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Merge branch 'develop' into eschnett/sympol

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This commit is contained in:
Erik Schnetter
2016-08-23 09:45:46 -04:00
parent e43eaad557 e81f3daa28
commit 64d3f87e60
929 changed files with 28519 additions and 6367 deletions
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40
var/spack/mock_configs/site_spackconfig/compilers.yaml Normal file
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@@ -0,0 +1,40 @@
compilers:
all:
clang@3.3:
cc: /path/to/clang
cxx: /path/to/clang++
f77: None
fc: None
modules: None
strategy: PATH
gcc@4.5.0:
cc: /path/to/gcc
cxx: /path/to/g++
f77: /path/to/gfortran
fc: /path/to/gfortran
modules: None
strategy: PATH
gcc@5.2.0:
cc: cc
cxx: CC
f77: ftn
fc: ftn
modules:
- PrgEnv-gnu
- gcc/5.2.0
strategy: MODULES
intel@15.0.1:
cc: cc
ccx: CC
f77: ftn
fc: ftn
modules:
- PrgEnv-intel
- intel/15.0.1
strategy: MODULES
intel@15.1.2:
cc: /path/to/icc
cxx: /path/to/ic++
f77: /path/to/ifort
fc: /path/to/ifort
strategy: PATH

1
var/spack/repos/builtin.mock/packages/a/package.py
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@@ -24,6 +24,7 @@
##############################################################################
from spack import *
class A(Package):
"""Simple package with no dependencies"""

1
var/spack/repos/builtin.mock/packages/b/package.py
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@@ -24,6 +24,7 @@
##############################################################################
from spack import *
class B(Package):
"""Simple package with no dependencies"""

1
var/spack/repos/builtin.mock/packages/c/package.py
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@@ -24,6 +24,7 @@
##############################################################################
from spack import *
class C(Package):
"""Simple package with no dependencies"""

1
var/spack/repos/builtin.mock/packages/callpath/package.py
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@@ -24,6 +24,7 @@
##############################################################################
from spack import *
class Callpath(Package):
homepage = "https://github.com/tgamblin/callpath"
url = "http://github.com/tgamblin/callpath-1.0.tar.gz"

17
var/spack/repos/builtin.mock/packages/cmake-client/package.py
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@@ -25,6 +25,7 @@
from spack import *
import os
def check(condition, msg):
"""Raise an install error if condition is False."""
if not condition:
@@ -38,8 +39,7 @@ class CmakeClient(Package):
version('1.0', '4cb3ff35b2472aae70f542116d616e63')
depends_on('cmake')
depends_on('cmake', type='build')
def setup_environment(self, spack_env, run_env):
spack_cc # Ensure spack module-scope variable is avaiabl
@@ -47,8 +47,8 @@ def setup_environment(self, spack_env, run_env):
"setup_environment couldn't read global set by cmake.")
check(self.spec['cmake'].link_arg == "test link arg",
"link arg on dependency spec not readable from setup_environment.")
"link arg on dependency spec not readable from "
"setup_environment.")
def setup_dependent_environment(self, spack_env, run_env, dspec):
spack_cc # Ensure spack module-scope variable is avaiable
@@ -56,8 +56,8 @@ def setup_dependent_environment(self, spack_env, run_env, dspec):
"setup_dependent_environment couldn't read global set by cmake.")
check(self.spec['cmake'].link_arg == "test link arg",
"link arg on dependency spec not readable from setup_dependent_environment.")
"link arg on dependency spec not readable from "
"setup_dependent_environment.")
def setup_dependent_package(self, module, dspec):
spack_cc # Ensure spack module-scope variable is avaiable
@@ -65,9 +65,8 @@ def setup_dependent_package(self, module, dspec):
"setup_dependent_package couldn't read global set by cmake.")
check(self.spec['cmake'].link_arg == "test link arg",
"link arg on dependency spec not readable from setup_dependent_package.")
"link arg on dependency spec not readable from "
"setup_dependent_package.")
def install(self, spec, prefix):
# check that cmake is in the global scope.

4
var/spack/repos/builtin.mock/packages/cmake/package.py
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@@ -25,6 +25,7 @@
from spack import *
import os
def check(condition, msg):
"""Raise an install error if condition is False."""
if not condition:
@@ -39,7 +40,6 @@ class Cmake(Package):
version('3.4.3', '4cb3ff35b2472aae70f542116d616e63',
url='https://cmake.org/files/v3.4/cmake-3.4.3.tar.gz')
def setup_environment(self, spack_env, run_env):
spack_cc # Ensure spack module-scope variable is avaiable
spack_env.set('for_install', 'for_install')
@@ -48,7 +48,6 @@ def setup_dependent_environment(self, spack_env, run_env, dspec):
spack_cc # Ensure spack module-scope variable is avaiable
spack_env.set('from_cmake', 'from_cmake')
def setup_dependent_package(self, module, dspec):
spack_cc # Ensure spack module-scope variable is avaiable
@@ -57,7 +56,6 @@ def setup_dependent_package(self, module, dspec):
self.spec.link_arg = "test link arg"
def install(self, spec, prefix):
mkdirp(prefix.bin)

1
var/spack/repos/builtin.mock/packages/direct_mpich/package.py
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@@ -24,6 +24,7 @@
##############################################################################
from spack import *
class DirectMpich(Package):
homepage = "http://www.example.com"
url = "http://www.example.com/direct_mpich-1.0.tar.gz"

18
var/spack/repos/builtin.mock/packages/dtbuild1/package.py Normal file
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@@ -0,0 +1,18 @@
from spack import *
class Dtbuild1(Package):
"""Package for use as a build tool for deptypes testing which has its own
deptree"""
homepage = "http://www.example.com"
url = "http://www.example.com/dtbuild1-1.0.tar.gz"
version('1.0', '0123456789abcdef0123456789abcdef')
depends_on('dtbuild2', type='build')
depends_on('dtlink2')
depends_on('dtrun2', type='run')
def install(self, spec, prefix):
pass

13
var/spack/repos/builtin.mock/packages/dtbuild2/package.py Normal file
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@@ -0,0 +1,13 @@
from spack import *
class Dtbuild2(Package):
"""Simple package which acts as a build dependency"""
homepage = "http://www.example.com"
url = "http://www.example.com/dtbuild2-1.0.tar.gz"
version('1.0', '0123456789abcdef0123456789abcdef')
def install(self, spec, prefix):
pass

13
var/spack/repos/builtin.mock/packages/dtbuild3/package.py Normal file
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@@ -0,0 +1,13 @@
from spack import *
class Dtbuild3(Package):
"""Simple package which acts as a build dependency"""
homepage = "http://www.example.com"
url = "http://www.example.com/dtbuild3-1.0.tar.gz"
version('1.0', '0123456789abcdef0123456789abcdef')
def install(self, spec, prefix):
pass

15
var/spack/repos/builtin.mock/packages/dtlink1/package.py Normal file
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@@ -0,0 +1,15 @@
from spack import *
class Dtlink1(Package):
"""Simple package which acts as a link dependency"""
homepage = "http://www.example.com"
url = "http://www.example.com/dtlink1-1.0.tar.gz"
version('1.0', '0123456789abcdef0123456789abcdef')
depends_on('dtlink3')
def install(self, spec, prefix):
pass

13
var/spack/repos/builtin.mock/packages/dtlink2/package.py Normal file
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@@ -0,0 +1,13 @@
from spack import *
class Dtlink2(Package):
"""Simple package which acts as a link dependency"""
homepage = "http://www.example.com"
url = "http://www.example.com/dtlink2-1.0.tar.gz"
version('1.0', '0123456789abcdef0123456789abcdef')
def install(self, spec, prefix):
pass

16
var/spack/repos/builtin.mock/packages/dtlink3/package.py Normal file
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@@ -0,0 +1,16 @@
from spack import *
class Dtlink3(Package):
"""Simple package which acts as a link dependency"""
homepage = "http://www.example.com"
url = "http://www.example.com/dtlink3-1.0.tar.gz"
version('1.0', '0123456789abcdef0123456789abcdef')
depends_on('dtbuild2', type='build')
depends_on('dtlink4')
def install(self, spec, prefix):
pass

13
var/spack/repos/builtin.mock/packages/dtlink4/package.py Normal file
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@@ -0,0 +1,13 @@
from spack import *
class Dtlink4(Package):
"""Simple package which acts as a link dependency"""
homepage = "http://www.example.com"
url = "http://www.example.com/dtlink4-1.0.tar.gz"
version('1.0', '0123456789abcdef0123456789abcdef')
def install(self, spec, prefix):
pass

13
var/spack/repos/builtin.mock/packages/dtlink5/package.py Normal file
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@@ -0,0 +1,13 @@
from spack import *
class Dtlink5(Package):
"""Simple package which acts as a link dependency"""
homepage = "http://www.example.com"
url = "http://www.example.com/dtlink5-1.0.tar.gz"
version('1.0', '0123456789abcdef0123456789abcdef')
def install(self, spec, prefix):
pass

16
var/spack/repos/builtin.mock/packages/dtrun1/package.py Normal file
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@@ -0,0 +1,16 @@
from spack import *
class Dtrun1(Package):
"""Simple package which acts as a run dependency"""
homepage = "http://www.example.com"
url = "http://www.example.com/dtrun1-1.0.tar.gz"
version('1.0', '0123456789abcdef0123456789abcdef')
depends_on('dtlink5')
depends_on('dtrun3', type='run')
def install(self, spec, prefix):
pass

13
var/spack/repos/builtin.mock/packages/dtrun2/package.py Normal file
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@@ -0,0 +1,13 @@
from spack import *
class Dtrun2(Package):
"""Simple package which acts as a run dependency"""
homepage = "http://www.example.com"
url = "http://www.example.com/dtrun2-1.0.tar.gz"
version('1.0', '0123456789abcdef0123456789abcdef')
def install(self, spec, prefix):
pass

15
var/spack/repos/builtin.mock/packages/dtrun3/package.py Normal file
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@@ -0,0 +1,15 @@
from spack import *
class Dtrun3(Package):
"""Simple package which acts as a run dependency"""
homepage = "http://www.example.com"
url = "http://www.example.com/dtrun3-1.0.tar.gz"
version('1.0', '0123456789abcdef0123456789abcdef')
depends_on('dtbuild3', type='build')
def install(self, spec, prefix):
pass

17
var/spack/repos/builtin.mock/packages/dttop/package.py Normal file
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@@ -0,0 +1,17 @@
from spack import *
class Dttop(Package):
"""Package with a complicated dependency tree"""
homepage = "http://www.example.com"
url = "http://www.example.com/dttop-1.0.tar.gz"
version('1.0', '0123456789abcdef0123456789abcdef')
depends_on('dtbuild1', type='build')
depends_on('dtlink1')
depends_on('dtrun1', type='run')
def install(self, spec, prefix):
pass

15
var/spack/repos/builtin.mock/packages/dtuse/package.py Normal file
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@@ -0,0 +1,15 @@
from spack import *
class Dtuse(Package):
"""Simple package which uses dttop"""
homepage = "http://www.example.com"
url = "http://www.example.com/dtuse-1.0.tar.gz"
version('1.0', '0123456789abcdef0123456789abcdef')
depends_on('dttop')
def install(self, spec, prefix):
pass

1
var/spack/repos/builtin.mock/packages/dyninst/package.py
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@@ -24,6 +24,7 @@
##############################################################################
from spack import *
class Dyninst(Package):
homepage = "https://paradyn.org"
url = "http://www.paradyn.org/release8.1/DyninstAPI-8.1.1.tgz"

1
var/spack/repos/builtin.mock/packages/e/package.py
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@@ -24,6 +24,7 @@
##############################################################################
from spack import *
class E(Package):
"""Simple package with no dependencies"""

38
var/spack/repos/builtin.mock/packages/externalmodule/package.py Normal file
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@@ -0,0 +1,38 @@
##############################################################################
# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-647188
#
# For details, see https://github.com/llnl/spack
# Please also see the LICENSE file for our notice and the LGPL.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License (as
# published by the Free Software Foundation) version 2.1, February 1999.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
# conditions of the GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
from spack import *
class Externalmodule(Package):
homepage = "http://somewhere.com"
url = "http://somewhere.com/module-1.0.tar.gz"
version('1.0', '1234567890abcdef1234567890abcdef')
depends_on('externalprereq')
def install(self, spec, prefix):
pass

1
var/spack/repos/builtin.mock/packages/externalprereq/package.py
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@@ -24,6 +24,7 @@
##############################################################################
from spack import *
class Externalprereq(Package):
homepage = "http://somewhere.com"
url = "http://somewhere.com/prereq-1.0.tar.gz"

1
var/spack/repos/builtin.mock/packages/externaltest/package.py
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@@ -24,6 +24,7 @@
##############################################################################
from spack import *
class Externaltest(Package):
homepage = "http://somewhere.com"
url = "http://somewhere.com/test-1.0.tar.gz"

1
var/spack/repos/builtin.mock/packages/externaltool/package.py
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@@ -24,6 +24,7 @@
##############################################################################
from spack import *
class Externaltool(Package):
homepage = "http://somewhere.com"
url = "http://somewhere.com/tool-1.0.tar.gz"

1
var/spack/repos/builtin.mock/packages/externalvirtual/package.py
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@@ -24,6 +24,7 @@
##############################################################################
from spack import *
class Externalvirtual(Package):
homepage = "http://somewhere.com"
url = "http://somewhere.com/stuff-1.0.tar.gz"

1
var/spack/repos/builtin.mock/packages/fake/package.py
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@@ -24,6 +24,7 @@
##############################################################################
from spack import *
class Fake(Package):
homepage = "http://www.fake-spack-example.org"
url = "http://www.fake-spack-example.org/downloads/fake-1.0.tar.gz"

1
var/spack/repos/builtin.mock/packages/git-test/package.py
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@@ -24,6 +24,7 @@
##############################################################################
from spack import *
class GitTest(Package):
"""Mock package that uses git for fetching."""
homepage = "http://www.git-fetch-example.com"

1
var/spack/repos/builtin.mock/packages/hg-test/package.py
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@@ -24,6 +24,7 @@
##############################################################################
from spack import *
class HgTest(Package):
"""Test package that does fetching with mercurial."""
homepage = "http://www.hg-fetch-example.com"

1
var/spack/repos/builtin.mock/packages/hypre/package.py
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@@ -24,6 +24,7 @@
##############################################################################
from spack import *
class Hypre(Package):
"""Hypre is included here as an example of a package that depends on
both LAPACK and BLAS."""

1
var/spack/repos/builtin.mock/packages/indirect_mpich/package.py
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@@ -24,6 +24,7 @@
##############################################################################
from spack import *
class IndirectMpich(Package):
"""Test case for a package that depends on MPI and one of its
dependencies requires a *particular version* of MPI.

2
var/spack/repos/builtin.mock/packages/libdwarf/package.py
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@@ -23,11 +23,11 @@
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
from spack import *
import os
# Only build certain parts of dwarf because the other ones break.
dwarf_dirs = ['libdwarf', 'dwarfdump2']
class Libdwarf(Package):
homepage = "http://www.prevanders.net/dwarf.html"
url = "http://www.prevanders.net/libdwarf-20130729.tar.gz"

1
var/spack/repos/builtin.mock/packages/libelf/package.py
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@@ -24,6 +24,7 @@
##############################################################################
from spack import *
class Libelf(Package):
homepage = "http://www.mr511.de/software/english.html"
url = "http://www.mr511.de/software/libelf-0.8.13.tar.gz"

1
var/spack/repos/builtin.mock/packages/mpich/package.py
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@@ -24,6 +24,7 @@
##############################################################################
from spack import *
class Mpich(Package):
homepage = "http://www.mpich.org"
url = "http://www.mpich.org/static/downloads/3.0.4/mpich-3.0.4.tar.gz"

1
var/spack/repos/builtin.mock/packages/mpich2/package.py
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@@ -24,6 +24,7 @@
##############################################################################
from spack import *
class Mpich2(Package):
homepage = "http://www.mpich.org"
url = "http://www.mpich.org/static/downloads/1.5/mpich2-1.5.tar.gz"

3
var/spack/repos/builtin.mock/packages/mpileaks/package.py
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@@ -24,6 +24,7 @@
##############################################################################
from spack import *
class Mpileaks(Package):
homepage = "http://www.llnl.gov"
url = "http://www.llnl.gov/mpileaks-1.0.tar.gz"
@@ -35,6 +36,8 @@ class Mpileaks(Package):
variant('debug', default=False, description='Debug variant')
variant('opt', default=False, description='Optimized variant')
variant('shared', default=True, description='Build shared library')
variant('static', default=True, description='Build static library')
depends_on("mpi")
depends_on("callpath")

37
var/spack/repos/builtin.mock/packages/multimethod/package.py
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@@ -23,6 +23,7 @@
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
from spack import *
import spack.architecture
class Multimethod(Package):
@@ -49,7 +50,6 @@ def no_version_2(self):
def no_version_2(self):
return 4
#
# These functions overlap, so there is ambiguity, but we'll take
# the first one.
@@ -62,7 +62,6 @@ def version_overlap(self):
def version_overlap(self):
return 2
#
# More complicated case with cascading versions.
#
@@ -81,7 +80,6 @@ def mpi_version(self):
def mpi_version(self):
return 1
#
# Use these to test whether the default method is called when no
# match is found. This also tests whether we can switch methods
@@ -98,31 +96,25 @@ def has_a_default(self):
def has_a_default(self):
return 'intel'
#
# Make sure we can switch methods on different architectures
# Make sure we can switch methods on different target
#
@when('arch=x86_64')
def different_by_architecture(self):
return 'x86_64'
@when('arch=ppc64')
def different_by_architecture(self):
return 'ppc64'
@when('arch=ppc32')
def different_by_architecture(self):
return 'ppc32'
@when('arch=arm64')
def different_by_architecture(self):
return 'arm64'
platform = spack.architecture.platform()
targets = platform.targets.values()
if len(targets) > 1:
targets = targets[:-1]
for target in targets:
@when('target=' + target.name)
def different_by_target(self):
if isinstance(self.spec.architecture.target, basestring):
return self.spec.architecture.target
else:
return self.spec.architecture.target.name
#
# Make sure we can switch methods on different dependencies
#
@when('^mpich')
def different_by_dep(self):
return 'mpich'
@@ -131,7 +123,6 @@ def different_by_dep(self):
def different_by_dep(self):
return 'zmpi'
#
# Make sure we can switch on virtual dependencies
#

1
var/spack/repos/builtin.mock/packages/netlib-blas/package.py
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@@ -24,6 +24,7 @@
##############################################################################
from spack import *
class NetlibBlas(Package):
homepage = "http://www.netlib.org/lapack/"
url = "http://www.netlib.org/lapack/lapack-3.5.0.tgz"

1
var/spack/repos/builtin.mock/packages/netlib-lapack/package.py
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@@ -24,6 +24,7 @@
##############################################################################
from spack import *
class NetlibLapack(Package):
homepage = "http://www.netlib.org/lapack/"
url = "http://www.netlib.org/lapack/lapack-3.5.0.tgz"

1
var/spack/repos/builtin.mock/packages/openblas-with-lapack/package.py
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@@ -24,6 +24,7 @@
##############################################################################
from spack import *
class OpenblasWithLapack(Package):
"""Dummy version of OpenBLAS that also provides LAPACK, for testing."""
homepage = "http://www.openblas.net"

1
var/spack/repos/builtin.mock/packages/openblas/package.py
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@@ -24,6 +24,7 @@
##############################################################################
from spack import *
class Openblas(Package):
"""OpenBLAS: An optimized BLAS library"""
homepage = "http://www.openblas.net"

1
var/spack/repos/builtin.mock/packages/optional-dep-test-2/package.py
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@@ -24,6 +24,7 @@
##############################################################################
from spack import *
class OptionalDepTest2(Package):
"""Depends on the optional-dep-test package"""

1
var/spack/repos/builtin.mock/packages/optional-dep-test-3/package.py
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@@ -24,6 +24,7 @@
##############################################################################
from spack import *
class OptionalDepTest3(Package):
"""Depends on the optional-dep-test package"""

1
var/spack/repos/builtin.mock/packages/optional-dep-test/package.py
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@@ -24,6 +24,7 @@
##############################################################################
from spack import *
class OptionalDepTest(Package):
"""Description"""

2
var/spack/repos/builtin.mock/packages/python/package.py
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@@ -24,6 +24,7 @@
##############################################################################
from spack import *
class Python(Package):
"""Dummy Python package to demonstrate preferred versions."""
homepage = "http://www.python.org"
@@ -40,4 +41,3 @@ class Python(Package):
def install(self, spec, prefix):
pass

1
var/spack/repos/builtin.mock/packages/svn-test/package.py
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@@ -24,6 +24,7 @@
##############################################################################
from spack import *
class SvnTest(Package):
"""Mock package that uses svn for fetching."""
url = "http://www.example.com/svn-test-1.0.tar.gz"

1
var/spack/repos/builtin.mock/packages/trivial_install_test_package/package.py
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@@ -24,6 +24,7 @@
##############################################################################
from spack import *
class TrivialInstallTestPackage(Package):
"""This package is a stub with a trivial install method. It allows us
to test the install and uninstall logic of spack."""

1
var/spack/repos/builtin.mock/packages/zmpi/package.py
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@@ -24,6 +24,7 @@
##############################################################################
from spack import *
class Zmpi(Package):
"""This is a fake MPI package used to demonstrate virtual package providers
with dependencies."""

2
var/spack/repos/builtin/packages/ImageMagick/package.py
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@@ -51,7 +51,7 @@ class Imagemagick(Package):
url="http://sourceforge.net/projects/imagemagick/files/old-sources/6.x/6.8/ImageMagick-6.8.9-10.tar.gz/download")
depends_on('jpeg')
depends_on('libtool')
depends_on('libtool', type='build')
depends_on('libpng')
depends_on('freetype')
depends_on('fontconfig')

1
var/spack/repos/builtin/packages/LuaJIT/package.py
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@@ -25,6 +25,7 @@
import os
from spack import *
class Luajit(Package):
"""Flast flexible JITed lua"""
homepage = "http://www.luajit.org"

1
var/spack/repos/builtin/packages/Mitos/package.py
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@@ -41,6 +41,7 @@ class Mitos(Package):
depends_on('dyninst@8.2.1:')
depends_on('hwloc')
depends_on('mpi')
depends_on('cmake', type='build')
def install(self, spec, prefix):
with working_dir('spack-build', create=True):

117
var/spack/repos/builtin/packages/R/package.py
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@@ -22,30 +22,25 @@
# License along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
import functools
import glob
import inspect
import os
import re
from contextlib import closing
import spack
from llnl.util.lang import match_predicate
from spack import *
from spack.util.environment import *
import shutil
class R(Package):
"""
R is 'GNU S', a freely available language and environment for statistical computing and graphics which provides a
wide variety of statistical and graphical techniques: linear and nonlinear modelling, statistical tests, time series
analysis, classification, clustering, etc. Please consult the R project homepage for further information.
"""
"""R is 'GNU S', a freely available language and environment for
statistical computing and graphics which provides a wide variety of
statistical and graphical techniques: linear and nonlinear modelling,
statistical tests, time series analysis, classification, clustering, etc.
Please consult the R project homepage for further information."""
homepage = "https://www.r-project.org"
url = "http://cran.cnr.berkeley.edu/src/base/R-3/R-3.1.2.tar.gz"
extendable = True
version('3.3.1', 'f50a659738b73036e2f5635adbd229c5')
version('3.3.0', '5a7506c8813432d1621c9725e86baf7a')
version('3.2.3', '1ba3dac113efab69e706902810cc2970')
version('3.2.2', '57cef5c2e210a5454da1979562a10e5b')
version('3.2.1', 'c2aac8b40f84e08e7f8c9068de9239a3')
@@ -53,7 +48,8 @@ class R(Package):
version('3.1.3', '53a85b884925aa6b5811dfc361d73fc4')
version('3.1.2', '3af29ec06704cbd08d4ba8d69250ae74')
variant('external-lapack', default=False, description='Links to externally installed BLAS/LAPACK')
variant('external-lapack', default=False,
description='Links to externally installed BLAS/LAPACK')
# Virtual dependencies
depends_on('blas', when='+external-lapack')
@@ -65,6 +61,7 @@ class R(Package):
depends_on('icu')
depends_on('glib')
depends_on('zlib')
depends_on('bzip2')
depends_on('libtiff')
depends_on('jpeg')
depends_on('cairo')
@@ -72,59 +69,107 @@ class R(Package):
depends_on('freetype')
depends_on('tcl')
depends_on('tk')
depends_on('curl')
depends_on('pcre')
depends_on('jdk')
@property
def etcdir(self):
return join_path(prefix, 'rlib', 'R', 'etc')
def install(self, spec, prefix):
rlibdir = join_path(prefix, 'rlib')
options = ['--prefix=%s' % prefix,
'--libdir=%s' % rlibdir,
'--enable-R-shlib',
'--enable-BLAS-shlib',
'--enable-R-framework=no']
configure_args = ['--prefix=%s' % prefix,
'--libdir=%s' % rlibdir,
'--enable-R-shlib',
'--enable-BLAS-shlib',
'--enable-R-framework=no']
if '+external-lapack' in spec:
options.extend(['--with-blas', '--with-lapack'])
configure_args.extend(['--with-blas', '--with-lapack'])
configure(*options)
configure(*configure_args)
make()
make('install')
# Make a copy of Makeconf because it will be needed to properly build R
# dependencies in Spack.
src_makeconf = join_path(self.etcdir, 'Makeconf')
dst_makeconf = join_path(self.etcdir, 'Makeconf.spack')
shutil.copy(src_makeconf, dst_makeconf)
self.filter_compilers(spec, prefix)
def filter_compilers(self, spec, prefix):
"""Run after install to tell the configuration files and Makefiles
to use the compilers that Spack built the package with.
If this isn't done, they'll have CC and CXX set to Spack's generic
cc and c++. We want them to be bound to whatever compiler
they were built with."""
kwargs = {'ignore_absent': True, 'backup': False, 'string': True}
filter_file(env['CC'], self.compiler.cc,
join_path(self.etcdir, 'Makeconf'), **kwargs)
filter_file(env['CXX'], self.compiler.cxx,
join_path(self.etcdir, 'Makeconf'), **kwargs)
filter_file(env['F77'], self.compiler.f77,
join_path(self.etcdir, 'Makeconf'), **kwargs)
filter_file(env['FC'], self.compiler.fc,
join_path(self.etcdir, 'Makeconf'), **kwargs)
# ========================================================================
# Set up environment to make install easy for R extensions.
# ========================================================================
@property
def r_lib_dir(self):
return os.path.join('rlib', 'R', 'library')
return join_path('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():
for d in extension_spec.traverse(deptype=nolink, deptype_query='run'):
if d.package.extends(self.spec):
r_libs_path.append(os.path.join(d.prefix, self.r_lib_dir))
r_libs_path.append(join_path(d.prefix, self.r_lib_dir))
r_libs_path = ':'.join(r_libs_path)
spack_env.set('R_LIBS', r_libs_path)
spack_env.set('R_MAKEVARS_SITE',
join_path(self.etcdir, 'Makeconf.spack'))
# For run time environment set only the path for extension_spec and prepend it to R_LIBS
# Use the number of make_jobs set in spack. The make program will
# determine how many jobs can actually be started.
spack_env.set('MAKEFLAGS', '-j{0}'.format(make_jobs))
# For run time environment set only the path for extension_spec and
# prepend it to R_LIBS
if extension_spec.package.extends(self.spec):
run_env.prepend_path('R_LIBS', os.path.join(extension_spec.prefix, self.r_lib_dir))
run_env.prepend_path('R_LIBS', join_path(
extension_spec.prefix, self.r_lib_dir))
def setup_environment(self, spack_env, run_env):
run_env.prepend_path('LIBRARY_PATH',
join_path(self.prefix, 'rlib', 'R', 'lib'))
run_env.prepend_path('LD_LIBRARY_PATH',
join_path(self.prefix, 'rlib', 'R', 'lib'))
run_env.prepend_path('CPATH',
join_path(self.prefix, 'rlib', 'R', 'include'))
def setup_dependent_package(self, module, ext_spec):
"""
Called before R modules' install() methods.
"""Called before R modules' install() methods. In most cases,
extensions will only need to have one line:
R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
self.stage.source_path)"""
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)
module.r_lib_dir = join_path(ext_spec.prefix, self.r_lib_dir)
# Make the site packages directory for extensions, if it does not exist already.
# Make the site packages directory for extensions, if it does not exist
# already.
if ext_spec.package.is_extension:
mkdirp(module.r_lib_dir)

10
var/spack/repos/builtin/packages/SAMRAI/package.py
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@@ -24,12 +24,14 @@
##############################################################################
from spack import *
class Samrai(Package):
"""SAMRAI (Structured Adaptive Mesh Refinement Application Infrastructure)
is an object-oriented C++ software library enables exploration of numerical,
algorithmic, parallel computing, and software issues associated with applying
structured adaptive mesh refinement (SAMR) technology in large-scale parallel
application development.
is an object-oriented C++ software library enables exploration of
numerical, algorithmic, parallel computing, and software issues
associated with applying structured adaptive mesh refinement
(SAMR) technology in large-scale parallel application development.
"""
homepage = "https://computation.llnl.gov/project/SAMRAI/"
url = "https://computation.llnl.gov/project/SAMRAI/download/SAMRAI-v3.9.1.tar.gz"

51
var/spack/repos/builtin/packages/ack/package.py Normal file
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@@ -0,0 +1,51 @@
##############################################################################
# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-647188
#
# For details, see https://github.com/llnl/spack
# Please also see the LICENSE file for our notice and the LGPL.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License (as
# published by the Free Software Foundation) version 2.1, February 1999.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
# conditions of the GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
from spack import *
class Ack(Package):
"""ack 2.14 is a tool like grep, optimized for programmers.
Designed for programmers with large heterogeneous trees of
source code, ack is written purely in portable Perl 5 and takes
advantage of the power of Perl's regular expressions."""
homepage = "http://beyondgrep.com/"
url = "http://beyondgrep.com/ack-2.14-single-file"
version('2.14', 'e74150a1609d28a70b450ef9cc2ed56b', expand=False)
depends_on('perl')
def install(self, spec, prefix):
mkdirp(prefix.bin)
ack = 'ack-{0}-single-file'.format(self.version)
# rewrite the script's #! line to call the perl dependency
shbang = '#!' + join_path(spec['perl'].prefix.bin, 'perl')
filter_file(r'^#!/usr/bin/env perl', shbang, ack)
install(ack, join_path(prefix.bin, "ack"))
set_executable(join_path(prefix.bin, "ack"))

7
var/spack/repos/builtin/packages/activeharmony/package.py
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@@ -24,8 +24,10 @@
##############################################################################
from spack import *
class Activeharmony(Package):
"""Active Harmony: a framework for auto-tuning (the automated search for values to improve the performance of a target application)."""
"""Active Harmony: a framework for auto-tuning (the automated search for
values to improve the performance of a target application)."""
homepage = "http://www.dyninst.org/harmony"
url = "http://www.dyninst.org/sites/default/files/downloads/harmony/ah-4.5.tar.gz"
@@ -34,6 +36,3 @@ class Activeharmony(Package):
def install(self, spec, prefix):
make("CFLAGS=-O3")
make("install", 'PREFIX=%s' % prefix)
from spack import *

2
var/spack/repos/builtin/packages/adept-utils/package.py
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@@ -24,6 +24,7 @@
##############################################################################
from spack import *
class AdeptUtils(Package):
"""Utility libraries for LLNL performance tools."""
@@ -35,6 +36,7 @@ class AdeptUtils(Package):
depends_on("boost")
depends_on("mpi")
depends_on('cmake', type='build')
def install(self, spec, prefix):
cmake(*std_cmake_args)

41
var/spack/repos/builtin/packages/adios/package.py Normal file
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@@ -0,0 +1,41 @@
import os
from spack import *
class Adios(Package):
"""
The Adaptable IO System (ADIOS) provides a simple,
flexible way for scientists to describe the
data in their code that may need to be written,
read, or processed outside of the running simulation
"""
homepage = "http://www.olcf.ornl.gov/center-projects/adios/"
url = "https://github.com/ornladios/ADIOS/archive/v1.9.0.tar.gz"
version('1.9.0', '310ff02388bbaa2b1c1710ee970b5678')
# Lots of setting up here for this package
# module swap PrgEnv-intel PrgEnv-$COMP
# module load cray-netcdf/4.3.3.1
# module load cray-hdf5/1.8.14
# module load python/2.7.10
depends_on('hdf5')
depends_on('mxml')
def install(self, spec, prefix):
configure_args = ["--prefix=%s" % prefix,
"--with-mxml=%s" % spec['mxml'].prefix,
"--with-hdf5=%s" % spec['hdf5'].prefix,
"--with-netcdf=%s" % os.environ["NETCDF_DIR"],
"--with-infiniband=no",
"MPICC=cc", "MPICXX=CC", "MPIFC=ftn",
"CPPFLAGS=-DMPICH_IGNORE_CXX_SEEK"]
if spec.satisfies('%gcc'):
configure_args.extend(["CC=gcc", "CXX=g++", "FC=gfortran"])
configure(*configure_args)
make()
make("install")

58
var/spack/repos/builtin/packages/adol-c/package.py
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@@ -23,21 +23,24 @@
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
from spack import *
import sys
class AdolC(Package):
"""A package for the automatic differentiation of first and higher derivatives of vector functions in C and C++ programs by operator overloading."""
"""A package for the automatic differentiation of first and higher
derivatives of vector functions in C and C++ programs by operator
overloading."""
homepage = "https://projects.coin-or.org/ADOL-C"
url = "http://www.coin-or.org/download/source/ADOL-C/ADOL-C-2.6.1.tgz"
version('head', svn='https://projects.coin-or.org/svn/ADOL-C/trunk/')
version('2.6.1', '1032b28427d6e399af4610e78c0f087b')
variant('doc', default=True, description='Install documentation')
variant('openmp', default=False, description='Enable OpenMP support')
variant('sparse', default=False, description='Enable sparse drivers')
variant('tests', default=True, description='Build all included examples as a test case')
variant('tests', default=True,
description='Build all included examples as a test case')
patch('openmp_exam.patch')
def install(self, spec, prefix):
@@ -49,10 +52,14 @@ def install(self, spec, prefix):
if '+openmp' in spec:
if spec.satisfies('%gcc'):
make_args.extend([
'--with-openmp-flag=-fopenmp' # FIXME: Is this required? -I <path to omp.h> -L <LLVM OpenMP library path>
# FIXME: Is this required? -I <path to omp.h> -L <LLVM
# OpenMP library path>
'--with-openmp-flag=-fopenmp'
])
else:
raise InstallError("OpenMP flags for compilers other than GCC are not implemented.")
raise InstallError(
"OpenMP flags for compilers other than GCC "
"are not implemented.")
if '+sparse' in spec:
make_args.extend([
@@ -63,7 +70,7 @@ def install(self, spec, prefix):
# whether Adol-C works as expected
if '+tests' in spec:
make_args.extend([
'--enable-docexa', # Documeted examples
'--enable-docexa', # Documeted examples
'--enable-addexa' # Additional examples
])
if '+openmp' in spec:
@@ -74,31 +81,36 @@ def install(self, spec, prefix):
configure(*make_args)
make()
make("install")
# Copy the config.h file, as some packages might require it
source_directory = self.stage.source_path
config_h = join_path(source_directory,'ADOL-C','src','config.h')
install(config_h, join_path(prefix.include,'adolc'))
config_h = join_path(source_directory, 'ADOL-C', 'src', 'config.h')
install(config_h, join_path(prefix.include, 'adolc'))
# Install documentation to {prefix}/share
if '+doc' in spec:
install_tree(join_path('ADOL-C','doc'),
join_path(prefix.share,'doc'))
install_tree(join_path('ADOL-C', 'doc'),
join_path(prefix.share, 'doc'))
# Install examples to {prefix}/share
if '+tests' in spec:
install_tree(join_path('ADOL-C','examples'),
join_path(prefix.share,'examples'))
install_tree(join_path('ADOL-C', 'examples'),
join_path(prefix.share, 'examples'))
# Run some examples that don't require user input
# TODO: Check that bundled examples produce the correct results
with working_dir(join_path(source_directory,'ADOL-C','examples')):
with working_dir(join_path(
source_directory, 'ADOL-C', 'examples')):
Executable('./tapeless_scalar')()
Executable('./tapeless_vector')()
with working_dir(join_path(source_directory,'ADOL-C','examples','additional_examples')):
with working_dir(join_path(
source_directory,
'ADOL-C', 'examples', 'additional_examples')):
Executable('./checkpointing/checkpointing')()
if '+openmp' in spec:
with working_dir(join_path(source_directory,'ADOL-C','examples','additional_examples')):
with working_dir(join_path(
source_directory,
'ADOL-C', 'examples', 'additional_examples')):
Executable('./checkpointing/checkpointing')()

16
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@@ -24,8 +24,9 @@
##############################################################################
from spack import *
class Antlr(Package):
homepage = "http://www.antlr.org"
url = "https://github.com/antlr/antlr/tarball/v2.7.7"
@@ -41,22 +42,23 @@ class Antlr(Package):
# 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')
# 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')
raise Error(
('Illegal variant %s; ' % v) + 'for now, '
'Spack only knows how to build antlr or antlr+cxx')
config_args = [
'--prefix=%s' % prefix,

55
var/spack/repos/builtin/packages/ape/package.py Normal file
View File

@@ -0,0 +1,55 @@
##############################################################################
# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-647188
#
# For details, see https://github.com/llnl/spack
# Please also see the LICENSE file for our notice and the LGPL.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License (as
# published by the Free Software Foundation) version 2.1, February 1999.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
# conditions of the GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
from spack import *
class Ape(Package):
"""A tool for generating atomic pseudopotentials within a Density-Functional
Theory framework"""
homepage = "http://www.tddft.org/programs/APE/"
url = "http://www.tddft.org/programs/APE/sites/default/files/ape-2.2.1.tar.gz"
version('2.2.1', 'ab81da85bd749c0c136af088c7f9ad58')
depends_on('gsl')
depends_on('libxc')
def install(self, spec, prefix):
args = []
args.extend([
'--prefix=%s' % prefix,
'--with-gsl-prefix=%s' % spec['gsl'].prefix,
'--with-libxc-prefix=%s' % spec['libxc'].prefix
])
if spec.satisfies('%clang') or spec.satisfies('%gcc'):
args.extend([
'FCFLAGS=-O2 -ffree-line-length-none'
])
configure(*args)
make()
make('install')

19
var/spack/repos/builtin/packages/apex/package.py
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@@ -25,6 +25,7 @@
from spack import *
from spack.util.environment import *
class Apex(Package):
homepage = "http://github.com/khuck/xpress-apex"
url = "http://github.com/khuck/xpress-apex/archive/v0.1.tar.gz"
@@ -33,23 +34,23 @@ class Apex(Package):
depends_on("binutils+libiberty")
depends_on("boost@1.54:")
depends_on("cmake@2.8.12:")
depends_on('cmake@2.8.12:', type='build')
depends_on("activeharmony@4.5:")
depends_on("ompt-openmp")
def install(self, spec, prefix):
path=get_path("PATH")
path = get_path("PATH")
path.remove(spec["binutils"].prefix.bin)
path_set("PATH", path)
with working_dir("build", create=True):
cmake('-DBOOST_ROOT=%s' % spec['boost'].prefix,
'-DUSE_BFD=TRUE',
'-DBFD_ROOT=%s' % spec['binutils'].prefix,
'-DUSE_ACTIVEHARMONY=TRUE',
'-DACTIVEHARMONY_ROOT=%s' % spec['activeharmony'].prefix,
'-DUSE_OMPT=TRUE',
'-DOMPT_ROOT=%s' % spec['ompt-openmp'].prefix,
'..', *std_cmake_args)
'-DUSE_BFD=TRUE',
'-DBFD_ROOT=%s' % spec['binutils'].prefix,
'-DUSE_ACTIVEHARMONY=TRUE',
'-DACTIVEHARMONY_ROOT=%s' % spec['activeharmony'].prefix,
'-DUSE_OMPT=TRUE',
'-DOMPT_ROOT=%s' % spec['ompt-openmp'].prefix,
'..', *std_cmake_args)
make()
make("install")

1
var/spack/repos/builtin/packages/apr-util/package.py
View File

@@ -24,6 +24,7 @@
##############################################################################
from spack import *
class AprUtil(Package):
"""Apache Portable Runtime Utility"""
homepage = 'https://apr.apache.org/'

1
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@@ -24,6 +24,7 @@
##############################################################################
from spack import *
class Apr(Package):
"""Apache portable runtime."""
homepage = 'https://apr.apache.org/'

69
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@@ -0,0 +1,69 @@
##############################################################################
# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-647188
#
# For details, see https://github.com/llnl/spack
# Please also see the LICENSE file for our notice and the LGPL.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License (as
# published by the Free Software Foundation) version 2.1, February 1999.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
# conditions of the GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
from spack import *
class Armadillo(Package):
"""Armadillo is a high quality linear algebra library (matrix maths)
for the C++ language, aiming towards a good balance between speed and
ease of use."""
homepage = "http://arma.sourceforge.net/"
url = "http://sourceforge.net/projects/arma/files/armadillo-7.200.1.tar.xz"
version('7.200.2', 'b21585372d67a8876117fd515d8cf0a2')
version('7.200.1', 'ed86d6df0058979e107502e1fe3e469e')
variant('hdf5', default=False, description='Include HDF5 support')
depends_on('cmake@2.8:', type='build')
depends_on('arpack-ng') # old arpack causes undefined symbols
depends_on('blas')
depends_on('lapack')
depends_on('superlu@5.2:')
depends_on('hdf5', when='+hdf5')
def install(self, spec, prefix):
cmake_args = [
# ARPACK support
'-DARPACK_LIBRARY={0}/libarpack.{1}'.format(
spec['arpack-ng'].prefix.lib, dso_suffix),
# BLAS support
'-DBLAS_LIBRARY={0}'.format(spec['blas'].blas_shared_lib),
# LAPACK support
'-DLAPACK_LIBRARY={0}'.format(spec['lapack'].lapack_shared_lib),
# SuperLU support
'-DSuperLU_INCLUDE_DIR={0}'.format(spec['superlu'].prefix.include),
'-DSuperLU_LIBRARY={0}/libsuperlu.a'.format(
spec['superlu'].prefix.lib64),
# HDF5 support
'-DDETECT_HDF5={0}'.format('ON' if '+hdf5' in spec else 'OFF')
]
cmake_args.extend(std_cmake_args)
cmake('.', *cmake_args)
make()
make('install')

24
var/spack/repos/builtin/packages/arpack-ng/make_install.patch Normal file
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@@ -0,0 +1,24 @@
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 607d221..50426c3 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -389,3 +389,19 @@ target_link_libraries(bug_1323 arpack ${BLAS_LIBRARIES} ${LAPACK_LIBRARIES})
add_test(bug_1323 Tests/bug_1323)
add_dependencies(check dnsimp_test bug_1315_single bug_1315_double bug_1323)
+
+############################
+# install
+############################
+# 'make install' to the correct location
+install(TARGETS arpack
+ ARCHIVE DESTINATION lib
+ LIBRARY DESTINATION lib
+ RUNTIME DESTINATION bin)
+
+if (MPI)
+ install(TARGETS parpack
+ ARCHIVE DESTINATION lib
+ LIBRARY DESTINATION lib
+ RUNTIME DESTINATION bin)
+endif ()

96
var/spack/repos/builtin/packages/arpack-ng/package.py
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@@ -27,7 +27,8 @@
class ArpackNg(Package):
"""
ARPACK-NG is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems.
ARPACK-NG is a collection of Fortran77 subroutines designed to solve large
scale eigenvalue problems.
Important Features:
@@ -38,43 +39,85 @@ class ArpackNg(Package):
Generalized Problems.
* Routines for Banded Matrices - Standard or Generalized Problems.
* Routines for The Singular Value Decomposition.
* Example driver routines that may be used as templates to implement numerous
Shift-Invert strategies for all problem types, data types and precision.
* Example driver routines that may be used as templates to implement
numerous Shift-Invert strategies for all problem types, data types and
precision.
This project is a joint project between Debian, Octave and Scilab in order to
provide a common and maintained version of arpack.
This project is a joint project between Debian, Octave and Scilab in order
to provide a common and maintained version of arpack.
Indeed, no single release has been published by Rice university for the last
few years and since many software (Octave, Scilab, R, Matlab...) forked it and
implemented their own modifications, arpack-ng aims to tackle this by providing
a common repository and maintained versions.
Indeed, no single release has been published by Rice university for the
last few years and since many software (Octave, Scilab, R, Matlab...)
forked it and implemented their own modifications, arpack-ng aims to tackle
this by providing a common repository and maintained versions.
arpack-ng is replacing arpack almost everywhere.
"""
homepage = 'https://github.com/opencollab/arpack-ng'
url = 'https://github.com/opencollab/arpack-ng/archive/3.3.0.tar.gz'
version('3.4.0', 'ae9ca13f2143a7ea280cb0e2fd4bfae4')
version('3.3.0', 'ed3648a23f0a868a43ef44c97a21bad5')
variant('shared', default=True, description='Enables the build of shared libraries')
variant('shared', default=True,
description='Enables the build of shared libraries')
variant('mpi', default=False, description='Activates MPI support')
# The function pdlamch10 does not set the return variable. This is fixed upstream
# The function pdlamch10 does not set the return variable.
# This is fixed upstream
# see https://github.com/opencollab/arpack-ng/issues/34
patch('pdlamch10.patch', when='@3.3:')
patch('pdlamch10.patch', when='@3.3.0')
patch('make_install.patch', when='@3.4.0')
patch('parpack_cmake.patch', when='@3.4.0')
depends_on('blas')
depends_on('lapack')
depends_on('automake')
depends_on('autoconf')
depends_on('libtool@2.4.2:')
depends_on('automake', when='@3.3.0', type='build')
depends_on('autoconf', when='@3.3.0', type='build')
depends_on('libtool@2.4.2:', when='@3.3.0', type='build')
depends_on('cmake@2.8.6:', when='@3.4.0:', type='build')
depends_on('mpi', when='+mpi')
@when('@3.4.0:')
def install(self, spec, prefix):
options = ['-DEXAMPLES=ON']
options.extend(std_cmake_args)
options.append('-DCMAKE_INSTALL_NAME_DIR:PATH=%s/lib' % prefix)
# Make sure we use Spack's blas/lapack:
options.extend([
'-DLAPACK_FOUND=true',
'-DLAPACK_INCLUDE_DIRS=%s' % spec['lapack'].prefix.include,
'-DLAPACK_LIBRARIES=%s' % (
spec['lapack'].lapack_shared_lib if '+shared' in spec else
spec['lapack'].lapack_static_lib),
'-DBLAS_FOUND=true',
'-DBLAS_INCLUDE_DIRS=%s' % spec['blas'].prefix.include,
'-DBLAS_LIBRARIES=%s' % (
spec['blas'].blas_shared_lib if '+shared' in spec else
spec['blas'].blas_static_lib)
])
if '+mpi' in spec:
options.append('-DMPI=ON')
# TODO: -DINTERFACE64=ON
if '+shared' in spec:
options.append('-DBUILD_SHARED_LIBS=ON')
cmake('.', *options)
make()
if self.run_tests:
make('test')
make('install')
@when('@3.3.0')
def install(self, spec, prefix):
# Apparently autotools are not bootstrapped
# TODO: switch to use the CMake build in the next version
# rather than bootstrapping.
which('libtoolize')()
bootstrap = Executable('./bootstrap')
@@ -83,13 +126,26 @@ def install(self, spec, prefix):
if '+mpi' in spec:
options.extend([
'--enable-mpi',
'F77=mpif77' #FIXME: avoid hardcoding MPI wrapper names
'F77=%s' % spec['mpi'].mpif77
])
if '~shared' in spec:
options.append('--enable-shared=no')
if '+shared' in spec:
options.extend([
'--with-blas=%s' % to_link_flags(
spec['blas'].blas_shared_lib),
'--with-lapack=%s' % to_link_flags(
spec['lapack'].lapack_shared_lib)
])
else:
options.extend([
'--with-blas=%s' % spec['blas'].blas_static_lib,
'--with-lapack=%s' % spec['lapack'].lapack_static_lib,
'--enable-shared=no'
])
bootstrap()
configure(*options)
make()
if self.run_tests:
make('check')
make('install')

18
var/spack/repos/builtin/packages/arpack-ng/parpack_cmake.patch Normal file
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@@ -0,0 +1,18 @@
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 607d221..345b7fc 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -113,11 +113,12 @@ set_target_properties(arpack PROPERTIES OUTPUT_NAME arpack${LIBSUFFIX})
if (MPI)
# add_library(parpack SHARED
- add_library(parpack
+ add_library(parpack
${parpacksrc_STAT_SRCS}
${parpackutil_STAT_SRCS})
target_link_libraries(parpack ${MPI_Fortran_LIBRARIES})
+ target_link_libraries(parpack arpack)
set_target_properties(parpack PROPERTIES OUTPUT_NAME parpack${LIBSUFFIX})
endif ()

40
var/spack/repos/builtin/packages/arpack/package.py
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@@ -24,12 +24,12 @@
##############################################################################
from spack import *
import os
import shutil
class Arpack(Package):
"""A collection of Fortran77 subroutines designed to solve large scale
eigenvalue problems.
"""
eigenvalue problems."""
homepage = "http://www.caam.rice.edu/software/ARPACK/"
url = "http://www.caam.rice.edu/software/ARPACK/SRC/arpack96.tar.gz"
@@ -39,27 +39,35 @@ class Arpack(Package):
depends_on('lapack')
def patch(self):
# Filter the cray makefile to make a spack one.
shutil.move('ARMAKES/ARmake.CRAY', 'ARmake.inc')
makefile = FileFilter('ARmake.inc')
# Be sure to use Spack F77 wrapper
makefile.filter('^FC.*', 'FC = f77')
makefile.filter('^FFLAGS.*', 'FFLAGS = -O2 -g')
# Section 1: Paths and Libraries
# Set up some variables.
makefile.filter('^PLAT.*', 'PLAT = ')
makefile.filter('^home.*', 'home = %s' % os.getcwd())
makefile.filter('^BLASdir.*', 'BLASdir = %s' % self.spec['blas'].prefix)
makefile.filter('^LAPACKdir.*', 'LAPACKdir = %s' % self.spec['lapack'].prefix)
# Change the build directory
makefile.filter('^home.*', 'home = %s' % os.getcwd())
# build the library in our own prefix.
makefile.filter('^ARPACKLIB.*', 'ARPACKLIB = %s/libarpack.a' % os.getcwd())
# Use external BLAS/LAPACK
makefile.filter('^BLASdir.*',
'BLASdir = %s' % self.spec['blas'].prefix)
makefile.filter('^LAPACKdir.*',
'LAPACKdir = %s' % self.spec['lapack'].prefix)
# Do not include the platform in the library name
makefile.filter('^PLAT.*', 'PLAT = ')
makefile.filter('^ARPACKLIB.*', 'ARPACKLIB = $(home)/libarpack.a')
# Section 2: Compilers
# Be sure to use the Spack compiler wrapper
makefile.filter('^FC.*', 'FC = {0}'.format(os.environ['F77']))
makefile.filter('^FFLAGS.*', 'FFLAGS = -O2 -g -fPIC')
if not which('ranlib'):
makefile.filter('^RANLIB.*', 'RANLIB = touch')
def install(self, spec, prefix):
with working_dir('SRC'):
make('all')
mkdirp(prefix.lib)
mkdir(prefix.lib)
install('libarpack.a', prefix.lib)

1
var/spack/repos/builtin/packages/asciidoc/package.py
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@@ -24,6 +24,7 @@
##############################################################################
from spack import *
class Asciidoc(Package):
""" A presentable text document format for writing articles, UNIX man
pages and other small to medium sized documents."""

10
var/spack/repos/builtin/packages/atk/package.py
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@@ -24,6 +24,7 @@
##############################################################################
from spack import *
class Atk(Package):
"""ATK provides the set of accessibility interfaces that are
implemented by other toolkits and applications. Using the ATK
@@ -32,9 +33,16 @@ class Atk(Package):
homepage = "https://developer.gnome.org/atk/"
url = "http://ftp.gnome.org/pub/gnome/sources/atk/2.14/atk-2.14.0.tar.xz"
version('2.20.0', '5187b0972f4d3905f285540b31395e20')
version('2.14.0', 'ecb7ca8469a5650581b1227d78051b8b')
depends_on("glib")
depends_on('glib')
depends_on('pkg-config', type='build')
def url_for_version(self, version):
"""Handle atk's version-based custom URLs."""
url = 'http://ftp.gnome.org/pub/gnome/sources/atk'
return 'url+/%s/atk-%s.tar.xz' % (version.up_to(2), version)
def install(self, spec, prefix):
configure("--prefix=%s" % prefix)

68
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@@ -23,20 +23,24 @@
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
from spack import *
from spack.package_test import *
from spack.util.executable import Executable
import os.path
class Atlas(Package):
"""
Automatically Tuned Linear Algebra Software, generic shared ATLAS is an approach for the automatic generation and
optimization of numerical software. Currently ATLAS supplies optimized versions for the complete set of linear
algebra kernels known as the Basic Linear Algebra Subroutines (BLAS), and a subset of the linear algebra routines
in the LAPACK library.
"""Automatically Tuned Linear Algebra Software, generic shared ATLAS is an
approach for the automatic generation and optimization of numerical
software. Currently ATLAS supplies optimized versions for the complete set
of linear algebra kernels known as the Basic Linear Algebra Subroutines
(BLAS), and a subset of the linear algebra routines in the LAPACK library.
"""
homepage = "http://math-atlas.sourceforge.net/"
version('3.10.2', 'a4e21f343dec8f22e7415e339f09f6da',
url='http://downloads.sourceforge.net/project/math-atlas/Stable/3.10.2/atlas3.10.2.tar.bz2', preferred=True)
url='https://sourceforge.net/projects/math-atlas/files/Stable/3.10.2/atlas3.10.2.tar.bz2', preferred=True)
# not all packages (e.g. Trilinos@12.6.3) stopped using deprecated in 3.6.0
# Lapack routines. Stick with 3.5.0 until this is fixed.
resource(name='lapack',
url='http://www.netlib.org/lapack/lapack-3.5.0.tgz',
md5='b1d3e3e425b2e44a06760ff173104bdf',
@@ -44,7 +48,7 @@ class Atlas(Package):
when='@3:')
version('3.11.34', '0b6c5389c095c4c8785fd0f724ec6825',
url='http://sourceforge.net/projects/math-atlas/files/Developer%20%28unstable%29/3.11.34/atlas3.11.34.tar.bz2/download')
url='http://sourceforge.net/projects/math-atlas/files/Developer%20%28unstable%29/3.11.34/atlas3.11.34.tar.bz2')
variant('shared', default=True, description='Builds shared library')
@@ -66,9 +70,24 @@ def install(self, spec, prefix):
options = []
if '+shared' in spec:
options.append('--shared')
options.extend([
'--shared'
])
# TODO: for non GNU add '-Fa', 'alg', '-fPIC' ?
# Lapack resource
# configure for 64-bit build
options.extend([
'-b', '64'
])
# set compilers:
options.extend([
'-C', 'ic', spack_cc,
'-C', 'if', spack_f77
])
# Lapack resource to provide full lapack build. Note that
# ATLAS only provides a few LAPACK routines natively.
lapack_stage = self.stage[1]
lapack_tarfile = os.path.basename(lapack_stage.fetcher.url)
lapack_tarfile_path = join_path(lapack_stage.path, lapack_tarfile)
@@ -81,4 +100,35 @@ def install(self, spec, prefix):
make('check')
make('ptcheck')
make('time')
if '+shared' in spec:
with working_dir('lib'):
make('shared_all')
make("install")
self.install_test()
def setup_dependent_package(self, module, dspec):
# libsatlas.[so,dylib,dll ] contains all serial APIs (serial lapack,
# serial BLAS), and all ATLAS symbols needed to support them. Whereas
# libtatlas.[so,dylib,dll ] is parallel (multithreaded) version.
name = 'libsatlas.%s' % dso_suffix
libdir = find_library_path(name,
self.prefix.lib64,
self.prefix.lib)
if '+shared' in self.spec:
self.spec.blas_shared_lib = join_path(libdir, name)
self.spec.lapack_shared_lib = self.spec.blas_shared_lib
def install_test(self):
source_file = join_path(os.path.dirname(self.module.__file__),
'test_cblas_dgemm.c')
blessed_file = join_path(os.path.dirname(self.module.__file__),
'test_cblas_dgemm.output')
include_flags = ["-I%s" % join_path(self.spec.prefix, "include")]
link_flags = ["-L%s" % join_path(self.spec.prefix, "lib"),
"-lsatlas"]
output = compile_c_and_execute(source_file, include_flags, link_flags)
compare_output_file(output, blessed_file)

49
var/spack/repos/builtin/packages/atlas/test_cblas_dgemm.c Normal file
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@@ -0,0 +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;
// 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\n", x[i]);
return 0;
}

12
var/spack/repos/builtin/packages/atlas/test_cblas_dgemm.output Normal file
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@@ -0,0 +1,12 @@
11.000000
-9.000000
5.000000
-9.000000
21.000000
-1.000000
5.000000
-1.000000
3.000000
-0.3
3.0
-3.0

3
var/spack/repos/builtin/packages/atop/package.py
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@@ -24,6 +24,7 @@
##############################################################################
from spack import *
class Atop(Package):
"""Atop is an ASCII full-screen performance monitor for Linux"""
homepage = "http://www.atoptool.nl/index.php"
@@ -37,4 +38,4 @@ def install(self, spec, prefix):
install("atop", join_path(prefix.bin, "atop"))
mkdirp(join_path(prefix.man, "man1"))
install(join_path("man", "atop.1"),
join_path(prefix.man, "man1", "atop.1"))
join_path(prefix.man, "man1", "atop.1"))

28
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@@ -24,18 +24,36 @@
##############################################################################
from spack import *
class Autoconf(Package):
"""Autoconf -- system configuration part of autotools"""
homepage = "https://www.gnu.org/software/autoconf/"
url = "http://ftp.gnu.org/gnu/autoconf/autoconf-2.69.tar.gz"
"""
Autoconf -- system configuration part of autotools
"""
homepage = 'https://www.gnu.org/software/autoconf/'
url = 'http://ftp.gnu.org/gnu/autoconf/autoconf-2.69.tar.gz'
version('2.69', '82d05e03b93e45f5a39b828dc9c6c29b')
version('2.62', '6c1f3b3734999035d77da5024aab4fbd')
depends_on("m4")
depends_on('m4', type='build')
def _make_executable(self, name):
return Executable(join_path(self.prefix.bin, name))
def setup_dependent_package(self, module, dependent_spec):
# Autoconf is very likely to be a build dependency,
# so we add the tools it provides to the dependent module
executables = ['autoconf',
'autoheader',
'autom4te',
'autoreconf',
'autoscan',
'autoupdate',
'ifnames']
for name in executables:
setattr(module, name, self._make_executable(name))
def install(self, spec, prefix):
configure("--prefix=%s" % prefix)
make()
make("install")

2
var/spack/repos/builtin/packages/automaded/package.py
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@@ -24,6 +24,7 @@
##############################################################################
from spack import *
class Automaded(Package):
"""AutomaDeD (Automata-based Debugging for Dissimilar parallel
tasks) is a tool for automatic diagnosis of performance and
@@ -44,6 +45,7 @@ class Automaded(Package):
depends_on('mpi')
depends_on('boost')
depends_on('callpath')
depends_on('cmake', type='build')
def install(self, spec, prefix):
cmake("-DSTATE_TRACKER_WITH_CALLPATH=ON", *std_cmake_args)

20
var/spack/repos/builtin/packages/automake/package.py
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@@ -24,10 +24,13 @@
##############################################################################
from spack import *
class Automake(Package):
"""Automake -- make file builder part of autotools"""
homepage = "http://www.gnu.org/software/automake/"
url = "http://ftp.gnu.org/gnu/automake/automake-1.14.tar.gz"
"""
Automake -- make file builder part of autotools
"""
homepage = 'http://www.gnu.org/software/automake/'
url = 'http://ftp.gnu.org/gnu/automake/automake-1.14.tar.gz'
version('1.15', '716946a105ca228ab545fc37a70df3a3')
version('1.14.1', 'd052a3e884631b9c7892f2efce542d75')
@@ -35,8 +38,17 @@ class Automake(Package):
depends_on('autoconf')
def _make_executable(self, name):
return Executable(join_path(self.prefix.bin, name))
def setup_dependent_package(self, module, dependent_spec):
# Automake is very likely to be a build dependency,
# so we add the tools it provides to the dependent module
executables = ['aclocal', 'automake']
for name in executables:
setattr(module, name, self._make_executable(name))
def install(self, spec, prefix):
configure("--prefix=%s" % prefix)
make()
make("install")

1
var/spack/repos/builtin/packages/bash/package.py
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@@ -24,6 +24,7 @@
##############################################################################
from spack import *
class Bash(Package):
"""The GNU Project's Bourne Again SHell."""

10
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@@ -24,18 +24,22 @@
##############################################################################
from spack import *
class Bbcp(Package):
"""Securely and quickly copy data from source to target"""
homepage = "http://www.slac.stanford.edu/~abh/bbcp/"
version('git', git='http://www.slac.stanford.edu/~abh/bbcp/bbcp.git', branch="master")
version('git', git='http://www.slac.stanford.edu/~abh/bbcp/bbcp.git',
branch="master")
def install(self, spec, prefix):
cd("src")
make()
# BBCP wants to build the executable in a directory whose name depends on the system type
# BBCP wants to build the executable in a directory whose name depends
# on the system type
makesname = Executable("../MakeSname")
bbcp_executable_path = "../bin/%s/bbcp" % makesname(output=str).rstrip("\n")
bbcp_executable_path = "../bin/%s/bbcp" % makesname(
output=str).rstrip("\n")
destination_path = "%s/bin/" % prefix
mkdirp(destination_path)
install(bbcp_executable_path, destination_path)

43
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@@ -0,0 +1,43 @@
##############################################################################
# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-647188
#
# For details, see https://github.com/llnl/spack
# Please also see the LICENSE file for our notice and the LGPL.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License (as
# published by the Free Software Foundation) version 2.1, February 1999.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
# conditions of the GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
from spack import *
class Bcftools(Package):
"""BCFtools is a set of utilities that manipulate variant calls in the
Variant Call Format (VCF) and its binary counterpart BCF. All
commands work transparently with both VCFs and BCFs, both
uncompressed and BGZF-compressed."""
homepage = "http://samtools.github.io/bcftools/"
url = "https://github.com/samtools/bcftools/releases/download/1.3.1/bcftools-1.3.1.tar.bz2"
version('1.3.1', '575001e9fca37cab0c7a7287ad4b1cdb')
depends_on('zlib')
def install(self, spec, prefix):
make("prefix=%s" % prefix, "all")
make("prefix=%s" % prefix, "install")

53
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@@ -0,0 +1,53 @@
##############################################################################
# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-647188
#
# For details, see https://github.com/llnl/spack
# Please also see the LICENSE file for our notice and the LGPL.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License (as
# published by the Free Software Foundation) version 2.1, February 1999.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
# conditions of the GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
from spack import *
class BdwGc(Package):
"""The Boehm-Demers-Weiser conservative garbage collector is a garbage
collecting replacement for C malloc or C++ new."""
homepage = "http://www.hboehm.info/gc/"
url = "http://www.hboehm.info/gc/gc_source/gc-7.4.4.tar.gz"
version('7.4.4', '96d18b0448a841c88d56e4ab3d180297')
variant('libatomic-ops', default=True,
description='Use external libatomic-ops')
depends_on('libatomic-ops', when='+libatomic-ops')
def install(self, spec, prefix):
config_args = [
'--prefix={0}'.format(prefix),
'--with-libatomic-ops={0}'.format(
'yes' if '+libatomic-ops' in spec else 'no')
]
configure(*config_args)
make()
make('check')
make('install')

6
var/spack/repos/builtin/packages/bear/package.py
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@@ -24,14 +24,16 @@
##############################################################################
from spack import *
class Bear(Package):
"""Bear is a tool that generates a compilation database for clang tooling from non-cmake build systems."""
"""Bear is a tool that generates a compilation database for clang tooling
from non-cmake build systems."""
homepage = "https://github.com/rizsotto/Bear"
url = "https://github.com/rizsotto/Bear/archive/2.0.4.tar.gz"
version('2.0.4', 'fd8afb5e8e18f8737ba06f90bd77d011')
depends_on("cmake")
depends_on('cmake', type='build')
depends_on("python")
def install(self, spec, prefix):

50
var/spack/repos/builtin/packages/bertini/package.py Normal file
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@@ -0,0 +1,50 @@
##############################################################################
# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-647188
#
# For details, see https://github.com/llnl/spack
# Please also see the LICENSE file for our notice and the LGPL.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License (as
# published by the Free Software Foundation) version 2.1, February 1999.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
# conditions of the GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
from spack import *
class Bertini(Package):
"""Bertini is a general-purpose solver, written in C, that was created
for research about polynomial continuation. It solves for the numerical
solution of systems of polynomial equations using homotopy continuation."""
homepage = "https://bertini.nd.edu/"
url = "https://bertini.nd.edu/BertiniSource_v1.5.tar.gz"
version('1.5', 'e3f6cc6e7f9a0cf1d73185e8671af707')
variant('mpi', default=True, description='Compile in parallel')
depends_on('flex', type='build')
depends_on('bison', type='build')
depends_on('gmp')
depends_on('mpfr')
depends_on('mpi', when='+mpi')
def install(self, spec, prefix):
configure('--prefix=%s' % prefix)
make()
make("install")

3
var/spack/repos/builtin/packages/bib2xhtml/package.py
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@@ -25,10 +25,11 @@
from spack import *
from glob import glob
class Bib2xhtml(Package):
"""bib2xhtml is a program that converts BibTeX files into HTML."""
homepage = "http://www.spinellis.gr/sw/textproc/bib2xhtml/"
url='http://www.spinellis.gr/sw/textproc/bib2xhtml/bib2xhtml-v3.0-15-gf506.tar.gz'
url = 'http://www.spinellis.gr/sw/textproc/bib2xhtml/bib2xhtml-v3.0-15-gf506.tar.gz'
version('3.0-15-gf506', 'a26ba02fe0053bbbf2277bdf0acf8645')

21
var/spack/repos/builtin/packages/binutils/package.py
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@@ -24,28 +24,33 @@
##############################################################################
from spack import *
class Binutils(Package):
"""GNU binutils, which contain the linker, assembler, objdump and others"""
homepage = "http://www.gnu.org/software/binutils/"
url = "https://ftp.gnu.org/gnu/binutils/binutils-2.25.tar.bz2"
url="https://ftp.gnu.org/gnu/binutils/binutils-2.25.tar.bz2"
# 2.26 is incompatible with py-pillow build for some reason.
version('2.26', '64146a0faa3b411ba774f47d41de239f')
version('2.25', 'd9f3303f802a5b6b0bb73a335ab89d66')
version('2.25', 'd9f3303f802a5b6b0bb73a335ab89d66', preferred=True)
version('2.24', 'e0f71a7b2ddab0f8612336ac81d9636b')
version('2.23.2', '4f8fa651e35ef262edc01d60fb45702e')
version('2.20.1', '2b9dc8f2b7dbd5ec5992c6e29de0b764')
depends_on('m4')
depends_on('flex')
depends_on('bison')
depends_on('m4', type='build')
depends_on('flex', type='build')
depends_on('bison', type='build')
# Add a patch that creates binutils libiberty_pic.a which is preferred by OpenSpeedShop and cbtf-krell
variant('krellpatch', default=False, description="build with openspeedshop based patch.")
# Add a patch that creates binutils libiberty_pic.a which is preferred by
# OpenSpeedShop and cbtf-krell
variant('krellpatch', default=False,
description="build with openspeedshop based patch.")
variant('gold', default=True, description="build the gold linker")
patch('binutilskrell-2.24.patch', when='@2.24+krellpatch')
patch('cr16.patch')
patch('update_symbol-2.26.patch', when='@2.26')
variant('libiberty', default=False, description='Also install libiberty.')

104
var/spack/repos/builtin/packages/binutils/update_symbol-2.26.patch Normal file
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@@ -0,0 +1,104 @@
From 544ddf9322b1b83982e5cb84a54d084ee7e718ea Mon Sep 17 00:00:00 2001
From: H.J. Lu <hjl.tools@gmail.com>
Date: Wed, 24 Feb 2016 15:13:35 -0800
Subject: [PATCH] Update symbol version for symbol from linker script
We need to update symbol version for symbols from linker script.
Backport from master
bfd/
PR ld/19698
* elflink.c (bfd_elf_record_link_assignment): Set versioned if
symbol version is unknown.
ld/
PR ld/19698
* testsuite/ld-elf/pr19698.d: New file.
* testsuite/ld-elf/pr19698.s: Likewise.
* testsuite/ld-elf/pr19698.t: Likewise.
---
bfd/ChangeLog | 9 +++++++++
bfd/elflink.c | 13 +++++++++++++
ld/ChangeLog | 10 ++++++++++
ld/testsuite/ld-elf/pr19698.d | 10 ++++++++++
ld/testsuite/ld-elf/pr19698.s | 5 +++++
ld/testsuite/ld-elf/pr19698.t | 11 +++++++++++
6 files changed, 58 insertions(+), 0 deletions(-)
create mode 100644 ld/testsuite/ld-elf/pr19698.d
create mode 100644 ld/testsuite/ld-elf/pr19698.s
create mode 100644 ld/testsuite/ld-elf/pr19698.t
diff --git a/bfd/elflink.c b/bfd/elflink.c
index ae8d148..8fcaadd 100644
--- a/bfd/elflink.c
+++ b/bfd/elflink.c
@@ -555,6 +555,19 @@ bfd_elf_record_link_assignment (bfd *output_bfd,
if (h == NULL)
return provide;
+ if (h->versioned == unknown)
+ {
+ /* Set versioned if symbol version is unknown. */
+ char *version = strrchr (name, ELF_VER_CHR);
+ if (version)
+ {
+ if (version > name && version[-1] != ELF_VER_CHR)
+ h->versioned = versioned_hidden;
+ else
+ h->versioned = versioned;
+ }
+ }
+
switch (h->root.type)
{
case bfd_link_hash_defined:
diff --git a/ld/testsuite/ld-elf/pr19698.d b/ld/testsuite/ld-elf/pr19698.d
new file mode 100644
index 0000000..a39f67a
--- /dev/null
+++ b/ld/testsuite/ld-elf/pr19698.d
@@ -0,0 +1,10 @@
+#ld: -shared $srcdir/$subdir/pr19698.t
+#readelf : --dyn-syms --wide
+#target: *-*-linux* *-*-gnu* *-*-solaris*
+
+Symbol table '\.dynsym' contains [0-9]+ entries:
+#...
+ +[0-9]+: +[0-9a-f]+ +[0-9a-f]+ +FUNC +GLOBAL +DEFAULT +[0-9]+ +foo@VERS.1
+#...
+ +[0-9]+: +[0-9a-f]+ +[0-9a-f]+ +FUNC +GLOBAL +DEFAULT +[0-9]+ +foo@@VERS.2
+#pass
diff --git a/ld/testsuite/ld-elf/pr19698.s b/ld/testsuite/ld-elf/pr19698.s
new file mode 100644
index 0000000..875dca4
--- /dev/null
+++ b/ld/testsuite/ld-elf/pr19698.s
@@ -0,0 +1,5 @@
+ .text
+ .globl foo
+ .type foo, %function
+foo:
+ .byte 0
diff --git a/ld/testsuite/ld-elf/pr19698.t b/ld/testsuite/ld-elf/pr19698.t
new file mode 100644
index 0000000..09d9125
--- /dev/null
+++ b/ld/testsuite/ld-elf/pr19698.t
@@ -0,0 +1,11 @@
+"foo@VERS.1" = foo;
+
+VERSION {
+VERS.2 {
+ global:
+ foo;
+};
+
+VERS.1 {
+};
+}
--
1.7.1

7
var/spack/repos/builtin/packages/bison/package.py
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@@ -24,9 +24,10 @@
##############################################################################
from spack import *
class Bison(Package):
"""Bison is a general-purpose parser generator that converts
an annotated context-free grammar into a deterministic LR or
"""Bison is a general-purpose parser generator that converts
an annotated context-free grammar into a deterministic LR or
generalized LR (GLR) parser employing LALR(1) parser tables."""
homepage = "http://www.gnu.org/software/bison/"
@@ -34,7 +35,7 @@ class Bison(Package):
version('3.0.4', 'a586e11cd4aff49c3ff6d3b6a4c9ccf8')
depends_on("m4")
depends_on("m4", type='build')
def install(self, spec, prefix):
configure("--prefix=%s" % prefix)

1
var/spack/repos/builtin/packages/blitz/package.py
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@@ -24,6 +24,7 @@
##############################################################################
from spack import *
class Blitz(Package):
"""N-dimensional arrays for C++"""
homepage = "http://github.com/blitzpp/blitz"

97
var/spack/repos/builtin/packages/boost/package.py
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@@ -25,9 +25,8 @@
from spack import *
import spack
import sys
import os
import sys
class Boost(Package):
"""Boost provides free peer-reviewed portable C++ source
@@ -75,23 +74,24 @@ class Boost(Package):
version('1.34.0', 'ed5b9291ffad776f8757a916e1726ad0')
default_install_libs = set(['atomic',
'chrono',
'date_time',
'filesystem',
'graph',
'iostreams',
'locale',
'log',
'math',
'program_options',
'random',
'regex',
'serialization',
'signals',
'system',
'test',
'thread',
'wave'])
'chrono',
'date_time',
'filesystem',
'graph',
'iostreams',
'locale',
'log',
'math',
'program_options',
'random',
'regex',
'serialization',
'signals',
'system',
'test',
'thread',
'timer',
'wave'])
# mpi/python are not installed by default because they pull in many
# dependencies and/or because there is a great deal of customization
@@ -102,13 +102,19 @@ class Boost(Package):
for lib in all_libs:
variant(lib, default=(lib not in default_noinstall_libs),
description="Compile with {0} library".format(lib))
description="Compile with {0} library".format(lib))
variant('debug', default=False, description='Switch to the debug version of Boost')
variant('shared', default=True, description="Additionally build shared libraries")
variant('multithreaded', default=True, description="Build multi-threaded versions of libraries")
variant('singlethreaded', default=True, description="Build single-threaded versions of libraries")
variant('icu_support', default=False, description="Include ICU support (for regex/locale libraries)")
variant('debug', default=False,
description='Switch to the debug version of Boost')
variant('shared', default=True,
description="Additionally build shared libraries")
variant('multithreaded', default=True,
description="Build multi-threaded versions of libraries")
variant('singlethreaded', default=True,
description="Build single-threaded versions of libraries")
variant('icu_support', default=False,
description="Include ICU support (for regex/locale libraries)")
variant('graph', default=False, description="Build the Boost Graph library")
depends_on('icu', when='+icu_support')
depends_on('python', when='+python')
@@ -120,15 +126,17 @@ class Boost(Package):
patch('boost_11856.patch', when='@1.60.0%gcc@4.4.7')
def url_for_version(self, version):
"""Handle Boost's weird URLs, which write the version two different ways."""
"""
Handle Boost's weird URLs,
which write the version two different ways.
"""
parts = [str(p) for p in Version(version)]
dots = ".".join(parts)
underscores = "_".join(parts)
return "http://downloads.sourceforge.net/project/boost/boost/%s/boost_%s.tar.bz2" % (
dots, underscores)
return "http://downloads.sourceforge.net/project/boost/boost/%s/boost_%s.tar.bz2" % (dots, underscores)
def determine_toolset(self, spec):
if spec.satisfies("arch=darwin-x86_64"):
if spec.satisfies("platform=darwin"):
return 'darwin'
toolsets = {'g++': 'gcc',
@@ -149,20 +157,20 @@ def determine_bootstrap_options(self, spec, withLibs, options):
if '+python' in spec:
options.append('--with-python=%s' %
join_path(spec['python'].prefix.bin, 'python'))
join_path(spec['python'].prefix.bin, 'python'))
with open('user-config.jam', 'w') as f:
compiler_wrapper = join_path(spack.build_env_path, 'c++')
f.write("using {0} : : {1} ;\n".format(boostToolsetId,
compiler_wrapper))
compiler_wrapper))
if '+mpi' in spec:
f.write('using mpi : %s ;\n' %
join_path(spec['mpi'].prefix.bin, 'mpicxx'))
join_path(spec['mpi'].prefix.bin, 'mpicxx'))
if '+python' in spec:
f.write('using python : %s : %s ;\n' %
(spec['python'].version,
join_path(spec['python'].prefix.bin, 'python')))
(spec['python'].version,
join_path(spec['python'].prefix.bin, 'python')))
def determine_b2_options(self, spec, options):
if '+debug' in spec:
@@ -178,8 +186,7 @@ def determine_b2_options(self, spec, options):
'-s', 'BZIP2_INCLUDE=%s' % spec['bzip2'].prefix.include,
'-s', 'BZIP2_LIBPATH=%s' % spec['bzip2'].prefix.lib,
'-s', 'ZLIB_INCLUDE=%s' % spec['zlib'].prefix.include,
'-s', 'ZLIB_LIBPATH=%s' % spec['zlib'].prefix.lib,
])
'-s', 'ZLIB_LIBPATH=%s' % spec['zlib'].prefix.lib])
linkTypes = ['static']
if '+shared' in spec:
@@ -191,7 +198,8 @@ def determine_b2_options(self, spec, options):
if '+singlethreaded' in spec:
threadingOpts.append('single')
if not threadingOpts:
raise RuntimeError("At least one of {singlethreaded, multithreaded} must be enabled")
raise RuntimeError("""At least one of {singlethreaded,
multithreaded} must be enabled""")
options.extend([
'toolset=%s' % self.determine_toolset(spec),
@@ -202,9 +210,9 @@ def determine_b2_options(self, spec, options):
def install(self, spec, prefix):
# On Darwin, Boost expects the Darwin libtool. However, one of the
# dependencies may have pulled in Spack's GNU libtool, and these two are
# not compatible. We thus create a symlink to Darwin's libtool and add
# it at the beginning of PATH.
# dependencies may have pulled in Spack's GNU libtool, and these two
# are not compatible. We thus create a symlink to Darwin's libtool
# and add it at the beginning of PATH.
if sys.platform == 'darwin':
newdir = os.path.abspath('darwin-libtool')
mkdirp(newdir)
@@ -217,7 +225,8 @@ def install(self, spec, prefix):
withLibs.append(lib)
if not withLibs:
# if no libraries are specified for compilation, then you dont have
# to configure/build anything, just copy over to the prefix directory.
# to configure/build anything, just copy over to the prefix
# directory.
src = join_path(self.stage.source_path, 'boost')
mkdirp(join_path(prefix, 'include'))
dst = join_path(prefix, 'include', 'boost')
@@ -235,6 +244,9 @@ def install(self, spec, prefix):
withLibs.remove('chrono')
if not spec.satisfies('@1.43.0:'):
withLibs.remove('random')
if '+graph' in spec and '+mpi' in spec:
withLibs.remove('graph')
withLibs.append('graph_parallel')
# to make Boost find the user-config.jam
env['BOOST_BUILD_PATH'] = './'
@@ -259,6 +271,7 @@ def install(self, spec, prefix):
for threadingOpt in threadingOpts:
b2('install', 'threading=%s' % threadingOpt, *b2_options)
# The shared libraries are not installed correctly on Darwin; correct this
# The shared libraries are not installed correctly
# on Darwin; correct this
if (sys.platform == 'darwin') and ('+shared' in spec):
fix_darwin_install_name(prefix.lib)

8
var/spack/repos/builtin/packages/bowtie2/package.py
View File

@@ -24,12 +24,15 @@
##############################################################################
from spack import *
from glob import glob
class Bowtie2(Package):
"""Description"""
homepage = "bowtie-bio.sourceforge.net/bowtie2/index.shtml"
version('2.2.5','51fa97a862d248d7ee660efc1147c75f', url = "http://downloads.sourceforge.net/project/bowtie-bio/bowtie2/2.2.5/bowtie2-2.2.5-source.zip")
version('2.2.5', '51fa97a862d248d7ee660efc1147c75f',
url="http://downloads.sourceforge.net/project/bowtie-bio/bowtie2/2.2.5/bowtie2-2.2.5-source.zip")
patch('bowtie2-2.5.patch',when='@2.2.5', level=0)
patch('bowtie2-2.5.patch', when='@2.2.5', level=0)
def install(self, spec, prefix):
make()
@@ -45,4 +48,3 @@ def install(self, spec, prefix):
# install('bowtie2-inspect',prefix.bin)
# install('bowtie2-inspect-l',prefix.bin)
# install('bowtie2-inspect-s',prefix.bin)

5
var/spack/repos/builtin/packages/boxlib/package.py
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@@ -24,17 +24,19 @@
##############################################################################
from spack import *
class Boxlib(Package):
"""BoxLib, a software framework for massively parallel
block-structured adaptive mesh refinement (AMR) codes."""
homepage = "https://ccse.lbl.gov/BoxLib/"
url = "https://ccse.lbl.gov/pub/Downloads/BoxLib.git";
url = "https://ccse.lbl.gov/pub/Downloads/BoxLib.git"
# TODO: figure out how best to version this. No tags in the repo!
version('master', git='https://ccse.lbl.gov/pub/Downloads/BoxLib.git')
depends_on('mpi')
depends_on('cmake', type='build')
def install(self, spec, prefix):
args = std_cmake_args
@@ -46,4 +48,3 @@ def install(self, spec, prefix):
cmake('.', *args)
make()
make("install")

41
var/spack/repos/builtin/packages/bpp-core/package.py Normal file
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@@ -0,0 +1,41 @@
##############################################################################
# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-647188
#
# For details, see https://github.com/llnl/spack
# Please also see the LICENSE file for our notice and the LGPL.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License (as
# published by the Free Software Foundation) version 2.1, February 1999.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
# conditions of the GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
from spack import *
class BppCore(Package):
"""Bio++ core library."""
homepage = "http://biopp.univ-montp2.fr/wiki/index.php/Installation"
url = "http://biopp.univ-montp2.fr/repos/sources/bpp-core-2.2.0.tar.gz"
version('2.2.0', '5789ed2ae8687d13664140cd77203477')
depends_on('cmake', type='build')
def install(self, spec, prefix):
cmake('-DBUILD_TESTING=FALSE', '.', *std_cmake_args)
make()
make('install')

43
var/spack/repos/builtin/packages/bpp-phyl/package.py Normal file
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@@ -0,0 +1,43 @@
##############################################################################
# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-647188
#
# For details, see https://github.com/llnl/spack
# Please also see the LICENSE file for our notice and the LGPL.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License (as
# published by the Free Software Foundation) version 2.1, February 1999.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
# conditions of the GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
from spack import *
class BppPhyl(Package):
"""Bio++ phylogeny library."""
homepage = "http://biopp.univ-montp2.fr/wiki/index.php/Installation"
url = "http://biopp.univ-montp2.fr/repos/sources/bpp-phyl-2.2.0.tar.gz"
version('2.2.0', '5c40667ec0bf37e0ecaba321be932770')
depends_on('cmake', type='build')
depends_on('bpp-core')
depends_on('bpp-seq')
def install(self, spec, prefix):
cmake('-DBUILD_TESTING=FALSE', '.', *std_cmake_args)
make()
make('install')

42
var/spack/repos/builtin/packages/bpp-seq/package.py Normal file
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@@ -0,0 +1,42 @@
##############################################################################
# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-647188
#
# For details, see https://github.com/llnl/spack
# Please also see the LICENSE file for our notice and the LGPL.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License (as
# published by the Free Software Foundation) version 2.1, February 1999.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
# conditions of the GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
from spack import *
class BppSeq(Package):
"""Bio++ seq library."""
homepage = "http://biopp.univ-montp2.fr/wiki/index.php/Installation"
url = "http://biopp.univ-montp2.fr/repos/sources/bpp-seq-2.2.0.tar.gz"
version('2.2.0', '44adef0ff4d5ca4e69ccf258c9270633')
depends_on('cmake', type='build')
depends_on('bpp-core')
def install(self, spec, prefix):
cmake('-DBUILD_TESTING=FALSE', '.', *std_cmake_args)
make()
make('install')

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##############################################################################
# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-647188
#
# For details, see https://github.com/llnl/spack
# Please also see the LICENSE file for our notice and the LGPL.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License (as
# published by the Free Software Foundation) version 2.1, February 1999.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
# conditions of the GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
from spack import *
class BppSuite(Package):
"""BppSuite is a suite of ready-to-use programs for phylogenetic and
sequence analysis."""
homepage = "http://biopp.univ-montp2.fr/wiki/index.php/BppSuite"
url = "http://biopp.univ-montp2.fr/repos/sources/bppsuite/bppsuite-2.2.0.tar.gz"
version('2.2.0', 'd8b29ad7ccf5bd3a7beb701350c9e2a4')
# FIXME: Add dependencies if required.
depends_on('cmake', type='build')
depends_on('texinfo', type='build')
depends_on('bpp-core')
depends_on('bpp-seq')
depends_on('bpp-phyl')
def install(self, spec, prefix):
cmake('.', *std_cmake_args)
make()
make('install')

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##############################################################################
# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-647188
#
# For details, see https://github.com/llnl/spack
# Please also see the LICENSE file for our notice and the LGPL.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License (as
# published by the Free Software Foundation) version 2.1, February 1999.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
# conditions of the GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
from spack import *
class Bwa(Package):
"""Burrow-Wheeler Aligner for pairwise alignment between DNA sequences."""
homepage = "http://github.com/lh3/bwa"
url = "https://github.com/lh3/bwa/releases/download/v0.7.15/bwa-0.7.15.tar.bz2"
version('0.7.15', 'fcf470a46a1dbe2f96a1c5b87c530554')
depends_on('zlib')
def install(self, spec, prefix):
filter_file(r'^INCLUDES=',
"INCLUDES=-I%s" % spec['zlib'].prefix.include, 'Makefile')
filter_file(r'^LIBS=', "LIBS=-L%s " % spec['zlib'].prefix.lib,
'Makefile')
make()
mkdirp(prefix.bin)
install('bwa', join_path(prefix.bin, 'bwa'))
set_executable(join_path(prefix.bin, 'bwa'))
mkdirp(prefix.doc)
install('README.md', prefix.doc)
install('NEWS.md', prefix.doc)
mkdirp(prefix.man1)
install('bwa.1', prefix.man1)

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##############################################################################
from spack import *
class Bzip2(Package):
"""bzip2 is a freely available, patent free high-quality data
compressor. It typically compresses files to within 10% to 15%
of the best available techniques (the PPM family of statistical
compressors), whilst being around twice as fast at compression
and six times faster at decompression.
compressor. It typically compresses files to within 10% to 15%
of the best available techniques (the PPM family of statistical
compressors), whilst being around twice as fast at compression
and six times faster at decompression."""
"""
homepage = "http://www.bzip.org"
url = "http://www.bzip.org/1.0.6/bzip2-1.0.6.tar.gz"
version('1.0.6', '00b516f4704d4a7cb50a1d97e6e8e15b')
def patch(self):
mf = FileFilter('Makefile-libbz2_so')
mf.filter(r'^CC=gcc', 'CC=cc')
# bzip2 comes with two separate Makefiles for static and dynamic builds
# Tell both to use Spack's compiler wrapper instead of GCC
filter_file(r'^CC=gcc', 'CC=cc', 'Makefile')
filter_file(r'^CC=gcc', 'CC=cc', 'Makefile-libbz2_so')
# Below stuff patches the link line to use RPATHs on Mac OS X.
# Patch the link line to use RPATHs on macOS
if 'darwin' in self.spec.architecture:
v = self.spec.version
v1, v2, v3 = (v.up_to(i) for i in (1,2,3))
v1, v2, v3 = (v.up_to(i) for i in (1, 2, 3))
mf.filter('$(CC) -shared -Wl,-soname -Wl,libbz2.so.{0} -o libbz2.so.{1} $(OBJS)'.format(v2, v3),
'$(CC) -dynamiclib -Wl,-install_name -Wl,@rpath/libbz2.{0}.dylib -current_version {1} -compatibility_version {2} -o libbz2.{3}.dylib $(OBJS)'.format(v1, v2, v3, v3), string=True)
kwargs = {'ignore_absent': False, 'backup': False, 'string': True}
mf.filter('$(CC) $(CFLAGS) -o bzip2-shared bzip2.c libbz2.so.{0}'.format(v3),
'$(CC) $(CFLAGS) -o bzip2-shared bzip2.c libbz2.{0}.dylib'.format(v3), string=True)
mf.filter('rm -f libbz2.so.{0}'.format(v2),
'rm -f libbz2.{0}.dylib'.format(v2), string=True)
mf.filter('ln -s libbz2.so.{0} libbz2.so.{1}'.format(v3, v2),
'ln -s libbz2.{0}.dylib libbz2.{1}.dylib'.format(v3, v2), string=True)
mf = FileFilter('Makefile-libbz2_so')
mf.filter('$(CC) -shared -Wl,-soname -Wl,libbz2.so.{0} -o libbz2.so.{1} $(OBJS)' # noqa
.format(v2, v3),
'$(CC) -dynamiclib -Wl,-install_name -Wl,@rpath/libbz2.{0}.dylib -current_version {1} -compatibility_version {2} -o libbz2.{3}.dylib $(OBJS)' # noqa
.format(v1, v2, v3, v3),
**kwargs)
mf.filter(
'$(CC) $(CFLAGS) -o bzip2-shared bzip2.c libbz2.so.{0}'.format(v3), # noqa
'$(CC) $(CFLAGS) -o bzip2-shared bzip2.c libbz2.{0}.dylib'
.format(v3), **kwargs)
mf.filter(
'rm -f libbz2.so.{0}'.format(v2),
'rm -f libbz2.{0}.dylib'.format(v2), **kwargs)
mf.filter(
'ln -s libbz2.so.{0} libbz2.so.{1}'.format(v3, v2),
'ln -s libbz2.{0}.dylib libbz2.{1}.dylib'.format(v3, v2),
**kwargs)
def install(self, spec, prefix):
# Build the dynamic library first
make('-f', 'Makefile-libbz2_so')
make('clean')
make("install", "PREFIX=%s" % prefix)
# Build the static library and everything else
make()
make('install', 'PREFIX={0}'.format(prefix))
install('bzip2-shared', join_path(prefix.bin, 'bzip2'))
v1, v2, v3 = (self.spec.version.up_to(i) for i in (1,2,3))
v1, v2, v3 = (self.spec.version.up_to(i) for i in (1, 2, 3))
if 'darwin' in self.spec.architecture:
lib = 'libbz2.dylib'
lib1, lib2, lib3 = ('libbz2.{0}.dylib'.format(v) for v in (v1, v2, v3))
lib1, lib2, lib3 = ('libbz2.{0}.dylib'.format(v)
for v in (v1, v2, v3))
else:
lib = 'libbz2.so'
lib1, lib2, lib3 = ('libbz2.so.{0}'.format(v) for v in (v1, v2, v3))
lib1, lib2, lib3 = ('libbz2.so.{0}'.format(v)
for v in (v1, v2, v3))
install(lib3, join_path(prefix.lib, lib3))
with working_dir(prefix.lib):

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##############################################################################
# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-647188
#
# For details, see https://github.com/llnl/spack
# Please also see the LICENSE file for our notice and the LGPL.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License (as
# published by the Free Software Foundation) version 2.1, February 1999.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
# conditions of the GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
import sys
from spack import *
class CBlosc(Package):
"""Blosc, an extremely fast, multi-threaded, meta-compressor library"""
homepage = "http://www.blosc.org"
url = "https://github.com/Blosc/c-blosc/archive/v1.9.2.tar.gz"
version('1.9.2', 'dd2d83069d74b36b8093f1c6b49defc5')
version('1.9.1', '7d708d3daadfacf984a87b71b1734ce2')
version('1.9.0', 'e4c1dc8e2c468e5cfa2bf05eeee5357a')
version('1.8.1', 'd73d5be01359cf271e9386c90dcf5b05')
version('1.8.0', '5b92ecb287695ba20cc33d30bf221c4f')
depends_on("cmake", type='build')
depends_on("snappy")
depends_on("zlib")
def install(self, spec, prefix):
cmake('.', *std_cmake_args)
make()
make("install")
if sys.platform == 'darwin':
fix_darwin_install_name(prefix.lib)

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