Index: head/science/gromacs/Makefile =================================================================== --- head/science/gromacs/Makefile (revision 467752) +++ head/science/gromacs/Makefile (revision 467753) @@ -1,84 +1,92 @@ # Created by: Stephen Montgomery-Smith # $FreeBSD$ PORTNAME= gromacs -PORTVERSION= 5.0.6 -PORTREVISION= 12 +DISTVERSION= 2018.1 CATEGORIES= science MASTER_SITES= ftp://ftp.gromacs.org/pub/gromacs/ -MAINTAINER= ports@FreeBSD.org +MAINTAINER= yuri@FreeBSD.org COMMENT= Compute molecular dynamics LICENSE= LGPL21 BUILD_DEPENDS= boost-libs>=1.44:devel/boost-libs +LIB_DEPENDS= libhwloc.so:devel/hwloc USES= cmake fortran perl5 pkgconfig shebangfix SHEBANG_FILES= admin/*.sh scripts/*.pl scripts/*.sh src/gromacs/selection/*.sh bash_CMD= ${SH} USE_GNOME= libxml2 CMAKE_ARGS= -DGMX_USE_RDTSCP:BOOL=OFF \ -DUSE_PYTHON_SCRIPTS:BOOL=OFF USE_LDCONFIG= yes -OPTIONS_DEFINE= ATLAS FLOAT OPENMP SIMD X11 -OPTIONS_RADIO= MPI -OPTIONS_RADIO_MPI= MPICH2 OPENMPI -OPTIONS_DEFAULT= FLOAT OPENMP X11 +OPTIONS_DEFINE= ATLAS FLOAT OPENCL OPENMP SIMD X11 +OPTIONS_SINGLE= MP +OPTIONS_SINGLE_MP= NOMP MPICH2 OPENMPI THREAD_MPI +OPTIONS_DEFAULT= FLOAT OPENMP THREAD_MPI X11 OPTIONS_SUB= yes ATLAS_DESC= Use ATLAS for BLAS and LAPACK ATLAS_USES= blaslapack:atlas ATLAS_USES_OFF= blaslapack ATLAS_CMAKE_ON= -DBLAS_LIBRARIES:FILEPATH="${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:math/fftw3 FLOAT_LIB_DEPENDS= libfftw3f.so:math/fftw3-float FLOAT_LIB_DEPENDS_OFF= libfftw3.so:math/fftw3 FLOAT_CMAKE_ON= -DGMX_DOUBLE:BOOL=OFF FLOAT_CMAKE_OFF= -DGMX_DOUBLE:BOOL=ON -MPICH2_LIB_DEPENDS= libmpich.so:net/mpich2 -MPICH2_CMAKE_ON= -DMPI_C_COMPILER:FILEPATH="${LOCALBASE}/bin/mpicc" +FLOAT_PLIST_SUB= SUFFIX_D="" +FLOAT_PLIST_SUB_OFF= SUFFIX_D="_d" + +OPENCL_CMAKE_BOOL= GMX_USE_OPENCL GMX_GPU +OPENCL_LIB_DEPENDS= libOpenCL.so:devel/ocl-icd + OPENMP_USES= compiler:openmp OPENMP_CMAKE_ON= -DGMX_CXX11:BOOL=OFF OPENMP_CMAKE_OFF= -DGMX_OPENMP:BOOL=OFF -OPENMPI_BUILD_DEPENDS= openmpi>0:net/openmpi -OPENMPI_RUN_DEPENDS= openmpi>0:net/openmpi -OPENMPI_CMAKE_ON= -DMPI_C_COMPILER:FILEPATH="${LOCALBASE}/mpi/openmpi/bin/mpicc" + SIMD_CMAKE_OFF= -DGMX_SIMD:STRING="None" -X11_USE= XORG=xext,x11 + +X11_USE= XORG=ice,sm,xext,x11 X11_CMAKE_ON= -DGMX_X11:BOOL=ON X11_CMAKE_OFF= -DGMX_X11:BOOL=OFF -.include +MP_DESC= Multiprocessing -.if ${PORT_OPTIONS:MFLOAT} -PLIST_SUB+= SUFFIX_D="" -.else -PLIST_SUB+= SUFFIX_D="_d" -.endif +NOMP_DESC= No multiprocessing support +NOMP_PLIST_SUB= SUFFIX_MPI="" -.if ${PORT_OPTIONS:MMPICH2} || ${PORT_OPTIONS:MOPENMPI} -CMAKE_ARGS+= -DGMX_MPI:BOOL=ON -PLIST_SUB+= SUFFIX_MPI="_mpi" -.else -CMAKE_ARGS+= -DGMX_MPI:BOOL=OFF -PLIST_SUB+= SUFFIX_MPI="" -.endif +MPICH2_LIB_DEPENDS= libmpich.so:net/mpich2 +MPICH2_CMAKE_ON= -DGMX_MPI:BOOL=ON \ + -DMPI_C_COMPILER:FILEPATH="${LOCALBASE}/bin/mpicc" +MPICH2_PLIST_SUB= SUFFIX_MPI="_mpi" + +OPENMPI_BUILD_DEPENDS= openmpi>0:net/openmpi +OPENMPI_RUN_DEPENDS= openmpi>0:net/openmpi +OPENMPI_CMAKE_ON= -DGMX_MPI:BOOL=ON \ + -DMPI_C_COMPILER:FILEPATH="${LOCALBASE}/mpi/openmpi/bin/mpicc" +OPENMPI_PLIST_SUB= SUFFIX_MPI="_mpi" + +THREAD_MPI_DESC= Build a thread-MPI-based multithreaded version of GROMACS +THREAD_MPI_CMAKE_BOOL= GMX_THREAD_MPI +THREAD_MPI_PLIST_SUB= SUFFIX_MPI="" post-patch: @${FIND} ${WRKSRC} -name "CMakeLists.txt" | ${XARGS} \ ${REINPLACE_CMD} -e \ 's|share/man|man| ; \ /pkgconfig/s|LIB_INSTALL_DIR}|CMAKE_INSTALL_PREFIX}/libdata|' @${FIND} ${WRKSRC} -name "GMXRC.*" | ${XARGS} ${REINPLACE_CMD} -e \ 's|LDLIB/pkgconfig|LDLIB/../libdata/pkgconfig| ; \ s|LDLIB}/pkgconfig|LDLIB}/../libdata/pkgconfig|' @${REINPLACE_CMD} -e '/CMAKE_REQUIRED_LIBRARIES/d' \ ${WRKSRC}/cmake/gmxTestdlopen.cmake .include Index: head/science/gromacs/distinfo =================================================================== --- head/science/gromacs/distinfo (revision 467752) +++ head/science/gromacs/distinfo (revision 467753) @@ -1,2 +1,3 @@ -SHA256 (gromacs-5.0.6.tar.gz) = e07e950c4cd6cb84b83b145b70a15c25338ad6a7d7d1a0a83cdbd51cad954952 -SIZE (gromacs-5.0.6.tar.gz) = 26351063 +TIMESTAMP = 1524116817 +SHA256 (gromacs-2018.1.tar.gz) = 4d3533340499323fece83b4a2d4251fa856376f2426c541e00b8e6b4c0d705cd +SIZE (gromacs-2018.1.tar.gz) = 29895119 Index: head/science/gromacs/pkg-plist =================================================================== --- head/science/gromacs/pkg-plist (revision 467752) +++ head/science/gromacs/pkg-plist (revision 467753) @@ -1,997 +1,708 @@ bin/GMXRC bin/GMXRC.bash bin/GMXRC.csh bin/GMXRC.zsh bin/demux.pl -bin/do_dssp%%SUFFIX_MPI%%%%SUFFIX_D%% -bin/editconf%%SUFFIX_MPI%%%%SUFFIX_D%% -bin/eneconv%%SUFFIX_MPI%%%%SUFFIX_D%% -bin/g_anadock%%SUFFIX_MPI%%%%SUFFIX_D%% 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%%DATADIR%%/top/gromos45a3.ff/tip4p.itp %%DATADIR%%/top/gromos45a3.ff/watermodels.dat %%DATADIR%%/top/gromos53a5.ff/aminoacids.c.tdb %%DATADIR%%/top/gromos53a5.ff/aminoacids.hdb %%DATADIR%%/top/gromos53a5.ff/aminoacids.n.tdb %%DATADIR%%/top/gromos53a5.ff/aminoacids.r2b %%DATADIR%%/top/gromos53a5.ff/aminoacids.rtp %%DATADIR%%/top/gromos53a5.ff/aminoacids.vsd %%DATADIR%%/top/gromos53a5.ff/atomname2type.n2t %%DATADIR%%/top/gromos53a5.ff/atomtypes.atp %%DATADIR%%/top/gromos53a5.ff/ff_dum.itp %%DATADIR%%/top/gromos53a5.ff/ffbonded.itp %%DATADIR%%/top/gromos53a5.ff/ffnonbonded.itp %%DATADIR%%/top/gromos53a5.ff/forcefield.doc %%DATADIR%%/top/gromos53a5.ff/forcefield.itp %%DATADIR%%/top/gromos53a5.ff/ions.itp %%DATADIR%%/top/gromos53a5.ff/spc.itp %%DATADIR%%/top/gromos53a5.ff/spce.itp %%DATADIR%%/top/gromos53a5.ff/tip3p.itp %%DATADIR%%/top/gromos53a5.ff/tip4p.itp %%DATADIR%%/top/gromos53a5.ff/watermodels.dat %%DATADIR%%/top/gromos53a6.ff/aminoacids.c.tdb %%DATADIR%%/top/gromos53a6.ff/aminoacids.hdb %%DATADIR%%/top/gromos53a6.ff/aminoacids.n.tdb %%DATADIR%%/top/gromos53a6.ff/aminoacids.r2b %%DATADIR%%/top/gromos53a6.ff/aminoacids.rtp %%DATADIR%%/top/gromos53a6.ff/aminoacids.vsd %%DATADIR%%/top/gromos53a6.ff/atomtypes.atp %%DATADIR%%/top/gromos53a6.ff/ff_dum.itp %%DATADIR%%/top/gromos53a6.ff/ffbonded.itp %%DATADIR%%/top/gromos53a6.ff/ffnonbonded.itp %%DATADIR%%/top/gromos53a6.ff/forcefield.doc %%DATADIR%%/top/gromos53a6.ff/forcefield.itp %%DATADIR%%/top/gromos53a6.ff/ions.itp %%DATADIR%%/top/gromos53a6.ff/spc.itp %%DATADIR%%/top/gromos53a6.ff/spce.itp %%DATADIR%%/top/gromos53a6.ff/tip3p.itp %%DATADIR%%/top/gromos53a6.ff/tip4p.itp %%DATADIR%%/top/gromos53a6.ff/watermodels.dat %%DATADIR%%/top/gromos54a7.ff/aminoacids.c.tdb %%DATADIR%%/top/gromos54a7.ff/aminoacids.hdb %%DATADIR%%/top/gromos54a7.ff/aminoacids.n.tdb %%DATADIR%%/top/gromos54a7.ff/aminoacids.r2b %%DATADIR%%/top/gromos54a7.ff/aminoacids.rtp %%DATADIR%%/top/gromos54a7.ff/aminoacids.vsd %%DATADIR%%/top/gromos54a7.ff/atomtypes.atp %%DATADIR%%/top/gromos54a7.ff/dppc.itp %%DATADIR%%/top/gromos54a7.ff/ff_dum.itp %%DATADIR%%/top/gromos54a7.ff/ffbonded.itp %%DATADIR%%/top/gromos54a7.ff/ffnonbonded.itp %%DATADIR%%/top/gromos54a7.ff/forcefield.doc %%DATADIR%%/top/gromos54a7.ff/forcefield.itp %%DATADIR%%/top/gromos54a7.ff/ions.itp %%DATADIR%%/top/gromos54a7.ff/popc.itp %%DATADIR%%/top/gromos54a7.ff/spc.itp %%DATADIR%%/top/gromos54a7.ff/spce.itp %%DATADIR%%/top/gromos54a7.ff/tip3p.itp %%DATADIR%%/top/gromos54a7.ff/tip4p.itp %%DATADIR%%/top/gromos54a7.ff/tmcl.itp %%DATADIR%%/top/gromos54a7.ff/watermodels.dat -%%DATADIR%%/top/gurgle.dat %%DATADIR%%/top/ha-shift.dat %%DATADIR%%/top/ions.itp %%DATADIR%%/top/nsfactor.dat %%DATADIR%%/top/oplsaa.ff/1propanol.itp %%DATADIR%%/top/oplsaa.ff/aminoacids.c.tdb %%DATADIR%%/top/oplsaa.ff/aminoacids.hdb %%DATADIR%%/top/oplsaa.ff/aminoacids.n.tdb %%DATADIR%%/top/oplsaa.ff/aminoacids.r2b 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