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.

10 files changed, 99 insertions, 241 deletions

diff --git a/parallel/openmpi/Makefile b/parallel/openmpi/Makefile
index 5623ceca31d..a324918a21e 100644
--- a/parallel/openmpi/Makefile
+++ b/parallel/openmpi/Makefile
@@ -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 @@ SHLIBTOOL_OVERRIDE=	${WRKSRC}/config/libtool.m4 \
 CONFIGURE_ARGS+=	--disable-mpi-f90
 CONFIGURE_ARGS+=	--without-sge
 CONFIGURE_ARGS+=	--without-slurm
+CONFIGURE_ARGS+=	--enable-contrib-no-build=vt # in separate package
 CONFIGURE_ARGS+=	--with-libltdl=external # use our libltdl
 CONFIGURE_ARGS+=	--with-hwloc=$(BUILDLINK_PREFIX.hwloc:Q) #external
 CONFIGURE_ARGS+=	--with-wrapper-ldflags="-L${PREFIX}/lib ${LINKER_RPATH_FLAG}${PREFIX}/lib"
@@ -51,4 +51,6 @@ TEST_TARGET=	check
 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 --git a/parallel/openmpi/PLIST b/parallel/openmpi/PLIST
index bbf800ddf77..cc302b10d11 100644
--- a/parallel/openmpi/PLIST
+++ b/parallel/openmpi/PLIST
@@ -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_ess_tool.la
 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_resilient.la
 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-resilient.txt
 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-plm-rsh.txt
 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 --git a/parallel/openmpi/PLIST.vt b/parallel/openmpi/PLIST.vt
deleted file mode 100644
index aec58893129..00000000000
--- a/parallel/openmpi/PLIST.vt
+++ /dev/null
@@ -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 --git a/parallel/openmpi/distinfo b/parallel/openmpi/distinfo
index 17d2732cd88..92ab601b80e 100644
--- a/parallel/openmpi/distinfo
+++ b/parallel/openmpi/distinfo
@@ -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 --git a/parallel/openmpi/options.mk b/parallel/openmpi/options.mk
index 05856e4c934..8acf3d9b5c9 100644
--- a/parallel/openmpi/options.mk
+++ b/parallel/openmpi/options.mk
@@ -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 \
-			$(PKG_SYSCONFDIR)/vt-java-default-filter.spec
-
-.include "../../graphics/freetype2/buildlink3.mk"
-.else
-CONFIGURE_ARGS+=	--enable-contrib-no-build=vt
-.endif
-
-PLIST_SRC+=	PLIST
diff --git a/parallel/openmpi/patches/patch-ai b/parallel/openmpi/patches/patch-ai
index 6ae57ce6f36..90a49e7e9b7 100644
--- a/parallel/openmpi/patches/patch-ai
+++ b/parallel/openmpi/patches/patch-ai
@@ -1,39 +1,55 @@
-$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)/$$file" ; \
++	      rm -f "$(DESTDIR)$(sysconfexampledir)/$$file" ; \
+ 	    fi ; \
+ 	  fi ; \
+ 	done
diff --git a/parallel/openmpi/patches/patch-aj b/parallel/openmpi/patches/patch-aj
index a8bcab1020e..191f61c5961 100644
--- a/parallel/openmpi/patches/patch-aj
+++ b/parallel/openmpi/patches/patch-aj
@@ -1,46 +1,62 @@
-$NetBSD: patch-aj,v 1.2 2010/12/16 21:00:54 asau Exp $
+$NetBSD: patch-aj,v 1.3 2012/10/17 23:27:35 asau Exp $
 
 Install configuration files into example directory.
 
---- opal/etc/Makefile.in.orig	2010-03-31 05:34:56.000000000 +0400
-+++ opal/etc/Makefile.in	2010-03-31 20:54:20.000000000 +0400
+--- opal/etc/Makefile.in.orig	2012-08-22 14:25:33.000000000 +0000
++++ opal/etc/Makefile.in
 @@ -35,6 +35,7 @@
  #
  VPATH = @srcdir@
  pkgdatadir = $(datadir)/@PACKAGE@
-+exampledir = $(pkgdatadir)/examples
++sysconfexampledir = $(pkgdatadir)/examples
  pkgincludedir = $(includedir)/@PACKAGE@
  pkglibdir = $(libdir)/@PACKAGE@
  pkglibexecdir = $(libexecdir)/@PACKAGE@
-@@ -1240,24 +1241,24 @@
+@@ -1302,24 +1303,24 @@ 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="$(opal_config_files)"; \
          if test "$(opal_file_from_platform)" = "yes"; then \
  	    if test -f "$$p"; then d=; else d="$(srcdir)/"; fi; \
 -	    echo " $(INSTALL_DATA) $$d$$p $(DESTDIR)$(sysconfdir)/openmpi-mca-params.conf"; \
 -	    $(INSTALL_DATA) $$d$$p $(DESTDIR)$(sysconfdir)/openmpi-mca-params.conf; \
-+	    echo " $(INSTALL_DATA) $$d$$p $(DESTDIR)$(exampledir)/openmpi-mca-params.conf"; \
-+	    $(INSTALL_DATA) $$d$$p $(DESTDIR)$(exampledir)/openmpi-mca-params.conf; \
++	    echo " $(INSTALL_DATA) $$d$$p $(DESTDIR)$(sysconfexampledir)/openmpi-mca-params.conf"; \
++	    $(INSTALL_DATA) $$d$$p $(DESTDIR)$(sysconfexampledir)/openmpi-mca-params.conf; \
          else \
              for file in $$p; do \
 -	        if test -f $(DESTDIR)$(sysconfdir)/openmpi-mca-params.conf; then \
-+	        if test -f $(DESTDIR)$(exampledir)/openmpi-mca-params.conf; then \
++	        if test -f $(DESTDIR)$(sysconfexampledir)/openmpi-mca-params.conf; 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 \
          fi;
+@@ -1331,11 +1332,11 @@ install-data-local:
+ uninstall-local:
+ 	@ p="$(opal_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)/$$file" ; \
++	      rm -f "$(DESTDIR)$(sysconfexampledir)/$$file" ; \
+ 	    fi ; \
+ 	  fi ; \
+ 	done
diff --git a/parallel/openmpi/patches/patch-ak b/parallel/openmpi/patches/patch-ak
index fceea66decb..f4777e31413 100644
--- a/parallel/openmpi/patches/patch-ak
+++ b/parallel/openmpi/patches/patch-ak
@@ -1,39 +1,55 @@
-$NetBSD: patch-ak,v 1.2 2010/12/16 21:00:54 asau Exp $
+$NetBSD: patch-ak,v 1.3 2012/10/17 23:27:35 asau Exp $
 
 Install configuration files into example directory.
 
---- ompi/etc/Makefile.in.orig	2010-03-31 05:34:04.000000000 +0400
-+++ ompi/etc/Makefile.in	2010-03-31 20:55:04.000000000 +0400
+--- ompi/etc/Makefile.in.orig	2012-08-22 14:24:34.000000000 +0000
++++ ompi/etc/Makefile.in
 @@ -35,6 +35,7 @@
  #
  VPATH = @srcdir@
  pkgdatadir = $(datadir)/@PACKAGE@
-+exampledir = $(pkgdatadir)/examples
++sysconfexampledir = $(pkgdatadir)/examples
  pkgincludedir = $(includedir)/@PACKAGE@
  pkglibdir = $(libdir)/@PACKAGE@
  pkglibexecdir = $(libexecdir)/@PACKAGE@
-@@ -1241,19 +1242,19 @@
+@@ -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="$(ompi_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="$(ompi_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)/$$file" ; \
++	      rm -f "$(DESTDIR)$(sysconfexampledir)/$$file" ; \
+ 	    fi ; \
+ 	  fi ; \
+ 	done
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
deleted file mode 100644
index 616dab4344e..00000000000
--- a/parallel/openmpi/patches/patch-ompi_contrib_vt_vt_etc_Makefile.in
+++ /dev/null
@@ -1,50 +0,0 @@
-$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
deleted file mode 100644
index 5f6053b7428..00000000000
--- a/parallel/openmpi/patches/patch-ompi_contrib_vt_vt_extlib_otf_tools_otfprofile_clustering.cpp
+++ /dev/null
@@ -1,14 +0,0 @@
-$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>