14 files changed, 230 insertions, 32 deletions

diff --git a/science/pnetcdf/Makefile b/science/pnetcdf/Makefile
index 752e9c76bbbb..2cd007080380 100644
--- a/science/pnetcdf/Makefile
+++ b/science/pnetcdf/Makefile
@@ -2,54 +2,44 @@
 # $FreeBSD$
 
 PORTNAME=	pnetcdf
-PORTVERSION=	1.3.1
-PORTREVISION=	1
+PORTVERSION=	1.4.1
 CATEGORIES=	science parallel
-MASTER_SITES=	http://ftp.mcs.anl.gov/pub/parallel-netcdf/ \
+MASTER_SITES=	http://cucis.ece.northwestern.edu/projects/PnetCDF/Release/ \
 		LOCAL/sunpoet
 DISTNAME=	parallel-netcdf-${PORTVERSION}
 
 MAINTAINER=	sunpoet@FreeBSD.org
 COMMENT=	Library providing high-performance I/O
 
-OPTIONS_DEFINE=	DOCS OPENMPI
-OPENMPI_DESC=	Use openmpi instead of mpich2
+OPTIONS_DEFINE=	DOCS
+OPTIONS_SINGLE=	MPI
+OPTIONS_SINGLE_MPI=	OPENMPI MPICH2
+OPTIONS_DEFAULT=OPENMPI
 
 CONFLICTS=	hdf-4.*
 
 CFLAGS+=	-fPIC -DPIC
 CONFIGURE_ENV=	M4FLAGS=""
 GNU_CONFIGURE=	yes
+MAKE_JOBS_UNSAFE=	yes
 USE_BZIP2=	yes
 USES=		fortran gmake
 
-MAN1=		ncmpidiff.1 ncmpidump.1 ncmpigen.1
-MAN3=		pnetcdf.3
 PORTDOCS=	COPYRIGHT INSTALL README
-PLIST_FILES=	bin/ncmpidiff bin/ncmpidump bin/ncmpigen bin/ncvalid \
-		include/pnetcdf.h include/pnetcdf.inc include/pnetcdf.mod \
-		lib/libpnetcdf.a
-
-NO_STAGE=	yes
-.include <bsd.port.options.mk>
-
-.if ${PORT_OPTIONS:MOPENMPI}
-BUILD_DEPENDS+=	${LOCALBASE}/mpi/openmpi/bin/mpicc:${PORTSDIR}/net/openmpi
-RUN_DEPENDS+=	${LOCALBASE}/mpi/openmpi/lib/libmpi.so:${PORTSDIR}/net/openmpi
-CONFIGURE_ARGS+=--with-mpi=${LOCALBASE}/mpi/openmpi
-.else
-BUILD_DEPENDS+=	${LOCALBASE}/bin/mpicc:${PORTSDIR}/net/mpich2
-RUN_DEPENDS+=	${LOCALBASE}/lib/libmpich.so:${PORTSDIR}/net/mpich2
-CONFIGURE_ARGS+=--with-mpi=${LOCALBASE}
-.endif
+
+#FORTRAN_CONFIGURE_OFF=	--disable-fortran
+#FORTRAN_CONFIGURE_ON=	--enable-fortran
+#FORTRAN_USES=		fortran
+MPICH2_CONFIGURE_ON=	--with-mpi=${LOCALBASE}
+MPICH2_LIB_DEPENDS=	libmpich.so:${PORTSDIR}/net/mpich2
+OPENMPI_CONFIGURE_ON=	--with-mpi=${LOCALBASE}/mpi/openmpi
+OPENMPI_LIB_DEPENDS=	libmpi.so:${PORTSDIR}/net/openmpi
 
 post-install:
-.for file in ncmpidiff ncmpidump ncmpigen ncvalid
-	${STRIP_CMD} ${PREFIX}/bin/${file}
+.for file in ncmpidiff ncmpidump ncmpigen ncmpivalid
+	${STRIP_CMD} ${STAGEDIR}${PREFIX}/bin/${file}
 .endfor
-.if ${PORT_OPTIONS:MDOCS}
-	${MKDIR} ${DOCSDIR}/
-	cd ${WRKSRC}/ && ${INSTALL_DATA} ${PORTDOCS} ${DOCSDIR}/
-.endif
+	${MKDIR} ${STAGEDIR}${DOCSDIR}/
+	cd ${WRKSRC}/ && ${INSTALL_DATA} ${PORTDOCS} ${STAGEDIR}${DOCSDIR}/
 
 .include <bsd.port.mk>
diff --git a/science/pnetcdf/distinfo b/science/pnetcdf/distinfo
index 725e29149322..888fb218e474 100644
--- a/science/pnetcdf/distinfo
+++ b/science/pnetcdf/distinfo
@@ -1,2 +1,2 @@
-SHA256 (parallel-netcdf-1.3.1.tar.bz2) = 8d8fc0dbec39bcc01a8d556a8f6f65199e7da42d2e15cd24a8d96a750fba8a61
-SIZE (parallel-netcdf-1.3.1.tar.bz2) = 1658379
+SHA256 (parallel-netcdf-1.4.1.tar.bz2) = a79e8bfebde5baaa17470ff4425cbdcf99bd3cd265efdf3a8aedeca91c057463
+SIZE (parallel-netcdf-1.4.1.tar.bz2) = 1622328
diff --git a/science/pnetcdf/files/patch-configure b/science/pnetcdf/files/patch-configure
new file mode 100644
index 000000000000..5e65c3b2d0f0
--- /dev/null
+++ b/science/pnetcdf/files/patch-configure
@@ -0,0 +1,29 @@
+--- configure.orig	2013-12-24 06:35:50.000000000 +0800
++++ configure	2014-03-09 22:42:45.285478789 +0800
+@@ -2886,10 +2886,11 @@
+ ac_configure="$SHELL $ac_aux_dir/configure"  # Please don't use this var.
+ 
+ 
++PNETCDF_VERSION_MAJOR=`echo ${PACKAGE_VERSION} | cut -d. -f1`
++PNETCDF_VERSION_MINOR=`echo ${PACKAGE_VERSION} | cut -d. -f2`
++PNETCDF_VERSION_SUB=`echo ${PACKAGE_VERSION} | cut -d. -f3`
++PNETCDF_VERSION_PRE=`echo ${PACKAGE_VERSION} | cut -d. -f4`
+ 
+-saved_IFS=${IFS}
+-IFS=. read PNETCDF_VERSION_MAJOR PNETCDF_VERSION_MINOR PNETCDF_VERSION_SUB PNETCDF_VERSION_PRE <<< "$PACKAGE_VERSION"
+-IFS=${saved_IFS}
+ 
+ PNETCDF_VERSION="${PNETCDF_VERSION_MAJOR}.${PNETCDF_VERSION_MINOR}"
+ if test x${PNETCDF_VERSION_SUB} != x ; then
+@@ -2899,11 +2900,6 @@
+    fi
+ fi
+ 
+-SVN_DATE="$LastChangedDate: 2013-12-23 16:32:11 -0600 (Mon, 23 Dec 2013) $"
+-saved_IFS=${IFS}
+-IFS="\ " read t_key PNETCDF_RELEASE_DATE2 t_time t_zone t_string <<< ${SVN_DATE}
+-IFS="() $," read t_day PNETCDF_RELEASE_DATE <<< $t_string
+-IFS=${saved_IFS}
+ 
+ _DEBUG=no
+ 
diff --git a/science/pnetcdf/files/patch-man-Makefile.in b/science/pnetcdf/files/patch-man-Makefile.in
new file mode 100644
index 000000000000..902d35b3b212
--- /dev/null
+++ b/science/pnetcdf/files/patch-man-Makefile.in
@@ -0,0 +1,17 @@
+--- man/Makefile.in.orig	2013-11-17 13:18:16.000000000 +0800
++++ man/Makefile.in	2014-03-09 22:42:45.288471552 +0800
+@@ -43,12 +43,12 @@
+ test:
+ 
+ install: $(MANUAL)
+-	$(INSTALL) -d -m 755 $(MANDIR)/man3
++	$(INSTALL) -d -m 755 $(DESTDIR)$(MANDIR)/man3
+ 	@for i in $(MANUAL) ; do ( \
+ 	    if test -f $(srcdir)/$$i; then file=$(srcdir)/$$i; \
+ 	    else file=$$i; fi; \
+ 	    fn=`basename $$i` ; \
+-	    $(INSTALL_DATA) $$file $(MANDIR)/man3/$$fn \
++	    $(INSTALL_DATA) $$file $(DESTDIR)$(MANDIR)/man3/$$fn \
+ 	; ) ; done
+ 
+ uninstall:
diff --git a/science/pnetcdf/files/patch-rules.make b/science/pnetcdf/files/patch-rules.make
new file mode 100644
index 000000000000..0d36c16a26a9
--- /dev/null
+++ b/science/pnetcdf/files/patch-rules.make
@@ -0,0 +1,32 @@
+--- rules.make.orig	2013-10-27 00:53:18.000000000 +0800
++++ rules.make	2014-03-09 22:42:45.290481492 +0800
+@@ -125,21 +125,21 @@
+ # $(INSTALL)ation:
+ 
+ $(INCDIR)/$(HEADER):	$(INCDIR) $(HEADER)
+-	$(INSTALL) $(srcdir)/$(HEADER) $@
++	$(INSTALL) $(srcdir)/$(HEADER) $(DESTDIR)$@
+ $(INCDIR)/$(HEADER1):	$(INCDIR) $(HEADER1)
+-	$(INSTALL) $(srcdir)/$(HEADER1) $@
++	$(INSTALL) $(srcdir)/$(HEADER1) $(DESTDIR)$@
+ $(INCDIR)/$(HEADER2):	$(INCDIR) $(HEADER2)
+-	$(INSTALL) $(srcdir)/$(HEADER2) $@
++	$(INSTALL) $(srcdir)/$(HEADER2) $(DESTDIR)$@
+ $(INCDIR)/$(HEADER3):	$(INCDIR) $(HEADER3)
+-	$(INSTALL) $(srcdir)/$(HEADER3) $@
++	$(INSTALL) $(srcdir)/$(HEADER3) $(DESTDIR)$@
+ 
+ $(LIBDIR)/$(LIBRARY):	$(LIBDIR) $(LIBRARY)
+-	$(INSTALL) -d -m 755 $(LIBDIR)
+-	$(INSTALL) -m 644  $(LIBRARY) $@
++	$(INSTALL) -d -m 755 $(DESTDIR)$(LIBDIR)
++	$(INSTALL) -m 644  $(LIBRARY) $(DESTDIR)$@
+ 
+ $(BINDIR)/$(PROGRAM):	$(BINDIR) $(PROGRAM)
+-	$(INSTALL) -d -m 755 $(BINDIR)
+-	$(INSTALL) -m 755  $(PROGRAM) $@
++	$(INSTALL) -d -m 755 $(DESTDIR)$(BINDIR)
++	$(INSTALL) -m 755  $(PROGRAM) $(DESTDIR)$@
+ 
+ #$(BINDIR) \
+ #$(INCDIR) \
diff --git a/science/pnetcdf/files/patch-src-lib-Makefile.in b/science/pnetcdf/files/patch-src-lib-Makefile.in
new file mode 100644
index 000000000000..00a613fb132e
--- /dev/null
+++ b/science/pnetcdf/files/patch-src-lib-Makefile.in
@@ -0,0 +1,17 @@
+--- src/lib/Makefile.in.orig	2013-11-17 02:02:38.000000000 +0800
++++ src/lib/Makefile.in	2014-03-09 22:42:45.293477277 +0800
+@@ -97,10 +97,10 @@
+ 	$(RANLIB) $@
+ 
+ install:
+-	$(INSTALL) -d -m 755 $(LIBDIR)
+-	$(INSTALL_DATA) $(LIBRARY) $(LIBDIR)/$(LIBRARY)
+-	$(INSTALL) -d -m 755 $(INCDIR)
+-	$(INSTALL_DATA) $(HEADER) $(INCDIR)/$(HEADER)
++	$(INSTALL) -d -m 755 $(DESTDIR)$(LIBDIR)
++	$(INSTALL_DATA) $(LIBRARY) $(DESTDIR)$(LIBDIR)/$(LIBRARY)
++	$(INSTALL) -d -m 755 $(DESTDIR)$(INCDIR)
++	$(INSTALL_DATA) $(HEADER) $(DESTDIR)$(INCDIR)/$(HEADER)
+ 
+ uninstall:
+ 	$(RM) -f $(LIBDIR)/$(LIBRARY)
diff --git a/science/pnetcdf/files/patch-src-libf-Makefile.in b/science/pnetcdf/files/patch-src-libf-Makefile.in
new file mode 100644
index 000000000000..c2f2bab730ee
--- /dev/null
+++ b/science/pnetcdf/files/patch-src-libf-Makefile.in
@@ -0,0 +1,13 @@
+--- src/libf/Makefile.in.orig	2013-10-27 00:53:18.000000000 +0800
++++ src/libf/Makefile.in	2014-03-09 22:42:45.296474221 +0800
+@@ -351,8 +351,8 @@
+ 	$(SED) -e "s%/\*%!%g" -e "s%\*/%%g" $< > $@
+ 
+ install: pnetcdf.inc
+-	$(INSTALL) -d -m 755 $(INCDIR)
+-	$(INSTALL_DATA) pnetcdf.inc $(INCDIR)
++	$(INSTALL) -d -m 755 $(DESTDIR)$(INCDIR)
++	$(INSTALL_DATA) pnetcdf.inc $(DESTDIR)$(INCDIR)
+ 
+ uninstall:
+ 	$(RM) -f $(INCDIR)/pnetcdf.inc
diff --git a/science/pnetcdf/files/patch-src-libf90-Makefile.in b/science/pnetcdf/files/patch-src-libf90-Makefile.in
new file mode 100644
index 000000000000..f255a1291642
--- /dev/null
+++ b/science/pnetcdf/files/patch-src-libf90-Makefile.in
@@ -0,0 +1,13 @@
+--- src/libf90/Makefile.in.orig	2013-12-15 01:17:42.000000000 +0800
++++ src/libf90/Makefile.in	2014-03-09 22:42:45.298473932 +0800
+@@ -71,8 +71,8 @@
+ 	$(RANLIB) $(LIBRARY)
+ 
+ install: $(PNETCDF_MOD)
+-	$(INSTALL) -d -m 755 $(INCDIR)
+-	$(INSTALL_DATA) $(PNETCDF_MOD) $(INCDIR)
++	$(INSTALL) -d -m 755 $(DESTDIR)$(INCDIR)
++	$(INSTALL_DATA) $(PNETCDF_MOD) $(DESTDIR)$(INCDIR)
+ 
+ uninstall:
+ 	$(RM) -f $(INCDIR)/$(PNETCDF_MOD)
diff --git a/science/pnetcdf/files/patch-src-utils-ncmpidiff-Makefile.in b/science/pnetcdf/files/patch-src-utils-ncmpidiff-Makefile.in
new file mode 100644
index 000000000000..6b2fd33fb48b
--- /dev/null
+++ b/science/pnetcdf/files/patch-src-utils-ncmpidiff-Makefile.in
@@ -0,0 +1,18 @@
+--- src/utils/ncmpidiff/Makefile.in.orig	2013-11-03 03:15:49.000000000 +0800
++++ src/utils/ncmpidiff/Makefile.in	2014-03-09 22:42:45.301478900 +0800
+@@ -37,11 +37,11 @@
+ 	set -e ; cd $(BUILDDIR)/src && $(MAKE) $(MFLAGS) all
+ 
+ install:	
+-	$(INSTALL) -d -m 755 $(MANDIR)/man1
+-	$(INSTALL_DATA) $(srcdir)/$(MANUAL) $(MANDIR)/man1/$(MANUAL)
++	$(INSTALL) -d -m 755 $(DESTDIR)$(MANDIR)/man1
++	$(INSTALL_DATA) $(srcdir)/$(MANUAL) $(DESTDIR)$(MANDIR)/man1/$(MANUAL)
+ 
+-	$(INSTALL) -d $(BINDIR)
+-	$(INSTALL) -m 755 $(PROGRAM) $(BINDIR)/$(PROGRAM)
++	$(INSTALL) -d $(DESTDIR)$(BINDIR)
++	$(INSTALL) -m 755 $(PROGRAM) $(DESTDIR)$(BINDIR)/$(PROGRAM)
+ 
+ uninstall:
+ 	$(RM) -f $(BINDIR)/$(PROGRAM)
diff --git a/science/pnetcdf/files/patch-src-utils-ncmpidump-Makefile.in b/science/pnetcdf/files/patch-src-utils-ncmpidump-Makefile.in
new file mode 100644
index 000000000000..9c19ca0c2e66
--- /dev/null
+++ b/science/pnetcdf/files/patch-src-utils-ncmpidump-Makefile.in
@@ -0,0 +1,18 @@
+--- src/utils/ncmpidump/Makefile.in.orig	2013-11-03 03:15:49.000000000 +0800
++++ src/utils/ncmpidump/Makefile.in	2014-03-09 22:42:45.303474265 +0800
+@@ -48,11 +48,11 @@
+ 	     echo "*** $(PROGRAM) test successful ***"
+ 
+ install:	
+-	$(INSTALL) -d -m 755 $(MANDIR)/man1
+-	$(INSTALL_DATA) $(srcdir)/$(MANUAL) $(MANDIR)/man1/$(MANUAL)
++	$(INSTALL) -d -m 755 $(DESTDIR)$(MANDIR)/man1
++	$(INSTALL_DATA) $(srcdir)/$(MANUAL) $(DESTDIR)$(MANDIR)/man1/$(MANUAL)
+ 
+-	$(INSTALL) -d $(BINDIR)
+-	$(INSTALL) -m 755 $(PROGRAM) $(BINDIR)/$(PROGRAM)
++	$(INSTALL) -d $(DESTDIR)$(BINDIR)
++	$(INSTALL) -m 755 $(PROGRAM) $(DESTDIR)$(BINDIR)/$(PROGRAM)
+ 
+ uninstall:
+ 	$(RM) -f $(BINDIR)/$(PROGRAM)
diff --git a/science/pnetcdf/files/patch-src-utils-ncmpigen-Makefile.in b/science/pnetcdf/files/patch-src-utils-ncmpigen-Makefile.in
new file mode 100644
index 000000000000..3fee3987692e
--- /dev/null
+++ b/science/pnetcdf/files/patch-src-utils-ncmpigen-Makefile.in
@@ -0,0 +1,18 @@
+--- src/utils/ncmpigen/Makefile.in.orig	2013-11-03 03:15:49.000000000 +0800
++++ src/utils/ncmpigen/Makefile.in	2014-03-09 22:42:45.306475408 +0800
+@@ -48,11 +48,11 @@
+ test:           $(PROGRAM) b-test c-test FORCE
+ 
+ install:	
+-	$(INSTALL) -d -m 755 $(MANDIR)/man1
+-	$(INSTALL_DATA) $(srcdir)/$(MANUAL) $(MANDIR)/man1/$(MANUAL)
++	$(INSTALL) -d -m 755 $(DESTDIR)$(MANDIR)/man1
++	$(INSTALL_DATA) $(srcdir)/$(MANUAL) $(DESTDIR)$(MANDIR)/man1/$(MANUAL)
+ 
+-	$(INSTALL) -d $(BINDIR)
+-	$(INSTALL) -m 755 $(PROGRAM) $(BINDIR)/$(PROGRAM)
++	$(INSTALL) -d $(DESTDIR)$(BINDIR)
++	$(INSTALL) -m 755 $(PROGRAM) $(DESTDIR)$(BINDIR)/$(PROGRAM)
+ 
+ uninstall:
+ 	$(RM) -f $(BINDIR)/$(PROGRAM)
diff --git a/science/pnetcdf/files/patch-src-utils-ncmpivalid-Makefile.in b/science/pnetcdf/files/patch-src-utils-ncmpivalid-Makefile.in
new file mode 100644
index 000000000000..e399882c5165
--- /dev/null
+++ b/science/pnetcdf/files/patch-src-utils-ncmpivalid-Makefile.in
@@ -0,0 +1,18 @@
+--- src/utils/ncmpivalid/Makefile.in.orig	2013-11-03 03:15:49.000000000 +0800
++++ src/utils/ncmpivalid/Makefile.in	2014-03-09 22:42:45.308476499 +0800
+@@ -37,11 +37,11 @@
+ 	set -e ; cd $(BUILDDIR)/src && $(MAKE) $(MFLAGS) all
+ 
+ install:	
+-	$(INSTALL) -d -m 755 $(MANDIR)/man1
+-	$(INSTALL_DATA) $(srcdir)/$(MANUAL) $(MANDIR)/man1/$(MANUAL)
++	$(INSTALL) -d -m 755 $(DESTDIR)$(MANDIR)/man1
++	$(INSTALL_DATA) $(srcdir)/$(MANUAL) $(DESTDIR)$(MANDIR)/man1/$(MANUAL)
+ 
+-	$(INSTALL) -d $(BINDIR)
+-	$(INSTALL) -m 755 $(PROGRAM) $(BINDIR)/$(PROGRAM)
++	$(INSTALL) -d $(DESTDIR)$(BINDIR)
++	$(INSTALL) -m 755 $(PROGRAM) $(DESTDIR)$(BINDIR)/$(PROGRAM)
+ 
+ uninstall:
+ 	$(RM) -f $(BINDIR)/$(PROGRAM)
diff --git a/science/pnetcdf/pkg-descr b/science/pnetcdf/pkg-descr
index 229c35732b2b..1bc495ec8dfb 100644
--- a/science/pnetcdf/pkg-descr
+++ b/science/pnetcdf/pkg-descr
@@ -5,4 +5,4 @@ However, it does so in a serial manner, making it difficult to achieve high
 I/O performance. By making some small changes to the API specified by NetCDF,
 we can use MPI-IO and its collective operations.
 
-WWW: http://www.mcs.anl.gov/parallel-netcdf
+WWW: http://trac.mcs.anl.gov/projects/parallel-netcdf
diff --git a/science/pnetcdf/pkg-plist b/science/pnetcdf/pkg-plist
new file mode 100644
index 000000000000..804045785fc2
--- /dev/null
+++ b/science/pnetcdf/pkg-plist
@@ -0,0 +1,15 @@
+bin/ncmpidiff
+bin/ncmpidump
+bin/ncmpigen
+bin/ncmpivalid
+include/pnetcdf.h
+include/pnetcdf.inc
+include/pnetcdf.mod
+lib/libpnetcdf.a
+man/man1/ncmpidiff.1.gz
+man/man1/ncmpidump.1.gz
+man/man1/ncmpigen.1.gz
+man/man1/ncmpivalid.1.gz
+man/man3/pnetcdf.3.gz
+man/man3/pnetcdf_f77.3.gz
+man/man3/pnetcdf_f90.3.gz