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Merge branch 'develop' of https://github.com/LLNL/spack into features/module_refresh

Browse source 
Conflicts:
	share/spack/setup-env.sh
This commit is contained in:
alalazo 2016-07-18 14:12:47 +02:00
commit a96eb7096d
25 changed files with 786 additions and 267 deletions
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9
lib/spack/docs/basic_usage.rst
View file

@ -183,7 +183,7 @@ To uninstall a package and every package that depends on it, you may give the
spack uninstall --dependents mpich
will display a list of all the packages that depends on `mpich` and, upon confirmation,
will display a list of all the packages that depend on `mpich` and, upon confirmation,
will uninstall them in the right order.
A line like
@ -543,11 +543,12 @@ More formally, a spec consists of the following pieces:
* ``+`` or ``-`` or ``~`` Optional variant specifiers (``+debug``,
``-qt``, or ``~qt``) for boolean variants
* ``name=<value>`` Optional variant specifiers that are not restricted to
boolean variants
boolean variants
* ``name=<value>`` Optional compiler flag specifiers. Valid flag names are
``cflags``, ``cxxflags``, ``fflags``, ``cppflags``, ``ldflags``, and ``ldlibs``.
``cflags``, ``cxxflags``, ``fflags``, ``cppflags``, ``ldflags``, and ``ldlibs``.
* ``target=<value> os=<value>`` Optional architecture specifier
(``target=haswell os=CNL10``) * ``^`` Dependency specs (``^callpath@1.1``)
(``target=haswell os=CNL10``)
* ``^`` Dependency specs (``^callpath@1.1``)
There are two things to notice here. The first is that specs are
recursively defined. That is, each dependency after ``^`` is a spec

16
lib/spack/docs/packaging_guide.rst
View file

@ -2627,14 +2627,14 @@ Spack packages with variants similar to already-existing Spack
packages should use the same name for their variants. Standard
variant names are:
======= ======== ========================
Name Default Description
------- -------- ------------------------
shared True Build shared libraries
static Build static libraries
mpi Use MPI
python Build Python extension
------- -------- ------------------------
======= ======== ========================
Name Default Description
======= ======== ========================
shared True Build shared libraries
static Build static libraries
mpi Use MPI
python Build Python extension
======= ======== ========================
If specified in this table, the corresponding default should be used
when declaring a variant.

12
lib/spack/llnl/util/filesystem.py
View file

@ -42,7 +42,7 @@
'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']
'fix_darwin_install_name', 'to_link_flags', 'to_lib_name']
def filter_file(regex, repl, *filenames, **kwargs):
@ -431,6 +431,13 @@ def fix_darwin_install_name(path):
break
def to_lib_name(library):
"""Transforms a path to the library /path/to/lib<name>.xyz into <name>
"""
# Assume libXYZ.suffix
return os.path.basename(library)[3:].split(".")[0]
def to_link_flags(library):
"""Transforms a path to a <library> into linking flags -L<dir> -l<name>.
@ -438,8 +445,7 @@ def to_link_flags(library):
A string of linking flags.
"""
dir = os.path.dirname(library)
# Assume libXYZ.suffix
name = os.path.basename(library)[3:].split(".")[0]
name = to_lib_name(library)
res = '-L%s -l%s' % (dir, name)
return res

6
lib/spack/spack/cmd/create.py
View file

@ -142,9 +142,9 @@ def __call__(self, stage):
# Build dependencies and extensions
dependenciesDict = {
'autotools': "# depends_on('foo')",
'cmake': "depends_on('cmake')",
'scons': "depends_on('scons')",
'python': "extends('python')",
'cmake': "depends_on('cmake', type='build')",
'scons': "depends_on('scons', type='build')",
'python': "extends('python', type=nolink)",
'R': "extends('R')",
'unknown': "# depends_on('foo')"
}

7
lib/spack/spack/cmd/info.py
View file

@ -29,9 +29,11 @@
description = "Get detailed information on a particular package"
def padder(str_list, extra=0):
"""Return a function to pad elements of a list."""
length = max(len(str(s)) for s in str_list) + extra
def pad(string):
string = str(string)
padding = max(0, length - len(string))
@ -40,7 +42,8 @@ def pad(string):
def setup_parser(subparser):
subparser.add_argument('name', metavar="PACKAGE", help="Name of package to get info for.")
subparser.add_argument(
'name', metavar="PACKAGE", help="Name of package to get info for.")
def print_text_info(pkg):
@ -84,7 +87,7 @@ def print_text_info(pkg):
for deptype in ('build', 'link', 'run'):
print
print "%s Dependencies:" % deptype.capitalize()
deps = pkg.dependencies(deptype)
deps = pkg.dependencies_of_type(deptype)
if deps:
colify(deps, indent=4)
else:

25
lib/spack/spack/database.py
View file

@ -60,7 +60,7 @@
_db_dirname = '.spack-db'
# DB version. This is stuck in the DB file to track changes in format.
_db_version = Version('0.9.1')
_db_version = Version('0.9.2')
# Default timeout for spack database locks is 5 min.
_db_lock_timeout = 60
@ -215,14 +215,10 @@ def _read_spec_from_yaml(self, hash_key, installs, parent_key=None):
# Add dependencies from other records in the install DB to
# form a full spec.
if 'dependencies' in spec_dict[spec.name]:
for dep in spec_dict[spec.name]['dependencies'].values():
if type(dep) == tuple:
dep_hash, deptypes = dep
else:
dep_hash = dep
deptypes = spack.alldeps
child = self._read_spec_from_yaml(dep_hash, installs, hash_key)
spec._add_dependency(child, deptypes)
yaml_deps = spec_dict[spec.name]['dependencies']
for dname, dhash, dtypes in Spec.read_yaml_dep_specs(yaml_deps):
child = self._read_spec_from_yaml(dhash, installs, hash_key)
spec._add_dependency(child, dtypes)
# Specs from the database need to be marked concrete because
# they represent actual installations.
@ -639,13 +635,14 @@ def _exit(self):
class CorruptDatabaseError(SpackError):
def __init__(self, path, msg=''):
super(CorruptDatabaseError, self).__init__(
"Spack database is corrupt: %s. %s." + \
"Try running `spack reindex` to fix." % (path, msg))
"Spack database is corrupt: %s. %s." % (path, msg),
"Try running `spack reindex` to fix.")
class InvalidDatabaseVersionError(SpackError):
def __init__(self, expected, found):
super(InvalidDatabaseVersionError, self).__init__(
"Expected database version %s but found version %s." + \
"Try running `spack reindex` to fix." %
(expected, found))
"Expected database version %s but found version %s."
% (expected, found),
"`spack reindex` may fix this, or you may need a newer "
"Spack version.")

13
lib/spack/spack/directory_layout.py
View file

@ -34,6 +34,7 @@
import llnl.util.tty as tty
from llnl.util.filesystem import join_path, mkdirp
import spack
from spack.spec import Spec
from spack.error import SpackError
@ -223,8 +224,14 @@ def write_spec(self, spec, path):
def read_spec(self, path):
"""Read the contents of a file and parse them as a spec"""
try:
with open(path) as f:
spec = Spec.from_yaml(f)
except Exception as e:
if spack.debug:
raise
raise SpecReadError(
'Unable to read file: %s' % path, 'Cause: ' + str(e))
# Specs read from actual installations are always concrete
spec._mark_concrete()
@ -456,10 +463,12 @@ def __init__(self, path):
"Install path %s already exists!")
class SpecReadError(DirectoryLayoutError):
"""Raised when directory layout can't read a spec."""
class InvalidExtensionSpecError(DirectoryLayoutError):
"""Raised when an extension file has a bad spec in it."""
def __init__(self, message):
super(InvalidExtensionSpecError, self).__init__(message)
class ExtensionAlreadyInstalledError(DirectoryLayoutError):

113
lib/spack/spack/package.py
View file

@ -37,7 +37,6 @@
import re
import textwrap
import time
import glob
import string
import llnl.util.tty as tty
@ -62,10 +61,10 @@
from spack.stage import Stage, ResourceStage, StageComposite
from spack.util.compression import allowed_archive
from spack.util.environment import dump_environment
from spack.util.executable import ProcessError, Executable, which
from spack.util.executable import ProcessError, which
from spack.version import *
from spack import directory_layout
from urlparse import urlparse
"""Allowed URL schemes for spack packages."""
_ALLOWED_URL_SCHEMES = ["http", "https", "ftp", "file", "git"]
@ -410,7 +409,6 @@ 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
@ -565,6 +563,11 @@ def fetcher(self):
def fetcher(self, f):
self._fetcher = f
def dependencies_of_type(self, *deptypes):
"""Get subset of the dependencies with certain types."""
return dict((name, conds) for name, conds in self.dependencies.items()
if any(d in self._deptypes[name] for d in deptypes))
@property
def extendee_spec(self):
"""
@ -687,7 +690,7 @@ def installed_dependents(self):
if self.name == spec.name:
continue
# XXX(deptype): Should build dependencies not count here?
#for dep in spec.traverse(deptype=('run')):
# for dep in spec.traverse(deptype=('run')):
for dep in spec.traverse(deptype=spack.alldeps):
if self.spec == dep:
dependents.append(spec)
@ -699,7 +702,7 @@ def prefix(self):
return self.spec.prefix
@property
#TODO: Change this to architecture
# TODO: Change this to architecture
def compiler(self):
"""Get the spack.compiler.Compiler object used to build this package"""
if not self.spec.concrete:
@ -761,7 +764,6 @@ def do_fetch(self, mirror_only=False):
self.stage.cache_local()
def do_stage(self, mirror_only=False):
"""Unpacks the fetched tarball, then changes into the expanded tarball
directory."""
@ -879,6 +881,7 @@ def _resource_stage(self, resource):
return resource_stage_folder
install_phases = set(['configure', 'build', 'install', 'provenance'])
def do_install(self,
keep_prefix=False,
keep_stage=False,
@ -890,7 +893,7 @@ def do_install(self,
fake=False,
explicit=False,
dirty=False,
install_phases = install_phases):
install_phases=install_phases):
"""Called by commands to install a package and its dependencies.
Package implementations should override install() to describe
@ -911,7 +914,8 @@ def do_install(self,
run_tests -- Runn tests within the package's install()
"""
if not self.spec.concrete:
raise ValueError("Can only install concrete packages: %s." % self.spec.name)
raise ValueError("Can only install concrete packages: %s."
% self.spec.name)
# No installation needed if package is external
if self.spec.external:
@ -920,7 +924,8 @@ def do_install(self,
return
# Ensure package is not already installed
if 'install' in install_phases and spack.install_layout.check_installed(self.spec):
layout = spack.install_layout
if 'install' in install_phases and layout.check_installed(self.spec):
tty.msg("%s is already installed in %s" % (self.name, self.prefix))
rec = spack.installed_db.get_record(self.spec)
if (not rec.explicit) and explicit:
@ -1001,20 +1006,17 @@ def build_process():
if 'install' in self.install_phases:
self.sanity_check_prefix()
# Copy provenance into the install directory on success
if 'provenance' in self.install_phases:
log_install_path = spack.install_layout.build_log_path(
self.spec)
env_install_path = spack.install_layout.build_env_path(
self.spec)
packages_dir = spack.install_layout.build_packages_path(
self.spec)
log_install_path = layout.build_log_path(self.spec)
env_install_path = layout.build_env_path(self.spec)
packages_dir = layout.build_packages_path(self.spec)
# Remove first if we're overwriting another build
# (can happen with spack setup)
try:
shutil.rmtree(packages_dir) # log_install_path and env_install_path are inside this
# log_install_path and env_install_path are here
shutil.rmtree(packages_dir)
except:
pass
@ -1041,7 +1043,7 @@ def build_process():
except directory_layout.InstallDirectoryAlreadyExistsError:
if 'install' in install_phases:
# Abort install if install directory exists.
# But do NOT remove it (you'd be overwriting someon else's stuff)
# But do NOT remove it (you'd be overwriting someone's data)
tty.warn("Keeping existing install prefix in place.")
raise
else:
@ -1533,24 +1535,29 @@ def _hms(seconds):
parts.append("%.2fs" % s)
return ' '.join(parts)
class StagedPackage(Package):
"""A Package subclass where the install() is split up into stages."""
def install_setup(self):
"""Creates an spack_setup.py script to configure the package later if we like."""
raise InstallError("Package %s provides no install_setup() method!" % self.name)
"""Creates a spack_setup.py script to configure the package later."""
raise InstallError(
"Package %s provides no install_setup() method!" % self.name)
def install_configure(self):
"""Runs the configure process."""
raise InstallError("Package %s provides no install_configure() method!" % self.name)
raise InstallError(
"Package %s provides no install_configure() method!" % self.name)
def install_build(self):
"""Runs the build process."""
raise InstallError("Package %s provides no install_build() method!" % self.name)
raise InstallError(
"Package %s provides no install_build() method!" % self.name)
def install_install(self):
"""Runs the install process."""
raise InstallError("Package %s provides no install_install() method!" % self.name)
raise InstallError(
"Package %s provides no install_install() method!" % self.name)
def install(self, spec, prefix):
if 'setup' in self.install_phases:
@ -1567,9 +1574,10 @@ def install(self, spec, prefix):
else:
# Create a dummy file so the build doesn't fail.
# That way, the module file will also be created.
with open(os.path.join(prefix, 'dummy'), 'w') as fout:
with open(os.path.join(prefix, 'dummy'), 'w'):
pass
# stackoverflow.com/questions/12791997/how-do-you-do-a-simple-chmod-x-from-within-python
def make_executable(path):
mode = os.stat(path).st_mode
@ -1577,9 +1585,7 @@ def make_executable(path):
os.chmod(path, mode)
class CMakePackage(StagedPackage):
def make_make(self):
import multiprocessing
# number of jobs spack will to build with.
@ -1593,37 +1599,41 @@ def make_make(self):
return make
def configure_args(self):
"""Returns package-specific arguments to be provided to the configure command."""
"""Returns package-specific arguments to be provided to
the configure command.
"""
return list()
def configure_env(self):
"""Returns package-specific environment under which the configure command should be run."""
"""Returns package-specific environment under which the
configure command should be run.
"""
return dict()
def spack_transitive_include_path(self):
def transitive_inc_path(self):
return ';'.join(
os.path.join(dep, 'include')
for dep in os.environ['SPACK_DEPENDENCIES'].split(os.pathsep)
)
def install_setup(self):
cmd = [str(which('cmake'))] + \
spack.build_environment.get_std_cmake_args(self) + \
['-DCMAKE_INSTALL_PREFIX=%s' % os.environ['SPACK_PREFIX'],
cmd = [str(which('cmake'))]
cmd += spack.build_environment.get_std_cmake_args(self)
cmd += ['-DCMAKE_INSTALL_PREFIX=%s' % os.environ['SPACK_PREFIX'],
'-DCMAKE_C_COMPILER=%s' % os.environ['SPACK_CC'],
'-DCMAKE_CXX_COMPILER=%s' % os.environ['SPACK_CXX'],
'-DCMAKE_Fortran_COMPILER=%s' % os.environ['SPACK_FC']] + \
self.configure_args()
'-DCMAKE_Fortran_COMPILER=%s' % os.environ['SPACK_FC']]
cmd += self.configure_args()
env = dict()
env['PATH'] = os.environ['PATH']
env['SPACK_TRANSITIVE_INCLUDE_PATH'] = self.spack_transitive_include_path()
env['CMAKE_PREFIX_PATH'] = os.environ['CMAKE_PREFIX_PATH']
env = {
'PATH': os.environ['PATH'],
'SPACK_TRANSITIVE_INCLUDE_PATH': self.transitive_inc_path(),
'CMAKE_PREFIX_PATH': os.environ['CMAKE_PREFIX_PATH']
}
setup_fname = 'spconfig.py'
with open(setup_fname, 'w') as fout:
fout.write(\
r"""#!%s
fout.write(r"""#!%s
#
import sys
@ -1639,34 +1649,39 @@ def cmdlist(str):
for name in env_vars:
val = env[name]
if string.find(name, 'PATH') < 0:
fout.write('env[%s] = %s\n' % (repr(name),repr(val)))
fout.write('env[%s] = %s\n' % (repr(name), repr(val)))
else:
if name == 'SPACK_TRANSITIVE_INCLUDE_PATH':
sep = ';'
else:
sep = ':'
fout.write('env[%s] = "%s".join(cmdlist("""\n' % (repr(name),sep))
fout.write('env[%s] = "%s".join(cmdlist("""\n'
% (repr(name), sep))
for part in string.split(val, sep):
fout.write(' %s\n' % part)
fout.write('"""))\n')
fout.write("env['CMAKE_TRANSITIVE_INCLUDE_PATH'] = env['SPACK_TRANSITIVE_INCLUDE_PATH'] # Deprecated\n")
fout.write("env['CMAKE_TRANSITIVE_INCLUDE_PATH'] = "
"env['SPACK_TRANSITIVE_INCLUDE_PATH'] # Deprecated\n")
fout.write('\ncmd = cmdlist("""\n')
fout.write('%s\n' % cmd[0])
for arg in cmd[1:]:
fout.write(' %s\n' % arg)
fout.write('""") + sys.argv[1:]\n')
fout.write('\nproc = subprocess.Popen(cmd, env=env)\nproc.wait()\n')
fout.write('\nproc = subprocess.Popen(cmd, env=env)\n')
fout.write('proc.wait()\n')
make_executable(setup_fname)
def install_configure(self):
cmake = which('cmake')
with working_dir(self.build_directory, create=True):
os.environ.update(self.configure_env())
os.environ['SPACK_TRANSITIVE_INCLUDE_PATH'] = self.spack_transitive_include_path()
options = self.configure_args() + spack.build_environment.get_std_cmake_args(self)
env = os.environ
env.update(self.configure_env())
env['SPACK_TRANSITIVE_INCLUDE_PATH'] = self.transitive_inc_path()
options = self.configure_args()
options += spack.build_environment.get_std_cmake_args(self)
cmake(self.source_directory, *options)
def install_build(self):

268
lib/spack/spack/spec.py
View file

@ -96,7 +96,6 @@
expansion when it is the first character in an id typed on the command line.
"""
import sys
import itertools
import hashlib
import base64
import imp
@ -116,8 +115,6 @@
import spack.error
import spack.compilers as compilers
# TODO: move display_specs to some other location.
from spack.cmd.find import display_specs
from spack.version import *
from spack.util.string import *
from spack.util.prefix import Prefix
@ -155,6 +152,7 @@
every time we call str()"""
_any_version = VersionList([':'])
# Special types of dependencies.
alldeps = ('build', 'link', 'run')
nolink = ('build', 'run')
@ -296,10 +294,15 @@ def __repr__(self):
@key_ordering
class DependencySpec(object):
"""
Dependencies have conditions in which they apply.
"""Dependencies can be one (or more) of several types:
This stores both what is depended on and why it is a dependency.
- build: needs to be in the PATH at build time.
- link: is linked to and added to compiler flags.
- run: needs to be in the PATH for the package to run.
Fields:
- spec: the spack.spec.Spec description of a dependency.
- deptypes: strings representing the type of dependency this is.
"""
def __init__(self, spec, deptypes):
self.spec = spec
@ -558,15 +561,15 @@ def dependents(self, deptype=None):
def _find_deps_dict(self, where, deptype):
deptype = self._deptype_norm(deptype)
return [(dep.spec.name, dep)
return dict((dep.spec.name, dep)
for dep in where.values()
if deptype and any(d in deptype for d in dep.deptypes)]
if deptype and any(d in deptype for d in dep.deptypes))
def dependencies_dict(self, deptype=None):
return dict(self._find_deps_dict(self._dependencies, deptype))
return self._find_deps_dict(self._dependencies, deptype)
def dependents_dict(self, deptype=None):
return dict(self._find_deps_dict(self._dependents, deptype))
return self._find_deps_dict(self._dependents, deptype)
#
# Private routines here are called by the parser when building a spec.
@ -644,7 +647,8 @@ def _set_platform(self, value):
mod = imp.load_source(mod_name, path)
class_name = mod_to_class(value)
if not hasattr(mod, class_name):
tty.die('No class %s defined in %s' % (class_name, mod_name))
tty.die(
'No class %s defined in %s' % (class_name, mod_name))
cls = getattr(mod, class_name)
if not inspect.isclass(cls):
tty.die('%s.%s is not a class' % (mod_name, class_name))
@ -667,13 +671,15 @@ def _set_platform(self, value):
def _set_os(self, value):
"""Called by the parser to set the architecture operating system"""
if self.architecture.platform:
self.architecture.platform_os = self.architecture.platform.operating_system(value)
arch = self.architecture
if arch.platform:
arch.platform_os = arch.platform.operating_system(value)
def _set_target(self, value):
"""Called by the parser to set the architecture target"""
if self.architecture.platform:
self.architecture.target = self.architecture.platform.target(value)
arch = self.architecture
if arch.platform:
arch.target = arch.platform.target(value)
def _add_dependency(self, spec, deptypes):
"""Called by the parser to add another spec as a dependency."""
@ -688,7 +694,8 @@ def _add_dependency(self, spec, deptypes):
#
@property
def fullname(self):
return (('%s.%s' % (self.namespace, self.name)) if self.namespace else
return (
('%s.%s' % (self.namespace, self.name)) if self.namespace else
(self.name if self.name else ''))
@property
@ -745,15 +752,15 @@ def concrete(self):
if self._concrete:
return True
self._concrete = bool(not self.virtual
and self.namespace is not None
and self.versions.concrete
and self.variants.concrete
and self.architecture
and self.architecture.concrete
and self.compiler and self.compiler.concrete
and self.compiler_flags.concrete
and self._dependencies.concrete)
self._concrete = bool(not self.virtual and
self.namespace is not None and
self.versions.concrete and
self.variants.concrete and
self.architecture and
self.architecture.concrete and
self.compiler and self.compiler.concrete and
self.compiler_flags.concrete and
self._dependencies.concrete)
return self._concrete
def traverse(self, visited=None, deptype=None, **kwargs):
@ -914,9 +921,11 @@ def to_node_dict(self):
d = {
'parameters': params,
'arch': self.architecture,
'dependencies': dict((d, (deps[d].spec.dag_hash(),
deps[d].deptypes))
for d in sorted(deps.keys()))
'dependencies': dict(
(name, {
'hash': dspec.spec.dag_hash(),
'type': [str(s) for s in dspec.deptypes]})
for name, dspec in deps.items())
}
# Older concrete specs do not have a namespace. Omit for
@ -982,13 +991,33 @@ def from_node_dict(node):
raise SpackRecordError(
"Did not find a valid format for variants in YAML file")
# XXX(deptypes): why are dependencies not meant to be read here?
#for name, dep_info in node['dependencies'].items():
# (dag_hash, deptypes) = dep_info
# spec._dependencies[name] = DependencySpec(dag_hash, deptypes)
# Don't read dependencies here; from_node_dict() is used by
# from_yaml() to read the root *and* each dependency spec.
return spec
@staticmethod
def read_yaml_dep_specs(dependency_dict):
"""Read the DependencySpec portion of a YAML-formatted Spec.
This needs to be backward-compatible with older spack spec
formats so that reindex will work on old specs/databases.
"""
for dep_name, elt in dependency_dict.items():
if isinstance(elt, basestring):
# original format, elt is just the dependency hash.
dag_hash, deptypes = elt, ['build', 'link']
elif isinstance(elt, tuple):
# original deptypes format: (used tuples, not future-proof)
dag_hash, deptypes = elt
elif isinstance(elt, dict):
# new format: elements of dependency spec are keyed.
dag_hash, deptypes = elt['hash'], elt['type']
else:
raise SpecError("Couldn't parse dependency types in spec.")
yield dep_name, dag_hash, list(deptypes)
@staticmethod
def from_yaml(stream):
"""Construct a spec from YAML.
@ -1000,27 +1029,30 @@ def from_yaml(stream):
represent more than the DAG does.
"""
deps = {}
spec = None
try:
yfile = yaml.load(stream)
except MarkedYAMLError, e:
raise SpackYAMLError("error parsing YAML spec:", str(e))
for node in yfile['spec']:
name = next(iter(node))
dep = Spec.from_node_dict(node)
if not spec:
spec = dep
deps[dep.name] = dep
nodes = yfile['spec']
for node in yfile['spec']:
# Read nodes out of list. Root spec is the first element;
# dependencies are the following elements.
dep_list = [Spec.from_node_dict(node) for node in nodes]
if not dep_list:
raise SpecError("YAML spec contains no nodes.")
deps = dict((spec.name, spec) for spec in dep_list)
spec = dep_list[0]
for node in nodes:
# get dependency dict from the node.
name = next(iter(node))
for dep_name, (dep, deptypes) in \
node[name]['dependencies'].items():
deps[name]._dependencies[dep_name] = \
DependencySpec(deps[dep_name], deptypes)
yaml_deps = node[name]['dependencies']
for dname, dhash, dtypes in Spec.read_yaml_dep_specs(yaml_deps):
# Fill in dependencies by looking them up by name in deps dict
deps[name]._dependencies[dname] = DependencySpec(
deps[dname], set(dtypes))
return spec
def _concretize_helper(self, presets=None, visited=None):
@ -1171,14 +1203,16 @@ def _expand_virtual_packages(self):
def feq(cfield, sfield):
return (not cfield) or (cfield == sfield)
if replacement is spec or (feq(replacement.name, spec.name) and
if replacement is spec or (
feq(replacement.name, spec.name) and
feq(replacement.versions, spec.versions) and
feq(replacement.compiler, spec.compiler) and
feq(replacement.architecture, spec.architecture) and
feq(replacement._dependencies, spec._dependencies) and
feq(replacement.variants, spec.variants) and
feq(replacement.external, spec.external) and
feq(replacement.external_module, spec.external_module)):
feq(replacement.external_module,
spec.external_module)):
continue
# Refine this spec to the candidate. This uses
# replace_with AND dup so that it can work in
@ -1235,10 +1269,10 @@ def concretize(self):
if s.namespace is None:
s.namespace = spack.repo.repo_for_pkg(s.name).namespace
for s in self.traverse(root=False):
if s.external_module:
compiler = spack.compilers.compiler_for_spec(s.compiler, s.architecture)
compiler = spack.compilers.compiler_for_spec(
s.compiler, s.architecture)
for mod in compiler.modules:
load_module(mod)
@ -1505,13 +1539,13 @@ def normalize(self, force=False):
# Ensure first that all packages & compilers in the DAG exist.
self.validate_names()
# Get all the dependencies into one DependencyMap
spec_deps = self.flat_dependencies_with_deptype(copy=False,
deptype_query=alldeps)
spec_deps = self.flat_dependencies_with_deptype(
copy=False, deptype_query=alldeps)
# Initialize index of virtual dependency providers if
# concretize didn't pass us one already
provider_index = ProviderIndex([s.spec for s in spec_deps.values()],
restrict=True)
provider_index = ProviderIndex(
[s.spec for s in spec_deps.values()], restrict=True)
# traverse the package DAG and fill out dependencies according
# to package files & their 'when' specs
@ -1584,20 +1618,17 @@ def constrain(self, other, deps=True):
other.variants[v])
# TODO: Check out the logic here
if self.architecture is not None and other.architecture is not None:
if self.architecture.platform is not None and other.architecture.platform is not None:
if self.architecture.platform != other.architecture.platform:
raise UnsatisfiableArchitectureSpecError(self.architecture,
other.architecture)
if self.architecture.platform_os is not None and other.architecture.platform_os is not None:
if self.architecture.platform_os != other.architecture.platform_os:
raise UnsatisfiableArchitectureSpecError(self.architecture,
other.architecture)
if self.architecture.target is not None and other.architecture.target is not None:
if self.architecture.target != other.architecture.target:
raise UnsatisfiableArchitectureSpecError(self.architecture,
other.architecture)
sarch, oarch = self.architecture, other.architecture
if sarch is not None and oarch is not None:
if sarch.platform is not None and oarch.platform is not None:
if sarch.platform != oarch.platform:
raise UnsatisfiableArchitectureSpecError(sarch, oarch)
if sarch.platform_os is not None and oarch.platform_os is not None:
if sarch.platform_os != oarch.platform_os:
raise UnsatisfiableArchitectureSpecError(sarch, oarch)
if sarch.target is not None and oarch.target is not None:
if sarch.target != oarch.target:
raise UnsatisfiableArchitectureSpecError(sarch, oarch)
changed = False
if self.compiler is not None and other.compiler is not None:
@ -1612,15 +1643,16 @@ def constrain(self, other, deps=True):
changed |= self.compiler_flags.constrain(other.compiler_flags)
old = str(self.architecture)
if self.architecture is None or other.architecture is None:
self.architecture = self.architecture or other.architecture
sarch, oarch = self.architecture, other.architecture
if sarch is None or other.architecture is None:
self.architecture = sarch or oarch
else:
if self.architecture.platform is None or other.architecture.platform is None:
self.architecture.platform = self.architecture.platform or other.architecture.platform
if self.architecture.platform_os is None or other.architecture.platform_os is None:
self.architecture.platform_os = self.architecture.platform_os or other.architecture.platform_os
if self.architecture.target is None or other.architecture.target is None:
self.architecture.target = self.architecture.target or other.architecture.target
if sarch.platform is None or oarch.platform is None:
self.architecture.platform = sarch.platform or oarch.platform
if sarch.platform_os is None or oarch.platform_os is None:
sarch.platform_os = sarch.platform_os or oarch.platform_os
if sarch.target is None or oarch.target is None:
sarch.target = sarch.target or oarch.target
changed |= (str(self.architecture) != old)
if deps:
@ -1751,15 +1783,25 @@ def satisfies(self, other, deps=True, strict=False):
# Architecture satisfaction is currently just string equality.
# If not strict, None means unconstrained.
if self.architecture and other.architecture:
if ((self.architecture.platform and other.architecture.platform and self.architecture.platform != other.architecture.platform) or
(self.architecture.platform_os and other.architecture.platform_os and self.architecture.platform_os != other.architecture.platform_os) or
(self.architecture.target and other.architecture.target and self.architecture.target != other.architecture.target)):
sarch, oarch = self.architecture, other.architecture
if sarch and oarch:
if ((sarch.platform and
oarch.platform and
sarch.platform != oarch.platform) or
(sarch.platform_os and
oarch.platform_os and
sarch.platform_os != oarch.platform_os) or
(sarch.target and
oarch.target and
sarch.target != oarch.target)):
return False
elif strict and ((other.architecture and not self.architecture) or
(other.architecture.platform and not self.architecture.platform) or
(other.architecture.platform_os and not self.architecture.platform_os) or
(other.architecture.target and not self.architecture.target)):
elif strict and ((oarch and not sarch) or
(oarch.platform and not sarch.platform) or
(oarch.platform_os and not sarch.platform_os) or
(oarch.target and not sarch.target)):
return False
if not self.compiler_flags.satisfies(
@ -1841,11 +1883,16 @@ def _dup(self, other, **kwargs):
# We don't count dependencies as changes here
changed = True
if hasattr(self, 'name'):
changed = (self.name != other.name and self.versions != other.versions and \
self.architecture != other.architecture and self.compiler != other.compiler and \
self.variants != other.variants and self._normal != other._normal and \
self.concrete != other.concrete and self.external != other.external and \
self.external_module != other.external_module and self.compiler_flags != other.compiler_flags)
changed = (self.name != other.name and
self.versions != other.versions and
self.architecture != other.architecture and
self.compiler != other.compiler and
self.variants != other.variants and
self._normal != other._normal and
self.concrete != other.concrete and
self.external != other.external and
self.external_module != other.external_module and
self.compiler_flags != other.compiler_flags)
# Local node attributes get copied first.
self.name = other.name
@ -2000,7 +2047,6 @@ def _cmp_node(self):
self.compiler,
self.compiler_flags)
def eq_node(self, other):
"""Equality with another spec, not including dependencies."""
return self._cmp_node() == other._cmp_node()
@ -2196,41 +2242,39 @@ def write(s, c):
def dep_string(self):
return ''.join("^" + dep.format() for dep in self.sorted_deps())
def __cmp__(self, other):
#Package name sort order is not configurable, always goes alphabetical
# Package name sort order is not configurable, always goes alphabetical
if self.name != other.name:
return cmp(self.name, other.name)
#Package version is second in compare order
# Package version is second in compare order
pkgname = self.name
if self.versions != other.versions:
return spack.pkgsort.version_compare(pkgname,
self.versions, other.versions)
return spack.pkgsort.version_compare(
pkgname, self.versions, other.versions)
#Compiler is third
# Compiler is third
if self.compiler != other.compiler:
return spack.pkgsort.compiler_compare(pkgname,
self.compiler, other.compiler)
return spack.pkgsort.compiler_compare(
pkgname, self.compiler, other.compiler)
#Variants
# Variants
if self.variants != other.variants:
return spack.pkgsort.variant_compare(pkgname,
self.variants, other.variants)
return spack.pkgsort.variant_compare(
pkgname, self.variants, other.variants)
#Target
# Target
if self.architecture != other.architecture:
return spack.pkgsort.architecture_compare(pkgname,
self.architecture, other.architecture)
return spack.pkgsort.architecture_compare(
pkgname, self.architecture, other.architecture)
#Dependency is not configurable
# Dependency is not configurable
if self._dependencies != other._dependencies:
return -1 if self._dependencies < other._dependencies else 1
#Equal specs
# Equal specs
return 0
def __str__(self):
return self.format() + self.dep_string()
@ -2244,12 +2288,14 @@ def tree(self, **kwargs):
indent = kwargs.pop('indent', 0)
fmt = kwargs.pop('format', '$_$@$%@+$+$=')
prefix = kwargs.pop('prefix', None)
deptypes = kwargs.pop('deptypes', ('build', 'link'))
check_kwargs(kwargs, self.tree)
out = ""
cur_id = 0
ids = {}
for d, node in self.traverse(order='pre', cover=cover, depth=True):
for d, node in self.traverse(
order='pre', cover=cover, depth=True, deptypes=deptypes):
if prefix is not None:
out += prefix(node)
out += " " * indent
@ -2303,8 +2349,8 @@ def __init__(self):
# Lexer is always the same for every parser.
_lexer = SpecLexer()
class SpecParser(spack.parse.Parser):
class SpecParser(spack.parse.Parser):
def __init__(self):
super(SpecParser, self).__init__(_lexer)
self.previous = None
@ -2357,8 +2403,8 @@ def do_parse(self):
except spack.parse.ParseError, e:
raise SpecParseError(e)
# If the spec has an os or a target and no platform, give it the default platform
# If the spec has an os or a target and no platform, give it
# the default platform
for spec in specs:
for s in spec.traverse():
if s.architecture.os_string or s.architecture.target_string:

62
lib/spack/spack/test/architecture.py
View file

@ -1,7 +1,31 @@
##############################################################################
# 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
##############################################################################
""" Test checks if the architecture class is created correctly and also that
the functions are looking for the correct architecture name
"""
import unittest
import itertools
import os
import platform as py_platform
import spack
@ -14,9 +38,8 @@
from spack.test.mock_packages_test import *
#class ArchitectureTest(unittest.TestCase):
class ArchitectureTest(MockPackagesTest):
class ArchitectureTest(MockPackagesTest):
def setUp(self):
super(ArchitectureTest, self).setUp()
self.platform = spack.architecture.platform()
@ -36,24 +59,22 @@ def test_dict_functions_for_architecture(self):
self.assertEqual(arch, new_arch)
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) )
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()
elif os.path.exists('/bgsys'):
@ -107,10 +128,11 @@ def test_user_input_combination(self):
combinations = itertools.product(os_list, target_list)
results = []
for arch in combinations:
o,t = arch
o, t = arch
spec = Spec("libelf os=%s target=%s" % (o, t))
spec.concretize()
results.append(spec.architecture.platform_os == self.platform.operating_system(o))
results.append(spec.architecture.platform_os ==
self.platform.operating_system(o))
results.append(spec.architecture.target == self.platform.target(t))
res = all(results)

3
share/spack/qa/run-flake8
View file

@ -18,7 +18,7 @@ if [[ ! $flake8 ]]; then
fi
# Check if changed files are flake8 conformant [framework]
changed=$(git diff --name-only develop... | grep '.py$')
changed=$(git diff --name-only --find-renames develop... | grep '.py$')
# Add approved style exemptions to the changed packages.
for file in $changed; do
@ -26,6 +26,7 @@ for file in $changed; do
cp "$file" "$file~"
# Exempt lines with urls and descriptions from overlong line errors.
perl -i -pe 's/^(\s*homepage\s*=.*)$/\1 # NOQA: ignore=E501/' $file
perl -i -pe 's/^(\s*url\s*=.*)$/\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

26
share/spack/setup-env.sh
View file

@ -57,6 +57,11 @@
########################################################################
function spack {
# Zsh does not do word splitting by default, this enables it for this function only
if [ -n "$ZSH_VERSION" ]; then
emulate -L sh
fi
# save raw arguments into an array before butchering them
args=( "$@" )
@ -93,11 +98,18 @@ function spack {
;;
"use"|"unuse"|"load"|"unload")
# Shift any other args for use off before parsing spec.
_sp_subcommand_args=""
_sp_module_args=""
if [[ "$1" =~ ^- ]]; then
_sp_module_args="$1"; shift
_sp_spec="$@"
while [[ "$1" =~ ^- ]]; do
if [ "$1" = "-r" -o "$1" = "--dependencies" ]; then
_sp_subcommand_args="$_sp_subcommand_args $1"
else
_sp_module_args="$_sp_module_args $1"
fi
shift
done
_sp_spec="$@"
# Here the user has run use or unuse with a spec. Find a matching
# spec using 'spack module find', then use the appropriate module
@ -105,19 +117,19 @@ function spack {
# If spack module command comes back with an error, do nothing.
case $_sp_subcommand in
"use")
if _sp_full_spec=$(command spack $_sp_flags module find --module-type dotkit $_sp_spec); then
if _sp_full_spec=$(command spack $_sp_flags module find $_sp_subcommand_args --module-type dotkit $_sp_spec); then
use $_sp_module_args $_sp_full_spec
fi ;;
"unuse")
if _sp_full_spec=$(command spack $_sp_flags module find --module-type dotkit $_sp_spec); then
if _sp_full_spec=$(command spack $_sp_flags module find $_sp_subcommand_args --module-type dotkit $_sp_spec); then
unuse $_sp_module_args $_sp_full_spec
fi ;;
"load")
if _sp_full_spec=$(command spack $_sp_flags module find --module-type tcl $_sp_spec); then
if _sp_full_spec=$(command spack $_sp_flags module find $_sp_subcommand_args --module-type tcl $_sp_spec); then
module load $_sp_module_args $_sp_full_spec
fi ;;
"unload")
if _sp_full_spec=$(command spack $_sp_flags module find --module-type tcl $_sp_spec); then
if _sp_full_spec=$(command spack $_sp_flags module find $_sp_subcommand_args --module-type tcl $_sp_spec); then
module unload $_sp_module_args $_sp_full_spec
fi ;;
esac

53
var/spack/repos/builtin/packages/gts/package.py Normal file
View file

@ -0,0 +1,53 @@
##############################################################################
# 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 Gts(Package):
"""GTS stands for the GNU Triangulated Surface Library.
It is an Open Source Free Software Library intended to provide a set of
useful functions to deal with 3D surfaces meshed with interconnected
triangles. The source code is available free of charge under the Free
Software LGPL license.
The code is written entirely in C with an object-oriented approach
based mostly on the design of GTK+. Careful attention is paid to
performance related issues as the initial goal of GTS is to provide a
simple and efficient library to scientists dealing with 3D computational
surface meshes.
"""
homepage = "http://gts.sourceforge.net/index.html"
url = "http://gts.sourceforge.net/tarballs/gts-snapshot-121130.tar.gz"
version('121130', '023ebb6b13b8707534182a3ef0d12908')
depends_on('glib')
def install(self, spec, prefix):
configure('--prefix={0}'.format(prefix))
make()
make('install')

76
var/spack/repos/builtin/packages/hmmer/package.py Normal file
View file

@ -0,0 +1,76 @@
##############################################################################
# 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 Hmmer(Package):
"""HMMER is used for searching sequence databases for sequence homologs,
and for making sequence alignments. It implements methods using
probabilistic models called profile hidden Markov models (profile HMMs).
"""
homepage = 'http://www.hmmer.org'
url = 'http://eddylab.org/software/hmmer3/3.1b2/hmmer-3.1b2.tar.gz'
version('3.1b2', 'c8c141018bc0ccd7fc37b33f2b945d5f')
version('3.0', '4cf685f3bc524ba5b5cdaaa070a83588')
version('2.4i', 'dab234c87e026ac1de942450750acd20')
version('2.3.2', '5f073340c0cf761288f961a73821228a')
version('2.3.1', 'c724413e5761c630892506698a4716e2')
variant('mpi', default=True, description='Compile with MPI')
variant('gsl', default=False, description='Compile with GSL')
depends_on('mpi', when='+mpi')
depends_on('gsl', when='+gsl')
def url_for_version(self, version):
base_url = 'http://eddylab.org/software'
if version >= Version('3.0'):
return '{0}/hmmer3/{1}/hmmer-{1}.tar.gz'.format(base_url, version)
else:
return '{0}/hmmer/{1}/hmmer-{1}.tar.gz'.format(base_url, version)
def install(self, spec, prefix):
configure_args = [
'--prefix={0}'.format(prefix)
]
if '+gsl' in self.spec:
configure_args.extend([
'--with-gsl',
'LIBS=-lgsl -lgslcblas'
])
if '+mpi' in self.spec:
configure_args.append('--enable-mpi')
configure(*configure_args)
make()
if self.run_tests:
make('check')
make('install')

45
var/spack/repos/builtin/packages/hypre/package.py
View file

@ -23,7 +23,9 @@
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
from spack import *
import os, sys
import os
import sys
class Hypre(Package):
"""Hypre is a library of high performance preconditioners that
@ -37,7 +39,7 @@ class Hypre(Package):
version('2.10.0b', '768be38793a35bb5d055905b271f5b8e')
# hypre does not know how to build shared libraries on Darwin
variant('shared', default=sys.platform!='darwin', description="Build shared library version (disables static library)")
variant('shared', default=(sys.platform != 'darwin'), description="Build shared library version (disables static library)")
# SuperluDist have conflicting headers with those in Hypre
variant('internal-superlu', default=True, description="Use internal Superlu routines")
@ -46,21 +48,26 @@ class Hypre(Package):
depends_on("lapack")
def install(self, spec, prefix):
blas_dir = spec['blas'].prefix
lapack_dir = spec['lapack'].prefix
mpi_dir = spec['mpi'].prefix
os.environ['CC'] = os.path.join(mpi_dir, 'bin', 'mpicc')
os.environ['CXX'] = os.path.join(mpi_dir, 'bin', 'mpicxx')
os.environ['F77'] = os.path.join(mpi_dir, 'bin', 'mpif77')
os.environ['CC'] = spec['mpi'].mpicc
os.environ['CXX'] = spec['mpi'].mpicxx
os.environ['F77'] = spec['mpi'].mpif77
# Since +shared does not build on macOS and also Atlas does not have
# a single static lib to build against, link against shared libs with
# a hope that --whole-archive linker option (or alike) was used
# to command the linker to include whole static libs' content into the
# shared lib
# Note: --with-(lapack|blas)_libs= needs space separated list of names
configure_args = [
"--prefix=%s" % prefix,
"--with-lapack-libs=lapack",
"--with-lapack-lib-dirs=%s/lib" % lapack_dir,
"--with-blas-libs=blas",
"--with-blas-lib-dirs=%s/lib" % blas_dir]
'--prefix=%s' % prefix,
'--with-lapack-libs=%s' % to_lib_name(
spec['lapack'].lapack_shared_lib),
'--with-lapack-lib-dirs=%s/lib' % spec['lapack'].prefix,
'--with-blas-libs=%s' % to_lib_name(
spec['blas'].blas_shared_lib),
'--with-blas-lib-dirs=%s/lib' % spec['blas'].prefix
]
if '+shared' in self.spec:
configure_args.append("--enable-shared")
@ -76,4 +83,12 @@ def install(self, spec, prefix):
configure(*configure_args)
make()
if self.run_tests:
make("check")
make("test")
Executable(join_path('test', 'ij'))()
sstruct = Executable(join_path('test', 'struct'))
sstruct()
sstruct('-in', 'test/sstruct.in.default', '-solver', '40',
'-rhsone')
make("install")

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

@ -63,6 +63,7 @@ class Openmpi(Package):
list_url = "http://www.open-mpi.org/software/ompi/"
list_depth = 3
version('2.0.0', 'cdacc800cb4ce690c1f1273cb6366674')
version('1.10.3', 'e2fe4513200e2aaa1500b762342c674b')
version('1.10.2', 'b2f43d9635d2d52826e5ef9feb97fd4c')
version('1.10.1', 'f0fcd77ed345b7eafb431968124ba16e')
@ -101,6 +102,7 @@ class Openmpi(Package):
provides('mpi@:2.2', when='@1.6.5')
provides('mpi@:3.0', when='@1.7.5:')
provides('mpi@:3.1', when='@2.0.0:')
depends_on('hwloc')
depends_on('sqlite', when='+sqlite3')
@ -169,7 +171,8 @@ def install(self, spec, prefix):
'--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', # NOQA: ignore=E501
('--enable-mpi-thread-multiple' if '+thread_multiple' in spec
else '--disable-mpi-thread-multiple'),
'--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'

4
var/spack/repos/builtin/packages/py-numpy/package.py
View file

@ -24,6 +24,7 @@
##############################################################################
from spack import *
class PyNumpy(Package):
"""NumPy is the fundamental package for scientific computing with Python.
It contains among other things: a powerful N-dimensional array object,
@ -38,7 +39,6 @@ class PyNumpy(Package):
version('1.9.2', 'a1ed53432dbcd256398898d35bc8e645')
version('1.9.1', '78842b73560ec378142665e712ae4ad9')
variant('blas', default=True)
variant('lapack', default=True)
@ -63,6 +63,6 @@ def install(self, spec, prefix):
f.write('[DEFAULT]\n')
f.write('libraries=%s\n' % ','.join(libraries))
f.write('library_dirs=%s\n' % ':'.join(library_dirs))
f.write('rpath=%s\n' % ':'.join(library_dirs))
python('setup.py', 'install', '--prefix=%s' % prefix)

23
var/spack/repos/builtin/packages/python/package.py
View file

@ -38,16 +38,29 @@ class Python(Package):
homepage = "http://www.python.org"
url = "http://www.python.org/ftp/python/2.7.8/Python-2.7.8.tgz"
version('3.5.2', '3fe8434643a78630c61c6464fe2e7e72')
version('3.5.1', 'be78e48cdfc1a7ad90efff146dce6cfe')
version('3.5.0', 'a56c0c0b45d75a0ec9c6dee933c41c36')
version('2.7.11', '6b6076ec9e93f05dd63e47eb9c15728b', preferred=True)
version('3.4.3', '4281ff86778db65892c05151d5de738d')
version('3.3.6', 'cdb3cd08f96f074b3f3994ccb51063e9')
version('3.2.6', '23815d82ae706e9b781ca65865353d39')
version('3.1.5', '02196d3fc7bc76bdda68aa36b0dd16ab')
version('2.7.12', '88d61f82e3616a4be952828b3694109d', preferred=True)
version('2.7.11', '6b6076ec9e93f05dd63e47eb9c15728b')
version('2.7.10', 'd7547558fd673bd9d38e2108c6b42521')
version('2.7.9', '5eebcaa0030dc4061156d3429657fb83')
version('2.7.8', 'd4bca0159acb0b44a781292b5231936f')
extendable = True
variant('ucs4', default=False, description='Enable UCS4 unicode strings')
variant('ucs4', default=False, description='Enable UCS4 (wide) unicode strings')
# From https://docs.python.org/2/c-api/unicode.html: Python's default
# builds use a 16-bit type for Py_UNICODE and store Unicode values
# internally as UCS2. It is also possible to build a UCS4 version of Python
# (most recent Linux distributions come with UCS4 builds of Python). These
# builds then use a 32-bit type for Py_UNICODE and store Unicode data
# internally as UCS4. Note that UCS2 and UCS4 Python builds are not binary
# compatible.
depends_on("openssl")
depends_on("bzip2")
@ -85,7 +98,13 @@ def install(self, spec, prefix):
]
if '+ucs4' in spec:
if spec.satisfies('@:2.7'):
config_args.append('--enable-unicode=ucs4')
elif spec.satisfies('@3.0:3.2'):
config_args.append('--with-wide-unicode')
elif spec.satisfies('@3.3:'):
# https://docs.python.org/3.3/whatsnew/3.3.html
raise ValueError('+ucs4 variant not compatible with Python 3.3 and beyond') # NOQA: ignore=E501
if spec.satisfies('@3:'):
config_args.append('--without-ensurepip')

51
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@ -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 RGgvis(Package):
"""An implementation of an interactive grammar of graphics, taking the best
parts of 'ggplot2', combining them with the reactive framework from 'shiny'
and web graphics from 'vega'."""
homepage = "http://ggvis.rstudio.com/"
url = "https://cran.r-project.org/src/contrib/ggvis_0.4.2.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/ggvis"
version('0.4.2', '039f45e5c7f1e0652779163d7d99f922')
extends('R')
depends_on('r-assertthat')
depends_on('r-jsonlite')
depends_on('r-shiny')
depends_on('r-magrittr')
depends_on('r-dplyr')
depends_on('r-lazyeval')
depends_on('r-htmltools')
def install(self, spec, prefix):
R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
self.stage.source_path)

44
var/spack/repos/builtin/packages/r-htmltools/package.py Normal file
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@ -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 RHtmltools(Package):
"""Tools for HTML generation and output."""
homepage = "https://github.com/rstudio/htmltools"
url = "https://cran.r-project.org/src/contrib/htmltools_0.3.5.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/htmltools"
version('0.3.5', '5f001aff4a39e329f7342dcec5139724')
extends('R')
depends_on('r-digest')
depends_on('r-rcpp')
def install(self, spec, prefix):
R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
self.stage.source_path)

49
var/spack/repos/builtin/packages/r-httpuv/package.py Normal file
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@ -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 RHttpuv(Package):
"""Provides low-level socket and protocol support for handling HTTP and
WebSocket requests directly from within R. It is primarily intended as a
building block for other packages, rather than making it particularly easy
to create complete web applications using httpuv alone. httpuv is built on
top of the libuv and http-parser C libraries, both of which were developed
by Joyent, Inc. (See LICENSE file for libuv and http-parser license
information.)"""
homepage = "https://github.com/rstudio/httpuv"
url = "https://cran.r-project.org/src/contrib/httpuv_1.3.3.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/httpuv"
version('1.3.3', 'c78ae068cf59e949b9791be987bb4489')
extends('R')
depends_on('r-rcpp')
def install(self, spec, prefix):
R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
self.stage.source_path)

52
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@ -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 RShiny(Package):
"""Makes it incredibly easy to build interactive web applications with R.
Automatic "reactive" binding between inputs and outputs and extensive
pre-built widgets make it possible to build beautiful, responsive, and
powerful applications with minimal effort."""
homepage = "http://shiny.rstudio.com/"
url = "https://cran.r-project.org/src/contrib/shiny_0.13.2.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/shiny"
version('0.13.2', 'cb5bff7a28ad59ec2883cd0912ca9611')
extends('R')
depends_on('r-httpuv')
depends_on('r-mime')
depends_on('r-jsonlite')
depends_on('r-xtable')
depends_on('r-digest')
depends_on('r-htmltools')
depends_on('r-R6')
def install(self, spec, prefix):
R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
self.stage.source_path)

41
var/spack/repos/builtin/packages/r-xtable/package.py Normal file
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@ -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 RXtable(Package):
"""Coerce data to LaTeX and HTML tables."""
homepage = "http://xtable.r-forge.r-project.org/"
url = "https://cran.r-project.org/src/contrib/xtable_1.8-2.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/xtable"
version('1.8-2', '239e4825cd046156a67efae3aac01d86')
extends('R')
def install(self, spec, prefix):
R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
self.stage.source_path)

1
var/spack/repos/builtin/packages/swiftsim/package.py
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@ -71,6 +71,7 @@ def install(self, spec, prefix):
# Configure and install
options = ['--prefix=%s' % prefix,
'--enable-mpi' if '+mpi' in spec else '--disable-mpi',
'--with-metis={0}'.format(spec['metis'].prefix),
'--enable-optimization']
configure(*options)
make()

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

@ -118,6 +118,7 @@ def install(self, spec, prefix):
options.extend(std_cmake_args)
mpi_bin = spec['mpi'].prefix.bin
# Note: -DXYZ_LIBRARY_NAMES= needs semicolon separated list of names
options.extend([
'-DTrilinos_ENABLE_ALL_PACKAGES:BOOL=ON',
'-DTrilinos_ENABLE_ALL_OPTIONAL_PACKAGES:BOOL=ON',
@ -131,10 +132,12 @@ def install(self, spec, prefix):
'-DTPL_ENABLE_MPI:BOOL=ON',
'-DMPI_BASE_DIR:PATH=%s' % spec['mpi'].prefix,
'-DTPL_ENABLE_BLAS=ON',
'-DBLAS_LIBRARY_NAMES=blas', # FIXME: don't hardcode names
'-DBLAS_LIBRARY_NAMES=%s' % to_lib_name(
spec['blas'].blas_shared_lib),
'-DBLAS_LIBRARY_DIRS=%s' % spec['blas'].prefix.lib,
'-DTPL_ENABLE_LAPACK=ON',
'-DLAPACK_LIBRARY_NAMES=lapack',
'-DLAPACK_LIBRARY_NAMES=%s' % to_lib_name(
spec['lapack'].lapack_shared_lib),
'-DLAPACK_LIBRARY_DIRS=%s' % spec['lapack'].prefix,
'-DTrilinos_ENABLE_EXPLICIT_INSTANTIATION:BOOL=ON',
'-DTrilinos_ENABLE_CXX11:BOOL=ON',