ports/151867: net/mpich2: upgrade to 1.3.

Thierry Thomas thierry at FreeBSD.org
Mon Nov 1 15:30:13 UTC 2010 

>Number:         151867
>Category:       ports
>Synopsis:       net/mpich2: upgrade to 1.3.
>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 15:30:12 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 at graf.pompo.net:/usr/obj/usr/src/sys/GRAF100821 i386


	
>Description:
	Upgrade MPICH2 to 1.3.

	This implies to modify several dependencies.

>How-To-Repeat:
	NA

>Fix:
	Please apply the hereunder patches:

--- mpich2.diff begins here ---
diff -urN net/mpich2.orig/Makefile net/mpich2/Makefile
--- net/mpich2.orig/Makefile	2010-03-15 18:45:51.000000000 +0100
+++ net/mpich2/Makefile	2010-10-27 08:03:47.000000000 +0200
@@ -6,19 +6,18 @@
 #
 
 PORTNAME=	mpich2
-DISTVERSION=	1.2.1p1
+PORTVERSION=	1.3
 PORTEPOCH=	5
 CATEGORIES=	net parallel
-MASTER_SITES=	http://www.mcs.anl.gov/research/projects/mpich2/downloads/tarballs/${DISTVERSION}/
+MASTER_SITES=	http://www.mcs.anl.gov/research/projects/mpich2/downloads/tarballs/${PORTVERSION}/
 DIST_SUBDIR=	mpich
-#PATCH_SITES=	ftp://ftp.mcs.anl.gov/pub/mpi/mpich2-patch/
-#PATCHFILES=
 
 MAINTAINER=	ports at FreeBSD.org
 COMMENT=	A portable implementation of MPI-1 and MPI-2
 
+BUILD_DEPENDS=	bash:${PORTSDIR}/shells/bash
 LIB_DEPENDS=	execinfo.1:${PORTSDIR}/devel/libexecinfo
-#BUILD_DEPENDS=	doctext:${PORTSDIR}/textproc/sowing
+RUN_DEPENDS=	bash:${PORTSDIR}/shells/bash
 
 #-----------------------------------------------------------------------
 # You may define these options:
@@ -40,7 +39,7 @@
 USE_GNOME=	pkgconfig
 
 GNU_CONFIGURE=	yes
-CONFIGURE_ARGS=	--enable-romio --enable-sharedlibs=gcc	\
+CONFIGURE_ARGS=	--enable-romio --enable-shared	\
 		--docdir=${DOCSDIR}
 CONFIGURE_ENV+=	PTHREAD_LIBS="${PTHREAD_LIBS}" CPPFLAGS="-I${LOCALBASE}/include"	\
 		LDFLAGS="-L${LOCALBASE}/lib -lexecinfo ${PTHREAD_LIBS}"			\
@@ -56,15 +55,16 @@
 CONFLICTS=	lam-7.* mpiexec-0.*
 
 USE_FORTRAN=	yes
-F90FLAGS+=	${FFLAGS}
-CONFIGURE_ENV+=	F90="${FC}" F90FLAGS="${F90FLAGS}"
+FCFLAGS+=	${FFLAGS}
+CONFIGURE_ENV+=	FC="${FC}" FCFLAGS="${FCFLAGS}"
 
 USE_LDCONFIG=	yes
 
 SUB_FILES=	pkg-message
 
-VERSO=		1.2
-PLIST_SUB=	VER=${VERSO}
+VERSO=		2.0
+VERSOM=		${VERSO:R}
+PLIST_SUB=	VER=${VERSO} VERM=${VERSOM}
 .if defined(WITHOUT_X11)
 CONFIGURE_ARGS+=	--disable-graphics
 WITHOUT_JAVA=	yes
@@ -95,8 +95,6 @@
 PLIST_SUB+=	PM_MPD="" PM_SMPD="@comment "
 .endif
 
-LIBSSO=		fmpich mpich mpichcxx mpichf90
-
 THREAD2FIX=	configure test/mpi/threads/comm/Makefile.in	\
 		test/mpi/threads/pt2pt/Makefile.in		\
 		src/mpe2/src/logging/configure			\
@@ -107,9 +105,9 @@
 		src/mpe2/src/graphics/configure
 DOC2PATCH=	Makefile.in src/mpe2/sbin/mpeinstall.in		\
 		src/openpa/Makefile.in src/mpi/romio/util/romioinstall.in
-CONFPFX2FIX1=	man/man1/mpd.1 src/pm/mpd/mpd.py
-CONFPFX2FIX2=	README doc/installguide/install.tex.vin		\
-		src/pm/mpd/mpdlib.py src/pm/mpd/mpdroot.c
+CONFPFX2FIX1=	src/pm/mpd/mpd.py
+CONFPFX2FIX2=	doc/installguide/install.tex.vin		\
+		src/pm/mpd/mpdroot.c
 
 .include <bsd.port.pre.mk>
 
@@ -182,14 +180,6 @@
 		${WRKSRC}/src/packaging/pkgconfig/mpich2-ch3.pc
 
 post-install:
-.for lib in ${LIBSSO}
-	${MV} ${PREFIX}/lib/lib${lib}.so.1.2 ${PREFIX}/lib/lib${lib}.so.1
-	${LN} -sf ${PREFIX}/lib/lib${lib}.so.1 ${PREFIX}/lib/lib${lib}.so
-	${LN} -sf ${PREFIX}/lib/lib${lib}.so.1 ${PREFIX}/lib/lib${lib}.so.1.2
-.endfor
-.if !defined(NOPORTDOCS)
-	${RM} ${MANPREFIX}/man/man1/mpd.1.bak
-.endif
 	@${PYTHON_CMD} ${PYTHON_LIBDIR}/compileall.py ${PREFIX}/bin
 	@${PYTHON_CMD} -O ${PYTHON_LIBDIR}/compileall.py ${PREFIX}/bin
 	@${ECHO_CMD} "MPD_SECRETWORD=change_on_install" > ${WRKDIR}/mpd.conf.dist
diff -urN net/mpich2.orig/distinfo net/mpich2/distinfo
--- net/mpich2.orig/distinfo	2010-03-08 22:29:34.000000000 +0100
+++ net/mpich2/distinfo	2010-10-23 10:53:52.000000000 +0200
@@ -1,3 +1,3 @@
-MD5 (mpich/mpich2-1.2.1p1.tar.gz) = fa7e8dc7c5fb60395ab26c5b239321ca
-SHA256 (mpich/mpich2-1.2.1p1.tar.gz) = a55d1682ee0b5ebbacc047f60620ed291e0a9b3ded3eaeb6a2c81a1598c4c964
-SIZE (mpich/mpich2-1.2.1p1.tar.gz) = 18014859
+MD5 (mpich/mpich2-1.3.tar.gz) = d19865b6244845198c29fc553a6bb8ad
+SHA256 (mpich/mpich2-1.3.tar.gz) = c76e869045ce274ee0494b0c72d884f9e2d3176a4689d362e684754ae0430e63
+SIZE (mpich/mpich2-1.3.tar.gz) = 19394388
diff -urN net/mpich2.orig/files/manpages net/mpich2/files/manpages
--- net/mpich2.orig/files/manpages	2009-11-25 18:48:02.000000000 +0100
+++ net/mpich2/files/manpages	2010-10-23 15:42:47.000000000 +0200
@@ -1,22 +1,5 @@
 MAN1= \
 MPI.1 \
-Zeroconf.1 \
-mpd.1 \
-mpdallexit.1 \
-mpdboot.1 \
-mpdcheck.1 \
-mpdchkpyver.1 \
-mpdcleanup.1 \
-mpdexit.1 \
-mpdgdbdrv.1 \
-mpdhelp.1 \
-mpdkilljob.1 \
-mpdlib.1 \
-mpdlistjobs.1 \
-mpdman.1 \
-mpdringtest.1 \
-mpdsigjob.1 \
-mpdtrace.1 \
 mpicc.1 \
 mpicxx.1 \
 mpiexec.1 \
diff -urN net/mpich2.orig/pkg-plist net/mpich2/pkg-plist
--- net/mpich2.orig/pkg-plist	2010-03-14 22:56:15.000000000 +0100
+++ net/mpich2/pkg-plist	2010-10-23 17:46:39.000000000 +0200
@@ -1,3 +1,4 @@
+bin/bt2line
 bin/check_callstack
 @comment SLOG-2 tools are not installed if NOPORTDOCS is set
 %%JAVA%%bin/clog2TOslog2
@@ -167,7 +168,7 @@
 lib/libampe.a
 lib/libfmpich.a
 lib/libfmpich.so
-lib/libfmpich.so.1
+lib/libfmpich.so.%%VERM%%
 lib/libfmpich.so.%%VER%%
 lib/liblmpe.a
 lib/libmpe.a
@@ -178,17 +179,24 @@
 lib/libmpe_null.a
 lib/libmpich.a
 lib/libmpich.so
-lib/libmpich.so.1
+lib/libmpich.so.%%VERM%%
 lib/libmpich.so.%%VER%%
 lib/libmpichcxx.a
 lib/libmpichcxx.so
-lib/libmpichcxx.so.1
+lib/libmpichcxx.so.%%VERM%%
 lib/libmpichcxx.so.%%VER%%
 lib/libmpichf90.a
 lib/libmpichf90.so
-lib/libmpichf90.so.1
+lib/libmpichf90.so.%%VERM%%
 lib/libmpichf90.so.%%VER%%
+lib/libmpl.a
+lib/libmpl.la
+lib/libmpl.so
+lib/libmpl.so.1
 lib/libopa.a
+lib/libopa.la
+lib/libopa.so
+lib/libopa.so.1
 lib/libtmpe.a
 %%JAVA%%lib/logconvertor.jar
 lib/mpe_prof.o
--- mpich2.diff ends here ---

--- valgrind.diff begins here ---
diff -urN devel/valgrind.orig/Makefile devel/valgrind/Makefile
--- devel/valgrind.orig/Makefile	2010-10-24 08:16:33.000000000 +0200
+++ devel/valgrind/Makefile	2010-11-01 15:48:49.000000000 +0100
@@ -7,7 +7,7 @@
 
 PORTNAME=	valgrind
 PORTVERSION=	3.6.0
-PORTREVISION=	2
+PORTREVISION=	3
 PORTEPOCH=	1
 CATEGORIES=	devel
 MASTER_SITES=	http://www.deglitch.com/dist/
@@ -44,7 +44,7 @@
 .endif
 
 .if defined(WITH_MPI) || exists(${LOCALBASE}/bin/mpicc)
-LIB_DEPENDS+=	mpich.1:${PORTSDIR}/net/mpich2
+LIB_DEPENDS+=	mpich.2:${PORTSDIR}/net/mpich2
 PLIST_SUB+=	MPI=""
 .else
 PLIST_SUB+=	MPI="@comment "
--- valgrind.diff ends here ---

--- aster.diff begins here ---
diff -urN french/aster.orig/Makefile french/aster/Makefile
--- french/aster.orig/Makefile	2010-09-20 18:45:56.000000000 +0200
+++ french/aster/Makefile	2010-10-25 23:56:55.000000000 +0200
@@ -7,6 +7,7 @@
 
 PORTNAME=		aster
 DISTVERSION=		${ASTER_DISTVERSION}
+PORTREVISION=		1
 CATEGORIES=		french cad
 
 MAINTAINER=	thierry at FreeBSD.org
@@ -131,13 +132,13 @@
 BUILD_DEPENDS+=	${LOCALBASE}/lib/libblacs.a:${PORTSDIR}/math/blacs	\
 		${LOCALBASE}/lib/libscalapack.a:${PORTSDIR}/math/scalapack
 MUMPS_PORT=	mumps-mpich
-MUMPSLIB=	-L${LOCALBASE}/lib -ldmumps -lzmumps -lmumps_common -lpord -lscalapack -lblacs -lblacsc -lblacs -L${LOCALBASE}/lib -lmpich
+MUMPSLIB=	-L${LOCALBASE}/lib -ldmumps -lzmumps -lmumps_common -lpord -lscalapack -lblacs -lblacsc -lblacs -L${LOCALBASE}/lib -lmpich -lmpl
 . endif
 BUILD_DEPENDS+=	${LOCALBASE}/lib/libcmumps.a:${PORTSDIR}/math/${MUMPS_PORT}
 .endif
 
 .if defined(WITH_MPI)
-BUILD_DEPENDS+=	${HOME_MPI}/include/mpif.h:${PORTSDIR}/net/mpich2
+LIB_DEPENDS+=	mpich.2:${PORTSDIR}/net/mpich2
 HOME_MPI=	${LOCALBASE}
 .endif
 
@@ -220,7 +221,7 @@
 
 pre-everything::
 .if defined(WITH_MPI)
-	@${ECHO_MSG} "To build Code_Aster with MPI enabled, you need to run `mpd &'"
+	@${ECHO_MSG} "To build Code_Aster with MPI enabled, you need to run \`mpd &'"
 .endif
 
 pre-configure:
@@ -337,6 +338,7 @@
 	${ECHO_CMD} "#?vers : VVV?" >> ${WRKSRC}/instdir/etc/codeaster/aster
 	${CP} -R ${LOCALBASE}/aster/ASTK/ASTK_SERV/bin		\
 		${LOCALBASE}/aster/ASTK/ASTK_SERV/asrun		\
+		${LOCALBASE}/aster/ASTK/ASTK_SERV/share		\
 		${WRKSRC}/instdir/
 	${REINPLACE_CMD} -e 's|${LOCALBASE}/aster|${WRKSRC}/instdir|'	\
 		${WRKSRC}/instdir/bin/as_run
diff -urN french/aster.orig/files/patch-products.py french/aster/files/patch-products.py
--- french/aster.orig/files/patch-products.py	2010-08-30 22:23:04.000000000 +0200
+++ french/aster/files/patch-products.py	2010-10-25 22:53:40.000000000 +0200
@@ -1,5 +1,5 @@
---- products.py.orig	2010-07-07 18:18:13.000000000 +0200
-+++ products.py	2010-08-12 19:08:43.000000000 +0200
+--- products.py.orig	2010-09-14 10:48:26.000000000 +0200
++++ products.py	2010-10-25 22:53:13.000000000 +0200
 @@ -907,16 +907,19 @@
             'HOME_PYTHON', 'PYTHON_EXE', 'PYTHONLIB',
             'HOME_MUMPS', 'HOME_ZMAT', 'HOME_MPI', 'INCLUDE_MUMPS', 'HOME_METIS',
@@ -40,7 +40,7 @@
 +      opt['FINCLUDE']   = ''
 +      cxxlibs.extend(['stdc++', 'supc++'])
 +      zmat_platform=''
-+      mpilibs.extend(['mpich'])
++      mpilibs.extend(['mpich', 'mpl'])
     elif cfg['IFDEF'] == 'LINUX64':
        opt['SYSLIB']     = '-Wl,--allow-multiple-definition -Wl,--export-dynamic -lieee -ldl -lutil -lm'
        opt['LDFLAGS']    = '-v'
--- aster.diff ends here ---

--- mumps.diff begins here ---
diff -urN math/mumps.orig/files/patch-Make.inc+Makefile.inc.generic math/mumps/files/patch-Make.inc+Makefile.inc.generic
--- math/mumps.orig/files/patch-Make.inc+Makefile.inc.generic	2010-01-01 17:09:44.000000000 +0100
+++ math/mumps/files/patch-Make.inc+Makefile.inc.generic	2010-10-26 19:32:50.000000000 +0200
@@ -52,7 +52,7 @@
  
  # LIBRARIES USED BY THE PARALLEL VERSION OF MUMPS: $(SCALAP) and MPI
 -LIBPAR  = $(SCALAP) -L/usr/lib -lmpi
-+LIBPAR  = -L at LOCALBASE@/lib -lfmpich -lmpich $(SCALAP)
++LIBPAR  = -L at LOCALBASE@/lib -lfmpich -lmpich -lmpl $(SCALAP)
  
  # The parallel version is not concerned by the next two lines.
  # They are related to the sequential library provided by MUMPS,
--- mumps.diff ends here ---

--- petsc.diff begins here ---
diff -urN math/petsc.orig/Makefile math/petsc/Makefile
--- math/petsc.orig/Makefile	2009-11-28 11:44:53.000000000 +0100
+++ math/petsc/Makefile	2010-10-27 22:50:27.000000000 +0200
@@ -28,8 +28,8 @@
 			PETSC_DIR=${WRKSRC}
 CONFIGURE_ARGS=		--prefix=${PREFIX}/${PFX} --COPTFLAGS="${CFLAGS}"	\
 			--CXXOPTFLAGS="${CXXFLAGS}" --FOPTFLAGS="${FFLAGS}"	\
-			--with-shared=1 --with-cc=${CC} --with-fc=${FC}	\
-			--CPPFLAGS="-I${LOCALBASE}/include"
+			--with-shared=1 --with-cc=${CC} --with-fc=${FC}		\
+			--CPPFLAGS="-I${LOCALBASE}/include" --LDFLAGS=${PTHREAD_LIBS}
 ALL_TARGET=		all
 MAKEFILE=		makefile
 MAKE_ENV=		PETSC_DIR=${WRKSRC}
@@ -258,6 +258,14 @@
 	${REINPLACE_CMD} -e "s|/bin/ksh|${LOCALBASE}/bin/ksh|"	\
 		${WRKSRC}/bin/popup
 	@${RM} ${WRKSRC}/bin/popup.bak
+.if defined (WITH_MPI)
+. for ps in ml.py MPE.py
+	${REINPLACE_CMD} -e "s|-lpmpich|-lmpl|"	\
+		${WRKSRC}/python/PETSc/packages/${ps}
+. endfor
+	${REINPLACE_CMD} -e "s|libpmpich|libmpl|"	\
+		${WRKSRC}/python/BuildSystem/config/packages/MPI.py
+.endif
 .if defined(PACKAGE_BUILDING)
 	${REINPLACE_CMD} -e "s|%%PACKAGE%%exit 1; ||"		\
 		-e "s|%%PACKAGE%%sys.exit(3)||"			\
--- petsc.diff ends here ---

--- fvm.diff begins here ---
diff -urN science/fvm.orig/Makefile science/fvm/Makefile
--- science/fvm.orig/Makefile	2010-01-01 17:10:48.000000000 +0100
+++ science/fvm/Makefile	2010-10-25 21:57:10.000000000 +0200
@@ -7,7 +7,7 @@
 
 PORTNAME=	fvm
 PORTVERSION=	0.12.0
-PORTREVISION=	1
+PORTREVISION=	2
 CATEGORIES=	science parallel
 MASTER_SITES=	http://rd.edf.com/fichiers/fckeditor/File/EDF%20RD/Code_Saturne/Fichiers/
 DISTNAME=	${PORTNAME}-${PORTVERSION:S/.//g}
@@ -52,6 +52,8 @@
 TESTSBIN=	fvm_file_test fvm_interface_test fvm_selector_postfix_test fvm_selector_test
 
 pre-configure:
+	${REINPLACE_CMD} -e 's|-lmpich|-lmpich -lmpl|'	\
+		${WRKSRC}/${CONFIGURE_SCRIPT}
 	# No useful doc there
 	${REINPLACE_CMD} -e 's|tests doc|tests|' ${WRKSRC}/Makefile.in
 
--- fvm.diff ends here ---

--- ncs.diff begins here ---
diff -urN science/ncs.orig/Makefile science/ncs/Makefile
--- science/ncs.orig/Makefile	2010-04-04 18:05:42.000000000 +0200
+++ science/ncs/Makefile	2010-10-27 22:59:18.000000000 +0200
@@ -67,7 +67,7 @@
 MPI_HOME=	${LOCALBASE}
 BUILD_DEPENDS+=	${MPI_HOME}/bin/mpicc:${PORTSDIR}/net/mpich2
 RUN_DEPENDS+=	${MPI_HOME}/bin/mpirun:${PORTSDIR}/net/mpich2
-MPI_LIBS=	-lmpich
+MPI_LIBS=	-lmpich -lmpl ${PTHREAD_LIBS}
 .endif
 
 .if !defined(NOPORTDOCS)
--- ncs.diff ends here ---


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