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[pkgsrc/trunk]: pkgsrc/parallel/openmpi Update to OpenMPI 1.6.2
details: https://anonhg.NetBSD.org/pkgsrc/rev/de2744522542
branches: trunk
changeset: 610091:de2744522542
user: asau <asau%pkgsrc.org@localhost>
date: Wed Oct 17 23:27:34 2012 +0000
description:
Update to OpenMPI 1.6.2
Don't build VampirTrace anymore, it will be introduced as separate package.
Changes in v1.6.2 as compared to v1.6.1:
- Fix issue with MX MTL. Thanks to Doug Eadline for raising the issue.
- Fix singleton MPI_COMM_SPAWN when the result job spans multiple nodes.
- Fix MXM hang, and update for latest version of MXM.
- Update to support Mellanox FCA 2.5.
- Fix startup hang for large jobs.
- Ensure MPI_TESTANY / MPI_WAITANY properly set the empty status when
count==0.
- Fix MPI_CART_SUB behavior of not copying periods to the new
communicator properly. Thanks to John Craske for the bug report.
- Add btl_openib_abort_not_enough_reg_mem MCA parameter to cause Open
MPI to abort MPI jobs if there is not enough registered memory
available on the system (vs. just printing a warning). Thanks to
Brock Palen for raising the issue.
- Minor fix to Fortran MPI_INFO_GET: only copy a value back to the
user's buffer if the flag is .TRUE.
- Fix VampirTrace compilation issue with the PGI compiler suite.
diffstat:
parallel/openmpi/Makefile | 8 +-
parallel/openmpi/PLIST | 7 +-
parallel/openmpi/PLIST.vt | 105 ----------
parallel/openmpi/distinfo | 16 +-
parallel/openmpi/options.mk | 20 +-
parallel/openmpi/patches/patch-ai | 40 ++-
parallel/openmpi/patches/patch-aj | 42 ++-
parallel/openmpi/patches/patch-ak | 38 ++-
parallel/openmpi/patches/patch-ompi_contrib_vt_vt_etc_Makefile.in | 50 ----
parallel/openmpi/patches/patch-ompi_contrib_vt_vt_extlib_otf_tools_otfprofile_clustering.cpp | 14 -
10 files changed, 99 insertions(+), 241 deletions(-)
diffs (truncated from 525 to 300 lines):
diff -r 61e1eecc8b4e -r de2744522542 parallel/openmpi/Makefile
--- a/parallel/openmpi/Makefile Wed Oct 17 22:25:02 2012 +0000
+++ b/parallel/openmpi/Makefile Wed Oct 17 23:27:34 2012 +0000
@@ -1,7 +1,6 @@
-# $NetBSD: Makefile,v 1.17 2012/10/03 21:57:14 wiz Exp $
+# $NetBSD: Makefile,v 1.18 2012/10/17 23:27:34 asau Exp $
-DISTNAME= openmpi-1.6
-PKGREVISION= 1
+DISTNAME= openmpi-1.6.2
CATEGORIES= parallel
MASTER_SITES= http://www.open-mpi.org/software/ompi/v1.6/downloads/
EXTRACT_SUFX= .tar.bz2
@@ -26,6 +25,7 @@
CONFIGURE_ARGS+= --disable-mpi-f90
CONFIGURE_ARGS+= --without-sge
CONFIGURE_ARGS+= --without-slurm
+CONFIGURE_ARGS+= --enable-contrib-no-build=vt # in separate package
CONFIGURE_ARGS+= --with-libltdl=external # use our libltdl
CONFIGURE_ARGS+= --with-hwloc=$(BUILDLINK_PREFIX.hwloc:Q) #external
CONFIGURE_ARGS+= --with-wrapper-ldflags="-L${PREFIX}/lib ${LINKER_RPATH_FLAG}${PREFIX}/lib"
@@ -51,4 +51,6 @@
LIBLTDL_CONVENIENCE_SUBDIR= opal/libltdl
.include "../../devel/libltdl/convenience.mk" # for "test" target to work
.include "../../devel/libltdl/buildlink3.mk"
+.include "../../parallel/hwloc/buildlink3.mk"
+.include "../../textproc/libxml2/buildlink3.mk" # should be reexported by hwloc?
.include "../../mk/bsd.pkg.mk"
diff -r 61e1eecc8b4e -r de2744522542 parallel/openmpi/PLIST
--- a/parallel/openmpi/PLIST Wed Oct 17 22:25:02 2012 +0000
+++ b/parallel/openmpi/PLIST Wed Oct 17 23:27:34 2012 +0000
@@ -1,4 +1,4 @@
-@comment $NetBSD: PLIST,v 1.9 2012/06/12 23:36:31 asau Exp $
+@comment $NetBSD: PLIST,v 1.10 2012/10/17 23:27:34 asau Exp $
bin/mpiCC
bin/mpic++
bin/mpicc
@@ -99,7 +99,6 @@
lib/openmpi/mca_filem_rsh.la
lib/openmpi/mca_grpcomm_bad.la
lib/openmpi/mca_grpcomm_basic.la
-lib/openmpi/mca_grpcomm_hier.la
lib/openmpi/mca_io_romio.la
lib/openmpi/mca_iof_hnp.la
lib/openmpi/mca_iof_orted.la
@@ -131,8 +130,6 @@
lib/openmpi/mca_rmaps_round_robin.la
lib/openmpi/mca_rmaps_seq.la
lib/openmpi/mca_rmaps_topo.la
-lib/openmpi/mca_rmcast_tcp.la
-lib/openmpi/mca_rmcast_udp.la
lib/openmpi/mca_rml_oob.la
lib/openmpi/mca_routed_binomial.la
lib/openmpi/mca_routed_cm.la
@@ -543,7 +540,6 @@
share/openmpi/help-orte-rmaps-rr.txt
share/openmpi/help-orte-rmaps-seq.txt
share/openmpi/help-orte-rmaps-topo.txt
-share/openmpi/help-orte-rmcast-udp.txt
share/openmpi/help-orte-runtime.txt
share/openmpi/help-orte-snapc-base.txt
share/openmpi/help-orte-top.txt
@@ -554,7 +550,6 @@
share/openmpi/help-ras-base.txt
share/openmpi/help-regex.txt
share/openmpi/help-rmaps_rank_file.txt
-share/openmpi/help-rmcast-base.txt
share/openmpi/mpiCC-wrapper-data.txt
share/openmpi/mpic++-wrapper-data.txt
share/openmpi/mpicc-wrapper-data.txt
diff -r 61e1eecc8b4e -r de2744522542 parallel/openmpi/PLIST.vt
--- a/parallel/openmpi/PLIST.vt Wed Oct 17 22:25:02 2012 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,105 +0,0 @@
-@comment $NetBSD: PLIST.vt,v 1.6 2012/06/12 23:36:31 asau Exp $
-bin/mpiCC-vt
-bin/mpic++-vt
-bin/mpicc-vt
-bin/mpicxx-vt
-bin/mpif77-vt
-bin/mpif90-vt
-bin/otfaux
-bin/otfcompress
-bin/otfconfig
-bin/otfdecompress
-bin/otfdump
-bin/otfinfo
-bin/otfmerge
-bin/otfmerge-mpi
-bin/otfprofile
-bin/otfprofile-mpi
-bin/otfshrink
-bin/vtCC
-bin/vtc++
-bin/vtcc
-bin/vtcxx
-bin/vtf77
-bin/vtf90
-bin/vtfilter
-bin/vtfilter-mpi
-bin/vtfiltergen
-bin/vtfiltergen-mpi
-bin/vtrun
-bin/vtunify
-bin/vtunify-mpi
-bin/vtwrapper
-include/vampirtrace/OTFAUX_MsgMatching.h
-include/vampirtrace/OTFAUX_Thumbnail.h
-include/vampirtrace/OTF_CopyHandler_stream.h
-include/vampirtrace/OTF_CopyHandler.h
-include/vampirtrace/OTF_Definitions.h
-include/vampirtrace/OTF_Errno.h
-include/vampirtrace/OTF_File.h
-include/vampirtrace/OTF_FileManager.h
-include/vampirtrace/OTF_Filenames.h
-include/vampirtrace/OTF_HandlerArray.h
-include/vampirtrace/OTF_KeyValue.h
-include/vampirtrace/OTF_MasterControl.h
-include/vampirtrace/OTF_RBuffer.h
-include/vampirtrace/OTF_RStream.h
-include/vampirtrace/OTF_Reader.h
-include/vampirtrace/OTF_Version.h
-include/vampirtrace/OTF_WBuffer.h
-include/vampirtrace/OTF_WStream.h
-include/vampirtrace/OTF_Writer.h
-include/vampirtrace/OTF_inttypes.h
-include/vampirtrace/OTF_inttypes_unix.h
-include/vampirtrace/otfaux.h
-include/vampirtrace/otf.h
-include/vampirtrace/vt_inttypes.h
-include/vampirtrace/vt_user.h
-include/vampirtrace/vt_user.inc
-include/vampirtrace/vt_user_comment.h
-include/vampirtrace/vt_user_comment.inc
-include/vampirtrace/vt_user_control.h
-include/vampirtrace/vt_user_control.inc
-include/vampirtrace/vt_user_count.h
-include/vampirtrace/vt_user_count.inc
-include/vampirtrace/vt_user_marker.h
-include/vampirtrace/vt_user_marker.inc
-include/vampirtrace/vt_user_message.h
-include/vampirtrace/vt_user_message.inc
-include/vampirtrace/vt_user_region.h
-include/vampirtrace/vt_user_region.inc
-include/vampirtrace/vt_wrap_pthread.h
-lib/libotfaux.la
-lib/libotf.la
-lib/libvt-hyb.la
-lib/libvt-mpi.la
-lib/libvt-mpi-unify.la
-lib/libvt-mt.la
-lib/libvt.la
-share/openmpi/mpiCC-vt-wrapper-data.txt
-share/openmpi/mpic++-vt-wrapper-data.txt
-share/openmpi/mpicc-vt-wrapper-data.txt
-share/openmpi/mpicxx-vt-wrapper-data.txt
-share/openmpi/mpif77-vt-wrapper-data.txt
-share/openmpi/mpif90-vt-wrapper-data.txt
-share/vampirtrace/FILTER.SPEC
-share/vampirtrace/GROUPS.SPEC
-share/vampirtrace/METRICS.SPEC
-share/vampirtrace/VampirTrace/examples/vt-java-default-filter.spec
-share/vampirtrace/doc/ChangeLog
-share/vampirtrace/doc/LICENSE
-share/vampirtrace/doc/UserManual.html
-share/vampirtrace/doc/UserManual.pdf
-share/vampirtrace/doc/otf/ChangeLog
-share/vampirtrace/doc/otf/LICENSE
-share/vampirtrace/doc/otf/otfprofile.pdf
-share/vampirtrace/doc/otf/otfprofile_clustering.pdf
-share/vampirtrace/doc/otf/otftools.pdf
-share/vampirtrace/doc/otf/specification.pdf
-share/vampirtrace/libtool
-share/vampirtrace/vtCC-wrapper-data.txt
-share/vampirtrace/vtc++-wrapper-data.txt
-share/vampirtrace/vtcc-wrapper-data.txt
-share/vampirtrace/vtcxx-wrapper-data.txt
-share/vampirtrace/vtf77-wrapper-data.txt
-share/vampirtrace/vtf90-wrapper-data.txt
diff -r 61e1eecc8b4e -r de2744522542 parallel/openmpi/distinfo
--- a/parallel/openmpi/distinfo Wed Oct 17 22:25:02 2012 +0000
+++ b/parallel/openmpi/distinfo Wed Oct 17 23:27:34 2012 +0000
@@ -1,11 +1,9 @@
-$NetBSD: distinfo,v 1.10 2012/06/12 23:36:31 asau Exp $
+$NetBSD: distinfo,v 1.11 2012/10/17 23:27:34 asau Exp $
-SHA1 (openmpi-1.6.tar.bz2) = 8b81eea712bb8f8120468003b5f29baecedf2367
-RMD160 (openmpi-1.6.tar.bz2) = 3a9a81a5ec61dcd5e0cc5e5bb6bfb0f9c2ad0c84
-Size (openmpi-1.6.tar.bz2) = 10034857 bytes
+SHA1 (openmpi-1.6.2.tar.bz2) = 694fd3bac911cdb22f77175884d819b6fea871df
+RMD160 (openmpi-1.6.2.tar.bz2) = 949539fc255592f51df6aac505e7474a92464703
+Size (openmpi-1.6.2.tar.bz2) = 10198489 bytes
SHA1 (patch-aa) = 6fa20775c6e2abae7c9a2ae858dbb941652beab8
-SHA1 (patch-ai) = 650906ec3701cc7bac6b7f916c87506ccb885341
-SHA1 (patch-aj) = dc85e6c9eb6db0eb40bb896a11c223afeda63c2f
-SHA1 (patch-ak) = f6ea4220d51dd0c84ac2067d695c265f00904a0f
-SHA1 (patch-ompi_contrib_vt_vt_etc_Makefile.in) = 913d3adbf073a1c0eec1fb499407c69cc0a2c057
-SHA1 (patch-ompi_contrib_vt_vt_extlib_otf_tools_otfprofile_clustering.cpp) = b2baee86e9787fec7d16073cbb63ece4e83c2333
+SHA1 (patch-ai) = 95d699d343a7df8d768e78a235036c842c24e2d2
+SHA1 (patch-aj) = 1408114e5fc07d5b0df3e9368b6d2c5b85f85991
+SHA1 (patch-ak) = d42271d1c6adeb5e9425cc6a183f5308c74dea59
diff -r 61e1eecc8b4e -r de2744522542 parallel/openmpi/options.mk
--- a/parallel/openmpi/options.mk Wed Oct 17 22:25:02 2012 +0000
+++ b/parallel/openmpi/options.mk Wed Oct 17 23:27:34 2012 +0000
@@ -1,26 +1,10 @@
-# $NetBSD: options.mk,v 1.3 2012/06/12 23:36:31 asau Exp $
+# $NetBSD: options.mk,v 1.4 2012/10/17 23:27:34 asau Exp $
PKG_OPTIONS_VAR= PKG_OPTIONS.openmpi
-PKG_SUPPORTED_OPTIONS= debug openmpi-vampirtrace
-PKG_SUGGESTED_OPTIONS= openmpi-vampirtrace
+PKG_SUPPORTED_OPTIONS= debug
.include "../../mk/bsd.options.mk"
.if !empty(PKG_OPTIONS:Mdebug)
CONFIGURE_ARGS+= --enable-debug
.endif
-
-# Allow coexistance of OpenMPI and libotf by disabling OpenMPI parts:
-.if !empty(PKG_OPTIONS:Mopenmpi-vampirtrace)
-CONFLICTS+= libotf-[0-9]*
-PLIST_SRC+= PLIST.vt
-
-CONF_FILES+= share/vampirtrace/VampirTrace/examples/vt-java-default-filter.spec \
- $(PKG_SYSCONFDIR)/vt-java-default-filter.spec
-
-.include "../../graphics/freetype2/buildlink3.mk"
-.else
-CONFIGURE_ARGS+= --enable-contrib-no-build=vt
-.endif
-
-PLIST_SRC+= PLIST
diff -r 61e1eecc8b4e -r de2744522542 parallel/openmpi/patches/patch-ai
--- a/parallel/openmpi/patches/patch-ai Wed Oct 17 22:25:02 2012 +0000
+++ b/parallel/openmpi/patches/patch-ai Wed Oct 17 23:27:34 2012 +0000
@@ -1,39 +1,55 @@
-$NetBSD: patch-ai,v 1.3 2011/03/23 05:32:29 asau Exp $
+$NetBSD: patch-ai,v 1.4 2012/10/17 23:27:35 asau Exp $
Install configuration files into example directory.
---- orte/etc/Makefile.in.orig 2011-03-09 17:51:05.000000000 +0300
-+++ orte/etc/Makefile.in 2011-03-11 00:11:49.000000000 +0300
-@@ -1051,6 +1051,7 @@
+--- orte/etc/Makefile.in.orig 2012-08-22 14:26:19.000000000 +0000
++++ orte/etc/Makefile.in
+@@ -1085,6 +1085,7 @@ sbindir = @sbindir@
sharedstatedir = @sharedstatedir@
srcdir = @srcdir@
sysconfdir = @sysconfdir@
-+exampledir = $(pkgdatadir)/examples
++sysconfexampledir = $(pkgdatadir)/examples
sysinfo_solaris_CFLAGS = @sysinfo_solaris_CFLAGS@
sysinfo_solaris_CPPFLAGS = @sysinfo_solaris_CPPFLAGS@
sysinfo_solaris_LDFLAGS = @sysinfo_solaris_LDFLAGS@
-@@ -1264,19 +1265,19 @@
+@@ -1303,19 +1304,19 @@ uninstall-am: uninstall-local
# details why the mkdir is in install-data-local.
install-data-local:
-- $(mkdir_p) $(DESTDIR)$(sysconfdir)
-+ $(mkdir_p) $(DESTDIR)$(exampledir)
+- $(MKDIR_P) $(DESTDIR)$(sysconfdir)
++ $(MKDIR_P) $(DESTDIR)$(sysconfexampledir)
@ p="$(orte_config_files)"; \
for file in $$p; do \
- if test -f $(DESTDIR)$(sysconfdir)/$$file; then \
-+ if test -f $(DESTDIR)$(exampledir)/$$file; then \
++ if test -f $(DESTDIR)$(sysconfexampledir)/$$file; then \
echo "******************************* WARNING ************************************"; \
echo "*** Not installing new $$file over existing file in:"; \
- echo "*** $(DESTDIR)$(sysconfdir)/$$file"; \
-+ echo "*** $(DESTDIR)$(exampledir)/$$file"; \
++ echo "*** $(DESTDIR)$(sysconfexampledir)/$$file"; \
echo "******************************* WARNING ************************************"; \
else \
if test -f "$$file"; then d=; else d="$(srcdir)/"; fi; \
f="`echo $$file | sed -e 's|^.*/||'`"; \
- echo " $(INSTALL_DATA) $$d$$file $(DESTDIR)$(sysconfdir)/$$f"; \
- $(INSTALL_DATA) $$d$$file $(DESTDIR)$(sysconfdir)/$$f; \
-+ echo " $(INSTALL_DATA) $$d$$file $(DESTDIR)$(exampledir)/$$f"; \
-+ $(INSTALL_DATA) $$d$$file $(DESTDIR)$(exampledir)/$$f; \
++ echo " $(INSTALL_DATA) $$d$$file $(DESTDIR)$(sysconfexampledir)/$$f"; \
++ $(INSTALL_DATA) $$d$$file $(DESTDIR)$(sysconfexampledir)/$$f; \
fi; \
done
+@@ -1326,11 +1327,11 @@ install-data-local:
+ uninstall-local:
+ @ p="$(orte_config_files)"; \
+ for file in $$p; do \
+- if test -f "$(DESTDIR)$(sysconfdir)/$$file"; then \
++ if test -f "$(DESTDIR)$(sysconfexampledir)/$$file"; then \
+ if test -f "$$file"; then d=; else d="$(srcdir)/"; fi; \
+- if diff "$(DESTDIR)$(sysconfdir)/$$file" "$$d$$file" > /dev/null 2>&1 ; then \
+- echo "rm -f $(DESTDIR)$(sysconfdir)/$$file" ; \
+- rm -f "$(DESTDIR)$(sysconfdir)/$$file" ; \
++ if diff "$(DESTDIR)$(sysconfexampledir)/$$file" "$$d$$file" > /dev/null 2>&1 ; then \
++ echo "rm -f $(DESTDIR)$(sysconfexampledir)/$$file" ; \
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