Update to MPICH2 1.3.1

Changes in 1.3.1

 # OVERALL: MPICH2 is now fully compliant with the CIFTS FTB standard
   MPI events (based on the draft standard).

 # OVERALL: Major improvements to RMA performance for long lists of
   RMA operations.

 # OVERALL: Performance improvements for Group_translate_ranks.

 # COLLECTIVES: Collective algorithm selection thresholds can now be controlled
   at runtime via environment variables.

 # ROMIO: PVFS error codes are now mapped to MPI error codes.

 # Several other minor bug fixes, memory leak fixes, and code cleanup.
   A full list of changes is available using:

     svn log -r7350:HEAD https://svn.mcs.anl.gov/repos/mpi/mpich2/tags/release/mpich2-1.3.1

     ... or at the following link:

     https://trac.mcs.anl.gov/projects/mpich2/log/mpich2/tags/release/mpich2-1.3.1?action=follow_copy&rev=HEAD&stop_rev=7350&mode=follow_copy


Changes in 1.3

 # OVERALL: Initial support for fine-grained threading in
   ch3:nemesis:tcp.

 # OVERALL: Support for Asynchronous Communication Progress.

 # OVERALL: The ssm and shm channels have been removed.

 # OVERALL: Checkpoint/restart support using BLCR.

 # OVERALL: Improved tolerance to process and communication failures
   when error handler is set to MPI_ERRORS_RETURN.  If a communication
   operation fails (e.g., due to a process failure) MPICH2 will return
   an error, and further communication to that process is not
   possible.  However, communication with other processes will still
   proceed normally.  Note, however, that the behavior collective
   operations on communicators containing the failed process is
   undefined, and may give incorrect results or hang some processes.

 # OVERALL: Experimental support for inter-library dependencies.

 # PM/PMI: Hydra is now the default process management framework
   replacing MPD.

 # PM/PMI: Added dynamic process support for Hydra.

 # PM/PMI: Added support for LSF, SGE and POE in Hydra.

 # PM/PMI: Added support for CPU and memory/cache topology aware
   process-core binding.

 # DEBUGGER: Improved support and bug fixes in the Totalview support.

 # Build system: Replaced F90/F90FLAGS by FC/FCFLAGS. F90/F90FLAGS are
   not longer supported in the configure.

 # Multi-compiler support: On systems where C compiler that is used to
   build mpich2 libraries supports multiple weak symbols and multiple aliases,
   the Fortran binding built in the mpich2 libraries can handle different
   Fortran compilers (than the one used to build mpich2).  Details in README.

 # Several other minor bug fixes, memory leak fixes, and code cleanup.
   A full list of changes is available using:

     svn log -r5762:HEAD https://svn.mcs.anl.gov/repos/mpi/mpich2/tags/release/mpich2-1.3

     ... or at the following link:

     https://trac.mcs.anl.gov/projects/mpich2/log/mpich2/tags/release/mpich2-1.3?action=follow_copy&rev=HEAD&stop_rev=5762&mode=follow_copy

4 files changed, 46 insertions, 141 deletions

diff --git a/parallel/mpi-ch/patches/patch-aa b/parallel/mpi-ch/patches/patch-aa
index 16a13b3ec65..c840e77f3f7 100644
--- a/parallel/mpi-ch/patches/patch-aa
+++ b/parallel/mpi-ch/patches/patch-aa
@@ -1,45 +1,57 @@
-$NetBSD: patch-aa,v 1.9 2009/12/13 18:38:11 asau Exp $
+$NetBSD: patch-aa,v 1.10 2010/12/17 02:47:18 asau Exp $
 
 Install configuration files into example directory.
 
---- src/env/Makefile.in.orig	2009-11-18 19:40:34.000000000 +0300
-+++ src/env/Makefile.in	2009-12-13 20:12:58.000000000 +0300
-@@ -19,6 +19,7 @@
+--- src/env/Makefile.in.orig	2010-11-17 19:51:55.000000000 +0300
++++ src/env/Makefile.in	2010-12-17 02:06:35.000000000 +0300
+@@ -19,6 +19,8 @@
  srcdir          = @srcdir@
  abs_srcdir      = @abs_srcdir@
  sysconfdir      = @sysconfdir@
 +datadir		= @datadir@
++exampledir	= ${datadir}/examples
  DEFS            = @DEFS@ -I. -I${srcdir}
  CPPFLAGS        = @CPPFLAGS@
  LIBS            = @LIBS@
-@@ -39,6 +40,8 @@
- INCLUDES = -I../include
- doc_sources = mpicc.txt mpif77.txt mpicxx.txt mpif90.txt mpiexec.txt
- 
-+exampledir =	$(datadir)/examples
-+
- .SUFFIXES:
- .SUFFIXES: .o .lo .c .man .html .latex .txt 
- .c.o:
-@@ -135,15 +138,15 @@
- 	$(INSTALL_PROGRAM) $(INSTALL_STRIP_FLAG) mpich2version ${DESTDIR}${bindir}/mpich2version
- 	$(INSTALL_SCRIPT) mpicc ${DESTDIR}${bindir}/mpicc
- 	$(INSTALL_SCRIPT) parkill ${DESTDIR}${bindir}/parkill
+@@ -95,15 +97,15 @@
+ 	$(INSTALL_PROGRAM) $(INSTALL_STRIP_FLAG)  mpich2version ${DESTDIR}${bindir}/mpich2version
+ 	$(INSTALL_SCRIPT)  mpicc ${DESTDIR}${bindir}/mpicc
+ 	$(INSTALL_SCRIPT)  parkill ${DESTDIR}${bindir}/parkill
 -	if [ ! -d ${DESTDIR}${sysconfdir} ] ; then $(MKDIR_P) ${DESTDIR}${sysconfdir} ; fi
--	$(INSTALL_DATA) mpixxx_opts.conf ${DESTDIR}${sysconfdir}/mpixxx_opts.conf
--	$(INSTALL_DATA) mpicc.conf ${DESTDIR}${sysconfdir}/mpicc.conf
+-	$(INSTALL_DATA)  mpixxx_opts.conf ${DESTDIR}${sysconfdir}/mpixxx_opts.conf
+-	$(INSTALL_DATA)  mpicc.conf ${DESTDIR}${sysconfdir}/mpicc.conf
 +	if [ ! -d ${DESTDIR}${exampledir} ] ; then $(MKDIR_P) ${DESTDIR}${exampledir} ; fi
-+	$(INSTALL_DATA) mpixxx_opts.conf ${DESTDIR}${exampledir}/mpixxx_opts.conf
-+	$(INSTALL_DATA) mpicc.conf ${DESTDIR}${exampledir}/mpicc.conf
- 	if [ -s mpicxx ] ; then $(INSTALL_SCRIPT) mpicxx ${DESTDIR}${bindir}/mpicxx ; fi
- 	if [ -s mpif77 ] ; then $(INSTALL_SCRIPT) mpif77 ${DESTDIR}${bindir}/mpif77 ; fi
- 	if [ -s mpif90 ] ; then $(INSTALL_SCRIPT) mpif90 ${DESTDIR}${bindir}/mpif90 ; fi
--	if [ -s mpicxx.conf ] ; then $(INSTALL_DATA) mpicxx.conf ${DESTDIR}${sysconfdir}/mpicxx.conf ; fi
--	if [ -s mpif77.conf ] ; then $(INSTALL_DATA) mpif77.conf ${DESTDIR}${sysconfdir}/mpif77.conf ; fi
--	if [ -s mpif90.conf ] ; then $(INSTALL_DATA) mpif90.conf ${DESTDIR}${sysconfdir}/mpif90.conf ; fi
-+	if [ -s mpicxx.conf ] ; then $(INSTALL_DATA) mpicxx.conf ${DESTDIR}${exampledir}/mpicxx.conf ; fi
-+	if [ -s mpif77.conf ] ; then $(INSTALL_DATA) mpif77.conf ${DESTDIR}${exampledir}/mpif77.conf ; fi
-+	if [ -s mpif90.conf ] ; then $(INSTALL_DATA) mpif90.conf ${DESTDIR}${exampledir}/mpif90.conf ; fi
++	$(INSTALL_DATA)  mpixxx_opts.conf ${DESTDIR}${exampledir}/mpixxx_opts.conf
++	$(INSTALL_DATA)  mpicc.conf ${DESTDIR}${exampledir}/mpicc.conf
+ 	if [ -s mpicxx ] ; then $(INSTALL_SCRIPT)  mpicxx ${DESTDIR}${bindir}/mpicxx ; fi
+ 	if [ -s mpif77 ] ; then $(INSTALL_SCRIPT)  mpif77 ${DESTDIR}${bindir}/mpif77 ; fi
+ 	if [ -s mpif90 ] ; then $(INSTALL_SCRIPT)  mpif90 ${DESTDIR}${bindir}/mpif90 ; fi
+-	if [ -s mpicxx.conf ] ; then $(INSTALL_DATA)  mpicxx.conf ${DESTDIR}${sysconfdir}/mpicxx.conf ; fi
+-	if [ -s mpif77.conf ] ; then $(INSTALL_DATA)  mpif77.conf ${DESTDIR}${sysconfdir}/mpif77.conf ; fi
+-	if [ -s mpif90.conf ] ; then $(INSTALL_DATA)  mpif90.conf ${DESTDIR}${sysconfdir}/mpif90.conf ; fi
++	if [ -s mpicxx.conf ] ; then $(INSTALL_DATA)  mpicxx.conf ${DESTDIR}${exampledir}/mpicxx.conf ; fi
++	if [ -s mpif77.conf ] ; then $(INSTALL_DATA)  mpif77.conf ${DESTDIR}${exampledir}/mpif77.conf ; fi
++	if [ -s mpif90.conf ] ; then $(INSTALL_DATA)  mpif90.conf ${DESTDIR}${exampledir}/mpif90.conf ; fi
  	${MAKE} install-postamble
  
  install-strip:
+@@ -112,14 +114,14 @@
+ 	-rm -f ${DESTDIR}${bindir}/mpich2version
+ 	-rm -f ${DESTDIR}${bindir}/mpicc
+ 	-rm -f ${DESTDIR}${bindir}/parkill
+-	-rm -f ${DESTDIR}${sysconfdir}/mpixxx_opts.conf
+-	-rm -f ${DESTDIR}${sysconfdir}/mpicc.conf
++	-rm -f ${DESTDIR}${exampledir}/mpixxx_opts.conf
++	-rm -f ${DESTDIR}${exampledir}/mpicc.conf
+ 	-rm -f ${DESTDIR}${bindir}/mpicxx
+ 	-rm -f ${DESTDIR}${bindir}/mpif77
+ 	-rm -f ${DESTDIR}${bindir}/mpif90
+-	-rm -f ${DESTDIR}${sysconfdir}/mpicxx.conf
+-	-rm -f ${DESTDIR}${sysconfdir}/mpif77.conf
+-	-rm -f ${DESTDIR}${sysconfdir}/mpif90.conf
++	-rm -f ${DESTDIR}${exampledir}/mpicxx.conf
++	-rm -f ${DESTDIR}${exampledir}/mpif77.conf
++	-rm -f ${DESTDIR}${exampledir}/mpif90.conf
+ 	${MAKE} uninstall-postamble
+ installcheck: 
+ # --------------------------------------------------------------------------
diff --git a/parallel/mpi-ch/patches/patch-ac b/parallel/mpi-ch/patches/patch-ac
index ada6322ad1b..159b71275b3 100644
--- a/parallel/mpi-ch/patches/patch-ac
+++ b/parallel/mpi-ch/patches/patch-ac
@@ -1,25 +1,10 @@
-$NetBSD: patch-ac,v 1.7 2009/12/13 18:38:11 asau Exp $
+$NetBSD: patch-ac,v 1.8 2010/12/17 02:47:18 asau Exp $
 
 Install sample configuration files in example directory.
 
---- src/mpe2/sbin/mpeinstall.in.orig	2009-10-16 03:50:22.000000000 +0400
-+++ src/mpe2/sbin/mpeinstall.in	2009-12-11 12:55:38.000000000 +0300
-@@ -40,12 +40,8 @@
- mandir=@mandir@
- # Since autoconf < 2.60 does not set @docdir@ and @htmldir@,
- # If not set, docdir=@docdir@ remains, set them accordingly.
--if [ "$docdir" = "@docdir@" ] ; then
--    docdir=${datadir}/doc/${PACKAGE}
--fi
--if [ "$htmldir" = "@htmldir@" ] ; then
--    htmldir=${docdir}
--fi
-+case "$docdir" in @docdir) docdir=${datadir}/doc/${PACKAGE} ;; esac
-+case "$htmldir" in @htmldir) htmldir=${docdir} ;; esac
- 
- # Assume PROF_LIBNAME=MPE_LIBNAME.
- PROF_LIBNAME=@MPE_LIBNAME@
-@@ -494,14 +490,16 @@
+--- src/mpe2/sbin/mpeinstall.in.orig	2009-01-31 02:56:35.000000000 +0300
++++ src/mpe2/sbin/mpeinstall.in	2009-03-22 21:29:26.000000000 +0300
+@@ -487,14 +487,16 @@
      fi
  fi
  
diff --git a/parallel/mpi-ch/patches/patch-ae b/parallel/mpi-ch/patches/patch-ae
deleted file mode 100644
index 595b4b7765a..00000000000
--- a/parallel/mpi-ch/patches/patch-ae
+++ /dev/null
@@ -1,15 +0,0 @@
-$NetBSD: patch-ae,v 1.6 2009/12/13 18:38:11 asau Exp $
-
-"test ==" portability fixes.
-
---- src/mpid/ch3/channels/nemesis/configure.orig	2009-11-18 19:41:17.000000000 +0300
-+++ src/mpid/ch3/channels/nemesis/configure	2009-12-11 06:15:44.000000000 +0300
-@@ -5947,7 +5947,7 @@
- 
-     fi;
- 
--    if test "${net}" == "newmad" ; then
-+    if test "${net}" = "newmad" ; then
-        if test "${ac_cv_header_nm_public_h+set}" = set; then
-   { $as_echo "$as_me:$LINENO: checking for nm_public.h" >&5
- $as_echo_n "checking for nm_public.h... " >&6; }
diff --git a/parallel/mpi-ch/patches/patch-af b/parallel/mpi-ch/patches/patch-af
deleted file mode 100644
index 3124f19a4bb..00000000000
--- a/parallel/mpi-ch/patches/patch-af
+++ /dev/null
@@ -1,77 +0,0 @@
-$NetBSD: patch-af,v 1.3 2009/12/13 18:38:11 asau Exp $
-
-Disable bundled OpenPA.
-
---- examples/Makefile.in.orig	2009-11-18 19:40:35.000000000 +0300
-+++ examples/Makefile.in	2009-12-11 15:41:31.000000000 +0300
-@@ -33,6 +33,8 @@
- INCLUDES = -I../src/include -I${top_srcdir}/src/include
- LIBS   =
- 
-+LIBOPA =
-+
- EXTRA_PROGRAMS = pmandel pmandel_spawn pmandel_service pmandel_spaserv 	         pmandel_fence hellow icpi parent child srtest srvec sr 		 spawn_merge_parent spawn_merge_child1 spawn_merge_child2
- 
- .SUFFIXES:
-@@ -105,47 +107,47 @@
- all-redirect: cpi
- 
- coverage: 
--parent: parent.o   ../lib/lib${MPILIBNAME}.a ../src/openpa/src/libopa.a
-+parent: parent.o   ../lib/lib${MPILIBNAME}.a $(LIBOPA)
- 	$(C_LINK) $(CFLAGS) $(LDFLAGS) -o parent parent.o  ${LIBS}
--hellow: hellow.o   ../lib/lib${MPILIBNAME}.a ../src/openpa/src/libopa.a
-+hellow: hellow.o   ../lib/lib${MPILIBNAME}.a $(LIBOPA)
- 	$(C_LINK) $(CFLAGS) $(LDFLAGS) -o hellow hellow.o  ${LIBS}
- pmandel_spawn: pmandel_spawn.o  \
--	 ../lib/lib${MPILIBNAME}.a ../src/openpa/src/libopa.a
-+	 ../lib/lib${MPILIBNAME}.a $(LIBOPA)
- 	$(C_LINK) $(CFLAGS) $(LDFLAGS) -o pmandel_spawn pmandel_spawn.o  -lm \
- 	${LIBS} 
--pmandel: pmandel.o   ../lib/lib${MPILIBNAME}.a ../src/openpa/src/libopa.a
-+pmandel: pmandel.o   ../lib/lib${MPILIBNAME}.a $(LIBOPA)
- 	$(C_LINK) $(CFLAGS) $(LDFLAGS) -o pmandel pmandel.o  -lm ${LIBS}
--icpi: icpi.o   ../lib/lib${MPILIBNAME}.a ../src/openpa/src/libopa.a
-+icpi: icpi.o   ../lib/lib${MPILIBNAME}.a $(LIBOPA)
- 	$(C_LINK) $(CFLAGS) $(LDFLAGS) -o icpi icpi.o  -lm ${LIBS}
--child: child.o   ../lib/lib${MPILIBNAME}.a ../src/openpa/src/libopa.a
-+child: child.o   ../lib/lib${MPILIBNAME}.a $(LIBOPA)
- 	$(C_LINK) $(CFLAGS) $(LDFLAGS) -o child child.o  ${LIBS}
- spawn_merge_child2: spawn_merge_child2.o  \
--	 ../lib/lib${MPILIBNAME}.a ../src/openpa/src/libopa.a
-+	 ../lib/lib${MPILIBNAME}.a $(LIBOPA)
- 	$(C_LINK) $(CFLAGS) $(LDFLAGS) -o spawn_merge_child2 \
- 	spawn_merge_child2.o  ${LIBS} 
--cpi: cpi.o   ../lib/lib${MPILIBNAME}.a ../src/openpa/src/libopa.a
-+cpi: cpi.o   ../lib/lib${MPILIBNAME}.a $(LIBOPA)
- 	$(C_LINK) $(CFLAGS) $(LDFLAGS) -o cpi cpi.o  -lm ${LIBS}
- pmandel_fence: pmandel_fence.o  \
--	 ../lib/lib${MPILIBNAME}.a ../src/openpa/src/libopa.a
-+	 ../lib/lib${MPILIBNAME}.a $(LIBOPA)
- 	$(C_LINK) $(CFLAGS) $(LDFLAGS) -o pmandel_fence pmandel_fence.o  -lm \
- 	${LIBS} 
- spawn_merge_parent: spawn_merge_parent.o  \
--	 ../lib/lib${MPILIBNAME}.a ../src/openpa/src/libopa.a
-+	 ../lib/lib${MPILIBNAME}.a $(LIBOPA)
- 	$(C_LINK) $(CFLAGS) $(LDFLAGS) -o spawn_merge_parent \
- 	spawn_merge_parent.o  ${LIBS} 
- spawn_merge_child1: spawn_merge_child1.o  \
--	 ../lib/lib${MPILIBNAME}.a ../src/openpa/src/libopa.a
-+	 ../lib/lib${MPILIBNAME}.a $(LIBOPA)
- 	$(C_LINK) $(CFLAGS) $(LDFLAGS) -o spawn_merge_child1 \
- 	spawn_merge_child1.o  ${LIBS} 
- pmandel_spaserv: pmandel_spaserv.o  \
--	 ../lib/lib${MPILIBNAME}.a ../src/openpa/src/libopa.a
-+	 ../lib/lib${MPILIBNAME}.a $(LIBOPA)
- 	$(C_LINK) $(CFLAGS) $(LDFLAGS) -o pmandel_spaserv pmandel_spaserv.o  \
- 	-lm ${LIBS} 
- pmandel_service: pmandel_service.o  \
--	 ../lib/lib${MPILIBNAME}.a ../src/openpa/src/libopa.a
-+	 ../lib/lib${MPILIBNAME}.a $(LIBOPA)
- 	$(C_LINK) $(CFLAGS) $(LDFLAGS) -o pmandel_service pmandel_service.o  \
- 	-lm ${LIBS} 
--srtest: srtest.o   ../lib/lib${MPILIBNAME}.a ../src/openpa/src/libopa.a
-+srtest: srtest.o   ../lib/lib${MPILIBNAME}.a $(LIBOPA)
- 	$(C_LINK) $(CFLAGS) $(LDFLAGS) -o srtest srtest.o  ${LIBS}
- # --------------------------------------------------------------------------
- htmldoc: