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Merge branch 'develop' of https://github.com/LLNL/spack into packages/swift_durham

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This commit is contained in:
alalazo
2016-06-27 09:08:37 +02:00
parent a2ba60f6a8 73213ac59d
commit f3f309a22a
23 changed files with 468 additions and 74 deletions
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23
var/spack/packages/adios/package.py → var/spack/repos/builtin/packages/adios/package.py
View File

@@ -1,15 +1,18 @@
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
"""
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 = "http://users.nccs.gov/~pnorbert/adios-1.9.0.tar.gz"
url = "http://users.nccs.gov/~pnorbert/adios-1.9.0.tar.gz"
version('1.9.0', 'dbf5cb10e32add2f04c9b4052b7ffa76')
@@ -22,13 +25,13 @@ class Adios(Package):
depends_on('mxml')
def install(self, spec, prefix):
configure_args = ["--prefix=%s" % prefix,
"--with-mxml=%s" % spec['mxml'].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"]
"MPICC=cc", "MPICXX=CC", "MPIFC=ftn",
"CPPFLAGS=-DMPICH_IGNORE_CXX_SEEK"]
if spec.satisfies('%gcc'):
configure_args.extend(["CC=gcc", "CXX=g++", "FC=gfortran"])

2
var/spack/repos/builtin/packages/curl/package.py
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@@ -24,6 +24,7 @@
##############################################################################
from spack import *
class Curl(Package):
"""cURL is an open source command line tool and library for
transferring data with URL syntax"""
@@ -31,6 +32,7 @@ class Curl(Package):
homepage = "http://curl.haxx.se"
url = "http://curl.haxx.se/download/curl-7.46.0.tar.bz2"
version('7.49.1', '6bb1f7af5b58b30e4e6414b8c1abccab')
version('7.47.1', '9ea3123449439bbd960cd25cf98796fb')
version('7.46.0', '9979f989a2a9930d10f1b3deeabc2148')
version('7.45.0', '62c1a352b28558f25ba6209214beadc8')

35
var/spack/repos/builtin/packages/emacs/package.py
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@@ -23,23 +23,44 @@
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
from spack import *
import llnl.util.tty as tty
class Emacs(Package):
"""The Emacs programmable text editor."""
homepage = "https://www.gnu.org/software/emacs"
url = "http://ftp.gnu.org/gnu/emacs/emacs-24.5.tar.gz"
version('24.5', 'd74b597503a68105e61b5b9f6d065b44')
variant('X', default=True, description="Enable a X toolkit (GTK+)")
variant('gtkplus', default=False, description="Enable a GTK+ as X toolkit (this variant is ignored if ~X)")
depends_on('ncurses')
# Emacs also depends on:
# GTK or other widget library
# libtiff, png, etc.
# For now, we assume the system provides all that stuff.
# For Ubuntu 14.04 LTS:
# sudo apt-get install libgtk-3-dev libxpm-dev libtiff5-dev libjpeg8-dev libgif-dev libpng12-dev
depends_on('libtiff', when='+X')
depends_on('libpng', when='+X')
depends_on('libxpm', when='+X')
depends_on('giflib', when='+X')
depends_on('gtkplus', when='+X+gtkplus')
def install(self, spec, prefix):
configure('--prefix=%s' % prefix)
args = []
if '+X' in spec:
if '+gtkplus' in spec:
toolkit = 'gtk{0}'.format(spec['gtkplus'].version.up_to(1))
else:
toolkit = 'no'
args = [
'--with-x',
'--with-x-toolkit={0}'.format(toolkit)
]
else:
args = ['--without-x']
if '+gtkplus' in spec:
tty.warn('The variant +gtkplus is ignored if ~X is selected.')
configure('--prefix={0}'.format(prefix), *args)
make()
make("install")

41
var/spack/repos/builtin/packages/giflib/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 Giflib(Package):
"""The GIFLIB project maintains the giflib service library, which has
been pulling images out of GIFs since 1989."""
homepage = "http://giflib.sourceforge.net/"
url = "https://downloads.sourceforge.net/project/giflib/giflib-5.1.4.tar.bz2"
version('5.1.4', '2c171ced93c0e83bb09e6ccad8e3ba2b')
def install(self, spec, prefix):
configure('--prefix=%s' % prefix)
make()
make("install")

34
var/spack/repos/builtin/packages/glib/g_date_strftime.patch Normal file
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@@ -0,0 +1,34 @@
From 00148329967adb196138372771052a3f606a6ea3 Mon Sep 17 00:00:00 2001
From: coypu <coypu@sdf.org>
Date: Wed, 2 Mar 2016 19:43:10 +0200
Subject: [PATCH 2/2] gdate: Suppress string format literal warning
Newer versions of GCC emit an error here, but we know it's safe.
https://bugzilla.gnome.org/761550
---
glib/gdate.c | 5 +++++
1 file changed, 5 insertions(+)
diff --git a/glib/gdate.c b/glib/gdate.c
index 4aece02..92c34d2 100644
--- a/glib/gdate.c
+++ b/glib/gdate.c
@@ -2439,6 +2439,9 @@ win32_strftime_helper (const GDate *d,
*
* Returns: number of characters written to the buffer, or 0 the buffer was too small
*/
+#pragma GCC diagnostic push
+#pragma GCC diagnostic ignored "-Wformat-nonliteral"
+
gsize
g_date_strftime (gchar *s,
gsize slen,
@@ -2549,3 +2552,5 @@ g_date_strftime (gchar *s,
return retval;
#endif
}
+
+#pragma GCC diagnostic pop
--
2.7.1

8
var/spack/repos/builtin/packages/glib/package.py
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@@ -25,20 +25,24 @@
from spack import *
import sys
class Glib(Package):
"""The GLib package contains a low-level libraries useful for
providing data structure handling for C, portability wrappers
and interfaces for such runtime functionality as an event loop,
threads, dynamic loading and an object system."""
homepage = "https://developer.gnome.org/glib/"
url = "http://ftp.gnome.org/pub/gnome/sources/glib/2.42/glib-2.42.1.tar.xz"
url = "http://ftp.gnome.org/pub/gnome/sources/glib/2.42/glib-2.42.1.tar.xz"
version('2.42.1', '89c4119e50e767d3532158605ee9121a')
depends_on("libffi")
depends_on("zlib")
depends_on("pkg-config")
depends_on('gettext', sys.platform=='darwin')
depends_on('gettext', sys.platform == 'darwin')
# The following patch is needed for gcc-6.1
patch('g_date_strftime.patch')
def install(self, spec, prefix):
configure("--prefix=%s" % prefix)

33
var/spack/repos/builtin/packages/julia/package.py
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@@ -22,8 +22,9 @@
# 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 *
import os
class Julia(Package):
"""The Julia Language: A fresh approach to technical computing"""
@@ -32,10 +33,14 @@ class Julia(Package):
version('master',
git='https://github.com/JuliaLang/julia.git', branch='master')
version('release-0.4',
git='https://github.com/JuliaLang/julia.git', branch='release-0.4')
version('0.4.6', 'd88db18c579049c23ab8ef427ccedf5d', preferred=True)
version('0.4.5', '69141ff5aa6cee7c0ec8c85a34aa49a6')
version('0.4.3', '8a4a59fd335b05090dd1ebefbbe5aaac')
patch('gc.patch')
patch('gc.patch', when='@0.4:0.4.5')
patch('gc.patch', when='@release-0.4')
patch('openblas.patch', when='@0.4:0.4.5')
# Build-time dependencies:
@@ -92,25 +97,21 @@ class Julia(Package):
depends_on("mpi")
def install(self, spec, prefix):
if '@master' in spec:
# Julia needs to know the offset from a specific commit
git = which('git')
git('fetch', '--unshallow')
# Explicitly setting CC, CXX, or FC breaks building libuv, one
# of Julia's dependencies. This might be a Darwin-specific
# problem. Given how Spack sets up compilers, Julia should
# still use Spack's compilers, even if we don't specify them
# explicitly.
options = [#"CC=cc",
#"CXX=c++",
#"FC=fc",
#"USE_SYSTEM_ARPACK=1",
#"USE_SYSTEM_FFTW=1",
#"USE_SYSTEM_GMP=1",
#"USE_SYSTEM_MPFR=1",
#TODO "USE_SYSTEM_PCRE=1",
"prefix=%s" % prefix]
options = [
# "CC=cc",
# "CXX=c++",
# "FC=fc",
# "USE_SYSTEM_ARPACK=1",
# "USE_SYSTEM_FFTW=1",
# "USE_SYSTEM_GMP=1",
# "USE_SYSTEM_MPFR=1",
# "USE_SYSTEM_PCRE=1",
"prefix=%s" % prefix]
with open('Make.user', 'w') as f:
f.write('\n'.join(options) + '\n')
make()

44
var/spack/repos/builtin/packages/libxpm/package.py Normal file
View File

@@ -0,0 +1,44 @@
##############################################################################
# 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 Libxpm(Package):
"""Xpm file format library"""
homepage = "https://www.x.org/"
url = "https://www.x.org/archive//individual/lib/libXpm-3.5.11.tar.gz"
version('3.5.11', '7c67c878ee048206b070bc0b24154f04')
version('3.5.10', 'a70507638d74541bf30a771f1e5938bb')
version('3.5.9', 'd6d4b0f76248a6b346eb42dfcdaa72a6')
version('3.5.8', '2d81d6633e67ac5562e2fbee126b2897')
version('3.5.7', '7bbc8f112f7143ed6961a58ce4e14558')
def install(self, spec, prefix):
configure('--prefix=%s' % prefix)
make()
make("install")

5
var/spack/repos/builtin/packages/mpich/package.py
View File

@@ -50,6 +50,11 @@ class Mpich(Package):
provides('mpi@:1.3', when='@1:')
def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
spack_env.set('MPICC', join_path(self.prefix.bin, 'mpicc'))
spack_env.set('MPICXX', join_path(self.prefix.bin, 'mpic++'))
spack_env.set('MPIF77', join_path(self.prefix.bin, 'mpif77'))
spack_env.set('MPIF90', join_path(self.prefix.bin, 'mpif90'))
spack_env.set('MPICH_CC', spack_cc)
spack_env.set('MPICH_CXX', spack_cxx)
spack_env.set('MPICH_F77', spack_f77)

5
var/spack/repos/builtin/packages/mvapich2/package.py
View File

@@ -191,6 +191,11 @@ def setup_environment(self, spack_env, run_env):
run_env.set('SLURM_MPI_TYPE', 'pmi2')
def setup_dependent_environment(self, spack_env, run_env, extension_spec):
spack_env.set('MPICC', join_path(self.prefix.bin, 'mpicc'))
spack_env.set('MPICXX', join_path(self.prefix.bin, 'mpicxx'))
spack_env.set('MPIF77', join_path(self.prefix.bin, 'mpif77'))
spack_env.set('MPIF90', join_path(self.prefix.bin, 'mpif90'))
spack_env.set('MPICH_CC', spack_cc)
spack_env.set('MPICH_CXX', spack_cxx)
spack_env.set('MPICH_F77', spack_f77)

15
var/spack/packages/mxml/package.py → var/spack/repos/builtin/packages/mxml/package.py
View File

@@ -1,14 +1,15 @@
import os
from spack import *
class Mxml(Package):
"""Mini-XML is a small XML library that you can use to read and write XML
and XML-like data files in your application without requiring large
non-standard libraries
"""
Mini-XML is a small XML library that you can use to read and write XML
and XML-like data files in your application without requiring large
non-standard libraries
"""
homepage = "http://www.msweet.org"
url = "http://www.msweet.org/files/project3/mxml-2.9.tar.gz"
url = "http://www.msweet.org/files/project3/mxml-2.9.tar.gz"
version('2.9', 'e21cad0f7aacd18f942aa0568a8dee19')
version('2.8', 'd85ee6d30de053581242c4a86e79a5d2')
@@ -16,11 +17,11 @@ class Mxml(Package):
version('2.6', '68977789ae64985dddbd1a1a1652642e')
version('2.5', 'f706377fba630b39fa02fd63642b17e5')
# module swap PrgEnv-intel PrgEnv-$COMP (Can use whatever compiler you want to use)
# module swap PrgEnv-intel PrgEnv-$COMP
# (Can use whatever compiler you want to use)
# Case statement to change CC and CXX flags
def install(self, spec, prefix):
configure('--prefix=%s' % prefix, "--disable-shared", 'CFLAGS=-static')
make()
make("install")

2
var/spack/repos/builtin/packages/netcdf-fortran/package.py
View File

@@ -24,12 +24,14 @@
##############################################################################
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('4.4.4', 'e855c789cd72e1b8bc1354366bf6ac72')
version('4.4.3', 'bfd4ae23a34635b273d3eb0d91cbde9e')
depends_on('netcdf')

5
var/spack/repos/builtin/packages/openmpi/package.py
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@@ -109,6 +109,11 @@ def url_for_version(self, version):
return "http://www.open-mpi.org/software/ompi/v%s/downloads/openmpi-%s.tar.bz2" % (version.up_to(2), version) # NOQA: ignore=E501
def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
spack_env.set('MPICC', join_path(self.prefix.bin, 'mpicc'))
spack_env.set('MPICXX', join_path(self.prefix.bin, 'mpic++'))
spack_env.set('MPIF77', join_path(self.prefix.bin, 'mpif77'))
spack_env.set('MPIF90', join_path(self.prefix.bin, 'mpif90'))
spack_env.set('OMPI_CC', spack_cc)
spack_env.set('OMPI_CXX', spack_cxx)
spack_env.set('OMPI_FC', spack_fc)

50
var/spack/repos/builtin/packages/py-protobuf/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 PyProtobuf(Package):
"""Protocol buffers are Google's language-neutral, platform-neutral,
extensible mechanism for serializing structured data - think XML, but
smaller, faster, and simpler. You define how you want your data to be
structured once, then you can use special generated source code to easily
write and read your structured data to and from a variety of data streams
and using a variety of languages."""
homepage = 'https://developers.google.com/protocol-buffers/'
url = 'https://pypi.python.org/packages/source/p/protobuf/protobuf-3.0.0b2.tar.gz'
version('3.0.0b2', 'f0d3bd2394345a9af4a277cd0302ae83')
version('2.6.1', '6bf843912193f70073db7f22e2ea55e2')
version('2.5.0', '338813f3629d59e9579fed9035ecd457')
version('2.4.1', '72f5141d20ab1bcae6b1e00acfb1068a')
version('2.3.0', 'bb020c962f252fe81bfda8fb433bafdd')
extends('python')
depends_on('py-setuptools')
def install(self, spec, prefix):
python('setup.py', 'install', '--prefix={0}'.format(prefix))