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Merge develop for v0.8.16 release.

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This commit is contained in:
Todd Gamblin 2015-03-13 23:41:59 -04:00
commit 1414480d3a
17 changed files with 304 additions and 124 deletions
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5
lib/spack/docs/site_configuration.rst
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@ -8,8 +8,9 @@ Site configuration
Temporary space
----------------------------
.. warning:: Temporary space configuration will be moved to configuration files.
The instructions here are old and refer to ``__init__.py``
.. warning:: Temporary space configuration will eventually be moved to
configuration files, but currently these settings are in
``lib/spack/spack/__init__.py``
By default, Spack will try to do all of its building in temporary
space. There are two main reasons for this. First, Spack is designed

1
lib/spack/env/clang vendored
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cc

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lib/spack/env/clang++ vendored
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cc

1
lib/spack/env/g++ vendored
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cc

1
lib/spack/env/gcc vendored
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cc

121
lib/spack/llnl/util/filesystem.py
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@ -22,9 +22,10 @@
# 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', 'expand_user', 'working_dir',
'touch', 'touchp', 'mkdirp', 'force_remove', 'join_path', 'ancestor',
'can_access', 'filter_file', 'change_sed_delimiter', 'is_exe']
__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',
'change_sed_delimiter', 'is_exe', 'force_symlink']
import os
import sys
@ -140,12 +141,7 @@ def set_install_permissions(path):
os.chmod(path, 0644)
def install(src, dest):
"""Manually install a file to a particular location."""
tty.info("Installing %s to %s" % (src, dest))
shutil.copy(src, dest)
set_install_permissions(dest)
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
@ -154,6 +150,24 @@ def install(src, dest):
os.chmod(dest, dest_mode)
def install(src, dest):
"""Manually install a file to a particular location."""
tty.info("Installing %s to %s" % (src, dest))
shutil.copy(src, dest)
set_install_permissions(dest)
copy_mode(src, dest)
def install_tree(src, dest, **kwargs):
"""Manually install a file to a particular location."""
tty.info("Installing %s to %s" % (src, dest))
shutil.copytree(src, dest, **kwargs)
for s, d in traverse_tree(src, dest, follow_nonexisting=False):
set_install_permissions(d)
copy_mode(s, d)
def is_exe(path):
"""True if path is an executable file."""
return os.path.isfile(path) and os.access(path, os.X_OK)
@ -210,6 +224,14 @@ def touchp(path):
touch(path)
def force_symlink(src, dest):
try:
os.symlink(src, dest)
except OSError, e:
os.remove(dest)
os.symlink(src, dest)
def join_path(prefix, *args):
path = str(prefix)
for elt in args:
@ -228,3 +250,84 @@ 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)
def traverse_tree(source_root, dest_root, rel_path='', **kwargs):
"""Traverse two filesystem trees simultaneously.
Walks the LinkTree directory in pre or post order. Yields each
file in the source directory with a matching path from the dest
directory, along with whether the file is a directory.
e.g., for this tree::
root/
a/
file1
file2
b/
file3
When called on dest, this yields::
('root', 'dest')
('root/a', 'dest/a')
('root/a/file1', 'dest/a/file1')
('root/a/file2', 'dest/a/file2')
('root/b', 'dest/b')
('root/b/file3', 'dest/b/file3')
Optional args:
order=[pre|post] -- Whether to do pre- or post-order traveral.
ignore=<predicate> -- Predicate indicating which files to ignore.
follow_nonexisting -- Whether to descend into directories in
src that do not exit in dest. Default True.
follow_links -- Whether to descend into symlinks in src.
"""
follow_nonexisting = kwargs.get('follow_nonexisting', True)
follow_links = kwargs.get('follow_link', False)
# Yield in pre or post order?
order = kwargs.get('order', 'pre')
if order not in ('pre', 'post'):
raise ValueError("Order must be 'pre' or 'post'.")
# List of relative paths to ignore under the src root.
ignore = kwargs.get('ignore', lambda filename: False)
# Don't descend into ignored directories
if ignore(rel_path):
return
source_path = os.path.join(source_root, rel_path)
dest_path = os.path.join(dest_root, rel_path)
# preorder yields directories before children
if order == 'pre':
yield (source_path, dest_path)
for f in os.listdir(source_path):
source_child = os.path.join(source_path, f)
dest_child = os.path.join(dest_path, f)
rel_child = os.path.join(rel_path, f)
# Treat as a directory
if os.path.isdir(source_child) and (
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
# Treat as a file.
elif not ignore(os.path.join(rel_path, f)):
yield (source_child, dest_child)
if order == 'post':
yield (source_path, dest_path)

82
lib/spack/llnl/util/link_tree.py
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@ -32,88 +32,6 @@
empty_file_name = '.spack-empty'
def traverse_tree(source_root, dest_root, rel_path='', **kwargs):
"""Traverse two filesystem trees simultaneously.
Walks the LinkTree directory in pre or post order. Yields each
file in the source directory with a matching path from the dest
directory, along with whether the file is a directory.
e.g., for this tree::
root/
a/
file1
file2
b/
file3
When called on dest, this yields::
('root', 'dest')
('root/a', 'dest/a')
('root/a/file1', 'dest/a/file1')
('root/a/file2', 'dest/a/file2')
('root/b', 'dest/b')
('root/b/file3', 'dest/b/file3')
Optional args:
order=[pre|post] -- Whether to do pre- or post-order traveral.
ignore=<predicate> -- Predicate indicating which files to ignore.
follow_nonexisting -- Whether to descend into directories in
src that do not exit in dest. Default True.
follow_links -- Whether to descend into symlinks in src.
"""
follow_nonexisting = kwargs.get('follow_nonexisting', True)
follow_links = kwargs.get('follow_link', False)
# Yield in pre or post order?
order = kwargs.get('order', 'pre')
if order not in ('pre', 'post'):
raise ValueError("Order must be 'pre' or 'post'.")
# List of relative paths to ignore under the src root.
ignore = kwargs.get('ignore', lambda filename: False)
# Don't descend into ignored directories
if ignore(rel_path):
return
source_path = os.path.join(source_root, rel_path)
dest_path = os.path.join(dest_root, rel_path)
# preorder yields directories before children
if order == 'pre':
yield (source_path, dest_path)
for f in os.listdir(source_path):
source_child = os.path.join(source_path, f)
dest_child = os.path.join(dest_path, f)
rel_child = os.path.join(rel_path, f)
# Treat as a directory
if os.path.isdir(source_child) and (
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
# Treat as a file.
elif not ignore(os.path.join(rel_path, f)):
yield (source_child, dest_child)
if order == 'post':
yield (source_path, dest_path)
class LinkTree(object):
"""Class to create trees of symbolic links from a source directory.

23
lib/spack/spack/build_environment.py
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@ -189,18 +189,19 @@ def set_module_variables_for_package(pkg):
m.std_cmake_args.append('-DCMAKE_INSTALL_RPATH=%s' % ":".join(get_rpaths(pkg)))
# 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.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.rmtree = shutil.rmtree
m.move = shutil.move
m.mkdirp = mkdirp
m.install = install
m.install_tree = install_tree
m.rmtree = shutil.rmtree
m.move = shutil.move
# Useful directories within the prefix are encapsulated in
# a Prefix object.

32
lib/spack/spack/package.py
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@ -62,6 +62,7 @@
from spack.stage import Stage
from spack.util.web import get_pages
from spack.util.compression import allowed_archive, extension
from spack.util.executable import ProcessError
"""Allowed URL schemes for spack packages."""
_ALLOWED_URL_SCHEMES = ["http", "https", "ftp", "file", "git"]
@ -805,6 +806,16 @@ def do_install(self, **kwargs):
# package naming scheme it likes.
spack.install_layout.make_path_for_spec(self.spec)
def cleanup():
if not keep_prefix:
# If anything goes wrong, remove the install prefix
self.remove_prefix()
else:
tty.warn("Keeping install prefix in place despite error.",
"Spack will think this package is installed." +
"Manually remove this directory to fix:",
self.prefix)
def real_work():
try:
tty.msg("Building %s." % self.name)
@ -837,15 +848,20 @@ def real_work():
% (_hms(self._fetch_time), _hms(build_time), _hms(self._total_time)))
print_pkg(self.prefix)
except:
if not keep_prefix:
# If anything goes wrong, remove the install prefix
self.remove_prefix()
except ProcessError, e:
# One of the processes returned an error code.
# Suppress detailed stack trace here unless in debug mode
if spack.debug:
raise e
else:
tty.warn("Keeping install prefix in place despite error.",
"Spack will think this package is installed." +
"Manually remove this directory to fix:",
self.prefix)
tty.error(e)
# Still need to clean up b/c there was an error.
cleanup()
except:
# other exceptions just clean up and raise.
cleanup()
raise
build_env.fork(self, real_work)

18
var/spack/packages/SAMRAI/package.py
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@ -7,10 +7,11 @@ class Samrai(Package):
structured adaptive mesh refinement (SAMR) technology in large-scale parallel
application development.
"""
homepage = "https://computation-rnd.llnl.gov/SAMRAI/confirm.php"
url = "https://computation-rnd.llnl.gov/SAMRAI/download/SAMRAI-v3.7.3.tar.gz"
homepage = "https://computation.llnl.gov/project/SAMRAI/"
url = "https://computation.llnl.gov/project/SAMRAI/download/SAMRAI-v3.9.1.tar.gz"
list_url = homepage
version('3.9.1', '232d04d0c995f5abf20d94350befd0b2')
version('3.7.3', '12d574eacadf8c9a70f1bb4cd1a69df6')
version('3.7.2', 'f6a716f171c9fdbf3cb12f71fa6e2737')
version('3.6.3-beta', 'ef0510bf2893042daedaca434e5ec6ce')
@ -24,22 +25,25 @@ class Samrai(Package):
depends_on("mpi")
depends_on("zlib")
depends_on("hdf5")
depends_on("boost@1.52.0")
depends_on("boost")
# don't build tools with gcc
patch('no-tool-build.patch', when='%gcc')
# TODO: currently hard-coded to use openmpi - be careful!
def install(self, spec, prefix):
mpi = next(m for m in ('openmpi', 'mpich', 'mvapich')
if m in spec)
configure(
"--prefix=%s" % prefix,
"--with-CXX=%s" % spec['openmpi'].prefix.bin + "/mpic++",
"--with-CC=%s" % spec['openmpi'].prefix.bin + "/mpicc",
"--with-CXX=%s" % spec[mpi].prefix.bin + "/mpic++",
"--with-CC=%s" % spec[mpi].prefix.bin + "/mpicc",
"--with-hdf5=%s" % spec['hdf5'].prefix,
"--with-boost=%s" % spec['boost'].prefix,
"--with-zlib=%s" % spec['zlib'].prefix,
"--disable-blas",
"--disable-lapack",
"--without-blas",
"--without-lapack",
"--with-hypre=no",
"--with-petsc=no",
"--enable-opt",

15
var/spack/packages/cram/package.py Normal file
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@ -0,0 +1,15 @@
from spack import *
class Cram(Package):
"""Cram runs many small MPI jobs inside one large MPI job."""
homepage = "https://github.com/scalability-llnl/cram"
url = "http://github.com/scalability-llnl/cram/archive/v1.0.1.tar.gz"
version('1.0.1', 'c73711e945cf5dc603e44395f6647f5e')
depends_on("mpi")
def install(self, spec, prefix):
cmake(".", *std_cmake_args)
make()
make("install")

32
var/spack/packages/metis/package.py Normal file
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@ -0,0 +1,32 @@
from spack import *
class Metis(Package):
"""METIS is a set of serial programs for partitioning graphs,
partitioning finite element meshes, and producing fill reducing
orderings for sparse matrices. The algorithms implemented in
METIS are based on the multilevel recursive-bisection,
multilevel k-way, and multi-constraint partitioning schemes
developed in our lab."""
homepage = "http://glaros.dtc.umn.edu/gkhome/metis/metis/overview"
url = "http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/metis-5.1.0.tar.gz"
version('5.1.0', '5465e67079419a69e0116de24fce58fe')
# FIXME: Add dependencies if this package requires them.
# depends_on("foo")
def patch(self):
filter_file(r'#define IDXTYPEWIDTH 32', '#define IDXTYPEWIDTH 64', 'include/metis.h',
string=True)
def install(self, spec, prefix):
with working_dir('spack-build', create=True):
cmake('..',
'-DGKLIB_PATH=../GKlib',
'-DBUILD_SHARED_LIBS=TRUE',
*std_cmake_args)
make()
make("install")

9
var/spack/packages/mpich/package.py
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@ -38,6 +38,15 @@ class Mpich(Package):
provides('mpi@:3', when='@3:')
provides('mpi@:1', when='@1:')
def setup_dependent_environment(self, module, spec, dep_spec):
"""For dependencies, make mpicc's use spack wrapper."""
os.environ['MPICH_CC'] = 'cc'
os.environ['MPICH_CXX'] = 'c++'
os.environ['MPICH_F77'] = 'f77'
os.environ['MPICH_F90'] = 'f90'
def install(self, spec, prefix):
config_args = ["--prefix=" + prefix,
"--enable-shared"]

3
var/spack/packages/muster/package.py
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@ -10,7 +10,8 @@ class Muster(Package):
homepage = "https://github.com/scalability-llnl/muster"
url = "https://github.com/scalability-llnl/muster/archive/v1.0.tar.gz"
version('1.0', '2eec6979a4a36d3a65a792d12969be16')
version('1.0.1', 'd709787db7e080447afb6571ac17723c')
version('1.0', '2eec6979a4a36d3a65a792d12969be16')
depends_on("boost")
depends_on("mpi")

21
var/spack/packages/otf/package.py Normal file
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@ -0,0 +1,21 @@
from spack import *
class Otf(Package):
"""To improve scalability for very large and massively parallel
traces the Open Trace Format (OTF) is developed at ZIH as a
successor format to the Vampir Trace Format (VTF3)."""
homepage = "http://tu-dresden.de/die_tu_dresden/zentrale_einrichtungen/zih/forschung/projekte/otf/index_html/document_view?set_language=en"
url = "http://wwwpub.zih.tu-dresden.de/%7Emlieber/dcount/dcount.php?package=otf&get=OTF-1.12.5salmon.tar.gz"
version('1.12.5salmon', 'bf260198633277031330e3356dcb4eec')
depends_on('zlib')
def install(self, spec, prefix):
configure('--prefix=%s' % prefix,
'--without-vtf3',
'--with-zlib',
'--with-zlibsymbols')
make()
make("install")

23
var/spack/packages/ravel/package.py Normal file
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@ -0,0 +1,23 @@
from spack import *
class Ravel(Package):
"""Ravel is a parallel communication trace visualization tool that
orders events according to logical time."""
homepage = "https://github.com/scalability-llnl/ravel"
url = 'https://github.com/scalability-llnl/ravel/archive/v1.0.0.tar.gz'
version('1.0.0', 'b25fece58331c2adfcce76c5036485c2')
# TODO: make this a build dependency
depends_on('cmake@2.8.9:')
depends_on('muster@1.0.1:')
depends_on('otf')
depends_on('otf2')
depends_on('qt@5:')
def install(self, spec, prefix):
cmake('-Wno-dev', *std_cmake_args)
make()
make("install")

40
var/spack/packages/scotch/package.py Normal file
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@ -0,0 +1,40 @@
from spack import *
import glob
import os
class Scotch(Package):
"""Scotch is a software package for graph and mesh/hypergraph
partitioning, graph clustering, and sparse matrix ordering."""
homepage = "http://www.labri.fr/perso/pelegrin/scotch/"
url = "http://gforge.inria.fr/frs/download.php/file/34099/scotch_6.0.3.tar.gz"
list_url = "http://gforge.inria.fr/frs/?group_id=248"
version('6.0.3', '10b0cc0f184de2de99859eafaca83cfc')
depends_on('mpi')
def patch(self):
with working_dir('src/Make.inc'):
makefiles = glob.glob('Makefile.inc.x86-64_pc_linux2*')
filter_file(r'^CCS\s*=.*$', 'CCS = cc', *makefiles)
filter_file(r'^CCD\s*=.*$', 'CCD = cc', *makefiles)
def install(self, spec, prefix):
# Currently support gcc and icc on x86_64 (maybe others with
# vanilla makefile)
makefile = 'Make.inc/Makefile.inc.x86-64_pc_linux2'
if spec.satisfies('%icc'):
makefile += '.icc'
with working_dir('src'):
force_symlink(makefile, 'Makefile.inc')
for app in ('scotch', 'ptscotch'):
make(app)
install_tree('bin', prefix.bin)
install_tree('lib', prefix.lib)
install_tree('include', prefix.include)
install_tree('man/man1', prefix.share_man1)