Update to OpenMPI 1.6

Disable automatic detection of SGE and SLURM to avoid PLIST divergence.


Changes in OpenMPI 1.6

v1.6 is a major release; it effectively deprecates both the v1.4.x
and v1.5.x series, and replaces v1.4.x as the current "super stable" series.
A forthcoming v1.7 series will become the new "feature" series.

*All users* -- including production users and downstream providers --
are encouraged to upgrade to v1.6.

Note that v1.6 is ABI compatible with the entire v1.5.x series,
but is not ABI compatible with the v1.4.x series.
See http://www.open-mpi.org/software/ompi/versions/ for a description
of Open MPI's release methodology.


Here is a list of changes in v1.6 as compared to v1.5.5:

- Fix some process affinity issues.  When binding a process, Open MPI
  will now bind to all available hyperthreads in a core (or socket,
  depending on the binding options specified).
  --> Note that "mpirun --bind-to-socket ..." does not work on POWER6-
      and POWER7-based systems with some Linux kernel versions.  See
      the FAQ on the Open MPI web site for more information.
- Add support for ARM5 and ARM6 (in addition to the existing ARM7
  support).  Thanks to Evan Clinton for the patch.
- Minor Mellanox MXM fixes.
- Properly detect FDR10, FDR, and EDR OpenFabrics devices.
- Minor fixes to the mpirun(1) and MPI_Comm_create(3) man pages.
- Prevent segv if COMM_SPAWN_MULTIPLE fails.  Thanks to Fujitsu for
  the patch.
- Disable interposed memory management in fakeroot environments.  This
  fixes a problem in some build environments.
- Minor hwloc updates.
- Array versions of MPI_TEST and MPI_WAIT with a count==0 will now
  return immediately with MPI_SUCCESS.  Thanks to Jeremiah Willcock
  for the suggestion.
- Update VampirTrace to v5.12.2.
- Properly handle forwarding stdin to all processes when "mpirun
  --stdin all" is used.
- Workaround XLC assembly bug.
- OS X Tiger (10.3) has not been supported for a while, so forcibly
  abort configure if we detect it.
- Fix segv in the openib BTL when running on SPARC 64 systems.
- Fix some include file ordering issues on some BSD-based platforms.
  Thanks to Paul Hargove for this (and many, many other) fixes.
- Properly handle .FALSE. return parameter value to attribute copy
  callback functions.
- Fix a bunch of minor C++ API issues; thanks to Fujitsu for the patch.
- Fixed the default hostfile MCA parameter behavior.
- Per the MPI spec, ensure not to touch the port_name parameter to
  MPI_CLOSE_PORT (it's an IN parameter).

7 files changed, 89 insertions, 33 deletions

diff --git a/parallel/openmpi/Makefile b/parallel/openmpi/Makefile
index 5114f9b57dc..a1b64e851ed 100644
--- a/parallel/openmpi/Makefile
+++ b/parallel/openmpi/Makefile
@@ -1,8 +1,8 @@
-# $NetBSD: Makefile,v 1.14 2012/05/28 18:38:17 asau Exp $
+# $NetBSD: Makefile,v 1.15 2012/06/12 23:36:30 asau Exp $
 
-DISTNAME=	openmpi-1.5.5
+DISTNAME=	openmpi-1.6
 CATEGORIES=	parallel
-MASTER_SITES=	http://www.open-mpi.org/software/ompi/v1.5/downloads/
+MASTER_SITES=	http://www.open-mpi.org/software/ompi/v1.6/downloads/
 EXTRACT_SUFX=	.tar.bz2
 
 MAINTAINER=	asau@inbox.ru
@@ -25,7 +25,10 @@ SHLIBTOOL_OVERRIDE=	${WRKSRC}/config/libtool.m4 \
 			${WRKSRC}/opal/libltdl/m4/libtool.m4
 
 CONFIGURE_ARGS+=	--disable-mpi-f90
+CONFIGURE_ARGS+=	--without-sge
+CONFIGURE_ARGS+=	--without-slurm
 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"
 CONFIGURE_ENV+=		ompi_cv_f77_have_INTEGERp8=no	# no "INTEGER*8"??
 CONFIGURE_ARGS+=	OPAL_HAVE_LTDL_ADVISE=0
@@ -35,13 +38,6 @@ BUILDLINK_TRANSFORM=	rm:-fopenmp
 
 USE_TOOLS+=		perl:run
 
-PLIST_VARS+=		vtlwraph
-.include "../../mk/bsd.prefs.mk"
-.if ${OPSYS} == "DragonFly"
-PLIST.vtlwraph= 	yes
-.endif
-
-
 .include "options.mk"
 
 TEST_TARGET=	check
@@ -53,5 +49,7 @@ TEST_TARGET=	check
 # pre-configure:	replace-interpreter
 # 	cd $(WRKSRC) && $(BASH) autogen.sh
 
+LIBLTDL_CONVENIENCE_SUBDIR=	opal/libltdl
+.include "../../devel/libltdl/convenience.mk" # for "test" target to work
 .include "../../devel/libltdl/buildlink3.mk"
 .include "../../mk/bsd.pkg.mk"
diff --git a/parallel/openmpi/PLIST b/parallel/openmpi/PLIST
index 719d9377f2c..bbf800ddf77 100644
--- a/parallel/openmpi/PLIST
+++ b/parallel/openmpi/PLIST
@@ -1,4 +1,4 @@
-@comment $NetBSD: PLIST,v 1.8 2012/05/28 18:38:17 asau Exp $
+@comment $NetBSD: PLIST,v 1.9 2012/06/12 23:36:31 asau Exp $
 bin/mpiCC
 bin/mpic++
 bin/mpicc
@@ -95,8 +95,6 @@ lib/openmpi/mca_ess_env.la
 lib/openmpi/mca_ess_hnp.la
 lib/openmpi/mca_ess_singleton.la
 lib/openmpi/mca_ess_slave.la
-lib/openmpi/mca_ess_slurm.la
-lib/openmpi/mca_ess_slurmd.la
 lib/openmpi/mca_ess_tool.la
 lib/openmpi/mca_filem_rsh.la
 lib/openmpi/mca_grpcomm_bad.la
@@ -119,7 +117,6 @@ lib/openmpi/mca_osc_pt2pt.la
 lib/openmpi/mca_osc_rdma.la
 lib/openmpi/mca_paffinity_hwloc.la
 lib/openmpi/mca_plm_rsh.la
-lib/openmpi/mca_plm_slurm.la
 lib/openmpi/mca_pml_bfo.la
 lib/openmpi/mca_pml_cm.la
 lib/openmpi/mca_pml_csum.la
@@ -127,8 +124,6 @@ lib/openmpi/mca_pml_ob1.la
 lib/openmpi/mca_pml_v.la
 lib/openmpi/mca_pubsub_orte.la
 lib/openmpi/mca_ras_cm.la
-lib/openmpi/mca_ras_gridengine.la
-lib/openmpi/mca_ras_slurm.la
 lib/openmpi/mca_rcache_vma.la
 lib/openmpi/mca_rmaps_load_balance.la
 lib/openmpi/mca_rmaps_rank_file.la
@@ -556,10 +551,7 @@ share/openmpi/help-orted.txt
 share/openmpi/help-orterun.txt
 share/openmpi/help-plm-base.txt
 share/openmpi/help-plm-rsh.txt
-share/openmpi/help-plm-slurm.txt
 share/openmpi/help-ras-base.txt
-share/openmpi/help-ras-gridengine.txt
-share/openmpi/help-ras-slurm.txt
 share/openmpi/help-regex.txt
 share/openmpi/help-rmaps_rank_file.txt
 share/openmpi/help-rmcast-base.txt
diff --git a/parallel/openmpi/PLIST.vt b/parallel/openmpi/PLIST.vt
index 1fe11e856b3..aec58893129 100644
--- a/parallel/openmpi/PLIST.vt
+++ b/parallel/openmpi/PLIST.vt
@@ -1,4 +1,4 @@
-@comment $NetBSD: PLIST.vt,v 1.5 2012/05/28 18:38:18 asau Exp $
+@comment $NetBSD: PLIST.vt,v 1.6 2012/06/12 23:36:31 asau Exp $
 bin/mpiCC-vt
 bin/mpic++-vt
 bin/mpicc-vt
@@ -30,13 +30,10 @@ bin/vtrun
 bin/vtunify
 bin/vtunify-mpi
 bin/vtwrapper
-etc/vt-java-default-filter.spec
-etc/vt-setup-config.dtd
-etc/vt-setup-config.xml
 include/vampirtrace/OTFAUX_MsgMatching.h
 include/vampirtrace/OTFAUX_Thumbnail.h
-include/vampirtrace/OTF_CopyHandler.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
@@ -54,8 +51,8 @@ include/vampirtrace/OTF_WStream.h
 include/vampirtrace/OTF_Writer.h
 include/vampirtrace/OTF_inttypes.h
 include/vampirtrace/OTF_inttypes_unix.h
-include/vampirtrace/otf.h
 include/vampirtrace/otfaux.h
+include/vampirtrace/otf.h
 include/vampirtrace/vt_inttypes.h
 include/vampirtrace/vt_user.h
 include/vampirtrace/vt_user.inc
@@ -72,12 +69,11 @@ include/vampirtrace/vt_user_message.inc
 include/vampirtrace/vt_user_region.h
 include/vampirtrace/vt_user_region.inc
 include/vampirtrace/vt_wrap_pthread.h
-${PLIST.vtlwraph}include/vampirtrace/vt_libwrap.h
-lib/libotf.la
 lib/libotfaux.la
+lib/libotf.la
 lib/libvt-hyb.la
-lib/libvt-mpi-unify.la
 lib/libvt-mpi.la
+lib/libvt-mpi-unify.la
 lib/libvt-mt.la
 lib/libvt.la
 share/openmpi/mpiCC-vt-wrapper-data.txt
@@ -89,6 +85,7 @@ share/openmpi/mpif90-vt-wrapper-data.txt
 share/vampirtrace/FILTER.SPEC
 share/vampirtrace/GROUPS.SPEC
 share/vampirtrace/METRICS.SPEC
+share/vampirtrace/VampirTrace/examples/vt-java-default-filter.spec
 share/vampirtrace/doc/ChangeLog
 share/vampirtrace/doc/LICENSE
 share/vampirtrace/doc/UserManual.html
diff --git a/parallel/openmpi/distinfo b/parallel/openmpi/distinfo
index acd3a6460ee..17d2732cd88 100644
--- a/parallel/openmpi/distinfo
+++ b/parallel/openmpi/distinfo
@@ -1,10 +1,11 @@
-$NetBSD: distinfo,v 1.9 2012/05/28 18:38:18 asau Exp $
+$NetBSD: distinfo,v 1.10 2012/06/12 23:36:31 asau Exp $
 
-SHA1 (openmpi-1.5.5.tar.bz2) = 206e555f6d376443f2342f721d944e67dd1a04ef
-RMD160 (openmpi-1.5.5.tar.bz2) = 6e7648ec0fa553c16b40f886b397d11863039eb2
-Size (openmpi-1.5.5.tar.bz2) = 10055601 bytes
+SHA1 (openmpi-1.6.tar.bz2) = 8b81eea712bb8f8120468003b5f29baecedf2367
+RMD160 (openmpi-1.6.tar.bz2) = 3a9a81a5ec61dcd5e0cc5e5bb6bfb0f9c2ad0c84
+Size (openmpi-1.6.tar.bz2) = 10034857 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
diff --git a/parallel/openmpi/options.mk b/parallel/openmpi/options.mk
index d94c48e0895..05856e4c934 100644
--- a/parallel/openmpi/options.mk
+++ b/parallel/openmpi/options.mk
@@ -1,4 +1,4 @@
-# $NetBSD: options.mk,v 1.2 2010/05/14 20:12:58 asau Exp $
+# $NetBSD: options.mk,v 1.3 2012/06/12 23:36:31 asau Exp $
 
 PKG_OPTIONS_VAR=	PKG_OPTIONS.openmpi
 PKG_SUPPORTED_OPTIONS=	debug openmpi-vampirtrace
@@ -14,6 +14,10 @@ CONFIGURE_ARGS+=	--enable-debug
 .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 \
+			$(PKG_SYSCONFDIR)/vt-java-default-filter.spec
+
 .include "../../graphics/freetype2/buildlink3.mk"
 .else
 CONFIGURE_ARGS+=	--enable-contrib-no-build=vt
diff --git a/parallel/openmpi/patches/patch-ompi_contrib_vt_vt_etc_Makefile.in b/parallel/openmpi/patches/patch-ompi_contrib_vt_vt_etc_Makefile.in
new file mode 100644
index 00000000000..616dab4344e
--- /dev/null
+++ b/parallel/openmpi/patches/patch-ompi_contrib_vt_vt_etc_Makefile.in
@@ -0,0 +1,50 @@
+$NetBSD: patch-ompi_contrib_vt_vt_etc_Makefile.in,v 1.1 2012/06/12 23:36:31 asau Exp $
+
+--- ompi/contrib/vt/vt/etc/Makefile.in.orig	2012-05-10 15:12:24.000000000 +0000
++++ ompi/contrib/vt/vt/etc/Makefile.in
+@@ -461,6 +461,7 @@ vtsysconf_DATA = \
+ 	vt-java-default-filter.spec
+ 
+ vtsysconfdir = $(sysconfdir)
++vtsysconfexampledir = $(pkgdatadir)/examples
+ EXTRA_DIST = $(vtsysconf_DATA)
+ all: all-am
+ 
+@@ -503,22 +504,22 @@ clean-libtool:
+ 	-rm -rf .libs _libs
+ install-vtsysconfDATA: $(vtsysconf_DATA)
+ 	@$(NORMAL_INSTALL)
+-	test -z "$(vtsysconfdir)" || $(MKDIR_P) "$(DESTDIR)$(vtsysconfdir)"
+-	@list='$(vtsysconf_DATA)'; test -n "$(vtsysconfdir)" || list=; \
++	test -z "$(vtsysconfdir)" || $(MKDIR_P) "$(DESTDIR)$(vtsysconfexampledir)"
++	@list='$(vtsysconf_DATA)'; test -n "$(vtsysconfexampledir)" || list=; \
+ 	for p in $$list; do \
+ 	  if test -f "$$p"; then d=; else d="$(srcdir)/"; fi; \
+ 	  echo "$$d$$p"; \
+ 	done | $(am__base_list) | \
+ 	while read files; do \
+-	  echo " $(INSTALL_DATA) $$files '$(DESTDIR)$(vtsysconfdir)'"; \
+-	  $(INSTALL_DATA) $$files "$(DESTDIR)$(vtsysconfdir)" || exit $$?; \
++	  echo " $(INSTALL_DATA) $$files '$(DESTDIR)$(vtsysconfexampledir)'"; \
++	  $(INSTALL_DATA) $$files "$(DESTDIR)$(vtsysconfexampledir)" || exit $$?; \
+ 	done
+ 
+ uninstall-vtsysconfDATA:
+ 	@$(NORMAL_UNINSTALL)
+-	@list='$(vtsysconf_DATA)'; test -n "$(vtsysconfdir)" || list=; \
++	@list='$(vtsysconf_DATA)'; test -n "$(vtsysconfexampledir)" || list=; \
+ 	files=`for p in $$list; do echo $$p; done | sed -e 's|^.*/||'`; \
+-	dir='$(DESTDIR)$(vtsysconfdir)'; $(am__uninstall_files_from_dir)
++	dir='$(DESTDIR)$(vtsysconfexampledir)'; $(am__uninstall_files_from_dir)
+ tags: TAGS
+ TAGS:
+ 
+@@ -560,7 +561,7 @@ check-am: all-am
+ check: check-am
+ all-am: Makefile $(DATA)
+ installdirs:
+-	for dir in "$(DESTDIR)$(vtsysconfdir)"; do \
++	for dir in "$(DESTDIR)$(vtsysconfexampledir)"; do \
+ 	  test -z "$$dir" || $(MKDIR_P) "$$dir"; \
+ 	done
+ install: install-am
diff --git a/parallel/openmpi/patches/patch-ompi_contrib_vt_vt_extlib_otf_tools_otfprofile_clustering.cpp b/parallel/openmpi/patches/patch-ompi_contrib_vt_vt_extlib_otf_tools_otfprofile_clustering.cpp
new file mode 100644
index 00000000000..5f6053b7428
--- /dev/null
+++ b/parallel/openmpi/patches/patch-ompi_contrib_vt_vt_extlib_otf_tools_otfprofile_clustering.cpp
@@ -0,0 +1,14 @@
+$NetBSD: patch-ompi_contrib_vt_vt_extlib_otf_tools_otfprofile_clustering.cpp,v 1.1 2012/06/12 23:36:31 asau Exp $
+
+Define WEXITSTATUS.
+
+--- ompi/contrib/vt/vt/extlib/otf/tools/otfprofile/clustering.cpp.orig	2011-12-14 01:44:13.000000000 +0000
++++ ompi/contrib/vt/vt/extlib/otf/tools/otfprofile/clustering.cpp
+@@ -3,6 +3,7 @@
+  Authors: Andreas Knuepfer, Robert Dietrich, Matthias Jurenz
+ */
+ 
++#include <sys/wait.h>
+ #include <fstream>
+ #include <iostream>
+ #include <sstream>