Update to MPICH2 1.4.1p1

===============================================================================
                               Changes in 1.4.1
===============================================================================

 # OVERALL: Several improvements to the ARMCI API implementation
   within MPICH2.

 # Build system: Added beta support for DESTDIR while installing
   MPICH2.

 # PM/PMI: Upgrade hwloc to 1.2.1rc2.

 # PM/PMI: Initial support for the PBS launcher.

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

     svn log -r8675:HEAD https://svn.mcs.anl.gov/repos/mpi/mpich2/tags/release/mpich2-1.4.1

     ... or at the following link:

     https://trac.mcs.anl.gov/projects/mpich2/log/mpich2/tags/release/mpich2-1.4.1?action=follow_copy&rev=HEAD&stop_rev=8675&mode=follow_copy


===============================================================================
                               Changes in 1.4
===============================================================================

 # OVERALL: Improvements to fault tolerance for collective
   operations. Thanks to Rui Wang @ ICT for reporting several of these
   issues.

 # OVERALL: Improvements to the universe size detection. Thanks to
   Yauheni Zelenko for reporting this issue.

 # OVERALL: Bug fixes for Fortran attributes on some systems. Thanks
   to Nicolai Stange for reporting this issue.

 # OVERALL: Added new ARMCI API implementation (experimental).

 # OVERALL: Added new MPIX_Group_comm_create function to allow
   non-collective creation of sub-communicators.

 # FORTRAN: Bug fixes in the MPI_DIST_GRAPH_ Fortran bindings.

 # PM/PMI: Support for a manual "none" launcher in Hydra to allow for
   higher-level tools to be built on top of Hydra. Thanks to Justin
   Wozniak for reporting this issue, for providing several patches for
   the fix, and testing it.

 # PM/PMI: Bug fixes in Hydra to handle non-uniform layouts of hosts
   better. Thanks to the MVAPICH group at OSU for reporting this issue
   and testing it.

 # PM/PMI: Bug fixes in Hydra to handle cases where only a subset of
   the available launchers or resource managers are compiled
   in. Thanks to Satish Balay @ Argonne for reporting this issue.

 # PM/PMI: Support for a different username to be provided for each
   host; this only works for launchers that support this (such as
   SSH).

 # PM/PMI: Bug fixes for using Hydra on AIX machines. Thanks to
   Kitrick Sheets @ NCSA for reporting this issue and providing the
   first draft of the patch.

 # PM/PMI: Bug fixes in memory allocation/management for environment
   variables that was showing up on older platforms. Thanks to Steven
   Sutphen for reporting the issue and providing detailed analysis to
   track down the bug.

 # PM/PMI: Added support for providing a configuration file to pick
   the default options for Hydra. Thanks to Saurabh T. for reporting
   the issues with the current implementation and working with us to
   improve this option.

 # PM/PMI: Improvements to the error code returned by Hydra.

 # PM/PMI: Bug fixes for handling "=" in environment variable values in
   hydra.

 # PM/PMI: Upgrade the hwloc version to 1.2.

 # COLLECTIVES: Performance and memory usage improvements for MPI_Bcast
   in certain cases.

 # VALGRIND: Fix incorrect Valgrind client request usage when MPICH2 is
   built for memory debugging.

 # BUILD SYSTEM: "--enable-fast" and "--disable-error-checking" are once
   again valid simultaneous options to configure.

 # TEST SUITE: Several new tests for MPI RMA operations.

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

     svn log -r7838:HEAD https://svn.mcs.anl.gov/repos/mpi/mpich2/tags/release/mpich2-1.4

     ... or at the following link:

     https://trac.mcs.anl.gov/projects/mpich2/log/mpich2/tags/release/mpich2-1.4?action=follow_copy&rev=HEAD&stop_rev=7838&mode=follow_copy


===============================================================================
                               Changes in 1.3.2
===============================================================================

 # OVERALL: MPICH2 now recognizes the OSX mach_absolute_time as a
   native timer type.

 # OVERALL: Performance improvements to MPI_Comm_split on large
   systems.

 # OVERALL: Several improvements to error returns capabilities in the
   presence of faults.

 # PM/PMI: Several fixes and improvements to Hydra's process binding
   capability.

 # PM/PMI: Upgrade the hwloc version to 1.1.1.

 # PM/PMI: Allow users to sort node lists allocated by resource
   managers in Hydra.

 # PM/PMI: Improvements to signal handling. Now Hydra respects Ctrl-Z
   signals and passes on the signal to the application.

 # PM/PMI: Improvements to STDOUT/STDERR handling including improved
   support for rank prepending on output. Improvements to STDIN
   handling for applications being run in the background.

 # PM/PMI: Split the bootstrap servers into "launchers" and "resource
   managers", allowing the user to pick a different resource manager
   from the launcher. For example, the user can now pick the "SLURM"
   resource manager and "SSH" as the launcher.

 # PM/PMI: The MPD process manager is deprecated.

 # PM/PMI: The PLPA process binding library support is deprecated.

 # WINDOWS: Adding support for gfortran and 64-bit gcc libs.

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

     svn log -r7457:HEAD https://svn.mcs.anl.gov/repos/mpi/mpich2/tags/release/mpich2-1.3.2

     ... or at the following link:

     https://trac.mcs.anl.gov/projects/mpich2/log/mpich2/tags/release/mpich2-1.3.2?action=follow_copy&rev=HEAD&stop_rev=7457&mode=follow_copy

6 files changed, 66 insertions, 25 deletions

diff --git a/parallel/mpi-ch/Makefile b/parallel/mpi-ch/Makefile
index 496cc8ba4fe..124879c003c 100644
--- a/parallel/mpi-ch/Makefile
+++ b/parallel/mpi-ch/Makefile
@@ -1,9 +1,8 @@
-# $NetBSD: Makefile,v 1.67 2012/01/11 02:46:01 sbd Exp $
+# $NetBSD: Makefile,v 1.68 2012/01/11 09:43:25 asau Exp $
 
-DISTNAME=	mpich2-1.3.1
-PKGREVISION=	1
+DISTNAME=	mpich2-1.4.1p1
 CATEGORIES=	parallel
-MASTER_SITES=	http://www.mcs.anl.gov/research/projects/mpich2/downloads/tarballs/1.3.1/
+MASTER_SITES=	http://www.mcs.anl.gov/research/projects/mpich2/downloads/tarballs/1.4.1p1/
 
 MAINTAINER=	asau@inbox.ru
 HOMEPAGE=	http://www.mcs.anl.gov/research/projects/mpich2/
@@ -29,7 +28,6 @@ CONFIGURE_ARGS+=	--docdir=${PREFIX}/share/doc/${PKGBASE}
 CONFIGURE_ARGS+=	--htmldir=${PREFIX}/share/doc/${PKGBASE}/html
 
 CONFIGURE_ARGS+=	--with-pm=hydra:gforker
-CONFIGURE_ARGS+=	--with-hydra-bindlib=plpa # problems with hwloc
 CONFIGURE_ARGS+=	--disable-fc		# problems?
 CONFIGURE_ARGS+=	--with-openpa-prefix=$(BUILDLINK_PREFIX.openpa:Q) # reuse it
 
diff --git a/parallel/mpi-ch/PLIST b/parallel/mpi-ch/PLIST
index d8b87afc7b5..70b5027c8b4 100644
--- a/parallel/mpi-ch/PLIST
+++ b/parallel/mpi-ch/PLIST
@@ -1,4 +1,4 @@
-@comment $NetBSD: PLIST,v 1.16 2012/01/11 02:46:01 sbd Exp $
+@comment $NetBSD: PLIST,v 1.17 2012/01/11 09:43:25 asau Exp $
 bin/bt2line
 bin/check_callstack
 bin/clog2_join
@@ -16,9 +16,6 @@ bin/mpiexec.gforker
 bin/mpiexec.hydra
 bin/mpif77
 bin/mpirun
-bin/parkill
-bin/plpa-info
-bin/plpa-taskset
 include/clog_commset.h
 include/clog_const.h
 include/clog_inttypes.h
@@ -35,7 +32,7 @@ include/mpicxx.h
 include/mpif.h
 include/mpio.h
 include/mpiof.h
-include/plpa.h
+include/mpix.h
 lib/libfmpich.a
 lib/liblmpe.a
 lib/libmpe.a
@@ -49,13 +46,17 @@ lib/libmpichcxx.a
 lib/libmpl.la
 lib/libtmpe.a
 lib/mpe_prof.o
-lib/pkgconfig/mpich2-ch3.pc
+lib/pkgconfig/mpich2-c.pc
+lib/pkgconfig/mpich2-cxx.pc
+lib/pkgconfig/mpich2-f77.pc
+lib/pkgconfig/mpich2-f90.pc
 man/man1/MPI.1
 man/man1/mpicc.1
 man/man1/mpicxx.1
 man/man1/mpiexec.1
 man/man1/mpif77.1
 man/man1/mpif90.1
+man/man3/MPIX_Group_comm_create.3
 man/man3/MPI_Abort.3
 man/man3/MPI_Accumulate.3
 man/man3/MPI_Add_error_class.3
@@ -414,6 +415,7 @@ share/doc/mpich2/html/www1/mpicxx.html
 share/doc/mpich2/html/www1/mpiexec.html
 share/doc/mpich2/html/www1/mpif77.html
 share/doc/mpich2/html/www1/mpif90.html
+share/doc/mpich2/html/www3/MPIX_Group_comm_create.html
 share/doc/mpich2/html/www3/MPI_Abort.html
 share/doc/mpich2/html/www3/MPI_Accumulate.html
 share/doc/mpich2/html/www3/MPI_Add_error_class.html
diff --git a/parallel/mpi-ch/distinfo b/parallel/mpi-ch/distinfo
index 13e68177103..cf7a02078ee 100644
--- a/parallel/mpi-ch/distinfo
+++ b/parallel/mpi-ch/distinfo
@@ -1,7 +1,9 @@
-$NetBSD: distinfo,v 1.17 2010/12/17 02:47:18 asau Exp $
+$NetBSD: distinfo,v 1.18 2012/01/11 09:43:25 asau Exp $
 
-SHA1 (mpich2-1.3.1.tar.gz) = 6fc6723d693c381b231aebc51745b73398bd37aa
-RMD160 (mpich2-1.3.1.tar.gz) = 70ea44bab15b127921b046f1b97088ac14309e8c
-Size (mpich2-1.3.1.tar.gz) = 19421084 bytes
-SHA1 (patch-aa) = 9d7f22f9401687ccf6114b915a26ad67958d8ccd
+SHA1 (mpich2-1.4.1p1.tar.gz) = 8dcc8888fb27232eb8f76c11cc890f1c3c483804
+RMD160 (mpich2-1.4.1p1.tar.gz) = 1d355cc07b8675af77b1c255fd10696844447298
+Size (mpich2-1.4.1p1.tar.gz) = 19502854 bytes
+SHA1 (patch-Makefile.in) = c7e8398952d3b60d1325661ef0055c72930c70f9
+SHA1 (patch-aa) = f7d5fc3be6b2679ef0937615cc9c5b4229acb22a
 SHA1 (patch-ac) = b956a355ef381d759077288916c40e32b022f178
+SHA1 (patch-src_pm_hydra_configure) = 9d42c909464fa24af7a079c03a75ae03aa3f8ee5
diff --git a/parallel/mpi-ch/patches/patch-Makefile.in b/parallel/mpi-ch/patches/patch-Makefile.in
new file mode 100644
index 00000000000..7764b93de73
--- /dev/null
+++ b/parallel/mpi-ch/patches/patch-Makefile.in
@@ -0,0 +1,26 @@
+$NetBSD: patch-Makefile.in,v 1.1 2012/01/11 09:43:26 asau Exp $
+
+--- Makefile.in.orig	2011-09-01 18:55:44.000000000 +0000
++++ Makefile.in
+@@ -202,16 +202,16 @@ install:  install-preamble FORCE_TARGET 
+ 	if [ -s $(srcdir)/doc/installguide/install.pdf ] ; then $(INSTALL_DATA)  $(srcdir)/doc/installguide/install.pdf ${DESTDIR}${docdir}/install.pdf ; fi
+ 	if [ -s $(srcdir)/doc/smpd/smpd_pmi.pdf ] ; then $(INSTALL_DATA)  $(srcdir)/doc/smpd/smpd_pmi.pdf ${DESTDIR}${docdir}/smpd_pmi.pdf ; fi
+ 	if [ -s $(srcdir)/doc/logging/logging.pdf ] ; then $(INSTALL_DATA)  $(srcdir)/doc/logging/logging.pdf ${DESTDIR}${docdir}/logging.pdf ; fi
+-	(cd src/env && $(MAKE) INSTALL_STRIP_FLAG=$(INSTALL_STRIP_FLAG) PACKAGE=$(PACKAGE) prefix=${DESTDIR}${prefix} exec_prefix=${DESTDIR}${exec_prefix} bindir=${DESTDIR}${bindir} libdir=${DESTDIR}${libdir} includedir=${DESTDIR}${includedir} install)
+-	(cd src/packaging/pkgconfig && $(MAKE) INSTALL_STRIP_FLAG=$(INSTALL_STRIP_FLAG) PACKAGE=$(PACKAGE) prefix=${DESTDIR}${prefix} exec_prefix=${DESTDIR}${exec_prefix} bindir=${DESTDIR}${bindir} libdir=${DESTDIR}${libdir} includedir=${DESTDIR}${includedir} install)
+-	(cd src/packaging/envmods && $(MAKE) INSTALL_STRIP_FLAG=$(INSTALL_STRIP_FLAG) PACKAGE=$(PACKAGE) prefix=${DESTDIR}${prefix} exec_prefix=${DESTDIR}${exec_prefix} bindir=${DESTDIR}${bindir} libdir=${DESTDIR}${libdir} includedir=${DESTDIR}${includedir} install)
++	(cd src/env && $(MAKE) INSTALL_STRIP_FLAG=$(INSTALL_STRIP_FLAG) PACKAGE=$(PACKAGE) prefix=${prefix} exec_prefix=${exec_prefix} bindir=${bindir} libdir=${libdir} includedir=${includedir} install)
++	(cd src/packaging/pkgconfig && $(MAKE) INSTALL_STRIP_FLAG=$(INSTALL_STRIP_FLAG) PACKAGE=$(PACKAGE) prefix=${prefix} exec_prefix=${exec_prefix} bindir=${bindir} libdir=${libdir} includedir=${includedir} install)
++	(cd src/packaging/envmods && $(MAKE) INSTALL_STRIP_FLAG=$(INSTALL_STRIP_FLAG) PACKAGE=$(PACKAGE) prefix=${prefix} exec_prefix=${exec_prefix} bindir=${bindir} libdir=${libdir} includedir=${includedir} install)
+ 	for dir in @bindings_dirs@ - ; do \
+ 		if [ "$$dir" = "-" ] ; then break ; fi ;\
+-		(cd $$dir && $(MAKE) INSTALL_STRIP_FLAG=$(INSTALL_STRIP_FLAG) PACKAGE=$(PACKAGE) prefix=${DESTDIR}${prefix} exec_prefix=${DESTDIR}${exec_prefix} bindir=${DESTDIR}${bindir} libdir=${DESTDIR}${libdir} includedir=${DESTDIR}${includedir} install) ;\
++		(cd $$dir && $(MAKE) INSTALL_STRIP_FLAG=$(INSTALL_STRIP_FLAG) PACKAGE=$(PACKAGE) prefix=${prefix} exec_prefix=${exec_prefix} bindir=${bindir} libdir=${libdir} includedir=${includedir} install) ;\
+ 	done
+ 	for dir in @other_install_dirs@ - ; do \
+ 		if [ "$$dir" = "-" ] ; then break ; fi ;\
+-		(cd $$dir && $(MAKE) INSTALL_STRIP_FLAG=$(INSTALL_STRIP_FLAG) PACKAGE=$(PACKAGE) prefix=${DESTDIR}${prefix} exec_prefix=${DESTDIR}${exec_prefix} bindir=${DESTDIR}${bindir} libdir=${DESTDIR}${libdir} includedir=${DESTDIR}${includedir} install) ;\
++		(cd $$dir && $(MAKE) INSTALL_STRIP_FLAG=$(INSTALL_STRIP_FLAG) PACKAGE=$(PACKAGE) prefix=${prefix} exec_prefix=${exec_prefix} bindir=${bindir} libdir=${libdir} includedir=${includedir} install) ;\
+ 	done
+ 
+ install-strip:
diff --git a/parallel/mpi-ch/patches/patch-aa b/parallel/mpi-ch/patches/patch-aa
index c840e77f3f7..e3a9aa986c4 100644
--- a/parallel/mpi-ch/patches/patch-aa
+++ b/parallel/mpi-ch/patches/patch-aa
@@ -1,10 +1,10 @@
-$NetBSD: patch-aa,v 1.10 2010/12/17 02:47:18 asau Exp $
+$NetBSD: patch-aa,v 1.11 2012/01/11 09:43:26 asau Exp $
 
 Install configuration files into example directory.
 
---- 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 @@
+--- src/env/Makefile.in.orig	2011-09-01 22:55:45.000000000 +0400
++++ src/env/Makefile.in	2011-11-09 21:08:59.000000000 +0400
+@@ -21,6 +21,8 @@
  srcdir          = @srcdir@
  abs_srcdir      = @abs_srcdir@
  sysconfdir      = @sysconfdir@
@@ -13,10 +13,10 @@ Install configuration files into example directory.
  DEFS            = @DEFS@ -I. -I${srcdir}
  CPPFLAGS        = @CPPFLAGS@
  LIBS            = @LIBS@
-@@ -95,15 +97,15 @@
+@@ -97,15 +99,15 @@
+ 	if [ ! -d ${DESTDIR}${bindir} ] ; then $(MKDIR_P) ${DESTDIR}${bindir} ; fi
  	$(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
@@ -32,13 +32,13 @@ Install configuration files into example directory.
 +	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
+ 	${MAKE} DESTDIR=${DESTDIR} prefix=${prefix} exec_prefix=${exec_prefix} bindir=${bindir} libdir=${libdir} includedir=${includedir} install-postamble
  
  install-strip:
-@@ -112,14 +114,14 @@
+@@ -113,14 +115,14 @@
+ uninstall: 
  	-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
diff --git a/parallel/mpi-ch/patches/patch-src_pm_hydra_configure b/parallel/mpi-ch/patches/patch-src_pm_hydra_configure
new file mode 100644
index 00000000000..03cfac33c63
--- /dev/null
+++ b/parallel/mpi-ch/patches/patch-src_pm_hydra_configure
@@ -0,0 +1,13 @@
+$NetBSD: patch-src_pm_hydra_configure,v 1.1 2012/01/11 09:43:26 asau Exp $
+
+--- src/pm/hydra/configure.orig	2011-09-01 18:54:46.000000000 +0000
++++ src/pm/hydra/configure
+@@ -13854,7 +13854,7 @@ fi
+ 
+ 
+ cat >>confdefs.h <<_ACEOF
+-#define HYDRA_CONFIGURE_ARGS_CLEAN "`echo $ac_configure_args`"
++#define HYDRA_CONFIGURE_ARGS_CLEAN "`echo -n $ac_configure_args`"
+ _ACEOF
+ 
+