science/gromacs: Upgrade version 4.6.5 => 5.0

PR:		191826
Submitted by:	Ports Fury

science/gromacs/Makefile

@@ -2,8 +2,7 @@
 # $FreeBSD$
 
 PORTNAME=	gromacs
-PORTVERSION=	4.6.5
-PORTREVISION=	3
+PORTVERSION=	5.0
 CATEGORIES=	science
 MASTER_SITES=	ftp://ftp.gromacs.org/pub/gromacs/
 
@@ -12,86 +11,68 @@ COMMENT=	Compute molecular dynamics
 
 LICENSE=	LGPL21
 
-OPTIONS_DEFINE=	ATLAS FLOAT GSL SIMD X11
-OPTIONS_DEFAULT=	FLOAT GSL X11
-OPTIONS_RADIO=	MPI
-OPTIONS_RADIO_MPI=	MPICH OMPI
-
-OPTIONS_SUB=	yes
-
-ATLAS_DESC=	Use ATLAS for BLAS and LAPACK
-FLOAT_DESC=	Use single instead of double precision
-GSL_DESC=	Extra analysis using math/gsl
-MPICH_DESC=	MPI support using net/mpich2
-OMPI_DESC=	MPI support using net/openmpi
+BUILD_DEPENDS=	boost-libs>=1.44:${PORTSDIR}/devel/boost-libs
 
 USES=		cmake fortran perl5 pkgconfig shebangfix
-SHEBANG_FILES=	admin/*.pl scripts/*.pl scripts/*.sh src/gmxlib/selection/*.sh
+SHEBANG_FILES=	admin/*.sh scripts/*.pl scripts/*.sh src/gromacs/selection/*.sh
 bash_CMD=	${SH}
-CMAKE_ARGS=	-DBLAS_LIBRARIES:FILEPATH="${BLAS_LIBS}" \
-		-DLAPACK_LIBRARIES:FILEPATH="${LAPACK_LIBS}"
+USE_GNOME=	libxml2
+CMAKE_ARGS=	-DGMX_USE_RDTSCP:BOOL=OFF \
+		-DUSE_PYTHON_SCRIPTS:BOOL=OFF
 USE_LDCONFIG=	yes
 
-GSL_LIB_DEPENDS=	libgsl.so:${PORTSDIR}/math/gsl
-GSL_CMAKE_ON=		-DGMX_GSL:BOOL=ON
-GSL_CMAKE_OFF=		-DGMX_GSL:BOOL=OFF
-
-SIMD_CMAKE_OFF=		-DGMX_CPU_ACCELERATION:STRING="None"
+OPTIONS_DEFINE=		ATLAS FLOAT SIMD X11
+OPTIONS_RADIO=		MPI
+OPTIONS_RADIO_MPI=	MPICH OMPI
+OPTIONS_DEFAULT=	FLOAT X11
+OPTIONS_SUB=		yes
 
+ATLAS_DESC=		Use ATLAS for BLAS and LAPACK
+ATLAS_LIB_DEPENDS=	libalapack.so:${PORTSDIR}/math/atlas
+ATLAS_LIB_DEPENDS_OFF=	libblas.so:${PORTSDIR}/math/blas \
+			liblapack.so:${PORTSDIR}/math/lapack
+ATLAS_CMAKE_ON=		-DBLAS_LIBRARIES:FILEPATH="${LOCALBASE}/lib/libcblas.so;${LOCALBASE}/lib/libf77blas.so" \
+			-DLAPACK_LIBRARIES:FILEPATH="${LOCALBASE}/lib/libalapack.so"
+ATLAS_CMAKE_OFF=	-DBLAS_LIBRARIES:FILEPATH="${LOCALBASE}/lib/libblas.so" \
+			-DLAPACK_LIBRARIES:FILEPATH="${LOCALBASE}/lib/liblapack.so"
+FLOAT_DESC=		Use single instead of double precision
+FLOAT_BUILD_DEPENDS=	fftw3>0:${PORTSDIR}/math/fftw3
+FLOAT_LIB_DEPENDS=	libfftw3f.so:${PORTSDIR}/math/fftw3-float
+FLOAT_LIB_DEPENDS_OFF=	libfftw3.so:${PORTSDIR}/math/fftw3
+FLOAT_CMAKE_ON=		-DGMX_DOUBLE:BOOL=OFF
+FLOAT_CMAKE_OFF=	-DGMX_DOUBLE:BOOL=ON
+MPICH_DESC=		MPI support using net/mpich2
+MPICH_LIB_DEPENDS=	libmpich.so:${PORTSDIR}/net/mpich2
+MPICH_CMAKE_ON= 	-DMPI_C_COMPILER:FILEPATH="${LOCALBASE}/bin/mpicc"
+OMPI_DESC=		MPI support using net/openmpi
+OMPI_BUILD_DEPENDS=	openmpi>0:${PORTSDIR}/net/openmpi
+OMPI_RUN_DEPENDS=	openmpi>0:${PORTSDIR}/net/openmpi
+OMPI_CMAKE_ON=		-DMPI_C_COMPILER:FILEPATH="${LOCALBASE}/mpi/openmpi/bin/mpicc"
+SIMD_CMAKE_OFF=		-DGMX_SIMD:STRING="None"
 X11_USE=		XORG=xext,x11
 X11_CMAKE_ON=		-DGMX_X11:BOOL=ON
 X11_CMAKE_OFF=		-DGMX_X11:BOOL=OFF
 
 .include <bsd.port.options.mk>
 
-.if ${PORT_OPTIONS:MATLAS}
-LIB_DEPENDS+=	libalapack.so:${PORTSDIR}/math/atlas
-BLAS_LIBS=	${LOCALBASE}/lib/libcblas.so;${LOCALBASE}/lib/libf77blas.so
-LAPACK_LIBS=	${LOCALBASE}/lib/libalapack.so
-.else
-LIB_DEPENDS+=	libblas.so:${PORTSDIR}/math/blas \
-		liblapack.so:${PORTSDIR}/math/lapack
-BLAS_LIBS=	${LOCALBASE}/lib/libblas.so
-LAPACK_LIBS=	${LOCALBASE}/lib/liblapack.so
-.endif
-
 .if ${PORT_OPTIONS:MFLOAT}
-BUILD_DEPENDS+=	fftw3>0:${PORTSDIR}/math/fftw3
-LIB_DEPENDS+=	libfftw3f.so:${PORTSDIR}/math/fftw3-float
-CMAKE_ARGS+=	-DGMX_DOUBLE:BOOL=OFF
 PLIST_SUB+=	SUFFIX_D=""
 .else
-LIB_DEPENDS+=	libfftw3.so:${PORTSDIR}/math/fftw3
-CMAKE_ARGS+=	-DGMX_DOUBLE:BOOL=ON
 PLIST_SUB+=	SUFFIX_D="_d"
 .endif
 
 .if ${PORT_OPTIONS:MMPICH} || ${PORT_OPTIONS:MOMPI}
-CMAKE_ARGS+=	-DGMX_MPI:BOOL=ON \
-		-DMPI_C_COMPILER:FILEPATH="${MPICC}"
+CMAKE_ARGS+=	-DGMX_MPI:BOOL=ON
 PLIST_SUB+=	SUFFIX_MPI="_mpi"
 .else
 CMAKE_ARGS+=	-DGMX_MPI:BOOL=OFF
 PLIST_SUB+=	SUFFIX_MPI=""
 .endif
 
-.if ${PORT_OPTIONS:MMPICH}
-BUILD_DEPENDS+=	${LOCALBASE}/bin/mpicc:${PORTSDIR}/net/mpich2
-RUN_DEPENDS+=	${LOCALBASE}/bin/mpicc:${PORTSDIR}/net/mpich2
-MPICC=		${LOCALBASE}/bin/mpicc
-.endif
-
-.if ${PORT_OPTIONS:MOMPI}
-BUILD_DEPENDS+=	${LOCALBASE}/mpi/openmpi/bin/mpicc:${PORTSDIR}/net/openmpi
-RUN_DEPENDS+=	${LOCALBASE}/mpi/openmpi/bin/mpicc:${PORTSDIR}/net/openmpi
-MPICC=		${LOCALBASE}/mpi/openmpi/bin/mpicc
-.endif
-
 post-patch:
 	@${FIND} ${WRKSRC} -name "CMakeLists.txt" | ${XARGS} \
 		${REINPLACE_CMD} -e \
 		's|share/man|man| ; \
-		 s|-lpthread|-pthread| ; \
 		 /pkgconfig/s|LIB_INSTALL_DIR}|CMAKE_INSTALL_PREFIX}/libdata|'
 	@${FIND} ${WRKSRC} -name "GMXRC.*" | ${XARGS} ${REINPLACE_CMD} -e \
 		's|LDLIB/pkgconfig|LDLIB/../libdata/pkgconfig| ; \

science/gromacs/distinfo

@@ -1,2 +1,2 @@
-SHA256 (gromacs-4.6.5.tar.gz) = a7242f315963a111e87fd28795696b1e818ac97479788356c4f73a04e9cdef09
-SIZE (gromacs-4.6.5.tar.gz) = 10991576
+SHA256 (gromacs-5.0.tar.gz) = c2c9b5e75e014785641f39fbbde9829ce200f963344b35fa942f041a0dcfeb20
+SIZE (gromacs-5.0.tar.gz) = 26862408

science/gromacs/files/patch-CMakeLists.txt

@@ -1,11 +0,0 @@
---- CMakeLists.txt.orig	2014-03-30 09:37:58.783039000 +0000
-+++ CMakeLists.txt
-@@ -431,7 +431,7 @@ include(TestBigEndian)
- test_big_endian(GMX_INTEGER_BIG_ENDIAN)
- 
- 
--if(APPLE OR CYGWIN OR ${CMAKE_SYSTEM_NAME} MATCHES "Linux|.*BSD")
-+if(APPLE OR CYGWIN OR ${CMAKE_SYSTEM_NAME} MATCHES "Linux|DragonFly|.*BSD")
-     # Maybe Solaris should be here? Patch this if you know!
-     SET(SHARED_LIBS_DEFAULT ON)
- elseif(WIN32 OR ${CMAKE_SYSTEM_NAME} MATCHES "BlueGene")

science/gromacs/files/patch-src__external__thread_mpi__src__atomic.c

@@ -1,5 +1,5 @@
---- src/gmxlib/thread_mpi/atomic.c.orig
-+++ src/gmxlib/thread_mpi/atomic.c
+--- src/external/thread_mpi/src/atomic.c.orig
++++ src/external/thread_mpi/src/atomic.c
 @@ -35,6 +35,14 @@
     files.
   */

science/gromacs/pkg-descr

@@ -1,5 +1,5 @@
-GROMACS is a versatile package to perform molecular dynamics, i.e. simulate
-the Newtonian equations of motion for systems with hundreds to millions of
-particles.
+GROMACS is a versatile package to perform molecular dynamics, i.e.
+simulate the Newtonian equations of motion for systems with hundreds to
+millions of particles.
 
 WWW: http://www.gromacs.org