Date: Mon, 1 Nov 2010 16:50:48 +0100 (CET) From: Thierry Thomas <thierry@FreeBSD.org> To: FreeBSD-gnats-submit@FreeBSD.org Cc: Maho Nakata <maho@FreeBSD.org> Subject: ports/151868: math/blacs, science/mbdyn & science/mpqc: chase net/mpich2 upgrade Message-ID: <20101101155048.11F5011449@graf.pompo.net> Resent-Message-ID: <201011011600.oA1G0RrW023205@freefall.freebsd.org>
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>Number: 151868 >Category: ports >Synopsis: math/blacs, science/mbdyn & science/mpqc: chase net/mpich2 upgrade >Confidential: no >Severity: non-critical >Priority: medium >Responsible: freebsd-ports-bugs >State: open >Quarter: >Keywords: >Date-Required: >Class: update >Submitter-Id: current-users >Arrival-Date: Mon Nov 01 16:00:27 UTC 2010 >Closed-Date: >Last-Modified: >Originator: Thierry Thomas >Release: FreeBSD 8.1-STABLE i386 >Organization: Kabbale Eros >Environment: System: FreeBSD graf.pompo.net 8.1-STABLE FreeBSD 8.1-STABLE #0: Sun Aug 22 11:07:29 CEST 2010 thierry@graf.pompo.net:/usr/obj/usr/src/sys/GRAF100821 i386 >Description: When upgrading net/mpich2 to 1.3, the ports math/blacs, science/mbdyn & science/mpqc must be modified. Please see the hereunder patches. net/mpich2 upgrade: PR ports/151867 http://www.freebsd.org/cgi/query-pr.cgi?pr=151867 Note about science/mbdyn: I have'nt been able to build it with MPI without enaabling SCHUR. >How-To-Repeat: - Upgrade net/mpich2 to 1.3 - see PR ports/151867; - then apply the attached patches. >Fix: --- blacs.diff begins here --- diff -urN math/blacs.orig/Makefile math/blacs/Makefile --- math/blacs.orig/Makefile 2010-01-01 17:09:41.000000000 +0100 +++ math/blacs/Makefile 2010-11-01 15:51:59.000000000 +0100 @@ -7,7 +7,7 @@ PORTNAME= blacs PORTVERSION= 1.7 -PORTREVISION= 12 +PORTREVISION= 13 CATEGORIES= math MASTER_SITES= ftp://ftp.netlib.org/blacs/ DISTNAME= BLACS @@ -32,12 +32,11 @@ .endif .if defined(WITH_OPENMPI) -BUILD_DEPENDS= ${LOCALBASE}/mpi/openmpi/lib/libmpi.so:${PORTSDIR}/net/openmpi -RUN_DEPENDS= ${LOCALBASE}/mpi/openmpi/bin/mpirun:${PORTSDIR}/net/openmpi +BUILD_DEPENDS+= ${LOCALBASE}/mpi/openmpi/lib/libmpi.so:${PORTSDIR}/net/openmpi +RUN_DEPENDS+= ${LOCALBASE}/mpi/openmpi/bin/mpirun:${PORTSDIR}/net/openmpi EXTRA_PATCHES+= ${FILESDIR}/Bmake.inc-openmpi.diff .else -LIB_DEPENDS= mpich:${PORTSDIR}/net/mpich2 -RUN_DEPENDS= ${LOCALBASE}/bin/mpirun:${PORTSDIR}/net/mpich2 +LIB_DEPENDS+= mpich:${PORTSDIR}/net/mpich2 EXTRA_PATCHES+= ${FILESDIR}/Bmake.inc-mpich.diff .endif diff -urN math/blacs.orig/files/Bmake.inc-mpich.diff math/blacs/files/Bmake.inc-mpich.diff --- math/blacs.orig/files/Bmake.inc-mpich.diff 2010-01-01 17:09:41.000000000 +0100 +++ math/blacs/files/Bmake.inc-mpich.diff 2010-10-25 22:30:19.000000000 +0200 @@ -35,7 +35,7 @@ MPILIBdir = $(MPIdir)/lib/ MPIINCdir = $(MPIdir)/include - MPILIB = $(MPILIBdir)/libmpich.a -+ MPILIB = $(MPILIBdir)/libmpich.a ++ MPILIB = $(MPILIBdir)/libmpich.a $(MPILIBdir)/libmpl.a -pthread # ------------------------------------- # All libraries required by the tester. --- blacs.diff ends here --- --- mbdyn.diff begins here --- diff -urN science/mbdyn.orig/Makefile science/mbdyn/Makefile --- science/mbdyn.orig/Makefile 2010-01-01 17:10:49.000000000 +0100 +++ science/mbdyn/Makefile 2010-11-01 15:45:59.000000000 +0100 @@ -7,7 +7,7 @@ PORTNAME= mbdyn PORTVERSION= 1.3.9 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= science MASTER_SITES= http://www.aero.polimi.it/~masarati/Download/mbdyn/ @@ -51,9 +51,12 @@ .if defined(WITH_MPI) LIB_DEPENDS+= mpich:${PORTSDIR}/net/mpich2 -CONFIGURE_ARGS+= --with-mpi=pmpi -CPPFLAGS+= -I${LOCALBASE}/include -I${LOCALBASE}/include/mpi2c++ -LDFLAGS+= -L${LOCALBASE}/lib +CONFIGURE_ARGS+= --with-mpi=yes --enable-schur +CPPFLAGS+= -I${LOCALBASE}/include +LDFLAGS+= "-L${LOCALBASE}/lib" +. if !defined(WITH_METIS) +WITH_CHACO= yes +. endif .else CONFIGURE_ARGS+= --with-mpi=no .endif diff -urN science/mbdyn.orig/files/patch-configure science/mbdyn/files/patch-configure --- science/mbdyn.orig/files/patch-configure 2009-08-05 07:25:45.000000000 +0200 +++ science/mbdyn/files/patch-configure 2010-10-31 22:20:11.000000000 +0100 @@ -1,16 +1,5 @@ ---- configure.in 2009-08-05 12:29:39.000000000 +0900 -+++ configure.in 2009-08-05 12:29:50.000000000 +0900 -@@ -765,7 +765,7 @@ - dnl Add fortran lib - dnl - case `basename "$F77"` in --gfortran) -+gfortran*) - F2C_LIBS="$F2C_LIBS -lgfortran" - ;; - *) ---- configure~ 2009-06-24 20:45:44.000000000 +0900 -+++ configure 2009-08-05 12:29:56.000000000 +0900 +--- configure.orig 2009-06-24 13:45:44.000000000 +0200 ++++ configure 2010-10-31 22:17:08.000000000 +0100 @@ -27344,7 +27344,7 @@ fi @@ -20,3 +9,56 @@ F2C_LIBS="$F2C_LIBS -lgfortran" ;; *) +@@ -33508,7 +33508,7 @@ + cat >>conftest.$ac_ext <<_ACEOF + /* end confdefs.h. */ + $ac_includes_default +-#include <$ac_header> ++#include <mpi.h> + _ACEOF + rm -f conftest.$ac_objext + if { (ac_try="$ac_compile" +@@ -33548,7 +33548,7 @@ + cat confdefs.h >>conftest.$ac_ext + cat >>conftest.$ac_ext <<_ACEOF + /* end confdefs.h. */ +-#include <$ac_header> ++#include <mpi.h> + _ACEOF + if { (ac_try="$ac_cpp conftest.$ac_ext" + case "(($ac_try" in +@@ -33643,7 +33643,7 @@ + elif test $ac_cv_header_mpicxx_h = yes ; then + have_mpi_cxx_header=yes + mpi_cxx_header="mpicxx.h" +- try_mpi_LIBS="-lmpi -lmpi_cxx" ++ try_mpi_LIBS="-lmpich -lmpichcxx -lmpl -pthread" + fi + + if test $ac_cv_header_mpi_h = yes -a $have_mpi_cxx_header = yes ; then +@@ -33655,7 +33655,6 @@ + ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' + ac_compiler_gnu=$ac_cv_cxx_compiler_gnu + +- try_mpi_LIBS= + save_LIBS=$LIBS + cat >conftest.$ac_ext <<_ACEOF + /* confdefs.h. */ +@@ -33664,7 +33663,7 @@ + cat >>conftest.$ac_ext <<_ACEOF + /* end confdefs.h. */ + +-#include <$mpi_cxx_header> ++#include <mpi.h> + + int + main () +@@ -33715,7 +33714,7 @@ + cat >>conftest.$ac_ext <<_ACEOF + /* end confdefs.h. */ + +-#include <mpi_cxx_header> ++#include <mpi.h> + + int + main () diff -urN science/mbdyn.orig/files/patch-include__ac__mpi.h science/mbdyn/files/patch-include__ac__mpi.h --- science/mbdyn.orig/files/patch-include__ac__mpi.h 1970-01-01 01:00:00.000000000 +0100 +++ science/mbdyn/files/patch-include__ac__mpi.h 2010-10-31 22:32:32.000000000 +0100 @@ -0,0 +1,11 @@ +--- ./include/ac/mpi.h.orig 2009-01-04 19:04:54.000000000 +0100 ++++ ./include/ac/mpi.h 2010-10-31 22:31:57.000000000 +0100 +@@ -35,7 +35,7 @@ + #ifdef HAVE_MPI___H + #include <mpi++.h> + #elif defined HAVE_MPICXX_H +-#include <mpicxx.h> ++#include <mpi.h> + #endif /* ! HAVE_MPI___H && ! HAVE_MPICXX_H */ + + #endif /* MPI_H */ diff -urN science/mbdyn.orig/files/patch-mbdyn__base__invsolver.cc science/mbdyn/files/patch-mbdyn__base__invsolver.cc --- science/mbdyn.orig/files/patch-mbdyn__base__invsolver.cc 1970-01-01 01:00:00.000000000 +0100 +++ science/mbdyn/files/patch-mbdyn__base__invsolver.cc 2010-10-31 23:15:16.000000000 +0100 @@ -0,0 +1,12 @@ +--- ./mbdyn/base/invsolver.cc.orig 2009-04-10 13:25:00.000000000 +0200 ++++ ./mbdyn/base/invsolver.cc 2010-10-31 23:14:49.000000000 +0100 +@@ -200,8 +200,8 @@ + } + } + +-#ifdef USE_SCHUR + int mpi_finalize = 0; ++#ifdef USE_SCHUR + + int MyRank = 0; + if (bParallel) { diff -urN science/mbdyn.orig/files/patch-mbdyn__base__solver.cc science/mbdyn/files/patch-mbdyn__base__solver.cc --- science/mbdyn.orig/files/patch-mbdyn__base__solver.cc 2009-08-05 23:44:49.000000000 +0200 +++ science/mbdyn/files/patch-mbdyn__base__solver.cc 2010-10-31 23:38:49.000000000 +0100 @@ -1,5 +1,5 @@ ---- mbdyn/base/solver.cc.orig 2009-06-24 23:13:44.000000000 +0900 -+++ mbdyn/base/solver.cc 2009-08-05 11:32:29.000000000 +0900 +--- mbdyn/base/solver.cc.orig 2009-06-24 16:13:44.000000000 +0200 ++++ mbdyn/base/solver.cc 2010-10-31 23:38:30.000000000 +0100 @@ -109,10 +109,17 @@ }; @@ -18,3 +18,13 @@ extern "C" void mbdyn_really_exit_handler(int signum) +@@ -456,8 +463,8 @@ + } + } + +-#ifdef USE_SCHUR + int mpi_finalize = 0; ++#ifdef USE_SCHUR + + int MyRank = 0; + if (bParallel) { --- mbdyn.diff ends here --- --- mpqc.diff begins here --- diff -urN science/mpqc.orig/Makefile science/mpqc/Makefile --- science/mpqc.orig/Makefile 2010-10-19 21:28:43.000000000 +0200 +++ science/mpqc/Makefile 2010-11-01 15:53:55.000000000 +0100 @@ -7,7 +7,7 @@ PORTNAME= mpqc PORTVERSION= 2.3.1 -PORTREVISION= 12 +PORTREVISION= 13 CATEGORIES= science parallel MASTER_SITES= SF @@ -74,6 +74,7 @@ .if defined(WITH_MPICH) CONFIGURE_ARGS+=--with-libdirs="-L${LOCALBASE}/lib -L${LOCALBASE}/lib"\ --enable-always-use-mpi +CONFIGURE_ENV+= PTHREAD_LIBS="${PTHREAD_LIBS}" .endif .if defined(WITH_MPICH) CONFIGURE_ARGS+=--with-include="-I${LOCALBASE}/include -I${WRKDIR} -I${LOCALBASE}/include" diff -urN science/mpqc.orig/files/patch-::configure.in science/mpqc/files/patch-::configure.in --- science/mpqc.orig/files/patch-::configure.in 2007-11-18 15:58:53.000000000 +0100 +++ science/mpqc/files/patch-::configure.in 2010-10-28 00:10:19.000000000 +0200 @@ -1,5 +1,5 @@ ---- configure.in.orig 2006-03-23 03:04:54.000000000 +0900 -+++ configure.in 2007-11-11 14:37:20.000000000 +0900 +--- configure.in.orig 2006-03-22 19:04:54.000000000 +0100 ++++ configure.in 2010-10-28 00:09:59.000000000 +0200 @@ -349,6 +349,31 @@ ac_default_prefix="/usr/local/mpqc/$SC_VERSION" @@ -165,7 +165,17 @@ AC_CHECK_FUNC(pthread_attr_getstacksize) AC_CHECK_FUNC(pthread_attr_setstacksize) AC_CHECK_FUNC(pthread_attr_setscope) -@@ -1769,10 +1793,10 @@ +@@ -1165,7 +1189,8 @@ + AC_CHECK_LIB(mpi,MPI_Init,[HAVE_MPI=yes;LIBS="-lmpi $LIBS"]) + fi + if test "$HAVE_MPI" = no; then +- AC_CHECK_LIB(mpich,MPI_Init,[HAVE_MPI=yes;LIBS="-lmpich $LIBS"]) ++ LIBS="-lmpl $PTHREAD_LIBS $LIBS" ++ AC_CHECK_LIB(mpich,MPI_Init,[HAVE_MPI=yes;LIBS="-lmpich -lmpl $PTHREAD_LIBS $LIBS"]) + fi + fi + if test X$HAVE_MPI = Xyes; then +@@ -1769,10 +1794,10 @@ dnl --------- CCA component configuration --------- --- mpqc.diff ends here --- >Release-Note: >Audit-Trail: >Unformatted:
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