTrue( isinstance(new_arch, spack.architecture.Arch) ) + self.assertTrue( isinstance(new_arch.platform, + spack.architecture.Platform) ) + self.assertTrue( isinstance(new_arch.platform_os, + spack.architecture.OperatingSystem) ) + self.assertTrue( isinstance(new_arch.target, + spack.architecture.Target) ) + + + def test_platform(self): + output_platform_class = spack.architecture.platform() my_arch_class = None if os.path.exists('/opt/cray/craype'): my_platform_class = CrayXc() diff --git a/lib/spack/spack/test/concretize.py b/lib/spack/spack/test/concretize.py index ab201f406a..ce02b08bc3 100644 --- a/lib/spack/spack/test/concretize.py +++ b/lib/spack/spack/test/concretize.py @@ -257,8 +257,8 @@ class ConcretizeTest(MockPackagesTest): def test_external_package_module(self): # No tcl modules on darwin/linux machines # TODO: improved way to check for this. - if (spack.architecture.sys_type().name == 'darwin' or - spack.architecture.sys_type().name == 'linux'): + if (spack.architecture.platform().name == 'darwin' or + spack.architecture.platform().name == 'linux'): return spec = Spec('externalmodule') 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..2396961888 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 +112,46 @@ 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() + + # This is sensitive to the user's environment; can include + # spurious entries for things like PS1 + # + # TODO: figure out how to make a bit more robust. + self.assertTrue(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/lib/spack/spack/test/install.py b/lib/spack/spack/test/install.py index cfe6ea9b27..390ec096a9 100644 --- a/lib/spack/spack/test/install.py +++ b/lib/spack/spack/test/install.py @@ -28,6 +28,7 @@ import tempfile import spack from llnl.util.filesystem import * from spack.directory_layout import YamlDirectoryLayout +from spack.database import Database from spack.fetch_strategy import URLFetchStrategy, FetchStrategyComposite from spack.test.mock_packages_test import * from spack.test.mock_repo import MockArchive @@ -49,7 +50,10 @@ class InstallTest(MockPackagesTest): # installed pkgs and mock packages. self.tmpdir = tempfile.mkdtemp() self.orig_layout = spack.install_layout + self.orig_db = spack.installed_db + spack.install_layout = YamlDirectoryLayout(self.tmpdir) + spack.installed_db = Database(self.tmpdir) def tearDown(self): @@ -61,6 +65,7 @@ class InstallTest(MockPackagesTest): # restore spack's layout. spack.install_layout = self.orig_layout + spack.installed_db = self.orig_db shutil.rmtree(self.tmpdir, ignore_errors=True) @@ -71,7 +76,7 @@ class InstallTest(MockPackagesTest): pkg.fetcher = fetcher - def ztest_install_and_uninstall(self): + def test_install_and_uninstall(self): # Get a basic concrete spec for the trivial install package. spec = Spec('trivial_install_test_package') spec.concretize() diff --git a/lib/spack/spack/test/mock_packages_test.py b/lib/spack/spack/test/mock_packages_test.py index a56bd8ebdc..e1acc32cb7 100644 --- a/lib/spack/spack/test/mock_packages_test.py +++ b/lib/spack/spack/test/mock_packages_test.py @@ -34,7 +34,7 @@ from ordereddict_backport import OrderedDict from spack.repository import RepoPath from spack.spec import Spec -platform = spack.architecture.sys_type() +platform = spack.architecture.platform() linux_os_name = 'debian' linux_os_version = '6' @@ -56,7 +56,7 @@ compilers: fc: None modules: 'None' - compiler: - spec: gcc@4.5.0 + spec: gcc@4.5.0 operating_system: {0}{1} paths: cc: /path/to/gcc @@ -144,7 +144,7 @@ compilers: fc: /path/to/gfortran operating_system: elcapitan spec: gcc@4.5.0 - modules: 'None' + modules: 'None' - compiler: spec: clang@3.3 operating_system: elcapitan @@ -201,6 +201,10 @@ class MockPackagesTest(unittest.TestCase): spack.config.ConfigScope('site', self.mock_site_config) spack.config.ConfigScope('user', self.mock_user_config) + # Keep tests from interfering with the actual module path. + self.real_share_path = spack.share_path + spack.share_path = tempfile.mkdtemp() + # Store changes to the package's dependencies so we can # restore later. self.saved_deps = {} @@ -235,6 +239,9 @@ class MockPackagesTest(unittest.TestCase): pkg.dependencies.clear() pkg.dependencies.update(deps) + shutil.rmtree(spack.share_path, ignore_errors=True) + spack.share_path = self.real_share_path + def setUp(self): self.initmock() diff --git a/lib/spack/spack/test/modules.py b/lib/spack/spack/test/modules.py index 582e067860..6d2e3705bd 100644 --- a/lib/spack/spack/test/modules.py +++ b/lib/spack/spack/test/modules.py @@ -27,6 +27,7 @@ from contextlib import contextmanager import StringIO import spack.modules +import unittest from spack.test.mock_packages_test import MockPackagesTest FILE_REGISTRY = collections.defaultdict(StringIO.StringIO) @@ -67,6 +68,24 @@ configuration_autoload_all = { } } +configuration_prerequisites_direct = { + 'enable': ['tcl'], + 'tcl': { + 'all': { + 'prerequisites': 'direct' + } + } +} + +configuration_prerequisites_all = { + 'enable': ['tcl'], + 'tcl': { + 'all': { + 'prerequisites': 'all' + } + } +} + configuration_alter_environment = { 'enable': ['tcl'], 'tcl': { @@ -74,8 +93,13 @@ configuration_alter_environment = { 'filter': {'environment_blacklist': ['CMAKE_PREFIX_PATH']} }, 'platform=test target=x86_64': { - 'environment': {'set': {'FOO': 'foo'}, - 'unset': ['BAR']} + 'environment': { + 'set': {'FOO': 'foo'}, + 'unset': ['BAR'] + } + }, + 'platform=test target=x86_32': { + 'load': ['foo/bar'] } } } @@ -83,7 +107,8 @@ configuration_alter_environment = { configuration_blacklist = { 'enable': ['tcl'], 'tcl': { - 'blacklist': ['callpath'], + 'whitelist': ['zmpi'], + 'blacklist': ['callpath', 'mpi'], 'all': { 'autoload': 'direct' } @@ -100,8 +125,68 @@ configuration_conflicts = { } } +configuration_wrong_conflicts = { + 'enable': ['tcl'], + 'tcl': { + 'naming_scheme': '{name}/{version}-{compiler.name}', + 'all': { + 'conflict': ['{name}/{compiler.name}'] + } + } +} + +configuration_suffix = { + 'enable': ['tcl'], + 'tcl': { + 'mpileaks': { + 'suffixes': { + '+debug': 'foo', + '~debug': 'bar' + } + } + } +} + + +class HelperFunctionsTests(MockPackagesTest): + + def test_update_dictionary_extending_list(self): + target = { + 'foo': { + 'a': 1, + 'b': 2, + 'd': 4 + }, + 'bar': [1, 2, 4], + 'baz': 'foobar' + } + update = { + 'foo': { + 'c': 3, + }, + 'bar': [3], + 'baz': 'foobaz', + 'newkey': { + 'd': 4 + } + } + spack.modules.update_dictionary_extending_lists(target, update) + self.assertTrue(len(target) == 4) + self.assertTrue(len(target['foo']) == 4) + self.assertTrue(len(target['bar']) == 4) + self.assertEqual(target['baz'], 'foobaz') + + def test_inspect_path(self): + env = spack.modules.inspect_path('/usr') + names = [item.name for item in env] + self.assertTrue('PATH' in names) + self.assertTrue('LIBRARY_PATH' in names) + self.assertTrue('LD_LIBRARY_PATH' in names) + self.assertTrue('CPATH' in names) + class TclTests(MockPackagesTest): + def setUp(self): super(TclTests, self).setUp() self.configuration_obj = spack.modules.CONFIGURATION @@ -116,7 +201,6 @@ class TclTests(MockPackagesTest): def get_modulefile_content(self, spec): spec.concretize() - print spec, '&&&&&' generator = spack.modules.TclModule(spec) generator.write() content = FILE_REGISTRY[generator.file_name].split('\n') @@ -127,6 +211,8 @@ class TclTests(MockPackagesTest): spec = spack.spec.Spec('mpich@3.0.4') content = self.get_modulefile_content(spec) self.assertTrue('module-whatis "mpich @3.0.4"' in content) + self.assertRaises(TypeError, spack.modules.dependencies, + spec, 'non-existing-tag') def test_autoload(self): spack.modules.CONFIGURATION = configuration_autoload_direct @@ -141,11 +227,21 @@ class TclTests(MockPackagesTest): self.assertEqual(len([x for x in content if 'is-loaded' in x]), 5) self.assertEqual(len([x for x in content if 'module load ' in x]), 5) + def test_prerequisites(self): + spack.modules.CONFIGURATION = configuration_prerequisites_direct + spec = spack.spec.Spec('mpileaks arch=x86-linux') + content = self.get_modulefile_content(spec) + self.assertEqual(len([x for x in content if 'prereq' in x]), 2) + + spack.modules.CONFIGURATION = configuration_prerequisites_all + spec = spack.spec.Spec('mpileaks arch=x86-linux') + content = self.get_modulefile_content(spec) + self.assertEqual(len([x for x in content if 'prereq' in x]), 5) + def test_alter_environment(self): spack.modules.CONFIGURATION = configuration_alter_environment spec = spack.spec.Spec('mpileaks platform=test target=x86_64') content = self.get_modulefile_content(spec) - print content self.assertEqual( len([x for x in content @@ -156,7 +252,6 @@ class TclTests(MockPackagesTest): spec = spack.spec.Spec('libdwarf %clang platform=test target=x86_32') content = self.get_modulefile_content(spec) - print content self.assertEqual( len([x for x in content @@ -164,6 +259,10 @@ class TclTests(MockPackagesTest): self.assertEqual( len([x for x in content if 'setenv FOO "foo"' in x]), 0) self.assertEqual(len([x for x in content if 'unsetenv BAR' in x]), 0) + self.assertEqual( + len([x for x in content if 'is-loaded foo/bar' in x]), 1) + self.assertEqual( + len([x for x in content if 'module load foo/bar' in x]), 1) def test_blacklist(self): spack.modules.CONFIGURATION = configuration_blacklist @@ -171,6 +270,13 @@ class TclTests(MockPackagesTest): content = self.get_modulefile_content(spec) self.assertEqual(len([x for x in content if 'is-loaded' in x]), 1) self.assertEqual(len([x for x in content if 'module load ' in x]), 1) + spec = spack.spec.Spec('callpath arch=x86-linux') + # Returns a StringIO instead of a string as no module file was written + self.assertRaises(AttributeError, self.get_modulefile_content, spec) + spec = spack.spec.Spec('zmpi arch=x86-linux') + content = self.get_modulefile_content(spec) + self.assertEqual(len([x for x in content if 'is-loaded' in x]), 1) + self.assertEqual(len([x for x in content if 'module load ' in x]), 1) def test_conflicts(self): spack.modules.CONFIGURATION = configuration_conflicts @@ -182,3 +288,57 @@ class TclTests(MockPackagesTest): len([x for x in content if x == 'conflict mpileaks']), 1) self.assertEqual( len([x for x in content if x == 'conflict intel/14.0.1']), 1) + + spack.modules.CONFIGURATION = configuration_wrong_conflicts + self.assertRaises(SystemExit, self.get_modulefile_content, spec) + + def test_suffixes(self): + spack.modules.CONFIGURATION = configuration_suffix + spec = spack.spec.Spec('mpileaks+debug arch=x86-linux') + spec.concretize() + generator = spack.modules.TclModule(spec) + self.assertTrue('foo' in generator.use_name) + + spec = spack.spec.Spec('mpileaks~debug arch=x86-linux') + spec.concretize() + generator = spack.modules.TclModule(spec) + self.assertTrue('bar' in generator.use_name) + + +configuration_dotkit = { + 'enable': ['dotkit'], + 'dotkit': { + 'all': { + 'prerequisites': 'direct' + } + } +} + + +class DotkitTests(MockPackagesTest): + + def setUp(self): + super(DotkitTests, self).setUp() + self.configuration_obj = spack.modules.CONFIGURATION + spack.modules.open = mock_open + # Make sure that a non-mocked configuration will trigger an error + spack.modules.CONFIGURATION = None + + def tearDown(self): + del spack.modules.open + spack.modules.CONFIGURATION = self.configuration_obj + super(DotkitTests, self).tearDown() + + def get_modulefile_content(self, spec): + spec.concretize() + generator = spack.modules.Dotkit(spec) + generator.write() + content = FILE_REGISTRY[generator.file_name].split('\n') + return content + + def test_dotkit(self): + spack.modules.CONFIGURATION = configuration_dotkit + spec = spack.spec.Spec('mpileaks arch=x86-linux') + content = self.get_modulefile_content(spec) + self.assertTrue('#c spack' in content) + self.assertTrue('#d mpileaks @2.3' in content) diff --git a/lib/spack/spack/test/multimethod.py b/lib/spack/spack/test/multimethod.py index 034e6b3923..c233ea4fd6 100644 --- a/lib/spack/spack/test/multimethod.py +++ b/lib/spack/spack/test/multimethod.py @@ -93,7 +93,7 @@ class MultiMethodTest(MockPackagesTest): def test_target_match(self): - platform = spack.architecture.sys_type() + platform = spack.architecture.platform() targets = platform.targets.values() for target in targets[:-1]: pkg = spack.repo.get('multimethod target='+target.name) diff --git a/lib/spack/spack/test/sbang.py b/lib/spack/spack/test/sbang.py index 6aea1a68c7..ed54ff90b0 100644 --- a/lib/spack/spack/test/sbang.py +++ b/lib/spack/spack/test/sbang.py @@ -34,10 +34,12 @@ from llnl.util.filesystem import * from spack.hooks.sbang import filter_shebangs_in_directory import spack -short_line = "#!/this/is/short/bin/bash\n" -long_line = "#!/this/" + ('x' * 200) + "/is/long\n" -sbang_line = '#!/bin/bash %s/bin/sbang\n' % spack.spack_root -last_line = "last!\n" +short_line = "#!/this/is/short/bin/bash\n" +long_line = "#!/this/" + ('x' * 200) + "/is/long\n" +lua_line = "#!/this/" + ('x' * 200) + "/is/lua\n" +lua_line_patched = "--!/this/" + ('x' * 200) + "/is/lua\n" +sbang_line = '#!/bin/bash %s/bin/sbang\n' % spack.spack_root +last_line = "last!\n" class SbangTest(unittest.TestCase): def setUp(self): @@ -59,6 +61,12 @@ class SbangTest(unittest.TestCase): f.write(long_line) f.write(last_line) + # Lua script with long shebang + self.lua_shebang = os.path.join(self.tempdir, 'lua') + with open(self.lua_shebang, 'w') as f: + f.write(lua_line) + f.write(last_line) + # Script already using sbang. self.has_shebang = os.path.join(self.tempdir, 'shebang') with open(self.has_shebang, 'w') as f: @@ -71,7 +79,6 @@ class SbangTest(unittest.TestCase): shutil.rmtree(self.tempdir, ignore_errors=True) - def test_shebang_handling(self): filter_shebangs_in_directory(self.tempdir) @@ -86,6 +93,12 @@ class SbangTest(unittest.TestCase): self.assertEqual(f.readline(), long_line) self.assertEqual(f.readline(), last_line) + # Make sure this got patched. + with open(self.lua_shebang, 'r') as f: + self.assertEqual(f.readline(), sbang_line) + self.assertEqual(f.readline(), lua_line_patched) + self.assertEqual(f.readline(), last_line) + # Make sure this is untouched with open(self.has_shebang, 'r') as f: self.assertEqual(f.readline(), sbang_line) diff --git a/lib/spack/spack/test/spec_dag.py b/lib/spack/spack/test/spec_dag.py index 712f07ac4d..c56c70b1fe 100644 --- a/lib/spack/spack/test/spec_dag.py +++ b/lib/spack/spack/test/spec_dag.py @@ -242,7 +242,7 @@ class SpecDagTest(MockPackagesTest): def test_unsatisfiable_architecture(self): - platform = spack.architecture.sys_type() + platform = spack.architecture.platform() self.set_pkg_dep('mpileaks', 'mpich platform=test target=be') spec = Spec('mpileaks ^mpich platform=test target=fe ^callpath ^dyninst ^libelf ^libdwarf') diff --git a/lib/spack/spack/test/spec_semantics.py b/lib/spack/spack/test/spec_semantics.py index 9876bfd5a8..b174e5305c 100644 --- a/lib/spack/spack/test/spec_semantics.py +++ b/lib/spack/spack/test/spec_semantics.py @@ -141,7 +141,6 @@ class SpecSematicsTest(MockPackagesTest): def test_satisfies_architecture(self): - platform = spack.architecture.sys_type() self.check_satisfies( 'foo platform=test target=frontend os=frontend', 'platform=test target=frontend os=frontend') @@ -396,7 +395,7 @@ class SpecSematicsTest(MockPackagesTest): self.check_constrain_changed('libelf', 'debug=2') self.check_constrain_changed('libelf', 'cppflags="-O3"') - platform = spack.architecture.sys_type() + platform = spack.architecture.platform() self.check_constrain_changed('libelf', 'target='+platform.target('default_target').name) self.check_constrain_changed('libelf', 'os='+platform.operating_system('default_os').name) @@ -412,7 +411,7 @@ class SpecSematicsTest(MockPackagesTest): self.check_constrain_not_changed('libelf debug=2', 'debug=2') self.check_constrain_not_changed('libelf cppflags="-O3"', 'cppflags="-O3"') - platform = spack.architecture.sys_type() + platform = spack.architecture.platform() default_target = platform.target('default_target').name self.check_constrain_not_changed('libelf target='+default_target, 'target='+default_target) @@ -425,7 +424,7 @@ class SpecSematicsTest(MockPackagesTest): self.check_constrain_changed('libelf^foo', 'libelf^foo+debug') self.check_constrain_changed('libelf^foo', 'libelf^foo~debug') - platform = spack.architecture.sys_type() + platform = spack.architecture.platform() default_target = platform.target('default_target').name self.check_constrain_changed('libelf^foo', 'libelf^foo target='+default_target) @@ -439,6 +438,6 @@ class SpecSematicsTest(MockPackagesTest): self.check_constrain_not_changed('libelf^foo~debug', 'libelf^foo~debug') self.check_constrain_not_changed('libelf^foo cppflags="-O3"', 'libelf^foo cppflags="-O3"') - platform = spack.architecture.sys_type() + platform = spack.architecture.platform() default_target = platform.target('default_target').name self.check_constrain_not_changed('libelf^foo target='+default_target, 'libelf^foo target='+default_target) 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.mock/packages/multimethod/package.py b/var/spack/repos/builtin.mock/packages/multimethod/package.py index 649afa5945..ca991632dd 100644 --- a/var/spack/repos/builtin.mock/packages/multimethod/package.py +++ b/var/spack/repos/builtin.mock/packages/multimethod/package.py @@ -106,17 +106,11 @@ class Multimethod(Package): # # Make sure we can switch methods on different target # -# for platform_name in ['cray_xc', 'darwin', 'linux']: -# file_path = join_path(spack.platform_path, platform_name) -# platform_mod = imp.load_source('spack.platforms', file_path + '.py') -# cls = getattr(platform_mod, mod_to_class(platform_name)) - -# platform = cls() - platform = spack.architecture.sys_type() + platform = spack.architecture.platform() targets = platform.targets.values() if len(targets) > 1: targets = targets[:-1] - + for target in targets: @when('target='+target.name) def different_by_target(self): 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/packages/adios/package.py b/var/spack/repos/builtin/packages/adios/package.py index 260dcbe851..9e0452ba6f 100644 --- a/var/spack/packages/adios/package.py +++ b/var/spack/repos/builtin/packages/adios/package.py @@ -1,15 +1,18 @@ import os from spack import * + + class Adios(Package): - """The Adaptable IO System (ADIOS) provides a simple, - flexible way for scientists to describe the - data in their code that may need to be written, - read, or processed outside of the running simulation """ - + The Adaptable IO System (ADIOS) provides a simple, + flexible way for scientists to describe the + data in their code that may need to be written, + read, or processed outside of the running simulation + """ + homepage = "http://www.olcf.ornl.gov/center-projects/adios/" - url = "http://users.nccs.gov/~pnorbert/adios-1.9.0.tar.gz" + url = "http://users.nccs.gov/~pnorbert/adios-1.9.0.tar.gz" version('1.9.0', 'dbf5cb10e32add2f04c9b4052b7ffa76') @@ -22,13 +25,13 @@ class Adios(Package): depends_on('mxml') def install(self, spec, prefix): - configure_args = ["--prefix=%s" % prefix, - "--with-mxml=%s" % spec['mxml'].prefix, + configure_args = ["--prefix=%s" % prefix, + "--with-mxml=%s" % spec['mxml'].prefix, "--with-hdf5=%s" % spec['hdf5'].prefix, "--with-netcdf=%s" % os.environ["NETCDF_DIR"], "--with-infiniband=no", - "MPICC=cc","MPICXX=CC","MPIFC=ftn", - "CPPFLAGS=-DMPICH_IGNORE_CXX_SEEK"] + "MPICC=cc", "MPICXX=CC", "MPIFC=ftn", + "CPPFLAGS=-DMPICH_IGNORE_CXX_SEEK"] if spec.satisfies('%gcc'): configure_args.extend(["CC=gcc", "CXX=g++", "FC=gfortran"]) 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/autoconf/package.py b/var/spack/repos/builtin/packages/autoconf/package.py index d920855a2f..770ceed48b 100644 --- a/var/spack/repos/builtin/packages/autoconf/package.py +++ b/var/spack/repos/builtin/packages/autoconf/package.py @@ -24,18 +24,36 @@ ############################################################################## from spack import * + class Autoconf(Package): - """Autoconf -- system configuration part of autotools""" - homepage = "https://www.gnu.org/software/autoconf/" - url = "http://ftp.gnu.org/gnu/autoconf/autoconf-2.69.tar.gz" + """ + Autoconf -- system configuration part of autotools + """ + homepage = 'https://www.gnu.org/software/autoconf/' + url = 'http://ftp.gnu.org/gnu/autoconf/autoconf-2.69.tar.gz' version('2.69', '82d05e03b93e45f5a39b828dc9c6c29b') version('2.62', '6c1f3b3734999035d77da5024aab4fbd') - depends_on("m4") + depends_on('m4') + + def _make_executable(self, name): + return Executable(join_path(self.prefix.bin, name)) + + def setup_dependent_package(self, module, dependent_spec): + # Autoconf is very likely to be a build dependency, + # so we add the tools it provides to the dependent module + executables = ['autoconf', + 'autoheader', + 'autom4te', + 'autoreconf', + 'autoscan', + 'autoupdate', + 'ifnames'] + for name in executables: + setattr(module, name, self._make_executable(name)) def install(self, spec, prefix): configure("--prefix=%s" % prefix) - make() make("install") diff --git a/var/spack/repos/builtin/packages/automake/package.py b/var/spack/repos/builtin/packages/automake/package.py index 331b364496..78b0a5b34f 100644 --- a/var/spack/repos/builtin/packages/automake/package.py +++ b/var/spack/repos/builtin/packages/automake/package.py @@ -24,10 +24,13 @@ ############################################################################## from spack import * + class Automake(Package): - """Automake -- make file builder part of autotools""" - homepage = "http://www.gnu.org/software/automake/" - url = "http://ftp.gnu.org/gnu/automake/automake-1.14.tar.gz" + """ + Automake -- make file builder part of autotools + """ + homepage = 'http://www.gnu.org/software/automake/' + url = 'http://ftp.gnu.org/gnu/automake/automake-1.14.tar.gz' version('1.15', '716946a105ca228ab545fc37a70df3a3') version('1.14.1', 'd052a3e884631b9c7892f2efce542d75') @@ -35,8 +38,17 @@ class Automake(Package): depends_on('autoconf') + def _make_executable(self, name): + return Executable(join_path(self.prefix.bin, name)) + + def setup_dependent_package(self, module, dependent_spec): + # Automake is very likely to be a build dependency, + # so we add the tools it provides to the dependent module + executables = ['aclocal', 'automake'] + for name in executables: + setattr(module, name, self._make_executable(name)) + def install(self, spec, prefix): configure("--prefix=%s" % prefix) - make() make("install") diff --git a/var/spack/repos/builtin/packages/binutils/package.py b/var/spack/repos/builtin/packages/binutils/package.py index 5f305abb02..35d52128c3 100644 --- a/var/spack/repos/builtin/packages/binutils/package.py +++ b/var/spack/repos/builtin/packages/binutils/package.py @@ -24,11 +24,12 @@ ############################################################################## from spack import * + class Binutils(Package): """GNU binutils, which contain the linker, assembler, objdump and others""" - homepage = "http://www.gnu.org/software/binutils/" - url="https://ftp.gnu.org/gnu/binutils/binutils-2.25.tar.bz2" + homepage = "http://www.gnu.org/software/binutils/" + url = "https://ftp.gnu.org/gnu/binutils/binutils-2.25.tar.bz2" # 2.26 is incompatible with py-pillow build for some reason. version('2.26', '64146a0faa3b411ba774f47d41de239f') @@ -41,12 +42,15 @@ class Binutils(Package): depends_on('flex') depends_on('bison') - # Add a patch that creates binutils libiberty_pic.a which is preferred by OpenSpeedShop and cbtf-krell - variant('krellpatch', default=False, description="build with openspeedshop based patch.") + # Add a patch that creates binutils libiberty_pic.a which is preferred by + # OpenSpeedShop and cbtf-krell + variant('krellpatch', default=False, + description="build with openspeedshop based patch.") variant('gold', default=True, description="build the gold linker") patch('binutilskrell-2.24.patch', when='@2.24+krellpatch') patch('cr16.patch') + patch('update_symbol-2.26.patch', when='@2.26') variant('libiberty', default=False, description='Also install libiberty.') diff --git a/var/spack/repos/builtin/packages/binutils/update_symbol-2.26.patch b/var/spack/repos/builtin/packages/binutils/update_symbol-2.26.patch new file mode 100644 index 0000000000..2601f63a6b --- /dev/null +++ b/var/spack/repos/builtin/packages/binutils/update_symbol-2.26.patch @@ -0,0 +1,104 @@ +From 544ddf9322b1b83982e5cb84a54d084ee7e718ea Mon Sep 17 00:00:00 2001 +From: H.J. Lu <hjl.tools@gmail.com> +Date: Wed, 24 Feb 2016 15:13:35 -0800 +Subject: [PATCH] Update symbol version for symbol from linker script + +We need to update symbol version for symbols from linker script. + +Backport from master + +bfd/ + + PR ld/19698 + * elflink.c (bfd_elf_record_link_assignment): Set versioned if + symbol version is unknown. + +ld/ + + PR ld/19698 + * testsuite/ld-elf/pr19698.d: New file. + * testsuite/ld-elf/pr19698.s: Likewise. + * testsuite/ld-elf/pr19698.t: Likewise. +--- + bfd/ChangeLog | 9 +++++++++ + bfd/elflink.c | 13 +++++++++++++ + ld/ChangeLog | 10 ++++++++++ + ld/testsuite/ld-elf/pr19698.d | 10 ++++++++++ + ld/testsuite/ld-elf/pr19698.s | 5 +++++ + ld/testsuite/ld-elf/pr19698.t | 11 +++++++++++ + 6 files changed, 58 insertions(+), 0 deletions(-) + create mode 100644 ld/testsuite/ld-elf/pr19698.d + create mode 100644 ld/testsuite/ld-elf/pr19698.s + create mode 100644 ld/testsuite/ld-elf/pr19698.t + +diff --git a/bfd/elflink.c b/bfd/elflink.c +index ae8d148..8fcaadd 100644 +--- a/bfd/elflink.c ++++ b/bfd/elflink.c +@@ -555,6 +555,19 @@ bfd_elf_record_link_assignment (bfd *output_bfd, + if (h == NULL) + return provide; + ++ if (h->versioned == unknown) ++ { ++ /* Set versioned if symbol version is unknown. */ ++ char *version = strrchr (name, ELF_VER_CHR); ++ if (version) ++ { ++ if (version > name && version[-1] != ELF_VER_CHR) ++ h->versioned = versioned_hidden; ++ else ++ h->versioned = versioned; ++ } ++ } ++ + switch (h->root.type) + { + case bfd_link_hash_defined: +diff --git a/ld/testsuite/ld-elf/pr19698.d b/ld/testsuite/ld-elf/pr19698.d +new file mode 100644 +index 0000000..a39f67a +--- /dev/null ++++ b/ld/testsuite/ld-elf/pr19698.d +@@ -0,0 +1,10 @@ ++#ld: -shared $srcdir/$subdir/pr19698.t ++#readelf : --dyn-syms --wide ++#target: *-*-linux* *-*-gnu* *-*-solaris* ++ ++Symbol table '\.dynsym' contains [0-9]+ entries: ++#... ++ +[0-9]+: +[0-9a-f]+ +[0-9a-f]+ +FUNC +GLOBAL +DEFAULT +[0-9]+ +foo@VERS.1 ++#... ++ +[0-9]+: +[0-9a-f]+ +[0-9a-f]+ +FUNC +GLOBAL +DEFAULT +[0-9]+ +foo@@VERS.2 ++#pass +diff --git a/ld/testsuite/ld-elf/pr19698.s b/ld/testsuite/ld-elf/pr19698.s +new file mode 100644 +index 0000000..875dca4 +--- /dev/null ++++ b/ld/testsuite/ld-elf/pr19698.s +@@ -0,0 +1,5 @@ ++ .text ++ .globl foo ++ .type foo, %function ++foo: ++ .byte 0 +diff --git a/ld/testsuite/ld-elf/pr19698.t b/ld/testsuite/ld-elf/pr19698.t +new file mode 100644 +index 0000000..09d9125 +--- /dev/null ++++ b/ld/testsuite/ld-elf/pr19698.t +@@ -0,0 +1,11 @@ ++"foo@VERS.1" = foo; ++ ++VERSION { ++VERS.2 { ++ global: ++ foo; ++}; ++ ++VERS.1 { ++}; ++} +-- +1.7.1 + 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/cairo/package.py b/var/spack/repos/builtin/packages/cairo/package.py index 5c7c2fae22..ddb8d2fd03 100644 --- a/var/spack/repos/builtin/packages/cairo/package.py +++ b/var/spack/repos/builtin/packages/cairo/package.py @@ -24,8 +24,10 @@ ############################################################################## from spack import * + class Cairo(Package): - """Cairo is a 2D graphics library with support for multiple output devices.""" + """Cairo is a 2D graphics library with support for multiple output + devices.""" homepage = "http://cairographics.org" url = "http://cairographics.org/releases/cairo-1.14.0.tar.xz" @@ -34,11 +36,12 @@ class Cairo(Package): depends_on("libpng") depends_on("glib") depends_on("pixman") - depends_on("fontconfig@2.10.91:") # Require newer version of fontconfig. + depends_on("freetype") + depends_on("fontconfig@2.10.91:") # Require newer version of fontconfig. def install(self, spec, prefix): configure("--prefix=%s" % prefix, - "--disable-trace", # can cause problems with libiberty + "--disable-trace", # can cause problems with libiberty "--enable-tee") make() make("install") diff --git a/var/spack/repos/builtin/packages/cantera/package.py b/var/spack/repos/builtin/packages/cantera/package.py new file mode 100644 index 0000000000..e9e5da4486 --- /dev/null +++ b/var/spack/repos/builtin/packages/cantera/package.py @@ -0,0 +1,197 @@ +############################################################################## +# 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 Cantera(Package): + """Cantera is a suite of object-oriented software tools for problems + involving chemical kinetics, thermodynamics, and/or transport processes.""" + + homepage = "http://www.cantera.org/docs/sphinx/html/index.html" + url = "https://github.com/Cantera/cantera/archive/v2.2.1.tar.gz" + + version('2.2.1', '9d1919bdef39ddec54485fc8a741a3aa') + + variant('lapack', default=True, description='Build with external BLAS/LAPACK libraries') + variant('threadsafe', default=True, description='Build threadsafe, requires Boost') + variant('sundials', default=True, description='Build with external Sundials') + variant('python', default=False, description='Build the Cantera Python module') + variant('matlab', default=False, description='Build the Cantera Matlab toolbox') + + # Required dependencies + depends_on('scons') + + # Recommended dependencies + depends_on('blas', when='+lapack') + depends_on('lapack', when='+lapack') + depends_on('boost', when='+threadsafe') + depends_on('sundials', when='+sundials') # must be compiled with -fPIC + + # Python module dependencies + extends('python', when='+python') + depends_on('py-numpy', when='+python') + depends_on('py-scipy', when='+python') + depends_on('py-cython', when='+python') + depends_on('py-3to2', when='+python') + # TODO: these "when" specs don't actually work + # depends_on('py-unittest2', when='+python^python@2.6') + # depends_on('py-unittest2py3k', when='+python^python@3.1') + + # Matlab toolbox dependencies + # TODO: add Matlab package + # TODO: allow packages to extend multiple other packages + # extends('matlab', when='+matlab') + + def install(self, spec, prefix): + # Required options + options = [ + 'prefix={0}'.format(prefix), + 'CC={0}'.format(os.environ['CC']), + 'CXX={0}'.format(os.environ['CXX']), + 'F77={0}'.format(os.environ['F77']), + 'FORTRAN={0}'.format(os.environ['FC']), + 'cc_flags=-fPIC', + # Allow Spack environment variables to propagate through to SCons + 'env_vars=all' + ] + + # BLAS/LAPACK support + if '+lapack' in spec: + options.extend([ + 'blas_lapack_libs=lapack,blas', + 'blas_lapack_dir={0}'.format(spec['lapack'].prefix.lib) + ]) + + # Threadsafe build, requires Boost + if '+threadsafe' in spec: + options.extend([ + 'build_thread_safe=yes', + 'boost_inc_dir={0}'.format(spec['boost'].prefix.include), + 'boost_lib_dir={0}'.format(spec['boost'].prefix.lib), + 'boost_thread_lib=boost_thread-mt,boost_system-mt' + ]) + else: + options.append('build_thread_safe=no') + + # Sundials support + if '+sundials' in spec: + options.extend([ + 'use_sundials=y', + 'sundials_include={0}'.format(spec['sundials'].prefix.include), + 'sundials_libdir={0}'.format(spec['sundials'].prefix.lib), + 'sundials_license={0}'.format( + join_path(spec['sundials'].prefix, 'LICENSE')) + ]) + else: + options.append('use_sundials=n') + + # Python module + if '+python' in spec: + options.extend([ + 'python_package=full', + 'python_cmd={0}'.format( + join_path(spec['python'].prefix.bin, 'python')), + 'python_array_home={0}'.format(spec['py-numpy'].prefix) + ]) + if spec['python'].satisfies('@3'): + options.extend([ + 'python3_package=y', + 'python3_cmd={0}'.format( + join_path(spec['python'].prefix.bin, 'python')), + 'python3_array_home={0}'.format(spec['py-numpy'].prefix) + ]) + else: + options.append('python3_package=n') + else: + options.append('python_package=none') + options.append('python3_package=n') + + # Matlab toolbox + if '+matlab' in spec: + options.extend([ + 'matlab_toolbox=y', + 'matlab_path={0}'.format(spec['matlab'].prefix) + ]) + else: + options.append('matlab_toolbox=n') + + scons('build', *options) + + if '+python' in spec: + # Tests will always fail if Python dependencies aren't built + # In addition, 3 of the tests fail when run in parallel + scons('test', parallel=False) + + scons('install') + + self.filter_compilers() + + def filter_compilers(self): + """Run after install to tell the Makefile and SConstruct files to use + the compilers that Spack built the package with. + + If this isn't done, they'll have CC, CXX, F77, and FC set to Spack's + generic cc, c++, f77, and f90. We want them to be bound to whatever + compiler they were built with.""" + + kwargs = {'ignore_absent': True, 'backup': False, 'string': True} + dirname = os.path.join(self.prefix, 'share/cantera/samples') + + cc_files = [ + 'cxx/rankine/Makefile', 'cxx/NASA_coeffs/Makefile', + 'cxx/kinetics1/Makefile', 'cxx/flamespeed/Makefile', + 'cxx/combustor/Makefile', 'f77/SConstruct' + ] + + cxx_files = [ + 'cxx/rankine/Makefile', 'cxx/NASA_coeffs/Makefile', + 'cxx/kinetics1/Makefile', 'cxx/flamespeed/Makefile', + 'cxx/combustor/Makefile' + ] + + f77_files = [ + 'f77/Makefile', 'f77/SConstruct' + ] + + fc_files = [ + 'f90/Makefile', 'f90/SConstruct' + ] + + for filename in cc_files: + filter_file(os.environ['CC'], self.compiler.cc, + os.path.join(dirname, filename), **kwargs) + + for filename in cxx_files: + filter_file(os.environ['CXX'], self.compiler.cxx, + os.path.join(dirname, filename), **kwargs) + + for filename in f77_files: + filter_file(os.environ['F77'], self.compiler.f77, + os.path.join(dirname, filename), **kwargs) + + for filename in fc_files: + filter_file(os.environ['FC'], self.compiler.fc, + os.path.join(dirname, filename), **kwargs) diff --git a/var/spack/repos/builtin/packages/curl/package.py b/var/spack/repos/builtin/packages/curl/package.py index e3de6ee5a1..79570205fa 100644 --- a/var/spack/repos/builtin/packages/curl/package.py +++ b/var/spack/repos/builtin/packages/curl/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Curl(Package): """cURL is an open source command line tool and library for transferring data with URL syntax""" @@ -31,6 +32,7 @@ class Curl(Package): homepage = "http://curl.haxx.se" url = "http://curl.haxx.se/download/curl-7.46.0.tar.bz2" + version('7.49.1', '6bb1f7af5b58b30e4e6414b8c1abccab') version('7.47.1', '9ea3123449439bbd960cd25cf98796fb') version('7.46.0', '9979f989a2a9930d10f1b3deeabc2148') version('7.45.0', '62c1a352b28558f25ba6209214beadc8') diff --git a/var/spack/repos/builtin/packages/dealii/package.py b/var/spack/repos/builtin/packages/dealii/package.py index 54b6426d36..068dbec10a 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([ @@ -246,7 +245,7 @@ class Dealii(Package): # change Linear Algebra to Trilinos # The below filter_file should be different for versions # before and after 8.4.0 - if spec.satisfies('@8.4.0:'): + if spec.satisfies('@8.4.0:') or spec.satisfies('@dev'): filter_file(r'(\/\/ #define FORCE_USE_OF_TRILINOS.*)', ('#define FORCE_USE_OF_TRILINOS'), 'step-40.cc') else: @@ -258,7 +257,7 @@ class Dealii(Package): # the rest of the tests on step 40 only works for # dealii version 8.4.0 and after - if spec.satisfies('@8.4.0:'): + if spec.satisfies('@8.4.0:') or spec.satisfies('@dev'): print('=====================================') print('=== Step-40 Trilinos SuperluDist ====') print('=====================================') @@ -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/eigen/package.py b/var/spack/repos/builtin/packages/eigen/package.py index e20fcffdd7..9ff4107619 100644 --- a/var/spack/repos/builtin/packages/eigen/package.py +++ b/var/spack/repos/builtin/packages/eigen/package.py @@ -28,7 +28,9 @@ from spack import * class Eigen(Package): """ - Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms + Eigen is a C++ template library for linear algebra + + Matrices, vectors, numerical solvers, and related algorithms """ homepage = 'http://eigen.tuxfamily.org/' @@ -42,16 +44,16 @@ class Eigen(Package): variant('scotch', default=True, description='Enables scotch backend') variant('fftw', default=True, description='Enables FFTW backend') variant('suitesparse', default=True, description='Enables SuiteSparse support') + variant('mpfr', default=True, description='Enables support for multi-precisions floating points via mpfr') # TODO : dependency on googlehash, superlu, adolc missing - depends_on('cmake') depends_on('metis@5:', when='+metis') depends_on('scotch', when='+scotch') depends_on('fftw', when='+fftw') depends_on('suite-sparse', when='+suitesparse') - depends_on('mpfr@2.3.0:') # Eigen 3.2.7 requires at least 2.3.0 - depends_on('gmp') + depends_on('mpfr@2.3.0:', when="+mpfr") + depends_on('gmp', when="+mpfr") def install(self, spec, prefix): diff --git a/var/spack/repos/builtin/packages/emacs/package.py b/var/spack/repos/builtin/packages/emacs/package.py index 4b05864a1e..a9ebd6d42f 100644 --- a/var/spack/repos/builtin/packages/emacs/package.py +++ b/var/spack/repos/builtin/packages/emacs/package.py @@ -23,23 +23,44 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## from spack import * +import llnl.util.tty as tty + class Emacs(Package): """The Emacs programmable text editor.""" + homepage = "https://www.gnu.org/software/emacs" url = "http://ftp.gnu.org/gnu/emacs/emacs-24.5.tar.gz" version('24.5', 'd74b597503a68105e61b5b9f6d065b44') + variant('X', default=True, description="Enable a X toolkit (GTK+)") + variant('gtkplus', default=False, description="Enable a GTK+ as X toolkit (this variant is ignored if ~X)") + depends_on('ncurses') - # Emacs also depends on: - # GTK or other widget library - # libtiff, png, etc. - # For now, we assume the system provides all that stuff. - # For Ubuntu 14.04 LTS: - # sudo apt-get install libgtk-3-dev libxpm-dev libtiff5-dev libjpeg8-dev libgif-dev libpng12-dev + depends_on('libtiff', when='+X') + depends_on('libpng', when='+X') + depends_on('libxpm', when='+X') + depends_on('giflib', when='+X') + depends_on('gtkplus', when='+X+gtkplus') def install(self, spec, prefix): - configure('--prefix=%s' % prefix) + args = [] + if '+X' in spec: + if '+gtkplus' in spec: + toolkit = 'gtk{0}'.format(spec['gtkplus'].version.up_to(1)) + else: + toolkit = 'no' + args = [ + '--with-x', + '--with-x-toolkit={0}'.format(toolkit) + ] + else: + args = ['--without-x'] + if '+gtkplus' in spec: + tty.warn('The variant +gtkplus is ignored if ~X is selected.') + + configure('--prefix={0}'.format(prefix), *args) + make() make("install") diff --git a/var/spack/repos/builtin/packages/fenics/package.py b/var/spack/repos/builtin/packages/fenics/package.py index 0845237656..465ab651be 100644 --- a/var/spack/repos/builtin/packages/fenics/package.py +++ b/var/spack/repos/builtin/packages/fenics/package.py @@ -57,6 +57,9 @@ class Fenics(Package): # variant('slepc4py', default=True, description='Uses SLEPc4py') # variant('pastix', default=True, description='Compile with Pastix') + patch('petsc-3.7.patch', when='^petsc@3.7:') + patch('petsc-version-detection.patch', when='@:1.6.1') + extends('python') depends_on('py-numpy') diff --git a/var/spack/repos/builtin/packages/fenics/petsc-3.7.patch b/var/spack/repos/builtin/packages/fenics/petsc-3.7.patch new file mode 100644 index 0000000000..c1ba5c4da6 --- /dev/null +++ b/var/spack/repos/builtin/packages/fenics/petsc-3.7.patch @@ -0,0 +1,394 @@ +diff -Naur dolfin-1.6.0/dolfin/common/SubSystemsManager.cpp dolfin-1.6.0.new/dolfin/common/SubSystemsManager.cpp +--- dolfin-1.6.0/dolfin/common/SubSystemsManager.cpp 2015-07-28 17:05:55.000000000 +0200 ++++ dolfin-1.6.0.new/dolfin/common/SubSystemsManager.cpp 2016-06-26 23:42:56.391929550 +0200 +@@ -179,7 +179,7 @@ + PetscInitialized(&is_initialized); + if (is_initialized) + { +- PetscOptionsInsert(&argc, &argv, PETSC_NULL); ++ PetscOptionsInsert(NULL, &argc, &argv, PETSC_NULL); + } + else + { +@@ -187,12 +187,12 @@ + PetscInitializeNoArguments(); + + // Set options to avoid common failures with some 3rd party solvers +- PetscOptionsSetValue("-mat_mumps_icntl_7", "0"); +- PetscOptionsSetValue("-mat_superlu_dist_colperm", "MMD_AT_PLUS_A"); ++ PetscOptionsSetValue(NULL, "-mat_mumps_icntl_7", "0"); ++ PetscOptionsSetValue(NULL, "-mat_superlu_dist_colperm", "MMD_AT_PLUS_A"); + + // Pass command line arguments to PETSc (will overwrite any + // default above) +- PetscOptionsInsert(&argc, &argv, PETSC_NULL); ++ PetscOptionsInsert(NULL, &argc, &argv, PETSC_NULL); + } + + // Set PETSc +diff -Naur dolfin-1.6.0/dolfin/la/PETScKrylovSolver.cpp dolfin-1.6.0.new/dolfin/la/PETScKrylovSolver.cpp +--- dolfin-1.6.0/dolfin/la/PETScKrylovSolver.cpp 2015-07-28 17:05:55.000000000 +0200 ++++ dolfin-1.6.0.new/dolfin/la/PETScKrylovSolver.cpp 2016-06-26 23:33:02.418351380 +0200 +@@ -564,6 +564,11 @@ + return solve(x, b); + } + //----------------------------------------------------------------------------- ++PetscErrorCode PETScKrylovSolver::ksp_monitor_norm(KSP ksp, PetscInt n, PetscReal rnorm, void *vf) ++{ ++ KSPMonitorTrueResidualNorm(ksp, n, rnorm, static_cast<PetscViewerAndFormat *>(vf)); ++} ++//----------------------------------------------------------------------------- + void PETScKrylovSolver::set_petsc_ksp_options() + { + PetscErrorCode ierr; +@@ -585,7 +590,8 @@ + const bool monitor_convergence = parameters["monitor_convergence"]; + if (monitor_convergence) + { +- ierr = KSPMonitorSet(_ksp, KSPMonitorTrueResidualNorm, 0, 0); ++ PetscViewerAndFormatCreate(PETSC_VIEWER_STDOUT_WORLD, PETSC_VIEWER_DEFAULT, &_vf); ++ ierr = KSPMonitorSet(_ksp, ksp_monitor_norm, _vf, 0); + if (ierr != 0) petsc_error(ierr, __FILE__, "KSPMonitorSet"); + } + +diff -Naur dolfin-1.6.0/dolfin/la/PETScKrylovSolver.h dolfin-1.6.0.new/dolfin/la/PETScKrylovSolver.h +--- dolfin-1.6.0/dolfin/la/PETScKrylovSolver.h 2015-07-28 17:05:55.000000000 +0200 ++++ dolfin-1.6.0.new/dolfin/la/PETScKrylovSolver.h 2016-06-26 23:19:40.767042975 +0200 +@@ -179,6 +179,12 @@ + // PETSc solver pointer + KSP _ksp; + ++ // viewer for monitoring ++ PetscViewerAndFormat* _vf; ++ ++ // monitoring function ++ static PetscErrorCode ksp_monitor_norm(KSP ksp, PetscInt n, PetscReal rnorm, void *ctx); ++ + // DOLFIN-defined PETScUserPreconditioner + PETScUserPreconditioner* pc_dolfin; + +diff -Naur dolfin-1.6.0/dolfin/la/PETScLUSolver.cpp dolfin-1.6.0.new/dolfin/la/PETScLUSolver.cpp +--- dolfin-1.6.0/dolfin/la/PETScLUSolver.cpp 2015-07-28 17:05:55.000000000 +0200 ++++ dolfin-1.6.0.new/dolfin/la/PETScLUSolver.cpp 2016-06-26 23:13:36.903732301 +0200 +@@ -246,14 +246,14 @@ + if (parameters["num_threads"].is_set()) + { + // Use number of threads specified for LU solver +- ierr = PetscOptionsSetValue("-mat_pastix_threadnbr", ++ ierr = PetscOptionsSetValue(NULL, "-mat_pastix_threadnbr", + parameters["num_threads"].value_str().c_str()); + if (ierr != 0) petsc_error(ierr, __FILE__, "PetscOptionsSetValue"); + } + else + { + // Use global number of threads +- ierr = PetscOptionsSetValue("-mat_pastix_threadnbr", ++ ierr = PetscOptionsSetValue(NULL, "-mat_pastix_threadnbr", + dolfin::parameters["num_threads"].value_str().c_str()); + if (ierr != 0) petsc_error(ierr, __FILE__, "PetscOptionsSetValue"); + } +diff -Naur dolfin-1.6.0/dolfin/la/PETScOptions.cpp dolfin-1.6.0.new/dolfin/la/PETScOptions.cpp +--- dolfin-1.6.0/dolfin/la/PETScOptions.cpp 2015-07-28 17:05:55.000000000 +0200 ++++ dolfin-1.6.0.new/dolfin/la/PETScOptions.cpp 2016-06-26 23:37:58.613121118 +0200 +@@ -54,7 +54,7 @@ + { + SubSystemsManager::init_petsc(); + PetscErrorCode ierr; +- ierr = PetscOptionsClearValue(option.c_str()); ++ ierr = PetscOptionsClearValue(NULL, option.c_str()); + if (ierr != 0) + { + dolfin_error("PETScOptions.cpp", +diff -Naur dolfin-1.6.0/dolfin/la/PETScOptions.h dolfin-1.6.0.new/dolfin/la/PETScOptions.h +--- dolfin-1.6.0/dolfin/la/PETScOptions.h 2015-07-28 17:05:55.000000000 +0200 ++++ dolfin-1.6.0.new/dolfin/la/PETScOptions.h 2016-06-26 23:37:54.352023709 +0200 +@@ -65,7 +65,7 @@ + + PetscErrorCode ierr; + std::string _option = "-" + option; +- ierr = PetscOptionsSetValue(_option.c_str(), ++ ierr = PetscOptionsSetValue(NULL, _option.c_str(), + boost::lexical_cast<std::string>(value).c_str()); + if (ierr != 0) + { +diff -Naur dolfin-1.6.0/dolfin/la/SLEPcEigenSolver.cpp dolfin-1.6.0.new/dolfin/la/SLEPcEigenSolver.cpp +--- dolfin-1.6.0/dolfin/la/SLEPcEigenSolver.cpp 2015-07-28 17:05:55.000000000 +0200 ++++ dolfin-1.6.0.new/dolfin/la/SLEPcEigenSolver.cpp 2016-06-26 23:35:25.930631132 +0200 +@@ -99,6 +99,19 @@ + solve(_matA->size(0)); + } + //----------------------------------------------------------------------------- ++PetscErrorCode SLEPcEigenSolver::eps_monitor(EPS eps, PetscInt its, PetscInt nconv, PetscScalar* eigr, ++ PetscScalar* eigi, PetscReal* errest, ++ PetscInt nest, void *vf) ++{ ++ EPSMonitorAll(eps, its, nconv, eigr, eigi, errest, nest, ++ static_cast<PetscViewerAndFormat *>(vf)); ++} ++//----------------------------------------------------------------------------- ++PetscErrorCode SLEPcEigenSolver::ksp_monitor(KSP ksp, PetscInt n, PetscReal rnorm, void *vf) ++{ ++ KSPMonitorDefault(ksp, n, rnorm, static_cast<PetscViewerAndFormat *>(vf)); ++} ++//----------------------------------------------------------------------------- + void SLEPcEigenSolver::solve(std::size_t n) + { + dolfin_assert(_matA); +@@ -139,10 +152,11 @@ + { + KSP ksp; + ST st; +- EPSMonitorSet(_eps, EPSMonitorAll, NULL, NULL); ++ PetscViewerAndFormatCreate(PETSC_VIEWER_STDOUT_WORLD, PETSC_VIEWER_DEFAULT, &_vf); ++ EPSMonitorSet(_eps, eps_monitor, _vf, NULL); + EPSGetST(_eps, &st); + STGetKSP(st, &ksp); +- KSPMonitorSet(ksp, KSPMonitorDefault, NULL, NULL); ++ KSPMonitorSet(ksp, ksp_monitor, _vf, NULL); + EPSView(_eps, PETSC_VIEWER_STDOUT_SELF); + } + +diff -Naur dolfin-1.6.0/dolfin/la/SLEPcEigenSolver.h dolfin-1.6.0.new/dolfin/la/SLEPcEigenSolver.h +--- dolfin-1.6.0/dolfin/la/SLEPcEigenSolver.h 2015-07-28 17:05:55.000000000 +0200 ++++ dolfin-1.6.0.new/dolfin/la/SLEPcEigenSolver.h 2016-06-26 23:36:08.784610612 +0200 +@@ -231,6 +231,11 @@ + // SLEPc solver pointer + EPS _eps; + ++ PetscViewerAndFormat* _vf; ++ static PetscErrorCode eps_monitor(EPS eps, int its, int nconv, PetscScalar *eigr, ++ PetscScalar *eigi, PetscReal* errest, ++ int nest, void *mctx); ++ static PetscErrorCode ksp_monitor(KSP ksp, PetscInt n, PetscReal rnorm, void *vf); + }; + + } +diff -Naur dolfin-1.6.0/dolfin/nls/PETScSNESSolver.cpp dolfin-1.6.0.new/dolfin/nls/PETScSNESSolver.cpp +--- dolfin-1.6.0/dolfin/nls/PETScSNESSolver.cpp 2015-07-28 17:05:55.000000000 +0200 ++++ dolfin-1.6.0.new/dolfin/nls/PETScSNESSolver.cpp 2016-06-26 23:19:40.166029256 +0200 +@@ -195,6 +195,15 @@ + return this->solve(nonlinear_problem, x); + } + //----------------------------------------------------------------------------- ++PetscErrorCode ++PETScSNESSolver::snes_monitor(SNES snes, PetscInt its, ++ PetscReal fgnorm, void *vf) ++{ ++ PetscViewerAndFormat * _vf = static_cast<PetscViewerAndFormat *>(vf); ++ SNESMonitorDefault(snes, its, fgnorm, _vf); ++ return(0); ++} ++//----------------------------------------------------------------------------- + void + PETScSNESSolver::init(NonlinearProblem& nonlinear_problem, + GenericVector& x) +@@ -237,9 +246,11 @@ + } + + // Set some options from the parameters +- if (report) +- SNESMonitorSet(_snes, SNESMonitorDefault, PETSC_NULL, PETSC_NULL); +- ++ if (report) { ++ PetscViewerAndFormatCreate(PETSC_VIEWER_STDOUT_WORLD, PETSC_VIEWER_DEFAULT, &_snes_ctx.vf); ++ SNESMonitorSet(_snes, PETScSNESSolver::snes_monitor, _snes_ctx.vf, PETSC_NULL); ++ } ++ + // Set the bounds, if any + set_bounds(x); + +@@ -293,8 +304,8 @@ + SNESGetLineSearch(_snes, &linesearch); + #endif + +- if (report) +- SNESLineSearchSetMonitor(linesearch, PETSC_TRUE); ++ // if (report) ++ // SNESLineSearchSetMonitor(linesearch, PETSC_TRUE); + const std::string line_search_type = std::string(parameters["line_search"]); + SNESLineSearchSetType(linesearch, line_search_type.c_str()); + +@@ -466,6 +477,24 @@ + } + #endif + //----------------------------------------------------------------------------- ++PetscErrorCode ++PETScSNESSolver::ksp_monitor(KSP ksp, PetscInt n, ++ PetscReal rnorm, void *vf) ++{ ++ PetscViewerAndFormat * _vf = static_cast<PetscViewerAndFormat *>(vf); ++ KSPMonitorDefault(ksp, n, rnorm, _vf); ++ return(0); ++} ++//----------------------------------------------------------------------------- ++PetscErrorCode ++PETScSNESSolver::ksp_monitor_norm(KSP ksp, PetscInt n, ++ PetscReal rnorm, void *vf) ++{ ++ PetscViewerAndFormat * _vf = static_cast<PetscViewerAndFormat *>(vf); ++ KSPMonitorTrueResidualNorm(ksp, n, rnorm, _vf); ++ return(0); ++} ++//----------------------------------------------------------------------------- + void PETScSNESSolver::set_linear_solver_parameters() + { + KSP ksp; +@@ -482,7 +511,7 @@ + PetscObjectGetComm((PetscObject)_snes, &comm); + + if (parameters["report"]) +- KSPMonitorSet(ksp, KSPMonitorDefault, PETSC_NULL, PETSC_NULL); ++ KSPMonitorSet(ksp, PETScSNESSolver::ksp_monitor, _snes_ctx.vf, PETSC_NULL); + + const std::string linear_solver = parameters["linear_solver"]; + const std::string preconditioner = parameters["preconditioner"]; +@@ -518,7 +547,7 @@ + KSPSetInitialGuessNonzero(ksp, PETSC_FALSE); + + if (krylov_parameters["monitor_convergence"]) +- KSPMonitorSet(ksp, KSPMonitorTrueResidualNorm, 0, 0); ++ KSPMonitorSet(ksp, PETScSNESSolver::ksp_monitor_norm, _snes_ctx.vf, 0); + + // Set tolerances + const int max_iters = krylov_parameters["maximum_iterations"]; +diff -Naur dolfin-1.6.0/dolfin/nls/PETScSNESSolver.h dolfin-1.6.0.new/dolfin/nls/PETScSNESSolver.h +--- dolfin-1.6.0/dolfin/nls/PETScSNESSolver.h 2015-07-28 17:05:55.000000000 +0200 ++++ dolfin-1.6.0.new/dolfin/nls/PETScSNESSolver.h 2016-06-26 22:31:21.554129282 +0200 +@@ -24,6 +24,7 @@ + + #include <map> + #include <petscsnes.h> ++#include <petscviewer.h> + #include <memory> + #include <dolfin/nls/NewtonSolver.h> + #include <dolfin/parameter/Parameters.h> +@@ -124,8 +125,15 @@ + Vec f_tmp; + const PETScVector* xl; + const PETScVector* xu; ++ PetscViewerAndFormat* vf; + }; + ++ ++ // monitoring functions ++ static PetscErrorCode snes_monitor(SNES snes, PetscInt its, PetscReal fgnorm, void* ctx); ++ static PetscErrorCode ksp_monitor(KSP ksp, PetscInt n, PetscReal rnorm, void *ctx); ++ static PetscErrorCode ksp_monitor_norm(KSP ksp, PetscInt n, PetscReal rnorm, void *ctx); ++ + // PETSc solver pointer + SNES _snes; + +diff -Naur dolfin-1.6.0/dolfin/nls/PETScTAOSolver.cpp dolfin-1.6.0.new/dolfin/nls/PETScTAOSolver.cpp +--- dolfin-1.6.0/dolfin/nls/PETScTAOSolver.cpp 2015-07-28 17:05:55.000000000 +0200 ++++ dolfin-1.6.0.new/dolfin/nls/PETScTAOSolver.cpp 2016-06-27 19:14:47.367885081 +0200 +@@ -186,6 +186,15 @@ + init(optimisation_problem, x.down_cast<PETScVector>(), lb, ub); + } + //----------------------------------------------------------------------------- ++PetscErrorCode ++PETScTAOSolver::ksp_monitor_norm(KSP ksp, PetscInt n, ++ PetscReal rnorm, void * vf) ++{ ++ PetscViewerAndFormat * _vf = static_cast<PetscViewerAndFormat *>(vf); ++ KSPMonitorTrueResidualNorm(ksp, n, rnorm, _vf); ++ return(0); ++} ++//----------------------------------------------------------------------------- + void PETScTAOSolver::init(OptimisationProblem& optimisation_problem, + PETScVector& x, + const PETScVector& lb, +@@ -365,9 +374,7 @@ + set_tao(parameters["method"]); + + // Set tolerances +- TaoSetTolerances(_tao, parameters["function_absolute_tol"], +- parameters["function_relative_tol"], +- parameters["gradient_absolute_tol"], ++ TaoSetTolerances(_tao, parameters["gradient_absolute_tol"], + parameters["gradient_relative_tol"], + parameters["gradient_t_tol"]); + +@@ -490,8 +497,10 @@ + KSPSetInitialGuessNonzero(ksp, PETSC_FALSE); + + // KSP monitor +- if (krylov_parameters["monitor_convergence"]) +- KSPMonitorSet(ksp, KSPMonitorTrueResidualNorm, 0, 0); ++ if (krylov_parameters["monitor_convergence"]) { ++ PetscViewerAndFormatCreate(PETSC_VIEWER_STDOUT_WORLD, PETSC_VIEWER_DEFAULT, &vf); ++ KSPMonitorSet(ksp, ksp_monitor_norm, vf, 0); ++ } + + // Get integer tolerances (to take care of casting to PetscInt) + const int max_iter = krylov_parameters["maximum_iterations"]; +diff -Naur dolfin-1.6.0/dolfin/nls/PETScTAOSolver.h dolfin-1.6.0.new/dolfin/nls/PETScTAOSolver.h +--- dolfin-1.6.0/dolfin/nls/PETScTAOSolver.h 2015-07-28 17:05:55.000000000 +0200 ++++ dolfin-1.6.0.new/dolfin/nls/PETScTAOSolver.h 2016-06-27 19:08:00.634361160 +0200 +@@ -146,6 +146,10 @@ + // TAO pointer + Tao _tao; + ++ // monitoring functions ++ PetscViewerAndFormat* vf; ++ static PetscErrorCode ksp_monitor_norm(KSP ksp, PetscInt n, PetscReal rnorm, void *ctx); ++ + // Update parameters when tao/ksp/pc_types are explictly given + void update_parameters(const std::string tao_type, + const std::string ksp_type, +diff -Naur dolfin-1.6.0/dolfin/nls/TAOLinearBoundSolver.cpp dolfin-1.6.0.new/dolfin/nls/TAOLinearBoundSolver.cpp +--- dolfin-1.6.0/dolfin/nls/TAOLinearBoundSolver.cpp 2015-07-28 17:05:55.000000000 +0200 ++++ dolfin-1.6.0.new/dolfin/nls/TAOLinearBoundSolver.cpp 2016-06-27 19:17:10.390216576 +0200 +@@ -313,9 +313,7 @@ + dolfin_assert(_tao); + + // Set tolerances +- TaoSetTolerances(_tao, parameters["function_absolute_tol"], +- parameters["function_relative_tol"], +- parameters["gradient_absolute_tol"], ++ TaoSetTolerances(_tao, parameters["gradient_absolute_tol"], + parameters["gradient_relative_tol"], + parameters["gradient_t_tol"]); + +@@ -340,6 +338,15 @@ + set_solver(method); + } + //----------------------------------------------------------------------------- ++PetscErrorCode ++TAOLinearBoundSolver::ksp_monitor_norm(KSP ksp, PetscInt n, ++ PetscReal rnorm, void * vf) ++{ ++ PetscViewerAndFormat * _vf = static_cast<PetscViewerAndFormat *>(vf); ++ KSPMonitorTrueResidualNorm(ksp, n, rnorm, _vf); ++ return(0); ++} ++//----------------------------------------------------------------------------- + void TAOLinearBoundSolver::set_ksp_options() + { + dolfin_assert(_tao); +@@ -360,8 +367,10 @@ + else + KSPSetInitialGuessNonzero(ksp, PETSC_FALSE); + +- if (krylov_parameters["monitor_convergence"]) +- KSPMonitorSet(ksp, KSPMonitorTrueResidualNorm, 0, 0); ++ if (krylov_parameters["monitor_convergence"]) { ++ PetscViewerAndFormatCreate(PETSC_VIEWER_STDOUT_WORLD, PETSC_VIEWER_DEFAULT, &vf); ++ KSPMonitorSet(ksp, ksp_monitor_norm, vf, 0); ++ } + + // Set tolerances + const int max_ksp_it = krylov_parameters["maximum_iterations"]; +diff -Naur dolfin-1.6.0/dolfin/nls/TAOLinearBoundSolver.h dolfin-1.6.0.new/dolfin/nls/TAOLinearBoundSolver.h +--- dolfin-1.6.0/dolfin/nls/TAOLinearBoundSolver.h 2015-07-28 17:05:55.000000000 +0200 ++++ dolfin-1.6.0.new/dolfin/nls/TAOLinearBoundSolver.h 2016-06-27 19:08:09.157561005 +0200 +@@ -174,6 +174,10 @@ + // Tao solver pointer + Tao _tao; + ++ // monitoring functions ++ PetscViewerAndFormat* vf; ++ static PetscErrorCode ksp_monitor_norm(KSP ksp, PetscInt n, PetscReal rnorm, void *ctx); ++ + // Petsc preconditioner + std::shared_ptr<PETScPreconditioner> preconditioner; + diff --git a/var/spack/repos/builtin/packages/fenics/petsc-version-detection.patch b/var/spack/repos/builtin/packages/fenics/petsc-version-detection.patch new file mode 100644 index 0000000000..1429cd7bc6 --- /dev/null +++ b/var/spack/repos/builtin/packages/fenics/petsc-version-detection.patch @@ -0,0 +1,39 @@ +--- dolfin-1.6.0.orig/cmake/modules/FindPETSc.cmake 2015-07-28 17:05:55.000000000 +0200 ++++ dolfin-1.6.0/cmake/modules/FindPETSc.cmake 2016-06-27 17:16:02.484402705 +0200 +@@ -207,13 +207,7 @@ + + endif() + +-# Build PETSc test program +-if (DOLFIN_SKIP_BUILD_TESTS) +- set(PETSC_TEST_RUNS TRUE) +- set(PETSC_VERSION "UNKNOWN") +- set(PETSC_VERSION_OK TRUE) +-elseif (FOUND_PETSC_CONF) +- ++if (FOUND_PETSC_CONF) + # Set flags for building test program + set(CMAKE_REQUIRED_INCLUDES ${PETSC_INCLUDE_DIRS}) + set(CMAKE_REQUIRED_LIBRARIES ${PETSC_LIBRARIES}) +@@ -271,7 +265,10 @@ + set(PETSC_VERSION_OK TRUE) + endif() + mark_as_advanced(PETSC_VERSION_OK) ++endif() + ++ # Build PETSc test program ++if (NOT DOLFIN_SKIP_BUILD_TESTS AND FOUND_PETSC_CONF) + # Run PETSc test program + set(PETSC_TEST_LIB_CPP + "${CMAKE_CURRENT_BINARY_DIR}/CMakeFiles/petsc_test_lib.cpp") +@@ -359,7 +356,9 @@ + else() + message(STATUS "PETSc configured without Cusp support") + endif() +- ++else() ++ set(PETSC_TEST_RUNS TRUE) ++ + endif() + + # Check sizeof(PetscInt) diff --git a/var/spack/repos/builtin/packages/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/foam-extend/package.py b/var/spack/repos/builtin/packages/foam-extend/package.py new file mode 100644 index 0000000000..4479fc9bee --- /dev/null +++ b/var/spack/repos/builtin/packages/foam-extend/package.py @@ -0,0 +1,235 @@ +from spack import * +from spack.environment import * + +import multiprocessing +import os + + +class FoamExtend(Package): + """The foam-extend project is a fork of the OpenFOAM open source library + for Computational Fluid Dynamics (CFD).""" + + homepage = "http://www.extend-project.de/" + + version('3.2', git='http://git.code.sf.net/p/foam-extend/foam-extend-3.2') + version('3.1', git='http://git.code.sf.net/p/foam-extend/foam-extend-3.1') + version('3.0', git='http://git.code.sf.net/p/foam-extend/foam-extend-3.0') + + variant('paraview', default=False, description='Enable ParaFOAM') + variant('scotch', default=True, description='Activate Scotch as a possible decomposition library') + variant('ptscotch', default=True, description='Activate PT-Scotch as a possible decomposition library') + variant('metis', default=True, description='Activate Metis as a possible decomposition library') + variant('parmetis', default=True, description='Activate Parmetis as a possible decomposition library') + variant('parmgridgen', default=True, description='Activate Parmgridgen support') + variant('source', default=True, description='Installs also the source folder') + + supported_compilers = {'clang': 'Clang', 'gcc': 'Gcc', 'intel': 'Icc'} + + depends_on('mpi') + depends_on('python') + depends_on('flex@:2.5.99') + depends_on('zlib') + + depends_on('scotch ~ metis', when='~ptscotch+scotch') + depends_on('scotch ~ metis + mpi', when='+ptscotch') + depends_on('metis@5:', when='+metis') + depends_on('parmetis', when='+parmetis') + depends_on('parmgridgen', when='+parmgridgen') + + depends_on('paraview', when='+paraview') + + def set_arch(self): + (sysname, nodename, release, version, machine) = os.uname() + + if self.compiler.name not in self.supported_compilers: + raise RuntimeError('{0} is not a supported compiler \ + to compile OpenFOAM'.format(self.compiler.name)) + + foam_compiler = self.supported_compilers[self.compiler.name] + if sysname == 'Linux': + arch = 'linux' + if foam_compiler == 'Clang': + raise RuntimeError('OS, compiler combination not\ + supported ({0} {1})'.format(sysname, foam_compiler)) + elif sysname == 'Darwin': + if machine == 'x86_64': + arch = 'darwinIntel' + if foam_compiler == 'Icc': + raise RuntimeError('OS, compiler combination not\ + supported ({0} {1})'.format(sysname, foam_compiler)) + else: + raise RuntimeError('{0} {1} is not a \ + supported architecture'.format(sysname, machine)) + + return (arch, foam_compiler) + + def get_openfoam_environment(self): + return EnvironmentModifications.from_sourcing_files( + join_path(self.stage.source_path, + 'etc/bashrc')) + + def patch(self): + # change names to match the package and not the one patch in + # the Third-Party of foam-extend + if '+parmgridgen' in self.spec: + filter_file(r'-lMGridGen', + r'-lmgrid', + 'src/dbns/Make/options') + + filter_file( + r'-lMGridGen', + r'-lmgrid', + 'src/fvAgglomerationMethods/MGridGenGamgAgglomeration/Make/options') # NOQA: ignore=501 + + # Get the wmake arch and compiler + (arch, foam_compiler) = self.set_arch() + + prefs_dict = { + 'compilerInstall': 'System', + 'WM_COMPILER': foam_compiler, + 'WM_ARCH_OPTION': '64', + 'WM_PRECISION_OPTION': 'DP', + 'WM_COMPILE_OPTION': 'SPACKOpt', + 'WM_MPLIB': 'SPACK', + + 'CMAKE_DIR': self.spec['cmake'].prefix, + 'CMAKE_BIN_DIR': self.spec['cmake'].prefix.bin, + 'PYTHON_DIR': self.spec['python'].prefix, + 'PYTHON_BIN_DIR': self.spec['python'].prefix.bin, + + 'FLEX_SYSTEM': 1, + 'FLEX_DIR': self.spec['flex'].prefix, + + 'BISON_SYSTEM': 1, + 'BISON_DIR': self.spec['flex'].prefix, + + 'ZLIB_SYSTEM': 1, + 'ZLIB_DIR': self.spec['zlib'].prefix, + } + + if '+scotch' in self.spec or '+ptscotch' in self.spec: + prefs_dict['SCOTCH_SYSTEM'] = 1 + prefs_dict['SCOTCH_DIR'] = self.spec['scotch'].prefix + prefs_dict['SCOTCH_BIN_DIR'] = self.spec['scotch'].prefix.bin + prefs_dict['SCOTCH_LIB_DIR'] = self.spec['scotch'].prefix.lib + prefs_dict['SCOTCH_INCLUDE_DIR'] = \ + self.spec['scotch'].prefix.include + + if '+metis' in self.spec: + prefs_dict['METIS_SYSTEM'] = 1 + prefs_dict['METIS_DIR'] = self.spec['metis'].prefix + prefs_dict['METIS_BIN_DIR'] = self.spec['metis'].prefix.bin + prefs_dict['METIS_LIB_DIR'] = self.spec['metis'].prefix.lib + prefs_dict['METIS_INCLUDE_DIR'] = self.spec['metis'].prefix.include + + if '+parmetis' in self.spec: + prefs_dict['PARMETIS_SYSTEM'] = 1 + prefs_dict['PARMETIS_DIR'] = self.spec['parmetis'].prefix + prefs_dict['PARMETIS_BIN_DIR'] = self.spec['parmetis'].prefix.bin + prefs_dict['PARMETIS_LIB_DIR'] = self.spec['parmetis'].prefix.lib + prefs_dict['PARMETIS_INCLUDE_DIR'] = \ + self.spec['parmetis'].prefix.include + + if '+parmgridgen' in self.spec: + prefs_dict['PARMGRIDGEN_SYSTEM'] = 1 + prefs_dict['PARMGRIDGEN_DIR'] = self.spec['parmgridgen'].prefix + prefs_dict['PARMGRIDGEN_BIN_DIR'] = \ + self.spec['parmgridgen'].prefix.bin + prefs_dict['PARMGRIDGEN_LIB_DIR'] = \ + self.spec['parmgridgen'].prefix.lib + prefs_dict['PARMGRIDGEN_INCLUDE_DIR'] = \ + self.spec['parmgridgen'].prefix.include + + if '+paraview' in self.spec: + prefs_dict['PARAVIEW_SYSTEM'] = 1 + prefs_dict['PARAVIEW_DIR'] = self.spec['paraview'].prefix, + prefs_dict['PARAVIEW_BIN_DIR'] = self.spec['paraview'].prefix.bin, + prefs_dict['QT_SYSTEM'] = 1 + prefs_dict['QT_DIR'] = self.spec['qt'].prefix, + prefs_dict['QT_BIN_DIR'] = self.spec['qt'].prefix.bin, + + # write the prefs files to define the configuration needed, + # only the prefs.sh is used by this script but both are + # installed for end users + with working_dir('.'): + with open("etc/prefs.sh", "w") as fh: + for key in sorted(prefs_dict): + fh.write('export {0}={1}\n'.format(key, prefs_dict[key])) + + with open("etc/prefs.csh", "w") as fh: + for key in sorted(prefs_dict): + fh.write('setenv {0}={1}\n'.format(key, prefs_dict[key])) + + # Defining a different mpi and optimisation file to be able to + # make wmake get spack info with minimum modifications on + # configurations scripts + mpi_info = [ + 'PFLAGS = -DOMPI_SKIP_MPICXX -DMPICH_IGNORE_CXX_SEEK', + 'PINC = -I{0}'.format(self.spec['mpi'].prefix.include), + 'PLIBS = -L{0} -lmpi'.format(self.spec['mpi'].prefix.lib) + ] + + arch_path = ''.join([arch, prefs_dict['WM_ARCH_OPTION'], + foam_compiler]) + option_path = ''.join([arch_path, + prefs_dict['WM_PRECISION_OPTION'], + prefs_dict['WM_COMPILE_OPTION']]) + rule_path = join_path("wmake", "rules", arch_path) + build_path = join_path(self.stage.source_path, 'lib', option_path) + install_path = \ + join_path(self.prefix, + 'foam-extend-{0}'.format(self.version.up_to(2)), + option_path) + + rpaths_foam = ' '.join([ + '{0}{1}'.format(self.compiler.cxx_rpath_arg, + install_path), + '{0}{1}'.format(self.compiler.cxx_rpath_arg, + build_path) + ]) + + compiler_flags = { + 'DBUG': rpaths_foam, + 'OPT': '-O3', + } + + with working_dir(rule_path): + with open('mplibSPACK', "w") as fh: + fh.write('\n'.join(mpi_info)) + + for comp in ['c', 'c++']: + with open('{0}SPACKOpt'.format(comp), "w") as fh: + for key, val in compiler_flags.iteritems(): + fh.write('{0}{1} = {2}\n'.format(comp, key, val)) + + def setup_environment(self, spack_env, run_env): + with working_dir(self.stage.path): + spack_env.set('FOAM_INST_DIR', os.path.abspath('.')) + + (arch, foam_compiler) = self.set_arch() + + run_env.set('FOAM_INST_DIR', self.prefix) + + def install(self, spec, prefix): + env_openfoam = self.get_openfoam_environment() + env_openfoam.apply_modifications() + + if self.parallel: + os.environ['WM_NCOMPPROCS'] = str(self.make_jobs) \ + if self.make_jobs else str(multiprocessing.cpu_count()) + + allwmake = Executable('./Allwmake') + allwmake() + + install_path = \ + join_path(self.prefix, + 'foam-extend-{0}'.format(self.version.up_to(2))) + + if '+source' in spec: + install_tree('src', join_path(install_path, 'src')) + + install_tree('lib', join_path(install_path, 'lib')) + install_tree('bin', join_path(install_path, 'bin')) + install_tree('applications', join_path(install_path, 'applications')) + install_tree('etc', join_path(install_path, 'etc')) + install_tree('wmake', join_path(install_path, 'wmake')) diff --git a/var/spack/repos/builtin/packages/freetype/package.py b/var/spack/repos/builtin/packages/freetype/package.py index 897c011396..dd181623d0 100644 --- a/var/spack/repos/builtin/packages/freetype/package.py +++ b/var/spack/repos/builtin/packages/freetype/package.py @@ -24,17 +24,18 @@ ############################################################################## from spack import * + class Freetype(Package): """Font package""" homepage = "http://http://www.freetype.org" url = "http://download.savannah.gnu.org/releases/freetype/freetype-2.5.3.tar.gz" - version('2.5.3' , 'cafe9f210e45360279c730d27bf071e9') + version('2.5.3', 'cafe9f210e45360279c730d27bf071e9') depends_on('libpng') def install(self, spec, prefix): - configure("--prefix=%s" % prefix) + configure("--prefix=%s" % prefix, "--with-harfbuzz=no") make() make("install") diff --git a/var/spack/repos/builtin/packages/giflib/package.py b/var/spack/repos/builtin/packages/giflib/package.py new file mode 100644 index 0000000000..7082384b9b --- /dev/null +++ b/var/spack/repos/builtin/packages/giflib/package.py @@ -0,0 +1,41 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class Giflib(Package): + """The GIFLIB project maintains the giflib service library, which has + been pulling images out of GIFs since 1989.""" + + homepage = "http://giflib.sourceforge.net/" + url = "https://downloads.sourceforge.net/project/giflib/giflib-5.1.4.tar.bz2" + + version('5.1.4', '2c171ced93c0e83bb09e6ccad8e3ba2b') + + def install(self, spec, prefix): + configure('--prefix=%s' % prefix) + + make() + make("install") diff --git a/var/spack/repos/builtin/packages/glib/g_date_strftime.patch b/var/spack/repos/builtin/packages/glib/g_date_strftime.patch new file mode 100644 index 0000000000..532c743277 --- /dev/null +++ b/var/spack/repos/builtin/packages/glib/g_date_strftime.patch @@ -0,0 +1,34 @@ +From 00148329967adb196138372771052a3f606a6ea3 Mon Sep 17 00:00:00 2001 +From: coypu <coypu@sdf.org> +Date: Wed, 2 Mar 2016 19:43:10 +0200 +Subject: [PATCH 2/2] gdate: Suppress string format literal warning + +Newer versions of GCC emit an error here, but we know it's safe. +https://bugzilla.gnome.org/761550 +--- + glib/gdate.c | 5 +++++ + 1 file changed, 5 insertions(+) + +diff --git a/glib/gdate.c b/glib/gdate.c +index 4aece02..92c34d2 100644 +--- a/glib/gdate.c ++++ b/glib/gdate.c +@@ -2439,6 +2439,9 @@ win32_strftime_helper (const GDate *d, + * + * Returns: number of characters written to the buffer, or 0 the buffer was too small + */ ++#pragma GCC diagnostic push ++#pragma GCC diagnostic ignored "-Wformat-nonliteral" ++ + gsize + g_date_strftime (gchar *s, + gsize slen, +@@ -2549,3 +2552,5 @@ g_date_strftime (gchar *s, + return retval; + #endif + } ++ ++#pragma GCC diagnostic pop +-- +2.7.1 + diff --git a/var/spack/repos/builtin/packages/glib/package.py b/var/spack/repos/builtin/packages/glib/package.py index b146ea63d8..342a61a6a1 100644 --- a/var/spack/repos/builtin/packages/glib/package.py +++ b/var/spack/repos/builtin/packages/glib/package.py @@ -25,20 +25,24 @@ from spack import * import sys + class Glib(Package): """The GLib package contains a low-level libraries useful for providing data structure handling for C, portability wrappers and interfaces for such runtime functionality as an event loop, threads, dynamic loading and an object system.""" homepage = "https://developer.gnome.org/glib/" - url = "http://ftp.gnome.org/pub/gnome/sources/glib/2.42/glib-2.42.1.tar.xz" + url = "http://ftp.gnome.org/pub/gnome/sources/glib/2.42/glib-2.42.1.tar.xz" version('2.42.1', '89c4119e50e767d3532158605ee9121a') depends_on("libffi") depends_on("zlib") depends_on("pkg-config") - depends_on('gettext', sys.platform=='darwin') + depends_on('gettext', sys.platform == 'darwin') + + # The following patch is needed for gcc-6.1 + patch('g_date_strftime.patch') def install(self, spec, prefix): configure("--prefix=%s" % prefix) diff --git a/var/spack/repos/builtin/packages/gmsh/package.py b/var/spack/repos/builtin/packages/gmsh/package.py index e425d460c2..0951b86d57 100644 --- a/var/spack/repos/builtin/packages/gmsh/package.py +++ b/var/spack/repos/builtin/packages/gmsh/package.py @@ -27,39 +27,51 @@ from spack import * class Gmsh(Package): """ - Gmsh is a free 3D finite element grid generator with a built-in CAD engine and post-processor. Its design goal is - to provide a fast, light and user-friendly meshing tool with parametric input and advanced visualization - capabilities. Gmsh is built around four modules: geometry, mesh, solver and post-processing. The specification of - any input to these modules is done either interactively using the graphical user interface or in ASCII text files - using Gmsh's own scripting language. + Gmsh is a free 3D finite element grid generator with a built-in CAD engine + and post-processor. Its design goal is to provide a fast, light and + user-friendly meshing tool with parametric input and advanced visualization + capabilities. Gmsh is built around four modules: geometry, mesh, solver and + post-processing. The specification of any input to these modules is done + either interactively using the graphical user interface or in ASCII text + files using Gmsh's own scripting language. """ homepage = 'http://gmsh.info' url = 'http://gmsh.info/src/gmsh-2.11.0-source.tgz' + version('2.12.0', '7fbd2ec8071e79725266e72744d21e902d4fe6fa9e7c52340ad5f4be5c159d09') version('2.11.0', 'f15b6e7ac9ca649c9a74440e1259d0db') - # FIXME : Misses dependencies on gmm, PetsC, TetGen - - variant('shared', default=True, description='Enables the build of shared libraries') - variant('debug', default=False, description='Builds the library in debug mode') - variant('mpi', default=False, description='Builds MPI support for parser and solver') - variant('fltk', default=False, description='Enables the build of the FLTK GUI') - variant('hdf5', default=False, description='Enables HDF5 support') - variant('compression', default=True, description='Enables IO compression through zlib') + variant('shared', default=True, description='Enables the build of shared libraries') + variant('debug', default=False, description='Builds the library in debug mode') + variant('mpi', default=False, description='Builds MPI support for parser and solver') + variant('fltk', default=False, description='Enables the build of the FLTK GUI') + variant('hdf5', default=False, description='Enables HDF5 support') + variant('compression', default=True, description='Enables IO compression through zlib') + variant('oce', default=False, description='Build with OCE') + variant('petsc', default=False, description='Build with PETSc') + variant('slepc', default=False, description='Build with SLEPc (only when PETSc is enabled)') depends_on('blas') depends_on('lapack') + depends_on('cmake@2.8:') depends_on('gmp') - depends_on('mpi', when='+mpi') - depends_on('fltk', when='+fltk') # Assumes OpenGL with GLU is already provided by the system + depends_on('mpi', when='+mpi') + # Assumes OpenGL with GLU is already provided by the system: + depends_on('fltk', when='+fltk') depends_on('hdf5', when='+hdf5') - depends_on('zlib', when='+compression') + depends_on('oce', when='+oce') + depends_on('petsc+mpi', when='+petsc+mpi') + depends_on('petsc', when='+petsc~mpi') + depends_on('slepc', when='+slepc+petsc') + depends_on('zlib', when='+compression') def install(self, spec, prefix): - options = [] options.extend(std_cmake_args) + # Make sure native file dialogs are used + options.extend(['-DENABLE_NATIVE_FILE_CHOOSER=ON']) + build_directory = join_path(self.stage.path, 'spack-build') source_directory = self.stage.source_path @@ -68,11 +80,45 @@ class Gmsh(Package): # Prevent GMsh from using its own strange directory structure on OSX options.append('-DENABLE_OS_SPECIFIC_INSTALL=OFF') + # Make sure GMSH picks up correct BlasLapack by providing linker flags + options.append('-DBLAS_LAPACK_LIBRARIES=%s %s' % + (to_link_flags(spec['lapack'].lapack_shared_lib), + to_link_flags(spec['blas'].blas_shared_lib))) + + # Gmsh does not have an option to compile against external metis. + # Its own Metis, however, fails to build + options.append('-DENABLE_METIS=OFF') + + if '+fltk' in spec: + options.append('-DENABLE_FLTK=ON') + else: + options.append('-DENABLE_FLTK=OFF') + + if '+oce' in spec: + env['CASROOT'] = self.spec['oce'].prefix + options.extend(['-DENABLE_OCC=ON']) + else: + options.extend(['-DENABLE_OCC=OFF']) + + if '+petsc' in spec: + env['PETSC_DIR'] = self.spec['petsc'].prefix + options.extend(['-DENABLE_PETSC=ON']) + else: + options.extend(['-DENABLE_PETSC=OFF']) + + if '+slepc' in spec: + env['SLEPC_DIR'] = self.spec['slepc'].prefix + options.extend(['-DENABLE_SLEPC=ON']) + else: + options.extend(['-DENABLE_SLEPC=OFF']) + if '+shared' in spec: + # Builds dynamic executable and installs shared library options.extend(['-DENABLE_BUILD_SHARED:BOOL=ON', - '-DENABLE_BUILD_DYNAMIC:BOOL=ON']) # Builds dynamic executable and installs shared library + '-DENABLE_BUILD_DYNAMIC:BOOL=ON']) else: - options.append('-DENABLE_BUILD_LIB:BOOL=ON') # Builds and installs static library + # Builds and installs static library + options.append('-DENABLE_BUILD_LIB:BOOL=ON') if '+debug' in spec: options.append('-DCMAKE_BUILD_TYPE:STRING=Debug') diff --git a/var/spack/repos/builtin/packages/harfbuzz/package.py b/var/spack/repos/builtin/packages/harfbuzz/package.py index e4c1b80de3..f8d73d651b 100644 --- a/var/spack/repos/builtin/packages/harfbuzz/package.py +++ b/var/spack/repos/builtin/packages/harfbuzz/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Harfbuzz(Package): """The Harfbuzz package contains an OpenType text shaping engine.""" homepage = "http://www.freedesktop.org/wiki/Software/HarfBuzz/" @@ -34,6 +35,8 @@ class Harfbuzz(Package): depends_on("glib") depends_on("icu") depends_on("freetype") + depends_on("cairo") + depends_on("zlib") def patch(self): change_sed_delimiter('@', ';', 'src/Makefile.in') diff --git a/var/spack/repos/builtin/packages/hdf5/package.py b/var/spack/repos/builtin/packages/hdf5/package.py index e46f432be5..51a5823aa5 100644 --- a/var/spack/repos/builtin/packages/hdf5/package.py +++ b/var/spack/repos/builtin/packages/hdf5/package.py @@ -70,7 +70,8 @@ class Hdf5(Package): raise RuntimeError(msg) if '+threadsafe' in spec and ('+cxx' in spec or '+fortran' in spec): - raise RuntimeError("cannot use variant +threadsafe with either +cxx or +fortran") + msg = 'cannot use variant +threadsafe with either +cxx or +fortran' + raise RuntimeError(msg) def install(self, spec, prefix): self.validate(spec) @@ -164,7 +165,7 @@ int main(int argc, char **argv) { """ expected = """\ HDF5 version {version} {version} -""".format(version=str(spec.version)) +""".format(version=str(spec.version.up_to(3))) with open("check.c", 'w') as f: f.write(source) if '+mpi' in spec: @@ -185,24 +186,30 @@ HDF5 version {version} {version} if not success: print "Produced output does not match expected output." print "Expected output:" - print '-'*80 + print '-' * 80 print expected - print '-'*80 + print '-' * 80 print "Produced output:" - print '-'*80 + print '-' * 80 print output - print '-'*80 + print '-' * 80 raise RuntimeError("HDF5 install check failed") shutil.rmtree(checkdir) def url_for_version(self, version): - v = str(version) + base_url = "http://www.hdfgroup.org/ftp/HDF5/releases" if version == Version("1.2.2"): - return "http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-" + v + ".tar.gz" + return "{0}/hdf5-{1}.tar.gz".format(base_url, version) + elif version < Version("1.6.6"): + return "{0}/hdf5-{1}/hdf5-{2}.tar.gz".format( + base_url, version.up_to(2), version) elif version < Version("1.7"): - return "http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-" + version.up_to(2) + "/hdf5-" + v + ".tar.gz" + return "{0}/hdf5-{1}/hdf5-{2}/src/hdf5-{2}.tar.gz".format( + base_url, version.up_to(2), version) elif version < Version("1.10"): - return "http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-" + v + "/src/hdf5-" + v + ".tar.gz" + return "{0}/hdf5-{1}/src/hdf5-{1}.tar.gz".format( + base_url, version) else: - return "http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-" + version.up_to(2) + "/hdf5-" + v + "/src/hdf5-" + v + ".tar.gz" + return "{0}/hdf5-{1}/hdf5-{2}/src/hdf5-{2}.tar.gz".format( + base_url, version.up_to(2), version) diff --git a/var/spack/repos/builtin/packages/julia/package.py b/var/spack/repos/builtin/packages/julia/package.py index 69b52130e9..99d138dcff 100644 --- a/var/spack/repos/builtin/packages/julia/package.py +++ b/var/spack/repos/builtin/packages/julia/package.py @@ -22,8 +22,9 @@ # 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 Julia(Package): """The Julia Language: A fresh approach to technical computing""" @@ -32,10 +33,14 @@ class Julia(Package): version('master', git='https://github.com/JuliaLang/julia.git', branch='master') + version('release-0.4', + git='https://github.com/JuliaLang/julia.git', branch='release-0.4') + version('0.4.6', 'd88db18c579049c23ab8ef427ccedf5d', preferred=True) version('0.4.5', '69141ff5aa6cee7c0ec8c85a34aa49a6') version('0.4.3', '8a4a59fd335b05090dd1ebefbbe5aaac') - patch('gc.patch') + patch('gc.patch', when='@0.4:0.4.5') + patch('gc.patch', when='@release-0.4') patch('openblas.patch', when='@0.4:0.4.5') # Build-time dependencies: @@ -92,25 +97,21 @@ class Julia(Package): depends_on("mpi") def install(self, spec, prefix): - if '@master' in spec: - # Julia needs to know the offset from a specific commit - git = which('git') - git('fetch', '--unshallow') - # Explicitly setting CC, CXX, or FC breaks building libuv, one # of Julia's dependencies. This might be a Darwin-specific # problem. Given how Spack sets up compilers, Julia should # still use Spack's compilers, even if we don't specify them # explicitly. - options = [#"CC=cc", - #"CXX=c++", - #"FC=fc", - #"USE_SYSTEM_ARPACK=1", - #"USE_SYSTEM_FFTW=1", - #"USE_SYSTEM_GMP=1", - #"USE_SYSTEM_MPFR=1", - #TODO "USE_SYSTEM_PCRE=1", - "prefix=%s" % prefix] + options = [ + # "CC=cc", + # "CXX=c++", + # "FC=fc", + # "USE_SYSTEM_ARPACK=1", + # "USE_SYSTEM_FFTW=1", + # "USE_SYSTEM_GMP=1", + # "USE_SYSTEM_MPFR=1", + # "USE_SYSTEM_PCRE=1", + "prefix=%s" % prefix] with open('Make.user', 'w') as f: f.write('\n'.join(options) + '\n') make() diff --git a/var/spack/repos/builtin/packages/libaio/package.py b/var/spack/repos/builtin/packages/libaio/package.py new file mode 100644 index 0000000000..735ced047b --- /dev/null +++ b/var/spack/repos/builtin/packages/libaio/package.py @@ -0,0 +1,43 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class Libaio(Package): + """This is the linux native Asynchronous I/O interface library.""" + + homepage = "https://git.fedorahosted.org/cgit/libaio.git" + url = "https://git.fedorahosted.org/cgit/libaio.git/snapshot/libaio-0.3.110-1.tar.gz" + + version('0.3.110-1', 'eb6b1b435afadb5b80c5dd80984249f6') + + def install(self, spec, prefix): + # libaio is not supported on OS X + if spec.satisfies('arch=darwin-x86_64'): + # create a dummy directory + mkdir(prefix.lib) + return + + make('prefix={0}'.format(prefix), 'install') diff --git a/var/spack/repos/builtin/packages/libtool/package.py b/var/spack/repos/builtin/packages/libtool/package.py index 90e7b3b643..0e410a5061 100644 --- a/var/spack/repos/builtin/packages/libtool/package.py +++ b/var/spack/repos/builtin/packages/libtool/package.py @@ -24,18 +24,30 @@ ############################################################################## from spack import * + class Libtool(Package): - """libtool -- library building part of autotools""" - homepage = "https://www.gnu.org/software/libtool/" - url = "http://ftpmirror.gnu.org/libtool/libtool-2.4.2.tar.gz" + """ + libtool -- library building part of autotools + """ + homepage = 'https://www.gnu.org/software/libtool/' + url = 'http://ftpmirror.gnu.org/libtool/libtool-2.4.2.tar.gz' - version('2.4.6' , 'addf44b646ddb4e3919805aa88fa7c5e') - version('2.4.2' , 'd2f3b7d4627e69e13514a40e72a24d50') + version('2.4.6', 'addf44b646ddb4e3919805aa88fa7c5e') + version('2.4.2', 'd2f3b7d4627e69e13514a40e72a24d50') depends_on('m4') + def _make_executable(self, name): + return Executable(join_path(self.prefix.bin, name)) + + def setup_dependent_package(self, module, dependent_spec): + # Automake is very likely to be a build dependency, + # so we add the tools it provides to the dependent module + executables = ['libtoolize', 'libtool'] + for name in executables: + setattr(module, name, self._make_executable(name)) + def install(self, spec, prefix): configure("--prefix=%s" % prefix) - make() make("install") diff --git a/var/spack/repos/builtin/packages/libxpm/package.py b/var/spack/repos/builtin/packages/libxpm/package.py new file mode 100644 index 0000000000..10ca8158c2 --- /dev/null +++ b/var/spack/repos/builtin/packages/libxpm/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 Libxpm(Package): + """Xpm file format library""" + + homepage = "https://www.x.org/" + url = "https://www.x.org/archive//individual/lib/libXpm-3.5.11.tar.gz" + + version('3.5.11', '7c67c878ee048206b070bc0b24154f04') + version('3.5.10', 'a70507638d74541bf30a771f1e5938bb') + version('3.5.9', 'd6d4b0f76248a6b346eb42dfcdaa72a6') + version('3.5.8', '2d81d6633e67ac5562e2fbee126b2897') + version('3.5.7', '7bbc8f112f7143ed6961a58ce4e14558') + + def install(self, spec, prefix): + configure('--prefix=%s' % prefix) + + make() + make("install") diff --git a/var/spack/repos/builtin/packages/lrzip/package.py b/var/spack/repos/builtin/packages/lrzip/package.py new file mode 100644 index 0000000000..42542acfdb --- /dev/null +++ b/var/spack/repos/builtin/packages/lrzip/package.py @@ -0,0 +1,61 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class Lrzip(Package): + """A compression utility that excels at compressing large files + (usually > 10-50 MB). Larger files and/or more free RAM means that the + utility will be able to more effectively compress your files (ie: faster / + smaller size), especially if the filesize(s) exceed 100 MB. You can either + choose to optimise for speed (fast compression / decompression) or size, + but not both.""" + + homepage = 'http://lrzip.kolivas.org' + url = 'https://github.com/ckolivas/lrzip/archive/v0.630.tar.gz' + + version('master', git='https://github.com/ckolivas/lrzip.git') + version('0.630', '3ca7f1d1365aa105089d1fbfc6b0924a') + version('0.621', '1f07227b39ae81a98934411e8611e341') + version('0.616', 'd40bdb046d0807ef602e36b1e9782cc0') + version('0.615', 'f1c01e7f3de07f54d916b61c989dfaf2') + + # depends_on('coreutils') + depends_on('lzo') + depends_on('zlib') + depends_on('bzip2') + + def install(self, spec, prefix): + set_executable('./autogen.sh') + autogen = Executable('./autogen.sh') + + configure_args = [ + '--prefix={0}'.format(prefix), + '--disable-dependency-tracking' + ] + autogen(*configure_args) + + make() + make('install') diff --git a/var/spack/repos/builtin/packages/lzo/package.py b/var/spack/repos/builtin/packages/lzo/package.py new file mode 100644 index 0000000000..0961bbb58c --- /dev/null +++ b/var/spack/repos/builtin/packages/lzo/package.py @@ -0,0 +1,49 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class Lzo(Package): + """Real-time data compression library""" + + homepage = 'https://www.oberhumer.com/opensource/lzo/' + url = 'https://www.oberhumer.com/opensource/lzo/download/lzo-2.09.tar.gz' + + version('2.09', 'c7ffc9a103afe2d1bba0b015e7aa887f') + version('2.08', 'fcec64c26a0f4f4901468f360029678f') + version('2.07', '4011935e95171e78ad4894f7335c982a') + version('2.06', '95380bd4081f85ef08c5209f4107e9f8') + version('2.05', 'c67cda5fa191bab761c7cb06fe091e36') + + def install(self, spec, prefix): + configure_args = [ + '--prefix={0}'.format(prefix), + '--disable-dependency-tracking', + '--enable-shared' + ] + configure(*configure_args) + make() + make('check') + make('install') diff --git a/var/spack/repos/builtin/packages/mariadb/package.py b/var/spack/repos/builtin/packages/mariadb/package.py new file mode 100644 index 0000000000..d9df200d02 --- /dev/null +++ b/var/spack/repos/builtin/packages/mariadb/package.py @@ -0,0 +1,59 @@ +############################################################################## +# 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 Mariadb(Package): + """MariaDB turns data into structured information in a wide array of + applications, ranging from banking to websites. It is an enhanced, drop-in + replacement for MySQL. MariaDB is used because it is fast, scalable and + robust, with a rich ecosystem of storage engines, plugins and many other + tools make it very versatile for a wide variety of use cases.""" + + homepage = "https://mariadb.org/about/" + url = "https://downloads.mariadb.org/f/mariadb-10.1.14/source/mariadb-10.1.14.tar.gz" + + version('10.1.14', '294925531e0fd2f0461e3894496a5adc') + version('5.5.49', '67b5a499a5f158b2a586e6e3bfb4f304') + + variant('nonblocking', default=True, description='Allow non blocking ' + 'operations in the mariadb client library.') + + depends_on('boost') + depends_on('cmake') + depends_on('jemalloc') + depends_on('libaio') + depends_on('libedit') + depends_on('libevent', when='+nonblocking') + depends_on('ncurses') + depends_on('zlib') + + def install(self, spec, prefix): + with working_dir('spack-build', create=True): + + cmake('..', *std_cmake_args) + + make() + make('install') diff --git a/var/spack/repos/builtin/packages/mpich/package.py b/var/spack/repos/builtin/packages/mpich/package.py index 164d9db541..90670ee517 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') @@ -50,6 +50,11 @@ class Mpich(Package): provides('mpi@:1.3', when='@1:') def setup_dependent_environment(self, spack_env, run_env, dependent_spec): + spack_env.set('MPICC', join_path(self.prefix.bin, 'mpicc')) + spack_env.set('MPICXX', join_path(self.prefix.bin, 'mpic++')) + spack_env.set('MPIF77', join_path(self.prefix.bin, 'mpif77')) + spack_env.set('MPIF90', join_path(self.prefix.bin, 'mpif90')) + spack_env.set('MPICH_CC', spack_cc) spack_env.set('MPICH_CXX', spack_cxx) spack_env.set('MPICH_F77', spack_f77) @@ -57,9 +62,9 @@ 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 +97,6 @@ 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 +106,20 @@ 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..da386445bb 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): @@ -192,6 +191,11 @@ class Mvapich2(Package): run_env.set('SLURM_MPI_TYPE', 'pmi2') def setup_dependent_environment(self, spack_env, run_env, extension_spec): + spack_env.set('MPICC', join_path(self.prefix.bin, 'mpicc')) + spack_env.set('MPICXX', join_path(self.prefix.bin, 'mpicxx')) + spack_env.set('MPIF77', join_path(self.prefix.bin, 'mpif77')) + spack_env.set('MPIF90', join_path(self.prefix.bin, 'mpif90')) + spack_env.set('MPICH_CC', spack_cc) spack_env.set('MPICH_CXX', spack_cxx) spack_env.set('MPICH_F77', spack_f77) @@ -245,27 +249,20 @@ 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/packages/mxml/package.py b/var/spack/repos/builtin/packages/mxml/package.py index f79251d312..254a5f1595 100644 --- a/var/spack/packages/mxml/package.py +++ b/var/spack/repos/builtin/packages/mxml/package.py @@ -1,14 +1,15 @@ -import os from spack import * + class Mxml(Package): - """Mini-XML is a small XML library that you can use to read and write XML - and XML-like data files in your application without requiring large - non-standard libraries + """ + Mini-XML is a small XML library that you can use to read and write XML + and XML-like data files in your application without requiring large + non-standard libraries """ homepage = "http://www.msweet.org" - url = "http://www.msweet.org/files/project3/mxml-2.9.tar.gz" + url = "http://www.msweet.org/files/project3/mxml-2.9.tar.gz" version('2.9', 'e21cad0f7aacd18f942aa0568a8dee19') version('2.8', 'd85ee6d30de053581242c4a86e79a5d2') @@ -16,11 +17,11 @@ class Mxml(Package): version('2.6', '68977789ae64985dddbd1a1a1652642e') version('2.5', 'f706377fba630b39fa02fd63642b17e5') - # module swap PrgEnv-intel PrgEnv-$COMP (Can use whatever compiler you want to use) + # module swap PrgEnv-intel PrgEnv-$COMP + # (Can use whatever compiler you want to use) # Case statement to change CC and CXX flags def install(self, spec, prefix): configure('--prefix=%s' % prefix, "--disable-shared", 'CFLAGS=-static') make() make("install") - diff --git a/var/spack/repos/builtin/packages/netcdf-fortran/package.py b/var/spack/repos/builtin/packages/netcdf-fortran/package.py index 3d1951ceee..e52ff1af87 100644 --- a/var/spack/repos/builtin/packages/netcdf-fortran/package.py +++ b/var/spack/repos/builtin/packages/netcdf-fortran/package.py @@ -24,12 +24,14 @@ ############################################################################## from spack import * + class NetcdfFortran(Package): """Fortran interface for NetCDF4""" homepage = "http://www.unidata.ucar.edu/software/netcdf" url = "http://www.unidata.ucar.edu/downloads/netcdf/ftp/netcdf-fortran-4.4.3.tar.gz" + version('4.4.4', 'e855c789cd72e1b8bc1354366bf6ac72') version('4.4.3', 'bfd4ae23a34635b273d3eb0d91cbde9e') depends_on('netcdf') diff --git a/var/spack/repos/builtin/packages/octave-splines/package.py b/var/spack/repos/builtin/packages/octave-splines/package.py new file mode 100644 index 0000000000..11c9cc5ba7 --- /dev/null +++ b/var/spack/repos/builtin/packages/octave-splines/package.py @@ -0,0 +1,44 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class OctaveSplines(Package): + """Additional spline functions.""" + + homepage = "http://octave.sourceforge.net/splines/index.html" + url = "http://downloads.sourceforge.net/octave/splines-1.3.1.tar.gz" + + version('1.3.1', 'f9665d780c37aa6a6e17d1f424c49bdeedb89d1192319a4e39c08784122d18f9') + + extends('octave@3.6.0:') + + def install(self, spec, prefix): + octave('--quiet', + '--norc', + '--built-in-docstrings-file=/dev/null', + '--texi-macros-file=/dev/null', + '--eval', 'pkg prefix %s; pkg install %s' % + (prefix, self.stage.archive_file)) diff --git a/var/spack/repos/builtin/packages/octave/package.py b/var/spack/repos/builtin/packages/octave/package.py index 72ff0ee6fc..f97bfc7d12 100644 --- a/var/spack/repos/builtin/packages/octave/package.py +++ b/var/spack/repos/builtin/packages/octave/package.py @@ -36,6 +36,8 @@ class Octave(Package): homepage = "https://www.gnu.org/software/octave/" url = "ftp://ftp.gnu.org/gnu/octave/octave-4.0.0.tar.gz" + extendable = True + version('4.0.2', 'c2a5cacc6e4c52f924739cdf22c2c687') version('4.0.0', 'a69f8320a4f20a8480c1b278b1adb799') @@ -212,3 +214,16 @@ class Octave(Package): make() make("install") + + # ======================================================================== + # Set up environment to make install easy for Octave extensions. + # ======================================================================== + + def setup_dependent_package(self, module, ext_spec): + """Called before Octave modules' install() methods. + + In most cases, extensions will only need to have one line: + octave('--eval', 'pkg install %s' % self.stage.archive_file) + """ + # Octave extension builds can have a global Octave executable function + module.octave = Executable(join_path(self.spec.prefix.bin, 'octave')) diff --git a/var/spack/repos/builtin/packages/openjpeg/package.py b/var/spack/repos/builtin/packages/openjpeg/package.py index 9b2063593a..1d00edb06d 100644 --- a/var/spack/repos/builtin/packages/openjpeg/package.py +++ b/var/spack/repos/builtin/packages/openjpeg/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Openjpeg(Package): """ OpenJPEG is an open-source JPEG 2000 codec written in C language. @@ -36,12 +37,13 @@ class Openjpeg(Package): homepage = "https://github.com/uclouvain/openjpeg" url = "https://github.com/uclouvain/openjpeg/archive/version.2.1.tar.gz" - version('2.1' , '3e1c451c087f8462955426da38aa3b3d') + version('2.1', '3e1c451c087f8462955426da38aa3b3d') version('2.0.1', '105876ed43ff7dbb2f90b41b5a43cfa5') - version('2.0' , 'cdf266530fee8af87454f15feb619609') + version('2.0', 'cdf266530fee8af87454f15feb619609') version('1.5.2', '545f98923430369a6b046ef3632ef95c') version('1.5.1', 'd774e4b5a0db5f0f171c4fc0aabfa14e') + depends_on('cmake') def install(self, spec, prefix): cmake('.', *std_cmake_args) diff --git a/var/spack/repos/builtin/packages/openmpi/package.py b/var/spack/repos/builtin/packages/openmpi/package.py index be3d1342fc..15c8eefe96 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 @@ -96,24 +106,44 @@ 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('MPICC', join_path(self.prefix.bin, 'mpicc')) + spack_env.set('MPICXX', join_path(self.prefix.bin, 'mpic++')) + spack_env.set('MPIF77', join_path(self.prefix.bin, 'mpif77')) + spack_env.set('MPIF90', join_path(self.prefix.bin, 'mpif90')) + spack_env.set('OMPI_CC', spack_cc) spack_env.set('OMPI_CXX', spack_cxx) spack_env.set('OMPI_FC', spack_fc) spack_env.set('OMPI_F77', spack_f77) def 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 +151,14 @@ 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 +169,7 @@ 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 +187,7 @@ 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 +204,33 @@ 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/parmgridgen/package.py b/var/spack/repos/builtin/packages/parmgridgen/package.py new file mode 100644 index 0000000000..02be777c36 --- /dev/null +++ b/var/spack/repos/builtin/packages/parmgridgen/package.py @@ -0,0 +1,71 @@ +############################################################################## +# 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 Parmgridgen(Package): + """MGRIDGEN is a serial library written entirely in ANSI C that implements + (serial) algorithms for obtaining a sequence of successive coarse grids + that are well-suited for geometric multigrid methods. + ParMGridGen is the parallel version of MGridGen + """ + + homepage = "http://www-users.cs.umn.edu/~moulitsa/software.html" + url = "http://www-users.cs.umn.edu/~moulitsa/download/ParMGridGen-1.0.tar.gz" + + version('1.0', '2872fa95b7fb91d6bd525490eed62038') + + depends_on('mpi') + + def install(self, spec, prefix): + make_opts = [ + 'make=make', + 'COPTIONS=-fPIC', + 'LDOPTIONS=-fPIC', + 'CC={0}'.format(self.compiler.cc), + 'PARCC={0}'.format(spec['mpi'].mpicc), + 'LD={0}'.format(self.compiler.cc), + 'PARLD={0}'.format(spec['mpi'].mpicc), + 'LIBDIR=-L../..', + 'PARLIBS=-L../../ -lparmgrid -lmgrid -lm', + 'LIBS=-L../../ -lmgrid -lm', + 'parallel' + ] + + make(*make_opts, parallel=False) + + mkdirp(prefix.include, prefix.lib, prefix.bin) + + install("mgridgen.h", prefix.include) + install("parmgridgen.h", prefix.include) + + install("MGridGen/IMlib/libIMlib.a", + join_path(prefix.lib, 'libIMlib.a')) + install("libmgrid.a", prefix.lib) + install("libparmgrid.a", prefix.lib) + + install("mgridgen", prefix.bin) + install("parmgridgen", prefix.bin) 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/postgresql/package.py b/var/spack/repos/builtin/packages/postgresql/package.py index 9362234881..caf3768362 100644 --- a/var/spack/repos/builtin/packages/postgresql/package.py +++ b/var/spack/repos/builtin/packages/postgresql/package.py @@ -24,18 +24,21 @@ ############################################################################## from spack import * + class Postgresql(Package): - """PostgreSQL is a powerful, open source object-relational - database system. It has more than 15 years of active - development and a proven architecture that has earned it a - strong reputation for reliability, data integrity, and - correctness.""" + """PostgreSQL is a powerful, open source object-relational database system. + It has more than 15 years of active development and a proven architecture + that has earned it a strong reputation for reliability, data integrity, and + correctness.""" + homepage = "http://www.postgresql.org/" url = "http://ftp.postgresql.org/pub/source/v9.3.4/postgresql-9.3.4.tar.bz2" version('9.3.4', 'd0a41f54c377b2d2fab4a003b0dac762') + version('9.5.3', '3f0c388566c688c82b01a0edf1e6b7a0') - depends_on("openssl") + depends_on('openssl') + depends_on('readline') def install(self, spec, prefix): configure("--prefix=%s" % prefix, 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/py-3to2/package.py b/var/spack/repos/builtin/packages/py-3to2/package.py new file mode 100644 index 0000000000..1071a3c209 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-3to2/package.py @@ -0,0 +1,40 @@ +############################################################################## +# 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 Py3to2(Package): + """lib3to2 is a set of fixers that are intended to backport code written + for Python version 3.x into Python version 2.x.""" + + homepage = "https://pypi.python.org/pypi/3to2" + url = "https://pypi.python.org/packages/source/3/3to2/3to2-1.1.1.zip" + + version('1.1.1', 'cbeed28e350dbdaef86111ace3052824') + + extends('python') + + def install(self, spec, prefix): + python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-basemap/package.py b/var/spack/repos/builtin/packages/py-basemap/package.py index 95d02bce91..13f604bacd 100644 --- a/var/spack/repos/builtin/packages/py-basemap/package.py +++ b/var/spack/repos/builtin/packages/py-basemap/package.py @@ -23,10 +23,12 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## from spack import * -import os + class PyBasemap(Package): - """The matplotlib basemap toolkit is a library for plotting 2D data on maps in Python.""" + """The matplotlib basemap toolkit is a library for plotting + 2D data on maps in Python.""" + homepage = "http://matplotlib.org/basemap/" url = "https://downloads.sourceforge.net/project/matplotlib/matplotlib-toolkits/basemap-1.0.7/basemap-1.0.7.tar.gz" @@ -36,7 +38,7 @@ class PyBasemap(Package): depends_on('py-setuptools') depends_on('py-numpy') depends_on('py-matplotlib+gui') - depends_on('py-pillow') + depends_on('pil') depends_on("geos") def install(self, spec, prefix): diff --git a/var/spack/repos/builtin/packages/py-pil/package.py b/var/spack/repos/builtin/packages/py-pil/package.py index dc4418fdfe..2b3cce26d3 100644 --- a/var/spack/repos/builtin/packages/py-pil/package.py +++ b/var/spack/repos/builtin/packages/py-pil/package.py @@ -24,14 +24,19 @@ ############################################################################## from spack import * + class PyPil(Package): - """The Python Imaging Library (PIL) adds image processing capabilities to your Python interpreter. This library supports many file formats, and provides powerful image processing and graphics capabilities.""" + """The Python Imaging Library (PIL) adds image processing capabilities + to your Python interpreter. This library supports many file formats, + and provides powerful image processing and graphics capabilities.""" homepage = "http://www.pythonware.com/products/pil/" url = "http://effbot.org/media/downloads/Imaging-1.1.7.tar.gz" version('1.1.7', 'fc14a54e1ce02a0225be8854bfba478e') + provides('pil') + extends('python') def install(self, spec, prefix): diff --git a/var/spack/repos/builtin/packages/py-pillow/package.py b/var/spack/repos/builtin/packages/py-pillow/package.py index cdbc57e0a5..25cf412b31 100644 --- a/var/spack/repos/builtin/packages/py-pillow/package.py +++ b/var/spack/repos/builtin/packages/py-pillow/package.py @@ -23,77 +23,108 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## from spack import * -import os + class PyPillow(Package): - """Pillow is the friendly PIL fork by Alex Clark and Contributors. PIL is the Python Imaging Library by Fredrik Lundh and Contributors. The Python Imaging Library (PIL) adds image processing capabilities to your Python interpreter. This library supports many file formats, and provides powerful image processing and graphics capabilities.""" + """Pillow is a fork of the Python Imaging Library (PIL). It adds image + processing capabilities to your Python interpreter. This library supports + many file formats, and provides powerful image processing and graphics + capabilities.""" - homepage = "https://python-pillow.github.io/" + homepage = "https://python-pillow.org/" url = "https://pypi.python.org/packages/source/P/Pillow/Pillow-3.0.0.tar.gz" + # TODO: This version should be deleted once the next release comes out. + # TODO: It fixes a bug that prevented us from linking to Tk/Tcl. + # TODO: Tk/Tcl support is necessary for tkinter bitmap and photo images. + # TODO: If you require this support, run the following command: + # TODO: `spack install py-pillow@3.3.0.dev0 ^python+tk` + version('3.3.0.dev0', git='https://github.com/python-pillow/Pillow.git', + commit='30eced62868141a6c859a4370efd40b9434a7c3f') + + version('3.2.0', '7cfd093c11205d9e2ebe3c51dfcad510', preferred=True) version('3.0.0', 'fc8ac44e93da09678eac7e30c9b7377d') - provides('PIL') + + provides('pil') # These defaults correspond to Pillow defaults variant('jpeg', default=True, description='Provide JPEG functionality') variant('zlib', default=True, description='Access to compressed PNGs') variant('tiff', default=False, description='Access to TIFF files') variant('freetype', default=False, description='Font related services') - variant('tk', default=False, description='Support for tkinter bitmap and photo images') variant('lcms', default=False, description='Color management') + variant('jpeg2000', default=False, description='Provide JPEG 2000 functionality') # Spack does not (yet) support these modes of building - # variant('webp', default=False, description='') - # variant('webpmux', default=False, description='') - # variant('jpeg2000', default=False, description='') + # variant('webp', default=False, description='Provide the WebP format') + # variant('webpmux', default=False, description='WebP metadata, relies on WebP support') # NOQA: ignore=E501 + # variant('imagequant', default=False, description='Provide improved color quantization') # NOQA: ignore=E501 + # Required dependencies extends('python') depends_on('binutils') depends_on('py-setuptools') - depends_on('jpeg', when='+jpeg') # BUG: It will use the system libjpeg anyway + # Recommended dependencies + depends_on('jpeg', when='+jpeg') depends_on('zlib', when='+zlib') - depends_on('tiff', when='+tiff') + + # Optional dependencies + depends_on('libtiff', when='+tiff') depends_on('freetype', when='+freetype') depends_on('lcms', when='+lcms') - depends_on('tcl', when='+tk') - depends_on('tk', when='+tk') + depends_on('openjpeg', when='+jpeg2000') - def install(self, spec, prefix): - libpath=[] + # Spack does not (yet) support these modes of building + # depends_on('webp', when='+webp') + # depends_on('webpmux', when='+webpmux') + # depends_on('imagequant', when='+imagequant') + + def patch(self): + """Patch setup.py to provide lib and include directories + for dependencies.""" + + spec = self.spec + setup = FileFilter('setup.py') if '+jpeg' in spec: - libpath.append(join_path(spec['jpeg'].prefix, 'lib')) + setup.filter('JPEG_ROOT = None', + 'JPEG_ROOT = ("{0}", "{1}")'.format( + spec['jpeg'].prefix.lib, + spec['jpeg'].prefix.include)) if '+zlib' in spec: - libpath.append(join_path(spec['zlib'].prefix, 'lib')) + setup.filter('ZLIB_ROOT = None', + 'ZLIB_ROOT = ("{0}", "{1}")'.format( + spec['zlib'].prefix.lib, + spec['zlib'].prefix.include)) if '+tiff' in spec: - libpath.append(join_path(spec['tiff'].prefix, 'lib')) + setup.filter('TIFF_ROOT = None', + 'TIFF_ROOT = ("{0}", "{1}")'.format( + spec['libtiff'].prefix.lib, + spec['libtiff'].prefix.include)) if '+freetype' in spec: - libpath.append(join_path(spec['freetype'].prefix, 'lib')) + setup.filter('FREETYPE_ROOT = None', + 'FREETYPE_ROOT = ("{0}", "{1}")'.format( + spec['freetype'].prefix.lib, + spec['freetype'].prefix.include)) if '+lcms' in spec: - libpath.append(join_path(spec['lcms'].prefix, 'lib')) - - # This has not been tested, and likely needs some other treatment. - #if '+tk' in spec: - # libpath.append(join_path(spec['tcl'].prefix, 'lib')) - # libpath.append(join_path(spec['tk'].prefix, 'lib')) - - # -------- Building - cmd = ['build_ext', - '--%s-jpeg' % ('enable' if '+jpeg' in spec else 'disable'), - '--%s-zlib' % ('enable' if '+zlib' in spec else 'disable'), - '--%s-tiff' % ('enable' if '+tiff' in spec else 'disable'), - '--%s-freetype' % ('enable' if '+freetype' in spec else 'disable'), - '--%s-lcms' % ('enable' if '+lcms' in spec else 'disable'), - '-L'+':'.join(libpath) # NOTE: This does not make it find libjpeg - ] - - #if '+tk' in spec: - # cmd.extend(['--enable-tcl', '--enable-tk']) - #else: - # cmd.extend(['--disable-tcl', '--disable-tk']) - - # --------- Installation - cmd.extend(['install', '--prefix=%s' % prefix]) - - python('setup.py', *cmd) + setup.filter('LCMS_ROOT = None', + 'LCMS_ROOT = ("{0}", "{1}")'.format( + spec['lcms'].prefix.lib, + spec['lcms'].prefix.include)) + if '+jpeg2000' in spec: + setup.filter('JPEG2K_ROOT = None', + 'JPEG2K_ROOT = ("{0}", "{1}")'.format( + spec['openjpeg'].prefix.lib, + spec['openjpeg'].prefix.include)) + + def install(self, spec, prefix): + def variant_to_flag(variant): + able = 'enable' if '+{0}'.format(variant) in spec else 'disable' + return '--{0}-{1}'.format(able, variant) + + variants = ['jpeg', 'zlib', 'tiff', 'freetype', 'lcms', 'jpeg2000'] + build_args = list(map(variant_to_flag, variants)) + + python('setup.py', 'build_ext', *build_args) + python('setup.py', 'install', '--prefix={0}'.format(prefix)) diff --git a/var/spack/repos/builtin/packages/py-protobuf/package.py b/var/spack/repos/builtin/packages/py-protobuf/package.py new file mode 100644 index 0000000000..da3a65c22e --- /dev/null +++ b/var/spack/repos/builtin/packages/py-protobuf/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 PyProtobuf(Package): + """Protocol buffers are Google's language-neutral, platform-neutral, + extensible mechanism for serializing structured data - think XML, but + smaller, faster, and simpler. You define how you want your data to be + structured once, then you can use special generated source code to easily + write and read your structured data to and from a variety of data streams + and using a variety of languages.""" + + homepage = 'https://developers.google.com/protocol-buffers/' + url = 'https://pypi.python.org/packages/source/p/protobuf/protobuf-3.0.0b2.tar.gz' + + version('3.0.0b2', 'f0d3bd2394345a9af4a277cd0302ae83') + version('2.6.1', '6bf843912193f70073db7f22e2ea55e2') + version('2.5.0', '338813f3629d59e9579fed9035ecd457') + version('2.4.1', '72f5141d20ab1bcae6b1e00acfb1068a') + version('2.3.0', 'bb020c962f252fe81bfda8fb433bafdd') + + extends('python') + + depends_on('py-setuptools') + + def install(self, spec, prefix): + python('setup.py', 'install', '--prefix={0}'.format(prefix)) diff --git a/var/spack/repos/builtin/packages/py-scikit-image/package.py b/var/spack/repos/builtin/packages/py-scikit-image/package.py index 0479e9eb0a..4c8fd0942a 100644 --- a/var/spack/repos/builtin/packages/py-scikit-image/package.py +++ b/var/spack/repos/builtin/packages/py-scikit-image/package.py @@ -24,8 +24,11 @@ ############################################################################## from spack import * + class PyScikitImage(Package): - """Image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.""" + """Image processing algorithms for SciPy, including IO, morphology, + filtering, warping, color manipulation, object detection, etc.""" + homepage = "http://scikit-image.org/" url = "https://pypi.python.org/packages/source/s/scikit-image/scikit-image-0.12.3.tar.gz" @@ -34,7 +37,7 @@ class PyScikitImage(Package): extends('python', ignore=r'bin/.*\.py$') depends_on('py-dask') - depends_on('py-pillow') + depends_on('pil') depends_on('py-networkx') depends_on('py-six') depends_on('py-scipy') diff --git a/var/spack/repos/builtin/packages/py-unittest2/package.py b/var/spack/repos/builtin/packages/py-unittest2/package.py new file mode 100644 index 0000000000..f669a500ec --- /dev/null +++ b/var/spack/repos/builtin/packages/py-unittest2/package.py @@ -0,0 +1,41 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class PyUnittest2(Package): + """unittest2 is a backport of the new features added to the unittest + testing framework in Python 2.7 and onwards.""" + + homepage = "https://pypi.python.org/pypi/unittest2" + url = "https://pypi.python.org/packages/source/u/unittest2/unittest2-1.1.0.tar.gz" + + version('1.1.0', 'f72dae5d44f091df36b6b513305ea000') + + extends('python') + depends_on('py-setuptools') + + def install(self, spec, prefix): + python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-unittest2py3k/package.py b/var/spack/repos/builtin/packages/py-unittest2py3k/package.py new file mode 100644 index 0000000000..ca857395fb --- /dev/null +++ b/var/spack/repos/builtin/packages/py-unittest2py3k/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 PyUnittest2py3k(Package): + """unittest2 is a backport of the new features added to the unittest + testing framework in Python 2.7 and 3.2. This is a Python 3 compatible + version of unittest2.""" + + homepage = "https://pypi.python.org/pypi/unittest2py3k" + url = "https://pypi.python.org/packages/source/u/unittest2py3k/unittest2py3k-0.5.1.tar.gz" + + version('0.5.1', '8824ff92044310d9365f90d892bf0f09') + + extends('python') + depends_on('py-setuptools') + + def install(self, spec, prefix): + python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/python/package.py b/var/spack/repos/builtin/packages/python/package.py index b6a62bf742..8033c52b91 100644 --- a/var/spack/repos/builtin/packages/python/package.py +++ b/var/spack/repos/builtin/packages/python/package.py @@ -203,8 +203,10 @@ class Python(Package): r'site-packages/site[^/]*\.pyc?$', r'site-packages/__pycache__/site[^/]*\.pyc?$' ]) + if ext_pkg.name != 'py-pygments': + patterns.append(r'bin/pygmentize$') if ext_pkg.name != 'py-numpy': - patterns.append(r'bin/f2py$') + patterns.append(r'bin/f2py3?$') return match_predicate(ignore_arg, patterns) 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-dbi/package.py b/var/spack/repos/builtin/packages/r-dbi/package.py new file mode 100644 index 0000000000..a1e06d5100 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-dbi/package.py @@ -0,0 +1,43 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RDbi(Package): + """A database interface definition for communication between R and + relational database management systems. All classes in this package are + virtual and need to be extended by the various R/DBMS implementations.""" + + homepage = "https://github.com/rstats-db/DBI" + url = "https://cran.r-project.org/src/contrib/DBI_0.4-1.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/DBI" + + version('0.4-1', 'c7ee8f1c5037c2284e99c62698d0f087') + + 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-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-foreign/package.py b/var/spack/repos/builtin/packages/r-foreign/package.py new file mode 100644 index 0000000000..df38fc5680 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-foreign/package.py @@ -0,0 +1,43 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RForeign(Package): + """Functions for reading and writing data stored by some versions of Epi + Info, Minitab, S, SAS, SPSS, Stata, Systat and Weka and for reading and + writing some dBase files.""" + + homepage = "https://cran.r-project.org/web/packages/foreign/index.html" + url = "https://cran.r-project.org/src/contrib/foreign_0.8-66.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/foreign" + + version('0.8-66', 'ff12190f4631dca31e30ca786c2c8f62') + + 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-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-rjava/package.py b/var/spack/repos/builtin/packages/r-rjava/package.py new file mode 100644 index 0000000000..0ce0942602 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-rjava/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 RRjava(Package): + """Low-level interface to Java VM very much like .C/.Call and friends. + Allows creation of objects, calling methods and accessing fields.""" + + homepage = "http://www.rforge.net/rJava/" + url = "https://cran.r-project.org/src/contrib/rJava_0.9-8.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/rJava" + + version('0.9-8', '51ae0d690ceed056ebe7c4be71fc6c7a') + + 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-rmysql/package.py b/var/spack/repos/builtin/packages/r-rmysql/package.py new file mode 100644 index 0000000000..774c166f8b --- /dev/null +++ b/var/spack/repos/builtin/packages/r-rmysql/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 RRmysql(Package): + """Implements 'DBI' Interface to 'MySQL' and 'MariaDB' Databases.""" + + homepage = "https://github.com/rstats-db/rmysql" + url = "https://cran.r-project.org/src/contrib/RMySQL_0.10.9.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/RMySQL" + + version('0.10.9', '3628200a1864ac3005cfd55cc7cde17a') + + extends('R') + + depends_on('r-DBI') + depends_on('mariadb') + + 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-rodbc/package.py b/var/spack/repos/builtin/packages/r-rodbc/package.py new file mode 100644 index 0000000000..9cc9aebd9a --- /dev/null +++ b/var/spack/repos/builtin/packages/r-rodbc/package.py @@ -0,0 +1,43 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RRodbc(Package): + """An ODBC database interface.""" + + homepage = "https://cran.rstudio.com/web/packages/RODBC/" + url = "https://cran.rstudio.com/src/contrib/RODBC_1.3-13.tar.gz" + list_url = "https://cran.rstudio.com/src/contrib/Archive/RODBC" + + version('1.3-13', 'c52ef9139c2ed85adc53ad6effa7d68e') + + extends('R') + + depends_on('unixODBC') + + 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-rpostgresql/package.py b/var/spack/repos/builtin/packages/r-rpostgresql/package.py new file mode 100644 index 0000000000..83c9b85525 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-rpostgresql/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 RRpostgresql(Package): + """Database interface and PostgreSQL driver for R This package provides a + Database Interface (DBI) compliant driver for R to access PostgreSQL + database systems. In order to build and install this package from source, + PostgreSQL itself must be present your system to provide PostgreSQL + functionality via its libraries and header files. These files are provided + as postgresql-devel package under some Linux distributions. On Microsoft + Windows system the attached libpq library source will be used. A wiki and + issue tracking system for the package are available at Google Code at + https://code.google.com/p/rpostgresql/.""" + + homepage = "https://code.google.com/p/rpostgresql/" + url = "https://cran.r-project.org/src/contrib/RPostgreSQL_0.4-1.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/RPostgreSQL" + + version('0.4-1', 'e7b22e212afbb2cbb88bab937f93e55a') + + extends('R') + + depends_on('r-DBI') + depends_on('postgresql') + + 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-rsqlite/package.py b/var/spack/repos/builtin/packages/r-rsqlite/package.py new file mode 100644 index 0000000000..9602f6d927 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-rsqlite/package.py @@ -0,0 +1,45 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RRsqlite(Package): + """This package embeds the SQLite database engine in R and provides an + interface compliant with the DBI package. The source for the SQLite engine + (version 3.8.6) is included.""" + + homepage = "https://github.com/rstats-db/RSQLite" + url = "https://cran.r-project.org/src/contrib/RSQLite_1.0.0.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/RSQLite" + + version('1.0.0', 'e6cbe2709612b687c13a10d30c7bad45') + + extends('R') + + depends_on('r-DBI') + + 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/r-xlconnect/package.py b/var/spack/repos/builtin/packages/r-xlconnect/package.py new file mode 100644 index 0000000000..919291a023 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-xlconnect/package.py @@ -0,0 +1,45 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RXlconnect(Package): + """Provides comprehensive functionality to read, write and format Excel + data.""" + + homepage = "http://miraisolutions.wordpress.com/" + url = "https://cran.r-project.org/src/contrib/XLConnect_0.2-11.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/XLConnect" + + version('0.2-11', '9d1769a103cda05665df399cc335017d') + + extends('R') + + depends_on('r-XLConnectJars') + depends_on('r-rJava') + + 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-xlconnectjars/package.py b/var/spack/repos/builtin/packages/r-xlconnectjars/package.py new file mode 100644 index 0000000000..15d08cc5af --- /dev/null +++ b/var/spack/repos/builtin/packages/r-xlconnectjars/package.py @@ -0,0 +1,43 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RXlconnectjars(Package): + """Provides external JAR dependencies for the XLConnect package.""" + + homepage = "http://miraisolutions.wordpress.com/" + url = "https://cran.r-project.org/src/contrib/XLConnectJars_0.2-9.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/XLConnectJars" + + version('0.2-9', 'e6d6b1acfede26acaa616ee421bd30fb') + + extends('R') + + depends_on('r-rJava') + + 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-xlsx/package.py b/var/spack/repos/builtin/packages/r-xlsx/package.py new file mode 100644 index 0000000000..0aac6cdd1f --- /dev/null +++ b/var/spack/repos/builtin/packages/r-xlsx/package.py @@ -0,0 +1,45 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RXlsx(Package): + """Provide R functions to read/write/format Excel 2007 and Excel + 97/2000/XP/2003 file formats.""" + + homepage = "http://code.google.com/p/rexcel/" + url = "https://cran.rstudio.com/src/contrib/xlsx_0.5.7.tar.gz" + list_url = "https://cran.rstudio.com/src/contrib/Archive/xlsx" + + version('0.5.7', '36b1b16f29c54b6089b1dae923180dd5') + + extends('R') + + depends_on('r-rJava') + depends_on('r-xlsxjars') + + 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-xlsxjars/package.py b/var/spack/repos/builtin/packages/r-xlsxjars/package.py new file mode 100644 index 0000000000..cff6e7427e --- /dev/null +++ b/var/spack/repos/builtin/packages/r-xlsxjars/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 RXlsxjars(Package): + """The xlsxjars package collects all the external jars required for the + xlxs package. This release corresponds to POI 3.10.1.""" + + homepage = "https://cran.rstudio.com/web/packages/xlsxjars/index.html" + url = "https://cran.rstudio.com/src/contrib/xlsxjars_0.6.1.tar.gz" + list_url = "https://cran.rstudio.com/src/contrib/Archive/xlsxjars" + + version('0.6.1', '5a1721d5733cb42f3a29e3f353e39166') + + extends('R') + + depends_on('r-rJava') + + 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/scotch/package.py b/var/spack/repos/builtin/packages/scotch/package.py index 3c2b4993ac..2f6e42c439 100644 --- a/var/spack/repos/builtin/packages/scotch/package.py +++ b/var/spack/repos/builtin/packages/scotch/package.py @@ -171,15 +171,13 @@ class Scotch(Package): target == 'ptscotch')) make(target, parallel=can_make_parallel) - # todo change this to take into account darwin systems - lib_ext = '.so' if '+shared' in self.spec else '.a' + lib_ext = dso_suffix if '+shared' in self.spec else 'a' # It seams easier to remove metis wrappers from the folder that will be # installed than to tweak the Makefiles if '+metis' not in self.spec: with working_dir('lib'): - lib_ext = '.so' if '+shared' in self.spec else '.a' - force_remove('libscotchmetis{0}'.format(lib_ext)) - force_remove('libptscotchparmetis{0}'.format(lib_ext)) + force_remove('libscotchmetis.{0}'.format(lib_ext)) + force_remove('libptscotchparmetis.{0}'.format(lib_ext)) with working_dir('include'): force_remove('metis.h') @@ -187,8 +185,8 @@ class Scotch(Package): if '~esmumps' in self.spec and self.spec.version < Version('6.0.0'): with working_dir('lib'): - force_remove('libesmumps{0}'.format(lib_ext)) - force_remove('libptesmumps{0}'.format(lib_ext)) + force_remove('libesmumps.{0}'.format(lib_ext)) + force_remove('libptesmumps.{0}'.format(lib_ext)) with working_dir('include'): force_remove('esmumps.h') diff --git a/var/spack/repos/builtin/packages/serf/package.py b/var/spack/repos/builtin/packages/serf/package.py index 817db68241..ff6fd2da9b 100644 --- a/var/spack/repos/builtin/packages/serf/package.py +++ b/var/spack/repos/builtin/packages/serf/package.py @@ -28,10 +28,11 @@ from spack import * class Serf(Package): """Apache Serf - a high performance C-based HTTP client library built upon the Apache Portable Runtime (APR) library""" + homepage = 'https://serf.apache.org/' url = 'https://archive.apache.org/dist/serf/serf-1.3.8.tar.bz2' - version('1.3.8', '1d45425ca324336ce2f4ae7d7b4cfbc5567c5446') + version('1.3.8', '1d45425ca324336ce2f4ae7d7b4cfbc5567c5446') depends_on('apr') depends_on('apr-util') @@ -41,8 +42,6 @@ class Serf(Package): depends_on('zlib') def install(self, spec, prefix): - scons = which("scons") - options = ['PREFIX=%s' % prefix] options.append('APR=%s' % spec['apr'].prefix) options.append('APU=%s' % spec['apr-util'].prefix) 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/sundials/package.py b/var/spack/repos/builtin/packages/sundials/package.py index ba2340f74c..c55198a850 100644 --- a/var/spack/repos/builtin/packages/sundials/package.py +++ b/var/spack/repos/builtin/packages/sundials/package.py @@ -23,17 +23,151 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## from spack import * +import os + class Sundials(Package): - """SUNDIALS (SUite of Nonlinear and DIfferential/ALgebraic equation Solvers)""" + """SUNDIALS (SUite of Nonlinear and DIfferential/ALgebraic equation + Solvers)""" + homepage = "http://computation.llnl.gov/casc/sundials/" - url = "http://computation.llnl.gov/casc/sundials/download/code/sundials-2.5.0.tar.gz" + url = "http://computation.llnl.gov/projects/sundials-suite-nonlinear-differential-algebraic-equation-solvers/download/sundials-2.6.2.tar.gz" + + version('2.6.2', '3deeb0ede9f514184c6bd83ecab77d95') - version('2.5.0', 'aba8b56eec600de3109cfb967aa3ba0f') + variant('mpi', default=True, description='Enable MPI support') + variant('lapack', default=True, description='Build with external BLAS/LAPACK libraries') + variant('klu', default=False, description='Build with SuiteSparse KLU libraries') + variant('superlu', default=False, description='Build with SuperLU_MT libraries') + variant('openmp', default=False, description='Enable OpenMP support') + variant('pthread', default=True, description='Enable POSIX threads support') - depends_on("mpi") + depends_on('mpi', when='+mpi') + depends_on('blas', when='+lapack') + depends_on('lapack', when='+lapack') + depends_on('suite-sparse', when='+klu') + depends_on('superlu-mt+openmp', when='+superlu+openmp') + depends_on('superlu-mt+pthread', when='+superlu+pthread') def install(self, spec, prefix): - configure("--prefix=%s" % prefix) - make() - make("install") + cmake_args = std_cmake_args[:] + cmake_args.extend([ + '-DBUILD_SHARED_LIBS=ON', + '-DCMAKE_C_FLAGS=-fPIC', + '-DCMAKE_Fortran_FLAGS=-fPIC', + '-DEXAMPLES_ENABLE=ON', + '-DEXAMPLES_INSTALL=ON', + '-DFCMIX_ENABLE=ON' + ]) + + # MPI support + if '+mpi' in spec: + cmake_args.extend([ + '-DMPI_ENABLE=ON', + '-DMPI_MPICC={0}'.format(spec['mpi'].mpicc), + '-DMPI_MPIF77={0}'.format(spec['mpi'].mpif77) + ]) + else: + cmake_args.append('-DMPI_ENABLE=OFF') + + # Building with LAPACK and BLAS + if '+lapack' in spec: + cmake_args.extend([ + '-DLAPACK_ENABLE=ON', + '-DLAPACK_LIBRARIES={0};{1}'.format( + spec['lapack'].lapack_shared_lib, + spec['blas'].blas_shared_lib + ) + ]) + else: + cmake_args.append('-DLAPACK_ENABLE=OFF') + + # Building with KLU + if '+klu' in spec: + cmake_args.extend([ + '-DKLU_ENABLE=ON', + '-DKLU_INCLUDE_DIR={0}'.format( + spec['suite-sparse'].prefix.include), + '-DKLU_LIBRARY_DIR={0}'.format( + spec['suite-sparse'].prefix.lib) + ]) + else: + cmake_args.append('-DKLU_ENABLE=OFF') + + # Building with SuperLU_MT + if '+superlu' in spec: + cmake_args.extend([ + '-DSUPERLUMT_ENABLE=ON', + '-DSUPERLUMT_INCLUDE_DIR={0}'.format( + spec['superlu-mt'].prefix.include), + '-DSUPERLUMT_LIBRARY_DIR={0}'.format( + spec['superlu-mt'].prefix.lib) + ]) + if '+openmp' in spec: + cmake_args.append('-DSUPERLUMT_THREAD_TYPE=OpenMP') + elif '+pthread' in spec: + cmake_args.append('-DSUPERLUMT_THREAD_TYPE=Pthread') + else: + msg = 'You must choose either +openmp or +pthread when ' + msg += 'building with SuperLU_MT' + raise RuntimeError(msg) + else: + cmake_args.append('-DSUPERLUMT_ENABLE=OFF') + + # OpenMP support + if '+openmp' in spec: + cmake_args.append('-DOPENMP_ENABLE=ON') + else: + cmake_args.append('-DOPENMP_ENABLE=OFF') + + # POSIX threads support + if '+pthread' in spec: + cmake_args.append('-DPTHREAD_ENABLE=ON') + else: + cmake_args.append('-DPTHREAD_ENABLE=OFF') + + with working_dir('build', create=True): + cmake('..', *cmake_args) + + make() + make('install') + + install('LICENSE', prefix) + + self.filter_compilers() + + def filter_compilers(self): + """Run after install to tell the Makefiles to use + the compilers that Spack built the package with. + + If this isn't done, they'll have CC, CPP, and F77 set to + Spack's generic cc and f77. We want them to be bound to + whatever compiler they were built with.""" + + kwargs = {'ignore_absent': True, 'backup': False, 'string': True} + dirname = os.path.join(self.prefix, 'examples') + + cc_files = [ + 'arkode/C_serial/Makefile', 'arkode/C_parallel/Makefile', + 'cvode/serial/Makefile', 'cvode/parallel/Makefile', + 'cvodes/serial/Makefile', 'cvodes/parallel/Makefile', + 'ida/serial/Makefile', 'ida/parallel/Makefile', + 'idas/serial/Makefile', 'idas/parallel/Makefile', + 'kinsol/serial/Makefile', 'kinsol/parallel/Makefile', + 'nvector/serial/Makefile', 'nvector/parallel/Makefile', + 'nvector/pthreads/Makefile' + ] + + f77_files = [ + 'arkode/F77_serial/Makefile', 'cvode/fcmix_serial/Makefile', + 'ida/fcmix_serial/Makefile', 'ida/fcmix_pthreads/Makefile', + 'kinsol/fcmix_serial/Makefile' + ] + + for filename in cc_files: + filter_file(os.environ['CC'], self.compiler.cc, + os.path.join(dirname, filename), **kwargs) + + for filename in f77_files: + filter_file(os.environ['F77'], self.compiler.f77, + os.path.join(dirname, filename), **kwargs) 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-mt/package.py b/var/spack/repos/builtin/packages/superlu-mt/package.py new file mode 100644 index 0000000000..5a9429d6e5 --- /dev/null +++ b/var/spack/repos/builtin/packages/superlu-mt/package.py @@ -0,0 +1,134 @@ +############################################################################## +# 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 glob +import os + + +class SuperluMt(Package): + """SuperLU is a general purpose library for the direct solution of large, + sparse, nonsymmetric systems of linear equations on high performance + machines. SuperLU_MT is designed for shared memory parallel machines.""" + + homepage = "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/#superlu_mt" + url = "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/superlu_mt_3.1.tar.gz" + + version('3.1', '06ac62f1b4b7d17123fffa0d0c315e91') + + variant('blas', default=True, description='Build with external BLAS library') + + # Must choose one or the other + variant('openmp', default=False, description='Build with OpenMP support') + variant('pthread', default=True, description='Build with POSIX threads support') + + # NOTE: must link with a single-threaded BLAS library + depends_on('blas', when='+blas') + + # Cannot be built in parallel + parallel = False + + def configure(self, spec): + # Validate chosen variants + if '+openmp' in spec and '+pthread' in spec: + msg = 'You cannot choose both +openmp and +pthread' + raise RuntimeError(msg) + if '~openmp' in spec and '~pthread' in spec: + msg = 'You must choose either +openmp or +pthread' + raise RuntimeError(msg) + + # List of configuration options + config = [] + + # The machine (platform) identifier to append to the library names + if '+openmp' in spec: + # OpenMP + config.extend([ + 'PLAT = _OPENMP', + 'TMGLIB = libtmglib.a', + 'MPLIB = {0}'.format(self.compiler.openmp_flag), + 'CFLAGS = {0}'.format(self.compiler.openmp_flag), + 'FFLAGS = {0}'.format(self.compiler.openmp_flag) + ]) + elif '+pthread' in spec: + # POSIX threads + config.extend([ + 'PLAT = _PTHREAD', + 'TMGLIB = libtmglib$(PLAT).a', + 'MPLIB = -lpthread' + ]) + + # The BLAS library + # NOTE: must link with a single-threaded BLAS library + if '+blas' in spec: + config.extend([ + 'BLASDEF = -DUSE_VENDOR_BLAS', + 'BLASLIB = -L{0} -lblas'.format(spec['blas'].prefix.lib) + ]) + else: + config.append('BLASLIB = ../lib/libblas$(PLAT).a') + + # Generic options + config.extend([ + # The name of the libraries to be created/linked to + 'SUPERLULIB = libsuperlu_mt$(PLAT).a', + 'MATHLIB = -lm', + # The archiver and the flag(s) to use when building archives + 'ARCH = ar', + 'ARCHFLAGS = cr', + 'RANLIB = {0}'.format('ranlib' if which('ranlib') else 'echo'), + # Definitions used by CPP + 'PREDEFS = -D_$(PLAT)', + # Compilers and flags + 'CC = {0}'.format(os.environ['CC']), + 'CFLAGS += $(PREDEFS) -D_LONGINT', + 'NOOPTS = -O0', + 'FORTRAN = {0}'.format(os.environ['FC']), + 'LOADER = {0}'.format(os.environ['CC']), + # C preprocessor defs for compilation + 'CDEFS = -DAdd_' + ]) + + # Write configuration options to include file + with open('make.inc', 'w') as inc: + for option in config: + inc.write('{0}\n'.format(option)) + + def install(self, spec, prefix): + # Set up make include file manually + self.configure(spec) + + # BLAS needs to be compiled separately if using internal BLAS library + if '+blas' not in spec: + make('blaslib') + + make() + + # Install manually + install_tree('lib', prefix.lib) + + headers = glob.glob(join_path('SRC', '*.h')) + mkdir(prefix.include) + for h in headers: + install(h, prefix.include) 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/swiftsim/package.py b/var/spack/repos/builtin/packages/swiftsim/package.py new file mode 100644 index 0000000000..42e8fb466a --- /dev/null +++ b/var/spack/repos/builtin/packages/swiftsim/package.py @@ -0,0 +1,77 @@ +############################################################################## +# 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 llnl.util.tty as tty + + +class Swiftsim(Package): + """ + SPH With Inter-dependent Fine-grained Tasking (SWIFT) provides + astrophysicists with a state of the art framework to perform + particle based simulations. + """ + + homepage = 'http://icc.dur.ac.uk/swift/' + url = 'http://gitlab.cosma.dur.ac.uk/swift/swiftsim/repository/archive.tar.gz?ref=v0.3.0' + + version('0.3.0', git='https://gitlab.cosma.dur.ac.uk/swift/swiftsim.git', commit='254cc1b563b2f88ddcf437b1f71da123bb9db733') + + variant('mpi', default=True, description='Enable distributed memory parallelism') + + # Build dependencies + depends_on('autoconf') + depends_on('automake') + depends_on('libtool') + depends_on('m4') + # link-time / run-time dependencies + depends_on('mpi', when='+mpi') + depends_on('metis') + depends_on('hdf5~mpi', when='~mpi') + depends_on('hdf5+mpi', when='+mpi') + + def setup_environment(self, spack_env, run_env): + # Needed to be able to download from the Durham gitlab repository + tty.warn('Setting "GIT_SSL_NO_VERIFY=1"') + tty.warn('This is needed to clone SWIFT repository') + spack_env.set('GIT_SSL_NO_VERIFY', 1) + + def install(self, spec, prefix): + # Generate configure from configure.ac + # and Makefile.am + libtoolize() + aclocal() + autoconf() + autogen = Executable('./autogen.sh') + autogen() + + # Configure and install + options = ['--prefix=%s' % prefix, + '--enable-mpi' if '+mpi' in spec else '--disable-mpi', + '--enable-optimization'] + configure(*options) + 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') diff --git a/var/spack/repos/builtin/packages/unixodbc/package.py b/var/spack/repos/builtin/packages/unixodbc/package.py new file mode 100644 index 0000000000..15de127b7e --- /dev/null +++ b/var/spack/repos/builtin/packages/unixodbc/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 Unixodbc(Package): + """ODBC is an open specification for providing application developers with + a predictable API with which to access Data Sources. Data Sources include + SQL Servers and any Data Source with an ODBC Driver.""" + + homepage = "http://www.unixodbc.org/" + url = "ftp://ftp.unixodbc.org/pub/unixODBC/unixODBC-2.3.4.tar.gz" + + version('2.3.4', 'bd25d261ca1808c947cb687e2034be81') + + def install(self, spec, prefix): + configure('--prefix={0}'.format(prefix)) + + make() + make('install') |