Update to OpenMPI 1.5.5

Changes in 1.5.5
----------------

- Many, many portability configure/build fixes courtesy of Paul
  Hargrove.  Thanks, Paul!
- Fixed shared memory fault tolerance support compiler errors.
- Removed not-production-quality rshd and tmd PLM launchers.
- Minor updates to the Open MPI SRPM spec file.
- Fixed mpirun's --bind-to-socket option.
- A few MPI_THREAD_MULTIPLE fixes in the shared memory BTL.
- Upgrade the GNU Autotools used to bootstrap the 1.5/1.6 series to
  all the latest versions at the time of this release.
- Categorically state in the README that if you're having a problem
  with Open MPI with the Linux Intel 12.1 compilers, *upgrade your
  Intel Compiler Suite to the latest patch version*, and the problems
  will go away. :-)
- Fix the --without-memory-manager configure option.
- Fixes for Totalview/DDT MPI-capable debuggers.
- Update rsh/ssh support to properly handle the Mac OS X library path
  (i.e., DYLD_LIBRARY_PATH).
- Make warning about shared memory backing files on a networked file
  system be optional (i.e., can be disabled via MCA parameter).
- Several fixes to processor and memory affinity.
- Various shared memory infrastructure improvements.
- Various checkpoint/restart fixes.
- Fix MPI_IN_PLACE (and other MPI sentinel values) on OS X.  Thanks to
  Dave Goodell for providing the magic OS X gcc linker flags necessary.
- Various man page corrections and typo fixes.  Thanks to Fujitsu for
  the patch.
- Updated wrapper compiler man pages to list the various --showme
  options that are available.
- Add PMI direct-launch support (e.g., "srun mpi_application" under
  SLURM).
- Correctly compute the aligned address when packing the
  datatype description. Thanks to Fujitsu for the patch.
- Fix MPI obscure corner case handling in packing MPI datatypes.
  Thanks to Fujitsu for providing the patch.
- Workaround an Intel compiler v12.1.0 2011.6.233 vector optimization
  bug.
- Output the MPI API in ompi_info output.
- Major VT update to 5.12.1.4.
- Rankfile 'P'hysical mapping is no longer available.
- Upgrade embedded Hardware Locality (hwloc) v1.3.2, plus some
  post-1.3.2-release bug fixes.  All processor and memory binding is
  now done through hwloc.  Woo hoo!  Note that this fixes core binding
  on AMD Opteron 6200 and 4200 series-based systems (sometimes known
  as Interlagos, Valencia, or other Bulldozer-based chips).
- New MCA parameters to control process-wide memory binding policy:
  hwloc_base_mem_alloc_policy, hwloc_base_mem_bind_failure_action (see
  ompi_info --param hwloc base).
- Removed direct support for libnuma.  Libnuma support may now be
  picked up through hwloc.
- Added MPI_IN_PLACE support to MPI_EXSCAN.
- Various fixes for building on Windows, including MinGW support.
- Removed support for the OpenFabrics IBCM connection manager.
- Updated Chelsio T4 and Intel NE OpenFabrics default buffer settings.
- Increased the default RDMA CM timeout to 30 seconds.
- Issue a warning if both btl_tcp_if_include and btl_tcp_if_exclude
  are specified.
- Many fixes to the Mellanox MXM transport.

5 files changed, 53 insertions, 23 deletions

diff --git a/parallel/openmpi/Makefile b/parallel/openmpi/Makefile
index be3fb3f9546..5114f9b57dc 100644
--- a/parallel/openmpi/Makefile
+++ b/parallel/openmpi/Makefile
@@ -1,7 +1,6 @@
-# $NetBSD: Makefile,v 1.13 2012/05/21 16:08:51 marino Exp $
+# $NetBSD: Makefile,v 1.14 2012/05/28 18:38:17 asau Exp $
 
-DISTNAME=	openmpi-1.5.4
-PKGREVISION=	1
+DISTNAME=	openmpi-1.5.5
 CATEGORIES=	parallel
 MASTER_SITES=	http://www.open-mpi.org/software/ompi/v1.5/downloads/
 EXTRACT_SUFX=	.tar.bz2
diff --git a/parallel/openmpi/PLIST b/parallel/openmpi/PLIST
index 32c79c77d7a..719d9377f2c 100644
--- a/parallel/openmpi/PLIST
+++ b/parallel/openmpi/PLIST
@@ -1,4 +1,4 @@
-@comment $NetBSD: PLIST,v 1.7 2011/08/27 19:32:55 asau Exp $
+@comment $NetBSD: PLIST,v 1.8 2012/05/28 18:38:17 asau Exp $
 bin/mpiCC
 bin/mpic++
 bin/mpicc
@@ -89,14 +89,14 @@ lib/openmpi/mca_coll_sm.la
 lib/openmpi/mca_coll_sync.la
 lib/openmpi/mca_coll_tuned.la
 lib/openmpi/mca_crs_none.la
-lib/openmpi/mca_debugger_mpir.la
-lib/openmpi/mca_debugger_mpirx.la
 lib/openmpi/mca_dpm_orte.la
 lib/openmpi/mca_errmgr_default.la
 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
@@ -107,6 +107,7 @@ lib/openmpi/mca_iof_hnp.la
 lib/openmpi/mca_iof_orted.la
 lib/openmpi/mca_iof_tool.la
 lib/openmpi/mca_maffinity_first_use.la
+lib/openmpi/mca_maffinity_hwloc.la
 lib/openmpi/mca_mpool_fake.la
 lib/openmpi/mca_mpool_rdma.la
 lib/openmpi/mca_mpool_sm.la
@@ -118,7 +119,7 @@ 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_rshd.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
@@ -126,6 +127,8 @@ 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
@@ -142,6 +145,8 @@ lib/openmpi/mca_routed_direct.la
 lib/openmpi/mca_routed_linear.la
 lib/openmpi/mca_routed_radix.la
 lib/openmpi/mca_routed_slave.la
+lib/openmpi/mca_shmem_mmap.la
+lib/openmpi/mca_shmem_sysv.la
 lib/openmpi/mca_topo_unity.la
 lib/openmpi/mca_vprotocol_pessimist.la
 lib/pkgconfig/ompi-c.pc
@@ -524,7 +529,10 @@ share/openmpi/help-oob-tcp.txt
 share/openmpi/help-opal-carto-file.txt
 share/openmpi/help-opal-crs-base.txt
 share/openmpi/help-opal-crs-none.txt
+share/openmpi/help-opal-maffinity-hwloc.txt
 share/openmpi/help-opal-runtime.txt
+share/openmpi/help-opal-shmem-mmap.txt
+share/openmpi/help-opal-shmem-sysv.txt
 share/openmpi/help-opal-util.txt
 share/openmpi/help-opal-wrapper.txt
 share/openmpi/help-orte-clean.txt
@@ -548,8 +556,10 @@ 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-rshd.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 c31d83a21b1..1fe11e856b3 100644
--- a/parallel/openmpi/PLIST.vt
+++ b/parallel/openmpi/PLIST.vt
@@ -1,4 +1,4 @@
-@comment $NetBSD: PLIST.vt,v 1.4 2012/05/21 16:08:51 marino Exp $
+@comment $NetBSD: PLIST.vt,v 1.5 2012/05/28 18:38:18 asau Exp $
 bin/mpiCC-vt
 bin/mpic++-vt
 bin/mpicc-vt
@@ -12,7 +12,9 @@ bin/otfdecompress
 bin/otfdump
 bin/otfinfo
 bin/otfmerge
+bin/otfmerge-mpi
 bin/otfprofile
+bin/otfprofile-mpi
 bin/otfshrink
 bin/vtCC
 bin/vtc++
@@ -21,17 +23,27 @@ 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
 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_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
@@ -43,6 +55,8 @@ 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/vt_inttypes.h
 include/vampirtrace/vt_user.h
 include/vampirtrace/vt_user.inc
 include/vampirtrace/vt_user_comment.h
@@ -53,12 +67,16 @@ 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
 ${PLIST.vtlwraph}include/vampirtrace/vt_libwrap.h
 lib/libotf.la
+lib/libotfaux.la
 lib/libvt-hyb.la
+lib/libvt-mpi-unify.la
 lib/libvt-mpi.la
 lib/libvt-mt.la
 lib/libvt.la
@@ -77,6 +95,8 @@ share/vampirtrace/doc/UserManual.html
 share/vampirtrace/doc/UserManual.pdf
 share/vampirtrace/doc/otf/ChangeLog
 share/vampirtrace/doc/otf/LICENSE
+share/vampirtrace/doc/otf/otfprofile.pdf
+share/vampirtrace/doc/otf/otfprofile_clustering.pdf
 share/vampirtrace/doc/otf/otftools.pdf
 share/vampirtrace/doc/otf/specification.pdf
 share/vampirtrace/libtool
diff --git a/parallel/openmpi/distinfo b/parallel/openmpi/distinfo
index bfde8b682fb..acd3a6460ee 100644
--- a/parallel/openmpi/distinfo
+++ b/parallel/openmpi/distinfo
@@ -1,9 +1,10 @@
-$NetBSD: distinfo,v 1.8 2011/08/27 19:32:55 asau Exp $
+$NetBSD: distinfo,v 1.9 2012/05/28 18:38:18 asau Exp $
 
-SHA1 (openmpi-1.5.4.tar.bz2) = 81f7736a83b2134ba20c2e5c380b4d267cfd9d9c
-RMD160 (openmpi-1.5.4.tar.bz2) = 6e172309b102cf6382b4b516d07e0133466485b3
-Size (openmpi-1.5.4.tar.bz2) = 7629620 bytes
-SHA1 (patch-aa) = 90f74e14eb686cd68bf29ea28cfb9818984f6408
+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 (patch-aa) = 6fa20775c6e2abae7c9a2ae858dbb941652beab8
 SHA1 (patch-ai) = 650906ec3701cc7bac6b7f916c87506ccb885341
 SHA1 (patch-aj) = dc85e6c9eb6db0eb40bb896a11c223afeda63c2f
 SHA1 (patch-ak) = f6ea4220d51dd0c84ac2067d695c265f00904a0f
+SHA1 (patch-ompi_contrib_vt_vt_extlib_otf_tools_otfprofile_clustering.cpp) = b2baee86e9787fec7d16073cbb63ece4e83c2333
diff --git a/parallel/openmpi/patches/patch-aa b/parallel/openmpi/patches/patch-aa
index 3852da2142c..b5f4f6ee98e 100644
--- a/parallel/openmpi/patches/patch-aa
+++ b/parallel/openmpi/patches/patch-aa
@@ -1,18 +1,18 @@
-$NetBSD: patch-aa,v 1.2 2010/12/16 21:00:54 asau Exp $
+$NetBSD: patch-aa,v 1.3 2012/05/28 18:38:18 asau Exp $
 
 Missing RPATH support.
 
---- opal/tools/wrappers/opal_wrapper.c.orig	2009-11-04 17:57:36.000000000 +0300
-+++ opal/tools/wrappers/opal_wrapper.c	2010-01-12 20:48:26.000000000 +0300
-@@ -58,6 +58,7 @@
- #if !defined(__WINDOWS__)
+--- opal/tools/wrappers/opal_wrapper.c.orig	2011-12-14 05:43:59.000000000 +0400
++++ opal/tools/wrappers/opal_wrapper.c	2012-02-16 18:10:03.000000000 +0400
+@@ -61,6 +61,7 @@
+ #else
  #define OPAL_INCLUDE_FLAG  "-I"
  #define OPAL_LIBDIR_FLAG   "-L"
 +#define OPAL_RPATH_FLAG    "-R"
- #else
- #define OPAL_INCLUDE_FLAG  "/I"
- #define OPAL_LIBDIR_FLAG   "/LIBPATH:"
-@@ -357,6 +358,8 @@
+ #endif  /* !defined(__WINDOWS__) && defined(_MSC_VER) */
+ 
+ struct options_data_t {
+@@ -363,6 +364,8 @@
  #else
              asprintf(&line, OPAL_LIBDIR_FLAG"%s", 
                       options_data[parse_options_idx].path_libdir);