Index: head/biology/hhsuite/Makefile =================================================================== --- head/biology/hhsuite/Makefile (revision 532094) +++ head/biology/hhsuite/Makefile (revision 532095) @@ -1,37 +1,36 @@ # $FreeBSD$ PORTNAME= hhsuite DISTVERSIONPREFIX= v DISTVERSION= 3.2.0 -PORTREVISION= 3 +PORTREVISION= 4 CATEGORIES= biology science MAINTAINER= yuri@FreeBSD.org COMMENT= Remote protein homology detection suite LICENSE= GPLv3 LICENSE_FILE= ${WRKSRC}/LICENSE -BUILD_DEPENDS= openmpi>0:net/openmpi -RUN_DEPENDS= openmpi>0:net/openmpi +LIB_DEPENDS= libmpi.so:net/openmpi USES= cmake compiler:c++11-lang perl5 python shebangfix SHEBANG_GLOB= *.pl *.py USE_GITHUB= yes GH_ACCOUNT= soedinglab GH_PROJECT= hh-suite LDFLAGS+= -Wl,-rpath,${LOCALBASE}/mpi/openmpi/lib -L${LOCALBASE}/mpi/openmpi/lib -lmpi # force linking to openmpi, and not to mpich .include .if ${ARCH} == amd64 || ${ARCH} == i386 || ${ARCH} == powerpc64 CMAKE_ON= HAVE_SSE2 .endif .if ${ARCH} == powerpc64 post-patch: ${REINPLACE_CMD} -e 's/-msse -msse2/-D_ARCH_PWR8 -DNO_WARN_X86_INTRINSICS -maltivec -mpower8-vector -mvsx/g' ${WRKSRC}/src/CMakeLists.txt .endif .include Index: head/math/dbcsr/Makefile =================================================================== --- head/math/dbcsr/Makefile (revision 532094) +++ head/math/dbcsr/Makefile (revision 532095) @@ -1,48 +1,48 @@ # $FreeBSD$ PORTNAME= dbcsr DISTVERSIONPREFIX= v DISTVERSION= 2.0.1 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= math MAINTAINER= yuri@FreeBSD.org COMMENT= Distributed Block Compressed Sparse Row matrix library LICENSE= GPLv3 LICENSE_FILE= ${WRKSRC}/LICENSE BUILD_DEPENDS= fypp:devel/py-fypp@${PY_FLAVOR} USES= blaslapack:openblas cmake:noninja compiler:c++14-lang fortran \ python:build USE_GITHUB= yes GH_ACCOUNT= cp2k USE_LDCONFIG= yes LDFLAGS+= -lopenblas CMAKE_ON= BUILD_SHARED_LIBS CMAKE_ARGS= -DBLA_VENDOR:STRING="OpenBLAS" TEST_TARGET= test # tests hang: https://github.com/cp2k/dbcsr/issues/72 OPTIONS_DEFINE= MPI OPENMP C_API # libxsmm is supposed to be supported, but cmake build lacks the corresponding option: https://github.com/cp2k/dbcsr/issues/73 OPTIONS_DEFAULT= MPI OPENMP C_API OPTIONS_SUB= yes MPI_CMAKE_BOOL= USE_MPI MPI_LIB_DEPENDS= libmpi.so:net/openmpi OPENMP_CMAKE_BOOL= USE_OPENMP C_API_DESC= Build the C API library C_API_CMAKE_BOOL= WITH_C_API do-test: # tests are broken: https://github.com/cp2k/dbcsr/issues/150 @cd ${BUILD_WRKSRC} && \ ${SETENV} ${CONFIGURE_ENV} ${CMAKE_BIN} ${CMAKE_ARGS} -DBUILD_TESTING:BOOL=ON ${CMAKE_SOURCE_PATH} && \ ${SETENV} ${MAKE_ENV} ${MAKE_CMD} ${MAKE_ARGS} ${ALL_TARGET} && \ ${SETENV} ${MAKE_ENV} ${MAKE_CMD} ${MAKE_ARGS} test .include Index: head/math/dune-alugrid/Makefile =================================================================== --- head/math/dune-alugrid/Makefile (revision 532094) +++ head/math/dune-alugrid/Makefile (revision 532095) @@ -1,40 +1,41 @@ # $FreeBSD$ PORTNAME= dune-alugrid DISTVERSIONPREFIX= v DISTVERSION= 2.6.0 +PORTREVISION= 1 CATEGORIES= math MAINTAINER= yuri@FreeBSD.org COMMENT= DUNE framework: grid implementation providing simplex or cube grids LICENSE= GPLv2 LICENSE_FILE= ${WRKSRC}/COPYING BUILD_DEPENDS= vc>0:devel/vc LIB_DEPENDS= libdunecommon.so:math/dune-common \ libdunegeometry.so:math/dune-geometry \ libdunegrid.so:math/dune-grid \ libmetis.so:math/metis \ libmpi.so:net/openmpi USES= cmake compiler:c++17-lang fortran pkgconfig USE_GITLAB= yes USE_LDCONFIG= yes GL_SITE= https://gitlab.dune-project.org GL_ACCOUNT= extensions GL_COMMIT= 9cec115318adc7c3f4faa16a626f61996710c533 CMAKE_ON= BUILD_SHARED_LIBS OPTIONS_DEFINE= DOCS OPTIONS_SUB= yes DOCS_CMAKE_BOOL= FREEBSD_INSTALL_DOCS DOCS_BUILD_DEPENDS= doxygen:devel/doxygen \ sphinx-build:textproc/py-sphinx PORTDOCS= * .include Index: head/math/dune-common/Makefile =================================================================== --- head/math/dune-common/Makefile (revision 532094) +++ head/math/dune-common/Makefile (revision 532095) @@ -1,44 +1,44 @@ # $FreeBSD$ PORTNAME= dune-common DISTVERSIONPREFIX= v DISTVERSION= 2.7.0 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= math MAINTAINER= yuri@FreeBSD.org COMMENT= DUNE framework: Build system, infrastructure and foundation classes LICENSE= GPLv2 LICENSE_FILE= ${WRKSRC}/LICENSE.md BUILD_DEPENDS= openmpi>0:net/openmpi \ vc>0:devel/vc LIB_DEPENDS= libopenblas.so:math/openblas \ libtbb.so:devel/tbb USES= cmake compiler:c++17-lang fortran pkgconfig python shebangfix SHEBANG_FILES= bin/dune-ctest USE_GITLAB= yes USE_LDCONFIG= yes GL_SITE= https://gitlab.dune-project.org GL_ACCOUNT= core GL_COMMIT= c5321673af09725a411bdd81aa2be5cfaf8bf9a6 CMAKE_ON= BUILD_SHARED_LIBS OPTIONS_DEFINE= DOCS OPTIONS_SUB= yes DOCS_CMAKE_BOOL= FREEBSD_INSTALL_DOCS DOCS_BUILD_DEPENDS= doxygen:devel/doxygen \ latex:print/tex-formats \ sphinx-build:textproc/py-sphinx PORTDOCS= * post-stage-DOCS-on: # https://gitlab.dune-project.org/core/dune-common/issues/191 @${RMDIR} ${STAGEDIR}${DOCSDIR}/comm .include Index: head/math/dune-geometry/Makefile =================================================================== --- head/math/dune-geometry/Makefile (revision 532094) +++ head/math/dune-geometry/Makefile (revision 532095) @@ -1,40 +1,40 @@ # $FreeBSD$ PORTNAME= dune-geometry DISTVERSIONPREFIX= v DISTVERSION= 2.7.0 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= math MAINTAINER= yuri@FreeBSD.org COMMENT= DUNE framework: Geometry transformations, reference elements, etc LICENSE= GPLv2 LICENSE_FILE= ${WRKSRC}/LICENSE.md BUILD_DEPENDS= openmpi>0:net/openmpi \ vc>0:devel/vc LIB_DEPENDS= libdunecommon.so:math/dune-common \ libopenblas.so:math/openblas \ libtbb.so:devel/tbb USES= cmake compiler:c++17-lang fortran pkgconfig python USE_GITLAB= yes USE_LDCONFIG= yes GL_SITE= https://gitlab.dune-project.org GL_ACCOUNT= core GL_COMMIT= bcf9e469f3c105d5f497dbf81801e8dbd09cde92 CMAKE_ON= BUILD_SHARED_LIBS OPTIONS_DEFINE= DOCS OPTIONS_SUB= yes DOCS_CMAKE_BOOL= FREEBSD_INSTALL_DOCS DOCS_BUILD_DEPENDS= doxygen:devel/doxygen \ sphinx-build:textproc/py-sphinx PORTDOCS= * .include Index: head/math/dune-grid/Makefile =================================================================== --- head/math/dune-grid/Makefile (revision 532094) +++ head/math/dune-grid/Makefile (revision 532095) @@ -1,42 +1,42 @@ # $FreeBSD$ PORTNAME= dune-grid DISTVERSIONPREFIX= v DISTVERSION= 2.7.0rc2 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= math MAINTAINER= yuri@FreeBSD.org COMMENT= DUNE framework: Geometry transformations, reference elements, etc LICENSE= GPLv2 LICENSE_FILE= ${WRKSRC}/LICENSE.md BUILD_DEPENDS= openmpi>0:net/openmpi \ vc>0:devel/vc LIB_DEPENDS= libdunecommon.so:math/dune-common \ libdunegeometry.so:math/dune-geometry \ libugL.so:math/dune-uggrid \ libopenblas.so:math/openblas \ libtbb.so:devel/tbb USES= cmake compiler:c++17-lang fortran pkgconfig python:build USE_GITLAB= yes USE_LDCONFIG= yes GL_SITE= https://gitlab.dune-project.org GL_ACCOUNT= core GL_COMMIT= 8a201c5f04f94b0a25c9879fb9fb97f2eb5f0840 CMAKE_ON= BUILD_SHARED_LIBS OPTIONS_DEFINE= DOCS OPTIONS_SUB= yes DOCS_CMAKE_BOOL= FREEBSD_INSTALL_DOCS DOCS_BUILD_DEPENDS= doxygen:devel/doxygen \ sphinx-build:textproc/py-sphinx PORTDOCS= * .include Index: head/math/dune-spgrid/Makefile =================================================================== --- head/math/dune-spgrid/Makefile (revision 532094) +++ head/math/dune-spgrid/Makefile (revision 532095) @@ -1,40 +1,41 @@ # $FreeBSD$ PORTNAME= dune-spgrid DISTVERSIONPREFIX= v DISTVERSION= 2.6.0rc1.20200105 +PORTREVISION= 1 CATEGORIES= math MAINTAINER= yuri@FreeBSD.org COMMENT= DUNE framework: A structured, parallel DUNE grid implementation LICENSE= GPLv2 LICENSE_FILE= ${WRKSRC}/LICENSE DUNE_DEPENDS= dune-common>0:math/dune-common \ dune-grid>0:math/dune-grid \ dune-geometry>0:math/dune-geometry BUILD_DEPENDS= ${DUNE_DEPENDS} \ openmpi>0:net/openmpi \ vc>0:devel/vc RUN_DEPENDS= ${DUNE_DEPENDS} USES= cmake compiler:c++17-lang fortran pkgconfig USE_GITLAB= yes GL_SITE= https://gitlab.dune-project.org GL_ACCOUNT= extensions GL_COMMIT= 3977013bee93d1b113b155cc5b881d28d3ee37f5 NO_ARCH= yes OPTIONS_DEFINE= DOCS OPTIONS_SUB= yes DOCS_CMAKE_BOOL= FREEBSD_INSTALL_DOCS DOCS_BUILD_DEPENDS= doxygen:devel/doxygen \ sphinx-build:textproc/py-sphinx PORTDOCS= * .include Index: head/math/dune-typetree/Makefile =================================================================== --- head/math/dune-typetree/Makefile (revision 532094) +++ head/math/dune-typetree/Makefile (revision 532095) @@ -1,40 +1,40 @@ # $FreeBSD$ PORTNAME= dune-typetree DISTVERSIONPREFIX= v DISTVERSION= 2.7.0rc2 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= math MAINTAINER= yuri@FreeBSD.org COMMENT= DUNE framework: The TypeTree library LICENSE= GPLv2 LICENSE_FILE= ${WRKSRC}/LICENSE.md BUILD_DEPENDS= dune-common>0:math/dune-common \ openmpi>0:net/openmpi \ vc>0:devel/vc RUN_DEPENDS= dune-common>0:math/dune-common \ openmpi>0:net/openmpi \ vc>0:devel/vc USES= cmake compiler:c++17-lang fortran pkgconfig USE_GITLAB= yes GL_SITE= https://gitlab.dune-project.org GL_ACCOUNT= staging GL_COMMIT= b6427163a5ef45996471edad672ecab584aa490c NO_ARCH= yes OPTIONS_DEFINE= DOCS OPTIONS_SUB= yes DOCS_CMAKE_BOOL= FREEBSD_INSTALL_DOCS DOCS_BUILD_DEPENDS= doxygen:devel/doxygen \ sphinx-build:textproc/py-sphinx PORTDOCS= * .include Index: head/math/dune-uggrid/Makefile =================================================================== --- head/math/dune-uggrid/Makefile (revision 532094) +++ head/math/dune-uggrid/Makefile (revision 532095) @@ -1,32 +1,32 @@ # $FreeBSD$ PORTNAME= dune-uggrid DISTVERSIONPREFIX= v DISTVERSION= 2.7.0rc2 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= math MAINTAINER= yuri@FreeBSD.org COMMENT= DUNE framework: The UG Grid Manager LICENSE= LGPL21 LICENSE_FILE= ${WRKSRC}/COPYING.LGPL-2.1 BUILD_DEPENDS= openmpi>0:net/openmpi \ vc>0:devel/vc LIB_DEPENDS= libdunecommon.so:math/dune-common \ libopenblas.so:math/openblas \ libtbb.so:devel/tbb RUN_DEPENDS= openmpi>0:net/openmpi USES= cmake compiler:c++17-lang fortran pkgconfig python USE_GITLAB= yes USE_LDCONFIG= yes GL_SITE= https://gitlab.dune-project.org GL_ACCOUNT= staging GL_COMMIT= 1fce83c6efe2e0f77d0ee1b3cf6335172f1ace37 CMAKE_ON= BUILD_SHARED_LIBS .include Index: head/math/fftw3/Makefile =================================================================== --- head/math/fftw3/Makefile (revision 532094) +++ head/math/fftw3/Makefile (revision 532095) @@ -1,169 +1,169 @@ # Created by: Lars Koeller # $FreeBSD$ PORTNAME= fftw3 DISTVERSION= 3.3.8 -PORTREVISION?= 5 +PORTREVISION?= 6 CATEGORIES= math MASTER_SITES= http://www.fftw.org/ \ ftp://ftp.fftw.org/pub/fftw/ PKGNAMESUFFIX= ${FFTW3_PKGNAMESUFFIX} DISTNAME= fftw-${DISTVERSION} MAINTAINER= jhale@FreeBSD.org COMMENT?= Fast C routines to compute the Discrete Fourier Transform LICENSE= GPLv2+ LICENSE_FILE= ${WRKSRC}/COPYING #current flavors: default, float, long, and quad FFTW3_FLAVOR?= default FFTW3_SUFX= GNU_CONFIGURE= yes INSTALL_TARGET= install-strip TEST_TARGET= smallcheck #bigcheck check exhaustive-check paranoid-check TEST_WRKSRC= ${WRKSRC}/tests USES= gmake libtool makeinfo pathfix perl5 pkgconfig USE_PERL5= build USE_LDCONFIG= yes CONFIGURE_ARGS= --enable-shared --enable-threads --disable-fortran MPIDIR?= ${LOCALBASE}/mpi/openmpi .if ${FFTW3_FLAVOR} == "default" INFO= fftw3 .else #For non-default flavors, build and install the flavor-dependent components #only, so that these flavors may coexist with the default flavor INSTALL_TARGET= install-cmakeDATA install-pkgconfigDATA install-libLTLIBRARIES install-exec .endif OPTIONS_DEFINE= G77_WRAPPERS OPENMP OPENMPI OPTIMIZED_CFLAGS SIMD OPTIONS_DEFAULT= OPTIMIZED_CFLAGS SIMD .if ${FFTW3_FLAVOR} == "quad" OPTIONS_EXCLUDE+= OPENMPI .endif OPTIONS_SUB= yes G77_WRAPPERS_DESC= Alter Fortran wrappers for use with g77 OPENMP_DESC= Build OpenMP multithreaded libraries OPENMP_USES= compiler:openmp OPENMP_USES_OFF= compiler:env OPENMP_CONFIGURE_ENABLE= openmp OPENMP_EXTRA_PATCHES= ${FILESDIR}/extrapatch-tests_fftw-bench.c OPENMPI_DESC= Build OpenMPI parallel libraries OPENMPI_LIB_DEPENDS= libmpi.so:net/openmpi OPENMPI_CONFIGURE_ENABLE= mpi OPENMPI_CONFIGURE_ENV= MPICC=${MPIDIR}/bin/mpicc \ MPIRUN=${MPIDIR}/bin/mpirun .include # Enable cycle counter via the CNTVCT_EL0 register for all variants on arm64. .if ${ARCH} == "aarch64" CONFIGURE_ARGS+=--enable-armv8-cntvct-el0 .endif #Users must add altivec to MACHINE_CPU when desired: #this is not currently done in bsd.cpu.mk .if ${FFTW3_FLAVOR} == "default" . if ${PORT_OPTIONS:MSIMD} . if !empty(MACHINE_CPU:Mavx) CONFIGURE_ARGS+=--enable-avx . endif . if !empty(MACHINE_CPU:Mavx2) CONFIGURE_ARGS+=--enable-avx2 --enable-fma . endif . if !empty(MACHINE_CPU:Msse2) CONFIGURE_ARGS+=--enable-sse2 . endif . endif .elif ${FFTW3_FLAVOR} == "float" FFTW3_SUFX= f FFTW3_PKGNAMESUFFIX= -float CONFIGURE_ARGS+=--enable-float . if ${PORT_OPTIONS:MSIMD} . if !empty(MACHINE_CPU:Mavx) CONFIGURE_ARGS+=--enable-avx . endif . if !empty(MACHINE_CPU:Mavx2) CONFIGURE_ARGS+=--enable-avx2 --enable-fma . endif . if !empty(MACHINE_CPU:Msse) CONFIGURE_ARGS+=--enable-sse2 . endif . if !empty(ARCH:Mpowerpc*) && !empty(MACHINE_CPU:Maltivec) CONFIGURE_ARGS+=--enable-altivec . endif . if ${ARCH} == "aarch64" CONFIGURE_ARGS+=--enable-neon . endif . endif .elif ${FFTW3_FLAVOR} == "long" FFTW3_SUFX= l FFTW3_PKGNAMESUFFIX= -long CONFIGURE_ARGS+=--enable-long-double .elif ${FFTW3_FLAVOR} == "quad" FFTW3_SUFX= q FFTW3_PKGNAMESUFFIX= -quad CONFIGURE_ARGS+=--enable-quad-precision ONLY_FOR_ARCHS= i386 amd64 USE_GCC= yes .endif .if ${FFTW3_FLAVOR} == "default" PLIST_SUB+= DEF="" NONDEF="@comment " .else PLIST_SUB+= DEF="@comment " NONDEF="" .endif PLIST_SUB+= FFTW3_SUFX="${FFTW3_SUFX}" .include .if ${PORT_OPTIONS:MOPTIMIZED_CFLAGS} CFLAGS+= -O3 -fstrict-aliasing . if !defined(WITH_DEBUG) CFLAGS+= -fomit-frame-pointer . endif . if ${ARCH} == "i386" && (${COMPILER_TYPE} == "gcc" || !empty(USE_GCC)) && !${PORT_OPTIONS:MOPENMPI} CFLAGS+= -malign-double . endif WITHOUT_NO_STRICT_ALIASING= yes .endif # end OPTIMIZED_CFLAGS post-patch: @${REINPLACE_CMD} -e 's|/etc/fftw|${PREFIX}/etc/fftw|' \ ${WRKSRC}/Makefile.in \ ${WRKSRC}/api/import-system-wisdom.c \ ${WRKSRC}/doc/fftw3* \ ${WRKSRC}/tools/* .if ${FFTW3_FLAVOR} != "default" @${REINPLACE_CMD} -E \ -e '/(DIST_COMMON|bin_SCRIPTS|BUILT_SOURCES|EXTRA_DIST) =/,\ /[^\]$$/s/[^[:blank:]]*fftw-wisdom-to-conf[^[:blank:]]*//' \ ${WRKSRC}/tools/Makefile.in .endif post-configure: #After issuing --disable-fortran in order to avoid using a Fortran compiler #during configuration, edit config.h to provide Fortran wrappers appropriate for #gfortran, with ac_cv_f77_mangling="lower case, underscore, no extra underscore" @${REINPLACE_CMD} -e '/DISABLE_FORTRAN/d' ${WRKSRC}/config.h @${ECHO_CMD} "#define F77_FUNC(name,NAME) name ## _" >> ${WRKSRC}/config.h @${ECHO_CMD} "#define F77_FUNC_(name,NAME) name ## _" >> ${WRKSRC}/config.h @${ECHO_CMD} "#define F77_FUNC_EQUIV 1" >> ${WRKSRC}/config.h post-configure-G77_WRAPPERS-on: @${ECHO_CMD} "#define WITH_G77_WRAPPERS 1" >> ${WRKSRC}/config.h .if ${FFTW3_FLAVOR} != "default" post-install: ${INSTALL_MAN} ${WRKSRC}/tools/fftw${FFTW3_SUFX}-wisdom.1 ${STAGEDIR}${PREFIX}/man/man1 ${STRIP_CMD} ${STAGEDIR}${PREFIX}/lib/lib*.so .endif .include Index: head/math/form/Makefile =================================================================== --- head/math/form/Makefile (revision 532094) +++ head/math/form/Makefile (revision 532095) @@ -1,55 +1,56 @@ # Created by: Emanuel Haupt # $FreeBSD$ PORTNAME= form PORTVERSION= 4.2.1 +PORTREVISION= 1 DISTVERSIONPREFIX= v CATEGORIES= math MAINTAINER= ehaupt@FreeBSD.org COMMENT= Symbolic Manipulation System LICENSE= GPLv3+ LICENSE_FILE= ${WRKSRC}/COPYING LIB_DEPENDS= libgmp.so:math/gmp USES= autoreconf gmake localbase USE_GITHUB= yes GNU_CONFIGURE= yes GH_ACCOUNT= vermaseren OPTIONS_DEFINE= DOXYGEN OPENMPI OPTIONS_SUB= yes CONFIGURE_ARGS+= --enable-scalar \ --enable-largefile \ --with-api=posix \ --disable-native MPICC?= ${LOCALBASE}/mpi/openmpi/bin/mpicc MPICXX?= ${LOCALBASE}/mpi/openmpi/bin/mpic++ DOXYGEN_BROKEN= fails to build DOXYGEN_BUILD_DEPENDS= doxygen:devel/doxygen OPENMPI_CONFIGURE_ENABLE= parform OPENMPI_CONFIGURE_ENV+= MPICC="${MPICC}" MPICXX="${MPICXX}" OPENMPI_LIB_DEPENDS= libmpi.so:net/openmpi \ libgcc_s.so.1:lang/gcc9 post-patch: @${REINPLACE_CMD} -e 's| -O3||' ${WRKSRC}/configure.ac post-build-DOXYGEN-on: (cd ${WRKSRC}/doc/manual; ${MAKE_CMD} html pdf) post-install-DOXYGEN-on: (cd ${WRKSRC}/doc/manual && ${COPYTREE_SHARE} html ${STAGEDIR}${DOCSDIR}) ${INSTALL_DATA} ${WRKSRC}/doc/manual/manual.pdf ${STAGEDIR}${DOCSDIR} .include Index: head/math/mathgl/Makefile =================================================================== --- head/math/mathgl/Makefile (revision 532094) +++ head/math/mathgl/Makefile (revision 532095) @@ -1,78 +1,78 @@ # $FreeBSD$ PORTNAME= mathgl DISTVERSION= 2.4.4 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= math graphics MASTER_SITES= SF/${PORTNAME}/${PORTNAME}/${PORTNAME}%20${PORTVERSION}/ MAINTAINER= yuri@FreeBSD.org COMMENT= Library for high-quality scientific data visualization LICENSE= GPLv3 LICENSE_FILE= ${WRKSRC}/COPYING DEPRECATED= Uses deprecated version of python EXPIRATION_DATE= 2020-08-15 LIB_DEPENDS= libgif.so:graphics/giflib \ libgsl.so:math/gsl \ libhdf5.so:science/hdf5 \ libhpdf.so:print/libharu \ libltdl.so:devel/libltdl \ libpng.so:graphics/png \ libsz.so:science/szip USES= cmake compiler:c++11-lang gettext-runtime gl jpeg python:2.7 \ xorg USE_GL= gl glu glut USE_XORG= xi xmu USE_LDCONFIG= yes .for v in double gif glut gsl hdf5 jpeg ltdl mgl2 opengl pdf png zlib CMAKE_ARGS+= -Denable-${v}=ON .endfor .for v in doc-info doc-html lgpl mgltex CMAKE_ARGS+= -Denable-${v}=OFF .endfor OPTIONS_DEFINE= PYTHON MPI OPTIONS_GROUP= GRAPHICS OPTIONS_GROUP_GRAPHICS= QT5 FLTK WXGTK OPTIONS_RADIO= THREADS OPTIONS_RADIO_THREADS= PTHREADS OPENMP OPTIONS_DEFAULT= QT5 OPTIONS_SUB= yes GRAPHICS_DESC= Graphics support PTHREADS_DESC= Enable POSIX threads support (broken, fix pending release) OPENMP_DESC= Parallel processing support via OpenMP (broken, cmake bug) FLTK_DESC= Enable fltk widget PLIST_SUB= SHLIB_VER=7.5.0 PYTHON_CMAKE_BOOL= enable-python PYTHON_BUILD_DEPENDS= swig3.0:devel/swig30 \ ${PYNUMPY} PYTHON_RUN_DEPENDS= ${PYNUMPY} MPI_CMAKE_BOOL= enable-mpi MPI_LIB_DEPENDS= libmpi.so:net/openmpi QT5_CMAKE_BOOL= enable-qt5 QT5_USE= QT=core,gui,opengl,printsupport,widgets,buildtools_build,qmake_build QT5_USES= desktop-file-utils qt:5 shared-mime-info FLTK_CMAKE_BOOL= enable-fltk FLTK_LIB_DEPENDS= libfltk.so:x11-toolkits/fltk FLTK_USE= XORG=ice,sm,x11,xext WXGTK_CMAKE_BOOL= wx WXGTK_USE= WX=3.0+ PTHREADS_CMAKE_BOOL= enable-pthread OPENMP_CMAKE_BOOL= enable-openmp post-patch-FLTK-on: @${REINPLACE_CMD} -e 's|#include Index: head/math/moab/Makefile =================================================================== --- head/math/moab/Makefile (revision 532094) +++ head/math/moab/Makefile (revision 532095) @@ -1,36 +1,38 @@ # $FreeBSD$ PORTNAME= moab DISTVERSION= 5.1.1 +PORTREVISION= 1 CATEGORIES= math MASTER_SITES= https://bitbucket.org/${BB_ACCOUNT}/${BB_PROJECT}/get/${BB_COMMIT}.tar.gz?dummy=/ MAINTAINER= yuri@FreeBSD.org COMMENT= Component for representing and evaluating mesh data LICENSE= LGPL3+ LICENSE_FILE= ${WRKSRC}/LICENSE LIB_DEPENDS= libhdf5.so:science/hdf5 \ libnetcdf.so:science/netcdf \ libopenblas.so:math/openblas USES= cmake:noninja compiler:c++11-lang eigen:3 fortran USE_LDCONFIG= yes -CMAKE_ARGS= -DBLAS_LIBRARIES:STRING=${LOCALBASE}/lib/libopenblas.so -DLAPACK_LIBRARIES:STRING=${LOCALBASE}/lib/libopenblas.so +CMAKE_ARGS= -DBLAS_LIBRARIES:STRING=${LOCALBASE}/lib/libopenblas.so \ + -DLAPACK_LIBRARIES:STRING=${LOCALBASE}/lib/libopenblas.so BB_ACCOUNT= fathomteam BB_PROJECT= ${PORTNAME} BB_COMMIT= 7bde9dfb84a8 WRKSRC= ${WRKDIR}/${BB_ACCOUNT}-${BB_PROJECT}-${BB_COMMIT} OPTIONS_DEFINE= MPI OPTIONS_DEFAULT= MPI OPTIONS_SUB= yes MPI_CMAKE_BOOL= ENABLE_MPI MPI_LIB_DEPENDS= libmpi.so:net/openmpi .include Index: head/math/parmgridgen/Makefile =================================================================== --- head/math/parmgridgen/Makefile (revision 532094) +++ head/math/parmgridgen/Makefile (revision 532095) @@ -1,45 +1,45 @@ # Created by: Stas Timokhin # $FreeBSD$ PORTNAME= parmgridgen PORTVERSION= 1.0 -PORTREVISION= 14 +PORTREVISION= 15 CATEGORIES= math science MASTER_SITES= http://www.mgnet.org/mgnet/Codes/parmgridgen/ \ http://www-users.cs.umn.edu/~moulitsa/download/ \ http://www.stasyan.com/devel/distfiles/ DISTNAME= ParMGridGen-${PORTVERSION} MAINTAINER= devel@stasyan.com COMMENT= Library for obtaining a sequence of successive coarse grids LIB_DEPENDS= libmpi.so:net/openmpi ALL_TARGET= parallel USES= gmake MAKE_JOBS_UNSAFE= yes OPTIONS_DEFINE= DOCS post-patch: @${REINPLACE_CMD} 's|make|$$(MAKE)|g' ${WRKSRC}/Makefile #respect CFLAGS . for f in IMlib Lib Programs @${REINPLACE_CMD} 's|CFLAGS =|CFLAGS+=|g' ${WRKSRC}/MGridGen/${f}/Makefile . endfor . for f in IMParMetis-2.0 ParLib Programs @${REINPLACE_CMD} 's|CFLAGS =|CFLAGS+=|g' ${WRKSRC}/ParMGridGen/${f}/Makefile . endfor do-install: ${INSTALL_PROGRAM} ${WRKSRC}/mgridgen ${STAGEDIR}${PREFIX}/bin/mgridgen ${INSTALL_PROGRAM} ${WRKSRC}/parmgridgen ${STAGEDIR}${PREFIX}/bin/parmgridgen ${INSTALL_DATA} ${WRKSRC}/libmgrid.a ${STAGEDIR}${PREFIX}/lib/libmgrid.a ${INSTALL_DATA} ${WRKSRC}/libparmgrid.a ${STAGEDIR}${PREFIX}/lib/libparmgrid.a ${INSTALL_DATA} ${WRKSRC}/mgridgen.h ${STAGEDIR}${PREFIX}/include/mgridgen.h do-install-DOCS-on: @${MKDIR} ${STAGEDIR}${DOCSDIR} ${INSTALL_DATA} ${WRKSRC}/README ${STAGEDIR}${DOCSDIR}/README .include Index: head/math/vtk8/Makefile =================================================================== --- head/math/vtk8/Makefile (revision 532094) +++ head/math/vtk8/Makefile (revision 532095) @@ -1,129 +1,129 @@ # $FreeBSD$ PORTNAME= vtk DISTVERSION= 8.1.2 -PORTREVISION= 5 +PORTREVISION= 6 CATEGORIES= math graphics MASTER_SITES= http://www.vtk.org/files/release/${VTK_SHORT_VER}/ PKGNAMESUFFIX= 8 DISTNAME= ${PORTNAME:tu}-${PORTVERSION} MAINTAINER= yuri@FreeBSD.org COMMENT= Visualization toolkit LICENSE= BSD3CLAUSE LIB_DEPENDS= libtiff.so:graphics/tiff \ libpng.so:graphics/png \ libfreetype.so:print/freetype2 \ libexpat.so:textproc/expat2 CONFLICTS= vtk5 vtk6 USES= alias cmake compiler:c++11-lang gl jpeg localbase xorg USE_LDCONFIG= ${PREFIX}/lib/vtk-${VTK_SHORT_VER} USE_XORG= ice x11 xt xext sm CMAKE_ON= BUILD_SHARED_LIBS \ VTK_INSTALL_NO_DOCUMENTATION VTK_USE_SYSTEM_EXPAT VTK_USE_SYSTEM_TIFF \ VTK_USE_SYSTEM_PNG VTK_USE_SYSTEM_JPEG VTK_USE_SYSTEM_FREETYPE VTK_USE_SYSTEM_ZLIB \ Module_vtkTestingCore Module_vtkTestingRendering CMAKE_ARGS+= -DVTK_INSTALL_LIBRARY_DIR=lib/vtk-${VTK_SHORT_VER} \ -DVTK_INSTALL_ARCHIVE_DIR=lib/vtk-${VTK_SHORT_VER} \ -DVTK_INSTALL_QT_DIR=/${QT_LIBDIR_REL}/plugins/designer \ -DSTAGEDIR=${STAGEDIR} VTK_SHORT_VER= ${PORTVERSION:R} DOCSDIR= ${PREFIX}/share/doc/vtk-${VTK_SHORT_VER} DATADIR= ${PREFIX}/share/vtk-${VTK_SHORT_VER} # Options OPTIONS_DEFINE= DESIGNER DOCS OSMESA QT5 EXAMPLES OPTIONS_DEFAULT= MPI QT5 OSMESA_DESC= Use Mesa for off-screen rendering DESIGNER_DESC= Build the Qt Designer plugin OPTIONS_SUB= yes # Options groups #VTK_GROUPS= Imaging MPI Qt Rendering StandAlone Views VTK_GROUPS= MPI VTK_WRAPS= JAVA TCLTK OPTIONS_GROUP= GROUPS WRAPPING OPTIONS_GROUP_GROUPS=${VTK_GROUPS} OPTIONS_GROUP_WRAPPING=${VTK_WRAPS} GROUPS_DESC= Groups WRAPPING_DESC= Wrapping .for g in ${VTK_GROUPS} $g_DESC= Build the $g group .endfor .for w in ${VTK_WRAPS} $w_DESC= $w wrapping .endfor QT5_USES= qt:5 QT5_USE= QT=core,gui,sql,uiplugin,widgets,x11extras,qmake_build,buildtools_build QT5_CMAKE_ON= -DVTK_QT_VERSION:STRING="5" \ -DCMAKE_PREFIX_PATH:STRING=${LOCALBASE}/lib/qt5 \ -DVTK_Group_Qt:BOOL=ON DESIGNER_CMAKE_BOOL= QT_DESIGNER_PLUGIN DESIGNER_USE= QT=designer DESIGNER_IMPLIES= QT5 MPI_LIB_DEPENDS= libmpi.so:net/openmpi MPI_CMAKE_ON= -DMPIEXEC=${LOCALBASE}/mpi/openmpi/bin/mpiexec OSMESA_CMAKE_ARGS= -DVTK_OPENGL_HAS_OSMESA:BOOL=ON \ -DOSMESA_INCLUDE_DIR:PATH=${LOCALBASE}/include/Mesa \ -DOSMESA_LIBRARY:FILEPATH=${LOCALBASE}/lib/libOSMesa.so \ -DOPENGL_gl_LIBRARY:FILEPATH=${LOCALBASE}/lib/libOSMesa.so \ -DVTK_USE_X:BOOL=OFF OSMESA_LIB_DEPENDS= libOSMesa.so:graphics/libosmesa # Wrapping JAVA_CATEGORIES= java JAVA_VARS= USE_JAVA=yes JAVA_CMAKE_BOOL= VTK_WRAP_JAVA Module_vtkWrappingJava JAVA_CMAKE_ON= -DJAVA_INCLUDE_PATH:PATH=${JAVA_HOME}/include \ -DJAVA_AWT_LIBRARY:PATH=${JAVA_HOME}/jre/lib/${ARCH}/libjawt.so \ -DJAVA_JVM_LIBRARY:PATH=${JAVA_HOME}/jre/lib/${ATCH}/libjava.so TCLTK_USES= tk TCLTK_CMAKE_BOOL= VTK_WRAP_TCL VTK_Group_Tk TCLTK_CMAKE_ON= -DTCL_INCLUDE_PATH:PATH=${TCL_INCLUDEDIR} \ -DTK_INCLUDE_PATH:PATH=${TK_INCLUDEDIR} \ -DVTK_INSTALL_TCL_DIR=lib/vtk-${VTK_SHORT_VER} DOCS_CMAKE_BOOL= BUILD_DOCUMENTATION DOCS_BUILD_DEPENDS= doxygen:devel/doxygen EXAMPLES_CMAKE_BOOL= BUILD_EXAMPLES # Mangling so that it will build when science/netcdf is installed. post-patch: @${MV} ${WRKSRC}/ThirdParty/netcdf/vtknetcdf/include/netcdf.h \ ${WRKSRC}/ThirdParty/netcdf/vtknetcdf/include/xxxnetcdf.h @${FIND} ${WRKSRC}/ThirdParty/netcdf -type f | ${XARGS} ${REINPLACE_CMD} \ -E 's/[[:<:]]netcdf\.h[[:>:]]/xxxnetcdf.h/' .include .for g in ${VTK_GROUPS} . if ${PORT_OPTIONS:M${g}} CMAKE_ARGS+= -DVTK_Group_${g}:BOOL=ON . else CMAKE_ARGS+= -DVTK_Group_${g}:BOOL=OFF . endif .endfor .if !${PORT_OPTIONS:MOSMESA} USES+= gl USE_GL= gl glu .endif post-install: # autoplist: thousands of files, complex dependencies on options @cd ${STAGEDIR}${PREFIX} && \ ${FIND} * -type f -or -type l >> ${TMPPLIST} .include Index: head/misc/adios2/Makefile =================================================================== --- head/misc/adios2/Makefile (revision 532094) +++ head/misc/adios2/Makefile (revision 532095) @@ -1,36 +1,37 @@ # $FreeBSD$ PORTNAME= adios2 DISTVERSIONPREFIX= v DISTVERSION= 2.5.0 +PORTREVISION= 1 CATEGORIES= misc science MAINTAINER= yuri@FreeBSD.org COMMENT= Next generation of ADIOS developed in the Exascale Computing Program LICENSE= APACHE20 LICENSE_FILE= ${WRKSRC}/LICENSE BUILD_DEPENDS= bash:shells/bash LIB_DEPENDS= libblosc.so:archivers/c-blosc \ libepoll-shim.so:devel/libepoll-shim \ libfabric.so:net/libfabric \ libffi.so:devel/libffi \ libmpi.so:net/openmpi \ libpng.so:graphics/png \ libzfp.so:devel/zfp RUN_DEPENDS= bash:shells/bash USES= bison cmake compiler:c++11-lang localbase:ldflags pkgconfig \ perl5 python shebangfix SHEBANG_FILES= cmake/install/post/adios2-config.pre.sh.in cmake/install/post/generate-adios2-config.sh.in source/utils/bp4dbg/bp4dbg.py \ source/utils/adios_deactivate_bp.sh USE_GITHUB= yes GH_ACCOUNT= ornladios GH_PROJECT= ADIOS2 USE_LDCONFIG= yes CMAKE_OFF= BUILD_TESTING LDFLAGS+= -lepoll-shim .include Index: head/net/aluminum/Makefile =================================================================== --- head/net/aluminum/Makefile (revision 532094) +++ head/net/aluminum/Makefile (revision 532095) @@ -1,24 +1,24 @@ # $FreeBSD$ PORTNAME= Aluminum DISTVERSIONPREFIX= v DISTVERSION= 0.3.3 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= net MAINTAINER= yuri@FreeBSD.org COMMENT= Generic interface to high-performance communication libraries LICENSE= APACHE20 LIB_DEPENDS= libhwloc.so:devel/hwloc \ libmpi.so:net/openmpi USES= cmake compiler:c11 USE_GITHUB= yes GH_ACCOUNT= LLNL USE_LDCONFIG= yes LDFLAGS+= -lexecinfo .include Index: head/net/openmpi/Makefile =================================================================== --- head/net/openmpi/Makefile (revision 532094) +++ head/net/openmpi/Makefile (revision 532095) @@ -1,88 +1,109 @@ # $FreeBSD$ -# TODO: -# - etc/*.sample support - PORTNAME= openmpi -PORTVERSION= 1.10.7 -PORTREVISION= 7 +PORTVERSION= 4.0.3 CATEGORIES= net parallel MASTER_SITES= http://www.open-mpi.org/software/ompi/v${PORTVERSION:R}/downloads/ MAINTAINER= danilo@FreeBSD.org COMMENT= High Performance Message Passing Library LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE +BROKEN_armv6= fails to package: pkg-static: mca_patcher_overwrite.la: No such file or directory +BROKEN_armv7= fails to package: pkg-static: mca_patcher_overwrite.la: No such file or directory +BROKEN_sparc64= fails to compile on sparc64 + LIB_DEPENDS= libhwloc.so:devel/hwloc \ libltdl.so:devel/libltdl \ - libevent.so:devel/libevent + libevent.so:devel/libevent \ + libmunge.so:security/munge -HAS_CONFIGURE= yes -INSTALL_TARGET= install-strip # :keepla because port uses lt_dlopen -USES= compiler:c11 fortran gmake libtool:keepla perl5 pkgconfig \ - tar:bzip2 +USES= fortran gmake libtool:keepla localbase perl5 \ + pkgconfig shebangfix tar:bzip2 + +HAS_CONFIGURE= yes USE_PERL5= build MPIBASE?= mpi MPIDIR?= ${MPIBASE}/${PKGBASE} PLIST_SUB+= MPIBASE=${MPIBASE} PLIST_SUB+= MPIDIR=${MPIDIR} +# Workaround for https://github.com/open-mpi/ompi/issues/7516 +CONFIGURE_ENV+= DISABLE_gds_ds12=1 DISABLE_gds_ds21=1 + CONFIGURE_ARGS+= --prefix=${PREFIX}/${MPIDIR} \ --mandir=${PREFIX}/${MPIDIR}/man \ --program-prefix= \ - --with-hwloc=${LOCALBASE} \ - --with-libltdl=${LOCALBASE} \ + --with-hwloc=external \ + --with-libltdl \ --enable-mpi-fortran=usempi \ + --enable-mpi-cxx \ + --enable-cxx-exceptions \ + --enable-mpi-thread-multiple \ --with-libevent=external \ + --enable-mca-no-build=verbs,btl_openib,oob_ud \ + --without-verbs \ --with-wrapper-ldflags=-Wl,-rpath=-Wl,-rpath=${LOCALBASE}/lib/gcc${_GCC_VER} \ ompi_cv_fortran_ignore_tkr_data=0 -LDFLAGS+= -L${LOCALBASE}/lib USE_LDCONFIG= ${PREFIX}/${MPIDIR}/lib \ ${PREFIX}/${MPIDIR}/lib/openmpi MANPREFIX= ${PREFIX}/${MPIDIR} -OPTIONS_DEFINE= IPV6 SLURM TORQUE VT +SHEBANG_FILES= ompi/mca/common/monitoring/profile2mat.pl \ + ompi/mca/common/monitoring/aggregate_profile.pl + +OPTIONS_DEFINE= DEBUG IPV6 SLURM TORQUE TORQUE_DESC= Enable Torque support SLURM_DESC= Enable SLURM support -VT_DESC= Enable VampirTrace support OPTIONS_DEFAULT= SLURM +OPTIONS_EXCLUDE_i386= SLURM OPTIONS_SUB= yes +DEBUG_CONFIGURE_ENABLE= debug +DEBUG_INSTALL_TARGET_OFF= install-strip + IPV6_CONFIGURE_ENABLE= ipv6 -TORQUE_CONFIGURE_ON= --with-tm=${LOCALBASE} -TORQUE_CONFIGURE_OFF= --without-tm +TORQUE_CONFIGURE_WITH= tm TORQUE_LIB_DEPENDS= libtorque.so:sysutils/torque TORQUE_PLIST_FILES= ${MPIDIR}/lib/openmpi/mca_plm_tm.so \ ${MPIDIR}/lib/openmpi/mca_plm_tm.la \ ${MPIDIR}/lib/openmpi/mca_ras_tm.la \ ${MPIDIR}/lib/openmpi/mca_ras_tm.so \ ${MPIDIR}/lib/openmpi/mca_ess_tm.so \ ${MPIDIR}/lib/openmpi/mca_ess_tm.la \ ${MPIDIR}/share/openmpi/help-plm-tm.txt \ ${MPIDIR}/share/openmpi/help-ras-tm.txt SLURM_CONFIGURE_WITH= slurm SLURM_LIB_DEPENDS= libslurm.so:sysutils/slurm-wlm SLURM_PLIST_FILES= ${MPIDIR}/lib/openmpi/mca_ess_slurm.la \ ${MPIDIR}/lib/openmpi/mca_ess_slurm.so \ ${MPIDIR}/lib/openmpi/mca_plm_slurm.la \ ${MPIDIR}/lib/openmpi/mca_plm_slurm.so \ ${MPIDIR}/lib/openmpi/mca_ras_slurm.la \ ${MPIDIR}/lib/openmpi/mca_ras_slurm.so \ + ${MPIDIR}/lib/openmpi/mca_schizo_slurm.la \ + ${MPIDIR}/lib/openmpi/mca_schizo_slurm.so \ ${MPIDIR}/share/openmpi/help-plm-slurm.txt \ ${MPIDIR}/share/openmpi/help-ras-slurm.txt -VT_CONFIGURE_OFF= --enable-contrib-no-build=vt --disable-vt -VT_USE= JAVA=yes - -BROKEN_sparc64= Does not compile on sparc64 +post-patch: + @${REINPLACE_CMD} -e 's|$$(libdir)/pkgconfig|${PREFIX}/${MPIDIR}/libdata/pkgconfig|g' \ + ${WRKSRC}/ompi/tools/wrappers/Makefile.am \ + ${WRKSRC}/ompi/tools/wrappers/Makefile.in \ + ${WRKSRC}/opal/tools/wrappers/Makefile.am \ + ${WRKSRC}/opal/tools/wrappers/Makefile.in \ + ${WRKSRC}/orte/tools/wrappers/Makefile.am \ + ${WRKSRC}/orte/tools/wrappers/Makefile.in + @${REINPLACE_CMD} 's|define MCA_hwloc_external_.*header "|&${LOCALBASE}/include/|' \ + ${WRKSRC}/configure .include Index: head/net/openmpi/distinfo =================================================================== --- head/net/openmpi/distinfo (revision 532094) +++ head/net/openmpi/distinfo (revision 532095) @@ -1,3 +1,3 @@ -TIMESTAMP = 1497724776 -SHA256 (openmpi-1.10.7.tar.bz2) = a089ece151fec974905caa35b0a59039b227bdea4e7933069e94bee4ed0e5a90 -SIZE (openmpi-1.10.7.tar.bz2) = 13435131 +TIMESTAMP = 1586692006 +SHA256 (openmpi-4.0.3.tar.bz2) = 1402feced8c3847b3ab8252165b90f7d1fa28c23b6b2ca4632b6e4971267fd03 +SIZE (openmpi-4.0.3.tar.bz2) = 9856669 Index: head/net/openmpi/files/patch-opal_mca_pmix_pmix3x_pmix_src_mca_pshmem_mmap_pshmem__mmap.c =================================================================== --- head/net/openmpi/files/patch-opal_mca_pmix_pmix3x_pmix_src_mca_pshmem_mmap_pshmem__mmap.c (nonexistent) +++ head/net/openmpi/files/patch-opal_mca_pmix_pmix3x_pmix_src_mca_pshmem_mmap_pshmem__mmap.c (revision 532095) @@ -0,0 +1,20 @@ +--- opal/mca/pmix/pmix3x/pmix/src/mca/pshmem/mmap/pshmem_mmap.c.orig 2020-04-12 11:49:10 UTC ++++ opal/mca/pmix/pmix3x/pmix/src/mca/pshmem/mmap/pshmem_mmap.c +@@ -79,6 +79,9 @@ static int _mmap_segment_create(pmix_pshmem_seg_t *sm_ + if (0 != (rc = posix_fallocate(sm_seg->seg_id, 0, size))) { + pmix_output_verbose(2, pmix_globals.debug_output, + "sys call posix_fallocate(2) fail\n"); ++ if (EINVAL == rc) { ++ goto ftruncate; ++ } + if (ENOSPC == rc) { + rc = PMIX_ERR_OUT_OF_RESOURCE; + goto out; +@@ -98,6 +101,7 @@ static int _mmap_segment_create(pmix_pshmem_seg_t *sm_ + goto map_memory; + } + #endif ++ftruncate: + if (0 != ftruncate(sm_seg->seg_id, size)) { + pmix_output_verbose(2, pmix_globals.debug_output, + "sys call ftruncate(2) fail\n"); Property changes on: head/net/openmpi/files/patch-opal_mca_pmix_pmix3x_pmix_src_mca_pshmem_mmap_pshmem__mmap.c ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/net/openmpi/pkg-plist =================================================================== --- head/net/openmpi/pkg-plist (revision 532094) +++ head/net/openmpi/pkg-plist (revision 532095) @@ -1,979 +1,898 @@ +%%MPIDIR%%/bin/aggregate_profile.pl %%MPIDIR%%/bin/mpiCC %%MPIDIR%%/bin/mpic++ %%MPIDIR%%/bin/mpicc %%MPIDIR%%/bin/mpicxx %%MPIDIR%%/bin/mpiexec %%MPIDIR%%/bin/mpif77 %%MPIDIR%%/bin/mpif90 %%MPIDIR%%/bin/mpifort %%MPIDIR%%/bin/mpirun %%MPIDIR%%/bin/ompi-clean -%%MPIDIR%%/bin/ompi-ps %%MPIDIR%%/bin/ompi-server -%%MPIDIR%%/bin/ompi-top %%MPIDIR%%/bin/ompi_info %%MPIDIR%%/bin/opal_wrapper %%MPIDIR%%/bin/orte-clean -%%MPIDIR%%/bin/orte-dvm %%MPIDIR%%/bin/orte-info -%%MPIDIR%%/bin/orte-ps %%MPIDIR%%/bin/orte-server -%%MPIDIR%%/bin/orte-submit -%%MPIDIR%%/bin/orte-top %%MPIDIR%%/bin/ortecc -%%MPIDIR%%/bin/orterun %%MPIDIR%%/bin/orted -%%VT%%%%MPIDIR%%/bin/mpiCC-vt -%%VT%%%%MPIDIR%%/bin/mpic++-vt -%%VT%%%%MPIDIR%%/bin/mpicc-vt -%%VT%%%%MPIDIR%%/bin/mpicxx-vt -%%VT%%%%MPIDIR%%/bin/mpif77-vt -%%VT%%%%MPIDIR%%/bin/mpif90-vt -%%VT%%%%MPIDIR%%/bin/mpifort-vt -%%VT%%%%MPIDIR%%/bin/otfaux -%%VT%%%%MPIDIR%%/bin/otfcompress -%%VT%%%%MPIDIR%%/bin/otfconfig -%%VT%%%%MPIDIR%%/bin/otfdecompress -%%VT%%%%MPIDIR%%/bin/otfinfo -%%VT%%%%MPIDIR%%/bin/otfmerge -%%VT%%%%MPIDIR%%/bin/otfmerge-mpi -%%VT%%%%MPIDIR%%/bin/otfprint -%%VT%%%%MPIDIR%%/bin/otfprofile -%%VT%%%%MPIDIR%%/bin/otfprofile-mpi -%%VT%%%%MPIDIR%%/bin/otfshrink -%%VT%%%%MPIDIR%%/bin/vtCC -%%VT%%%%MPIDIR%%/bin/vtc++ -%%VT%%%%MPIDIR%%/bin/vtcc -%%VT%%%%MPIDIR%%/bin/vtcxx -%%VT%%%%MPIDIR%%/bin/vtf77 -%%VT%%%%MPIDIR%%/bin/vtf90 -%%VT%%%%MPIDIR%%/bin/vtfilter -%%VT%%%%MPIDIR%%/bin/vtfilter-mpi -%%VT%%%%MPIDIR%%/bin/vtfiltergen -%%VT%%%%MPIDIR%%/bin/vtfiltergen-mpi -%%VT%%%%MPIDIR%%/bin/vtfort -%%VT%%%%MPIDIR%%/bin/vtrun -%%VT%%%%MPIDIR%%/bin/vtsetup -%%VT%%%%MPIDIR%%/bin/vtsetup.jar -%%VT%%%%MPIDIR%%/bin/vtunify -%%VT%%%%MPIDIR%%/bin/vtunify-mpi -%%VT%%%%MPIDIR%%/bin/vtwrapper -%%VT%%%%MPIDIR%%/etc/vtsetup-config.dtd -%%VT%%%%MPIDIR%%/etc/vtsetup-config.xml -%%VT%%%%MPIDIR%%/include/vampirtrace/open-trace-format/OTFAUX_MsgMatching.h -%%VT%%%%MPIDIR%%/include/vampirtrace/open-trace-format/OTFAUX_State.h -%%VT%%%%MPIDIR%%/include/vampirtrace/open-trace-format/OTFAUX_Thumbnail.h -%%VT%%%%MPIDIR%%/include/vampirtrace/open-trace-format/OTF_CopyHandler.h -%%VT%%%%MPIDIR%%/include/vampirtrace/open-trace-format/OTF_CopyHandler_stream.h -%%VT%%%%MPIDIR%%/include/vampirtrace/open-trace-format/OTF_Definitions.h -%%VT%%%%MPIDIR%%/include/vampirtrace/open-trace-format/OTF_Errno.h -%%VT%%%%MPIDIR%%/include/vampirtrace/open-trace-format/OTF_File.h -%%VT%%%%MPIDIR%%/include/vampirtrace/open-trace-format/OTF_FileManager.h -%%VT%%%%MPIDIR%%/include/vampirtrace/open-trace-format/OTF_File_iofsl.h -%%VT%%%%MPIDIR%%/include/vampirtrace/open-trace-format/OTF_Filenames.h -%%VT%%%%MPIDIR%%/include/vampirtrace/open-trace-format/OTF_HandlerArray.h -%%VT%%%%MPIDIR%%/include/vampirtrace/open-trace-format/OTF_KeyValue.h -%%VT%%%%MPIDIR%%/include/vampirtrace/open-trace-format/OTF_MasterControl.h -%%VT%%%%MPIDIR%%/include/vampirtrace/open-trace-format/OTF_RBuffer.h -%%VT%%%%MPIDIR%%/include/vampirtrace/open-trace-format/OTF_RStream.h -%%VT%%%%MPIDIR%%/include/vampirtrace/open-trace-format/OTF_Reader.h -%%VT%%%%MPIDIR%%/include/vampirtrace/open-trace-format/OTF_Version.h -%%VT%%%%MPIDIR%%/include/vampirtrace/open-trace-format/OTF_WBuffer.h -%%VT%%%%MPIDIR%%/include/vampirtrace/open-trace-format/OTF_WStream.h -%%VT%%%%MPIDIR%%/include/vampirtrace/open-trace-format/OTF_Writer.h -%%VT%%%%MPIDIR%%/include/vampirtrace/open-trace-format/OTF_inttypes.h -%%VT%%%%MPIDIR%%/include/vampirtrace/open-trace-format/OTF_inttypes_unix.h -%%VT%%%%MPIDIR%%/include/vampirtrace/open-trace-format/otf.h -%%VT%%%%MPIDIR%%/include/vampirtrace/open-trace-format/otfaux.h -%%VT%%%%MPIDIR%%/include/vampirtrace/vt_inttypes.h -%%VT%%%%MPIDIR%%/include/vampirtrace/vt_user.h -%%VT%%%%MPIDIR%%/include/vampirtrace/vt_user.inc 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%%MPIDIR%%/man/man7/orte_snapc.7.gz %%MPIDIR%%/man/man7/orte_sstore.7.gz %%MPIDIR%%/%%DATADIR%%/amca-param-sets/example.conf %%MPIDIR%%/%%DATADIR%%/help-btl-vader.txt %%MPIDIR%%/%%DATADIR%%/help-coll-sync.txt %%MPIDIR%%/%%DATADIR%%/help-dash-host.txt -%%MPIDIR%%/%%DATADIR%%/help-db-base.txt %%MPIDIR%%/%%DATADIR%%/help-errmgr-base.txt %%MPIDIR%%/%%DATADIR%%/help-ess-base.txt -%%MPIDIR%%/%%DATADIR%%/help-ess-hnp.txt %%MPIDIR%%/%%DATADIR%%/help-hostfile.txt %%MPIDIR%%/%%DATADIR%%/help-mca-base.txt %%MPIDIR%%/%%DATADIR%%/help-mca-bml-r2.txt %%MPIDIR%%/%%DATADIR%%/help-mca-coll-base.txt -%%MPIDIR%%/%%DATADIR%%/help-mca-op-base.txt +%%MPIDIR%%/%%DATADIR%%/help-mca-hook-base.txt %%MPIDIR%%/%%DATADIR%%/help-mca-var.txt %%MPIDIR%%/%%DATADIR%%/help-mpi-api.txt %%MPIDIR%%/%%DATADIR%%/help-mpi-btl-base.txt %%MPIDIR%%/%%DATADIR%%/help-mpi-btl-sm.txt %%MPIDIR%%/%%DATADIR%%/help-mpi-btl-tcp.txt -%%MPIDIR%%/%%DATADIR%%/help-mpi-coll-ml.txt %%MPIDIR%%/%%DATADIR%%/help-mpi-coll-sm.txt %%MPIDIR%%/%%DATADIR%%/help-mpi-common-sm.txt %%MPIDIR%%/%%DATADIR%%/help-mpi-errors.txt -%%MPIDIR%%/%%DATADIR%%/help-mpi-pml-bfo.txt %%MPIDIR%%/%%DATADIR%%/help-mpi-pml-ob1.txt %%MPIDIR%%/%%DATADIR%%/help-mpi-runtime.txt %%MPIDIR%%/%%DATADIR%%/help-mpool-base.txt -%%MPIDIR%%/%%DATADIR%%/help-ompi-crcp-base.txt -%%MPIDIR%%/%%DATADIR%%/help-ompi-dpm-base.txt -%%MPIDIR%%/%%DATADIR%%/help-ompi-dpm-orte.txt -%%MPIDIR%%/%%DATADIR%%/help-ompi-pubsub-orte.txt %%MPIDIR%%/%%DATADIR%%/help-oob-base.txt %%MPIDIR%%/%%DATADIR%%/help-oob-tcp.txt -%%MPIDIR%%/%%DATADIR%%/help-opal-compress-base.txt -%%MPIDIR%%/%%DATADIR%%/help-opal-compress-bzip.txt -%%MPIDIR%%/%%DATADIR%%/help-opal-compress-gzip.txt -%%MPIDIR%%/%%DATADIR%%/help-opal-crs-base.txt %%MPIDIR%%/%%DATADIR%%/help-opal-crs-none.txt %%MPIDIR%%/%%DATADIR%%/help-opal-hwloc-base.txt %%MPIDIR%%/%%DATADIR%%/help-opal-runtime.txt %%MPIDIR%%/%%DATADIR%%/help-opal-shmem-mmap.txt %%MPIDIR%%/%%DATADIR%%/help-opal-shmem-posix.txt %%MPIDIR%%/%%DATADIR%%/help-opal-shmem-sysv.txt %%MPIDIR%%/%%DATADIR%%/help-opal-util.txt %%MPIDIR%%/%%DATADIR%%/help-opal-wrapper.txt %%MPIDIR%%/%%DATADIR%%/help-opal_info.txt %%MPIDIR%%/%%DATADIR%%/help-orte-clean.txt -%%MPIDIR%%/%%DATADIR%%/help-orte-filem-base.txt %%MPIDIR%%/%%DATADIR%%/help-orte-filem-raw.txt %%MPIDIR%%/%%DATADIR%%/help-orte-info.txt %%MPIDIR%%/%%DATADIR%%/help-orte-odls-base.txt %%MPIDIR%%/%%DATADIR%%/help-orte-odls-default.txt -%%MPIDIR%%/%%DATADIR%%/help-orte-ps.txt +%%MPIDIR%%/%%DATADIR%%/help-orte-odls-pspawn.txt %%MPIDIR%%/%%DATADIR%%/help-orte-rmaps-base.txt %%MPIDIR%%/%%DATADIR%%/help-orte-rmaps-md.txt %%MPIDIR%%/%%DATADIR%%/help-orte-rmaps-ppr.txt %%MPIDIR%%/%%DATADIR%%/help-orte-rmaps-resilient.txt %%MPIDIR%%/%%DATADIR%%/help-orte-rmaps-rr.txt %%MPIDIR%%/%%DATADIR%%/help-orte-rmaps-seq.txt +%%MPIDIR%%/%%DATADIR%%/help-orte-rtc-base.txt +%%MPIDIR%%/%%DATADIR%%/help-orte-rtc-hwloc.txt %%MPIDIR%%/%%DATADIR%%/help-orte-runtime.txt %%MPIDIR%%/%%DATADIR%%/help-orte-server.txt %%MPIDIR%%/%%DATADIR%%/help-orte-snapc-base.txt -%%MPIDIR%%/%%DATADIR%%/help-orte-sstore-base.txt -%%MPIDIR%%/%%DATADIR%%/help-orte-top.txt %%MPIDIR%%/%%DATADIR%%/help-orted.txt %%MPIDIR%%/%%DATADIR%%/help-orterun.txt +%%MPIDIR%%/%%DATADIR%%/help-osc-pt2pt.txt %%MPIDIR%%/%%DATADIR%%/help-plm-base.txt %%MPIDIR%%/%%DATADIR%%/help-plm-rsh.txt +%%MPIDIR%%/%%DATADIR%%/help-pmix-base.txt +%%MPIDIR%%/%%DATADIR%%/help-pmix-pmix3x.txt %%MPIDIR%%/%%DATADIR%%/help-ras-base.txt %%MPIDIR%%/%%DATADIR%%/help-ras-simulator.txt +%%MPIDIR%%/%%DATADIR%%/help-rcache-base.txt %%MPIDIR%%/%%DATADIR%%/help-regex.txt %%MPIDIR%%/%%DATADIR%%/help-rmaps_rank_file.txt -%%MPIDIR%%/%%DATADIR%%/help-sec-base.txt -%%MPIDIR%%/%%DATADIR%%/help-state-staged-hnp.txt -%%MPIDIR%%/%%DATADIR%%/mca-coll-ml.config +%%MPIDIR%%/%%DATADIR%%/help-state-base.txt %%MPIDIR%%/%%DATADIR%%/mpiCC-wrapper-data.txt %%MPIDIR%%/%%DATADIR%%/mpic++-wrapper-data.txt %%MPIDIR%%/%%DATADIR%%/mpicc-wrapper-data.txt %%MPIDIR%%/%%DATADIR%%/mpicxx-wrapper-data.txt %%MPIDIR%%/%%DATADIR%%/mpif77-wrapper-data.txt %%MPIDIR%%/%%DATADIR%%/mpif90-wrapper-data.txt %%MPIDIR%%/%%DATADIR%%/mpifort-wrapper-data.txt %%MPIDIR%%/%%DATADIR%%/openmpi-valgrind.supp %%MPIDIR%%/%%DATADIR%%/ortecc-wrapper-data.txt +%%MPIDIR%%/share/pmix/help-pmix-mca-base.txt +%%MPIDIR%%/share/pmix/help-pmix-mca-var.txt +%%MPIDIR%%/share/pmix/help-pmix-plog.txt +%%MPIDIR%%/share/pmix/help-pmix-psensor-file.txt +%%MPIDIR%%/share/pmix/help-pmix-psensor-heartbeat.txt +%%MPIDIR%%/share/pmix/help-pmix-runtime.txt +%%MPIDIR%%/share/pmix/help-pmix-server.txt +%%MPIDIR%%/share/pmix/pmix-valgrind.supp Index: head/science/chrono/Makefile =================================================================== --- head/science/chrono/Makefile (revision 532094) +++ head/science/chrono/Makefile (revision 532095) @@ -1,64 +1,64 @@ # $FreeBSD$ PORTNAME= chrono DISTVERSION= 5.0.1 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= science devel PKGNAMESUFFIX= -physics-simulation-engine MAINTAINER= yuri@FreeBSD.org COMMENT= C++ library for multi-physics simulation LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE BROKEN_i386= use of overloaded operator '[]' is ambiguous (with operand types 'chrono::quaternion' and 'int'): https://github.com/projectchrono/chrono/issues/158 BUILD_DEPENDS= openmpi>0:net/openmpi USES= cmake compiler:c++14-lang eigen:3 fortran USE_GITHUB= yes GH_ACCOUNT= project${PORTNAME} USE_LDCONFIG= yes OPTIONS_DEFINE= HDF5 DEMOS PARALLEL TESTS OPTIONS_DEFAULT= HDF5 PARALLEL OPTIONS_SUB= yes HDF5_CMAKE_BOOL= ENABLE_HDF5 HDF5_LIB_DEPENDS= libhdf5.so:science/hdf5 DEMOS_DESC= Build and install demo programs DEMOS_CMAKE_BOOL= BUILD_DEMOS PARALLEL_DESC= Enable parallelism PARALLEL_CMAKE_BOOL= ENABLE_MODULE_PARALLEL PARALLEL_CMAKE_ON= -DBLAZE_DIR:STRING=${LOCALBASE}/include PARALLEL_BUILD_DEPENDS= blaze>0:math/blaze \ thrust>0:devel/thrust TESTS_DESC= Build and install unit test programs TESTS_CMAKE_BOOL= BUILD_TESTING PORTSCOUT= skipv:3.0.0 # their development continues under the branch 2.X. 3.0.0 should be ignored until they release a higher version .include .if ${CHOSEN_COMPILER_TYPE} == gcc CXXFLAGS+= -Wno-error=narrowing .endif post-extract: @${RM} ${WRKSRC}/data/opensim/Rajagopal2015.orig post-patch: @${FIND} ${WRKSRC} -name CMakeLists.txt -o -name "*.cmake*" | ${XARGS} ${REINPLACE_CMD} -i '' 's|lib64|lib|' @${REINPLACE_CMD} -e 's/ -march=native//' \ ${WRKSRC}/cmake/FindAVX.cmake \ ${WRKSRC}/cmake/FindFMA.cmake \ ${WRKSRC}/cmake/FindSSE.cmake post-stage: # https://github.com/projectchrono/chrono/issues/153 @${RMDIR} ${STAGEDIR}${PREFIX}/include/chrono_thirdparty/googlebenchmark ${STAGEDIR}${PREFIX}/include/chrono_thirdparty/googletest .include Index: head/science/fvcom-mpi/Makefile =================================================================== --- head/science/fvcom-mpi/Makefile (revision 532094) +++ head/science/fvcom-mpi/Makefile (revision 532095) @@ -1,17 +1,17 @@ # $FreeBSD$ -PORTREVISION= 14 +PORTREVISION= 15 PKGNAMESUFFIX= -openmpi MPIPREFIX= mpi/openmpi/ MAINTAINER= jwb@FreeBSD.org LIB_DEPENDS+= libmpi.so:net/openmpi MASTERDIR= ${.CURDIR}/../fvcom MAKE_ARGS+= FC=${LOCALBASE}/${MPIPREFIX}bin/mpif90 \ PORT_CPP_FLAGS+=-DMULTIPROCESSOR .include "${MASTERDIR}/Makefile" Index: head/science/gromacs/Makefile =================================================================== --- head/science/gromacs/Makefile (revision 532094) +++ head/science/gromacs/Makefile (revision 532095) @@ -1,95 +1,95 @@ # Created by: Stephen Montgomery-Smith # $FreeBSD$ PORTNAME= gromacs DISTVERSION= 2020.1 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= science MASTER_SITES= ftp://ftp.gromacs.org/pub/gromacs/ MAINTAINER= yuri@FreeBSD.org COMMENT= Compute molecular dynamics LICENSE= LGPL21 LICENSE_FILE= ${WRKSRC}/COPYING BROKEN_i386= undefined reference to `__atomic_load' and `__atomic_compare_exchange' BUILD_DEPENDS= boost-libs>=1.44:devel/boost-libs LIB_DEPENDS= libhwloc.so:devel/hwloc USES= cmake compiler:c++14-lang fortran gnome perl5 pkgconfig shebangfix xorg SHEBANG_FILES= admin/*.sh scripts/*.pl scripts/*.sh src/gromacs/selection/*.sh bash_CMD= ${SH} USE_GNOME= libxml2 CMAKE_OFF= GMX_USE_RDTSCP \ USE_PYTHON_SCRIPTS USE_LDCONFIG= yes OPTIONS_DEFINE= ATLAS FLOAT OPENCL OPENMP SIMD X11 OPTIONS_SINGLE= MP OPTIONS_SINGLE_MP= NOMP MPICH 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 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_CMAKE_ON= -DGMX_CXX11:BOOL=OFF OPENMP_CMAKE_OFF= -DGMX_OPENMP:BOOL=OFF SIMD_CMAKE_OFF= -DGMX_SIMD:STRING="None" X11_USE= XORG=ice,sm,xext,x11 X11_CMAKE_BOOL= GMX_X11 MP_DESC= Multiprocessing NOMP_DESC= No multiprocessing support NOMP_PLIST_SUB= SUFFIX_MPI="" MPICH_DESC= Parallel processing support via MPICH MPICH_LIB_DEPENDS= libmpich.so:net/mpich MPICH_CMAKE_ON= -DGMX_MPI:BOOL=ON \ -DMPI_C_COMPILER:FILEPATH="${LOCALBASE}/bin/mpicc" MPICH_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/pkg-plist =================================================================== --- head/science/gromacs/pkg-plist (revision 532094) +++ head/science/gromacs/pkg-plist (revision 532095) @@ -1,594 +1,594 @@ bin/GMXRC bin/GMXRC.bash bin/GMXRC.csh bin/GMXRC.zsh bin/demux.pl bin/gmx%%SUFFIX_MPI%%%%SUFFIX_D%% bin/gmx-completion-gmx%%SUFFIX_MPI%%%%SUFFIX_D%%.bash 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lib/libgromacs%%SUFFIX_MPI%%%%SUFFIX_D%%.so.5.0.0 libdata/pkgconfig/libgromacs%%SUFFIX_MPI%%%%SUFFIX_D%%.pc -share/cmake/gmxapi%%SUFFIX_MPI%%%%SUFFIX_D%%/gmxapi-config-version.cmake -share/cmake/gmxapi%%SUFFIX_MPI%%%%SUFFIX_D%%/gmxapi-config.cmake -share/cmake/gmxapi%%SUFFIX_MPI%%%%SUFFIX_D%%/gmxapi-%%CMAKE_BUILD_TYPE%%.cmake -share/cmake/gmxapi%%SUFFIX_MPI%%%%SUFFIX_D%%/gmxapi.cmake +share/cmake/gmxapi/gmxapi-config-version.cmake +share/cmake/gmxapi/gmxapi-config.cmake +share/cmake/gmxapi/gmxapi-%%CMAKE_BUILD_TYPE%%.cmake +share/cmake/gmxapi/gmxapi.cmake share/cmake/gromacs%%SUFFIX_MPI%%%%SUFFIX_D%%/gromacs%%SUFFIX_MPI%%%%SUFFIX_D%%-config-version.cmake share/cmake/gromacs%%SUFFIX_MPI%%%%SUFFIX_D%%/gromacs%%SUFFIX_MPI%%%%SUFFIX_D%%-config.cmake -share/cmake/gromacs%%SUFFIX_MPI%%%%SUFFIX_D%%/gromacs%%SUFFIX_MPI%%%%SUFFIX_D%%-toolchain.cmake +share/cmake/gromacs%%SUFFIX_MPI%%%%SUFFIX_D%%/gromacs-toolchain%%SUFFIX_MPI%%%%SUFFIX_D%%.cmake 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man/man1/gmx-rdf.1.gz man/man1/gmx-report-methods.1.gz man/man1/gmx-rms.1.gz man/man1/gmx-rmsdist.1.gz man/man1/gmx-rmsf.1.gz man/man1/gmx-rotacf.1.gz man/man1/gmx-rotmat.1.gz man/man1/gmx-saltbr.1.gz man/man1/gmx-sans.1.gz man/man1/gmx-sasa.1.gz man/man1/gmx-saxs.1.gz man/man1/gmx-select.1.gz man/man1/gmx-sham.1.gz man/man1/gmx-sigeps.1.gz man/man1/gmx-solvate.1.gz man/man1/gmx-sorient.1.gz man/man1/gmx-spatial.1.gz man/man1/gmx-spol.1.gz man/man1/gmx-tcaf.1.gz man/man1/gmx-traj.1.gz man/man1/gmx-trajectory.1.gz man/man1/gmx-trjcat.1.gz man/man1/gmx-trjconv.1.gz man/man1/gmx-trjorder.1.gz man/man1/gmx-tune_pme.1.gz man/man1/gmx-vanhove.1.gz man/man1/gmx-velacc.1.gz man/man1/gmx-view.1.gz man/man1/gmx-wham.1.gz man/man1/gmx-wheel.1.gz man/man1/gmx-x2top.1.gz man/man1/gmx-xpm2ps.1.gz man/man1/gmx.1.gz Index: head/science/hypre/Makefile =================================================================== --- head/science/hypre/Makefile (revision 532094) +++ head/science/hypre/Makefile (revision 532095) @@ -1,77 +1,77 @@ # Created by: Pedro Giffuni # $FreeBSD$ PORTNAME= hypre DISTVERSIONPREFIX= v DISTVERSION= 2.18.2 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org COMMENT= Scalable Linear Solvers and Multigrid Methods LICENSE= APACHE20 MIT LICENSE_COMB= dual LICENSE_FILE_APACHE20= ${WRKSRC}/../LICENSE-APACHE LICENSE_FILE_MIT= ${WRKSRC}/../LICENSE-MIT BROKEN_powerpc64= fails to compile: ./DistributedMatrixPilutSolver.h:97:20: expected ')' before '->' token USES= blaslapack fortran gmake localbase # gmake is only for the 'test' target USE_GITHUB= yes GH_ACCOUNT= hypre-space USE_LDCONFIG= yes WRKSRC_SUBDIR= src HAS_CONFIGURE= yes CONFIGURE_ARGS= --with-blas --with-blas-lib=${BLASLIB} \ --with-lapack --with-lapack-lib=${LAPACKLIB} \ --enable-shared OPTIONS_DEFINE= DOCS OPTIONS_SINGLE= MPI OPTIONS_SINGLE_MPI= NOMPI MPICH OPENMPI OPTIONS_DEFAULT= MPICH NOMPI_DESC= Build without parallel processing support NOMPI_CONFIGURE_ON= --without-MPI MPICH_DESC= Parallel processing support via MPICH MPICH_LIB_DEPENDS= libmpich.so:net/mpich MPICH_CONFIGURE_ENV= CC=${LOCALBASE}/bin/mpicc CXX=${LOCALBASE}/bin/mpicxx MPICH_CONFIGURE_WITH= MPI-include=${LOCALBASE}/include \ MPI-lib-dirs=${LOCALBASE}/lib OPENMPI_LIB_DEPENDS= libmpi.so:net/openmpi OPENMPI_CONFIGURE_ENV= CC=${LOCALBASE}/mpi/openmpi/bin/mpicc \ CXX=${LOCALBASE}/mpi/openmpi/bin/mpicxx OPENMPI_CONFIGURE_WITH= MPI-include=${LOCALBASE}/mpi/openmpi/include \ MPI-lib-dirs=${LOCALBASE}/mpi/openmpi/lib TEST_TARGET= check SHL3= ${PORTVERSION} SHL2= ${SHL3:R} SHL1= ${SHL2:R} PORTDOCS= * post-patch: # Avoid conflict with C++20 by ignoring <...> under WRKSRC @${REINPLACE_CMD} -i .c++20 '/utilities/s/-I/-iquote/' \ ${WRKSRC}/FEI_mv/*/Makefile do-install: ${INSTALL_DATA} ${WRKSRC}/hypre/include/* ${STAGEDIR}${PREFIX}/include ${INSTALL_LIB} ${WRKSRC}/hypre/lib/libHYPRE-${SHL3}.so \ ${STAGEDIR}${PREFIX}/lib/libHYPRE.so.${SHL2} ${RLN} ${STAGEDIR}${PREFIX}/lib/libHYPRE.so.${SHL2} \ ${STAGEDIR}${PREFIX}/lib/libHYPRE.so.${SHL1} ${RLN} ${STAGEDIR}${PREFIX}/lib/libHYPRE.so.${SHL2} \ ${STAGEDIR}${PREFIX}/lib/libHYPRE.so post-install-DOCS-on: ${MKDIR} ${STAGEDIR}${DOCSDIR} ${COPYTREE_SHARE} ${WRKSRC}/docs/usr-manual ${STAGEDIR}${DOCSDIR} .include Index: head/science/lammps/Makefile =================================================================== --- head/science/lammps/Makefile (revision 532094) +++ head/science/lammps/Makefile (revision 532095) @@ -1,74 +1,74 @@ # $FreeBSD$ PORTNAME= lammps PORTVERSION= ${GH_TAGNAME:C/(stable|patch)_([0-9]{1,2})([A-Z][a-z][a-z])([0-9]{4})/\4.\3.\2/S/Jan/01/S/Feb/02/S/Mar/03/S/Apr/04/S/May/05/S/Jun/06/S/Jul/07/S/Aug/08/S/Sep/09/S/Oct/10/S/Nov/11/S/Dec/12/} -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org COMMENT= Classical molecular dynamics code with a focus on materials modeling LICENSE= GPLv2 LICENSE_FILE= ${WRKSRC}/LICENSE BROKEN_i386= undefined reference to `__atomic_load' CONFLICTS_BUILD= ga # conflicts with include/error.h, already fixed in the head USES= blaslapack:openblas cmake:noninja eigen:3 fortran localbase:ldflags shebangfix USE_GITHUB= yes GH_TAGNAME= patch_19Mar2020 SHEBANG_GLOB= *.sh *.bash SHEBANG_FILES= lib/kokkos/bin/nvcc_wrapper CMAKE_SOURCE_PATH= ${WRKSRC}/cmake CMAKE_ARGS= -DBLA_VENDOR:STRING="OpenBLAS" ${CMAKE_ARGS_${CHOSEN_COMPILER_TYPE}} CMAKE_ARGS_gcc= -DBUILD_OMP:BOOL=false OPTIONS_DEFINE= JPEG PNG GZIP FFMPEG VORONOI LATTE OPTIONS_DEFINE_clang= OPENMP OPTIONS_GROUP= PARALLEL OPTIONS_GROUP_PARALLEL= MPI ${OPTIONS_DEFINE_${CHOSEN_COMPILER_TYPE}} OPTIONS_DEFAULT= MPI JPEG PNG GZIP FFMPEG VORONOI LATTE ${OPTIONS_DEFAULT_${CHOSEN_COMPILER_TYPE}} OPTIONS_DEFAULT_clang= OPENMP PARALLEL_DESC= Enable parallelizations: MPI_CMAKE_BOOL= BUILD_MPI MPI_LIB_DEPENDS= libmpi.so:net/openmpi MPI_USES= compiler:c11 FFMPEG_BUILD_DEPENDS= ffmpeg:multimedia/ffmpeg FFMPEG_RUN_DEPENDS= ffmpeg:multimedia/ffmpeg JPEG_CMAKE_BOOL= WITH_JPEG JPEG_USES= jpeg PNG_CMAKE_BOOL= WITH_PNG PNG_LIB_DEPENDS= libpng.so:graphics/png GZIP_CMAKE_BOOL= WITH_GZIP FFMPEG_CMAKE_BOOL= WITH_FFMPEG VORONOI_DESC= Use voro++, Voronoi tessellation package VORONOI_CMAKE_BOOL= PKG_VORONOI VORONOI_LIB_DEPENDS= libvoro++.so:science/voro++ LATTE_DESC= Use LATTE package LATTE_CMAKE_BOOL= PKG_LATTE LATTE_LIB_DEPENDS= liblatte.so:science/latte PORTSCOUT= ignore:1 # due to a special version tagging scheme that this project uses portscout fails to find new versions, watching their GitHub release page instead .include .if ${PORT_OPTIONS:MOPENMP} CMAKE_ARGS+= -DBUILD_OMP:BOOL=true .endif post-patch: @${REINPLACE_CMD} 's|SHELL = /bin/bash|SHELL = ${LOCALBASE}/bin/bash|' ${WRKSRC}/src/Makefile post-patch-FFMPEG-off: @${REINPLACE_CMD} 's|find_program(FFMPEG_EXECUTABLE|#&|' ${WRKSRC}/cmake/CMakeLists.txt .include Index: head/science/latte/Makefile =================================================================== --- head/science/latte/Makefile (revision 532094) +++ head/science/latte/Makefile (revision 532095) @@ -1,46 +1,46 @@ # $FreeBSD$ PORTNAME= latte DISTVERSIONPREFIX= v DISTVERSION= 1.2.1 -PORTREVISION= 7 +PORTREVISION= 8 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org COMMENT= Quantum chemistry: Density functional tight binding molecular dynamics LICENSE= GPLv3 LICENSE_FILE= ${WRKSRC}/LICENSE_GPL-2.0 USES= blaslapack:openblas cmake:noninja fortran shebangfix SHEBANG_FILES= tests/run_test.sh USE_GITHUB= yes GH_ACCOUNT= lanl GH_PROJECT= ${PORTNAME:tu} USE_LDCONFIG= yes CMAKE_SOURCE_PATH= ${WRKSRC}/cmake CMAKE_ON= BUILD_SHARED_LIBS CMAKE_ARGS= -DBLA_VENDOR:STRING="OpenBLAS" OPTIONS_DEFINE= DBCSR OPENMP MPI # TODO PROGRESS needs to be ported OPTIONS_DEFAULT= OPENMP MPI DBCSR_DESC= Use distributed block compressed sparse row matrix library DBCSR_CMAKE_BOOL= DBCSR_OPT DBCSR_LIB_DEPENDS= libdbcsr.so:math/dbcsr DBCSR_BROKEN= see https://github.com/lanl/LATTE/issues/92 OPENMP_CMAKE_BOOL= OPENMP MPI_CMAKE_BOOL= DO_MPI MPI_LIB_DEPENDS= libmpi.so:net/openmpi MPI_LDFLAGS= ${LOCALBASE}/mpi/openmpi/lib/libmpi_mpifh.so MPI_PLIST_FILES= bin/LATTE_MPI_DOUBLE MPI_PLIST_FILES_OFF= bin/LATTE_DOUBLE PLIST_FILES= lib/liblatte.so CONFLICTS_INSTALL= latte-integrale .include Index: head/science/liggghts/Makefile =================================================================== --- head/science/liggghts/Makefile (revision 532094) +++ head/science/liggghts/Makefile (revision 532095) @@ -1,40 +1,41 @@ # $FreeBSD$ PORTNAME= liggghts DISTVERSION= 3.8.0 -PORTREVISION= 5 +PORTREVISION= 6 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org COMMENT= Discrete element method particle simulation software LICENSE= GPLv2 LICENSE_FILE= ${WRKSRC}/../LICENSE BUILD_DEPENDS= gsed:textproc/gsed LIB_DEPENDS= libexpat.so:textproc/expat2 \ libfreetype.so:print/freetype2 \ libmpi.so:net/openmpi \ libpng.so:graphics/png \ libtiff.so:graphics/tiff \ libvtkViewsCore-8.1.so:math/vtk8 USES= compiler:c++17-lang cmake fortran jpeg qt:5 xorg USE_GITHUB= yes GH_ACCOUNT= CFDEMproject GH_PROJECT= ${PORTNAME:tu}-PUBLIC USE_XORG= ice sm x11 xext xt USE_QT= core gui sql widgets qmake_build buildtools_build USE_LDCONFIG= yes -CMAKE_ARGS= -DMPI_C_COMPILER:FILEPATH="${LOCALBASE}/mpi/openmpi/bin/mpicc" -DMPI_CXX_COMPILER:FILEPATH="${LOCALBASE}/mpi/openmpi/bin/mpicxx" \ +CMAKE_ARGS= -DMPI_C_COMPILER:FILEPATH="${LOCALBASE}/mpi/openmpi/bin/mpicc" \ + -DMPI_CXX_COMPILER:FILEPATH="${LOCALBASE}/mpi/openmpi/bin/mpicxx" \ -DVTK_DIR:FILEPATH="${LOCALBASE}/lib/cmake/vtk-8.1" WRKSRC_SUBDIR= src CFLAGS+= -fPIC CXXFLAGS+= -fPIC BINARY_ALIAS= sed=gsed .include Index: head/science/pnetcdf/Makefile =================================================================== --- head/science/pnetcdf/Makefile (revision 532094) +++ head/science/pnetcdf/Makefile (revision 532095) @@ -1,53 +1,50 @@ # Created by: Chao Shin # $FreeBSD$ PORTNAME= pnetcdf PORTVERSION= 1.8.1 -PORTREVISION= 9 +PORTREVISION= 10 CATEGORIES= science parallel 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 OPTIONS_SINGLE= MPI -OPTIONS_SINGLE_MPI= OPENMPI OPENMPI2 OPENMPI3 MPICH -OPTIONS_DEFAULT=OPENMPI3 -OPENMPI_DESC= Parallel processing support via Open MPI 1.x -OPENMPI2_DESC= Parallel processing support via Open MPI 2.x +OPTIONS_SINGLE_MPI= OPENMPI OPENMPI3 MPICH +OPTIONS_DEFAULT=OPENMPI +OPENMPI_DESC= Parallel processing support via Open MPI (current) OPENMPI3_DESC= Parallel processing support via Open MPI 3.x CONFLICTS_INSTALL= hdf-4.* CFLAGS+= -fPIC CONFIGURE_ARGS= ac_cv_fc_compiler_nag=no GNU_CONFIGURE= yes MAKE_JOBS_UNSAFE= yes USE_PERL5= build USES= fortran gmake pathfix perl5 tar:bzip2 PORTDOCS= COPYRIGHT INSTALL README MPICH_CONFIGURE_ON= --with-mpi=${LOCALBASE} MPICH_LIB_DEPENDS= libmpich.so:net/mpich OPENMPI_CONFIGURE_ON= --with-mpi=${LOCALBASE}/mpi/openmpi OPENMPI_LIB_DEPENDS= libmpi.so:net/openmpi -OPENMPI2_CONFIGURE_ON= --with-mpi=${LOCALBASE}/mpi/openmpi2 -OPENMPI2_LIB_DEPENDS= libmpi.so:net/openmpi2 OPENMPI3_CONFIGURE_ON= --with-mpi=${LOCALBASE}/mpi/openmpi3 OPENMPI3_LIB_DEPENDS= libmpi.so:net/openmpi3 post-patch: @${REINPLACE_CMD} -e '/$$(INSTALL.*$$(PREFIX)/ s|$$(PREFIX)|$$(DESTDIR)&|' ${WRKSRC}/Makefile.in post-install: ${STRIP_CMD} ${STAGEDIR}${PREFIX}/bin/n* ${STAGEDIR}${PREFIX}/bin/pnetcdf_version post-install-DOCS-on: ${MKDIR} ${STAGEDIR}${DOCSDIR}/ cd ${WRKSRC}/ && ${INSTALL_DATA} ${PORTDOCS} ${STAGEDIR}${DOCSDIR}/ .include Index: head/science/sparta/Makefile =================================================================== --- head/science/sparta/Makefile (revision 532094) +++ head/science/sparta/Makefile (revision 532095) @@ -1,48 +1,51 @@ # $FreeBSD$ PORTNAME= sparta PORTVERSION= ${GH_TAGNAME:C/([0-9]{1,2})([A-Z][a-z][a-z])([0-9]{4})/\3.\2.\1/S/Jan/01/S/Feb/02/S/Mar/03/S/Apr/04/S/May/05/S/Jun/06/S/Jul/07/S/Aug/08/S/Sep/09/S/Oct/10/S/Nov/11/S/Dec/12/} +PORTREVISION= 1 CATEGORIES= science PKGNAMESUFFIX= -dsmc # Direct Simulation Monte Carlo MAINTAINER= yuri@FreeBSD.org COMMENT= Gas simulator: SPARTA DSMC software package LICENSE= GPLv2 LICENSE_FILE= ${WRKSRC}/../LICENSE BUILD_DEPENDS= bash:shells/bash USES= compiler:c++11-lang gmake localbase USE_GITHUB= yes GH_TAGNAME= 24Jan2020 CXXFLAGS+= -DSPARTA_UNORDERED_MAP WRKSRC_SUBDIR= src MAKE_ARGS= CC=${CXX} CCFLAGS="${CXXFLAGS}" LINK=${CXX} LINKFLAGS="${LDFLAGS}" mode=exe OPTIONS_SINGLE= PARALLEL OPTIONS_SINGLE_PARALLEL= SERIAL MPI OPTIONS_DEFAULT= MPI PARALLEL_DESC= Parallelization SERIAL_DESC= Serial: no parallelization SERIAL_ALL_TARGET= serial SERIAL_PLIST_FILES= bin/spa_serial MPI_ALL_TARGET= mpi MPI_PLIST_FILES= bin/spa_mpi MPI_CXXFLAGS= -I${LOCALBASE}/mpi/openmpi/include -MPI_LDFLAGS= ${LOCALBASE}/mpi/openmpi/lib/libmpi.so ${LOCALBASE}/mpi/openmpi/lib/libmpi_cxx.so -Wl,-rpath=${LOCALBASE}/mpi/openmpi/lib +MPI_LDFLAGS= ${LOCALBASE}/mpi/openmpi/lib/libmpi.so \ + ${LOCALBASE}/mpi/openmpi/lib/libmpi_cxx.so \ + -Wl,-rpath=${LOCALBASE}/mpi/openmpi/lib MPI_LIB_DEPENDS= libmpi.so:net/openmpi PORTSCOUT= ignore:1 # due to a special version tagging scheme that this project uses portscout fails to find new versions, watching their release page instead post-patch: @${REINPLACE_CMD} 's|SHELL = /bin/bash|SHELL = ${LOCALBASE}/bin/bash|' ${WRKSRC}/Makefile do-install: ${INSTALL_PROGRAM} ${WRKSRC}/spa_* ${STAGEDIR}${PREFIX}/bin/ .include