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Merge branch 'mplegendre-multi_pkgsrc_roots' into develop

Browse Source 
- This moves var/spack/packages to var/spack/repos/builtin/packages.

- Packages that did not exist in the source branch, or were changed in
  develop, were moved into var/spack/repos/builtin/packages as part of
  the integration.

Conflicts:
	lib/spack/spack/test/unit_install.py
	var/spack/repos/builtin/packages/clang/package.py
This commit is contained in:
Todd Gamblin
2016-01-17 19:42:28 -08:00
parent d802165e03 97b492756a
commit 8d6342c53d
445 changed files with 6902 additions and 840 deletions
Download Patch File Download Diff File Expand all files Collapse all files

11
var/spack/repos/builtin/packages/openmpi/ad_lustre_rwcontig_open_source.patch Normal file
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@@ -0,0 +1,11 @@
--- a/ompi/mca/io/romio/romio/adio/ad_lustre/ad_lustre_rwcontig.c 2013-12-10 12:05:44.806417000 -0800
+++ b/ompi/mca/io/romio/romio/adio/ad_lustre/ad_lustre_rwcontig.c 2013-12-10 11:53:03.295622000 -0800
@@ -8,7 +8,7 @@
* Copyright (C) 2008 Sun Microsystems, Lustre group
*/
-#define _XOPEN_SOURCE 600
+//#define _XOPEN_SOURCE 600
#include <stdlib.h>
#include <malloc.h>
#include "ad_lustre.h"

31
var/spack/repos/builtin/packages/openmpi/configure.patch Normal file
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@@ -0,0 +1,31 @@
This patch addresses <https://github.com/open-mpi/ompi/issues/576>.
--- a/configure
+++ b/configure
@@ -301130,10 +301130,11 @@
case ${prev}${p} in
-L* | -R* | -l*)
- # Some compilers place space between "-{L,R}" and the path.
+ # Some compilers place space between "-{L,R,l}" and the path.
# Remove the space.
if test $p = "-L" ||
- test $p = "-R"; then
+ test $p = "-R" ||
+ test $p = "-l"; then
prev=$p
continue
fi
@@ -303036,10 +303037,11 @@
case ${prev}${p} in
-L* | -R* | -l*)
- # Some compilers place space between "-{L,R}" and the path.
+ # Some compilers place space between "-{L,R,l}" and the path.
# Remove the space.
if test $p = "-L" ||
- test $p = "-R"; then
+ test $p = "-R" ||
+ test $p = "-l"; then
prev=$p
continue
fi

151
var/spack/repos/builtin/packages/openmpi/llnl-platforms.patch Normal file
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@@ -0,0 +1,151 @@
diff -Nuar openmpi-1.6.5.orig/contrib/platform/llnl/optimized openmpi-1.6.5.llnl/contrib/platform/llnl/optimized
--- openmpi-1.6.5.orig/contrib/platform/llnl/optimized 1969-12-31 16:00:00.000000000 -0800
+++ openmpi-1.6.5.llnl/contrib/platform/llnl/optimized 2013-08-08 23:47:12.704029000 -0700
@@ -0,0 +1,29 @@
+enable_dlopen=no
+enable_mem_debug=no
+enable_mem_profile=no
+enable_debug_symbols=no
+enable_binaries=yes
+enable_heterogeneous=no
+enable_debug=no
+enable_shared=yes
+enable_static=yes
+enable_memchecker=no
+enable_ipv6=no
+enable_mpi_f77=yes
+enable_mpi_f90=yes
+enable_mpi_cxx=yes
+enable_mpi_cxx_seek=yes
+enable_cxx_exceptions=no
+enable_ft_thread=no
+enable_per_user_config_files=no
+enable_mca_no_build=carto,crs,filem,routed-linear,snapc,pml-dr,pml-crcp2,pml-crcpw,pml-v,pml-example,crcp,btl-tcp
+enable_contrib_no_build=libnbc,vt
+with_slurm=yes
+with_pmi=yes
+with_tm=no
+with_openib=yes
+with_psm=yes
+with_devel_headers=yes
+with_io_romio_flags=--with-file-system=ufs+nfs+lustre
+with_memory_manager=ptmalloc2
+with_valgrind=no
diff -Nuar openmpi-1.6.5.orig/contrib/platform/llnl/optimized.conf openmpi-1.6.5.llnl/contrib/platform/llnl/optimized.conf
--- openmpi-1.6.5.orig/contrib/platform/llnl/optimized.conf 1969-12-31 16:00:00.000000000 -0800
+++ openmpi-1.6.5.llnl/contrib/platform/llnl/optimized.conf 2013-08-08 23:43:52.907553000 -0700
@@ -0,0 +1,114 @@
+#
+# Copyright (c) 2004-2005 The Trustees of Indiana University and Indiana
+# University Research and Technology
+# Corporation. All rights reserved.
+# Copyright (c) 2004-2005 The University of Tennessee and The University
+# of Tennessee Research Foundation. All rights
+# reserved.
+# Copyright (c) 2004-2005 High Performance Computing Center Stuttgart,
+# University of Stuttgart. All rights reserved.
+# Copyright (c) 2004-2005 The Regents of the University of California.
+# All rights reserved.
+# Copyright (c) 2006 Cisco Systems, Inc. All rights reserved.
+# Copyright (c) 2011 Los Alamos National Security, LLC.
+# All rights reserved.
+# $COPYRIGHT$
+#
+# Additional copyrights may follow
+#
+# $HEADER$
+#
+
+# This is the default system-wide MCA parameters defaults file.
+# Specifically, the MCA parameter "mca_param_files" defaults to a
+# value of
+# "$HOME/.openmpi/mca-params.conf:$sysconf/openmpi-mca-params.conf"
+# (this file is the latter of the two). So if the default value of
+# mca_param_files is not changed, this file is used to set system-wide
+# MCA parameters. This file can therefore be used to set system-wide
+# default MCA parameters for all users. Of course, users can override
+# these values if they want, but this file is an excellent location
+# for setting system-specific MCA parameters for those users who don't
+# know / care enough to investigate the proper values for them.
+
+# Note that this file is only applicable where it is visible (in a
+# filesystem sense). Specifically, MPI processes each read this file
+# during their startup to determine what default values for MCA
+# parameters should be used. mpirun does not bundle up the values in
+# this file from the node where it was run and send them to all nodes;
+# the default value decisions are effectively distributed. Hence,
+# these values are only applicable on nodes that "see" this file. If
+# $sysconf is a directory on a local disk, it is likely that changes
+# to this file will need to be propagated to other nodes. If $sysconf
+# is a directory that is shared via a networked filesystem, changes to
+# this file will be visible to all nodes that share this $sysconf.
+
+# The format is straightforward: one per line, mca_param_name =
+# rvalue. Quoting is ignored (so if you use quotes or escape
+# characters, they'll be included as part of the value). For example:
+
+# Disable run-time MPI parameter checking
+# mpi_param_check = 0
+
+# Note that the value "~/" will be expanded to the current user's home
+# directory. For example:
+
+# Change component loading path
+# component_path = /usr/local/lib/openmpi:~/my_openmpi_components
+
+# See "ompi_info --param all all" for a full listing of Open MPI MCA
+# parameters available and their default values.
+#
+
+# Basic behavior to smooth startup
+mca_component_show_load_errors = 0
+orte_abort_timeout = 10
+opal_set_max_sys_limits = 1
+orte_report_launch_progress = 1
+
+# Define timeout for daemons to report back during launch
+orte_startup_timeout = 10000
+
+## Protect the shared file systems
+orte_no_session_dirs = /p,/usr/local,/usr/global,/nfs/tmp1,/nfs/tmp2
+orte_tmpdir_base = /tmp
+
+## Require an allocation to run - protects the frontend
+## from inadvertent job executions
+orte_allocation_required = 1
+
+## MPI behavior
+## Do NOT specify mpi_leave_pinned so system
+## can figure out for itself whether or not
+## it is supported and usable
+orte_notifier = syslog
+
+## Add the interface for out-of-band communication
+## and set it up
+oob_tcp_if_include=ib0
+oob_tcp_peer_retries = 1000
+oob_tcp_disable_family = IPv6
+oob_tcp_listen_mode = listen_thread
+oob_tcp_sndbuf = 32768
+oob_tcp_rcvbuf = 32768
+
+## Define the MPI interconnects
+btl = sm,openib,self
+
+## We are using the PSM MTL by default
+## There can only be one!
+pml = cm
+
+## Setup OpenIB - just in case
+btl_openib_want_fork_support = 0
+btl_openib_cpc_include = oob
+btl_openib_receive_queues = S,4096,1024:S,12288,512:S,65536,512
+
+## Enable cpu affinity
+opal_paffinity_alone = 1
+
+## Setup MPI options
+mpi_show_handle_leaks = 0
+mpi_warn_on_fork = 1
+mpi_abort_print_stack = 0
+

136
var/spack/repos/builtin/packages/openmpi/package.py Normal file
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@@ -0,0 +1,136 @@
import os
from spack import *
class Openmpi(Package):
"""Open MPI is a project combining technologies and resources from
several other projects (FT-MPI, LA-MPI, LAM/MPI, and PACX-MPI)
in order to build the best MPI library available. A completely
new MPI-2 compliant implementation, Open MPI offers advantages
for system and software vendors, application developers and
computer science researchers.
"""
homepage = "http://www.open-mpi.org"
url = "http://www.open-mpi.org/software/ompi/v1.10/downloads/openmpi-1.10.1.tar.bz2"
list_url = "http://www.open-mpi.org/software/ompi/"
list_depth = 3
version('1.10.1', 'f0fcd77ed345b7eafb431968124ba16e')
version('1.10.0', '280cf952de68369cebaca886c5ce0304')
version('1.8.8', '0dab8e602372da1425e9242ae37faf8c')
version('1.6.5', '03aed2a4aa4d0b27196962a2a65fc475')
patch('ad_lustre_rwcontig_open_source.patch', when="@1.6.5")
patch('llnl-platforms.patch', when="@1.6.5")
patch('configure.patch', when="@1.10.0:")
variant('psm', default=False, description='Build support for the PSM library.')
variant('verbs', default=False, description='Build support for OpenFabrics verbs.')
provides('mpi@:2.2', when='@1.6.5')
provides('mpi@:3.0', when='@1.7.5:')
depends_on('hwloc')
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)
def setup_dependent_environment(self, module, spec, dep_spec):
"""For dependencies, make mpicc's use spack wrapper."""
os.environ['OMPI_CC'] = 'cc'
os.environ['OMPI_CXX'] = 'c++'
os.environ['OMPI_FC'] = 'f90'
os.environ['OMPI_F77'] = 'f77'
def install(self, spec, prefix):
config_args = ["--prefix=%s" % prefix,
"--with-hwloc=%s" % spec['hwloc'].prefix,
"--with-tm", # necessary for Torque support
"--enable-shared",
"--enable-static"]
# Variants
if '+psm' in spec:
config_args.append("--with-psm")
if '+verbs' in spec:
# Up through version 1.6, this option was previously named --with-openib
if spec.satisfies('@:1.6'):
config_args.append("--with-openib")
# In version 1.7, it was renamed to be --with-verbs
elif spec.satisfies('@1.7:'):
config_args.append("--with-verbs")
# TODO: use variants for this, e.g. +lanl, +llnl, etc.
# use this for LANL builds, but for LLNL builds, we need:
# "--with-platform=contrib/platform/llnl/optimized"
if self.version == ver("1.6.5") and '+lanl' in spec:
config_args.append("--with-platform=contrib/platform/lanl/tlcc2/optimized-nopanasas")
# TODO: Spack should make it so that you can't actually find
# these compilers if they're "disabled" for the current
# compiler configuration.
if not self.compiler.f77 and not self.compiler.fc:
config_args.append("--enable-mpi-fortran=no")
configure(*config_args)
make()
make("install")
self.filter_compilers()
def filter_compilers(self):
"""Run after install to make the MPI compilers use the
compilers that Spack built the package with.
If this isn't done, they'll have CC, CXX and FC set
to Spack's generic cc, c++ and f90. We want them to
be bound to whatever compiler they were built with.
"""
kwargs = { 'ignore_absent' : True, 'backup' : False, 'string' : False }
dir = os.path.join(self.prefix, 'share/openmpi/')
cc_wrappers = ['mpicc-vt-wrapper-data.txt', 'mpicc-wrapper-data.txt',
'ortecc-wrapper-data.txt', 'shmemcc-wrapper-data.txt']
cxx_wrappers = ['mpic++-vt-wrapper-data.txt', 'mpic++-wrapper-data.txt',
'ortec++-wrapper-data.txt']
fc_wrappers = ['mpifort-vt-wrapper-data.txt',
'mpifort-wrapper-data.txt', 'shmemfort-wrapper-data.txt']
for wrapper in cc_wrappers:
filter_file('compiler=.*', 'compiler=%s' % self.compiler.cc,
os.path.join(dir, wrapper), **kwargs)
for wrapper in cxx_wrappers:
filter_file('compiler=.*', 'compiler=%s' % self.compiler.cxx,
os.path.join(dir, wrapper), **kwargs)
for wrapper in fc_wrappers:
filter_file('compiler=.*', 'compiler=%s' % self.compiler.fc,
os.path.join(dir, wrapper), **kwargs)
# These are symlinks in newer versions, so check that here
f77_wrappers = ['mpif77-vt-wrapper-data.txt', 'mpif77-wrapper-data.txt']
f90_wrappers = ['mpif90-vt-wrapper-data.txt', 'mpif90-wrapper-data.txt']
for wrapper in f77_wrappers:
path = os.path.join(dir, wrapper)
if not os.path.islink(path):
filter_file('compiler=.*', 'compiler=%s' % self.compiler.f77,
path, **kwargs)
for wrapper in f90_wrappers:
path = os.path.join(dir, wrapper)
if not os.path.islink(path):
filter_file('compiler=.*', 'compiler=%s' % self.compiler.fc,
path, **kwargs)