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Merge remote-tracking branch 'upstream/develop' into develop

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This commit is contained in:
Jim Galarowicz 2016-04-04 17:07:53 -07:00
commit 9d2ef9f453
9 changed files with 193 additions and 37 deletions
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28
lib/spack/docs/basic_usage.rst
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@ -794,6 +794,34 @@ Environment modules
Spack provides some limited integration with environment module
systems to make it easier to use the packages it provides.
Installing Environment Modules
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In order to use Spack's generated environment modules, you must have
installed the *Environment Modules* package. On many Linux
distributions, this can be installed from the vendor's repository.
For example: ```yum install environment-modules``
(Fedora/RHEL/CentOS). If your Linux distribution does not have
Environment Modules, you can get it with Spack:
1. Install with::
spack install environment-modules
2. Activate with::
MODULES_HOME=`spack location -i environment-modules`
MODULES_VERSION=`ls -1 $MODULES_HOME/Modules | head -1`
${MODULES_HOME}/Modules/${MODULES_VERSION}/bin/add.modules
This adds to your ``.bashrc`` (or similar) files, enabling Environment
Modules when you log in. It will ask your permission before changing
any files.
Spack and Environment Modules
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
You can enable shell support by sourcing some files in the
``/share/spack`` directory.

3
lib/spack/spack/build_environment.py
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@ -304,7 +304,7 @@ def setup_package(pkg):
# traverse in postorder so package can use vars from its dependencies
spec = pkg.spec
for dspec in pkg.spec.traverse(order='post'):
for dspec in pkg.spec.traverse(order='post', root=False):
# If a user makes their own package repo, e.g.
# spack.repos.mystuff.libelf.Libelf, and they inherit from
# an existing class like spack.repos.original.libelf.Libelf,
@ -321,6 +321,7 @@ def setup_package(pkg):
dpkg.setup_dependent_package(pkg.module, spec)
dpkg.setup_dependent_environment(spack_env, run_env, spec)
set_module_variables_for_package(pkg, pkg.module)
pkg.setup_environment(spack_env, run_env)
# Make sure nothing's strange about the Spack environment.

19
var/spack/repos/builtin/packages/dealii/package.py
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@ -23,8 +23,10 @@ class Dealii(Package):
# required dependencies, light version
depends_on ("blas")
depends_on ("boost", when='~mpi')
depends_on ("boost+mpi", when='+mpi')
# Boost 1.58 is blacklisted, see https://github.com/dealii/dealii/issues/1591
# require at least 1.59
depends_on ("boost@1.59.0:", when='~mpi')
depends_on ("boost@1.59.0:+mpi", when='+mpi')
depends_on ("bzip2")
depends_on ("cmake")
depends_on ("lapack")
@ -174,6 +176,19 @@ def install(self, spec, prefix):
make('release')
make('run',parallel=False)
# An example which uses Metis + PETSc
# FIXME: switch step-18 to MPI
with working_dir('examples/step-18'):
print('=====================================')
print('============= Step-18 ===============')
print('=====================================')
# list the number of cycles to speed up
filter_file(r'(end_time = 10;)', ('end_time = 3;'), 'step-18.cc')
if '^petsc' in spec and '^metis' in spec:
cmake('.')
make('release')
make('run',parallel=False)
# take step-40 which can use both PETSc and Trilinos
# FIXME: switch step-40 to MPI run
with working_dir('examples/step-40'):

38
var/spack/repos/builtin/packages/environment-modules/package.py Normal file
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@ -0,0 +1,38 @@
from spack import *
class EnvironmentModules(Package):
"""The Environment Modules package provides for the dynamic
modification of a user's environment via modulefiles."""
homepage = "https://sourceforge.net/p/modules/wiki/Home/"
url = "http://prdownloads.sourceforge.net/modules/modules-3.2.10.tar.gz"
version('3.2.10', '8b097fdcb90c514d7540bb55a3cb90fb')
# Dependencies:
depends_on('tcl')
def install(self, spec, prefix):
tcl_spec = spec['tcl']
# See: https://sourceforge.net/p/modules/bugs/62/
CPPFLAGS = ['-DUSE_INTERP_ERRORLINE']
config_args = [
"--without-tclx",
"--with-tclx-ver=0.0",
"--prefix=%s" % prefix,
"--with-tcl=%s" % join_path(tcl_spec.prefix, 'lib'), # It looks for tclConfig.sh
"--with-tcl-ver=%d.%d" % (tcl_spec.version.version[0], tcl_spec.version.version[1]),
'--disable-debug',
'--disable-dependency-tracking',
'--disable-silent-rules',
'--disable-versioning',
'--datarootdir=%s' % prefix.share,
'CPPFLAGS=%s' % ' '.join(CPPFLAGS)
]
configure(*config_args)
make()
make('install')

51
var/spack/repos/builtin/packages/ipopt/package.py Normal file
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@ -0,0 +1,51 @@
from spack import *
class Ipopt(Package):
"""Ipopt (Interior Point OPTimizer, pronounced eye-pea-Opt) is a
software package for large-scale nonlinear optimization."""
homepage = "https://projects.coin-or.org/Ipopt"
url = "http://www.coin-or.org/download/source/Ipopt/Ipopt-3.12.4.tgz"
version('3.12.4', '12a8ecaff8dd90025ddea6c65b49cb03')
version('3.12.3', 'c560cbfa9cbf62acf8b485823c255a1b')
version('3.12.2', 'ec1e855257d7de09e122c446506fb00d')
version('3.12.1', 'ceaf895ce80c77778f2cab68ba9f17f3')
version('3.12.0', 'f7dfc3aa106a6711a85214de7595e827')
depends_on("blas")
depends_on("lapack")
depends_on("pkg-config")
depends_on("mumps+double~mpi")
def install(self, spec, prefix):
# Dependency directories
blas_dir = spec['blas'].prefix
lapack_dir = spec['lapack'].prefix
mumps_dir = spec['mumps'].prefix
# Add directory with fake MPI headers in sequential MUMPS
# install to header search path
mumps_flags = "-ldmumps -lmumps_common -lpord -lmpiseq"
mumps_libcmd = "-L%s " % mumps_dir.lib + mumps_flags
# By convention, spack links blas & lapack libs to libblas & liblapack
blas_lib = "-L%s" % blas_dir.lib + " -lblas"
lapack_lib = "-L%s" % lapack_dir.lib + " -llapack"
configure_args = [
"--prefix=%s" % prefix,
"--with-mumps-incdir=%s" % mumps_dir.include,
"--with-mumps-lib=%s" % mumps_libcmd,
"--enable-shared",
"--with-blas-incdir=%s" % blas_dir.include,
"--with-blas-lib=%s" % blas_lib,
"--with-lapack-incdir=%s" % lapack_dir.include,
"--with-lapack-lib=%s" % lapack_lib
]
configure(*configure_args)
# IPOPT does not build correctly in parallel on OS X
make(parallel=False)
make("test", parallel=False)
make("install", parallel=False)

18
var/spack/repos/builtin/packages/metis/package.py
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@ -79,10 +79,28 @@ def install(self, spec, prefix):
if '+double' in spec:
filter_file('REALTYPEWIDTH 32', 'REALTYPEWIDTH 64', metis_header)
# Make clang 7.3 happy.
# Prevents "ld: section __DATA/__thread_bss extends beyond end of file"
# See upstream LLVM issue https://llvm.org/bugs/show_bug.cgi?id=27059
# Adopted from https://github.com/Homebrew/homebrew-science/blob/master/metis.rb
if spec.satisfies('%clang@7.3.0'):
filter_file('#define MAX_JBUFS 128', '#define MAX_JBUFS 24', join_path(source_directory, 'GKlib', 'error.c'))
with working_dir(build_directory, create=True):
cmake(source_directory, *options)
make()
make("install")
# now run some tests:
for f in ["4elt", "copter2", "mdual"]:
graph = join_path(source_directory,'graphs','%s.graph' % f)
Executable(join_path(prefix.bin,'graphchk'))(graph)
Executable(join_path(prefix.bin,'gpmetis'))(graph,'2')
Executable(join_path(prefix.bin,'ndmetis'))(graph)
graph = join_path(source_directory,'graphs','test.mgraph')
Executable(join_path(prefix.bin,'gpmetis'))(graph,'2')
graph = join_path(source_directory,'graphs','metis.mesh')
Executable(join_path(prefix.bin,'mpmetis'))(graph,'2')
# install GKlib headers, which will be needed for ParMETIS
GKlib_dist = join_path(prefix.include,'GKlib')

25
var/spack/repos/builtin/packages/modules/package.py
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@ -1,25 +0,0 @@
from spack import *
class Modules(Package):
""" The Environment Modules package provides for the dynamic modification of a user's environment via modulefiles. """
homepage = "http://modules.sf.net"
url = "http://downloads.sourceforge.net/project/modules/Modules/modules-3.2.10/modules-3.2.10.tar.gz"
version('3.2.10', '8b097fdcb90c514d7540bb55a3cb90fb')
depends_on("tcl")
def install(self, spec, prefix):
options = ['--prefix=%s' % prefix,
'--disable-debug',
'--disable-dependency-tracking',
'--disable-silent-rules',
'--disable-versioning',
'--datarootdir=%s' % prefix.share,
'CPPFLAGS=-DUSE_INTERP_ERRORLINE']
configure(*options)
make()
make("install")

7
var/spack/repos/builtin/packages/mumps/package.py
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@ -1,5 +1,5 @@
from spack import *
import os, sys
import os, sys, glob
class Mumps(Package):
"""MUMPS: a MUltifrontal Massively Parallel sparse direct Solver"""
@ -164,10 +164,13 @@ def install(self, spec, prefix):
install_tree('lib', prefix.lib)
install_tree('include', prefix.include)
if '~mpi' in spec:
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

41
var/spack/repos/builtin/packages/suite-sparse/package.py
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@ -10,10 +10,18 @@ class SuiteSparse(Package):
version('4.5.1', 'f0ea9aad8d2d1ffec66a5b6bfeff5319')
# FIXME: (see below)
# variant('tbb', default=True, description='Build with Intel TBB')
depends_on('blas')
depends_on('lapack')
depends_on('metis@5.1.0', when='@4.5.1')
# FIXME:
# in @4.5.1. TBB support in SPQR seems to be broken as TBB-related linkng flags
# does not seem to be used, which leads to linking errors on Linux.
# Try re-enabling in future versions.
# depends_on('tbb', when='+tbb')
def install(self, spec, prefix):
# The build system of SuiteSparse is quite old-fashioned
@ -21,16 +29,35 @@ def install(self, spec, prefix):
# with a lot of convoluted logic in it.
# Any kind of customization will need to go through filtering of that file
# FIXME : this actually uses the current workaround
# FIXME : (blas / lapack always provide libblas and liblapack as aliases)
make('install', 'INSTALL=%s' % prefix,
make_args = ['INSTALL=%s' % prefix]
# inject Spack compiler wrappers
# inject Spack compiler wrappers
make_args.extend([
'AUTOCC=no',
'CC=cc',
'CXX=c++',
'F77=f77',
])
# BLAS arguments require path to libraries
'BLAS=-lblas',
'LAPACK=-llapack')
# use Spack's metis in CHOLMOD/Partition module,
# otherwise internal Metis will be compiled
make_args.extend([
'MY_METIS_LIB=-L%s -lmetis' % spec['metis'].prefix.lib,
'MY_METIS_INC=%s' % spec['metis'].prefix.include,
])
# Intel TBB in SuiteSparseQR
if '+tbb' in spec:
make_args.extend([
'SPQR_CONFIG=-DHAVE_TBB',
'TBB=-L%s -ltbb' % spec['tbb'].prefix.lib,
])
# BLAS arguments require path to libraries
# FIXME : (blas / lapack always provide libblas and liblapack as aliases)
make_args.extend([
'BLAS=-lblas',
'LAPACK=-llapack'
])
make('install', *make_args)