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-rw-r--r--.coveragerc34
-rw-r--r--.gitignore2
-rw-r--r--.style.yapf3
-rw-r--r--.travis.yml18
-rw-r--r--README.md3
-rwxr-xr-xbin/spack2
-rw-r--r--flake8.ini3
-rw-r--r--lib/spack/spack/build_environment.py4
-rw-r--r--lib/spack/spack/cmd/compiler.py13
-rw-r--r--lib/spack/spack/cmd/create.py8
-rw-r--r--lib/spack/spack/compiler.py4
-rw-r--r--lib/spack/spack/config.py10
-rw-r--r--lib/spack/spack/test/config.py33
-rw-r--r--lib/spack/spack/url.py3
-rw-r--r--lib/spack/spack/util/executable.py2
-rw-r--r--var/spack/repos/builtin/packages/R/package.py59
-rw-r--r--var/spack/repos/builtin/packages/antlr/package.py47
-rw-r--r--var/spack/repos/builtin/packages/binutils/package.py1
-rw-r--r--var/spack/repos/builtin/packages/bison/package.py2
-rw-r--r--var/spack/repos/builtin/packages/cbtf-argonavis/package.py90
-rw-r--r--var/spack/repos/builtin/packages/cbtf-krell/package.py262
-rw-r--r--var/spack/repos/builtin/packages/cbtf-lanl/package.py65
-rw-r--r--var/spack/repos/builtin/packages/cbtf/package.py88
-rw-r--r--var/spack/repos/builtin/packages/fftw/package.py13
-rw-r--r--var/spack/repos/builtin/packages/gdb/package.py1
-rw-r--r--var/spack/repos/builtin/packages/glib/package.py3
-rw-r--r--var/spack/repos/builtin/packages/gmsh/package.py4
-rw-r--r--var/spack/repos/builtin/packages/hdf5/package.py61
-rw-r--r--var/spack/repos/builtin/packages/kripke/package.py32
-rw-r--r--var/spack/repos/builtin/packages/libxcb/package.py1
-rw-r--r--var/spack/repos/builtin/packages/nccmp/package.py23
-rw-r--r--var/spack/repos/builtin/packages/nco/package.py30
-rw-r--r--var/spack/repos/builtin/packages/openblas/package.py82
-rw-r--r--var/spack/repos/builtin/packages/openblas/test_cblas_dgemm.c54
-rw-r--r--var/spack/repos/builtin/packages/openblas/test_cblas_dgemm.output3
-rw-r--r--var/spack/repos/builtin/packages/openspeedshop/package.py300
-rw-r--r--var/spack/repos/builtin/packages/parallel-netcdf/package.py18
-rw-r--r--var/spack/repos/builtin/packages/py-argcomplete/package.py14
-rw-r--r--var/spack/repos/builtin/packages/r-BiocGenerics/package.py14
-rw-r--r--var/spack/repos/builtin/packages/r-abind/package.py18
-rw-r--r--var/spack/repos/builtin/packages/r-filehash/package.py22
-rw-r--r--var/spack/repos/builtin/packages/r-magic/package.py19
-rw-r--r--var/spack/repos/builtin/packages/scotch/Makefile.esmumps5
-rw-r--r--var/spack/repos/builtin/packages/scotch/package.py152
-rw-r--r--var/spack/repos/builtin/packages/silo/package.py4
-rw-r--r--var/spack/repos/builtin/packages/visit/package.py31
46 files changed, 1331 insertions, 329 deletions
diff --git a/.coveragerc b/.coveragerc
new file mode 100644
index 0000000000..a1271a94fc
--- /dev/null
+++ b/.coveragerc
@@ -0,0 +1,34 @@
+# -*- conf -*-
+# .coveragerc to control coverage.py
+[run]
+branch = True
+source = lib
+omit =
+ lib/spack/spack/test/*
+ lib/spack/env/*
+ lib/spack/docs/*
+ lib/spack/external/*
+
+[report]
+# Regexes for lines to exclude from consideration
+exclude_lines =
+ # Have to re-enable the standard pragma
+ pragma: no cover
+
+ # Don't complain about missing debug-only code:
+ def __repr__
+ if self\.debug
+
+ # Don't complain if tests don't hit defensive assertion code:
+ raise AssertionError
+ raise NotImplementedError
+
+ # Don't complain if non-runnable code isn't run:
+ if 0:
+ if False:
+ if __name__ == .__main__.:
+
+ignore_errors = True
+
+[html]
+directory = htmlcov
diff --git a/.gitignore b/.gitignore
index 4b97de5d50..643e5d9b03 100644
--- a/.gitignore
+++ b/.gitignore
@@ -9,3 +9,5 @@
/share/spack/dotkit
/share/spack/modules
/TAGS
+/htmlcov
+.coverage
diff --git a/.style.yapf b/.style.yapf
new file mode 100644
index 0000000000..4741fb4f3b
--- /dev/null
+++ b/.style.yapf
@@ -0,0 +1,3 @@
+[style]
+based_on_style = pep8
+column_limit = 80
diff --git a/.travis.yml b/.travis.yml
index 1bed6b0874..4ff4d5f483 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -6,20 +6,32 @@ python:
# Use new Travis infrastructure (Docker can't sudo yet)
sudo: false
-# No need to install any deps.
-install: true
+# Install coveralls to obtain code coverage
+install:
+ - "pip install coveralls"
+ - "pip install flake8"
before_install:
# Need this for the git tests to succeed.
- git config --global user.email "spack@example.com"
- git config --global user.name "Test User"
+ # Need this to be able to compute the list of changed files
+ - git fetch origin develop:develop
script:
- . share/spack/setup-env.sh
- spack compilers
- spack config get compilers
- - spack test
- spack install -v libdwarf
+ # Run unit tests with code coverage
+ - coverage run bin/spack test
+ # Checks if the file that have been changed are flake8 conformant
+ - CHANGED_PYTHON_FILES=`git diff develop... --name-only | perl -ne 'print if /\.py$/'`
+ - if [[ ${CHANGED_PYTHON_FILES} ]] ; then flake8 --format pylint --config flake8.ini ${CHANGED_PYTHON_FILES} ; fi
+
+
+after_success:
+ - coveralls
notifications:
email:
diff --git a/README.md b/README.md
index 1977a4fee9..1f7bcc5c61 100644
--- a/README.md
+++ b/README.md
@@ -1,7 +1,8 @@
![image](share/spack/logo/spack-logo-text-64.png "Spack")
============
-[![Build Status](https://travis-ci.org/LLNL/spack.png?branch=develop)](https://travis-ci.org/LLNL/spack)
+[![Build Status](https://travis-ci.org/LLNL/spack.svg?branch=develop)](https://travis-ci.org/LLNL/spack)
+[![Coverage Status](https://coveralls.io/repos/github/LLNL/spack/badge.svg?branch=develop)](https://coveralls.io/github/LLNL/spack?branch=develop)
Spack is a package management tool designed to support multiple
versions and configurations of software on a wide variety of platforms
diff --git a/bin/spack b/bin/spack
index 31165bba9d..f51cb8a4ec 100755
--- a/bin/spack
+++ b/bin/spack
@@ -152,7 +152,7 @@ def main():
command = spack.cmd.get_command(args.command)
try:
return_val = command(parser, args)
- except SpackError, e:
+ except SpackError as e:
e.die()
except KeyboardInterrupt:
sys.stderr.write('\n')
diff --git a/flake8.ini b/flake8.ini
new file mode 100644
index 0000000000..757c71705e
--- /dev/null
+++ b/flake8.ini
@@ -0,0 +1,3 @@
+[flake8]
+ignore = W391,F403
+max-line-length = 120 \ No newline at end of file
diff --git a/lib/spack/spack/build_environment.py b/lib/spack/spack/build_environment.py
index 411425549a..8961886049 100644
--- a/lib/spack/spack/build_environment.py
+++ b/lib/spack/spack/build_environment.py
@@ -181,8 +181,8 @@ def set_build_environment_variables(pkg, env):
# Add any pkgconfig directories to PKG_CONFIG_PATH
pkg_config_dirs = []
for p in dep_prefixes:
- for libdir in ('lib', 'lib64'):
- pcdir = join_path(p, libdir, 'pkgconfig')
+ for maybe in ('lib', 'lib64', 'share'):
+ pcdir = join_path(p, maybe, 'pkgconfig')
if os.path.isdir(pcdir):
pkg_config_dirs.append(pcdir)
env.set_path('PKG_CONFIG_PATH', pkg_config_dirs)
diff --git a/lib/spack/spack/cmd/compiler.py b/lib/spack/spack/cmd/compiler.py
index a8e9e2a7a5..d3f8779d32 100644
--- a/lib/spack/spack/cmd/compiler.py
+++ b/lib/spack/spack/cmd/compiler.py
@@ -22,19 +22,18 @@
# along with this program; if not, write to the Free Software Foundation,
# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
-import sys
import argparse
+import sys
import llnl.util.tty as tty
-from llnl.util.tty.color import colorize
-from llnl.util.tty.colify import colify
-from llnl.util.lang import index_by
-
import spack.compilers
-import spack.spec
import spack.config
-from spack.util.environment import get_path
+import spack.spec
+from llnl.util.lang import index_by
+from llnl.util.tty.colify import colify
+from llnl.util.tty.color import colorize
from spack.spec import CompilerSpec
+from spack.util.environment import get_path
description = "Manage compilers"
diff --git a/lib/spack/spack/cmd/create.py b/lib/spack/spack/cmd/create.py
index f0cd50b8df..e3a31806ab 100644
--- a/lib/spack/spack/cmd/create.py
+++ b/lib/spack/spack/cmd/create.py
@@ -124,10 +124,12 @@ class ConfigureGuesser(object):
autotools = "configure('--prefix=%s' % prefix)"
cmake = "cmake('.', *std_cmake_args)"
python = "python('setup.py', 'install', '--prefix=%s' % prefix)"
+ r = "R('CMD', 'INSTALL', '--library=%s' % self.module.r_lib_dir, '%s' % self.stage.archive_file)"
config_lines = ((r'/configure$', 'autotools', autotools),
(r'/CMakeLists.txt$', 'cmake', cmake),
- (r'/setup.py$', 'python', python))
+ (r'/setup.py$', 'python', python),
+ (r'/NAMESPACE$', 'r', r))
# Peek inside the tarball.
tar = which('tar')
@@ -272,6 +274,10 @@ def create(parser, args):
if guesser.build_system == 'python':
name = 'py-%s' % name
+ # Prepend 'r-' to R package names, by convention.
+ if guesser.build_system == 'r':
+ name = 'r-%s' % name
+
# Create a directory for the new package.
pkg_path = repo.filename_for_package_name(name)
if os.path.exists(pkg_path) and not args.force:
diff --git a/lib/spack/spack/compiler.py b/lib/spack/spack/compiler.py
index 976d96825c..0f208caaf3 100644
--- a/lib/spack/spack/compiler.py
+++ b/lib/spack/spack/compiler.py
@@ -244,6 +244,10 @@ class Compiler(object):
return None
successful = [key for key in parmap(check, checks) if key is not None]
+ # The 'successful' list is ordered like the input paths.
+ # Reverse it here so that the dict creation (last insert wins)
+ # does not spoil the intented precedence.
+ successful.reverse()
return dict(((v, p, s), path) for v, p, s, path in successful)
@classmethod
diff --git a/lib/spack/spack/config.py b/lib/spack/spack/config.py
index 14e5aaf4fb..336d47cbb7 100644
--- a/lib/spack/spack/config.py
+++ b/lib/spack/spack/config.py
@@ -539,14 +539,16 @@ def update_config(section, update_data, scope=None):
other yaml-ish structure.
"""
+ validate_section_name(section) # validate section name
+ scope = validate_scope(scope) # get ConfigScope object from string.
+
# read in the config to ensure we've got current data
- get_config(section)
+ configuration = get_config(section)
- validate_section_name(section) # validate section name
- scope = validate_scope(scope) # get ConfigScope object from string.
+ configuration.update(update_data)
# read only the requested section's data.
- scope.sections[section] = { section : update_data }
+ scope.sections[section] = {section: configuration}
scope.write_section(section)
diff --git a/lib/spack/spack/test/config.py b/lib/spack/spack/test/config.py
index 0562d2d620..3977f0e7d4 100644
--- a/lib/spack/spack/test/config.py
+++ b/lib/spack/spack/test/config.py
@@ -33,7 +33,7 @@ from spack.test.mock_packages_test import *
# Some sample compiler config data
a_comps = {
- "all": {
+ "x86_64_E5v2_IntelIB": {
"gcc@4.7.3" : {
"cc" : "/gcc473",
"cxx": "/g++473",
@@ -53,7 +53,7 @@ a_comps = {
}
b_comps = {
- "all": {
+ "x86_64_E5v3": {
"icc@10.0" : {
"cc" : "/icc100",
"cxx": "/icc100",
@@ -85,27 +85,24 @@ class ConfigTest(MockPackagesTest):
super(ConfigTest, self).tearDown()
shutil.rmtree(self.tmp_dir, True)
-
- def check_config(self, comps, *compiler_names):
+ def check_config(self, comps, arch, *compiler_names):
"""Check that named compilers in comps match Spack's config."""
config = spack.config.get_config('compilers')
compiler_list = ['cc', 'cxx', 'f77', 'fc']
for key in compiler_names:
for c in compiler_list:
- expected = comps['all'][key][c]
- actual = config['all'][key][c]
+ expected = comps[arch][key][c]
+ actual = config[arch][key][c]
self.assertEqual(expected, actual)
-
def test_write_key_in_memory(self):
# Write b_comps "on top of" a_comps.
spack.config.update_config('compilers', a_comps, 'test_low_priority')
spack.config.update_config('compilers', b_comps, 'test_high_priority')
# Make sure the config looks how we expect.
- self.check_config(a_comps, 'gcc@4.7.3', 'gcc@4.5.0')
- self.check_config(b_comps, 'icc@10.0', 'icc@11.1', 'clang@3.3')
-
+ self.check_config(a_comps, 'x86_64_E5v2_IntelIB', 'gcc@4.7.3', 'gcc@4.5.0')
+ self.check_config(b_comps, 'x86_64_E5v3', 'icc@10.0', 'icc@11.1', 'clang@3.3')
def test_write_key_to_disk(self):
# Write b_comps "on top of" a_comps.
@@ -116,5 +113,17 @@ class ConfigTest(MockPackagesTest):
spack.config.clear_config_caches()
# Same check again, to ensure consistency.
- self.check_config(a_comps, 'gcc@4.7.3', 'gcc@4.5.0')
- self.check_config(b_comps, 'icc@10.0', 'icc@11.1', 'clang@3.3')
+ self.check_config(a_comps, 'x86_64_E5v2_IntelIB', 'gcc@4.7.3', 'gcc@4.5.0')
+ self.check_config(b_comps, 'x86_64_E5v3', 'icc@10.0', 'icc@11.1', 'clang@3.3')
+
+ def test_write_to_same_priority_file(self):
+ # Write b_comps in the same file as a_comps.
+ spack.config.update_config('compilers', a_comps, 'test_low_priority')
+ spack.config.update_config('compilers', b_comps, 'test_low_priority')
+
+ # Clear caches so we're forced to read from disk.
+ spack.config.clear_config_caches()
+
+ # Same check again, to ensure consistency.
+ self.check_config(a_comps, 'x86_64_E5v2_IntelIB', 'gcc@4.7.3', 'gcc@4.5.0')
+ self.check_config(b_comps, 'x86_64_E5v3', 'icc@10.0', 'icc@11.1', 'clang@3.3')
diff --git a/lib/spack/spack/url.py b/lib/spack/spack/url.py
index f51f05cad7..ad51da9d47 100644
--- a/lib/spack/spack/url.py
+++ b/lib/spack/spack/url.py
@@ -206,6 +206,9 @@ def parse_version_offset(path):
# e.g. lame-398-1
(r'-((\d)+-\d)', stem),
+ # e.g. foobar_1.2-3
+ (r'_((\d+\.)+\d+(-\d+)?[a-z]?)', stem),
+
# e.g. foobar-4.5.1
(r'-((\d+\.)*\d+)$', stem),
diff --git a/lib/spack/spack/util/executable.py b/lib/spack/spack/util/executable.py
index fc27b789d0..25819b6fc7 100644
--- a/lib/spack/spack/util/executable.py
+++ b/lib/spack/spack/util/executable.py
@@ -144,7 +144,7 @@ class Executable(object):
cmd = self.exe + list(args)
- cmd_line = ' '.join(cmd)
+ cmd_line = "'%s'" % "' '".join(map(lambda arg: arg.replace("'", "'\"'\"'"), cmd))
tty.debug(cmd_line)
try:
diff --git a/var/spack/repos/builtin/packages/R/package.py b/var/spack/repos/builtin/packages/R/package.py
index 2471dff09b..7c4aa3520c 100644
--- a/var/spack/repos/builtin/packages/R/package.py
+++ b/var/spack/repos/builtin/packages/R/package.py
@@ -1,4 +1,14 @@
+import functools
+import glob
+import inspect
+import os
+import re
+from contextlib import closing
+
+import spack
+from llnl.util.lang import match_predicate
from spack import *
+from spack.util.environment import *
class R(Package):
@@ -9,6 +19,8 @@ class R(Package):
"""
homepage = "https://www.r-project.org"
url = "http://cran.cnr.berkeley.edu/src/base/R-3/R-3.1.2.tar.gz"
+
+ extendable = True
version('3.2.3', '1ba3dac113efab69e706902810cc2970')
version('3.2.2', '57cef5c2e210a5454da1979562a10e5b')
@@ -38,12 +50,57 @@ class R(Package):
depends_on('tk')
def install(self, spec, prefix):
+ rlibdir = join_path(prefix, 'rlib')
options = ['--prefix=%s' % prefix,
+ '--libdir=%s' % rlibdir,
'--enable-R-shlib',
- '--enable-BLAS-shlib']
+ '--enable-BLAS-shlib',
+ '--enable-R-framework=no']
if '+external-lapack' in spec:
options.extend(['--with-blas', '--with-lapack'])
configure(*options)
make()
make('install')
+
+ # ========================================================================
+ # Set up environment to make install easy for R extensions.
+ # ========================================================================
+
+ @property
+ def r_lib_dir(self):
+ return os.path.join('rlib', 'R', 'library')
+
+ def setup_dependent_environment(self, spack_env, run_env, extension_spec):
+ # Set R_LIBS to include the library dir for the
+ # extension and any other R extensions it depends on.
+ r_libs_path = []
+ for d in extension_spec.traverse():
+ if d.package.extends(self.spec):
+ r_libs_path.append(os.path.join(d.prefix, self.r_lib_dir))
+
+ r_libs_path = ':'.join(r_libs_path)
+ spack_env.set('R_LIBS', r_libs_path)
+
+ # For run time environment set only the path for extension_spec and prepend it to R_LIBS
+ if extension_spec.package.extends(self.spec):
+ run_env.prepend_path('R_LIBS', os.path.join(extension_spec.prefix, self.r_lib_dir))
+
+
+ def setup_dependent_package(self, module, ext_spec):
+ """
+ Called before R modules' install() methods.
+
+ In most cases, extensions will only need to have one line::
+
+ R('CMD', 'INSTALL', '--library=%s' % self.module.r_lib_dir, '%s' % self.stage.archive_file)
+ """
+ # R extension builds can have a global R executable function
+ module.R = Executable(join_path(self.spec.prefix.bin, 'R'))
+
+ # Add variable for library directry
+ module.r_lib_dir = os.path.join(ext_spec.prefix, self.r_lib_dir)
+
+ # Make the site packages directory for extensions, if it does not exist already.
+ if ext_spec.package.is_extension:
+ mkdirp(module.r_lib_dir)
diff --git a/var/spack/repos/builtin/packages/antlr/package.py b/var/spack/repos/builtin/packages/antlr/package.py
new file mode 100644
index 0000000000..c7c7e3e850
--- /dev/null
+++ b/var/spack/repos/builtin/packages/antlr/package.py
@@ -0,0 +1,47 @@
+from spack import *
+
+class Antlr(Package):
+
+ homepage = "http://www.antlr.org"
+ url = "https://github.com/antlr/antlr/tarball/v2.7.7"
+
+ # NOTE: This requires that a system Java be available.
+ # Spack does not yet know how to install Java compilers
+
+ # Notes from http://nco.sourceforge.net/#bld
+ # The first steps to build (i.e., compile, for the most part) NCO from
+ # source code are to install the pre-requisites: ANTLR version 2.7.7
+ # (like this one not version 3.x or 4.x!) (required for ncap2)... ANTLR
+ # binaries from major distributions are pre-built with the source patch
+ # necessary to allow NCO to link to ANTLR... The ANTLR source file
+ # CharScanner.hpp must include this line: #include <cstring> or else
+ # ncap2 will not compile (this tarball is already patched).
+ version('2.7.7', '914865e853fe8e1e61a9f23d045cb4ab',
+ # Patched version as described above
+ url='http://dust.ess.uci.edu/tmp/antlr-2.7.7.tar.gz')
+ # Unpatched version
+ # url='http://dust.ess.uci.edu/nco/antlr-2.7.7.tar.gz')
+
+ variant('cxx', default=False, description='Enable ANTLR for C++')
+ variant('java', default=False, description='Enable ANTLR for Java')
+ variant('python', default=False, description='Enable ANTLR for Python')
+ variant('csharp', default=False, description='Enable ANTLR for Csharp')
+
+
+ def install(self, spec, prefix):
+ # Check for future enabling of variants
+ for v in ('+java', '+python', '+csharp'):
+ if v in spec:
+ raise Error('Illegal variant %s; for now, Spack only knows how to build antlr or antlr+cxx')
+
+ config_args = [
+ '--prefix=%s' % prefix,
+ '--%s-cxx' % ('enable' if '+cxx' in spec else 'disable'),
+ '--%s-java' % ('enable' if '+java' in spec else 'disable'),
+ '--%s-python' % ('enable' if '+python' in spec else 'disable'),
+ '--%s-csharp' % ('enable' if '+csharp' in spec else 'disable')]
+
+ # which('autoreconf')('-iv')
+ configure(*config_args)
+ make()
+ make("install")
diff --git a/var/spack/repos/builtin/packages/binutils/package.py b/var/spack/repos/builtin/packages/binutils/package.py
index b8064093d2..158d722046 100644
--- a/var/spack/repos/builtin/packages/binutils/package.py
+++ b/var/spack/repos/builtin/packages/binutils/package.py
@@ -29,6 +29,7 @@ class Binutils(Package):
configure_args = [
'--prefix=%s' % prefix,
'--disable-dependency-tracking',
+ '--disable-werror',
'--enable-interwork',
'--enable-multilib',
'--enable-shared',
diff --git a/var/spack/repos/builtin/packages/bison/package.py b/var/spack/repos/builtin/packages/bison/package.py
index 7c526fb958..9a2ddcbf96 100644
--- a/var/spack/repos/builtin/packages/bison/package.py
+++ b/var/spack/repos/builtin/packages/bison/package.py
@@ -10,6 +10,8 @@ class Bison(Package):
version('3.0.4', 'a586e11cd4aff49c3ff6d3b6a4c9ccf8')
+ depends_on("m4")
+
def install(self, spec, prefix):
configure("--prefix=%s" % prefix)
diff --git a/var/spack/repos/builtin/packages/cbtf-argonavis/package.py b/var/spack/repos/builtin/packages/cbtf-argonavis/package.py
index 7b07933911..90789a98f2 100644
--- a/var/spack/repos/builtin/packages/cbtf-argonavis/package.py
+++ b/var/spack/repos/builtin/packages/cbtf-argonavis/package.py
@@ -1,5 +1,5 @@
################################################################################
-# Copyright (c) 2015 Krell Institute. All Rights Reserved.
+# Copyright (c) 2015-2016 Krell Institute. All Rights Reserved.
#
# This program is free software; you can redistribute it and/or modify it under
# the terms of the GNU General Public License as published by the Free Software
@@ -24,43 +24,83 @@ class CbtfArgonavis(Package):
homepage = "http://sourceforge.net/p/cbtf/wiki/Home/"
# Mirror access template example
- #url = "file:/g/g24/jeg/cbtf-argonavis-1.5.tar.gz"
- #version('1.5', '1f7f6512f55409ed2135cfceabe26b82')
+ #url = "file:/home/jeg/OpenSpeedShop_ROOT/SOURCES/cbtf-argonavis-1.6.tar.gz"
+ #version('1.6', '0fafa0008478405c2c2319450f174ed4')
- version('1.6', branch='master', git='http://git.code.sf.net/p/cbtf-argonavis/cbtf-argonavis')
+ version('1.6', branch='master', git='https://github.com/OpenSpeedShop/cbtf-argonavis.git')
- depends_on("cmake@3.0.2:")
+ depends_on("cmake@3.0.2")
+ depends_on("boost@1.50.0:")
depends_on("papi")
+ depends_on("mrnet@5.0.1:+lwthreads+krellpatch")
depends_on("cbtf")
depends_on("cbtf-krell")
- depends_on("cuda")
+ depends_on("cuda@6.0.37")
+ #depends_on("cuda")
parallel = False
+ def adjustBuildTypeParams_cmakeOptions(self, spec, cmakeOptions):
+ # Sets build type parameters into cmakeOptions the options that will enable the cbtf-krell built type settings
+
+ compile_flags="-O2 -g"
+ BuildTypeOptions = []
+
+ # Set CMAKE_BUILD_TYPE to what cbtf-krell wants it to be, not the stdcmakeargs
+ for word in cmakeOptions[:]:
+ if word.startswith('-DCMAKE_BUILD_TYPE'):
+ cmakeOptions.remove(word)
+ if word.startswith('-DCMAKE_CXX_FLAGS'):
+ cmakeOptions.remove(word)
+ if word.startswith('-DCMAKE_C_FLAGS'):
+ cmakeOptions.remove(word)
+ if word.startswith('-DCMAKE_VERBOSE_MAKEFILE'):
+ cmakeOptions.remove(word)
+ BuildTypeOptions.extend([
+ '-DCMAKE_VERBOSE_MAKEFILE=ON',
+ '-DCMAKE_BUILD_TYPE=None',
+ '-DCMAKE_CXX_FLAGS=%s' % compile_flags,
+ '-DCMAKE_C_FLAGS=%s' % compile_flags
+ ])
+
+ cmakeOptions.extend(BuildTypeOptions)
+
+
def install(self, spec, prefix):
# Look for package installation information in the cbtf and cbtf-krell prefixes
cmake_prefix_path = join_path(spec['cbtf'].prefix) + ':' + join_path(spec['cbtf-krell'].prefix)
- # FIXME, hard coded for testing purposes, we will alter when the external package feature is available
- cuda_prefix_path = "/usr/local/cudatoolkit-6.0"
- cupti_prefix_path = "/usr/local/cudatoolkit-6.0/extras/CUPTI"
-
-
with working_dir('CUDA'):
with working_dir('build', create=True):
- cmake('..',
- '-DCMAKE_INSTALL_PREFIX=%s' % prefix,
- '-DCMAKE_LIBRARY_PATH=%s' % prefix.lib64,
- '-DCMAKE_PREFIX_PATH=%s' % cmake_prefix_path,
- '-DCUDA_INSTALL_PATH=%s' % cuda_prefix_path,
- '-DCUDA_ROOT=%s' % cuda_prefix_path,
- '-DCUPTI_ROOT=%s' % cupti_prefix_path,
- '-DCUDA_DIR=%s' % cuda_prefix_path,
- '-DPAPI_ROOT=%s' % spec['papi'].prefix,
- '-DCBTF_PREFIX=%s' % spec['cbtf'].prefix,
- *std_cmake_args)
- make("clean")
- make()
- make("install")
+ cmakeOptions = []
+ cmakeOptions.extend(['-DCMAKE_INSTALL_PREFIX=%s' % prefix,
+ '-DCMAKE_PREFIX_PATH=%s' % cmake_prefix_path,
+ '-DCUDA_DIR=%s' % spec['cuda'].prefix,
+ '-DCUDA_INSTALL_PATH=%s' % spec['cuda'].prefix,
+ '-DCUDA_TOOLKIT_ROOT_DIR=%s' % spec['cuda'].prefix,
+ '-DCUPTI_DIR=%s' % join_path(spec['cuda'].prefix + '/extras/CUPTI'),
+ '-DCUPTI_ROOT=%s' % join_path(spec['cuda'].prefix + '/extras/CUPTI'),
+ '-DPAPI_ROOT=%s' % spec['papi'].prefix,
+ '-DCBTF_DIR=%s' % spec['cbtf'].prefix,
+ '-DCBTF_KRELL_DIR=%s' % spec['cbtf-krell'].prefix,
+ '-DBOOST_ROOT=%s' % spec['boost'].prefix,
+ '-DBoost_DIR=%s' % spec['boost'].prefix,
+ '-DBOOST_LIBRARYDIR=%s' % spec['boost'].prefix.lib,
+ '-DMRNET_DIR=%s' % spec['mrnet'].prefix,
+ '-DBoost_NO_SYSTEM_PATHS=ON'
+ ])
+
+ # Add in the standard cmake arguments
+ cmakeOptions.extend(std_cmake_args)
+
+ # Adjust the standard cmake arguments to what we want the build type, etc to be
+ self.adjustBuildTypeParams_cmakeOptions(spec, cmakeOptions)
+
+ # Invoke cmake
+ cmake('..', *cmakeOptions)
+
+ make("clean")
+ make()
+ make("install")
diff --git a/var/spack/repos/builtin/packages/cbtf-krell/package.py b/var/spack/repos/builtin/packages/cbtf-krell/package.py
index 9458ac113c..e6050cb4a9 100644
--- a/var/spack/repos/builtin/packages/cbtf-krell/package.py
+++ b/var/spack/repos/builtin/packages/cbtf-krell/package.py
@@ -1,5 +1,5 @@
################################################################################
-# Copyright (c) 2015 Krell Institute. All Rights Reserved.
+# Copyright (c) 2015-2016 Krell Institute. All Rights Reserved.
#
# This program is free software; you can redistribute it and/or modify it under
# the terms of the GNU General Public License as published by the Free Software
@@ -26,21 +26,30 @@ class CbtfKrell(Package):
homepage = "http://sourceforge.net/p/cbtf/wiki/Home/"
# optional mirror access template
- #url = "file:/g/g24/jeg/cbtf-krell-1.5.tar.gz"
- #version('1.5', 'b13f6df6a93c44149d977773dd776d2f')
+ #url = "file:/home/jeg/cbtf-krell-1.6.tar.gz"
+ #version('1.6', 'edeb61cd488f16e7b124f77db9ce762d')
- version('1.6', branch='master', git='http://git.code.sf.net/p/cbtf-krell/cbtf-krell')
+ version('1.6', branch='master', git='https://github.com/OpenSpeedShop/cbtf-krell.git')
+ # MPI variants
+ variant('openmpi', default=False, description="Build mpi experiment collector for openmpi MPI when this variant is enabled.")
+ variant('mpt', default=False, description="Build mpi experiment collector for SGI MPT MPI when this variant is enabled.")
+ variant('mvapich2', default=False, description="Build mpi experiment collector for mvapich2 MPI when this variant is enabled.")
+ variant('mvapich', default=False, description="Build mpi experiment collector for mvapich MPI when this variant is enabled.")
+ variant('mpich2', default=False, description="Build mpi experiment collector for mpich2 MPI when this variant is enabled.")
+ variant('mpich', default=False, description="Build mpi experiment collector for mpich MPI when this variant is enabled.")
# Dependencies for cbtf-krell
+ depends_on("cmake@3.0.2")
# For binutils service
depends_on("binutils@2.24+krellpatch")
# collectionTool
- depends_on("boost@1.50.0")
- depends_on("dyninst@8.2.1")
- depends_on("mrnet@4.1.0:+lwthreads")
+ depends_on("boost@1.50.0:")
+ depends_on("dyninst@8.2.1:")
+ depends_on("mrnet@5.0.1:+lwthreads+krellpatch")
+
depends_on("xerces-c@3.1.1:")
depends_on("cbtf")
@@ -51,66 +60,207 @@ class CbtfKrell(Package):
# MPI Installations
# These have not worked either for build or execution, commenting out for now
- #depends_on("openmpi")
- #depends_on("mvapich2@2.0")
- #depends_on("mpich")
+ depends_on("openmpi", when='+openmpi')
+ depends_on("mpich", when='+mpich')
+ depends_on("mpich2", when='+mpich2')
+ depends_on("mvapich2", when='+mvapich2')
+ depends_on("mvapich", when='+mvapich')
+ depends_on("mpt", when='+mpt')
parallel = False
+ def adjustBuildTypeParams_cmakeOptions(self, spec, cmakeOptions):
+ # Sets build type parameters into cmakeOptions the options that will enable the cbtf-krell built type settings
+
+ compile_flags="-O2 -g"
+ BuildTypeOptions = []
+ # Set CMAKE_BUILD_TYPE to what cbtf-krell wants it to be, not the stdcmakeargs
+ for word in cmakeOptions[:]:
+ if word.startswith('-DCMAKE_BUILD_TYPE'):
+ cmakeOptions.remove(word)
+ if word.startswith('-DCMAKE_CXX_FLAGS'):
+ cmakeOptions.remove(word)
+ if word.startswith('-DCMAKE_C_FLAGS'):
+ cmakeOptions.remove(word)
+ if word.startswith('-DCMAKE_VERBOSE_MAKEFILE'):
+ cmakeOptions.remove(word)
+ BuildTypeOptions.extend([
+ '-DCMAKE_VERBOSE_MAKEFILE=ON',
+ '-DCMAKE_BUILD_TYPE=None',
+ '-DCMAKE_CXX_FLAGS=%s' % compile_flags,
+ '-DCMAKE_C_FLAGS=%s' % compile_flags
+ ])
+
+ cmakeOptions.extend(BuildTypeOptions)
+
+
+
+ def set_mpi_cmakeOptions(self, spec, cmakeOptions):
+ # Appends to cmakeOptions the options that will enable the appropriate MPI implementations
+
+ MPIOptions = []
+
+ # openmpi
+ if '+openmpi' in spec:
+ MPIOptions.extend([
+ '-DOPENMPI_DIR=%s' % spec['openmpi'].prefix
+ ])
+ # mpich
+ if '+mpich' in spec:
+ MPIOptions.extend([
+ '-DMPICH_DIR=%s' % spec['mpich'].prefix
+ ])
+ # mpich2
+ if '+mpich2' in spec:
+ MPIOptions.extend([
+ '-DMPICH2_DIR=%s' % spec['mpich2'].prefix
+ ])
+ # mvapich
+ if '+mvapich' in spec:
+ MPIOptions.extend([
+ '-DMVAPICH_DIR=%s' % spec['mvapich'].prefix
+ ])
+ # mvapich2
+ if '+mvapich2' in spec:
+ MPIOptions.extend([
+ '-DMVAPICH2_DIR=%s' % spec['mvapich2'].prefix
+ ])
+ # mpt
+ if '+mpt' in spec:
+ MPIOptions.extend([
+ '-DMPT_DIR=%s' % spec['mpt'].prefix
+ ])
+
+ cmakeOptions.extend(MPIOptions)
+
def install(self, spec, prefix):
# Add in paths for finding package config files that tell us where to find these packages
- cmake_prefix_path = join_path(spec['cbtf'].prefix) + ':' + join_path(spec['dyninst'].prefix)
-
- # FIXME - hard code path until external package support is available
- # Need to change this path and/or add additional paths for MPI experiment support on different platforms
- #openmpi_prefix_path = "/opt/openmpi-1.8.2"
- #mvapich_prefix_path = "/usr/local/tools/mvapich-gnu"
-
- # Other possibilities, they will need a -DMVAPICH_DIR=, etc clause in the cmake command to be recognized
- # mvapich_prefix_path = "<mvapich install path>"
- # mvapich2_prefix_path = "<mvapich2 install path>"
- # mpich2_prefix_path = "<mpich2 install path>"
- # mpich_prefix_path = "<mpich install path>"
- # mpt_prefix_path = "<mpt install path>"
-
- # Add in paths for cuda if requested via the cuda variant
- # FIXME - hard code path until external package support is available
- #if '+cuda' in spec:
- # cuda_prefix_path = "/usr/local/cuda-6.0"
- # cupti_prefix_path = "/usr/local/cuda-6.0/extras/CUPTI"
- #else:
- # cuda_prefix_path = ""
- # cupti_prefix_path = ""
-
- #'-DMVAPICH2_DIR=%s' % spec['mvapich2'].prefix,
- #'-DOPENMPI_DIR=%s' % spec['openmpi'].prefix,
- #'-DMPICH_DIR=%s' % spec['mpich'].prefix,
- #'-DCMAKE_LIBRARY_PATH=%s' % prefix.lib64,
- #'-DOPENMPI_DIR=%s' % openmpi_prefix_path,
- #'-DMVAPICH_DIR=%s' % mvapich_prefix_path,
- #'-DLIB_SUFFIX=64',
- #'-DCUDA_DIR=%s' % cuda_prefix_path,
- #'-DCUPTI_DIR=%s' % cupti_prefix_path,
+ #cmake_prefix_path = join_path(spec['cbtf'].prefix) + ':' + join_path(spec['dyninst'].prefix)
+ #'-DCMAKE_PREFIX_PATH=%s' % cmake_prefix_path
# Build cbtf-krell with cmake
with working_dir('build_cbtf_krell', create=True):
- cmake('..',
- '-DCMAKE_BUILD_TYPE=Debug',
- '-DCMAKE_INSTALL_PREFIX=%s' % prefix,
- '-DCBTF_DIR=%s' % spec['cbtf'].prefix,
- '-DBINUTILS_DIR=%s' % spec['binutils'].prefix,
- '-DLIBMONITOR_DIR=%s' % spec['libmonitor'].prefix,
- '-DLIBUNWIND_DIR=%s' % spec['libunwind'].prefix,
- '-DPAPI_DIR=%s' % spec['papi'].prefix,
- '-DBOOST_DIR=%s' % spec['boost'].prefix,
- '-DMRNET_DIR=%s' % spec['mrnet'].prefix,
- '-DDYNINST_DIR=%s' % spec['dyninst'].prefix,
- '-DXERCESC_DIR=%s' % spec['xerces-c'].prefix,
- '-DCMAKE_PREFIX_PATH=%s' % cmake_prefix_path,
- *std_cmake_args)
+ cmakeOptions = []
+ cmakeOptions.extend(['-DCMAKE_INSTALL_PREFIX=%s' % prefix,
+ '-DCBTF_DIR=%s' % spec['cbtf'].prefix,
+ '-DBINUTILS_DIR=%s' % spec['binutils'].prefix,
+ '-DLIBMONITOR_DIR=%s' % spec['libmonitor'].prefix,
+ '-DLIBUNWIND_DIR=%s' % spec['libunwind'].prefix,
+ '-DPAPI_DIR=%s' % spec['papi'].prefix,
+ '-DBOOST_DIR=%s' % spec['boost'].prefix,
+ '-DMRNET_DIR=%s' % spec['mrnet'].prefix,
+ '-DDYNINST_DIR=%s' % spec['dyninst'].prefix,
+ '-DXERCESC_DIR=%s' % spec['xerces-c'].prefix
+ ])
+
+
+ # Add any MPI implementations coming from variant settings
+ self.set_mpi_cmakeOptions(spec, cmakeOptions)
+
+ # Add in the standard cmake arguments
+ cmakeOptions.extend(std_cmake_args)
+
+ # Adjust the standard cmake arguments to what we want the build type, etc to be
+ self.adjustBuildTypeParams_cmakeOptions(spec, cmakeOptions)
+
+ # Invoke cmake
+ cmake('..', *cmakeOptions)
make("clean")
make()
make("install")
+
+
+ #if '+cray' in spec:
+ #if 'cray' in self.spec.architecture:
+ # if '+runtime' in spec:
+ # with working_dir('build_cbtf_cray_runtime', create=True):
+ # python_vers='%d.%d' % spec['python'].version[:2]
+ # cmake .. \
+ # -DCMAKE_BUILD_TYPE=Debug \
+ # -DTARGET_OS="cray" \
+ # -DRUNTIME_ONLY="true" \
+ # -DCMAKE_INSTALL_PREFIX=${CBTF_KRELL_PREFIX} \
+ # -DCMAKE_PREFIX_PATH=${CBTF_ROOT} \
+ # -DCBTF_DIR=${CBTF_ROOT} \
+ # -DBOOST_ROOT=${BOOST_INSTALL_PREFIX} \
+ # -DXERCESC_DIR=${XERCESC_INSTALL_PREFIX} \
+ # -DBINUTILS_DIR=${KRELL_ROOT} \
+ # -DLIBMONITOR_DIR=${KRELL_ROOT_COMPUTE} \
+ # -DLIBUNWIND_DIR=${KRELL_ROOT_COMPUTE} \
+ # -DPAPI_DIR=${PAPI_ROOT} \
+ # -DDYNINST_DIR=${DYNINST_CN_ROOT} \
+ # -DMRNET_DIR=${MRNET_INSTALL_PREFIX} \
+ # -DMPICH2_DIR=/opt/cray/mpt/7.0.1/gni/mpich2-gnu/48
+ # else:
+ # with working_dir('build_cbtf_cray_frontend', create=True):
+ # python_vers='%d.%d' % spec['python'].version[:2]
+ # cmake .. \
+ # -DCMAKE_BUILD_TYPE=Debug \
+ # -DCMAKE_INSTALL_PREFIX=${CBTF_KRELL_PREFIX} \
+ # -DCMAKE_PREFIX_PATH=${CBTF_ROOT} \
+ # -DCBTF_DIR=${CBTF_ROOT} \
+ # -DRUNTIME_TARGET_OS="cray" \
+ # -DCBTF_KRELL_CN_RUNTIME_DIR=${CBTF_KRELL_CN_RUNTIME_ROOT} \
+ # -DCBTF_CN_RUNTIME_DIR=${CBTF_CN_RUNTIME_ROOT} \
+ # -DLIBMONITOR_CN_RUNTIME_DIR=${LIBMONITOR_CN_ROOT} \
+ # -DLIBUNWIND_CN_RUNTIME_DIR=${LIBUNWIND_CN_ROOT} \
+ # -DPAPI_CN_RUNTIME_DIR=${PAPI_CN_ROOT} \
+ # -DXERCESC_CN_RUNTIME_DIR=/${XERCESC_CN_ROOT} \
+ # -DMRNET_CN_RUNTIME_DIR=${MRNET_CN_ROOT} \
+ # -DBOOST_CN_RUNTIME_DIR=${BOOST_CN_ROOT} \
+ # -DDYNINST_CN_RUNTIME_DIR=${DYNINST_CN_ROOT} \
+ # -DBOOST_ROOT=/${KRELL_ROOT} \
+ # -DXERCESC_DIR=/${KRELL_ROOT} \
+ # -DBINUTILS_DIR=/${KRELL_ROOT} \
+ # -DLIBMONITOR_DIR=${KRELL_ROOT} \
+ # -DLIBUNWIND_DIR=${KRELL_ROOT} \
+ # -DPAPI_DIR=${PAPI_ROOT} \
+ # -DDYNINST_DIR=${KRELL_ROOT} \
+ # -DMRNET_DIR=${KRELL_ROOT} \
+ # -DMPICH2_DIR=/opt/cray/mpt/7.0.1/gni/mpich2-gnu/48
+ # fi
+#
+# make("clean")
+# make()
+# make("install")
+#
+# elif '+mic' in spec:
+# if '+runtime' in spec:
+# with working_dir('build_cbtf_mic_runtime', create=True):
+# python_vers='%d.%d' % spec['python'].version[:2]
+# cmake .. \
+#
+# else:
+# with working_dir('build_cbtf_cray_frontend', create=True):
+# python_vers='%d.%d' % spec['python'].version[:2]
+# cmake .. \
+# fi
+#
+# else:
+# # Build cbtf-krell with cmake
+# with working_dir('build_cbtf_krell', create=True):
+# cmake('..',
+# '-DCMAKE_BUILD_TYPE=Debug',
+# '-DCMAKE_INSTALL_PREFIX=%s' % prefix,
+# '-DCBTF_DIR=%s' % spec['cbtf'].prefix,
+# '-DBINUTILS_DIR=%s' % spec['binutils'].prefix,
+# '-DLIBMONITOR_DIR=%s' % spec['libmonitor'].prefix,
+# '-DLIBUNWIND_DIR=%s' % spec['libunwind'].prefix,
+# '-DPAPI_DIR=%s' % spec['papi'].prefix,
+# '-DBOOST_DIR=%s' % spec['boost'].prefix,
+# '-DMRNET_DIR=%s' % spec['mrnet'].prefix,
+# '-DDYNINST_DIR=%s' % spec['dyninst'].prefix,
+# '-DXERCESC_DIR=%s' % spec['xerces-c'].prefix,
+# '-DOPENMPI_DIR=%s' % openmpi_prefix_path,
+# '-DCMAKE_PREFIX_PATH=%s' % cmake_prefix_path,
+# *std_cmake_args)
+#
+# make("clean")
+# make()
+# make("install")
+#
+# fi
+#
diff --git a/var/spack/repos/builtin/packages/cbtf-lanl/package.py b/var/spack/repos/builtin/packages/cbtf-lanl/package.py
index 2da9e8a1f7..5ca88601f3 100644
--- a/var/spack/repos/builtin/packages/cbtf-lanl/package.py
+++ b/var/spack/repos/builtin/packages/cbtf-lanl/package.py
@@ -1,5 +1,5 @@
################################################################################
-# Copyright (c) 2015 Krell Institute. All Rights Reserved.
+# Copyright (c) 2015-2016 Krell Institute. All Rights Reserved.
#
# This program is free software; you can redistribute it and/or modify it under
# the terms of the GNU General Public License as published by the Free Software
@@ -29,32 +29,65 @@ class CbtfLanl(Package):
version('1.6', branch='master', git='http://git.code.sf.net/p/cbtf-lanl/cbtf-lanl')
-
+ depends_on("cmake@3.0.2")
# Dependencies for cbtf-krell
- depends_on("boost@1.50")
- depends_on("mrnet@4.1.0:+lwthreads")
+ depends_on("mrnet@5.0.1:+lwthreads+krellpatch")
depends_on("xerces-c@3.1.1:")
depends_on("cbtf")
depends_on("cbtf-krell")
parallel = False
+ def adjustBuildTypeParams_cmakeOptions(self, spec, cmakeOptions):
+ # Sets build type parameters into cmakeOptions the options that will enable the cbtf-krell built type settings
+
+ compile_flags="-O2 -g"
+ BuildTypeOptions = []
+ # Set CMAKE_BUILD_TYPE to what cbtf-krell wants it to be, not the stdcmakeargs
+ for word in cmakeOptions[:]:
+ if word.startswith('-DCMAKE_BUILD_TYPE'):
+ cmakeOptions.remove(word)
+ if word.startswith('-DCMAKE_CXX_FLAGS'):
+ cmakeOptions.remove(word)
+ if word.startswith('-DCMAKE_C_FLAGS'):
+ cmakeOptions.remove(word)
+ if word.startswith('-DCMAKE_VERBOSE_MAKEFILE'):
+ cmakeOptions.remove(word)
+ BuildTypeOptions.extend([
+ '-DCMAKE_VERBOSE_MAKEFILE=ON',
+ '-DCMAKE_BUILD_TYPE=None',
+ '-DCMAKE_CXX_FLAGS=%s' % compile_flags,
+ '-DCMAKE_C_FLAGS=%s' % compile_flags
+ ])
+
+ cmakeOptions.extend(BuildTypeOptions)
+
def install(self, spec, prefix):
# Add in paths for finding package config files that tell us where to find these packages
cmake_prefix_path = join_path(spec['cbtf'].prefix) + ':' + join_path(spec['cbtf-krell'].prefix)
with working_dir('build', create=True):
- cmake('..',
- '-DCBTF_DIR=%s' % spec['cbtf'].prefix,
- '-DCBTF_KRELL_DIR=%s' % spec['cbtf-krell'].prefix,
- '-DMRNET_DIR=%s' % spec['mrnet'].prefix,
- '-DXERCESC_DIR=%s' % spec['xerces-c'].prefix,
- '-DCMAKE_PREFIX_PATH=%s' % cmake_prefix_path,
- '-DCMAKE_MODULE_PATH=%s' % join_path(prefix.share,'KrellInstitute','cmake'),
- *std_cmake_args)
-
- make("clean")
- make()
- make("install")
+ cmakeOptions = []
+ cmakeOptions.extend(['-DCMAKE_INSTALL_PREFIX=%s' % prefix,
+ '-DCBTF_DIR=%s' % spec['cbtf'].prefix,
+ '-DCBTF_KRELL_DIR=%s' % spec['cbtf-krell'].prefix,
+ '-DMRNET_DIR=%s' % spec['mrnet'].prefix,
+ '-DXERCESC_DIR=%s' % spec['xerces-c'].prefix,
+ '-DCMAKE_PREFIX_PATH=%s' % cmake_prefix_path,
+ '-DCMAKE_MODULE_PATH=%s' % join_path(prefix.share,'KrellInstitute','cmake')
+ ])
+
+ # Add in the standard cmake arguments
+ cmakeOptions.extend(std_cmake_args)
+
+ # Adjust the standard cmake arguments to what we want the build type, etc to be
+ self.adjustBuildTypeParams_cmakeOptions(spec, cmakeOptions)
+
+ # Invoke cmake
+ cmake('..', *cmakeOptions)
+
+ make("clean")
+ make()
+ make("install")
diff --git a/var/spack/repos/builtin/packages/cbtf/package.py b/var/spack/repos/builtin/packages/cbtf/package.py
index 52e6a07020..7ce1cd382b 100644
--- a/var/spack/repos/builtin/packages/cbtf/package.py
+++ b/var/spack/repos/builtin/packages/cbtf/package.py
@@ -1,5 +1,5 @@
################################################################################
-# Copyright (c) 2015 Krell Institute. All Rights Reserved.
+# Copyright (c) 2015-2016 Krell Institute. All Rights Reserved.
#
# This program is free software; you can redistribute it and/or modify it under
# the terms of the GNU General Public License as published by the Free Software
@@ -25,21 +25,44 @@ class Cbtf(Package):
homepage = "http://sourceforge.net/p/cbtf/wiki/Home"
# Mirror access template example
- #url = "file:/g/g24/jeg/cbtf-1.5.tar.gz"
- #version('1.6', '1ca88a8834759c4c74452cb97fe7b70a')
+ #url = "file:/home/jeg/cbtf-1.6.tar.gz"
+ #version('1.6', 'c1ef4e5aa4e470dffb042abdba0b9987')
# Use when the git repository is available
- version('1.6', branch='master', git='http://git.code.sf.net/p/cbtf/cbtf')
+ version('1.6', branch='master', git='https://github.com/OpenSpeedShop/cbtf.git')
- depends_on("cmake")
- #depends_on("boost@1.42.0:")
- depends_on("boost@1.50.0")
- depends_on("mrnet@4.1.0+lwthreads")
+ variant('runtime', default=False, description="build only the runtime libraries and collectors.")
+
+ depends_on("cmake@3.0.2")
+ depends_on("boost@1.50.0:")
+ depends_on("mrnet@5.0.1:+lwthreads+krellpatch")
depends_on("xerces-c@3.1.1:")
- depends_on("libxml2")
+ # Work around for spack libxml2 package bug, take off python when fixed
+ depends_on("libxml2+python")
parallel = False
+ def adjustBuildTypeParams_cmakeOptions(self, spec, cmakeOptions):
+ # Sets build type parameters into cmakeOptions the options that will enable the cbtf-krell built type settings
+
+ compile_flags="-O2 -g"
+ BuildTypeOptions = []
+ # Set CMAKE_BUILD_TYPE to what cbtf-krell wants it to be, not the stdcmakeargs
+ for word in cmakeOptions[:]:
+ if word.startswith('-DCMAKE_BUILD_TYPE'):
+ cmakeOptions.remove(word)
+ if word.startswith('-DCMAKE_CXX_FLAGS'):
+ cmakeOptions.remove(word)
+ if word.startswith('-DCMAKE_C_FLAGS'):
+ cmakeOptions.remove(word)
+ BuildTypeOptions.extend([
+ '-DCMAKE_BUILD_TYPE=None',
+ '-DCMAKE_CXX_FLAGS=%s' % compile_flags,
+ '-DCMAKE_C_FLAGS=%s' % compile_flags
+ ])
+
+ cmakeOptions.extend(BuildTypeOptions)
+
def install(self, spec, prefix):
with working_dir('build', create=True):
@@ -48,14 +71,45 @@ class Cbtf(Package):
# or BOOST_INCLUDEDIR). Useful when specifying BOOST_ROOT.
# Defaults to OFF.
- cmake('..',
- '--debug-output',
- '-DBoost_NO_SYSTEM_PATHS=TRUE',
- '-DXERCESC_DIR=%s' % spec['xerces-c'].prefix,
- '-DBOOST_ROOT=%s' % spec['boost'].prefix,
- '-DMRNET_DIR=%s' % spec['mrnet'].prefix,
- '-DCMAKE_MODULE_PATH=%s' % join_path(prefix.share,'KrellInstitute','cmake'),
- *std_cmake_args)
+ if '+runtime' in spec:
+ # Install message tag include file for use in Intel MIC cbtf-krell build
+ # FIXME
+ cmakeOptions = []
+ cmakeOptions.extend(['-DCMAKE_INSTALL_PREFIX=%s' % prefix,
+ '-DBoost_NO_SYSTEM_PATHS=TRUE',
+ '-DXERCESC_DIR=%s' % spec['xerces-c'].prefix,
+ '-DBOOST_ROOT=%s' % spec['boost'].prefix,
+ '-DMRNET_DIR=%s' % spec['mrnet'].prefix,
+ '-DCMAKE_MODULE_PATH=%s' % join_path(prefix.share,'KrellInstitute','cmake')
+ ])
+
+ # Add in the standard cmake arguments
+ cmakeOptions.extend(std_cmake_args)
+
+ # Adjust the standard cmake arguments to what we want the build type, etc to be
+ self.adjustBuildTypeParams_cmakeOptions(spec, cmakeOptions)
+
+ # Invoke cmake
+ cmake('..', *cmakeOptions)
+
+ else:
+ cmakeOptions = []
+ cmakeOptions.extend(['-DCMAKE_INSTALL_PREFIX=%s' % prefix,
+ '-DBoost_NO_SYSTEM_PATHS=TRUE',
+ '-DXERCESC_DIR=%s' % spec['xerces-c'].prefix,
+ '-DBOOST_ROOT=%s' % spec['boost'].prefix,
+ '-DMRNET_DIR=%s' % spec['mrnet'].prefix,
+ '-DCMAKE_MODULE_PATH=%s' % join_path(prefix.share,'KrellInstitute','cmake')
+ ])
+
+ # Add in the standard cmake arguments
+ cmakeOptions.extend(std_cmake_args)
+
+ # Adjust the standard cmake arguments to what we want the build type, etc to be
+ self.adjustBuildTypeParams_cmakeOptions(spec, cmakeOptions)
+
+ # Invoke cmake
+ cmake('..', *cmakeOptions)
make("clean")
make()
diff --git a/var/spack/repos/builtin/packages/fftw/package.py b/var/spack/repos/builtin/packages/fftw/package.py
index bc129aaf1a..4ffc787594 100644
--- a/var/spack/repos/builtin/packages/fftw/package.py
+++ b/var/spack/repos/builtin/packages/fftw/package.py
@@ -42,7 +42,7 @@ class Fftw(Package):
variant('float', default=True, description='Produces a single precision version of the library')
variant('long_double', default=True, description='Produces a long double precision version of the library')
variant('quad', default=False, description='Produces a quad precision version of the library (works only with GCC and libquadmath)')
-
+ variant('openmp', default=False, description="Enable OpenMP support.")
variant('mpi', default=False, description='Activate MPI support')
depends_on('mpi', when='+mpi')
@@ -52,8 +52,15 @@ class Fftw(Package):
def install(self, spec, prefix):
options = ['--prefix=%s' % prefix,
'--enable-shared',
- '--enable-threads',
- '--enable-openmp']
+ '--enable-threads']
+ # Add support for OpenMP
+ if '+openmp' in spec:
+ # Note: Apple's Clang does not support OpenMP.
+ if spec.satisfies('%clang'):
+ ver = str(self.compiler.version)
+ if ver.endswith('-apple'):
+ raise InstallError("Apple's clang does not support OpenMP")
+ options.append('--enable-openmp')
if not self.compiler.f77 or not self.compiler.fc:
options.append("--disable-fortran")
if '+mpi' in spec:
diff --git a/var/spack/repos/builtin/packages/gdb/package.py b/var/spack/repos/builtin/packages/gdb/package.py
index b346fe80c2..0e9e8fc099 100644
--- a/var/spack/repos/builtin/packages/gdb/package.py
+++ b/var/spack/repos/builtin/packages/gdb/package.py
@@ -34,6 +34,7 @@ class Gdb(Package):
homepage = "https://www.gnu.org/software/gdb"
url = "http://ftp.gnu.org/gnu/gdb/gdb-7.10.tar.gz"
+ version('7.11', 'f585059252836a981ea5db9a5f8ce97f')
version('7.10.1', 'b93a2721393e5fa226375b42d567d90b')
version('7.10', 'fa6827ad0fd2be1daa418abb11a54d86')
version('7.9.1', 'f3b97de919a9dba84490b2e076ec4cb0')
diff --git a/var/spack/repos/builtin/packages/glib/package.py b/var/spack/repos/builtin/packages/glib/package.py
index 67ead5f941..a3fc3f79eb 100644
--- a/var/spack/repos/builtin/packages/glib/package.py
+++ b/var/spack/repos/builtin/packages/glib/package.py
@@ -1,4 +1,5 @@
from spack import *
+import sys
class Glib(Package):
"""The GLib package contains a low-level libraries useful for
@@ -12,6 +13,8 @@ class Glib(Package):
depends_on("libffi")
depends_on("zlib")
+ depends_on("pkg-config")
+ depends_on('gettext', sys.platform=='darwin')
def install(self, spec, prefix):
configure("--prefix=%s" % prefix)
diff --git a/var/spack/repos/builtin/packages/gmsh/package.py b/var/spack/repos/builtin/packages/gmsh/package.py
index eb2981bba2..5f659c56df 100644
--- a/var/spack/repos/builtin/packages/gmsh/package.py
+++ b/var/spack/repos/builtin/packages/gmsh/package.py
@@ -62,7 +62,9 @@ class Gmsh(Package):
build_directory = join_path(self.stage.path, 'spack-build')
source_directory = self.stage.source_path
-
+
+ options.append('-DCMAKE_INSTALL_NAME_DIR:PATH=%s/lib' % prefix)
+
# Prevent GMsh from using its own strange directory structure on OSX
options.append('-DENABLE_OS_SPECIFIC_INSTALL=OFF')
diff --git a/var/spack/repos/builtin/packages/hdf5/package.py b/var/spack/repos/builtin/packages/hdf5/package.py
index 470969832f..cae46d3301 100644
--- a/var/spack/repos/builtin/packages/hdf5/package.py
+++ b/var/spack/repos/builtin/packages/hdf5/package.py
@@ -24,6 +24,7 @@
##############################################################################
from spack import *
+import shutil
class Hdf5(Package):
@@ -114,14 +115,16 @@ class Hdf5(Package):
# this is not actually a problem.
extra_args.extend([
"--enable-parallel",
- "CC=%s" % spec['mpi'].prefix.bin + "/mpicc",
+ "CC=%s" % join_path(spec['mpi'].prefix.bin, "mpicc"),
])
if '+cxx' in spec:
- extra_args.append("CXX=%s" % spec['mpi'].prefix.bin + "/mpic++")
+ extra_args.append("CXX=%s" % join_path(spec['mpi'].prefix.bin,
+ "mpic++"))
if '+fortran' in spec:
- extra_args.append("FC=%s" % spec['mpi'].prefix.bin + "/mpifort")
+ extra_args.append("FC=%s" % join_path(spec['mpi'].prefix.bin,
+ "mpifort"))
if '+szip' in spec:
extra_args.append("--with-szlib=%s" % spec['szip'].prefix)
@@ -138,6 +141,58 @@ class Hdf5(Package):
*extra_args)
make()
make("install")
+ self.check_install(spec)
+
+ def check_install(self, spec):
+ "Build and run a small program to test the installed HDF5 library"
+ print "Checking HDF5 installation..."
+ checkdir = "spack-check"
+ with working_dir(checkdir, create=True):
+ source = r"""
+#include <hdf5.h>
+#include <assert.h>
+#include <stdio.h>
+int main(int argc, char **argv) {
+ unsigned majnum, minnum, relnum;
+ herr_t herr = H5get_libversion(&majnum, &minnum, &relnum);
+ assert(!herr);
+ printf("HDF5 version %d.%d.%d %u.%u.%u\n", H5_VERS_MAJOR, H5_VERS_MINOR,
+ H5_VERS_RELEASE, majnum, minnum, relnum);
+ return 0;
+}
+"""
+ expected = """\
+HDF5 version {version} {version}
+""".format(version=str(spec.version))
+ with open("check.c", 'w') as f:
+ f.write(source)
+ if '+mpi' in spec:
+ cc = which(join_path(spec['mpi'].prefix.bin, "mpicc"))
+ else:
+ cc = which('cc')
+ # TODO: Automate these path and library settings
+ cc('-c', "-I%s" % join_path(spec.prefix, "include"), "check.c")
+ cc('-o', "check", "check.o",
+ "-L%s" % join_path(spec.prefix, "lib"), "-lhdf5",
+ "-lz")
+ try:
+ check = Executable('./check')
+ output = check(return_output=True)
+ except:
+ output = ""
+ success = output == expected
+ if not success:
+ print "Produced output does not match expected output."
+ print "Expected output:"
+ print '-'*80
+ print expected
+ print '-'*80
+ print "Produced output:"
+ print '-'*80
+ print output
+ print '-'*80
+ raise RuntimeError("HDF5 install check failed")
+ shutil.rmtree(checkdir)
def url_for_version(self, version):
v = str(version)
diff --git a/var/spack/repos/builtin/packages/kripke/package.py b/var/spack/repos/builtin/packages/kripke/package.py
new file mode 100644
index 0000000000..7d067ea44d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/kripke/package.py
@@ -0,0 +1,32 @@
+from spack import *
+
+class Kripke(Package):
+ """Kripke is a simple, scalable, 3D Sn deterministic particle
+ transport proxy/mini app.
+ """
+ homepage = "https://codesign.llnl.gov/kripke.php"
+ url = "https://codesign.llnl.gov/downloads/kripke-openmp-1.1.tar.gz"
+
+ version('1.1', '7fe6f2b26ed983a6ce5495ab701f85bf')
+
+ variant('mpi', default=True, description='Build with MPI.')
+ variant('openmp', default=True, description='Build with OpenMP enabled.')
+
+ depends_on('mpi', when="+mpi")
+
+ def install(self, spec, prefix):
+ with working_dir('build', create=True):
+ def enabled(variant):
+ return (1 if variant in spec else 0)
+
+ cmake('-DCMAKE_INSTALL_PREFIX:PATH=.',
+ '-DENABLE_OPENMP=%d' % enabled('+openmp'),
+ '-DENABLE_MPI=%d' % enabled('+mpi'),
+ '..',
+ *std_cmake_args)
+ make()
+
+ # Kripke does not provide install target, so we have to copy
+ # things into place.
+ mkdirp(prefix.bin)
+ install('kripke', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/libxcb/package.py b/var/spack/repos/builtin/packages/libxcb/package.py
index d7d94c4546..b2543be5da 100644
--- a/var/spack/repos/builtin/packages/libxcb/package.py
+++ b/var/spack/repos/builtin/packages/libxcb/package.py
@@ -13,6 +13,7 @@ class Libxcb(Package):
version('1.11.1', '118623c15a96b08622603a71d8789bf3')
depends_on("python")
depends_on("xcb-proto")
+ depends_on("pkg-config")
# depends_on('pthread') # Ubuntu: apt-get install libpthread-stubs0-dev
# depends_on('xau') # Ubuntu: apt-get install libxau-dev
diff --git a/var/spack/repos/builtin/packages/nccmp/package.py b/var/spack/repos/builtin/packages/nccmp/package.py
new file mode 100644
index 0000000000..72e86831c6
--- /dev/null
+++ b/var/spack/repos/builtin/packages/nccmp/package.py
@@ -0,0 +1,23 @@
+from spack import *
+
+class Nccmp(Package):
+ """Compare NetCDF Files"""
+ homepage = "http://nccmp.sourceforge.net/"
+ url = "http://downloads.sourceforge.net/project/nccmp/nccmp-1.8.2.0.tar.gz"
+
+ version('1.8.2.0', '81e6286d4413825aec4327e61a28a580')
+
+ depends_on('netcdf')
+
+ def install(self, spec, prefix):
+ # Configure says: F90 and F90FLAGS are replaced by FC and
+ # FCFLAGS respectively in this configure, please unset
+ # F90/F90FLAGS and set FC/FCFLAGS instead and rerun configure
+ # again.
+ env.pop('F90', None)
+ env.pop('F90FLAGS', None)
+
+ configure('--prefix=%s' % prefix)
+ make()
+ make("check")
+ make("install")
diff --git a/var/spack/repos/builtin/packages/nco/package.py b/var/spack/repos/builtin/packages/nco/package.py
new file mode 100644
index 0000000000..3a9aeaa656
--- /dev/null
+++ b/var/spack/repos/builtin/packages/nco/package.py
@@ -0,0 +1,30 @@
+from spack import *
+import os
+
+class Nco(Package):
+ """The NCO toolkit manipulates and analyzes data stored in
+ netCDF-accessible formats"""
+
+ homepage = "https://sourceforge.net/projects/nco"
+ url = "https://github.com/nco/nco/archive/4.5.5.tar.gz"
+
+ version('4.5.5', '9f1f1cb149ad6407c5a03c20122223ce')
+
+ # See "Compilation Requirements" at:
+ # http://nco.sourceforge.net/#bld
+
+ depends_on('netcdf')
+ depends_on('antlr@2.7.7+cxx') # (required for ncap2)
+ depends_on('gsl') # (desirable for ncap2)
+ depends_on('udunits2') # (allows dimensional unit transformations)
+ # depends_on('opendap') # (enables network transparency),
+
+ def install(self, spec, prefix):
+ opts = [
+ '--prefix=%s' % prefix,
+ '--disable-openmp', # TODO: Make this a variant
+ '--disable-dap', # TODO: Make this a variant
+ '--disable-esmf']
+ configure(*opts)
+ make()
+ make("install")
diff --git a/var/spack/repos/builtin/packages/openblas/package.py b/var/spack/repos/builtin/packages/openblas/package.py
index 99649da9ca..d147533491 100644
--- a/var/spack/repos/builtin/packages/openblas/package.py
+++ b/var/spack/repos/builtin/packages/openblas/package.py
@@ -8,13 +8,14 @@ class Openblas(Package):
homepage = "http://www.openblas.net"
url = "http://github.com/xianyi/OpenBLAS/archive/v0.2.15.tar.gz"
+ version('0.2.18', '805e7f660877d588ea7e3792cda2ee65')
version('0.2.17', '664a12807f2a2a7cda4781e3ab2ae0e1')
version('0.2.16', 'fef46ab92463bdbb1479dcec594ef6dc')
version('0.2.15', 'b1190f3d3471685f17cfd1ec1d252ac9')
- variant('shared', default=True, description="Build shared libraries as well as static libs.")
- variant('openmp', default=True, description="Enable OpenMP support.")
- variant('fpic', default=True, description="Build position independent code")
+ variant('shared', default=True, description="Build shared libraries as well as static libs.")
+ variant('openmp', default=False, description="Enable OpenMP support.")
+ variant('fpic', default=True, description="Build position independent code")
# virtual dependency
provides('blas')
@@ -45,8 +46,13 @@ class Openblas(Package):
make_defs += ['BUILD_LAPACK_DEPRECATED=1']
# Add support for OpenMP
- # Note: Make sure your compiler supports OpenMP
if '+openmp' in spec:
+ # Note: Apple's most recent Clang 7.3.0 still does not support OpenMP.
+ # What is worse, Openblas (as of 0.2.18) hardcoded that OpenMP cannot
+ # be used with any (!) compiler named clang, bummer.
+ if spec.satisfies('%clang'):
+ raise InstallError('OpenBLAS does not support OpenMP with clang!')
+
make_defs += ['USE_OPENMP=1']
make_args = make_defs + make_targets
@@ -88,48 +94,33 @@ class Openblas(Package):
self.spec.lapack_shared_lib = self.spec.blas_shared_lib
def check_install(self, spec):
- "Build and run a small program to test that we have Lapack symbols"
+ # TODO: Pull this out to the framework function which recieves a pair of xyz.c and xyz.output
print "Checking Openblas installation..."
- checkdir = "spack-check"
- with working_dir(checkdir, create=True):
- source = r"""
-#include <cblas.h>
-#include <stdio.h>
-int main(void) {
-int i=0;
-double A[6] = {1.0, 2.0, 1.0, -3.0, 4.0, -1.0};
-double B[6] = {1.0, 2.0, 1.0, -3.0, 4.0, -1.0};
-double C[9] = {.5, .5, .5, .5, .5, .5, .5, .5, .5};
-cblas_dgemm(CblasColMajor, CblasNoTrans, CblasTrans,
- 3, 3, 2, 1, A, 3, B, 3, 2, C, 3);
-for (i = 0; i < 9; i++)
- printf("%f\n", C[i]);
-return 0;
-}
-"""
- expected = """\
-11.000000
--9.000000
-5.000000
--9.000000
-21.000000
--1.000000
-5.000000
--1.000000
-3.000000
-"""
- with open("check.c", 'w') as f:
- f.write(source)
- cc = which('cc')
- # TODO: Automate these path and library settings
- cc('-c', "-I%s" % join_path(spec.prefix, "include"), "check.c")
- cc('-o', "check", "check.o",
- "-L%s" % join_path(spec.prefix, "lib"), "-llapack", "-lblas", "-lpthread")
- try:
- check = Executable('./check')
- output = check(return_output=True)
- except:
- output = ""
+ source_file = join_path(os.path.dirname(self.module.__file__),
+ 'test_cblas_dgemm.c')
+ output_file = join_path(os.path.dirname(self.module.__file__),
+ 'test_cblas_dgemm.output')
+
+ with open(output_file, 'r') as f:
+ expected = f.read()
+
+ cc = which('cc')
+ cc('-c', "-I%s" % join_path(spec.prefix, "include"), source_file)
+ link_flags = ["-L%s" % join_path(spec.prefix, "lib"),
+ "-llapack",
+ "-lblas",
+ "-lpthread"
+ ]
+ if '+openmp' in spec:
+ link_flags.extend([self.compiler.openmp_flag])
+ cc('-o', "check", "test_cblas_dgemm.o",
+ *link_flags)
+
+ try:
+ check = Executable('./check')
+ output = check(return_output=True)
+ except:
+ output = ""
success = output == expected
if not success:
print "Produced output does not match expected output."
@@ -142,4 +133,3 @@ return 0;
print output
print '-'*80
raise RuntimeError("Openblas install check failed")
- shutil.rmtree(checkdir)
diff --git a/var/spack/repos/builtin/packages/openblas/test_cblas_dgemm.c b/var/spack/repos/builtin/packages/openblas/test_cblas_dgemm.c
index 634e99d20b..3813a23b69 100644
--- a/var/spack/repos/builtin/packages/openblas/test_cblas_dgemm.c
+++ b/var/spack/repos/builtin/packages/openblas/test_cblas_dgemm.c
@@ -1,13 +1,49 @@
#include <cblas.h>
#include <stdio.h>
+
+double m[] = {
+ 3, 1, 3,
+ 1, 5, 9,
+ 2, 6, 5
+};
+
+double x[] = {
+ -1, 3, -3
+};
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+ void dgesv_(int *n, int *nrhs, double *a, int *lda,
+ int *ipivot, double *b, int *ldb, int *info);
+
+#ifdef __cplusplus
+}
+#endif
+
int main(void) {
-int i=0;
-double A[6] = {1.0, 2.0, 1.0, -3.0, 4.0, -1.0};
-double B[6] = {1.0, 2.0, 1.0, -3.0, 4.0, -1.0};
-double C[9] = {.5, .5, .5, .5, .5, .5, .5, .5, .5};
-cblas_dgemm(CblasColMajor, CblasNoTrans, CblasTrans,
- 3, 3, 2, 1, A, 3, B, 3, 2, C, 3);
-for (i = 0; i < 9; i++)
- printf("%f\n", C[i]);
-return 0;
+ int i;
+ // blas:
+ double A[6] = {1.0, 2.0, 1.0, -3.0, 4.0, -1.0};
+ double B[6] = {1.0, 2.0, 1.0, -3.0, 4.0, -1.0};
+ double C[9] = {.5, .5, .5, .5, .5, .5, .5, .5, .5};
+ cblas_dgemm(CblasColMajor, CblasNoTrans, CblasTrans,
+ 3, 3, 2, 1, A, 3, B, 3, 2, C, 3);
+ for (i = 0; i < 9; i++)
+ printf("%f\n", C[i]);
+
+ // lapack:
+ int ipiv[3];
+ int j;
+ int info;
+ int n = 1;
+ int nrhs = 1;
+ int lda = 3;
+ int ldb = 3;
+ dgesv_(&n,&nrhs, &m[0], &lda, ipiv, &x[0], &ldb, &info);
+ for (i=0; i<3; ++i)
+ printf("%5.1f %3d\n", x[i], ipiv[i]);
+
+ return 0;
}
diff --git a/var/spack/repos/builtin/packages/openblas/test_cblas_dgemm.output b/var/spack/repos/builtin/packages/openblas/test_cblas_dgemm.output
index b8316d7477..9c235e314f 100644
--- a/var/spack/repos/builtin/packages/openblas/test_cblas_dgemm.output
+++ b/var/spack/repos/builtin/packages/openblas/test_cblas_dgemm.output
@@ -7,3 +7,6 @@
5.000000
-1.000000
3.000000
+ -0.3 1
+ 3.0 1499101120
+ -3.0 32767
diff --git a/var/spack/repos/builtin/packages/openspeedshop/package.py b/var/spack/repos/builtin/packages/openspeedshop/package.py
index 8c71bcb7c3..bcd77351aa 100644
--- a/var/spack/repos/builtin/packages/openspeedshop/package.py
+++ b/var/spack/repos/builtin/packages/openspeedshop/package.py
@@ -1,5 +1,5 @@
################################################################################
-# Copyright (c) 2015 Krell Institute. All Rights Reserved.
+# Copyright (c) 2015-2016 Krell Institute. All Rights Reserved.
#
# This program is free software; you can redistribute it and/or modify it under
# the terms of the GNU General Public License as published by the Free Software
@@ -28,20 +28,15 @@ class Openspeedshop(Package):
as open source code primarily under LGPL.
"""
-
homepage = "http://www.openspeedshop.org"
- url = "http://sourceforge.net/projects/openss/files/openss/openspeedshop-2.2/openspeedshop-2.2.tar.gz/download"
+ url = "https://github.com/OpenSpeedShop"
version('2.2', '16cb051179c2038de4e8a845edf1d573')
+ # Use when the git repository is available
+ version('2.2', branch='master', git='https://github.com/OpenSpeedShop/openspeedshop.git')
- #homepage = "http://www.openspeedshop.org"
- #url = "http://sourceforge.net/projects/openss/files/openss/openspeedshop-2.1/openspeedshop-2.1.tar.gz/download"
- #version('2.1', 'bdaa57c1a0db9d0c3e0303fd8496c507')
-
- # optional mirror template
- #url = "file:/g/g24/jeg/openspeedshop-2.1.tar.gz"
- #version('2.1', '64ee17166519838c7b94a1adc138e94f')
-
-
+ # Optional mirror template
+ #url = "file:/home/jeg/OpenSpeedShop_ROOT/SOURCES/openspeedshop-2.2.tar.gz"
+ #version('2.2', '643337740dc6c2faca60f42d3620b0e1')
parallel = False
@@ -51,11 +46,17 @@ class Openspeedshop(Package):
variant('frontend', default=False, description="build only the front-end tool using the runtime_dir to point to the target build.")
variant('cuda', default=False, description="build with cuda packages included.")
variant('ptgf', default=False, description="build with the PTGF based gui package enabled.")
- variant('intelmic', default=False, description="build for the Intel MIC platform.")
- variant('cray', default=False, description="build for Cray platforms.")
- variant('bluegene', default=False, description="build for Cray platforms.")
variant('rtfe', default=False, description="build for generic cluster platforms that have different processors on the fe and be nodes.")
+ # MPI variants
+ variant('openmpi', default=False, description="Build mpi experiment collector for openmpi MPI when this variant is enabled.")
+ variant('mpt', default=False, description="Build mpi experiment collector for SGI MPT MPI when this variant is enabled.")
+ variant('mvapich2', default=False, description="Build mpi experiment collector for mvapich2 MPI when this variant is enabled.")
+ variant('mvapich', default=False, description="Build mpi experiment collector for mvapich MPI when this variant is enabled.")
+ variant('mpich2', default=False, description="Build mpi experiment collector for mpich2 MPI when this variant is enabled.")
+ variant('mpich', default=False, description="Build mpi experiment collector for mpich MPI when this variant is enabled.")
+
+ depends_on("cmake@3.0.2")
# Dependencies for openspeedshop that are common to all the variants of the OpenSpeedShop build
depends_on("bison")
depends_on("flex")
@@ -63,8 +64,8 @@ class Openspeedshop(Package):
depends_on("libelf")
depends_on("libdwarf")
depends_on("sqlite")
- depends_on("boost@1.50.0")
- depends_on("dyninst@8.2.1")
+ depends_on("boost@1.50.0:")
+ depends_on("dyninst@9.1.0")
depends_on("python")
depends_on("qt@3.3.8b+krellpatch")
@@ -72,15 +73,78 @@ class Openspeedshop(Package):
depends_on("libunwind", when='+offline')
depends_on("papi", when='+offline')
depends_on("libmonitor+krellpatch", when='+offline')
- #depends_on("openmpi+krelloptions", when='+offline')
- #depends_on("openmpi", when='+offline')
- #depends_on("mpich", when='+offline')
+ depends_on("openmpi", when='+offline+openmpi')
+ depends_on("mpich", when='+offline+mpich')
+ depends_on("mpich2", when='+offline+mpich2')
+ depends_on("mvapich2", when='+offline+mvapich2')
+ depends_on("mvapich", when='+offline+mvapich')
+ depends_on("mpt", when='+offline+mpt')
# Dependencies only for the openspeedshop cbtf package.
depends_on("cbtf", when='+cbtf')
depends_on("cbtf-krell", when='+cbtf')
- depends_on("cbtf-argonavis", when='+cbtf')
- depends_on("mrnet@4.1.0:+lwthreads", when='+cbtf')
+ depends_on("cbtf-argonavis", when='+cbtf+cuda')
+ depends_on("mrnet@5.0.1:+lwthreads+krellpatch", when='+cbtf')
+
+ def adjustBuildTypeParams_cmakeOptions(self, spec, cmakeOptions):
+ # Sets build type parameters into cmakeOptions the options that will enable the cbtf-krell built type settings
+
+ compile_flags="-O2 -g"
+ BuildTypeOptions = []
+ # Set CMAKE_BUILD_TYPE to what cbtf-krell wants it to be, not the stdcmakeargs
+ for word in cmakeOptions[:]:
+ if word.startswith('-DCMAKE_BUILD_TYPE'):
+ cmakeOptions.remove(word)
+ if word.startswith('-DCMAKE_CXX_FLAGS'):
+ cmakeOptions.remove(word)
+ if word.startswith('-DCMAKE_C_FLAGS'):
+ cmakeOptions.remove(word)
+ BuildTypeOptions.extend([
+ '-DCMAKE_BUILD_TYPE=None',
+ '-DCMAKE_CXX_FLAGS=%s' % compile_flags,
+ '-DCMAKE_C_FLAGS=%s' % compile_flags
+ ])
+
+ cmakeOptions.extend(BuildTypeOptions)
+
+ def set_mpi_cmakeOptions(self, spec, cmakeOptions):
+ # Appends to cmakeOptions the options that will enable the appropriate MPI implementations
+
+ MPIOptions = []
+
+ # openmpi
+ if '+openmpi' in spec:
+ MPIOptions.extend([
+ '-DOPENMPI_DIR=%s' % spec['openmpi'].prefix
+ ])
+ # mpich
+ if '+mpich' in spec:
+ MPIOptions.extend([
+ '-DMPICH_DIR=%s' % spec['mpich'].prefix
+ ])
+ # mpich2
+ if '+mpich2' in spec:
+ MPIOptions.extend([
+ '-DMPICH2_DIR=%s' % spec['mpich2'].prefix
+ ])
+ # mvapich
+ if '+mvapich' in spec:
+ MPIOptions.extend([
+ '-DMVAPICH_DIR=%s' % spec['mvapich'].prefix
+ ])
+ # mvapich2
+ if '+mvapich2' in spec:
+ MPIOptions.extend([
+ '-DMVAPICH2_DIR=%s' % spec['mvapich2'].prefix
+ ])
+ # mpt
+ if '+mpt' in spec:
+ MPIOptions.extend([
+ '-DMPT_DIR=%s' % spec['mpt'].prefix
+ ])
+
+ cmakeOptions.extend(MPIOptions)
+
def install(self, spec, prefix):
@@ -100,51 +164,118 @@ class Openspeedshop(Package):
instrumentor_setting = "offline"
if '+runtime' in spec:
with working_dir('build_runtime', create=True):
- cmake('..',
- '-DCMAKE_INSTALL_PREFIX=%s' % prefix,
- '-DCMAKE_LIBRARY_PATH=%s' % prefix.lib64,
- '-DINSTRUMENTOR=%s' % instrumentor_setting,
- '-DLIBMONITOR_DIR=%s' % spec['libmonitor'].prefix,
- '-DLIBUNWIND_DIR=%s' % spec['libunwind'].prefix,
- '-DPAPI_DIR=%s' % spec['papi'].prefix,
- *std_cmake_args)
+
+ cmakeOptions = []
+ cmakeOptions.extend(['-DCMAKE_INSTALL_PREFIX=%s' % prefix,
+ '-DCMAKE_LIBRARY_PATH=%s' % prefix.lib64,
+ '-DINSTRUMENTOR=%s' % instrumentor_setting,
+ '-DLIBMONITOR_DIR=%s' % spec['libmonitor'].prefix,
+ '-DLIBUNWIND_DIR=%s' % spec['libunwind'].prefix,
+ '-DPAPI_DIR=%s' % spec['papi'].prefix
+ ])
+
+ # Add any MPI implementations coming from variant settings
+ self.set_mpi_cmakeOptions(spec, cmakeOptions)
+ cmakeOptions.extend(std_cmake_args)
+
+ # Adjust the build options to the favored ones for this build
+ self.adjustBuildTypeParams_cmakeOptions(spec, cmakeOptions)
+
+ cmake('..', *cmakeOptions)
+
make("clean")
make()
make("install")
else:
cmake_prefix_path = join_path(spec['dyninst'].prefix)
with working_dir('build', create=True):
+
#python_vers=join_path(spec['python'].version[:2])
#'-DOPENMPI_DIR=%s' % openmpi_prefix_path,
#'-DMVAPICH_DIR=%s' % mvapich_prefix_path,
+ #'-DMPICH_DIR=%s' % spec['mpich'].prefix,
+ #'-DMPICH2_DIR=%s' % spec['mpich2'].prefix,
+ #'-DBoost_NO_SYSTEM_PATHS=TRUE',
+ #'-DBOOST_ROOT=%s' % spec['boost'].prefix,
+ #'-DOPENMPI_DIR=%s' % spec['openmpi'].prefix,
+
python_vers='%d.%d' % spec['python'].version[:2]
- cmake('..',
- '-DCMAKE_INSTALL_PREFIX=%s' % prefix,
- '-DCMAKE_LIBRARY_PATH=%s' % prefix.lib64,
- '-DCMAKE_PREFIX_PATH=%s' % cmake_prefix_path,
- '-DINSTRUMENTOR=%s' % instrumentor_setting,
- '-DBINUTILS_DIR=%s' % spec['binutils'].prefix,
- '-DLIBELF_DIR=%s' % spec['libelf'].prefix,
- '-DLIBDWARF_DIR=%s' % spec['libdwarf'].prefix,
- '-DLIBMONITOR_DIR=%s' % spec['libmonitor'].prefix,
- '-DLIBUNWIND_DIR=%s' % spec['libunwind'].prefix,
- '-DPAPI_DIR=%s' % spec['papi'].prefix,
- '-DSQLITE3_DIR=%s' % spec['sqlite'].prefix,
- '-DQTLIB_DIR=%s' % spec['qt'].prefix,
- '-DPYTHON_EXECUTABLE=%s' % join_path(spec['python'].prefix + '/bin/python'),
- '-DPYTHON_INCLUDE_DIR=%s' % join_path(spec['python'].prefix.include) + '/python' + python_vers,
- '-DPYTHON_LIBRARY=%s' % join_path(spec['python'].prefix.lib) + '/libpython' + python_vers + '.so',
- '-DBoost_NO_SYSTEM_PATHS=TRUE',
- '-DBOOST_ROOT=%s' % spec['boost'].prefix,
- '-DDYNINST_DIR=%s' % spec['dyninst'].prefix,
- *std_cmake_args)
+
+ cmakeOptions = []
+ cmakeOptions.extend(['-DCMAKE_INSTALL_PREFIX=%s' % prefix,
+ '-DCMAKE_LIBRARY_PATH=%s' % prefix.lib64,
+ '-DCMAKE_PREFIX_PATH=%s' % cmake_prefix_path,
+ '-DINSTRUMENTOR=%s' % instrumentor_setting,
+ '-DBINUTILS_DIR=%s' % spec['binutils'].prefix,
+ '-DLIBELF_DIR=%s' % spec['libelf'].prefix,
+ '-DLIBDWARF_DIR=%s' % spec['libdwarf'].prefix,
+ '-DLIBMONITOR_DIR=%s' % spec['libmonitor'].prefix,
+ '-DLIBUNWIND_DIR=%s' % spec['libunwind'].prefix,
+ '-DPAPI_DIR=%s' % spec['papi'].prefix,
+ '-DSQLITE3_DIR=%s' % spec['sqlite'].prefix,
+ '-DQTLIB_DIR=%s' % spec['qt'].prefix,
+ '-DPYTHON_EXECUTABLE=%s' % join_path(spec['python'].prefix + '/bin/python'),
+ '-DPYTHON_INCLUDE_DIR=%s' % join_path(spec['python'].prefix.include) + '/python' + python_vers,
+ '-DPYTHON_LIBRARY=%s' % join_path(spec['python'].prefix.lib) + '/libpython' + python_vers + '.so',
+ '-DBoost_NO_SYSTEM_PATHS=TRUE',
+ '-DBOOST_ROOT=%s' % spec['boost'].prefix,
+ '-DDYNINST_DIR=%s' % spec['dyninst'].prefix
+ ])
+
+ # Add any MPI implementations coming from variant settings
+ self.set_mpi_cmakeOptions(spec, cmakeOptions)
+ cmakeOptions.extend(std_cmake_args)
+
+ # Adjust the build options to the favored ones for this build
+ self.adjustBuildTypeParams_cmakeOptions(spec, cmakeOptions)
+
+ cmake('..', *cmakeOptions)
+
make("clean")
make()
make("install")
elif '+cbtf' in spec:
instrumentor_setting = "cbtf"
+ resolve_symbols = "symtabapi"
cmake_prefix_path = join_path(spec['cbtf'].prefix) + ':' + join_path(spec['cbtf-krell'].prefix) + ':' + join_path(spec['dyninst'].prefix)
+ #runtime_platform_cray = "cray"
+ #if '+cray' in spec:
+ # if '+runtime' in spec:
+ # #-DCBTF_KRELL_CN_RUNTIME_DIR=${CBTF_KRELL_CN_INSTALL_DIR} \
+ # with working_dir('build_cbtf_cray_runtime', create=True):
+ # python_vers='%d.%d' % spec['python'].version[:2]
+ # cmake('..',
+ # '-DCMAKE_INSTALL_PREFIX=%s' % prefix,
+ # '-DCMAKE_LIBRARY_PATH=%s' % prefix.lib64,
+ # '-DRUNTIME_PLATFORM=%s' % runtime_platform_cray,
+ # '-DCMAKE_PREFIX_PATH=%s' % cmake_prefix_path,
+ # '-DRESOLVE_SYMBOLS=%s' % resolve_symbols,
+ # '-DINSTRUMENTOR=%s' % instrumentor_setting,
+ # '-DCBTF_DIR=%s' % spec['cbtf'].prefix,
+ # '-DCBTF_KRELL_DIR=%s' % spec['cbtf-krell'].prefix,
+ # '-DCBTF_KRELL_CN_RUNTIME_DIR=%s' % spec['cbtf-krell'].prefix,
+ # '-DBINUTILS_DIR=%s' % spec['binutils'].prefix,
+ # '-DLIBELF_DIR=%s' % spec['libelf'].prefix,
+ # '-DLIBDWARF_DIR=%s' % spec['libdwarf'].prefix,
+ # '-DLIBUNWIND_DIR=%s' % spec['libunwind'].prefix,
+ # '-DPAPI_DIR=%s' % spec['papi'].prefix,
+ # '-DDYNINST_DIR=%s' % spec['dyninst'].prefix,
+ # '-DXERCESC_DIR=%s' % spec['xerces-c'].prefix,
+ # '-DMRNET_DIR=%s' % spec['mrnet'].prefix,
+ # '-DBoost_NO_SYSTEM_PATHS=TRUE',
+ # '-DBOOST_ROOT=%s' % spec['boost'].prefix,
+ # *std_cmake_args)
+
+ # make("clean")
+ # make()
+ # make("install")
+
+
+ #elif '+mic' in spec:
+ # comment out else and shift over the default case below until arch detection is in
+ #else:
+
if '+runtime' in spec:
with working_dir('build_cbtf_runtime', create=True):
python_vers='%d.%d' % spec['python'].version[:2]
@@ -203,14 +334,63 @@ class Openspeedshop(Package):
# tbd
- #if '+intelmic' in spec:
- # with working_dir('build_intelmic_compute', create=True):
- # tbd
- # with working_dir('build_intelmic_frontend', create=True):
- # tbd
- #if '+cray' in spec:
- # with working_dir('build_cray_compute', create=True):
- # tbd
- # with working_dir('build_cray_frontend', create=True):
- # tbd
+ #if '+cbtf' in spec:
+ # if cray build type detected:
+ # if '+runtime' in spec:
+ # with working_dir('build_cray_cbtf_compute', create=True):
+ # tbd
+ # else:
+ # with working_dir('build_cray_cbtf_frontend', create=True):
+ # tbd
+ # with working_dir('build_cray_osscbtf_frontend', create=True):
+ # tbd
+ # fi
+ # elif '+intelmic' in spec:
+ # if '+runtime' in spec:
+ # with working_dir('build_intelmic_cbtf_compute', create=True):
+ # tbd
+ # else:
+ # with working_dir('build_intelmic_cbtf_frontend', create=True):
+ # tbd
+ # with working_dir('build_intelmic_osscbtf_frontend', create=True):
+ # fi
+ # else
+ # with working_dir('build_cluster_cbtf', create=True):
+ # tbd
+ # with working_dir('build_cluster osscbtf', create=True):
+ # tbd
+ # fi
+ #elif '+offline' in spec:
+ # if cray build type detected:
+ # if '+runtime' in spec:
+ # with working_dir('build_cray_ossoff_compute', create=True):
+ # tbd
+ # else:
+ # with working_dir('build_cray_ossoff_frontend', create=True):
+ # tbd
+ # fi
+ # elif '+intelmic' in spec:
+ # if '+runtime' in spec:
+ # with working_dir('build_intelmic_ossoff_compute', create=True):
+ # tbd
+ # else:
+ # with working_dir('build_intelmic_ossoff_frontend', create=True):
+ # tbd
+ # fi
+ # elif bgq build type detected:
+ # if '+runtime' in spec:
+ # with working_dir('build_bgq_ossoff_compute', create=True):
+ # tbd
+ # else:
+ # with working_dir('build_bgq_ossoff_frontend', create=True):
+ # tbd
+ # fi
+ # else
+ # with working_dir('build_cluster ossoff', create=True):
+ # tbd
+ # fi
+ #fi
+
+
+
diff --git a/var/spack/repos/builtin/packages/parallel-netcdf/package.py b/var/spack/repos/builtin/packages/parallel-netcdf/package.py
index e6f8cf026b..1bbd24781e 100644
--- a/var/spack/repos/builtin/packages/parallel-netcdf/package.py
+++ b/var/spack/repos/builtin/packages/parallel-netcdf/package.py
@@ -11,11 +11,25 @@ class ParallelNetcdf(Package):
version('1.7.0', '267eab7b6f9dc78c4d0e6def2def3aea4bc7c9f0')
version('1.6.1', '62a094eb952f9d1e15f07d56e535052604f1ac34')
+ variant('cxx', default=True, description='Build the C++ Interface')
+ variant('fortran', default=True, description='Build the Fortran Interface')
+ variant('fpic', default=True, description='Produce position-independent code (for use with shared libraries)')
+
depends_on("m4")
depends_on("mpi")
+ # See: https://trac.mcs.anl.gov/projects/parallel-netcdf/browser/trunk/INSTALL
def install(self, spec, prefix):
- configure("--prefix=%s" % prefix,
- "--with-mpi=%s" % spec['mpi'].prefix)
+ args = list()
+ if '+fpic' in spec:
+ args.extend(['CFLAGS=-fPIC', 'CXXFLAGS=-fPIC', 'FFLAGS=-fPIC'])
+ if '~cxx' in spec:
+ args.append('--disable-cxx')
+ if '~fortran' in spec:
+ args.append('--disable-fortran')
+
+ args.extend(["--prefix=%s" % prefix,
+ "--with-mpi=%s" % spec['mpi'].prefix])
+ configure(*args)
make()
make("install")
diff --git a/var/spack/repos/builtin/packages/py-argcomplete/package.py b/var/spack/repos/builtin/packages/py-argcomplete/package.py
new file mode 100644
index 0000000000..c94ef7238b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-argcomplete/package.py
@@ -0,0 +1,14 @@
+from spack import *
+
+class PyArgcomplete(Package):
+ """Bash tab completion for argparse."""
+
+ homepage = "https://pypi.python.org/pypi/argcomplete"
+ url = "https://pypi.python.org/packages/source/a/argcomplete/argcomplete-1.1.1.tar.gz"
+
+ version('1.1.1', '89a3839096c9f991ad33828e72d21abf')
+
+ extends('python')
+
+ def install(self, spec, prefix):
+ python('setup.py', 'install', '--prefix=%s' % prefix)
diff --git a/var/spack/repos/builtin/packages/r-BiocGenerics/package.py b/var/spack/repos/builtin/packages/r-BiocGenerics/package.py
new file mode 100644
index 0000000000..2d92c1c4d8
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-BiocGenerics/package.py
@@ -0,0 +1,14 @@
+from spack import *
+
+class RBiocgenerics(Package):
+ """S4 generic functions needed by many Bioconductor packages."""
+
+ homepage = 'https://www.bioconductor.org/packages/release/bioc/html/BiocGenerics.html'
+ url = "https://www.bioconductor.org/packages/release/bioc/src/contrib/BiocGenerics_0.16.1.tar.gz"
+
+ version('0.16.1', 'c2148ffd86fc6f1f819c7f68eb2c744f', expand=False)
+
+ extends('R')
+
+ def install(self, spec, prefix):
+ R('CMD', 'INSTALL', '--library=%s' % self.module.r_lib_dir, '%s' % self.stage.archive_file)
diff --git a/var/spack/repos/builtin/packages/r-abind/package.py b/var/spack/repos/builtin/packages/r-abind/package.py
new file mode 100644
index 0000000000..d06c7e9240
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-abind/package.py
@@ -0,0 +1,18 @@
+from spack import *
+
+class RAbind(Package):
+ """Combine multidimensional arrays into a single array. This is a
+ generalization of 'cbind' and 'rbind'. Works with vectors, matrices, and
+ higher-dimensional arrays. Also provides functions 'adrop', 'asub', and
+ 'afill' for manipulating, extracting and replacing data in arrays."""
+
+ homepage = "https://cran.r-project.org/"
+ url = "https://cran.r-project.org/src/contrib/abind_1.4-3.tar.gz"
+
+ version('1.4-3', '10fcf80c677b991bf263d38be35a1fc5', expand=False)
+
+ extends('R')
+
+ def install(self, spec, prefix):
+
+ R('CMD', 'INSTALL', '--library=%s' % self.module.r_lib_dir, '%s' % self.stage.archive_file)
diff --git a/var/spack/repos/builtin/packages/r-filehash/package.py b/var/spack/repos/builtin/packages/r-filehash/package.py
new file mode 100644
index 0000000000..4911c636b4
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-filehash/package.py
@@ -0,0 +1,22 @@
+from spack import *
+
+class RFilehash(Package):
+ """Implements a simple key-value style database where character string keys
+ are associated with data values that are stored on the disk. A simple
+ interface is provided for inserting, retrieving, and deleting data from the
+ database. Utilities are provided that allow 'filehash' databases to be
+ treated much like environments and lists are already used in R. These
+ utilities are provided to encourage interactive and exploratory analysis on
+ large datasets. Three different file formats for representing the database
+ are currently available and new formats can easily be incorporated by third
+ parties for use in the 'filehash' framework."""
+
+ homepage = 'https://cran.r-project.org/'
+ url = "https://cran.r-project.org/src/contrib/filehash_2.3.tar.gz"
+
+ version('2.3', '01fffafe09b148ccadc9814c103bdc2f', expand=False)
+
+ extends('R')
+
+ def install(self, spec, prefix):
+ R('CMD', 'INSTALL', '--library=%s' % self.module.r_lib_dir, '%s' % self.stage.archive_file)
diff --git a/var/spack/repos/builtin/packages/r-magic/package.py b/var/spack/repos/builtin/packages/r-magic/package.py
new file mode 100644
index 0000000000..e900cdb216
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-magic/package.py
@@ -0,0 +1,19 @@
+from spack import *
+
+class RMagic(Package):
+ """A collection of efficient, vectorized algorithms for the creation and
+ investigation of magic squares and hypercubes, including a variety of
+ functions for the manipulation and analysis of arbitrarily dimensioned
+ arrays."""
+
+ homepage = "https://cran.r-project.org/"
+ url = "https://cran.r-project.org/src/contrib/magic_1.5-6.tar.gz"
+
+ version('1.5-6', 'a68e5ced253b2196af842e1fc84fd029', expand=False)
+
+ extends('R')
+
+ depends_on('r-abind')
+
+ def install(self, spec, prefix):
+ R('CMD', 'INSTALL', '--library=%s' % self.module.r_lib_dir, '%s' % self.stage.archive_file)
diff --git a/var/spack/repos/builtin/packages/scotch/Makefile.esmumps b/var/spack/repos/builtin/packages/scotch/Makefile.esmumps
new file mode 100644
index 0000000000..4bfc760197
--- /dev/null
+++ b/var/spack/repos/builtin/packages/scotch/Makefile.esmumps
@@ -0,0 +1,5 @@
+esmumps : scotch
+ (cd esmumps ; $(MAKE) scotch && $(MAKE) install)
+
+ptesmumps : ptscotch
+ (cd esmumps ; $(MAKE) ptscotch && $(MAKE) ptinstall)
diff --git a/var/spack/repos/builtin/packages/scotch/package.py b/var/spack/repos/builtin/packages/scotch/package.py
index 8229ed8686..8fad74b24f 100644
--- a/var/spack/repos/builtin/packages/scotch/package.py
+++ b/var/spack/repos/builtin/packages/scotch/package.py
@@ -1,88 +1,125 @@
from spack import *
-import os
+import os, re
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"
+ url = "http://gforge.inria.fr/frs/download.php/latestfile/298/scotch_6.0.3.tar.gz"
+ base_url = "http://gforge.inria.fr/frs/download.php/latestfile/298"
list_url = "http://gforge.inria.fr/frs/?group_id=248"
version('6.0.3', '10b0cc0f184de2de99859eafaca83cfc')
+ version('6.0.0', 'c50d6187462ba801f9a82133ee666e8e')
+ version('5.1.10b', 'f587201d6cf5cf63527182fbfba70753')
variant('mpi', default=False, description='Activate the compilation of PT-Scotch')
variant('compression', default=True, description='Activate the posibility to use compressed files')
variant('esmumps', default=False, description='Activate the compilation of the lib esmumps needed by mumps')
variant('shared', default=True, description='Build shared libraries')
- depends_on('mpi', when='+mpi')
- depends_on('zlib', when='+compression')
depends_on('flex')
depends_on('bison')
+ depends_on('mpi', when='+mpi')
+ depends_on('zlib', when='+compression')
- def compiler_specifics(self, makefile_inc, defines):
- if self.compiler.name == 'gcc':
- defines.append('-Drestrict=__restrict')
- elif self.compiler.name == 'intel':
- defines.append('-restrict')
+ # NOTE: Versions of Scotch up to version 6.0.0 don't include support for
+ # building with 'esmumps' in their default packages. In order to enable
+ # support for this feature, we must grab the 'esmumps' enabled archives
+ # from the Scotch hosting site. These alternative archives include a strict
+ # superset of the behavior in their default counterparts, so we choose to
+ # always grab these versions for older Scotch versions for simplicity.
+ @when('@:6.0.0')
+ def url_for_version(self, version):
+ return '%s/scotch_%s_esmumps.tar.gz' % (Scotch.base_url, version)
+
+ @when('@6.0.1:')
+ def url_for_version(self, version):
+ return super(Scotch, self).url_for_version(version)
+
+ # NOTE: Several of the 'esmumps' enabled Scotch releases up to version 6.0.0
+ # have broken build scripts that don't properly build 'esmumps' as a separate
+ # target, so we need a patch procedure to remove 'esmumps' from existing targets
+ # and to add it as a standalone target.
+ @when('@:6.0.0')
+ def patch(self):
+ makefile_path = os.path.join('src', 'Makefile')
+ with open(makefile_path, 'r') as makefile:
+ esmumps_enabled = any(re.search(r'^esmumps(\s*):(.*)$', line) for line in makefile.readlines())
- makefile_inc.append('CCS = $(CC)')
+ if not esmumps_enabled:
+ mff = FileFilter(makefile_path)
+ mff.filter(r'^.*((esmumps)|(ptesmumps)).*(install).*$', '')
- if '+mpi' in self.spec:
+ makefile_esmumps_path = os.path.join(os.path.dirname(os.path.realpath(__file__)), 'Makefile.esmumps')
+ with open(makefile_path, 'a') as makefile:
+ makefile.write('\ninclude %s\n' % makefile_esmumps_path)
+
+ @when('@6.0.1:')
+ def patch(self):
+ pass
+
+ # NOTE: Configuration of Scotch is achieved by writing a 'Makefile.inc' file
+ # that contains all of the configuration variables and their desired values
+ # for the installation. This function writes this file based on the given
+ # installation variants.
+ def configure(self):
+ makefile_inc = []
+ cflags = [
+ '-O3',
+ '-DCOMMON_RANDOM_FIXED_SEED',
+ '-DSCOTCH_DETERMINISTIC',
+ '-DSCOTCH_RENAME',
+ '-DIDXSIZE64'
+ ]
+
+ ## Library Build Type ##
+
+ if '+shared' in self.spec:
makefile_inc.extend([
- 'CCP = %s' % os.path.join(self.spec['mpi'].prefix.bin, 'mpicc'),
- 'CCD = $(CCP)'
- ])
+ 'LIB = .so',
+ 'CLIBFLAGS = -shared -fPIC',
+ 'RANLIB = echo',
+ 'AR = $(CC)',
+ 'ARFLAGS = -shared $(LDFLAGS) -o'
+ ])
+ cflags.append('-fPIC')
else:
makefile_inc.extend([
- 'CCP = mpicc', # It is set but not used
- 'CCD = $(CCS)'
- ])
+ 'LIB = .a',
+ 'CLIBFLAGS = ',
+ 'RANLIB = ranlib',
+ 'AR = ar',
+ 'ARFLAGS = -ruv '
+ ])
+ ## Compiler-Specific Options ##
+ if self.compiler.name == 'gcc':
+ cflags.append('-Drestrict=__restrict')
+ elif self.compiler.name == 'intel':
+ cflags.append('-restrict')
- def library_build_type(self, makefile_inc, defines):
- makefile_inc.extend([
- 'LIB = .a',
- 'CLIBFLAGS = ',
- 'RANLIB = ranlib',
- 'AR = ar',
- 'ARFLAGS = -ruv '
- ])
+ makefile_inc.append('CCS = $(CC)')
+ makefile_inc.append('CCP = %s' %
+ (self.spec['mpi'].mpicc if '+mpi' in self.spec else 'mpicc'))
+ makefile_inc.append('CCD = $(CCS)')
- @when('+shared')
- def library_build_type(self, makefile_inc, defines):
- makefile_inc.extend([
- 'LIB = .so',
- 'CLIBFLAGS = -shared -fPIC',
- 'RANLIB = echo',
- 'AR = $(CC)',
- 'ARFLAGS = -shared $(LDFLAGS) -o'
- ])
+ ## Extra Features ##
- def extra_features(self, makefile_inc, defines):
ldflags = []
-
+
if '+compression' in self.spec:
- defines.append('-DCOMMON_FILE_COMPRESS_GZ')
+ cflags.append('-DCOMMON_FILE_COMPRESS_GZ')
ldflags.append('-L%s -lz' % (self.spec['zlib'].prefix.lib))
- defines.append('-DCOMMON_PTHREAD')
+ cflags.append('-DCOMMON_PTHREAD')
ldflags.append('-lm -lrt -pthread')
-
- makefile_inc.append('LDFLAGS = %s' % ' '.join(ldflags))
- def patch(self):
- makefile_inc = []
- defines = [
- '-DCOMMON_RANDOM_FIXED_SEED',
- '-DSCOTCH_DETERMINISTIC',
- '-DSCOTCH_RENAME',
- '-DIDXSIZE64' ]
+ makefile_inc.append('LDFLAGS = %s' % ' '.join(ldflags))
- self.library_build_type(makefile_inc, defines)
- self.compiler_specifics(makefile_inc, defines)
- self.extra_features(makefile_inc, defines)
+ ## General Features ##
makefile_inc.extend([
'EXE =',
@@ -93,18 +130,19 @@ class Scotch(Package):
'MKDIR = mkdir',
'MV = mv',
'CP = cp',
- 'CFLAGS = -O3 %s' % (' '.join(defines)),
+ 'CFLAGS = %s' % ' '.join(cflags),
'LEX = %s -Pscotchyy -olex.yy.c' % os.path.join(self.spec['flex'].prefix.bin , 'flex'),
'YACC = %s -pscotchyy -y -b y' % os.path.join(self.spec['bison'].prefix.bin, 'bison'),
- 'prefix = %s' % self.prefix,
- ''
+ 'prefix = %s' % self.prefix
])
with working_dir('src'):
with open('Makefile.inc', 'w') as fh:
fh.write('\n'.join(makefile_inc))
-
+
def install(self, spec, prefix):
+ self.configure()
+
targets = ['scotch']
if '+mpi' in self.spec:
targets.append('ptscotch')
@@ -115,12 +153,10 @@ class Scotch(Package):
targets.append('ptesmumps')
with working_dir('src'):
- for app in targets:
- make(app, parallel=(not app=='ptesmumps'))
+ for target in targets:
+ make(target, parallel=(target!='ptesmumps'))
-
install_tree('bin', prefix.bin)
install_tree('lib', prefix.lib)
install_tree('include', prefix.include)
install_tree('man/man1', prefix.share_man1)
-
diff --git a/var/spack/repos/builtin/packages/silo/package.py b/var/spack/repos/builtin/packages/silo/package.py
index b7894e4d2b..7e68663c6e 100644
--- a/var/spack/repos/builtin/packages/silo/package.py
+++ b/var/spack/repos/builtin/packages/silo/package.py
@@ -1,5 +1,6 @@
from spack import *
+
class Silo(Package):
"""Silo is a library for reading and writing a wide variety of scientific
data to binary, disk files."""
@@ -12,6 +13,7 @@ class Silo(Package):
version('4.8', 'b1cbc0e7ec435eb656dc4b53a23663c9')
variant('fortran', default=True, description='Enable Fortran support')
+ variant('shared', default=True, description='Build shared libraries')
variant('silex', default=False, description='Builds Silex, a GUI for viewing Silo files')
depends_on('hdf5')
@@ -21,6 +23,7 @@ class Silo(Package):
config_args = [
'--enable-fortran' if '+fortran' in spec else '--disable-fortran',
'--enable-silex' if '+silex' in spec else '--disable-silex',
+ '--enable-shared' if '+shared' in spec else '--disable-shared',
]
if '+silex' in spec:
@@ -30,6 +33,7 @@ class Silo(Package):
'--prefix=%s' % prefix,
'--with-hdf5=%s,%s' % (spec['hdf5'].prefix.include, spec['hdf5'].prefix.lib),
'--with-zlib=%s,%s' % (spec['zlib'].prefix.include, spec['zlib'].prefix.lib),
+ '--enable-install-lite-headers',
*config_args)
make()
diff --git a/var/spack/repos/builtin/packages/visit/package.py b/var/spack/repos/builtin/packages/visit/package.py
new file mode 100644
index 0000000000..14e3b6a0c1
--- /dev/null
+++ b/var/spack/repos/builtin/packages/visit/package.py
@@ -0,0 +1,31 @@
+from spack import *
+
+
+class Visit(Package):
+ """VisIt is an Open Source, interactive, scalable, visualization, animation and analysis tool."""
+ homepage = "https://wci.llnl.gov/simulation/computer-codes/visit/"
+ url = "http://portal.nersc.gov/project/visit/releases/2.10.1/visit2.10.1.tar.gz"
+
+ version('2.10.1', '3cbca162fdb0249f17c4456605c4211e')
+ version('2.10.2', '253de0837a9d69fb689befc98ea4d068')
+
+ depends_on("vtk@6.1.0~opengl2")
+ depends_on("qt@4.8.6")
+ depends_on("python")
+ depends_on("silo+shared")
+
+ def install(self, spec, prefix):
+ with working_dir('spack-build', create=True):
+
+ feature_args = std_cmake_args[:]
+ feature_args.extend(["-DVTK_MAJOR_VERSION=6",
+ "-DVTK_MINOR_VERSION=1",
+ "-DVISIT_LOC_QMAKE_EXE:FILEPATH=%s/qmake-qt4" % spec['qt'].prefix.bin,
+ "-DPYTHON_EXECUTABLE:FILEPATH=%s/python" % spec['python'].prefix.bin,
+ "-DVISIT_SILO_DIR:PATH=%s" % spec['silo'].prefix,
+ "-DVISIT_HDF5_DIR:PATH=%s" % spec['hdf5'].prefix])
+
+ cmake('../src', *feature_args)
+
+ make()
+ make("install")