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

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This commit is contained in:
Kelly (KT) Thompson
2016-03-09 12:38:48 -07:00
parent 8174489787 ad7d89b165
commit 113e942c3c
93 changed files with 1477 additions and 850 deletions
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1
var/spack/repos/builtin/packages/autoconf/package.py
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@@ -6,6 +6,7 @@ class Autoconf(Package):
url = "http://ftp.gnu.org/gnu/autoconf/autoconf-2.69.tar.gz"
version('2.69', '82d05e03b93e45f5a39b828dc9c6c29b')
version('2.62', '6c1f3b3734999035d77da5024aab4fbd')
def install(self, spec, prefix):
configure("--prefix=%s" % prefix)

2
var/spack/repos/builtin/packages/automake/package.py
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@@ -5,7 +5,9 @@ class Automake(Package):
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')
version('1.11.6', '0286dc30295b62985ca51919202ecfcc')
depends_on('autoconf')

15
var/spack/repos/builtin/packages/blitz/package.py Normal file
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@@ -0,0 +1,15 @@
from spack import *
class Blitz(Package):
"""N-dimensional arrays for C++"""
homepage = "http://github.com/blitzpp/blitz"
url = "https://github.com/blitzpp/blitz/tarball/1.0.0"
version('1.0.0', '9f040b9827fe22228a892603671a77af')
# No dependencies
def install(self, spec, prefix):
configure('--prefix=%s' % prefix)
make()
make("install")

1
var/spack/repos/builtin/packages/cgal/package.py
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@@ -46,6 +46,7 @@ class Cgal(Package):
depends_on('mpfr')
depends_on('gmp')
depends_on('zlib')
depends_on('cmake')
# FIXME : Qt5 dependency missing (needs Qt5 and OpenGL)
# FIXME : Optional third party libraries missing

1
var/spack/repos/builtin/packages/expat/package.py
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@@ -7,6 +7,7 @@ class Expat(Package):
version('2.1.0', 'dd7dab7a5fea97d2a6a43f511449b7cd')
depends_on('cmake')
def install(self, spec, prefix):

28
var/spack/repos/builtin/packages/hypre/package.py
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@@ -1,4 +1,5 @@
from spack import *
import os
class Hypre(Package):
"""Hypre is a library of high performance preconditioners that
@@ -8,8 +9,11 @@ class Hypre(Package):
homepage = "http://computation.llnl.gov/project/linear_solvers/software.php"
url = "http://computation.llnl.gov/project/linear_solvers/download/hypre-2.10.0b.tar.gz"
version('2.10.1', 'dc048c4cabb3cd549af72591474ad674')
version('2.10.0b', '768be38793a35bb5d055905b271f5b8e')
variant('shared', default=True, description="Build shared library version (disables static library)")
depends_on("mpi")
depends_on("blas")
depends_on("lapack")
@@ -17,16 +21,26 @@ class Hypre(Package):
def install(self, spec, prefix):
blas_dir = spec['blas'].prefix
lapack_dir = spec['lapack'].prefix
mpi_dir = spec['mpi'].prefix
os.environ['CC'] = os.path.join(mpi_dir, 'bin', 'mpicc')
os.environ['CXX'] = os.path.join(mpi_dir, 'bin', 'mpicxx')
os.environ['F77'] = os.path.join(mpi_dir, 'bin', 'mpif77')
configure_args = [
"--prefix=%s" % prefix,
"--with-lapack-libs=lapack",
"--with-lapack-lib-dirs=%s/lib" % lapack_dir,
"--with-blas-libs=blas",
"--with-blas-lib-dirs=%s/lib" % blas_dir]
if '+shared' in self.spec:
configure_args.append("--enable-shared")
# Hypre's source is staged under ./src so we'll have to manually
# cd into it.
with working_dir("src"):
configure(
"--prefix=%s" % prefix,
"--with-blas-libs=blas",
"--with-blas-lib-dirs=%s/lib" % blas_dir,
"--with-lapack-libs=\"lapack blas\"",
"--with-lapack-lib-dirs=%s/lib" % lapack_dir,
"--with-MPI")
configure(*configure_args)
make()
make("install")

4
var/spack/repos/builtin/packages/jdk/package.py
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@@ -28,7 +28,7 @@ class Jdk(Package):
'-H', # specify required License Agreement cookie
'Cookie: oraclelicense=accept-securebackup-cookie']
def do_fetch(self):
def do_fetch(self, mirror_only=False):
# Add our custom curl commandline options
tty.msg(
"[Jdk] Adding required commandline options to curl " +
@@ -39,7 +39,7 @@ def do_fetch(self):
spack.curl.add_default_arg(option)
# Now perform the actual fetch
super(Jdk, self).do_fetch()
super(Jdk, self).do_fetch(mirror_only)
def install(self, spec, prefix):

9
var/spack/repos/builtin/packages/libevent/package.py
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@@ -22,9 +22,16 @@ class Libevent(Package):
version('2.0.13', 'af786b4b3f790c9d3279792edf7867fc')
version('2.0.12', '42986228baf95e325778ed328a93e070')
variant('openssl', default=True, description="Build with encryption enabled at the libevent level.")
depends_on('openssl', when='+openssl')
def install(self, spec, prefix):
configure("--prefix=%s" % prefix)
configure_args = []
if '+openssl' in spec:
configure_args.append('--enable-openssl')
else:
configure_args.append('--enable-openssl')
configure("--prefix=%s" % prefix, *configure_args)
make()
make("install")

15
var/spack/repos/builtin/packages/libsigsegv/package.py Normal file
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@@ -0,0 +1,15 @@
from spack import *
class Libsigsegv(Package):
"""GNU libsigsegv is a library for handling page faults in user mode."""
homepage = "https://www.gnu.org/software/libsigsegv/"
url = "ftp://ftp.gnu.org/gnu/libsigsegv/libsigsegv-2.10.tar.gz"
version('2.10', '7f96fb1f65b3b8cbc1582fb7be774f0f')
def install(self, spec, prefix):
configure('--prefix=%s' % prefix,
'--enable-shared')
make()
make("install")

38
var/spack/repos/builtin/packages/llvm/package.py
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@@ -1,5 +1,5 @@
##############################################################################
# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
# Copyright (c) 2016, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
@@ -34,7 +34,7 @@ class Llvm(Package):
it is the full name of the project.
"""
homepage = 'http://llvm.org/'
url = 'http://llvm.org/releases/3.7.0/llvm-3.7.0.src.tar.xz'
url = 'http://llvm.org/releases/3.7.1/llvm-3.7.1.src.tar.xz'
version('3.0', 'a8e5f5f1c1adebae7b4a654c376a6005', url='http://llvm.org/releases/3.0/llvm-3.0.tar.gz') # currently required by mesa package
@@ -132,6 +132,21 @@ class Llvm(Package):
'llvm-libunwind' : 'http://llvm.org/svn/llvm-project/libunwind/trunk',
}
},
{
'version' : '3.7.1',
'md5':'bf8b3a2c79e61212c5409041dfdbd319',
'resources' : {
'compiler-rt' : '1c6975daf30bb3b0473b53c3a1a6ff01',
'openmp' : 'b4ad08cda4e5c22e42b66062b140438e',
'polly' : '3a2a7367002740881637f4d47bca4dc3',
'libcxx' : 'f9c43fa552a10e14ff53b94d04bea140',
'libcxxabi' : '52d925afac9f97e9dcac90745255c169',
'clang' : '0acd026b5529164197563d135a8fd83e',
'clang-tools-extra' : '5d49ff745037f061a7c86aeb6a24c3d2',
'lldb' : 'a106d8a0d21fc84d76953822fbaf3398',
'llvm-libunwind' : '814bd52c9247c5d04629658fbcb3ab8c',
}
},
{
'version' : '3.7.0',
'md5':'b98b9495e5655a672d6cb83e1a180f8e',
@@ -196,25 +211,6 @@ class Llvm(Package):
when='@%(version)s' % release,
placement=resources[name].get('placement', None))
# SVN - current develop
version('develop', svn='http://llvm.org/svn/llvm-project/llvm/trunk')
resource(name='clang', svn='http://llvm.org/svn/llvm-project/cfe/trunk',
destination='tools', when='@develop', placement='clang')
resource(name='compiler-rt', svn='http://llvm.org/svn/llvm-project/compiler-rt/trunk',
destination='projects', when='@develop', placement='compiler-rt')
resource(name='openmp', svn='http://llvm.org/svn/llvm-project/openmp/trunk',
destination='projects', when='@develop', placement='openmp')
resource(name='libcxx', svn='http://llvm.org/svn/llvm-project/libcxx/trunk',
destination='projects', when='@develop', placement='libcxx')
resource(name='libcxxabi', svn='http://llvm.org/svn/llvm-project/libcxxabi/trunk',
destination='projects', when='@develop', placement='libcxxabi')
resource(name='polly', svn='http://llvm.org/svn/llvm-project/polly/trunk',
destination='tools', when='@develop', placement='polly')
resource(name='lldb', svn='http://llvm.org/svn/llvm-project/lldb/trunk',
destination='tools', when='@develop', placement='lldb')
def install(self, spec, prefix):
env['CXXFLAGS'] = self.compiler.cxx11_flag
cmake_args = [ arg for arg in std_cmake_args if 'BUILD_TYPE' not in arg ]

14
var/spack/repos/builtin/packages/m4/package.py
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@@ -7,7 +7,19 @@ class M4(Package):
version('1.4.17', 'a5e9954b1dae036762f7b13673a2cf76')
patch('pgi.patch', when='@1.4.17')
variant('sigsegv', default=True, description="Build the libsigsegv dependency")
depends_on('libsigsegv', when='+sigsegv')
def install(self, spec, prefix):
configure("--prefix=%s" % prefix)
configure_args = []
if 'libsigsegv' in spec:
configure_args.append('--with-libsigsegv-prefix=%s' % spec['libsigsegv'].prefix)
else:
configure_args.append('--without-libsigsegv-prefix')
configure("--prefix=%s" % prefix, *configure_args)
make()
make("install")

10
var/spack/repos/builtin/packages/m4/pgi.patch Normal file
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@@ -0,0 +1,10 @@
--- a/lib/config.hin
+++ b/lib/config.hin
@@ -1510,6 +1510,7 @@
? defined __GNUC_STDC_INLINE__ && __GNUC_STDC_INLINE__ \
: (199901L <= __STDC_VERSION__ \
&& !defined __HP_cc \
+ && !defined __PGI \
&& !(defined __SUNPRO_C && __STDC__))) \
&& !defined _GL_EXTERN_INLINE_APPLE_BUG)
# define _GL_INLINE inline

6
var/spack/repos/builtin/packages/mpc/package.py
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@@ -37,6 +37,12 @@ class Mpc(Package):
depends_on("gmp")
depends_on("mpfr")
def url_for_version(self, version):
if version < Version("1.0.1"):
return "http://www.multiprecision.org/mpc/download/mpc-%s.tar.gz" % version
else:
return "ftp://ftp.gnu.org/gnu/mpc/mpc-%s.tar.gz" % version
def install(self, spec, prefix):
configure("--prefix=%s" % prefix)
make()

15
var/spack/repos/builtin/packages/netcdf-cxx4/package.py Normal file
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@@ -0,0 +1,15 @@
from spack import *
class NetcdfCxx4(Package):
"""C++ interface for NetCDF4"""
homepage = "http://www.unidata.ucar.edu/software/netcdf"
url = "http://www.unidata.ucar.edu/downloads/netcdf/ftp/netcdf-cxx4-4.2.tar.gz"
version('4.2', 'd019853802092cf686254aaba165fc81')
depends_on('netcdf')
def install(self, spec, prefix):
configure('--prefix=%s' % prefix)
make()
make("install")

16
var/spack/repos/builtin/packages/netcdf-fortran/package.py Normal file
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@@ -0,0 +1,16 @@
from spack import *
class NetcdfFortran(Package):
"""Fortran interface for NetCDF4"""
homepage = "http://www.unidata.ucar.edu/software/netcdf"
url = "http://www.unidata.ucar.edu/downloads/netcdf/ftp/netcdf-fortran-4.4.3.tar.gz"
version('4.4.3', 'bfd4ae23a34635b273d3eb0d91cbde9e')
depends_on('netcdf')
def install(self, spec, prefix):
configure("--prefix=%s" % prefix)
make()
make("install")

14
var/spack/repos/builtin/packages/netcdf/package.py
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@@ -6,14 +6,13 @@ class Netcdf(Package):
data formats that support the creation, access, and sharing of array-oriented
scientific data."""
homepage = "http://www.unidata.ucar.edu/software/netcdf/"
homepage = "http://www.unidata.ucar.edu/software/netcdf"
url = "ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-4.3.3.tar.gz"
version('4.4.0', 'cffda0cbd97fdb3a06e9274f7aef438e')
version('4.3.3', '5fbd0e108a54bd82cb5702a73f56d2ae')
variant('mpi', default=True, description='Enables MPI parallelism')
variant('fortran', default=False, description="Download and install NetCDF-Fortran")
variant('hdf4', default=False, description="Enable HDF4 support")
# Dependencies:
@@ -66,11 +65,7 @@ def install(self, spec, prefix):
# Fortran support
# In version 4.2+, NetCDF-C and NetCDF-Fortran have split.
# They can be installed separately, but this bootstrap procedure
# should be able to install both at the same time.
# Note: this is a new experimental feature.
if '+fortran' in spec:
config_args.append("--enable-remote-fortran-bootstrap")
# Use the netcdf-fortran package to install Fortran support.
config_args.append('CPPFLAGS=%s' % ' '.join(CPPFLAGS))
config_args.append('LDFLAGS=%s' % ' '.join(LDFLAGS))
@@ -79,8 +74,3 @@ def install(self, spec, prefix):
configure(*config_args)
make()
make("install")
# After installing NetCDF-C, install NetCDF-Fortran
if '+fortran' in spec:
make("build-netcdf-fortran")
make("install-netcdf-fortran")

1
var/spack/repos/builtin/packages/openssl/package.py
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@@ -17,6 +17,7 @@ class Openssl(Package):
version('1.0.2d', '38dd619b2e77cbac69b99f52a053d25a')
version('1.0.2e', '5262bfa25b60ed9de9f28d5d52d77fc5')
version('1.0.2f', 'b3bf73f507172be9292ea2a8c28b659d')
version('1.0.2g', 'f3c710c045cdee5fd114feb69feba7aa')
depends_on("zlib")
parallel = False

2
var/spack/repos/builtin/packages/pango/package.py
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@@ -16,4 +16,4 @@ class Pango(Package):
def install(self, spec, prefix):
configure("--prefix=%s" % prefix)
make()
make("install")
make("install", parallel=False)

13
var/spack/repos/builtin/packages/paraview/package.py
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@@ -2,9 +2,11 @@
class Paraview(Package):
homepage = 'http://www.paraview.org'
url = 'http://www.paraview.org/files/v4.4/ParaView-v4.4.0-source.tar.gz'
url = 'http://www.paraview.org/files/v5.0/ParaView-v'
_url_str = 'http://www.paraview.org/files/v%s/ParaView-v%s-source.tar.gz'
version('4.4.0', 'fa1569857dd680ebb4d7ff89c2227378', url='http://www.paraview.org/files/v4.4/ParaView-v4.4.0-source.tar.gz')
version('4.4.0', 'fa1569857dd680ebb4d7ff89c2227378')
version('5.0.0', '4598f0b421460c8bbc635c9a1c3bdbee')
variant('python', default=False, description='Enable Python support')
@@ -25,8 +27,8 @@ class Paraview(Package):
depends_on('bzip2')
depends_on('freetype')
depends_on('hdf5')
depends_on('hdf5+mpi', when='+mpi')
depends_on('hdf5~mpi', when='~mpi')
depends_on('jpeg')
depends_on('libpng')
depends_on('libtiff')
@@ -35,6 +37,11 @@ class Paraview(Package):
#depends_on('protobuf') # version mismatches?
#depends_on('sqlite') # external version not supported
depends_on('zlib')
def url_for_version(self, version):
"""Handle ParaView version-based custom URLs."""
return self._url_str % (version.up_to(2), version)
def install(self, spec, prefix):
with working_dir('spack-build', create=True):

92
var/spack/repos/builtin/packages/petsc/package.py
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@@ -1,40 +1,86 @@
import os
from spack import *
class Petsc(Package):
"""PETSc is a suite of data structures and routines for the
scalable (parallel) solution of scientific applications modeled by
partial differential equations."""
"""
PETSc is a suite of data structures and routines for the scalable (parallel) solution of scientific applications
modeled by partial differential equations.
"""
homepage = "http://www.mcs.anl.gov/petsc/index.html"
url = "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-3.5.3.tar.gz"
url = "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-3.5.3.tar.gz"
version('3.6.3', '91dd3522de5a5ef039ff8f50800db606')
version('3.5.3', 'd4fd2734661e89f18ac6014b5dd1ef2f')
version('3.5.2', 'ad170802b3b058b5deb9cd1f968e7e13')
version('3.5.1', 'a557e029711ebf425544e117ffa44d8f')
depends_on("python @2.6:2.9") # requires Python for building
variant('shared', default=True, description='Enables the build of shared libraries')
variant('mpi', default=True, description='Activates MPI support')
variant('double', default=True, description='Switches between single and double precision')
depends_on("boost")
depends_on("blas")
depends_on("lapack")
depends_on("hypre")
depends_on("parmetis")
depends_on("metis")
depends_on("hdf5+mpi")
depends_on("mpi")
variant('metis', default=True, description='Activates support for metis and parmetis')
variant('hdf5', default=True, description='Activates support for HDF5 (only parallel)')
variant('boost', default=True, description='Activates support for Boost')
variant('hypre', default=True, description='Activates support for Hypre')
# Build dependencies
depends_on('python @2.6:2.9') # requires Python for building
# Virtual dependencies
depends_on('blas')
depends_on('lapack')
depends_on('mpi', when='+mpi')
# Other dependencies
depends_on('boost', when='+boost')
depends_on('metis', when='+metis')
depends_on('hdf5~cxx~unsupported+mpi', when='+hdf5+mpi')
depends_on('parmetis', when='+metis+mpi')
depends_on('hypre', when='+hypre+mpi')
def mpi_dependent_options(self):
if '~mpi' in self.spec:
compiler_opts = [
'--with-cc=%s' % os.environ['CC'],
'--with-cxx=%s' % (os.environ['CXX'] if self.compiler.cxx is not None else '0'),
'--with-fc=%s' % (os.environ['FC'] if self.compiler.fc is not None else '0'),
'--with-mpi=0'
]
error_message_fmt = '\t{library} support requires "+mpi" to be activated'
errors = [error_message_fmt.format(library=x) for x in ('hdf5', 'hypre') if ('+'+x) in self.spec]
if errors:
errors = ['incompatible variants given'] + errors
raise RuntimeError('\n'.join(errors))
else:
compiler_opts = [
'--with-mpi=1',
'--with-mpi-dir=%s' % self.spec['mpi'].prefix,
]
return compiler_opts
def install(self, spec, prefix):
configure("--prefix=%s" % prefix,
"--with-blas-lib=%s/libblas.a" % spec['blas'].prefix.lib,
"--with-lapack-lib=%s/liblapack.a" % spec['lapack'].prefix.lib,
"--with-boost-dir=%s" % spec['boost'].prefix,
"--with-hypre-dir=%s" % spec['hypre'].prefix,
"--with-parmetis-dir=%s" % spec['parmetis'].prefix,
"--with-metis-dir=%s" % spec['metis'].prefix,
"--with-hdf5-dir=%s" % spec['hdf5'].prefix,
"--with-mpi-dir=%s" % spec['mpi'].prefix,
"--with-shared-libraries=0")
options = []
options.extend(self.mpi_dependent_options())
options.extend([
'--with-precision=%s' % ('double' if '+double' in spec else 'single'),
'--with-shared-libraries=%s' % ('1' if '+shared' in spec else '0'),
'--with-blas-lapack-dir=%s' % spec['lapack'].prefix
])
# Activates library support if needed
for library in ('metis', 'boost', 'hfd5', 'hypre', 'parmetis'):
options.append(
'--with-{library}={value}'.format(library=library, value=('1' if library in spec else '0'))
)
if library in spec:
options.append(
'--with-{library}-dir={path}'.format(library=library, path=spec[library].prefix)
)
configure('--prefix=%s' % prefix, *options)
# PETSc has its own way of doing parallel make.
make('MAKE_NP=%s' % make_jobs, parallel=False)
make("install")

20
var/spack/repos/builtin/packages/proj/package.py Normal file
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@@ -0,0 +1,20 @@
from spack import *
class Proj(Package):
"""Cartographic Projections"""
homepage = "https://github.com/OSGeo/proj.4/wiki"
url = "http://download.osgeo.org/proj/proj-4.9.2.tar.gz"
version('4.9.2', '9843131676e31bbd903d60ae7dc76cf9')
version('4.9.1', '3cbb2a964fd19a496f5f4265a717d31c')
version('4.8.0', 'd815838c92a29179298c126effbb1537')
version('4.7.0', '927d34623b52e0209ba2bfcca18fe8cd')
version('4.6.1', '7dbaab8431ad50c25669fd3fb28dc493')
# No dependencies
def install(self, spec, prefix):
configure('--prefix=%s' % prefix)
make()
make("install")

19
var/spack/repos/builtin/packages/silo/package.py
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@@ -1,19 +1,28 @@
from spack import *
class Silo(Package):
"""Silo is a library for reading and writing a wide variety of scientific data to binary, disk files."""
"""Silo is a library for reading and writing a wide variety of scientific
data to binary, disk files."""
homepage = "http://wci.llnl.gov/simulation/computer-codes/silo"
url = "https://wci.llnl.gov/content/assets/docs/simulation/computer-codes/silo/silo-4.8/silo-4.8.tar.gz"
#version('4.9', 'a83eda4f06761a86726e918fc55e782a')
version('4.8', 'b1cbc0e7ec435eb656dc4b53a23663c9')
depends_on("hdf5@:1.8.12")
variant('fortran', default=True, description='Enable Fortran support')
depends_on("hdf5")
def install(self, spec, prefix):
configure("--prefix=%s" % prefix,
"--with-hdf5=%s" %spec['hdf5'].prefix)
config_args = [
'--enable-fortran' if '+fortran' in spec else '--disable-fortran',
]
configure(
"--prefix=%s" % prefix,
"--with-hdf5=%s,%s" % (spec['hdf5'].prefix.include, spec['hdf5'].prefix.lib),
"--with-zlib=%s,%s" % (spec['zlib'].prefix.include, spec['zlib'].prefix.lib),
*config_args)
make()
make("install")

16
var/spack/repos/builtin/packages/udunits2/package.py Normal file
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@@ -0,0 +1,16 @@
from spack import *
class Udunits2(Package):
"""Automated units conversion"""
homepage = "http://www.unidata.ucar.edu/software/udunits"
url = "ftp://ftp.unidata.ucar.edu/pub/udunits/udunits-2.2.20.tar.gz"
version('2.2.20', '1586b70a49dfe05da5fcc29ef239dce0')
depends_on('expat')
def install(self, spec, prefix):
configure("--prefix=%s" % prefix)
make()
make("install")

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var/spack/repos/builtin/packages/zfp/package.py Normal file
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from spack import *
class Zfp(Package):
"""zfp is an open source C library for compressed floating-point arrays that supports
very high throughput read and write random acces, target error bounds or bit rates.
Although bit-for-bit lossless compression is not always possible, zfp is usually
accurate to within machine epsilon in near-lossless mode, and is often orders of
magnitude more accurate than other lossy compressors.
"""
homepage = "http://computation.llnl.gov/projects/floating-point-compression"
url = "http://computation.llnl.gov/projects/floating-point-compression/download/zfp-0.5.0.tar.gz"
version('0.5.0', '2ab29a852e65ad85aae38925c5003654')
def install(self, spec, prefix):
make("shared")
# No install provided
mkdirp(prefix.lib)
mkdirp(prefix.include)
install('lib/libzfp.so', prefix.lib)
install('inc/zfp.h', prefix.include)
install('inc/types.h', prefix.include)
install('inc/bitstream.h', prefix.include)
install('inc/system.h', prefix.include)