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authorasau <asau@pkgsrc.org>2016-10-23 14:02:28 +0000
committerasau <asau@pkgsrc.org>2016-10-23 14:02:28 +0000
commit938d3bf4c149eddc51e8172e4b3510d73320499d (patch)
treea50f9b0024b211ca1a52a906a1f22b17f6afc5f9 /parallel
parent88c1c3d959d33088f56805baf8cbe9dec9eff45e (diff)
downloadpkgsrc-938d3bf4c149eddc51e8172e4b3510d73320499d.tar.gz
Update to OpenMPI 1.10.4
Prompted by Nicolas Joly in private mail. 1.10.4 - 01 Sept 2016 ------ - Fix assembler support for MIPS - Improve memory handling for temp buffers in collectives - Fix [all]reduce with non-zero lower bound datatypes Thanks Hristo Iliev for the report - Fix non-standard ddt handling. Thanks Yuki Matsumoto for the report - Various libnbc fixes. Thanks Yuki Matsumoto for the report - Fix typos in request RMA bindings for Fortran. Thanks to @alazzaro and @vondele for the assist - Various bug fixes and enhancements to collective support - Fix predefined types mapping in hcoll - Revive the coll/sync component to resolve unexpected message issues during tight loops across collectives - Fix typo in wrapper compiler for Fortran static builds 1.10.3 - 15 June 2016 ------ - Fix zero-length datatypes. Thanks to Wei-keng Liao for reporting the issue. - Minor manpage cleanups - Implement atomic support in OSHMEM/UCX - Fix support of MPI_COMBINER_RESIZED. Thanks to James Ramsey for the report - Fix computation of #cpus when --use-hwthread-cpus is used - Add entry points for Allgatherv, iAllgatherv, Reduce, and iReduce for the HCOLL library - Fix an HCOLL integration bug that could signal completion of request while still being worked - Fix computation of cores when SMT is enabled. Thanks to Ben Menadue for the report - Various USNIC fixes - Create a datafile in the per-proc directory in order to make it unique per communicator. Thanks to Peter Wind for the report - Fix zero-size malloc in one-sided pt-to-pt code. Thanks to Lisandro Dalcin for the report - Fix MPI_Get_address when passed MPI_BOTTOM to not return an error. Thanks to Lisandro Dalcin for the report - Fix MPI_TYPE_SET_ATTR with NULL value. Thanks to Lisandro Dalcin for the report - Fix various Fortran08 binding issues - Fix memchecker no-data case. Thanks to Clinton Stimpson for the report - Fix CUDA support under OS-X - Fix various OFI/MTL integration issues - Add MPI_T man pages - Fix one-sided pt-to-pt issue by preventing communication from happening before a target enters a fence, even in the no-precede case - Fix a bug that disabled Totalview for MPMD use-case - Correctly support MPI_UNWEIGHTED in topo-graph-neighbors. Thanks to Jun Kudo for the report - Fix singleton operations under SLURM when PMI2 is enabled - Do not use MPI_IN_PLACE in neighborhood collectives for non-blocking collectives (libnbc). Thanks to Jun Kudo for the report - Silence autogen deprecation warnings for newer versions of Perl - Do not return MPI_ERR_PENDING from collectives - Use type int* for MPI_WIN_DISP_UNIT, MPI_WIN_CREATE_FLAVOR, and MPI_WIN_MODEL. Thanks to Alastair McKinstry for the report - Fix register_datarep stub function in IO/OMPIO. Thanks to Eric Chamberland for the report - Fix a bus error on MPI_WIN_[POST,START] in the shared memory one-sided component - Add several missing MPI_WIN_FLAVOR constants to the Fortran support - Enable connecting processes from different subnets using the openib BTL - Fix bug in basic/barrier algorithm in OSHMEM - Correct process binding for the --map-by node case - Include support for subnet-to-subnet routing over InfiniBand networks - Fix usnic resource check - AUTHORS: Fix an errant reference to Subversion IDs - Fix affinity for MPMD jobs running under LSF - Fix many Fortran binding bugs - Fix `MPI_IN_PLACE`-related bugs - Fix PSM/PSM2 support for singleton operations - Ensure MPI transports continue to progress during RTE barriers - Update HWLOC to 1.9.1 end-of-series - Fix a bug in the Java command line parser when the -Djava.library.path options was given by the user - Update the MTL/OFI provider selection behavior - Add support for clock_gettime on Linux. - Correctly detect and configure for Solaris Studio 12.5 beta compilers - Correctly compute #slots when -host is used for MPMD case - Fix a bug in the hcoll collectives due to an uninitialized field - Do not set a binding policy when oversubscribing a node - Fix hang in intercommunicator operations when oversubscribed - Speed up process termination during MPI_Abort - Disable backtrace support by default in the PSM/PSM2 libraries to prevent unintentional conflicting behavior. 1.10.2: 26 Jan 2016 ------------------- ********************************************************************** * OSHMEM is now 1.2 compliant ********************************************************************** - Fix NBC_Copy for legitimate zero-size messages - Fix multiple bugs in OSHMEM - Correctly handle mpirun --host <user>@<ip-address> - Centralize two MCA params to avoid duplication between OMPI and OSHMEM layers: opal_abort_delay and opal_abort_print_stack - Add support for Fujitsu compilers - Add UCX support for OMPI and OSHMEM - Correctly handle oversubscription when not given directives to permit it. Thanks to @ammore1 for reporting it - Fix rpm spec file to not include the /usr directory - Add Intel HFI1 default parameters for the openib BTL - Resolve symbol conflicts in the PSM2 library - Add ability to empty the rgpusm cache when full if requested - Fix another libtool bug when -L requires a space between it and the path. Thanks to Eric Schnetter for the patch. - Add support for OSHMEM v1.2 APIs - Improve efficiency of oshmem_preconnect_all algorithm - Fix bug in buffered sends support - Fix double free in edge case of mpirun. Thanks to @jsharpe for the patch - Multiple one-sided support fixes - Fix integer overflow in the tuned "reduce" collective when using buffers larger than INT_MAX in size - Fix parse of user environment variables in mpirun. Thanks to Stefano Garzarella for the patch - Performance improvements in PSM2 support - Fix NBS iBarrier for inter-communicators - Fix bug in vader BTL during finalize - Improved configure support for Fortran compilers - Fix rank_file mapper to support default --slot-set. Thanks to Matt Thompson for reporting it - Update MPI_Testsome man page. Thanks to Eric Schnetter for the suggestion - Fix missing resize of the returned type for subarray and darray types. Thanks to Keith Bennett and Dan Garmann for reporting it - Fix Java support on OSX 10.11. Thanks to Alexander Daryin for reporting the problem - Fix some compilation issues on Solaris 11.2. Thanks to Paul Hargrove for his continued help in such areas
Diffstat (limited to 'parallel')
-rw-r--r--parallel/openmpi/Makefile7
-rw-r--r--parallel/openmpi/distinfo18
-rw-r--r--parallel/openmpi/patches/patch-ai12
-rw-r--r--parallel/openmpi/patches/patch-aj18
-rw-r--r--parallel/openmpi/patches/patch-ak18
-rw-r--r--parallel/openmpi/patches/patch-configure72
6 files changed, 93 insertions, 52 deletions
diff --git a/parallel/openmpi/Makefile b/parallel/openmpi/Makefile
index 135f9501dcb..e0f6c3dfc4d 100644
--- a/parallel/openmpi/Makefile
+++ b/parallel/openmpi/Makefile
@@ -1,14 +1,13 @@
-# $NetBSD: Makefile,v 1.35 2016/07/09 06:38:48 wiz Exp $
+# $NetBSD: Makefile,v 1.36 2016/10/23 14:02:28 asau Exp $
-DISTNAME= openmpi-1.10.1
-PKGREVISION= 2
+DISTNAME= openmpi-1.10.4
CATEGORIES= parallel
MASTER_SITES= http://www.open-mpi.org/software/ompi/v1.10/downloads/
EXTRACT_SUFX= .tar.bz2
MAINTAINER= asau@inbox.ru
HOMEPAGE= http://www.open-mpi.org/
-COMMENT= Open source MPI-2 implementation
+COMMENT= Open source MPI-3.1 implementation
GNU_CONFIGURE= yes
USE_LANGUAGES= c c++ fortran77
diff --git a/parallel/openmpi/distinfo b/parallel/openmpi/distinfo
index 7705751c48e..6974e914c82 100644
--- a/parallel/openmpi/distinfo
+++ b/parallel/openmpi/distinfo
@@ -1,13 +1,13 @@
-$NetBSD: distinfo,v 1.17 2016/02/28 19:47:41 joerg Exp $
+$NetBSD: distinfo,v 1.18 2016/10/23 14:02:28 asau Exp $
-SHA1 (openmpi-1.10.1.tar.bz2) = caf6885f323a38b9c106a7815711313843409478
-RMD160 (openmpi-1.10.1.tar.bz2) = 70de0da1f31793333b51eda328a18c01c4ffa3c0
-SHA512 (openmpi-1.10.1.tar.bz2) = 2ebdb6ca29d937bdada25d56b162cddceeed5256a4971b990ac8093e31de931473eb3aff3d18168d2c407b38ec0250b508d0b393ec677288adedb9b5156eaf15
-Size (openmpi-1.10.1.tar.bz2) = 13210778 bytes
+SHA1 (openmpi-1.10.4.tar.bz2) = 1676a7da6cc8cde1d46f6296f38d575249b46cd9
+RMD160 (openmpi-1.10.4.tar.bz2) = cea15b9fe8852805a5f8c1591b31907d996587c7
+SHA512 (openmpi-1.10.4.tar.bz2) = 58bcdc48a4d539f2656480751a9d8129597a0460f7b6ecc6f4d0094703c5f1a3f560eaf80b819d902dee91a77a0d21994f6e42728305969647d3170beefe39df
+Size (openmpi-1.10.4.tar.bz2) = 13430203 bytes
SHA1 (patch-aa) = 6fa20775c6e2abae7c9a2ae858dbb941652beab8
-SHA1 (patch-ai) = 5ddce5ee190ac7bf6964176e23c0a6e624c8c1dd
-SHA1 (patch-aj) = 547fa12b56bd5fe4c4b58d3558d78773bd9dc5c2
-SHA1 (patch-ak) = f79e69fc02510de8da3834729f471799e175bb9c
+SHA1 (patch-ai) = 33667fb853caef7ae9a22c7f2e6a016929eb1a13
+SHA1 (patch-aj) = ec79dc2137107d1253e47811c3ea7d00ff988b06
+SHA1 (patch-ak) = fce9064c50f62334ebc30c8488dbf9cc7500a634
SHA1 (patch-config_opal__setup__wrappers.m4) = c3fe3cb5ff7cedcb5c847f25eea129d4299dd5d2
-SHA1 (patch-configure) = 8717730bd4958fff225d64f34d10dc70a1bc2d92
+SHA1 (patch-configure) = 10b38cc45614258e236b70057c963a0615032e93
SHA1 (patch-ompi_mpi_java_java_Makefile.in) = bd61f02f56e03af9799d2ba86d66c1ded35f62f4
diff --git a/parallel/openmpi/patches/patch-ai b/parallel/openmpi/patches/patch-ai
index edcead76388..34b3c66ea90 100644
--- a/parallel/openmpi/patches/patch-ai
+++ b/parallel/openmpi/patches/patch-ai
@@ -1,16 +1,16 @@
-$NetBSD: patch-ai,v 1.5 2015/12/12 22:41:19 asau Exp $
+$NetBSD: patch-ai,v 1.6 2016/10/23 14:02:28 asau Exp $
---- orte/etc/Makefile.in.orig 2015-06-17 19:57:45.000000000 +0000
+--- orte/etc/Makefile.in.orig 2016-09-02 01:30:19.000000000 +0000
+++ orte/etc/Makefile.in
-@@ -1451,6 +1451,7 @@ spml_ikrit_LDFLAGS = @spml_ikrit_LDFLAGS
- spml_ikrit_LIBS = @spml_ikrit_LIBS@
+@@ -1515,6 +1515,7 @@ spml_ucx_LDFLAGS = @spml_ucx_LDFLAGS@
+ spml_ucx_LIBS = @spml_ucx_LIBS@
srcdir = @srcdir@
sysconfdir = @sysconfdir@
+sysconfexampledir = $(pkgdatadir)/examples
target = @target@
target_alias = @target_alias@
target_cpu = @target_cpu@
-@@ -1667,19 +1668,19 @@ uninstall-am: uninstall-local
+@@ -1731,19 +1732,19 @@ uninstall-am: uninstall-local
# details why the mkdir is in install-data-local.
install-data-local:
@@ -35,7 +35,7 @@ $NetBSD: patch-ai,v 1.5 2015/12/12 22:41:19 asau Exp $
fi; \
done
-@@ -1690,11 +1691,11 @@ install-data-local:
+@@ -1754,11 +1755,11 @@ install-data-local:
uninstall-local:
@ p="$(orte_config_files)"; \
for file in $$p; do \
diff --git a/parallel/openmpi/patches/patch-aj b/parallel/openmpi/patches/patch-aj
index 7769f2e0fed..dcdf22e4426 100644
--- a/parallel/openmpi/patches/patch-aj
+++ b/parallel/openmpi/patches/patch-aj
@@ -1,18 +1,16 @@
-$NetBSD: patch-aj,v 1.4 2015/12/12 22:41:19 asau Exp $
+$NetBSD: patch-aj,v 1.5 2016/10/23 14:02:28 asau Exp $
-Install configuration files into example directory.
-
---- opal/etc/Makefile.in.orig 2013-01-15 14:43:13.000000000 +0100
-+++ opal/etc/Makefile.in 2013-01-24 12:34:41.090709828 +0100
-@@ -51,6 +51,7 @@
- test $$am__dry = yes; \
- }
+--- opal/etc/Makefile.in.orig 2016-09-02 01:30:16.000000000 +0000
++++ opal/etc/Makefile.in
+@@ -89,6 +89,7 @@ am__make_running_with_option = \
+ am__make_dryrun = (target_option=n; $(am__make_running_with_option))
+ am__make_keepgoing = (target_option=k; $(am__make_running_with_option))
pkgdatadir = $(datadir)/@PACKAGE@
+sysconfexampledir = $(pkgdatadir)/examples
pkgincludedir = $(includedir)/@PACKAGE@
pkglibdir = $(libdir)/@PACKAGE@
pkglibexecdir = $(libexecdir)/@PACKAGE@
-@@ -1535,24 +1536,24 @@
+@@ -1730,24 +1731,24 @@ uninstall-am: uninstall-local
# details why the mkdir is in install-data-local.
install-data-local:
@@ -44,7 +42,7 @@ Install configuration files into example directory.
fi; \
done \
fi;
-@@ -1564,11 +1565,11 @@
+@@ -1759,11 +1760,11 @@ install-data-local:
uninstall-local:
@ p="$(opal_config_files)"; \
for file in $$p; do \
diff --git a/parallel/openmpi/patches/patch-ak b/parallel/openmpi/patches/patch-ak
index 4ff7f773e8b..7387adac0f3 100644
--- a/parallel/openmpi/patches/patch-ak
+++ b/parallel/openmpi/patches/patch-ak
@@ -1,18 +1,16 @@
-$NetBSD: patch-ak,v 1.4 2015/12/12 22:41:19 asau Exp $
+$NetBSD: patch-ak,v 1.5 2016/10/23 14:02:28 asau Exp $
-Install configuration files into example directory.
-
---- ompi/etc/Makefile.in.orig 2013-01-15 14:41:30.000000000 +0100
-+++ ompi/etc/Makefile.in 2013-01-24 12:36:01.150707935 +0100
-@@ -51,6 +51,7 @@
- test $$am__dry = yes; \
- }
+--- ompi/etc/Makefile.in.orig 2016-09-02 01:30:09.000000000 +0000
++++ ompi/etc/Makefile.in
+@@ -89,6 +89,7 @@ am__make_running_with_option = \
+ am__make_dryrun = (target_option=n; $(am__make_running_with_option))
+ am__make_keepgoing = (target_option=k; $(am__make_running_with_option))
pkgdatadir = $(datadir)/@PACKAGE@
+sysconfexampledir = $(pkgdatadir)/examples
pkgincludedir = $(includedir)/@PACKAGE@
pkglibdir = $(libdir)/@PACKAGE@
pkglibexecdir = $(libexecdir)/@PACKAGE@
-@@ -1536,19 +1537,19 @@
+@@ -1731,19 +1732,19 @@ uninstall-am: uninstall-local
# details why the mkdir is in install-data-local.
install-data-local:
@@ -37,7 +35,7 @@ Install configuration files into example directory.
fi; \
done
-@@ -1559,11 +1560,11 @@
+@@ -1754,11 +1755,11 @@ install-data-local:
uninstall-local:
@ p="$(ompi_config_files)"; \
for file in $$p; do \
diff --git a/parallel/openmpi/patches/patch-configure b/parallel/openmpi/patches/patch-configure
index 1041c9cc7d6..596039e0b62 100644
--- a/parallel/openmpi/patches/patch-configure
+++ b/parallel/openmpi/patches/patch-configure
@@ -1,16 +1,8 @@
-$NetBSD: patch-configure,v 1.1 2016/02/28 19:47:41 joerg Exp $
+$NetBSD: patch-configure,v 1.2 2016/10/23 14:02:28 asau Exp $
---- configure.orig 2016-02-24 13:44:02.424420285 +0000
+--- configure.orig 2016-09-02 01:30:27.000000000 +0000
+++ configure
-@@ -307902,6 +307902,7 @@ fi
-
-
- # Unwind the index
-+
- ompi_scope_index=`expr $ompi_scope_index - 1`
- ompi_scope_test=`expr $ompi_scope_index \> 0`
- if test "$ompi_scope_test" = "0"; then
-@@ -307922,112 +307923,6 @@ $as_echo "$as_me: WARNING: This usually
+@@ -314733,166 +314734,6 @@ $as_echo "$as_me: WARNING: This usually
done
@@ -28,7 +20,7 @@ $NetBSD: patch-configure,v 1.1 2016/02/28 19:47:41 joerg Exp $
- # This is a simple sanity check to ensure we're not already
- # overwriting pre-existing variables (that have a non-empty
- # value). It's not a perfect check, but at least it's something.
-- for ompi_var in LDFLAGS_save; do
+- for ompi_var in LDFLAGS_save rpath_script rpath_outfile wl_fc; do
- ompi_str="ompi_str=\"\$$ompi_var\""
- eval $ompi_str
-
@@ -47,7 +39,7 @@ $NetBSD: patch-configure,v 1.1 2016/02/28 19:47:41 joerg Exp $
-
- # Ok, we passed the simple sanity check. Save all these names so
- # that we can unset them at the end of the scope.
-- ompi_str="ompi_scope_$ompi_scope_index=\"LDFLAGS_save\""
+- ompi_str="ompi_scope_$ompi_scope_index=\"LDFLAGS_save rpath_script rpath_outfile wl_fc\""
- eval $ompi_str
- unset ompi_str
-
@@ -95,6 +87,60 @@ $NetBSD: patch-configure,v 1.1 2016/02/28 19:47:41 joerg Exp $
-ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
-ac_compiler_gnu=$ac_cv_c_compiler_gnu
-
+- # Output goes into globally-visible $rpath_args. Run this in a
+- # sub-process so that we don't pollute the current process
+- # environment.
+- rpath_script=conftest.$$.sh
+- rpath_outfile=conftest.$$.out
+- rm -f $rpath_script $rpath_outfile
+- cat > $rpath_script <<EOF
+-#!/bin/sh
+-
+-# Slurp in the libtool config into my environment
+-
+-# Apparently, "libtoool --config" calls "exit", so we can't source it
+-# (because if script A sources script B, and B calls "exit", then both
+-# B and A will exit). Instead, we have to send the output to a file
+-# and then source that.
+-$OMPI_TOP_BUILDDIR/libtool --tag=FC --config > $rpath_outfile
+-
+-chmod +x $rpath_outfile
+-. ./$rpath_outfile
+-rm -f $rpath_outfile
+-
+-wl="\`eval echo \$wl\`"
+-echo \$wl
+-
+-# Done
+-exit 0
+-EOF
+- chmod +x $rpath_script
+- wl_fc=`./$rpath_script`
+- rm -f $rpath_script
+-
+- LDFLAGS="$LDFLAGS_save ${wl_fc}--enable-new-dtags"
+- ac_ext=${ac_fc_srcext-f}
+-ac_compile='$FC -c $FCFLAGS $ac_fcflags_srcext conftest.$ac_ext >&5'
+-ac_link='$FC -o conftest$ac_exeext $FCFLAGS $LDFLAGS $ac_fcflags_srcext conftest.$ac_ext $LIBS >&5'
+-ac_compiler_gnu=$ac_cv_fc_compiler_gnu
+-
+- cat > conftest.$ac_ext <<_ACEOF
+-program test
+-end program
+-_ACEOF
+-if ac_fn_fc_try_link "$LINENO"; then :
+- runpath_fc_args="${wl_fc}--enable-new-dtags"
+-else
+- runpath_fc_args=""
+-fi
+-rm -f core conftest.err conftest.$ac_objext \
+- conftest$ac_exeext conftest.$ac_ext
+- ac_ext=c
+-ac_cpp='$CPP $CPPFLAGS'
+-ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+-ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+-ac_compiler_gnu=$ac_cv_c_compiler_gnu
+-
- LDFLAGS=$LDFLAGS_save
-
-