diff --git a/benchmarks/hpl/Makefile b/benchmarks/hpl/Makefile index c56cad3f2158..cf702a8022c7 100644 --- a/benchmarks/hpl/Makefile +++ b/benchmarks/hpl/Makefile @@ -1,72 +1,72 @@ PORTNAME= hpl DISTVERSION= 2.3 -PORTREVISION= 7 +PORTREVISION= 8 CATEGORIES= benchmarks MASTER_SITES= NETLIB/benchmark/hpl MAINTAINER= oliver@FreeBSD.org COMMENT= High Performance Computing Linpack Benchmark WWW= https://www.netlib.org/benchmark/hpl/ LICENSE= BSD4CLAUSE LICENSE_FILE= ${WRKSRC}/www/copyright.html USES= fortran pkgconfig HPL_ARCH?= FreeBSD_PIV_CBLAS MAKE_ARGS= arch=${HPL_ARCH} ALL_TARGET= build OPTIONS_DEFINE= DOCS OPTIONS_RADIO= BLAS MPI OPTIONS_RADIO_BLAS= ATLAS BLIS FLEXIBLAS NETLIB OPENBLAS OPENBLAS64 OPTIONS_RADIO_MPI= MPICH OPENMPI OPTIONS_DEFAULT= NETLIB MPICH BLIS_DESC= BLAS implementation from FLAME FLEXIBLAS_DESC= BLAS and LAPACK wrapper library OPENBLAS64_DESC= OpenBLAS with 8 byte integers support ATLAS_USES= blaslapack:atlas BLIS_USES= blaslapack:blis FLEXIBLAS_USES= blaslapack:flexiblas NETLIB_USES= blaslapack:netlib OPENBLAS_USES= blaslapack:openblas OPENBLAS64_USES= blaslapack:openblas64 MPICH_USES= mpi:mpich OPENMPI_USES= mpi:openmpi CFLAGS+= -fomit-frame-pointer -funroll-loops OPENBLAS64_CFLAGS= -DF77_INTEGER=long pre-configure: ${REINPLACE_CMD} -e 's|^TOPdir[ ]*=.*$$|TOPdir = ${WRKSRC}| ; \ s|^MPdir[ ]*=.*$$|MPdir = ${LOCALBASE}| ; \ s|^LAdir[ ]*=.*$$|LAdir = ${LOCALBASE}| ; \ s|^CC[ ]*=.*$$|CC = ${CC}| ; \ s|^CCFLAGS[ ]*=.*$$|CCFLAGS = $$\(HPL_DEFS\) ${CFLAGS}| ; \ s|^LINKER[ ]*=.*$$|LINKER = ${FC}| ; \ s|^LINKFLAGS[ ]*=\(.*\)$$|LINKFLAGS =\1 ${LDFLAGS}| ; \ s|^ARCHIVER[ ]*=.*$$|ARCHIVER = ${AR}| ; \ s|ARCH[ )]|_&|g ; \ s|^HPL_OPTS[ ]*=.*$$|HPL_OPTS =| ; \ s|^LAlib[ ]*=.*$$|LAlib = ${BLASLIB}| ; \ s|^MPdir[ ]*=.*$$|MPdir = ${MPI_HOME}| ; \ s|^MPinc[ ]*=.*$$|MPinc = ${MPI_CFLAGS}| ; \ s|^MPlib[ ]*=.*$$|MPlib = ${MPI_LIBS}|' \ ${WRKSRC}/setup/Make.${HPL_ARCH} ${REINPLACE_CMD} -e 's|HPL\.dat|${PREFIX}/etc/${PORTNAME}/&|' \ ${WRKSRC}/testing/ptest/HPL_pdinfo.c ${CP} ${WRKSRC}/setup/Make.${HPL_ARCH} ${WRKSRC}/ ${REINPLACE_CMD} -e '/^build/s|$$| startup|' ${WRKSRC}/Makefile do-install: ${MKDIR} ${STAGEDIR}${ETCDIR} ${INSTALL_PROGRAM} ${WRKSRC}/bin/${HPL_ARCH}/xhpl ${STAGEDIR}${PREFIX}/bin/ ${INSTALL_DATA} ${WRKSRC}/bin/${HPL_ARCH}/HPL.dat ${STAGEDIR}${ETCDIR} ${INSTALL_MAN} ${WRKSRC}/man/man3/*.3 ${STAGEDIR}${PREFIX}/share/man/man3/ @${MKDIR} ${STAGEDIR}${DOCSDIR} .for doc in BUGS COPYRIGHT HISTORY README TODO TUNING ${INSTALL_DATA} ${WRKSRC}/${doc} ${STAGEDIR}${DOCSDIR} .endfor .include diff --git a/benchmarks/imb/Makefile b/benchmarks/imb/Makefile index 972ad15e1214..fb099b78a81c 100644 --- a/benchmarks/imb/Makefile +++ b/benchmarks/imb/Makefile @@ -1,60 +1,60 @@ PORTNAME= IMB DISTVERSIONPREFIX= v DISTVERSION= 2021.7 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= benchmarks parallel MASTER_SITES= https://github.com/intel/mpi-benchmarks/archive/refs/tags/ MAINTAINER= ports@FreeBSD.org COMMENT= Intel MPI Benchmark WWW= https://software.intel.com/en-us/imb-user-guide LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/license/license.txt #USE_GITHUB= yes #GH_ACCOUNT= intel #GH_PROJECT= mpi-benchmarks USES= gmake localbase USE_CXXSTD= c++14 BINARY_ALIAS= make=${GMAKE} WRKSRC= ${WRKDIR}/mpi-benchmarks-${DISTNAME} # Intel hardcodes -O3 in make_mpich. Replacing it with system defaults # would make it impossible to compare benchmark results with other systems. # By putting it here we make it easier for somebody to change it, if they # _really_ want it. OPT_CFLAGS= -O3 CC= ${MPICC} CXX= ${MPICXX} CFLAGS+= ${OPT_CFLAGS} ${MPI_CFLAGS} LDFLAGS+= ${MPI_LIBS} MAKE_ENV= MPI_HOME=${MPI_HOME} OPTIONS_DEFINE= CHECK_RESULTS DOCS OPTIONS_RADIO= MPI OPTIONS_RADIO_MPI= MPICH OPENMPI OPTIONS_DEFAULT= MPICH # Attention: -DCHECK results are not valid as real benchmark data! Don't # forget to deactivate DCHECK and recompile in order to get proper results. CHECK_RESULTS_DESC= Check results (not valid as real benchmark data) CHECK_RESULTS_CFLAGS= -DCHECK MPICH_USES= mpi:mpich OPENMPI_USES= mpi:openmpi do-install: (cd ${WRKSRC} && ${INSTALL_PROGRAM} IMB-* ${STAGEDIR}${PREFIX}/bin) do-install-DOCS-on: @${MKDIR} ${STAGEDIR}${DOCSDIR} ${INSTALL_DATA} ${WRKSRC}/ReadMe_IMB.txt ${STAGEDIR}${DOCSDIR} ${INSTALL_DATA} ${WRKSRC}/license/third-party-programs.txt ${STAGEDIR}${DOCSDIR} ${INSTALL_DATA} ${WRKSRC}/license/use-of-trademark-license.txt \ ${STAGEDIR}${DOCSDIR} .include diff --git a/benchmarks/ior/Makefile b/benchmarks/ior/Makefile index d7bc7e8fb134..70ff2524710d 100644 --- a/benchmarks/ior/Makefile +++ b/benchmarks/ior/Makefile @@ -1,31 +1,32 @@ PORTNAME= ior DISTVERSION= 4.0.0 +PORTREVISION= 1 CATEGORIES= benchmarks MAINTAINER= yuri@FreeBSD.org COMMENT= IOR and mdtest, parallel IO storage benchmark WWW= https://github.com/hpc/ior LICENSE= GPLv2 USES= autoreconf gmake localbase:ldflags mpi:mpich pkgconfig USE_GITHUB= yes GH_ACCOUNT= hpc GNU_CONFIGURE= yes GNU_CONFIGURE_MANPREFIX= ${PREFIX}/share TEST_TARGET= check PLIST_FILES= bin/ior \ bin/md-workbench \ bin/mdtest \ share/man/man1/mdtest.1.gz post-install: # see https://github.com/hpc/ior/issues/454 @${RM} \ ${STAGEDIR}${PREFIX}/lib/libaiori.a \ ${STAGEDIR}${PREFIX}/share/USER_GUIDE .include diff --git a/benchmarks/mdtest/Makefile b/benchmarks/mdtest/Makefile index 1a152a66b7df..aa5022313749 100644 --- a/benchmarks/mdtest/Makefile +++ b/benchmarks/mdtest/Makefile @@ -1,41 +1,41 @@ PORTNAME= mdtest PORTVERSION= 1.9.3 -PORTREVISION= 16 +PORTREVISION= 17 CATEGORIES= benchmarks MASTER_SITES= SF/${PORTNAME}/${PORTNAME}%20latest/${PORTNAME}-${PORTVERSION} MAINTAINER= ports@FreeBSD.org COMMENT= Filesystem metadata benchmark utility WWW= https://sourceforge.net/projects/mdtest/ LICENSE= GPLv2 USES= tar:tgz NO_WRKSUBDIR= yes CFLAGS+= -DDarwin PLIST_FILES= bin/${PORTNAME} share/man/man1/${PORTNAME}.1.gz PORTEXAMPLES= * OPTIONS_DEFINE= OPENMPI EXAMPLES OPENMPI_DESC= Use Open MPI instead of MPICH OPENMPI_BUILD_DEPENDS= ${LOCALBASE}/mpi/openmpi/bin/mpicc:net/openmpi OPENMPI_RUN_DEPENDS= ${LOCALBASE}/mpi/openmpi/bin/mpirun:net/openmpi OPENMPI_VARS= MPICC=${LOCALBASE}/mpi/openmpi/bin/mpicc OPENMPI_BUILD_DEPENDS_OFF= ${LOCALBASE}/bin/mpicc:net/mpich OPENMPI_RUN_DEPENDS_OFF= ${LOCALBASE}/bin/mpirun:net/mpich OPENMPI_VARS_OFF= MPICC=${LOCALBASE}/bin/mpicc do-build: (cd ${WRKSRC} && ${MPICC} ${CFLAGS} -o ${PORTNAME} ${PORTNAME}.c -lm) do-install: ${INSTALL_PROGRAM} ${WRKSRC}/${PORTNAME} ${STAGEDIR}${PREFIX}/bin ${INSTALL_MAN} ${WRKSRC}/${PORTNAME}.1 ${STAGEDIR}${PREFIX}/share/man/man1 @${MKDIR} ${STAGEDIR}${EXAMPLESDIR} ${INSTALL_DATA} ${WRKSRC}/scripts/* ${STAGEDIR}${EXAMPLESDIR} .include diff --git a/biology/abyss/Makefile b/biology/abyss/Makefile index 2b189670b288..e2b984a5d940 100644 --- a/biology/abyss/Makefile +++ b/biology/abyss/Makefile @@ -1,53 +1,54 @@ PORTNAME= abyss DISTVERSION= 2.3.10 +PORTREVISION= 1 CATEGORIES= biology MAINTAINER= yuri@FreeBSD.org COMMENT= Assembly By Short Sequences: parallel, paired-end sequence assembler WWW= https://www.bcgsc.ca/resources/software/abyss/ LICENSE= GPLv3 LICENSE_FILE= ${WRKSRC}/LICENSE BROKEN_i386= result of comparison of constant 18446744073709551615 with expression of type 'size_t', see https://github.com/bcgsc/abyss/issues/310 BUILD_DEPENDS= ${LOCALBASE}/include/boost/version.hpp:devel/boost-libs \ ghc:lang/ghc \ pandoc:textproc/hs-pandoc # pandoc is required just for one man page: abyss-sealer LIB_DEPENDS= libbtllib.so:biology/btllib \ libffi.so:devel/libffi \ libgmp.so:math/gmp \ libmpich.so:net/mpich # binaries aren't linked with libmpich.so for some reason RUN_DEPENDS= bash:shells/bash \ gmake:devel/gmake USES= autoreconf compiler:c++11-lang gmake iconv:wchar_t localbase:ldflags shebangfix sqlite USE_GITHUB= yes GH_ACCOUNT= bcgsc SHEBANG_FILES= bin/${PORTNAME}-* DataBase/abyss-db-txt SHEBANG_LANG= make make_OLD_CMD= /usr/bin/make make_CMD= ${GMAKE} GNU_CONFIGURE= yes CONFIGURE_ARGS= --without-sparsehash # configure fails to find std::hash, reported to the ML: https://groups.google.com/forum/#!topic/trans-abyss/SZDBKR5bKxs TEST_TARGET= check PORTSCOUT= limit:^[0-9\.]*$$ # to ignore alpha-numeric tags PORTDOCS= * OPTIONS_DEFINE= DOCS TESTING_UNSAFE= yes # tests fail to compile, see https://github.com/bcgsc/abyss/issues/453 .include .if ${OPSYS} == FreeBSD CFLAGS+= -Wno-error=unused-but-set-variable .endif .include diff --git a/cad/scotch/Makefile b/cad/scotch/Makefile index 624357ac79ac..73e9ad06b4b0 100644 --- a/cad/scotch/Makefile +++ b/cad/scotch/Makefile @@ -1,94 +1,94 @@ PORTNAME= scotch DISTVERSION= 6.0.4-aster7 -PORTREVISION= 6 +PORTREVISION= 7 CATEGORIES= cad science MAINTAINER= thierry@FreeBSD.org COMMENT= Package for graph and mesh partitioning and sparse matrix ordering WWW= https://www.labri.fr/perso/pelegrin/scotch/ LICENSE= CeCILL_C LICENSE_NAME= CeCILL-C LICENSE_FILE= ${WRKSRC}/doc/CeCILL-C_V1-en.txt LICENSE_PERMS= dist-mirror dist-sell pkg-mirror pkg-sell auto-accept USES= bison:alias gmake localbase CONFLICTS_INSTALL= gbase gmap # bin/gbase bin/gmap MAKE_JOBS_UNSAFE=yes OPTIONS_DEFINE= DOCS EXAMPLES MPICH OPTIONS_DEFAULT=MPICH OPTIONS_SUB= yes WRKSRC= ${WRKDIR}/${PORTNAME}-${PORTVERSION:R} BUILD_WRKSRC= ${WRKSRC}/src INSTALL_WRKSRC= ${BUILD_WRKSRC} TEST_WRKSRC= ${BUILD_WRKSRC} ALL_TARGET= esmumps TEST_TARGET= check CFLAGS= -Wno-implicit-function-declaration MAKE_ENV= prefix=${STAGEDIR}${PREFIX} mandir=${STAGEDIR}${PREFIX}/share/man \ -DSCOTCH_PTHREAD_NUMBER=2 USE_LDCONFIG= yes DOCVER= ${PORTVERSION:R:R} PORTDOCS= ptscotch_user${DOCVER}.pdf scotch_user${DOCVER}.pdf scotch_example.f LIBS= esmumps scotch scotcherr scotcherrexit scotchmetis MPICH_USES= mpi:mpich MPICH_ALL_TARGET= ptesmumps MPICH_TEST_TARGET= ptcheck MPICH_LIBS+= ptesmumps ptscotch ptscotcherr ptscotcherrexit ptscotchparmetis .include .if ${ARCH} == "i386" MF= i686 .else MF= x86-64 .endif pre-everything:: .if !defined(WITHOUT_MPICH) @${ECHO_MSG} @${ECHO_MSG} "Define WITHOUT_MPI if PT-Scotch is not wanted." @${ECHO_MSG} .endif pre-configure: ${REINPLACE_CMD} -e 's/-lthread/-pthread/;s/-lpthread/-pthread/'\ ${WRKSRC}/src/Make.inc/Makefile.inc.${MF}_pc_freebsd ${LN} -sf ${WRKSRC}/src/Make.inc/Makefile.inc.${MF}_pc_freebsd \ ${WRKSRC}/src/Makefile.inc ${REINPLACE_CMD} -E -e 's|cd (.*) ; * \$$\(MAKE\)|\$$(MAKE) -C \1|' \ -e 's|\&\& \$$\(MAKE\)||' ${WRKSRC}/src/Makefile post-stage: ${STRIP_CMD} ${STAGEDIR}${PREFIX}/bin/* ${STAGEDIR}${PREFIX}/lib/lib* .for l in ${LIBS} ${MV} ${STAGEDIR}${PREFIX}/lib/lib${l}.so ${STAGEDIR}${PREFIX}/lib/lib${l}.so.0 ${LN} -sf lib${l}.so.0 ${STAGEDIR}${PREFIX}/lib/lib${l}.so .endfor do-install-DOCS-on: ${MKDIR} ${STAGEDIR}${DOCSDIR} ${INSTALL_DATA} ${PORTDOCS:S|^|${WRKSRC}/doc/|} ${STAGEDIR}${DOCSDIR} do-install-EXAMPLES-on: ${MKDIR} ${STAGEDIR}${EXAMPLESDIR}/grf ${STAGEDIR}${EXAMPLESDIR}/tgt ${INSTALL_DATA} ${WRKSRC}/grf/* ${STAGEDIR}${EXAMPLESDIR}/grf ${INSTALL_DATA} ${WRKSRC}/tgt/* ${STAGEDIR}${EXAMPLESDIR}/tgt .if !defined(WITHOUT_MPI) pre-test: . if !exists(${HOME}/.mpd.conf) @${ECHO_CMD} "MPD_SECRETWORD=change_on_install" > ${HOME}/.mpd.conf ${CHMOD} go-r ${HOME}/.mpd.conf @${ECHO_MSG} "${HOME}/.mpd.conf has been generated - please change the secret word!" . endif .endif .include "${.CURDIR}/../../french/aster/bsd.aster.mk" .include diff --git a/devel/babelflow/Makefile b/devel/babelflow/Makefile index 59c1849e04d1..1dde4260423c 100644 --- a/devel/babelflow/Makefile +++ b/devel/babelflow/Makefile @@ -1,36 +1,36 @@ PORTNAME= babelflow DISTVERSIONPREFIX= v DISTVERSION= 1.1.0 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= devel MAINTAINER= yuri@FreeBSD.org COMMENT= Embedded Domain Specific Language to describe task graph abstraction WWW= https://github.com/sci-visus/BabelFlow LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE USES= cmake compiler:c++11-lang USE_LDCONFIG= yes USE_GITHUB= yes GH_ACCOUNT= sci-visus GH_PROJECT= BabelFlow CMAKE_ARGS= -DRUNTIME_TYPE:STRING="MPI" OPTIONS_SINGLE= MPI OPTIONS_SINGLE_MPI= MPICH OPENMPI OPTIONS_SINGLE_MPI= MPICH OPENMPI OPTIONS_DEFINE= EXAMPLES OPTIONS_DEFAULT= EXAMPLES MPICH OPTIONS_SUB= yes EXAMPLES_CMAKE_BOOL= BUILD_EXAMPLES MPICH_USES= mpi:mpich OPENMPI_USES= mpi:openmpi .include diff --git a/devel/ga/Makefile b/devel/ga/Makefile index e8e392c11ab8..a588b6d3f9fa 100644 --- a/devel/ga/Makefile +++ b/devel/ga/Makefile @@ -1,54 +1,55 @@ PORTNAME= ga DISTVERSION= 5.9.2 +PORTREVISION= 1 CATEGORIES= devel MASTER_SITES= https://github.com/GlobalArrays/ga/releases/download/v${DISTVERSION}/ MAINTAINER= yuri@FreeBSD.org COMMENT= Partitioned Global Address Space (PGAS) library for distributed arrays WWW= https://globalarrays.github.io/ \ https://github.com/GlobalArrays/ga LICENSE= BSD3CLAUSE LIB_DEPENDS= libblas.so:math/blas \ liblapack.so:math/lapack \ libscalapack.so:math/scalapack USES= autoreconf fortran gmake libtool localbase USE_LDCONFIG= yes GNU_CONFIGURE= yes CONFIGURE_ARGS= --disable-peigs --enable-shared --disable-static --with-scalapack # PeIGS is part of NWChem, usure why the --enable-peigs even exists here LDFLAGS+= -lscalapack INSTALL_TARGET= install-strip TEST_TARGET= check # test asserts, see https://github.com/GlobalArrays/ga/issues/312 MPIEXEC_ARGS= -np 2 OPTIONS_RADIO= BLAS_SIZE MPI OPTIONS_RADIO_BLAS_SIZE= BLAS_SIZE_4 BLAS_SIZE_8 # the default BLAS_SIZE below should be same as the same choice in science/nwchem and in math/blas or math/openblas OPTIONS_RADIO_MPI= MPICH OPENMPI # the default MPI choice below should be the same as for the MPI option in math/scalapack OPTIONS_DEFAULT= BLAS_SIZE_4 MPICH BLAS_SIZE_DESC= BLAS_SIZE value to use during build (should be same as in devel/ga) BLAS_SIZE_4_DESC= BLAS_SIZE=4 BLAS_SIZE_4_CONFIGURE_ON= --with-blas4 BLAS_SIZE_8_DESC= BLAS_SIZE=8 BLAS_SIZE_8_CONFIGURE_ON= --with-blas8 MPICH_LIB_DEPENDS= libmpich.so:net/mpich MPICH_VARS= TEST_ARGS+=MPIEXEC="${LOCALBASE}/bin/mpiexec ${MPIEXEC_ARGS}" OPENMPI_BUILD_DEPENDS= openmpi>0:net/openmpi OPENMPI_RUN_DEPENDS= openmpi>0:net/openmpi OPENMPI_CONFIGURE_ENV= CC=${LOCALBASE}/mpi/openmpi/bin/mpicc MPICC=${LOCALBASE}/mpi/openmpi/bin/mpicc \ CXX=${LOCALBASE}/mpi/openmpi/bin/mpic++ MPICXX=${LOCALBASE}/mpi/openmpi/bin/mpic++ \ F77=${LOCALBASE}/mpi/openmpi/bin/mpif77 MPIF77=${LOCALBASE}/mpi/openmpi/bin/mpif77 \ FC=${LOCALBASE}/mpi/openmpi/bin/mpif90 MPIFC=${LOCALBASE}/mpi/openmpi/bin/mpif90 \ LDFLAGS="-L${LOCALBASE}/mpi/openmpi/lib -Wl,-rpath,${LOCALBASE}/mpi/openmpi/lib" OPENMPI_MAKE_ARGS= FREEBSD_LINK_FLAGS="-L${LOCALBASE}/mpi/openmpi/lib -Wl,-rpath,${LOCALBASE}/mpi/openmpi/lib -lmpi" OPENMPI_VARS= TEST_ARGS+=MPIEXEC="${LOCALBASE}/mpi/openmpi/bin/mpiexec ${MPIEXEC_ARGS}" .include diff --git a/graphics/glvis/Makefile b/graphics/glvis/Makefile index 9446149b0e47..cd151060704d 100644 --- a/graphics/glvis/Makefile +++ b/graphics/glvis/Makefile @@ -1,45 +1,46 @@ PORTNAME= glvis DISTVERSION= 4.4 +PORTREVISION= 1 CATEGORIES= graphics MASTER_SITES= https://glvis.github.io/releases/ PKGNAMESUFFIX= -mesh-visualizer # other software also has the name glvis DISTFILES= ${DISTNAME}${EXTRACT_SUFX} MAINTAINER= yuri@FreeBSD.org COMMENT= Lightweight tool for accurate & flexible finite element visualization WWW= https://glvis.org \ https://github.com/glvis/glvis LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE BUILD_DEPENDS= glm>0:math/glm \ xxd:editors/vim LIB_DEPENDS= libfontconfig.so:x11-fonts/fontconfig \ libfreetype.so:print/freetype2 \ libHYPRE.so:science/hypre \ libmetis.so:math/metis \ libmfem.so:math/mfem \ libpng.so:graphics/png TEST_DEPENDS= ${PYTHON_PKGNAMEPREFIX}scikit-image>0:graphics/py-scikit-image@${PY_FLAVOR} USES= cmake:testing gl mpi:mpich python:test sdl tar:tgz USE_GL= gl glew USE_SDL= sdl2 # the mpi dependency is inherited from math/mfem and not set here for simplicity USE_GITHUB= nodefault GH_TUPLE= GLVis:data:b8092cc:data/tests/data CMAKE_TESTING_ON= ENABLE_TESTS # 5 tests fail, likely because test baseline is for ubuntu CMAKE_ARGS= -DGLVIS_BASELINE_SYS=ubuntu-20.04 # baseline for tests PLIST_FILES= bin/${PORTNAME} BINARY_ALIAS= python3=${PYTHON_CMD} do-install: # workaround for https://github.com/GLVis/glvis/issues/234 ${INSTALL_PROGRAM} ${BUILD_WRKSRC}/glvis ${STAGEDIR}${PREFIX}/bin .include diff --git a/graphics/vv/Makefile b/graphics/vv/Makefile index 949a0af9f166..b22b9830da77 100644 --- a/graphics/vv/Makefile +++ b/graphics/vv/Makefile @@ -1,70 +1,71 @@ PORTNAME= vv DISTVERSIONPREFIX= v DISTVERSION= 1.4.0-406 +PORTREVISION= 1 DISTVERSIONSUFFIX= -gd33ac3e8 CATEGORIES= graphics MAINTAINER= yuri@FreeBSD.org COMMENT= Fast and simple 4D image viewer WWW= https://github.com/open-vv/vv LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE.txt BUILD_DEPENDS= googletest>0:devel/googletest # error: unable to find library -lGTest::GTest, see https://github.com/open-vv/vv/issues/74 LIB_DEPENDS= libexpat.so:textproc/expat2 \ libfreetype.so:print/freetype2 \ libgdcmCommon.so:devel/gdcm \ libhdf5_cpp.so:science/hdf5 \ libITKLabelMap-5.0.so:science/InsightToolkit501 \ libmpi.so:net/mpich \ libnetcdf.so:science/netcdf \ libpng16.so:graphics/png \ libtiff.so:graphics/tiff \ libvtkIOSQL-${VTK_VER}.so:math/vtk9 USES= cmake compiler:c++11-lang eigen:3 jpeg python:build,run qt:5 xorg USE_GITHUB= yes GH_ACCOUNT= open-vv USE_QT= core designer gui network opengl declarative sql widgets xml buildtools:build qmake:build USE_XORG= ice sm x11 xext xt USE_CXXSTD= c++11 CMAKE_ARGS= -DVTK_DIR:PATH=${LOCALBASE}/lib/vtk-8.2/cmake/vtk-8.2 PLIST_FILES= bin/vv .include .if ${ARCH} == i386 CXXFLAGS+= -msse2 # workaround for ITK failing to add -msse2 on i386: https://github.com/open-vv/vv/issues/83 & https://github.com/InsightSoftwareConsortium/ITK/issues/2011 .endif post-patch: @${REINPLACE_CMD} -e 's/VTK_OVERRIDE/override/g' \ ${WRKSRC}/vv/vtkVOXImageWriter.h \ ${WRKSRC}/vv/vvAnimatedGIFWriter.h \ ${WRKSRC}/vv/vvBlendImageActor.h \ ${WRKSRC}/vv/vvClipPolyData.h \ ${WRKSRC}/vv/vvGlyph2D.h \ ${WRKSRC}/vv/vvGlyphSource.h \ ${WRKSRC}/vv/vvInteractorStyleNavigator.h \ ${WRKSRC}/vv/vvLandmarksGlyph.h \ ${WRKSRC}/vv/vvSlicer.h @${REINPLACE_CMD} -e 's/Widget()->GetRenderWindow()/Widget()->renderWindow()/g' \ ${WRKSRC}/vv/vvToolHistogramCommand.cxx @${REINPLACE_CMD} -e 's/Widget->GetRenderWindow()/Widget->renderWindow()/g' \ ${WRKSRC}/vv/vvMainWindow.cxx \ ${WRKSRC}/vv/vvSegmentationDialog.cxx \ ${WRKSRC}/vv/vvSurfaceViewerDialog.cxx \ ${WRKSRC}/vv/vvToolHistogram.cxx \ ${WRKSRC}/vv/vvToolProfile.cxx @${REINPLACE_CMD} -e 's/widget->GetRenderWindow()/widget->renderWindow()/g' \ ${WRKSRC}/vv/vvMainWindow.cxx post-configure: # workaround for "error: unable to find library -lGTest::GTest", see https://github.com/open-vv/vv/issues/74 @${REINPLACE_CMD} -E 's/ -lGTest::(GTest|Main) / /g' ${BUILD_WRKSRC}/build.ninja @${REINPLACE_CMD} -E 's|/usr/local/lib/libtiff\.so\.[0-9]+\.[0-9]+\.[0-9]+|/usr/local/lib/libtiff.so|g' ${BUILD_WRKSRC}/build.ninja .include <../../math/vtk9/Makefile.version> .include diff --git a/lang/opencoarrays/Makefile b/lang/opencoarrays/Makefile index 83f779100eac..29e78531b930 100644 --- a/lang/opencoarrays/Makefile +++ b/lang/opencoarrays/Makefile @@ -1,69 +1,69 @@ PORTNAME= opencoarrays DISTVERSION= 2.10.1 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= lang parallel MAINTAINER= miguel@gocobachi.dev COMMENT= Transport layer for coarray Fortran compilers WWW= http://www.opencoarrays.org/ LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE BROKEN_aarch64= lack of IEEE754 support in gcc causes "Cannot find an intrinsic module named 'ieee_arithmetic'", see bug #255890 BUILD_DEPENDS= bash:shells/bash RUN_DEPENDS= bash:shells/bash USES= cmake fortran USE_CSTD= gnu99 USE_GCC= yes USE_GITHUB= yes GH_ACCOUNT= sourceryinstitute GH_PROJECT= OpenCoarrays USE_LDCONFIG= yes CFLAGS+= -fpermissive PLIST_SUB= GCC_VER=${_GCC_VER} \ PORTVERSION=${PORTVERSION} \ SOVERSION=3 OPTIONS_SINGLE= MPI OPTIONS_SINGLE_MPI= MPICH OPENMPI OPTIONS_DEFAULT= MPICH OPTIONS_EXCLUDE_armv6= MPICH OPTIONS_EXCLUDE_armv7= MPICH OPTIONS_EXCLUDE_i386= MPICH OPTIONS_EXCLUDE_mips= MPICH OPTIONS_EXCLUDE_powerpc= MPICH OPTIONS_EXCLUDE_powerpcspe= MPICH OPTIONS_DEFAULT_armv6= OPENMPI OPTIONS_DEFAULT_armv7= OPENMPI OPTIONS_DEFAULT_i386= OPENMPI OPTIONS_DEFAULT_mips= OPENMPI OPTIONS_DEFAULT_powerpc= OPENMPI OPTIONS_DEFAULT_powerpcspe= OPENMPI CMAKE_C_COMPILER= gcc MPICH_BUILD_DEPENDS= mpif90:net/mpich MPICH_RUN_DEPENDS= mpif90:net/mpich MPICH_CONFIGURE_ENV= MPI_HOME=${LOCALBASE} OPENMPI_BUILD_DEPENDS= ${LOCALBASE}/mpi/openmpi/bin/mpif90:net/openmpi OPENMPI_RUN_DEPENDS= ${LOCALBASE}/mpi/openmpi/bin/mpif90:net/openmpi OPENMPI_CONFIGURE_ENV= MPI_HOME=${LOCALBASE}/mpi/openmpi OPENMPI_CMAKE_ON= -DMPI_C_COMPILE_OPTIONS="-lpthread" \ -DMPI_Fortran_COMPILE_OPTIONS="-lpthread" .include post-patch: @${REINPLACE_CMD} '/mod_dir_tail/s/$${CMAKE_Fortran_COMPILER_VERSION}/${_GCC_VER}/' \ ${WRKSRC}/CMakeLists.txt do-test: (cd ${TEST_WRKSRC} && ctest) .include diff --git a/math/arpack-ng/Makefile b/math/arpack-ng/Makefile index 76ccea6597fe..6c6ae2ea1cc0 100644 --- a/math/arpack-ng/Makefile +++ b/math/arpack-ng/Makefile @@ -1,57 +1,57 @@ PORTNAME= arpack-ng DISTVERSION= 3.9.1 -PORTREVISION= 4 +PORTREVISION= 5 CATEGORIES= math MAINTAINER= yuri@FreeBSD.org COMMENT= Revised Argand library for solving large-scale eigenvalue problems WWW= https://forge.scilab.org/index.php/p/arpack-ng/ LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/COPYING LIB_DEPENDS= libmpich.so:net/mpich # MPI is incremental: it adds the libparpack.so lib, it is a candidate for a sub-package USES= autoreconf fortran libtool localbase pkgconfig USE_GITHUB= yes GH_ACCOUNT= opencollab GNU_CONFIGURE= yes CONFIGURE_ARGS= --with-blas="${BLASLIB}" \ --with-lapack="${LAPACKLIB}" \ --enable-mpi \ --disable-static \ --enable-icb TEST_TARGET= check USE_LDCONFIG= yes PIE_UNSAFE= yes PORTDOCS= * PORTEXAMPLES= * CONFLICTS_INSTALL= arpack OPTIONS_DEFINE= DOCS EXAMPLES OPTIONS_SINGLE= BLASLIB OPTIONS_SINGLE_BLASLIB= ATLAS NETLIB OPENBLAS OPTIONS_DEFAULT= NETLIB ATLAS_USES= blaslapack:atlas NETLIB_USES= blaslapack:netlib OPENBLAS_USES= blaslapack:openblas pre-configure: cd ${WRKSRC} && ./bootstrap post-install: @${STRIP_CMD} ${STAGEDIR}${PREFIX}/lib/lib*arpack.so.*.* post-install-DOCS-on: @${MKDIR} ${STAGEDIR}${DOCSDIR} cd ${WRKSRC}/DOCUMENTS && ${COPYTREE_SHARE} \* ${STAGEDIR}${DOCSDIR} post-install-EXAMPLES-on: @${MKDIR} ${STAGEDIR}${EXAMPLESDIR} cd ${WRKSRC}/EXAMPLES && ${COPYTREE_SHARE} . ${STAGEDIR}${EXAMPLESDIR} .include diff --git a/math/blacs/Makefile b/math/blacs/Makefile index f550f55ff9a4..1ca159e37841 100644 --- a/math/blacs/Makefile +++ b/math/blacs/Makefile @@ -1,126 +1,126 @@ PORTNAME= blacs PORTVERSION= 1.7 -PORTREVISION= 41 +PORTREVISION= 42 CATEGORIES= math MASTER_SITES= NETLIB/blacs DISTNAME= BLACS DISTFILES= mpiblacs.tgz blacstester.tgz mpiblacs-patch03.tgz DIST_SUBDIR= blacs EXTRACT_ONLY= mpiblacs.tgz blacstester.tgz mpiblacs-patch03.tgz MAINTAINER= ports@FreeBSD.org COMMENT= BLACS (Basic Linear Algebra Communication Subprograms) WWW= https://www.netlib.org/blacs/ # See http://icl.cs.utk.edu/lapack-forum/archives/lapack/msg01200.html LICENSE= BSD3CLAUSE SUB_FILES= pkg-message USES= fortran gmake localbase USE_LDCONFIG= yes OPTIONS_DEFINE= DOCS OPTIONS_RADIO= MPI OPTIONS_RADIO_MPI= MPICH OPENMPI OPTIONS_DEFAULT= DOCS MPICH DOCS_DISTFILES= blacs_install.ps f77blacsqref.ps lawn94.ps \ cblacsqref.ps mpi_prop.ps mpiblacs_issues.ps OPENMPI_USES= mpi:openmpi OPENMPI_EXTRA_PATCHES= ${FILESDIR}/Bmake.inc-openmpi.diff MPICH_USES= mpi:mpich MPICH_EXTRA_PATCHES= ${FILESDIR}/Bmake.inc-mpich.diff .include F77EXTRAFLAGS= #-w -fno-globals -fugly-complex .if ${FORTRAN_DEFAULT} == gfortran && ${GCC_DEFAULT} >= 10 # workaround for Rank mismatch between actual argument at (1) and actual argument at (2) (scalar and rank-1) F77EXTRAFLAGS+= -fallow-argument-mismatch .endif DEBUG_LEVEL= 0 .if ${ARCH} == "amd64" FPIC= -fPIC .else FPIC= -fpic .endif WRKSRC_SHARED=${WRKSRC}_shared CFLAGS_SHARED=${CFLAGS} ${FPIC} FFLAGS_SHARED=${FFLAGS} ${FPIC} SVERSION=1 .if defined(WITH_OPTIMIZED_FLAGS) .if ${ARCH} == "amd64" FFLAGS+= -pipe -O3 -ffast-math -funroll-all-loops -fpeel-loops -ftracer -funswitch-loops -funit-at-a-time CFLAGS+= -pipe -O3 -ffast-math -funroll-all-loops -fpeel-loops -ftracer -funswitch-loops -funit-at-a-time .elif ${ARCH} == "i386" FFLAGS+= -O3 -ffast-math -finline-functions -fomit-frame-pointer -funroll-loops -fexpensive-optimizations -malign-double -mcpu=i686 -march=i686 -mfancy-math-387 -mpreferred-stack-boundary=3 CFLAGS+= -O3 -ffast-math -finline-functions -fomit-frame-pointer -funroll-loops -fexpensive-optimizations -malign-double -mcpu=i686 -march=i686 -mfancy-math-387 -mpreferred-stack-boundary=3 .else FFLAGS+= -O3 -ffast-math -finline-functions -fomit-frame-pointer -funroll-loops -fexpensive-optimizations -Wno-multichar CFLAGS+= -O3 -ffast-math -finline-functions -fomit-frame-pointer -funroll-loops -fexpensive-optimizations -Wno-multichar .endif .endif pre-patch: (${CP} ${WRKSRC}/BMAKES/Bmake.MPI-LINUX ${WRKSRC}/Bmake.inc) post-patch: ${CP} -r ${WRKSRC} ${WRKSRC_SHARED} pre-configure: (${REINPLACE_CMD} -e 's|@WRKSRC@|${WRKSRC}|g ; s|@DEBUG_LEVEL@|${DEBUG_LEVEL}|g ; s|@LOCALBASE@|${LOCALBASE}|g ; s|@CC@|${CC}|g ; s|@CFLAGS@|${CFLAGS}|g ; s|@F77@|${F77}|g ; s|@FFLAGS@|${FFLAGS}|g ; s|@F77EXTRAFLAGS@|${F77EXTRAFLAGS}|g ; s| ARCH *.= ar| ARCMD = ar|' ${WRKSRC}/Bmake.inc) (${REINPLACE_CMD} -e 's|@WRKSRC@|${WRKSRC_SHARED}|g ; s|@DEBUG_LEVEL@|${DEBUG_LEVEL}|g ; s|@LOCALBASE@|${LOCALBASE}|g ; s|@CC@|${CC}|g ; s|@CFLAGS@|${CFLAGS_SHARED}|g ; s|@F77@|${F77}|g ; s|@FFLAGS@|${FFLAGS_SHARED}|g ; s|@F77EXTRAFLAGS@|${F77EXTRAFLAGS}|g ; s| ARCH *.= ar| ARCMD = ar|' ${WRKSRC_SHARED}/Bmake.inc) ${REINPLACE_CMD} -e 's|\$$(ARCH)|$$(ARCMD)|' ${WRKSRC}/SRC/MPI/Makefile ${REINPLACE_CMD} -e 's|\$$(ARCH)|$$(ARCMD)|' ${WRKSRC_SHARED}/SRC/MPI/Makefile do-build: (cd ${WRKSRC}; make mpi; make tester) (cd ${WRKSRC_SHARED}; make mpi; make tester) post-build: ${RM} -r ${WRKDIR}/tmp_shared ${MKDIR} ${WRKDIR}/tmp_shared ${MV} ${WRKSRC_SHARED}/LIB/blacs_MPI-FreeBSD-${DEBUG_LEVEL}.a ${WRKSRC_SHARED}/LIB/libblacsc.a ${MV} ${WRKSRC_SHARED}/LIB/blacsF77init_MPI-FreeBSD-${DEBUG_LEVEL}.a ${WRKSRC_SHARED}/LIB/libblacsf77.a ${MV} ${WRKSRC_SHARED}/LIB/blacsCinit_MPI-FreeBSD-${DEBUG_LEVEL}.a ${WRKSRC_SHARED}/LIB/libblacs.a ${FIND} ${WRKSRC_SHARED} -name "*\.a" -exec ${MV} {} ${WRKDIR}/tmp_shared \; cd ${WRKDIR}/tmp_shared ; for i in `ls *.a | ${SED} 's/\.a//' `; do \ ${LD} -Bshareable -o $${i}.so.${SVERSION} -x -soname $${i}.so.${SVERSION} --whole-archive $${i}.a ;\ ${LN} -s $${i}.so.${SVERSION} $${i}.so ;\ done do-install: ${INSTALL_DATA} ${WRKSRC}/LIB/blacsCinit_MPI-FreeBSD-${DEBUG_LEVEL}.a ${STAGEDIR}${PREFIX}/lib/libblacsc.a ${INSTALL_DATA} ${WRKSRC}/LIB/blacsF77init_MPI-FreeBSD-${DEBUG_LEVEL}.a ${STAGEDIR}${PREFIX}/lib/libblacsf77.a ${INSTALL_DATA} ${WRKSRC}/LIB/blacs_MPI-FreeBSD-${DEBUG_LEVEL}.a ${STAGEDIR}${PREFIX}/lib/libblacs.a .for lib in libblacsc libblacsf77 libblacs ${INSTALL_LIB} ${WRKDIR}/tmp_shared/${lib}.so.${SVERSION} ${STAGEDIR}${PREFIX}/lib/${lib}.so.${SVERSION} ${LN} -s ${lib}.so.${SVERSION} ${STAGEDIR}${PREFIX}/lib/${lib}.so .endfor ${MKDIR} ${STAGEDIR}${PREFIX}/share/BLACS/TESTING ( cd ${WRKSRC_SHARED}/TESTING/EXE ; \ ${INSTALL_PROGRAM} xCbtest_MPI-FreeBSD-${DEBUG_LEVEL} ${STAGEDIR}${PREFIX}/share/BLACS/TESTING/xCbtest_MPI-FreeBSD; \ ${INSTALL_PROGRAM} xFbtest_MPI-FreeBSD-${DEBUG_LEVEL} ${STAGEDIR}${PREFIX}/share/BLACS/TESTING/xFbtest_MPI-FreeBSD; \ ${INSTALL_DATA} bsbr.dat ${STAGEDIR}${PREFIX}/share/BLACS/TESTING; \ ${INSTALL_DATA} bt.dat ${STAGEDIR}${PREFIX}/share/BLACS/TESTING; \ ${INSTALL_DATA} comb.dat ${STAGEDIR}${PREFIX}/share/BLACS/TESTING; \ ${INSTALL_DATA} sdrv.dat ${STAGEDIR}${PREFIX}/share/BLACS/TESTING) .if ${PORT_OPTIONS:MDOCS} @${MKDIR} ${STAGEDIR}${DOCSDIR} ${CAT} ${DISTDIR}/${DIST_SUBDIR}/blacs_install.ps | ${GZIP_CMD} > ${STAGEDIR}${DOCSDIR}/blacs_install.ps.gz ${CAT} ${DISTDIR}/${DIST_SUBDIR}/cblacsqref.ps | ${GZIP_CMD} > ${STAGEDIR}${DOCSDIR}/cblacsqref.ps.gz ${CAT} ${DISTDIR}/${DIST_SUBDIR}/f77blacsqref.ps | ${GZIP_CMD} > ${STAGEDIR}${DOCSDIR}/f77blacsqref.ps.gz ${CAT} ${DISTDIR}/${DIST_SUBDIR}/lawn94.ps | ${GZIP_CMD} > ${STAGEDIR}${DOCSDIR}/lawn94.ps.gz ${CAT} ${DISTDIR}/${DIST_SUBDIR}/mpi_prop.ps | ${GZIP_CMD} > ${STAGEDIR}${DOCSDIR}/mpi_prop.ps.gz ${CAT} ${DISTDIR}/${DIST_SUBDIR}/mpiblacs_issues.ps | ${GZIP_CMD} > ${STAGEDIR}${DOCSDIR}/mpiblacs_issues.ps.gz .endif .include diff --git a/math/blocksolve95/Makefile b/math/blocksolve95/Makefile index 05f8cdbbf7d1..a8978720724d 100644 --- a/math/blocksolve95/Makefile +++ b/math/blocksolve95/Makefile @@ -1,76 +1,76 @@ PORTNAME= blocksolve95 PORTVERSION= 3.0 -PORTREVISION= 32 +PORTREVISION= 33 CATEGORIES= math parallel MASTER_SITES= ftp://ftp.mcs.anl.gov/pub/BlockSolve95/ \ http://ftp.mcs.anl.gov/pub/BlockSolve95/ DISTNAME= BlockSolve95 DIST_SUBDIR= ${PORTNAME}-${PORTVERSION} MAINTAINER= ports@FreeBSD.org COMMENT= Software for the efficient solution of large, sparse linear systems WWW= https://ftp.mcs.anl.gov/pub/BlockSolve95/ LICENSE= AS-IS LICENSE_NAME= AS-IS LICENSE_FILE= ${WRKSRC}/COPYRIGHT LICENSE_PERMS= dist-mirror dist-sell pkg-mirror pkg-sell auto-accept LIB_DEPENDS= libf2c.so:lang/f2c \ libmpich.so:net/mpich USES= fortran gmake tar:Z OPTIONS_DEFINE= DOCS EXAMPLES OPTIONS_RADIO= BLAS OPTIONS_RADIO_BLAS= REFERENCE ATLAS OPTIONS_DEFAULT= REFERENCE REFERENCE_DESC= Blas / Lapack REFERENCE_USES= blaslapack:netlib ATLAS_DESC= ATLAS ATLAS_USES= blaslapack:atlas MAKEFILE= makefile MAKE_ARGS= GMAKE=${MAKE_CMD} PETSC_ARCH=${PETSC_ARCH} BOPT=${BOPT} \ BLAS_LIB="${BLASLIB}" LAPACK_LIB="-L${LOCALBASE}/lib ${LAPACKLIB}" MPIDIR= ${LOCALBASE} PETSC_ARCH= freebsd BOPT?= O FFLAGS+= -O2 INCLUDES= BMmsg.h BSdepend.h BSlog.h BSmy_blas.h BSprivate.h BSsparse.h PORTDOCS= manual.ps do-install: ${INSTALL_DATA} ${WRKSRC}/lib/lib${BOPT}/${PETSC_ARCH}/libBS95.a \ ${STAGEDIR}${PREFIX}/lib ${INSTALL_DATA} ${INCLUDES:S|^|${WRKSRC}/include/|} ${STAGEDIR}${PREFIX}/include ${INSTALL_MAN} ${WRKSRC}/doc/man/man3/* ${STAGEDIR}${PREFIX}/share/man/man3 do-install-DOCS-on: @${MKDIR} ${STAGEDIR}${DOCSDIR} ${INSTALL_DATA} ${PORTDOCS:S|^|${WRKSRC}/doc/manual/|} ${STAGEDIR}${DOCSDIR} do-install-EXAMPLES-on: @${MKDIR} ${STAGEDIR}${EXAMPLESDIR} ${INSTALL_DATA} ${WRKSRC}/examples/* ${STAGEDIR}${EXAMPLESDIR} @${RM} ${STAGEDIR}${EXAMPLESDIR}/makefile.orig .if defined(MAINTAINER_MODE) do-test: . if !exists(${HOME}/.mpd.conf) @${ECHO_CMD} "MPD_SECRETWORD=change_on_install" > ${HOME}/.mpd.conf ${CHMOD} go-r ${HOME}/.mpd.conf @${ECHO_MSG} "${HOME}/.mpd.conf has been generated - please change the secret word!" . endif ${LOCALBASE}/bin/mpd & (cd ${BUILD_WRKSRC}/examples && \ ${SETENV} ${MAKE_ENV:C|HOME=|wHOME=|} ${MAKE_CMD} ${MAKE_FLAGS} ${MAKEFILE} ${MAKE_ARGS} bsrunexamples clean) ${LOCALBASE}/bin/mpdallexit .endif .include diff --git a/math/combblas/Makefile b/math/combblas/Makefile index a1cae68fdf34..58d14d212c47 100644 --- a/math/combblas/Makefile +++ b/math/combblas/Makefile @@ -1,40 +1,40 @@ PORTNAME= CombBLAS DISTVERSIONPREFIX= v DISTVERSION= 2.0.0 -PORTREVISION= 2 +PORTREVISION= 3 MASTER_SITES= https://portal.nersc.gov/project/m1982/CombBLAS/:test_data CATEGORIES= math DISTFILES= testdata_combblas1.6.1.tgz:test_data MAINTAINER= yuri@FreeBSD.org COMMENT= Combinatorial BLAS library: an extensible parallel graph library WWW= https://people.eecs.berkeley.edu/~aydin/CombBLAS/html/ LICENSE= MIT LICENSE_FILE= ${WRKSRC}/LICENSE ONLY_FOR_ARCHS= amd64 powerpc64 powerpc64le ONLY_FOR_ARCHS_REASON= fails to build: uses x86 asm LIB_DEPENDS= libmpi.so:net/mpich RUN_DEPENDS= ${LOCALBASE}/lib/gcc${GCC_DEFAULT}/libgcc_s.so.1:lang/gcc${GCC_DEFAULT} # because of the link flags induced by mpich USES= cmake:testing compiler:c++14-lang localbase:ldflags tar:tgz USE_LDCONFIG= yes USE_GITHUB= yes GH_ACCOUNT= PASSIONLab CMAKE_ON= BUILD_SHARED_LIBS # many tests fail, see https://github.com/PASSIONLab/CombBLAS/issues/15 post-extract: @cd ${WRKSRC}/include && ${RM} .DS_Store ._.DS_Store CombBLAS/._CombBLAS.h pre-test: @if [ ! -L ${TEST_WRKSRC}TESTDATA ]; then \ ${RLN} ${WRKDIR}/TESTDATA ${TEST_WRKSRC}/; \ fi .include diff --git a/math/costa/Makefile b/math/costa/Makefile index b636911a3242..85ac4007ba63 100644 --- a/math/costa/Makefile +++ b/math/costa/Makefile @@ -1,47 +1,47 @@ PORTNAME= costa DISTVERSIONPREFIX= v DISTVERSION= 2.2.2 -PORTREVISION= 3 +PORTREVISION= 4 CATEGORIES= math MAINTAINER= yuri@FreeBSD.org COMMENT= Distributed Communication-Optimal Shuffle and Transpose Algorithm WWW= https://github.com/eth-cscs/COSTA LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE LIB_DEPENDS= libopenblas.so:math/openblas \ libscalapack.so:math/scalapack USES= cmake:testing pkgconfig USE_LDCONFIG= yes USE_GITHUB= yes GH_ACCOUNT= eth-cscs GH_PROJECT= COSTA CMAKE_ON= BUILD_SHARED_LIBS CMAKE_ARGS= -DCOSTA_SCALAPACK=CUSTOM CMAKE_OFF= COSTA_WITH_TESTS CMAKE_TESTING_ON= COSTA_WITH_TESTS .if !exists(/usr/include/omp.h) BROKEN= requires OpenMP support that is missing on this architecture .endif OPTIONS_SINGLE= MPI OPTIONS_SINGLE_MPI= MPICH OPENMPI OPTIONS_DEFAULT= MPICH MPICH_USES= mpi:mpich OPENMPI_USES= mpi:openmpi post-install: # workaround for https://github.com/eth-cscs/COSTA/issues/9 @cd ${STAGEDIR}${PREFIX} && ${RMDIR} \ include/costa/pxtran \ include/costa/pxtranc \ include/costa/pxtranu .include diff --git a/math/dbcsr/Makefile b/math/dbcsr/Makefile index 34c86d042a6e..5ef26ad406ee 100644 --- a/math/dbcsr/Makefile +++ b/math/dbcsr/Makefile @@ -1,59 +1,59 @@ PORTNAME= dbcsr DISTVERSIONPREFIX= v DISTVERSION= 2.8.0 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= math MAINTAINER= yuri@FreeBSD.org COMMENT= Distributed Block Compressed Sparse Row matrix library WWW= https://www.cp2k.org/dbcsr LICENSE= GPLv3 LICENSE_FILE= ${WRKSRC}/LICENSE .if !exists(/usr/include/omp.h) BROKEN= requires OpenMP support that is missing on this architecture .endif BUILD_DEPENDS= fypp:devel/py-fypp@${PY_FLAVOR} USES= blaslapack:openblas cmake:noninja,testing compiler:c++14-lang fortran \ python:build USE_GCC= yes # OpenMP is used from both Fortan and C code, therefore C code should be compiled with GCC, otherwise it fails at run-time (same in cp2k) USE_LDCONFIG= yes USE_GITHUB= yes GH_ACCOUNT= cp2k FFLAGS+= -D__NO_STATM_ACCESS # disable /proc/self/statm access LDFLAGS+= -lopenblas CMAKE_ON= BUILD_SHARED_LIBS CMAKE_OFF= BUILD_TESTING WITH_EXAMPLES CMAKE_ARGS= -DBLA_VENDOR:STRING="OpenBLAS" -DPython_EXECUTABLE=${PYTHON_CMD} BINARY_ALIAS= git=false # with git sonames get messed up OPTIONS_DEFINE= C_API MPIX OPENMP # libxsmm is supposed to be supported, but cmake build lacks the corresponding option: https://github.com/cp2k/dbcsr/issues/73 OPTIONS_DEFAULT= C_API MPIX OPENMP OPTIONS_SUB= yes MPIX_DESC= Enable MPI MPIX_CMAKE_BOOL= USE_MPI USE_MPI_F08 MPIX_USES= mpi:mpich OPENMP_CMAKE_BOOL= USE_OPENMP C_API_DESC= Build the C API library C_API_CMAKE_BOOL= WITH_C_API C_API_IMPLIES= MPIX # the ISO_C_BINDINGS require MPI unconditionally .include . if ${GCC_DEFAULT} >= 10 CMAKE_ARGS+= -DCMAKE_Fortran_FLAGS="${FFLAGS} -fallow-argument-mismatch" # -fallow-argument-mismatch is a workaround of https://github.com/cp2k/dbcsr/issues/387 for gcc10+ . else CMAKE_ARGS+= -DCMAKE_Fortran_FLAGS="${FFLAGS}" . endif .include diff --git a/math/deal.ii/Makefile b/math/deal.ii/Makefile index e58d1b01593f..971fa0004632 100644 --- a/math/deal.ii/Makefile +++ b/math/deal.ii/Makefile @@ -1,118 +1,118 @@ PORTNAME= deal.II DISTVERSION= 9.6.2 -PORTREVISION= 11 +PORTREVISION= 12 CATEGORIES= math MASTER_SITES= https://github.com/dealii/dealii/releases/download/v${DISTVERSION}/ DISTNAME= dealii-${DISTVERSION} MAINTAINER= yuri@FreeBSD.org COMMENT= Finite element Differential Equations Analysis Library (DEAL) WWW= https://www.dealii.org/ \ https://github.com/dealii/dealii LICENSE= APACHE20 LGPL21 LICENSE_COMB= dual LICENSE_FILE_APACHE20= ${WRKSRC}/LICENSE.md LICENSE_FILE_LGPL21= ${WRKSRC}/LICENSE.md BROKEN_aarch64= error: use of undeclared identifier '__TBB_machine_fetchadd4' BROKEN_armv7= clang runs out of memory BROKEN_i386= compilation fails: Kokkos assumes 64-bit build; i.e., 8-byte pointers BUILD_DEPENDS= ${LOCALBASE}/include/boost/config.hpp:devel/boost-libs LIB_DEPENDS= libblis.so:math/blis \ libboost_serialization.so:devel/boost-libs \ libhdf5.so:science/hdf5 \ libmetis.so:math/metis \ libvtkCommonCore-${VTK_VER}.so:math/vtk${VTK_VER:R} # libkokkoscore.so:devel/kokkos TMP commented out for bundled kokkos, tests fail for non-bundled kokkos, see https://github.com/dealii/dealii/issues/15692 USES= blaslapack cmake:testing compiler:c++17-lang localbase:ldflags xorg USE_LDCONFIG= yes CMAKE_OFF= DEAL_II_ALLOW_BUNDLED DEAL_II_COMPONENT_EXAMPLES \ DEAL_II_WITH_P4EST DEAL_II_WITH_TRILINOS DEAL_II_WITH_UMFPACK \ DEAL_II_WITH_NANOFLANN DEAL_II_WITH_MUPARSER DEAL_II_WITH_ASSIMP \ DEAL_II_WITH_HDF5 CMAKE_ON= DEAL_II_FORCE_BUNDLED_TBB # instead of LIB_DEPENDS+=libtbb.so:devel/onetbb, pending https://github.com/dealii/dealii/issues/11561 CMAKE_ON+= FORCE_BUNDLED_KOKKOS # TMP turn on bundled kokkos CMAKE_TESTING_ON= FREEBSD_ENABLE_TESTS LDFLAGS+= -lomp LDFLAGS+= -lexecinfo # TMP for bundled kokkos XARCH!= uname -p OPTIONS_DEFINE= ADOLC ARPACK GSL LAPACK MPI OPENCASCADE PETSC SCALAPACK SLEPC SUNDIALS # for all options see contrib/docker/Dockerfile, TODO some of them need to be enabled here OPTIONS_DEFAULT= GSL LAPACK MPI OPENCASCADE PETSC SCALAPACK SLEPC SUNDIALS ADOLC_DESC= Compile with ADOL-C ADOLC_CMAKE_BOOL= DEAL_II_WITH_ADOLC ADOLC_LIB_DEPENDS= libadolc.so:math/adol-c ADOLC_BROKEN= requires the development version: see https://github.com/dealii/dealii/issues/7293 ARPACK_DESC= Compile with Arpack and PArpack (only with MPI, LAPACK) ARPACK_CMAKE_BOOL= DEAL_II_WITH_ARPACK ARPACK_CMAKE_ON= -DARPACK_LINKER_FLAGS:STRING="${LDFLAGS}" ARPACK_BUILD_DEPENDS= arpack-ng>0:math/arpack-ng ARPACK_RUN_DEPENDS= arpack-ng>0:math/arpack-ng # itself doesn't link to arpack, but makes depending project link to it ARPACK_IMPLIES= LAPACK GSL_DESC= Compile with gsl GSL_CMAKE_BOOL= DEAL_II_WITH_GSL GSL_LIB_DEPENDS= libgsl.so:math/gsl LAPACK_DESC= Compile with LAPACK for matrix operations LAPACK_USES= fortran LAPACK_CMAKE_BOOL= DEAL_II_WITH_LAPACK LAPACK_CMAKE_ON= -DLAPACK_LINKER_FLAGS:STRING="${LDFLAGS}" LAPACK_LIB_DEPENDS= libopenblas.so:math/openblas MPI_DESC= MPI support (math/sundials must be compiled with MPI) MPI_USES= fortran MPI_CMAKE_BOOL= DEAL_II_WITH_MPI MPI_CMAKE_ON= -DMPI_LINKER_FLAGS:STRING="${LDFLAGS}" MPI_LIB_DEPENDS= libboost_iostreams.so:devel/boost-libs \ libmpich.so:net/mpich OPENCASCADE_DESC= Compile with OpenCascade OPENCASCADE_CMAKE_BOOL= DEAL_II_WITH_OPENCASCADE OPENCASCADE_CMAKE_ON= -DOPENCASCADE_INCLUDE_DIR:STRING=${LOCALBASE}/include/OpenCASCADE OPENCASCADE_LIB_DEPENDS= libTKernel.so:cad/opencascade PETSC_DESC= Compile with Petsc (only with MPI) PETSC_USES= xorg PETSC_USE= XORG=x11 # PETSc adds x11 through interface libraries PETSC_CMAKE_BOOL= DEAL_II_WITH_PETSC PETSC_LIB_DEPENDS= libpetsc.so:science/PETSc PETSC_IMPLIES= MPI # has to use the same MPI as PETSc uses .if ${XARCH:M*64*} # match index size width being set to 64 in science/PETSc and math/metis PETSC_CMAKE_BOOL+= DEAL_II_WITH_64BIT_INDICES # as opposed to 32-bit indices that are default in deal.II .endif SCALAPACK_DESC= Compile with ScaLAPACK (only with MPI) SCALAPACK_CMAKE_BOOL= DEAL_II_WITH_SCALAPACK SCALAPACK_IMPLIES= MPI LAPACK SCALAPACK_LIB_DEPENDS= libscalapack.so:math/scalapack SLEPC_DESC= Compile with Slepc (only with MPI) SLEPC_USES= xorg SLEPC_USE= XORG=x11 # SLEPc adds x11 through interface libraries SLEPC_CMAKE_BOOL= DEAL_II_WITH_SLEPC SLEPC_LIB_DEPENDS= libslepc.so:math/slepc SLEPC_IMPLIES= MPI # has to use the same MPI as PETSc uses SUNDIALS_DESC= Compile with SUNDIALS SUNDIALS_CMAKE_BOOL= DEAL_II_WITH_SUNDIALS SUNDIALS_LIB_DEPENDS= libsundials_arkode.so:math/sundials post-patch: # unbundle boost @${RM} -r ${WRKSRC}/dealii/bundled/boost-* post-stage: @${RM} ${STAGEDIR}${PREFIX}/*.log # the testsuite is excluded from the tarball: https://github.com/dealii/dealii/issues/17951 .include <../../math/vtk9/Makefile.version> .include diff --git a/math/dihydrogen/Makefile b/math/dihydrogen/Makefile index ec267713f6b2..48df29eedb5a 100644 --- a/math/dihydrogen/Makefile +++ b/math/dihydrogen/Makefile @@ -1,43 +1,43 @@ PORTNAME= dihydrogen DISTVERSIONPREFIX= v DISTVERSION= 0.2.1-36 DISTVERSIONSUFFIX= -g4bda15e -PORTREVISION= 8 +PORTREVISION= 9 CATEGORIES= math MAINTAINER= yuri@FreeBSD.org COMMENT= Dense and sparse linear algebra, conic optimization, lattice reduction WWW= https://github.com/LLNL/DiHydrogen LICENSE= BSD2CLAUSE LIB_DEPENDS= libepoll-shim.so:devel/libepoll-shim \ libfabric.so:net/libfabric \ libfmt.so:devel/libfmt \ libhwloc.so:devel/hwloc2 \ libjson-c.so:devel/json-c \ libspdlog.so:devel/spdlog \ libze_loader.so:devel/level-zero TEST_DEPENDS= catch>0:devel/catch USES= cmake:testing compiler:c++17-lang USE_GITHUB= yes GH_ACCOUNT= LLNL GH_PROJECT= DiHydrogen LDFLAGS+= ${MPI_LIBS} # no MPI libs linkage might be intentional in the project (to allow lazy linking to any MPI implementaton) CMAKE_ON= BUILD_SHARED_LIBS CMAKE_OFF= H2_ENABLE_TESTS CMAKE_TESTING_ON= H2_ENABLE_TESTS OPTIONS_SINGLE= MPI OPTIONS_SINGLE_MPI= MPICH OPENMPI OPTIONS_DEFAULT= MPICH # should be same as in misc/lbann MPICH_USES= mpi:mpich OPENMPI_USES= mpi:openmpi .include diff --git a/math/hydrogen/Makefile b/math/hydrogen/Makefile index 0ce033f41927..1d37d6ab5426 100644 --- a/math/hydrogen/Makefile +++ b/math/hydrogen/Makefile @@ -1,44 +1,44 @@ PORTNAME= hydrogen DISTVERSIONPREFIX= v DISTVERSION= 1.5.3 -PORTREVISION= 4 +PORTREVISION= 5 CATEGORIES= math PKGNAMESUFFIX= -linear-algebra MAINTAINER= yuri@FreeBSD.org COMMENT= Dense and sparse linear algebra, conic optimization, lattice reduction WWW= https://github.com/LLNL/Elemental LICENSE= BSD2CLAUSE BUILD_DEPENDS= cereal>0:devel/cereal \ half>0:math/half LIB_DEPENDS= libopenblas.so:math/openblas RUN_DEPENDS= half>0:math/half USES= cmake:testing compiler:c++17-lang localbase:ldflags USE_GITHUB= yes GH_ACCOUNT= LLNL GH_PROJECT= Elemental CMAKE_ON= BUILD_SHARED_LIBS \ Hydrogen_ENABLE_HALF \ Hydrogen_ENABLE_MPC \ Hydrogen_ENABLE_QD #Hydrogen_ENABLE_ALUMINUM # depends on OpenMPI - so we disable it for now CMAKE_OFF= Hydrogen_ENABLE_TESTING CMAKE_TESTING_ON= Hydrogen_ENABLE_TESTING CMAKE_TESTING_TARGET= test OPTIONS_SINGLE= MPI OPTIONS_SINGLE_MPI= MPICH OPENMPI OPTIONS_DEFAULT= MPICH # should be same as in misc/lbann MPICH_USES= mpi:mpich OPENMPI_USES= mpi:openmpi BINARY_ALIAS= git=false .include diff --git a/math/kahip/Makefile b/math/kahip/Makefile index 8d4ea7f28cea..3e7e1c672de6 100644 --- a/math/kahip/Makefile +++ b/math/kahip/Makefile @@ -1,24 +1,25 @@ PORTNAME= kahip DISTVERSIONPREFIX= v DISTVERSION= 3.22 +PORTREVISION= 1 CATEGORIES= math MAINTAINER= yuri@FreeBSD.org COMMENT= Karlsruhe high quality graph partitioning WWW= https://kahip.github.io/ \ https://github.com/KaHIP/KaHIP LICENSE= MIT LICENSE_FILE= ${WRKSRC}/LICENSE LIB_DEPENDS= libmetis.so:math/metis \ libmpi.so:net/mpich USES= cmake localbase USE_LDCONFIG= yes USE_GITHUB= yes GH_ACCOUNT= KaHIP GH_PROJECT= KaHIP .include diff --git a/math/mfem/Makefile b/math/mfem/Makefile index 7434da47b5d9..81b862dc3f67 100644 --- a/math/mfem/Makefile +++ b/math/mfem/Makefile @@ -1,54 +1,55 @@ PORTNAME= mfem DISTVERSIONPREFIX= v DISTVERSION= 4.8 +PORTREVISION= 1 CATEGORIES= math MAINTAINER= yuri@FreeBSD.org COMMENT= Lightweight, general, scalable C++ library for finite element methods WWW= https://mfem.org \ https://github.com/mfem/mfem LICENSE= LGPL21 LICENSE_FILE= ${WRKSRC}/LICENSE USES= cmake:testing compiler:c++11-lang USE_GITHUB= yes USE_LDCONFIG= yes CMAKE_ON= BUILD_SHARED_LIBS CMAKE_TESTING_ON= MFEM_ENABLE_TESTING # tests are broken, see https://github.com/mfem/mfem/issues/3163 CMAKE_TESTING_TARGET= exec test OPTIONS_DEFINE= METIS SUPERLU OPTIONS_SINGLE= MPI OPTIONS_SINGLE_MPI= NOMPI MPICH OPENMPI OPTIONS_DEFAULT= METIS MPICH SUPERLU # should be the same MPI choice as in science/hypre OPTIONS_SUB= yes NOMPI_DESC= Build without parallel processing support OPENMPI_CMAKE_ON= -DTPL_ENABLE_MPI=OFF MPICH_USES= mpi:mpich MPICH_CMAKE_ON= -DTPL_ENABLE_MPI=ON MPICH_LIB_DEPENDS= libHYPRE.so:science/hypre \ libmetis.so:math/metis OPENMPI_USES= mpi:openmpi OPENMPI_CMAKE_ON= -DTPL_ENABLE_MPI=ON OPENMPI_LIB_DEPENDS= libHYPRE.so:science/hypre \ libmetis.so:math/metis METIS_DESC= Build with metis METIS_CMAKE_BOOL= MFEM_USE_METIS METIS_LIB_DEPENDS= libmetis.so:math/metis SUPERLU_DESC= Enable SuperLU use SUPERLU_CMAKE_BOOL= MFEM_USE_SUPERLU SUPERLU_CMAKE_ON= -DSuperLUDist_DIR=${LOCALBASE} -DSuperLUDist_INCLUDE_DIRS=${LOCALBASE}/include/superlu SUPERLU_LIB_DEPENDS= libsuperlu_dist.so:math/superlu-dist SUPERLU_LDFLAGS= -L${LOCALBASE}/lib -lsuperlu_dist # workaround for https://github.com/mfem/mfem/issues/3171#issuecomment-1236591028 post-install-SUPERLU-on: # workaround for https://github.com/mfem/mfem/issues/3191 @${REINPLACE_CMD} -e 's|;${LOCALBASE}/include/superlu||' ${STAGEDIR}${PREFIX}/lib/cmake/mfem/MFEMConfig.cmake .include diff --git a/math/ntpoly/Makefile b/math/ntpoly/Makefile index c96204640e2d..34fc117a83d9 100644 --- a/math/ntpoly/Makefile +++ b/math/ntpoly/Makefile @@ -1,60 +1,60 @@ PORTNAME= NTPoly DISTVERSIONPREFIX= ${PORTNAME:tl}-v DISTVERSION= 3.1.1 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= math MAINTAINER= thierry@FreeBSD.org COMMENT= Library for computing the functions of sparse matrices WWW= https://william-dawson.github.io/NTPoly LICENSE= MIT LICENSE_FILE= ${WRKSRC}/LICENSE BUILD_DEPENDS= swig>0:devel/swig TEST_DEPENDS= ${PYNUMPY} \ bash:shells/bash \ ${PYTHON_PKGNAMEPREFIX}mpi4py-mpich>0:net/py-mpi4py-mpich@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}scipy>0:science/py-scipy@${PY_FLAVOR} USE_GITHUB= yes GH_ACCOUNT= william-dawson USES= blaslapack:openblas cmake fortran mpi python FFLAGS+= -fopenmp -fallow-argument-mismatch CXXFLAGS+= -fopenmp CMAKE_ARGS= -DCMAKE_TOOLCHAIN_FILE=${TOOLCHAIN} CMAKE_ON= BUILD_SHARED_LIBS USE_LDCONFIG= yes TOOLCHAIN= ${WRKSRC}/Targets/${OPSYS}.cmake NTPLIBS= ${PORTNAME} ${PORTNAME}CPP ${PORTNAME}Wrapper pre-configure: ${ECHO_CMD} 'set(CMAKE_SYSTEM_NAME ${OPSYS})' > ${TOOLCHAIN} ${ECHO_CMD} 'set(CMAKE_C_COMPILER ${MPICC})' >> ${TOOLCHAIN} ${ECHO_CMD} 'set(CMAKE_Fortran_COMPILER ${MPIFC})' >> ${TOOLCHAIN} ${ECHO_CMD} 'set(CMAKE_CXX_COMPILER ${MPICXX})' >> ${TOOLCHAIN} ${ECHO_CMD} 'set(TOOLCHAIN_LIBS "${BLASLIB}")' >> ${TOOLCHAIN} ${ECHO_CMD} 'set(F_TOOLCHAINFLAGS_RELEASE "${FFLAGS}")' >> ${TOOLCHAIN} ${ECHO_CMD} 'set(CXX_TOOLCHAINFLAGS_DEBUG "${CXXFLAGS}")' >> ${TOOLCHAIN} ${ECHO_CMD} 'set(F_TOOLCHAINFLAGS_DEBUG "${FFLAGS}")' >> ${TOOLCHAIN} ${ECHO_CMD} 'set(TARGET_SUPPORTS_SHARED_LIBS Yes)' >> ${TOOLCHAIN} post-install: .for l in ${NTPLIBS} ${MV} ${STAGEDIR}${PREFIX}/lib/lib${l}.so \ ${STAGEDIR}${PREFIX}/lib/lib${l}.so.0 ${RLN} ${STAGEDIR}${PREFIX}/lib/lib${l}.so.0 \ ${STAGEDIR}${PREFIX}/lib/lib${l}.so .endfor do-test: @${ECHO_MSG} "/!\\ WARNING /!\\" @${ECHO_MSG} "net/py-mpi4py must be built against MPICH!" cd ${BUILD_WRKSRC} && \ ${SETENV} ${MAKE_ENV} ${MAKE_CMD} ${MAKE_ARGS} ${ALL_TARGET} && \ ${SETENV} ${MAKE_ENV} ${MAKE_CMD} ${MAKE_ARGS} test .include diff --git a/math/petiga/Makefile b/math/petiga/Makefile index 91ffa5a1763b..01d5939c0261 100644 --- a/math/petiga/Makefile +++ b/math/petiga/Makefile @@ -1,37 +1,37 @@ PORTNAME= petiga DISTVERSION= g20221208 -PORTREVISION= 7 +PORTREVISION= 8 CATEGORIES= math python MAINTAINER= yuri@FreeBSD.org COMMENT= Framework for High Performance Isogeometric Analysis WWW= https://github.com/dalcinl/PetIGA LICENSE= BSD2CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE.rst LIB_DEPENDS= libblas.so:math/blas \ liblapack.so:math/lapack \ libmpich.so:net/mpich \ libpetsc.so:science/PETSc USES= gmake compiler:c++14-lang fortran xorg USE_LDCONFIG= yes USE_XORG= x11 MAKEFILE= makefile MAKE_ENV= PETSC_DIR=${LOCALBASE} MAKE_ARGS= PREFIX=${STAGEDIR}${PREFIX} USE_GITHUB= yes GH_ACCOUNT= dalcinl GH_PROJECT= PetIGA GH_TAGNAME= 218fdfa TEST_TARGET= check post-install: @${STRIP_CMD} ${STAGEDIR}${PREFIX}/lib/libpetiga.so .include diff --git a/math/py-petsc4py/Makefile b/math/py-petsc4py/Makefile index daf3936362f1..e0c3d24d8791 100644 --- a/math/py-petsc4py/Makefile +++ b/math/py-petsc4py/Makefile @@ -1,38 +1,39 @@ PORTNAME= petsc4py DISTVERSION= 3.22.4 +PORTREVISION= 1 CATEGORIES= math python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= yuri@FreeBSD.org COMMENT= PETSc for Python WWW= https://gitlab.com/petsc/petsc LICENSE= BSD2CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE.rst BROKEN_armv7= compilation fails: LLVM ERROR: out of memory BUILD_DEPENDS= ${PYNUMPY} LIB_DEPENDS= libpetsc.so:science/PETSc RUN_DEPENDS= ${PYNUMPY} USES= python USE_PYTHON= autoplist cython distutils pytest # tests fail to run, see https://gitlab.com/petsc/petsc/-/issues/1301 MAKE_ENV= PETSC_DIR=${LOCALBASE} OPTIONS_SINGLE= MPI OPTIONS_SINGLE_MPI= MPICH OPENMPI OPTIONS_DEFAULT= MPICH MPICH_USES= mpi:mpich OPENMPI_USES= mpi:openmpi TEST_ENV= ${MAKE_ENV} PYTHONPATH=${STAGEDIR}${PYTHONPREFIX_SITELIBDIR} post-install: @${STRIP_CMD} ${STAGEDIR}${PYTHON_SITELIBDIR}/petsc4py/lib/PETSc${PYTHON_TAG}.so .include diff --git a/math/py-slepc4py/Makefile b/math/py-slepc4py/Makefile index bec7ada0b407..6ee8e849d186 100644 --- a/math/py-slepc4py/Makefile +++ b/math/py-slepc4py/Makefile @@ -1,33 +1,33 @@ PORTNAME= slepc4py DISTVERSION= 3.22.2 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= math python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= yuri@FreeBSD.org COMMENT= SLEPc for Python WWW= https://bitbucket.org/slepc/slepc4py LICENSE= BSD2CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE.rst PY_DEPENDS= ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}petsc4py>0:math/py-petsc4py@${PY_FLAVOR} BUILD_DEPENDS= ${PY_DEPENDS} RUN_DEPENDS= ${PY_DEPENDS} LIB_DEPENDS= libmpich.so:net/mpich \ libpetsc.so:science/PETSc \ libslepc.so:math/slepc RUN_DEPENDS= ${PYNUMPY} USES= fortran python USE_PYTHON= autoplist cython distutils pytest MAKE_ENV= PETSC_DIR=${LOCALBASE} SLEPC_DIR=${LOCALBASE} TEST_ENV= ${MAKE_ENV} PYTHONPATH=${STAGEDIR}${PYTHONPREFIX_SITELIBDIR} post-install: @${STRIP_CMD} ${STAGEDIR}${PYTHON_SITELIBDIR}/slepc4py/lib/SLEPc${PYTHON_TAG}.so .include diff --git a/math/scalapack/Makefile b/math/scalapack/Makefile index c9020ac6731d..2c5f892286a7 100644 --- a/math/scalapack/Makefile +++ b/math/scalapack/Makefile @@ -1,99 +1,99 @@ PORTNAME= scalapack PORTVERSION= 2.2.2 -PORTREVISION= 1 +PORTREVISION= 2 DISTVERSIONPREFIX= v CATEGORIES= math MAINTAINER= fortran@FreeBSD.org COMMENT= ScaLAPACK Scalable LAPACK library WWW= https://www.netlib.org/scalapack/ LICENSE= BSD2CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE CONFLICTS= elmer-mathlibs-1* USE_GITHUB= yes GH_ACCOUNT= Reference-ScaLAPACK USES= cmake fortran pathfix USE_LDCONFIG= yes CMAKE_ARGS= -DBUILD_STATIC_LIBS:BOOL=ON ARCH2FIX= PBLAS/SRC PBLAS/SRC/PBBLAS PBLAS/SRC/PTOOLS PBLAS/SRC/PTZBLAS \ REDIST/SRC SRC TOOLS TOOLS/LAPACK DATADIR= ${PREFIX}/share/${PORTNAME:tu} EXAMPLESDIR= ${PREFIX}/share/examples/${PORTNAME:tu} SUB_FILES= pkg-message PLIST_SUB= SVERSION=${SVERSION} PORTVERSION=2.2.1 VER=${PORTVERSION:R} OPTIONS_DEFINE= EXAMPLES OPTIONS_RADIO= LA MPI OPTIONS_RADIO_LA= ATLAS BLAS LA_DESC= Linear Algebra library support BLAS_DESC= LAPACK blass implementation OPTIONS_RADIO_MPI= MPICH OPENMPI OPTIONS_DEFAULT= BLAS EXAMPLES MPICH ATLAS_USES= blaslapack:atlas BLAS_USES= blaslapack:openblas MPICH_USES= mpi:mpich MPICH_CMAKE_ON= -DMPI_BASE_DIR=${LOCALBASE} OPENMPI_USES= mpi:openmpi OPENMPI_CMAKE_ON=-DMPI_BASE_DIR=${LOCALBASE}/mpi/openmpi .include BLAS= ${BLASLIB} LAPACK= ${LAPACKLIB} .if ${ARCH} == "amd64" FPIC= -fPIC .else FPIC= -fpic .endif CFLAGS+= ${FPIC} ${MPI_CFLAGS} FFLAGS+= ${FPIC} LDFLAGS+= ${MPI_LIBS} SVERSION= ${PORTVERSION:R:R} .if ${FORTRAN_DEFAULT} == gfortran && ${GCC_DEFAULT} >= 10 # workaround for Rank mismatch between actual argument at (1) and actual argument at (2) (scalar and rank-1) FFLAGS+= -fallow-argument-mismatch .endif # USES=fortran already forces FC to a supported fortran compiler; # assume mpicc points to a compatible compiler and force that, too. CC= ${MPICC} post-build: ${RM} -r ${WRKSRC}/CMakeFiles ${WRKSRC}/CMakeCache.txt (cd ${WRKSRC} && \ ${SETENV} ${CONFIGURE_ENV} ${CMAKE_BIN} ${CMAKE_ARGS:C|BUILD_STATIC_LIBS|BUILD_SHARED_LIBS|} ${CMAKE_SOURCE_PATH}) (cd ${WRKSRC} && ${DO_MAKE_BUILD} ${ALL_TARGET}) post-install: ${INSTALL_LIB} ${WRKSRC}/lib/libscalapack.so ${STAGEDIR}${PREFIX}/lib/libscalapack.so.${PORTVERSION:R} ${LN} -sf libscalapack.so.${PORTVERSION:R} ${STAGEDIR}${PREFIX}/lib/libscalapack.so ${LN} -sf libscalapack.so.${PORTVERSION:R} ${STAGEDIR}${PREFIX}/lib/libscalapack.so.${SVERSION} ${MKDIR} ${STAGEDIR}${PREFIX}/share/SCALAPACK/TESTING (cd ${BUILD_WRKSRC}/TESTING/ ;\ ${INSTALL_PROGRAM} x* ${STAGEDIR}${PREFIX}/share/SCALAPACK/TESTING ;\ ${INSTALL_DATA} *.dat ${STAGEDIR}${PREFIX}/share/SCALAPACK/TESTING) ${INSTALL_DATA} ${FILESDIR}/scalapack.h ${STAGEDIR}${PREFIX}/include ${INSTALL_DATA} ${WRKSRC}/PBLAS/SRC/*.h ${STAGEDIR}${PREFIX}/include post-install-EXAMPLES-on: ${MKDIR} ${STAGEDIR}${PREFIX}/share/examples/SCALAPACK ${INSTALL_DATA} ${FILESDIR}/Makefile ${STAGEDIR}${PREFIX}/share/examples/SCALAPACK ${INSTALL_DATA} ${FILESDIR}/example1.cc ${STAGEDIR}${PREFIX}/share/examples/SCALAPACK ${INSTALL_DATA} ${FILESDIR}/example1.f ${STAGEDIR}${PREFIX}/share/examples/SCALAPACK do-test: (cd ${BUILD_WRKSRC}/TESTING && ${MAKE_CMD} test) .include diff --git a/math/scalapackfx/Makefile b/math/scalapackfx/Makefile index 0d4e7d640914..250c26315b41 100644 --- a/math/scalapackfx/Makefile +++ b/math/scalapackfx/Makefile @@ -1,33 +1,33 @@ PORTNAME= scalapackfx DISTVERSION= 1.2 -PORTREVISION= 5 +PORTREVISION= 6 CATEGORIES= math MAINTAINER= yuri@FreeBSD.org COMMENT= Modern Fortran wrappers around ScaLAPACK routines WWW= https://github.com/dftbplus/scalapackfx LICENSE= BSD2CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE BUILD_DEPENDS= fypp:devel/py-fypp@${PY_FLAVOR} LIB_DEPENDS= libmpi.so:net/mpich \ libmpifort.so:net/mpich \ libopenblas.so:math/openblas \ libscalapack.so:math/scalapack USES= cmake fortran python:build USE_LDCONFIG= yes USE_GITHUB= yes GH_ACCOUNT= dftbplus CMAKE_ARGS= -DSCALAPACK_LIBRARY=${LOCALBASE} LDFLAGS+= -lscalapack CMAKE_ON= BUILD_SHARED_LIBS do-test: @cd ${WRKSRC}/test && mpirun -n 2 ${BUILD_WRKSRC}/test/test_det .include diff --git a/math/scorec-core/Makefile b/math/scorec-core/Makefile index 9bfd733f69e4..2d22a95f6313 100644 --- a/math/scorec-core/Makefile +++ b/math/scorec-core/Makefile @@ -1,52 +1,53 @@ PORTNAME= scorec-core DISTVERSIONPREFIX= v DISTVERSION= 3.0.2 +PORTREVISION= 1 CATEGORIES= math MAINTAINER= yuri@FreeBSD.org COMMENT= Parallel finite element unstructured meshes WWW= https://github.com/SCOREC/core LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE LIB_DEPENDS= \ libepoll-shim.so:devel/libepoll-shim \ libfabric.so:net/libfabric \ libhwloc.so:devel/hwloc2 \ libjson-c.so:devel/json-c \ libze_loader.so:devel/level-zero USES= cmake:testing compiler:c++11-lang pkgconfig USE_LDCONFIG= yes USE_GITHUB= yes GH_ACCOUNT= SCOREC GH_PROJECT= core GH_TUPLE= SCOREC:pumi-meshes:7b84de7:meshes/pumi-meshes CFLAGS+= ${MPI_CFLAGS} CXXFLAGS+= ${MPI_CFLAGS} LDFLAGS+= ${MPI_LIBS} CMAKE_ON= BUILD_SHARED_LIBS CMAKE_TESTING_ON= IS_TESTING # some tests fail possibly because they need a larger MPI cluster OPTIONS_DEFINE= FORTRAN OPTIONS_SINGLE= MPI OPTIONS_SINGLE_MPI= MPICH OPENMPI OPTIONS_DEFAULT= FORTRAN MPICH OPTIONS_SUB= yes FORTRAN_USES= fortran FORTRAN_CMAKE_BOOL= PUMI_FORTRAN_INTERFACE MPICH_USES= mpi:mpich OPENMPI_USES= mpi:openmpi PORTSCOUT= limit:^.*[0-9]\.[0-9].* # prevent tags like remove_viz # 3 tests fail, see https://github.com/SCOREC/core/issues/410 .include diff --git a/math/slepc/Makefile b/math/slepc/Makefile index 862edc2e9c16..356194150d7e 100644 --- a/math/slepc/Makefile +++ b/math/slepc/Makefile @@ -1,45 +1,45 @@ PORTNAME= slepc DISTVERSION= 3.22.2 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= math devel MASTER_SITES= http://slepc.upv.es/download/distrib/ MAINTAINER= yuri@FreeBSD.org COMMENT= Scalable Library for Eigenvalue Problem Computations WWW= http://slepc.upv.es/ LICENSE= BSD2CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE.md LIB_DEPENDS= libblas.so:math/blas \ libblis.so:math/blis \ liblapack.so:math/lapack \ libmetis.so:math/metis \ libmpich.so:net/mpich \ libpetsc.so:science/PETSc USES= gmake fortran python shebangfix xorg USE_XORG= x11 # not really needed, but is inherited from the PETSc setup USE_LDCONFIG= yes SHEBANG_FILES= configure SHEBANG_GLOB= *.py MAKEFILE= makefile MAKE_ENV= PETSC_DIR=${LOCALBASE} PETSC_ARCH="" SLEPC_DIR=${WRKSRC} PYTHON=${PYTHON_CMD} TEST_TARGET= test # 1 of 2568 tests fail because some file can't be opened BINARY_ALIAS= python=${PYTHON_CMD} OPTIONS_DEFINE= EXAMPLES PORTEXAMPLES= * do-configure: @cd ${WRKSRC} && ${SETENV} ${MAKE_ENV} ./configure --prefix=${PREFIX} post-install: @${STRIP_CMD} ${STAGEDIR}${PREFIX}/lib/libslepc.so.${PORTVERSION} .include diff --git a/math/spfft/Makefile b/math/spfft/Makefile index f043d2ede192..dee39d4d762c 100644 --- a/math/spfft/Makefile +++ b/math/spfft/Makefile @@ -1,62 +1,63 @@ PORTNAME= spfft DISTVERSIONPREFIX= v DISTVERSION= 1.1.1 +PORTREVISION= 1 CATEGORIES= math MAINTAINER= yuri@FreeBSD.org COMMENT= Sparse 3D FFT library WWW= https://github.com/eth-cscs/SpFFT LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE LIB_DEPENDS= libfftw3.so:math/fftw3 TEST_DEPENDS= cli11>0:devel/cli11 \ googletest>0:devel/googletest \ nlohmann-json>0:devel/nlohmann-json USES= cmake:testing compiler:c++11-lang USE_LDCONFIG= yes USE_GITHUB= yes GH_ACCOUNT= eth-cscs GH_PROJECT= SpFFT CMAKE_TESTING_ON= SPFFT_BUILD_TESTS CMAKE_TESTING_ARGS= -DSPFFT_BUNDLED_CLI11=OFF \ -DSPFFT_BUNDLED_GOOGLETEST=OFF \ -DSPFFT_BUNDLED_JSON=OFF CMAKE_TESTING_TARGET= ${ALL_TARGET} OPTIONS_DEFINE= FORTRAN OPENMP OPTIONS_SINGLE= MPI OPTIONS_SINGLE_MPI= NOMPI MPICH OPENMPI OPTIONS_DEFAULT= FORTRAN MPICH OPTIONS_SUB= yes FORTRAN_USES= fortran FORTRAN_CMAKE_BOOL= SPFFT_FORTRAN NOMPI_DESC= Build without parallel processing support NOMPI_CMAKE_ON= -DSPFFT_MPI=OFF MPICH_USES= mpi:mpich MPICH_CMAKE_ON= -DSPFFT_MPI=ON OPENMPI_USES= mpi:openmpi OPENMPI_CMAKE_ON= -DSPFFT_MPI=ON OPENMP_CMAKE_BOOL= SPFFT_OMP .if exists(/usr/include/omp.h) OPTIONS_DEFAULT+= OPENMP .endif post-test: @cd ${BUILD_WRKSRC}/tests && \ ./run_local_tests && \ ./run_mpi_tests # tests as of 1.1.1: [ PASSED ] 6500 tests. .include diff --git a/math/spla/Makefile b/math/spla/Makefile index d9d4645a39c9..2bb881ea53aa 100644 --- a/math/spla/Makefile +++ b/math/spla/Makefile @@ -1,45 +1,45 @@ PORTNAME= spla DISTVERSIONPREFIX= v DISTVERSION= 1.6.1 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= math MAINTAINER= yuri@FreeBSD.org COMMENT= Specialized Parallel Linear Algebra WWW= https://github.com/eth-cscs/spla LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE LIB_DEPENDS= libopenblas.so:math/openblas TEST_DEPENDS= scalapack>0:math/scalapack USES= cmake:testing compiler:c++17-lang USE_LDCONFIG= yes USE_GITHUB= yes GH_ACCOUNT= eth-cscs CMAKE_TESTING_ON= SPLA_BUILD_TESTS # tests fail to link, see https://github.com/eth-cscs/spla/issues/24 CMAKE_TESTING_ARGS= -DFETCHCONTENT_FULLY_DISCONNECTED:BOOL=OFF # to allow to download google test CMAKE_TESTING_TARGET= ${ALL_TARGET} OPTIONS_DEFINE= FORTRAN OPENMP OPTIONS_SINGLE= MPI OPTIONS_SINGLE_MPI= MPICH OPENMPI OPTIONS_DEFAULT= FORTRAN MPICH OPENMP OPTIONS_SUB= yes FORTRAN_USES= fortran FORTRAN_CMAKE_BOOL= SPLA_FORTRAN MPICH_USES= mpi:mpich OPENMPI_USES= mpi:openmpi OPENMP_CMAKE_BOOL= SPLA_OMP post-test: # run tests cd ${WRKSRC} && ${BUILD_WRKSRC}/tests/run_tests .include diff --git a/math/spooles/Makefile b/math/spooles/Makefile index 5e57ffba90e1..ab65e6baa6a6 100644 --- a/math/spooles/Makefile +++ b/math/spooles/Makefile @@ -1,112 +1,112 @@ PORTNAME= spooles PORTVERSION= 2.2 -PORTREVISION= 16 +PORTREVISION= 17 CATEGORIES= math MASTER_SITES= NETLIB/linalg/spooles .ifdef WITH_MPI PKGNAMESUFFIX= -mpich .endif DISTNAME= ${PORTNAME}.${PORTVERSION} DIST_SUBDIR= spooles EXTRACT_ONLY= ${DISTNAME}${EXTRACT_SUFX} MAINTAINER= bofh@FreeBSD.org COMMENT= SParse Object Oriented Linear Equations Solver WWW= https://www.netlib.org/linalg/spooles/spooles.2.2.html LICENSE= PD .if defined(WITH_MPI) LIB_DEPENDS= libmpich.so:net/mpich .endif USES= gmake tar:tgz .if defined(WITH_MPI) CONFLICTS= spooles-2* PLIST_SUB= MPI="" MT="@comment " .else CONFLICTS= spooles-mpich-2* PLIST_SUB= MPI="@comment " MT="" .endif OPTIONS_DEFINE= DOCS DOCS_DISTFILES= ${DISTNAME}${EXTRACT_SUFX} AllInOne.ps.gz Eigen.ps.gz \ Install.ps.gz LinSol.ps.gz Ordering.ps.gz \ PP99.ps.gz ReferenceManual.ps.gz PICFLAG?= -fpic .include .if ${OPSYS} == FreeBSD CFLAGS+= -Wno-error=int-conversion .endif .SILENT: pre-everything:: .if !defined(WITH_MPI) ${ECHO_MSG} "make WITH_MPI=yes for mpich version" .endif do-extract: ${MKDIR} ${WRKSRC} ; cd ${WRKSRC} ; ${TAR} ${EXTRACT_BEFORE_ARGS} ${_DISTDIR}/${DISTNAME}${EXTRACT_SUFX} ${EXTRACT_AFTER_ARGS} post-patch: ${MKDIR} ${WRKSRC}_SHARED ; ${CP} -r ${WRKSRC}/* ${WRKSRC}_SHARED @${REINPLACE_CMD} -e 's+%%LOCALBASE%%+${LOCALBASE}+g;' \ -e 's+%%CFLAGS%%+${CFLAGS}+g;' \ -e 's+%%CC%%+${CC}+g;' ${WRKSRC}/Make.inc @${REINPLACE_CMD} -e 's+%%LOCALBASE%%+${LOCALBASE}+g;' \ -e 's+%%CFLAGS%%+${CFLAGS} ${PICFLAG}+g;' \ -e 's+%%CC%%+${CC}+g;' ${WRKSRC}_SHARED/Make.inc do-build: .if defined(WITH_MPI) @(cd ${WRKSRC}/MPI/src ; ${SETENV} ${MAKE_ENV} ${MAKE_CMD} -f makeGlobalLib) @(cd ${WRKSRC}_SHARED/MPI/src; ${SETENV} ${MAKE_ENV} ${MAKE_CMD} -f makeGlobalLib) @(cd ${WRKSRC}_SHARED ; ld -Bshareable -o libspooles.so.1 -x -soname libspooles.so.1 --whole-archive spooles.a ) .else @(cd ${WRKSRC}; ${SETENV} ${MAKE_ENV} ${MAKE_CMD} global -f makefile) @(cd ${WRKSRC}/MT/src; ${SETENV} ${MAKE_ENV} ${MAKE_CMD} -f makeGlobalLib) @(cd ${WRKSRC}_SHARED; ${SETENV} ${MAKE_ENV} ${MAKE_CMD} global -f makefile) @(cd ${WRKSRC}_SHARED/MT/src; ${SETENV} ${MAKE_ENV} ${MAKE_CMD} -f makeGlobalLib) @(cd ${WRKSRC}_SHARED ; ld -Bshareable -o libspooles.so.1 -x -soname libspooles.so.1 --whole-archive spooles.a ) .endif do-install: ${MKDIR} ${STAGEDIR}${PREFIX}/include/spooles ${INSTALL_DATA} ${WRKSRC}/spooles.a ${STAGEDIR}${PREFIX}/lib/libspooles.a ${INSTALL_DATA} ${WRKSRC}_SHARED/libspooles.so.1 ${STAGEDIR}${PREFIX}/lib ${LN} -sf libspooles.so.1 ${STAGEDIR}${PREFIX}/lib/libspooles.so .if defined(WITH_MPI) ${MKDIR} ${STAGEDIR}${PREFIX}/include/spooles/MPI ${INSTALL_DATA} ${WRKSRC}/MPI/*.h ${STAGEDIR}${PREFIX}/include/spooles/MPI .else ${MKDIR} ${STAGEDIR}${PREFIX}/include/spooles/MT ${INSTALL_DATA} ${WRKSRC}/MT/*.h ${STAGEDIR}${PREFIX}/include/spooles/MT .endif ${INSTALL_DATA} ${WRKSRC}/*.h ${STAGEDIR}${PREFIX}/include/spooles/ .for i in A2 BPG Chv ChvList ChvManager Coords DenseMtx DSTree Drand \ DV ETree FrontMtx GPart Graph I2Ohash IIheap IV IVL Ideq InpMtx \ Lock MSMD PatchAndGoInfo Pencil SolveMap SubMtx SubMtxList SubMtxManager \ SymbFac Tree Utilities ZV misc ${MKDIR} ${STAGEDIR}${PREFIX}/include/spooles/${i} ${INSTALL_DATA} ${WRKSRC}/${i}/*.h ${STAGEDIR}${PREFIX}/include/spooles/${i} .endfor do-install-DOCS-on: @${MKDIR} ${STAGEDIR}${DOCSDIR} ${INSTALL_DATA} ${DISTDIR}/${DIST_SUBDIR}/AllInOne.ps.gz ${STAGEDIR}${DOCSDIR} ${INSTALL_DATA} ${DISTDIR}/${DIST_SUBDIR}/Eigen.ps.gz ${STAGEDIR}${DOCSDIR} ${INSTALL_DATA} ${DISTDIR}/${DIST_SUBDIR}/Install.ps.gz ${STAGEDIR}${DOCSDIR} ${INSTALL_DATA} ${DISTDIR}/${DIST_SUBDIR}/LinSol.ps.gz ${STAGEDIR}${DOCSDIR} ${INSTALL_DATA} ${DISTDIR}/${DIST_SUBDIR}/Ordering.ps.gz ${STAGEDIR}${DOCSDIR} ${INSTALL_DATA} ${DISTDIR}/${DIST_SUBDIR}/PP99.ps.gz ${STAGEDIR}${DOCSDIR} ${INSTALL_DATA} ${DISTDIR}/${DIST_SUBDIR}/ReferenceManual.ps.gz ${STAGEDIR}${DOCSDIR} .include diff --git a/math/sprng/Makefile b/math/sprng/Makefile index 3ee83905b18e..6b03d720ef51 100644 --- a/math/sprng/Makefile +++ b/math/sprng/Makefile @@ -1,66 +1,66 @@ PORTNAME= SPRNG PORTVERSION= 5.0 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= math science MASTER_SITES= http://www.sprng.org/Version${PORTVERSION}/ DISTNAME= ${PORTNAME:tl}${PORTVERSION:R} MAINTAINER= thierry@FreeBSD.org COMMENT= Scalable Parallel Pseudo Random Number Generators Library WWW= http://www.sprng.org/ LICENSE= CC-BY-NC-SA-4.0 LICENSE_FILE= ${WRKSRC}/LICENSE LIB_DEPENDS= libtestu01.so:math/testu01 USES= compiler dos2unix fortran gmake localbase tar:bz2 DOS2UNIX_GLOB= LICENSE FFLAGS= -I${LOCALBASE}/include GNU_CONFIGURE= yes CONFIGURE_ARGS= --with-testu01=${LOCALBASE} \ --with-testu01lib=${LOCALBASE}/lib \ --with-testu01inc=${LOCALBASE}/include/TestU01 TEST_TARGET= check PORTEXAMPLES= * OPTIONS_DEFINE= EXAMPLES MPICH OPTIONS_DEFAULT= EXAMPLES MPICH OPTIONS_SUB= yes MPICH_USES= mpi:mpich MPICH_CONFIGURE_WITH= mpi ASCII_TEXTS= checkcmrg checklcg checklcg64 checklfg checkmlfg checkpmlcg \ checksprng timecmrg timelcg timelcg64 timelfg timemlfg timepmlcg\ timesprng .include pre-configure: .if ${CHOSEN_COMPILER_TYPE} == clang ${FIND} ${WRKSRC} -name Makefile.in | \ ${XARGS} ${REINPLACE_CMD} -e 's|-lstdc++|-lc++|' .endif .for s in check_gen.cpp check_gen_simple.cpp ${FIND} ${WRKSRC} -name ${s} | \ ${XARGS} ${REINPLACE_CMD} -e 's|using namespace std;||' .endfor post-stage: (cd ${STAGEDIR}${PREFIX}/share && \ ${RM} .insertlib gencheck gentime insertlib) (cd ${STAGEDIR}${PREFIX}/bin && ${RM} ${ASCII_TEXTS}) post-install-EXAMPLES-on: ${MKDIR} ${STAGEDIR}${EXAMPLESDIR} (cd ${WRKSRC}/EXAMPLES && \ ${COPYTREE_SHARE} . ${STAGEDIR}${EXAMPLESDIR}) (cd ${STAGEDIR}${EXAMPLESDIR} && ${RM} -r .deps) .if !defined(WITH_DEBUG) ${FIND} ${STAGEDIR}${EXAMPLESDIR} -name "*.sprng" | \ ${XARGS} ${STRIP_CMD} .endif .include diff --git a/math/sundials/Makefile b/math/sundials/Makefile index 2c4f5e8c7455..530f2a1d9ea4 100644 --- a/math/sundials/Makefile +++ b/math/sundials/Makefile @@ -1,87 +1,88 @@ PORTNAME= sundials DISTVERSION= 7.5.0 +PORTREVISION= 1 CATEGORIES= math MASTER_SITES= https://github.com/LLNL/sundials/releases/download/v${DISTVERSION}/ MAINTAINER= yuri@FreeBSD.org COMMENT= SUite of Nonlinear and DIfferential/ALgebraic Equation Solvers WWW= https://computing.llnl.gov/projects/sundials \ https://github.com/LLNL/sundials LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE USES= cmake:testing fortran localbase:ldflags python:build # 4 tests fail, see https://github.com/LLNL/sundials/issues/220 USE_LDCONFIG= yes CMAKE_ARGS= -DCMAKE_C_STANDARD=99 CMAKE_ON= ENABLE_PTHREAD CMAKE_OFF= BUILD_STATIC_LIBS \ EXAMPLES_ENABLE_C EXAMPLES_ENABLE_CXX EXAMPLES_ENABLE_F77 EXAMPLES_ENABLE_F90 CMAKE_TESTING_ON= SUNDIALS_TEST_UNITTESTS \ EXAMPLES_ENABLE_C EXAMPLES_ENABLE_CXX EXAMPLES_ENABLE_F77 EXAMPLES_ENABLE_F90 FCFLAGS:= ${FFLAGS} # project checks that these flags are equal OPTIONS_DEFINE= BLAS EXAMPLES KLU LAPACK MPI OPENMP OPTIONS_DEFAULT= KLU LAPACK MPI OPENMP # no OpenMP on armv7 .if !exists(/usr/include/omp.h) OPTIONS_EXCLUDE= OPENMP .endif OPTIONS_GROUP= VECTORS OPTIONS_GROUP_VECTORS= HYPRE PETSC VECTORS_DESC= Alternative vector libraries OPTIONS_SUB= yes BLAS_DESC= Enable BLAS support BLAS_CMAKE_BOOL= ENABLE_BLAS BLAS_USES= blaslapack:openblas #EXAMPLES_CMAKE_BOOL= EXAMPLES_ENABLE_C EXAMPLES_ENABLE_CXX EXAMPLES_ENABLE_F77 EXAMPLES_ENABLE_F90 #EXAMPLES_CMAKE_ON= -DEXAMPLES_INSTALL_PATH=${EXAMPLESDIR} #PORTEXAMPLES= * HYPRE_DESC= HYPRE vectors support (also enables MPI) HYPRE_CMAKE_BOOL= ENABLE_HYPRE HYPRE_CMAKE_ON= -DHYPRE_INCLUDE_DIR=${LOCALBASE}/include \ -DHYPRE_LIBRARY_DIR=${LOCALBASE}/lib HYPRE_LIB_DEPENDS= libHYPRE.so:science/hypre # maybe is broken due to https://github.com/hypre-space/hypre/issues/464 HYPRE_IMPLIES= MPI HYPRE_PREVENTS= LAPACK # error: Incompatible sunindextype for LAPACK; disable LAPACK and rebuild HYPRE_BROKEN= ERROR: SUNDIALS interface to HYPRE is not functional. KLU_DESC= Use KLU package that is part of suitesparse KLU_CMAKE_BOOL= ENABLE_KLU KLU_CMAKE_ON= -DKLU_INCLUDE_DIR=${LOCALBASE}/include/suitesparse -DKLU_LIBRARY_DIR=${LOCALBASE}/lib KLU_LIB_DEPENDS= libamd.so:math/suitesparse-amd \ libbtf.so:math/suitesparse-btf \ libcolamd.so:math/suitesparse-colamd \ libklu.so:math/suitesparse-klu \ libsuitesparseconfig.so:math/suitesparse-config LAPACK_DESC= Use Lapack linear algebra (sets SUNDIALS_INDEX_TYPE=int32) LAPACK_USES= blaslapack:openblas LAPACK_CMAKE_BOOL= ENABLE_LAPACK MPI_CMAKE_BOOL= ENABLE_MPI MPI_LIB_DEPENDS= libmpich.so:net/mpich OPENMP_CMAKE_BOOL= ENABLE_OPENMP PETSC_DESC= PETSc vectors support (also enables MPI) PETSC_CMAKE_BOOL= ENABLE_PETSC PETSC_CMAKE_ON= -DPETSC_DIR=${LOCALBASE} \ -DPETSC_INCLUDE_DIR=${LOCALBASE}/include \ -DPETSC_LIBRARY_DIR=${LOCALBASE}/lib PETSC_LIB_DEPENDS= libpetsc.so:science/PETSc PETSC_IMPLIES= MPI PETSC_PREVENTS= LAPACK # error: Incompatible sunindextype for LAPACK; disable LAPACK and rebuild PETSC_BROKEN= ERROR: PETSc not functional due to index size mismatch: SUNDIALS_INDEX_SIZE=64, but PETSc was built with 32-bit indices post-install: @${RM} ${STAGEDIR}${PREFIX}/include/sundials/LICENSE # tests as of 7.5.0: 97% tests passed, 5 tests failed out of 190, see https://github.com/LLNL/sundials/issues/792 .include diff --git a/math/superlu-dist/Makefile b/math/superlu-dist/Makefile index 932f05dc86fc..3d9e10a2142a 100644 --- a/math/superlu-dist/Makefile +++ b/math/superlu-dist/Makefile @@ -1,58 +1,58 @@ PORTNAME= superlu-dist DISTVERSIONPREFIX= v DISTVERSION= 9.1.0 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= math MAINTAINER= yuri@FreeBSD.org COMMENT= Distributed memory, MPI based SuperLU WWW= https://portal.nersc.gov/project/sparse/superlu/ LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/License.txt USES= cmake:testing fortran pkgconfig USE_LDCONFIG= yes USE_GITHUB= yes GH_ACCOUNT= xiaoyeli GH_PROJECT= superlu_dist CMAKE_ON= USE_XSDK_DEFAULTS BUILD_SHARED_LIBS CMAKE_OFF= enable_tests enable_examples TPL_ENABLE_PARMETISLIB CMAKE_TESTING_ON= enable_tests # many tests fail, see https://github.com/xiaoyeli/superlu_dist/issues/113 OPTIONS_DEFINE= DOCS FORTRAN OPTIONS_SINGLE= BLAS MPI OPTIONS_SINGLE_BLAS= ATLAS OPENBLAS REFERENCE OPTIONS_SINGLE_MPI= MPICH OPENMPI OPTIONS_DEFAULT= FORTRAN MPICH REFERENCE OPTIONS_SUB= yes # all BLAS-related options ATLAS_USES= blaslapack:atlas ATLAS_CMAKE_ON= -DBLA_VENDOR:STRING="ATLAS" OPENBLAS_USES= blaslapack:openblas OPENBLAS_CMAKE_ON= -DBLA_VENDOR:STRING="OpenBLAS" REFERENCE_DESC= Reference blas implementation REFERENCE_USES= blaslapack REFERENCE_CMAKE_ON= -DBLA_VENDOR:STRING="Generic" # other options FORTRAN_CMAKE_BOOL= XSDK_ENABLE_Fortran MPICH_USES= mpi:mpich OPENMPI_USES= mpi:openmpi post-install-DOCS-on: @${MKDIR} ${STAGEDIR}${DOCSDIR} cd ${WRKSRC}/DOC && ${COPYTREE_SHARE} "ug.pdf" ${STAGEDIR}${DOCSDIR} post-install-FORTRAN-on: # workaround for https://github.com/xiaoyeli/superlu_dist/issues/112 @${RM} -r ${STAGEDIR}${PREFIX}/include/FORTRAN/CMakeFiles # move .mod files to a proper location @cd ${STAGEDIR}${PREFIX}/include && \ ${MV} FORTRAN/* . && \ ${RMDIR} FORTRAN .include diff --git a/misc/adios2/Makefile b/misc/adios2/Makefile index a7a9a44f5023..f87af0134b60 100644 --- a/misc/adios2/Makefile +++ b/misc/adios2/Makefile @@ -1,64 +1,64 @@ PORTNAME= adios2 DISTVERSIONPREFIX= v DISTVERSION= 2.10.2 -PORTREVISION= 4 +PORTREVISION= 5 CATEGORIES= misc science MAINTAINER= yuri@FreeBSD.org COMMENT= Next generation of ADIOS developed in the Exascale Computing Program WWW= https://github.com/ornladios/ADIOS2 LICENSE= APACHE20 LICENSE_FILE= ${WRKSRC}/LICENSE BROKEN_armv7= compilation fails: non-constant-expression cannot be narrowed from type 'uint64_t' (aka 'unsigned long long') to 'size_t' (aka 'unsigned int') in initializer list [-Wc++11-narrowing] BROKEN_i386= constant expression evaluates to 18446744073709551613 which cannot be narrowed to type 'unsigned int': https://github.com/ornladios/ADIOS2/issues/2469 BROKEN_powerpc= constant expression evaluates to 18446744073709551613 which cannot be narrowed to type 'unsigned int': https://github.com/ornladios/ADIOS2/issues/2469 PY_DEPENDS= ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}mpi4py-mpich>=3.0.3:net/py-mpi4py-mpich@${PY_FLAVOR} BUILD_DEPENDS= bash:shells/bash \ pybind11>0:devel/pybind11 \ ${PYTHON_PKGNAMEPREFIX}pybind11>=2.4:devel/py-pybind11@${PY_FLAVOR} \ ${PY_DEPENDS} LIB_DEPENDS= libblosc2.so:archivers/c-blosc2 \ libepoll-shim.so:devel/libepoll-shim \ libfabric.so:net/libfabric \ libhdf5.so:science/hdf5 \ liblz4.so:archivers/liblz4 \ libmpi.so:net/mpich \ libpng16.so:graphics/png \ libsodium.so:security/libsodium \ libzmq.so:net/libzmq4 \ libzfp.so:devel/zfp \ libzstd.so:archivers/zstd RUN_DEPENDS= bash:shells/bash \ ${PY_DEPENDS} USES= bison cmake:testing compiler:c++11-lang fortran localbase:ldflags pkgconfig \ perl5 python shebangfix sqlite USE_LDCONFIG= yes SHEBANG_FILES= cmake/install/post/adios2-config.pre.sh.in cmake/install/post/generate-adios2-config.sh.in \ source/utils/adios_reorganize/adios2_reorganize_wrapper source/utils/adios2_deactivate_bp SHEBANG_GLOB= *.sh *.py USE_GITHUB= yes GH_ACCOUNT= ornladios GH_PROJECT= ADIOS2 CMAKE_ARGS= -DFREEBSD_PYTHON_VERSION=${PYTHON_VER} CMAKE_OFF= BUILD_TESTING ADIOS2_BUILD_EXAMPLES LDFLAGS+= -lepoll-shim OPTIONS_DEFINE= DOCS DOCSDIR= ${PREFIX}/share/doc/ADIOS2 PORTDOCS= * # several tests fail, see https://github.com/ornladios/ADIOS2/issues/3286 post-install: @${STRIP_CMD} ${STAGEDIR}${PYTHON_SITELIBDIR}/adios2/bindings/adios2_bindings${PYTHON_TAG}.so .include diff --git a/net/mpifx/Makefile b/net/mpifx/Makefile index 3052c6d24c32..b49ce4325cb3 100644 --- a/net/mpifx/Makefile +++ b/net/mpifx/Makefile @@ -1,38 +1,39 @@ PORTNAME= mpifx DISTVERSION= 1.5 +PORTREVISION= 1 CATEGORIES= net devel MAINTAINER= yuri@FreeBSD.org COMMENT= Modern Fortran wrappers around MPI routines WWW= https://github.com/dftbplus/mpifx LICENSE= BSD2CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE BUILD_DEPENDS= fypp:devel/py-fypp@${PY_FLAVOR} USES= cmake:testing fortran mpi:mpich python:build USE_GITHUB= yes GH_ACCOUNT= dftbplus CMAKE_ON= BUILD_SHARED_LIBS post-patch: ${REINPLACE_CMD} -e '/include(CTest)/d' ${WRKSRC}/CMakeLists.txt post-test: # run test programs # at least one test crashes, see https://github.com/dftbplus/mpifx/issues/35 .for f in test_allgather test_allgatherv test_allreduce test_bcast test_comm_split test_gather test_gatherv test_reduce test_scatter test_scatterv cd ${BUILD_WRKSRC}/test && ./${f} .endfor .include .if ${FORTRAN_DEFAULT} == gfortran && ${GCC_DEFAULT} >= 10 # workaround for Type mismatch in argument 'cc' at (1); passed COMPLEX(8) to REAL(8) FFLAGS+= -fallow-argument-mismatch .endif # tests fail to run: https://github.com/dftbplus/mpifx/issues/49 .include diff --git a/net/py-mpi4py-mpich/Makefile b/net/py-mpi4py-mpich/Makefile index c1761bdc0868..deb6668cd715 100644 --- a/net/py-mpi4py-mpich/Makefile +++ b/net/py-mpi4py-mpich/Makefile @@ -1,11 +1,12 @@ PORTNAME= mpi4py COMMENT= Python bindings for MPI (MPICH) +PORTREVISION= 1 PKGNAMESUFFIX= -mpich MASTERDIR= ${.CURDIR}/../py-mpi4py MP= MPICH .include "${MASTERDIR}/Makefile" diff --git a/science/PETSc/Makefile b/science/PETSc/Makefile index b7ab3e403b9f..b61b17824b26 100644 --- a/science/PETSc/Makefile +++ b/science/PETSc/Makefile @@ -1,72 +1,72 @@ PORTNAME= PETSc DISTVERSION= 3.22.4 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= science devel MASTER_SITES= https://web.cels.anl.gov/projects/petsc/download/release-snapshots/ DISTNAME= ${PORTNAME:tl}-${DISTVERSION} MAINTAINER= yuri@FreeBSD.org COMMENT= Suite of data structures and routines from Argonne National Laboratory WWW= https://petsc.org/release/ \ https://gitlab.com/petsc/petsc \ https://github.com/petsc/petsc LICENSE= BSD2CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE LIB_DEPENDS= libblis.so:math/blis \ libmpich.so:net/mpich USES= blaslapack cmake:indirect fortran gmake python shebangfix xorg USE_LDCONFIG= yes USE_XORG= x11 SHEBANG_FILES= configure lib/petsc/bin/*.py lib/petsc/bin/saws/SAWs.py lib/petsc/bin/saws/*.bash config/*.py \ lib/petsc/bin/petscnagfor share/petsc/chkerrconvert.py XARCH!= uname -p GNU_CONFIGURE= yes CONFIGURE_LOG= configure.log CONFIGURE_ARGS= --with-shared-libraries=1 \ --with-mpi-dir=${LOCALBASE} \ --with-python=1 --with-python-pkg-config=${LOCALBASE}/libdata/pkgconfig \ FCFLAGS="${FCFLAGS}" FFLAGS="${FCFLAGS}" \ ${CONFIGURE_ARGS_${ARCH}} CPPFLAGS="${CPPFLAGS}" \ AR=${AR} RANLIB=${RANLIB} \ MAKEFLAGS="${MAKEFLAGS}" LDFLAGS="${LDFLAGS}" LIBS="" CONFIGURE_ARGS_amd64= CFLAGS="${CFLAGS} -msse2" CXXFLAGS="${CXXFLAGS} -msse2" CONFIGURE_ARGS_i386= CFLAGS="${CFLAGS} -msse2" CXXFLAGS="${CXXFLAGS} -msse2" .if ${XARCH:M*64*} # match IDXTYPEWIDTH being set to 64 in math/metis CONFIGURE_ARGS+= --with-64-bit-indices # as opposed to 32-bit indices that are default .endif MAKEFILE= makefile TEST_TARGET= test # 152 of 11396 tests (1.3%) fail due to missing files like /usr/local/share/petsc/datafiles/meshes/square_periodic.msh (tests expect the packe to be installed) LDFLAGS+= ${LOCALBASE}/lib/libmpi.so DATADIR= ${PREFIX}/share/${PORTNAME:tl} BINARY_ALIAS= python=${PYTHON_CMD} PLIST_SUB= SHLIB=${DISTVERSION} SHL=${DISTVERSION:C/\.[0-9]$//} OPTIONS_DEFINE= METIS OPTIONS_DEFAULT= METIS METIS_DESC= Enable metis support for graph partitioning algorithms METIS_LIB_DEPENDS= libmetis.so:math/metis METIS_CONFIGURE_ON= --with-metis=1 # --with-parmetis=1 to use include/parmetis.h post-install: @${STRIP_CMD} ${STAGEDIR}${PREFIX}/lib/libpetsc.so.${DISTVERSION} @${FIND} ${STAGEDIR}${PREFIX} -name "*.html" -delete @cd ${STAGEDIR}${PREFIX} && ${RM} -r bin/win32fe lib/petsc/conf/uninstall.py @${REINPLACE_CMD} -i '' -e 's|^PYTHON = .*|PYTHON = ${PYTHON_CMD}|' ${STAGEDIR}${PREFIX}/lib/petsc/conf/petscvariables @${REINPLACE_CMD} -i '' -e 's|#!/.*|#!${PYTHON_CMD}|' ${STAGEDIR}${PREFIX}/lib/petsc/conf/reconfigure-arch-*-c-debug.py @${RMDIR} ${STAGEDIR}${PREFIX}/lib/petsc/bin/__pycache__ # stray directory # the file /usr/local/share/petsc/examples/config/gmakegen.py is expected by some dependencies, at least by math/slepc .include diff --git a/science/ascent/Makefile b/science/ascent/Makefile index 1687ea96d527..7edcc270d62c 100644 --- a/science/ascent/Makefile +++ b/science/ascent/Makefile @@ -1,58 +1,58 @@ PORTNAME= ascent DISTVERSIONPREFIX= v DISTVERSION= 0.9.5 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= science PKGNAMESUFFIX= -visualizer MAINTAINER= yuri@FreeBSD.org COMMENT= Visualization and analysis runtime for multi-physics HPC simulations WWW= https://ascent.readthedocs.io/en/latest/ \ https://github.com/Alpine-DAV/ascent LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/../LICENSE BROKEN_FreeBSD_15= compilation fails with clang-19, see https://github.com/Alpine-DAV/ascent/issues/1422 LIB_DEPENDS= libconduit.so:science/conduit \ libhdf5.so:science/hdf5 \ libsiloh5.so:science/silo \ libsysinfo.so:devel/libsysinfo \ libsz.so:science/libaec USES= cmake:testing compiler:c++11-lang fortran localbase:ldflags USE_GITHUB= yes GH_ACCOUNT= Alpine-DAV GH_TUPLE= Alpine-DAV:spack_configs:26ea412:spack_configs/../scripts/uberenv_configs/spack_configs \ LLNL:blt:9ff7734:blt/blt \ llnl:uberenv:105e384:uberenv/../scripts/uberenv CMAKE_OFF= ENABLE_PYTHON ENABLE_DOCS ENABLE_TESTS ENABLE_EXAMPLES CMAKE_OFF+= ENABLE_UTILS # utils are installed into a non-standard path, see https://github.com/Alpine-DAV/ascent/issues/814 CMAKE_ARGS= -DCONDUIT_DIR=${LOCALBASE} CMAKE_TESTING_ON= ENABLE_TESTS # one testcase fails because conduit lacks HDF5, see https://github.com/LLNL/conduit/issues/840 LDFLAGS+= -lsysinfo WRKSRC_SUBDIR= src OPTIONS_SINGLE= MPI OPTIONS_SINGLE_MPI= NOMPI MPICH OPENMPI OPTIONS_DEFAULT= MPICH OPTIONS_SUB= yes NOMPI_DESC= Build without parallel processing support NOMPI_CMAKE_ON= -DENABLE_MPI=OFF MPICH_USES= mpi:mpich MPICH_CMAKE_ON= -DENABLE_MPI=ON OPENMPI_USES= mpi:openmpi OPENMPI_CMAKE_ON= -DENABLE_MPI=ON OPENMPI_BROKEN= still chooses mpich, see https://github.com/Alpine-DAV/ascent/issues/1091 # tests as of 0.9.5: 100% tests passed, 0 tests failed out of 97 .include diff --git a/science/axom/Makefile b/science/axom/Makefile index 254bf8397995..fe6b49151517 100644 --- a/science/axom/Makefile +++ b/science/axom/Makefile @@ -1,81 +1,81 @@ PORTNAME= axom DISTVERSIONPREFIX= v DISTVERSION= 0.10.1 -PORTREVISION= 3 +PORTREVISION= 4 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org COMMENT= Infrastructure for development of multi-physics applications and tools WWW= https://github.com/LLNL/axom \ https://axom.readthedocs.io/en/develop LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/../LICENSE BROKEN_armv7= use of overloaded operator '[]' is ambiguous, see https://github.com/LLNL/axom/issues/743 BROKEN_i386= use of overloaded operator '[]' is ambiguous, see https://github.com/LLNL/axom/issues/743 BROKEN_powerpc= use of overloaded operator '[]' is ambiguous, see https://github.com/LLNL/axom/issues/743 LIB_DEPENDS= libconduit.so:science/conduit \ libhdf5.so:science/hdf5 \ libHYPRE.so:science/hypre \ libmetis.so:math/metis \ libsiloh5.so:science/silo RUN_DEPENDS= sparsehash>0:devel/sparsehash USES= cmake:testing,noninja compiler:c++11-lang USE_GITHUB= yes GH_ACCOUNT= LLNL GH_TUPLE= LLNL:axom_data:1bff47e:axom_data/../data \ LLNL:blt:9cfe8ae:blt/cmake/blt \ LLNL:uberenv:e7dd3d9:uberenv/../scripts/uberenv CMAKE_OFF= AXOM_ENABLE_DOCS AXOM_ENABLE_EXAMPLES AXOM_ENABLE_TESTS AXOM_ENABLE_EXAMPLES CMAKE_ON= BUILD_SHARED_LIBS CMAKE_TESTING_ON= AXOM_ENABLE_TESTS AXOM_ENABLE_EXAMPLES CMAKE_TESTING_TARGET= all test CMAKE_ARGS= -DCONDUIT_DIR=${LOCALBASE} \ -DHDF5_DIR=${LOCALBASE} \ -DBLT_CXX_STD=c++14 # BLT_CXX_STD=c++14 is required for LLNL/serac LDFLAGS+= -lexecinfo WRKSRC_SUBDIR= src CONFLICTS_INSTALL= libfmt # bundles and installs an incompatible libfmt version: https://github.com/LLNL/axom/issues/561, axom headers include fmt unnecessarily OPTIONS_DEFINE= LUA MFEM OPENMP OPTIONS_SINGLE= MPI OPTIONS_SINGLE_MPI= NOMPI MPICH OPENMPI OPTIONS_DEFAULT= LUA MFEM MPICH #OPENMP LUA,MFEM,MPI are required for LLNL/serac OPTIONS_SUB= yes LUA_USES= lua:54 LUA_CMAKE_ON= -DLUA_DIR=${LUA_BASE} \ -DFREEBSD_LUA_VER_STR=${LUA_VER_STR} \ -DFREEBSD_LUA_VER=${LUA_VER} MFEM_DESC= Use mfem - library for finite element methods MFEM_CMAKE_ON= -DMFEM_DIR=${LOCALBASE} MFEM_LIB_DEPENDS= libmfem.so:math/mfem NOMPI_DESC= Build without parallel processing support NOMPI_BROKEN= https://github.com/LLNL/axom/issues/913 MPICH_USES= mpi:mpich MPICH_CMAKE_ON= -DENABLE_MPI=ON OPENMPI_USES= mpi:openmpi OPENMPI_CMAKE_ON= -DENABLE_MPI=ON OPENMP_CMAKE_BOOL= ENABLE_OPENMP OPENMP_BROKEN= https://github.com/LLNL/axom/issues/911 post-install: # installs headers of a third party library sparsehash: https://github.com/LLNL/axom/issues/365 @${RM} -r ${STAGEDIR}${PREFIX}/include/sparsehash # 2 tests are known to fail, see https://github.com/LLNL/axom/issues/912 # tests don't run in newer revisions, see https://github.com/LLNL/axom/issues/1492 .include diff --git a/science/bagel/Makefile b/science/bagel/Makefile index eba1ca2b2705..cdc1992d6691 100644 --- a/science/bagel/Makefile +++ b/science/bagel/Makefile @@ -1,62 +1,62 @@ PORTNAME= bagel DISTVERSIONPREFIX= v DISTVERSION= 1.2.2-132 -PORTREVISION= 17 +PORTREVISION= 18 DISTVERSIONSUFFIX= -g2955e4d1a CATEGORIES= science MAINTAINER= yuri@FreeBSD.org COMMENT= Brilliantly Advanced General Electronic-structure Library WWW= https://nubakery.org/ \ https://github.com/qsimulate-open/bagel LICENSE= GPLv3 LICENSE_FILE= ${WRKSRC}/COPYING BROKEN_armv7= error: static_assert failed "size_t is assumed to be the same size as unsigned long long" BROKEN_i386= error: static_assert failed "size_t is assumed to be the same size as unsigned long long" LIB_DEPENDS= libboost_serialization.so:devel/boost-libs TEST_DEPENDS= cblas>0:math/cblas USES= autoreconf blaslapack:openblas compiler:c++11-lang fortran gmake libtool localbase python:build USE_CXXSTD= c++11 USE_LDCONFIG= yes USE_GITHUB= yes GH_ACCOUNT= qsimulate-open GNU_CONFIGURE= yes CONFIGURE_ARGS= --datarootdir=${DATADIR} INSTALL_TARGET= install-strip OPTIONS_DEFINE= MPI LIBXC SCALAPACK SMITH # SLATER (needs a separate lib) OPTIONS_DEFAULT= MPI LIBXC SCALAPACK SMITH MPI_CONFIGURE_ON= --with-mpi=openmpi MPI_CONFIGURE_OFF= --with-mpi=no MPI_LIB_DEPENDS= libmpicxx.so:net/mpich # openmpi option erroneously links to mpich (due to a name clash) LIBXC_DESC= Build DFT with libxc LIBXC_CONFIGURE_WITH= libxc LIBXC_LIB_DEPENDS= libxc.so:science/libxc SCALAPACK_DESC= Use ScaLapack library for parallelized linear algebra SCALAPACK_CONFIGURE_ENABLE= scalapack SCALAPACK_VARS= LDFLAGS+="-lscalapack" SCALAPACK_VARS_OFF= LDFLAGS+="${BLASLIB} ${LAPACKLIB}" # -llapack -lblas are a replacement of libscalapack SCALAPACK_LIB_DEPENDS= libscalapack.so:math/scalapack SCALAPACK_IMPLIES= MPI SMITH_DESC= Compile SMITH generated code SMITH_CONFIGURE_ENABLE= smith SMITH_IMPLIES= MPI TEST_TARGET= check TEST_ARGS= LDFLAGS+="-lcblas -lblas" ${TEST_TARGET} post-test: # tests fail, see https://github.com/qsimulate-open/bagel/issues/248 @cd ${WRKSRC}/src && ./TestSuite --log_level=all .include diff --git a/science/bout++/Makefile b/science/bout++/Makefile index 88dce44c18f9..7d7c387f8264 100644 --- a/science/bout++/Makefile +++ b/science/bout++/Makefile @@ -1,138 +1,138 @@ PORTNAME= bout++ DISTVERSIONPREFIX= v DISTVERSION= 5.1.1 -PORTREVISION= 5 +PORTREVISION= 6 CATEGORIES= science math # physics MAINTAINER= yuri@FreeBSD.org COMMENT= Plasma fluid finite-difference simulation code WWW= https://boutproject.github.io/ LICENSE= GPLv3 LICENSE_FILE= ${WRKSRC}/LICENSE BUILD_DEPENDS= gmake:devel/gmake LIB_DEPENDS= libfftw3.so:math/fftw3 \ libfmt.so:devel/libfmt \ libopenblas.so:math/openblas \ libuuid.so:misc/libuuid RUN_DEPENDS= bash:shells/bash \ ${PYTHON_PKGNAMEPREFIX}matplotlib>=3.2.1:math/py-matplotlib@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}natsort>=8.1.0:devel/py-natsort@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}netCDF4>=0:science/py-netCDF4@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}numpy>=1.22.0:math/py-numpy@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}scipy>=1.4.1:science/py-scipy@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}sympy>=1.5.1:math/py-sympy@${PY_FLAVOR} USES= cmake:testing gettext python gettext-runtime shebangfix USE_LDCONFIG= yes USE_GITHUB= yes GH_ACCOUNT= boutproject GH_PROJECT= BOUT-dev GH_TUPLE= google:googletest:0953a17a4281fc26831da647ad3fcd5e21e6473b:google_googletest/externalpackages/googletest \ meitar:git-archive-all.sh:fc86194f00b678438f9210859597f6eead28e765:meitar_git_archive_all_sh/externalpackages/git-archive-all.sh \ mpark:variant:23cb94f027d4ef33bf48133acc2695c7e5c6f1e7:mpark_variant/externalpackages/mpark.variant \ boutproject:boutdata:e458cf0cf2af6ff68db91da39ef3e15a7e9e6b3d:boutproject_boutdata/externalpackages/boutdata \ abseil:googletest:695cf7c96249de50360a7d2951dc88eb3aea0695:abseil_googletest/externalpackages/mpark.variant/3rdparty/googletest SHEBANG_GLOB= *.sh *.py SHEBANG_FILES= bin/bout-add-mod-path \ bin/bout-boutdata-restart-create \ bin/bout-pylib-cmd-to-bin \ bin/bout-sonnet \ bin/bout-stop-script \ bin/bout_3to4.py \ bin/bout_4to5 CMAKE_ON= BUILD_SHARED_LIBS \ BOUT_USE_SYSTEM_FMT CMAKE_OFF= BOUT_TESTS CMAKE_TESTING_ON= BOUT_TESTS TESTING_UNSAFE= 6 tests fail, see https://github.com/boutproject/BOUT-dev/issues/2980 CXXFLAGS+= -I${WRKSRC}/include LDFLAGS+= -lexecinfo OPTIONS_DEFINE= OPENMP PETSC SLEPC SUNDIALS OPTIONS_MULTI= FORMAT OPTIONS_MULTI_FORMAT= HDF5 NETCDF OPTIONS_SINGLE= MPI OPTIONS_SINGLE_MPI= MPICH OPENMPI OPTIONS_DEFAULT= MPICH NETCDF # PETSC SLEPC: not compatible with the latest petsc-3.18.4 FORMAT_DESC= File format support HDF5_CMAKE_BOOL= BOUT_USE_HDF5 HDF5_LIB_DEPENDS= libhdf5.so:science/hdf5 NETCDF_USES= localbase:ldflags pkgconfig # because of the cmake patch in files/ NETCDF_CMAKE_BOOL= BOUT_USE_NETCDF NETCDF_LIB_DEPENDS= libnetcdf_c++4.so:science/netcdf-cxx \ libnetcdf.so:science/netcdf MPICH_USES= mpi:mpich OPENMP_CMAKE_BOOL= BOUT_ENABLE_OPENMP OPRNMP_BROKEN= SEGV when OpenMP is enabled, see https://github.com/boutproject/BOUT-dev/issues/2620 OPENMPI_USES= mpi:openmpi PETSC_DESC= Build with PETSc support PETSC_CMAKE_BOOL= BOUT_USE_PETSC PETSC_LIB_DEPENDS= libpetsc.so:science/PETSc SLEPC_DESC= Build with SLEPc support SLEPC_CMAKE_BOOL= BOUT_USE_SLEPC SLEPC_LIB_DEPENDS= libslepc.so:math/slepc SLEPC_IMPLIES= PETSC # build breaks w/out petsc SUNDIALS_DESC= Build with Sundials support SUNDIALS_CMAKE_BOOL= BOUT_USE_SUNDIALS SUNDIALS_CMAKE_ON= -DBOUT_DOWNLOAD_SUNDIALS=OFF SUNDIALS_BROKEN= fails to build with sundials, see https://github.com/boutproject/BOUT-dev/issues/2617 BINARY_ALIAS= make=${GMAKE} \ python3=${PYTHON_CMD} .if defined(WITH_EXAMPLES) # Build executables demonstrating BOUT++ capabilities. They aren't installed and don't need to be built for packaging. CMAKE_ON+= BOUT_BUILD_EXAMPLES .endif post-patch: # fix the version number in the code that it can't obtain from git @${REINPLACE_CMD} \ -e 's|__version__ = version(__name__)|__version__ = "${PORTVERSION}"|' \ ${WRKSRC}/tools/pylib/boutdata/__init__.py \ ${WRKSRC}/externalpackages/boutdata/src/boututils/__init__.py post-install: # workaround for /usr/local/lib/cmake/bout++/bout++Config.cmake:if @${REINPLACE_CMD} -i '' \ -e 's|${BUILD_WRKSRC}/externalpackages/mpark.variant|${PREFIX}/lib/cmake/mpark_variant|' \ -e 's|${BUILD_WRKSRC}/externalpackages/PVODE|${PREFIX}/lib/cmake/PVODE|' \ -e 's|${WRKSRC}/cmake|${PREFIX}/lib/cmake/bout++|' \ ${STAGEDIR}${PREFIX}/lib/cmake/bout++/bout++Config.cmake # remove *.orig files created by patching @${RM} ${STAGEDIR}${PREFIX}/include/*.orig # install missing PVODE cmake files @${RM} ${STAGEDIR}${PREFIX}/lib/cmake/PVODE/* ${INSTALL_DATA} ${BUILD_WRKSRC}/externalpackages/PVODE/PVODEConfig.cmake ${STAGEDIR}${PREFIX}/lib/cmake/PVODE ${INSTALL_DATA} ${BUILD_WRKSRC}/externalpackages/PVODE/PVODEConfigVersion.cmake ${STAGEDIR}${PREFIX}/lib/cmake/PVODE @${REINPLACE_CMD} -i '' \ -e 's|${BUILD_WRKSRC}/lib|${PREFIX}/lib|' \ -e 's|${PORTSDIR}/.*/BOUT-dev-${PORTVERSION}/externalpackages/PVODE/include|${PREFIX}/include|g' \ ${STAGEDIR}${PREFIX}/lib/cmake/PVODE/* @${REINPLACE_CMD} -i '' \ -e 's|INTERFACE_INCLUDE_DIRECTORIES .*|INTERFACE_INCLUDE_DIRECTORIES "${PREFIX}/include"|' \ ${STAGEDIR}${PREFIX}/lib/cmake/PVODE/PVODEConfig.cmake # remove broken link, see https://github.com/boutproject/BOUT-dev/issues/2623 @${RM} ${STAGEDIR}${PREFIX}/bin/bout-squashoutput pre-test: # build tests @cd ${BUILD_WRKSRC} && \ ${SETENVI} ${WRK_ENV} ${CONFIGURE_ENV} ${CMAKE_BIN} ${CMAKE_ARGS} ${CMAKE_TESTING_ARGS} ${CMAKE_SOURCE_PATH} && \ ${SETENVI} ${WRK_ENV} ${MAKE_ENV} ${TEST_ENV} ${MAKE_CMD} ${_MAKE_JOBS} ${MAKE_ARGS} build-check .include diff --git a/science/cardioid/Makefile b/science/cardioid/Makefile index 6cdeefa06769..42dbb8e05320 100644 --- a/science/cardioid/Makefile +++ b/science/cardioid/Makefile @@ -1,62 +1,62 @@ PORTNAME= cardioid PORTVERSION= g20211026 -PORTREVISION= 4 +PORTREVISION= 5 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org COMMENT= Cardiac simulation toolkit WWW= https://github.com/LLNL/cardioid LICENSE= MIT LICENSE_FILE= ${WRKSRC}/LICENSE LIB_DEPENDS= libblas.so:math/blas \ liblapack.so:math/lapack RUN_DEPENDS= bash:shells/bash USES= cmake:testing shebangfix USE_GITHUB= yes GH_ACCOUNT= LLNL GH_TAGNAME= 2f66d9f GH_TUPLE= mfem:mfem:v4.4:mfem SHEBANG_FILES= elec/compileReaction.template CMAKE_TESTING_ON= ENABLE_TESTS PLIST_FILES= bin/cardioid \ bin/compileReaction \ bin/singleCell OPTIONS_DEFINE= MFEM OPENMP OPTIONS_SINGLE= MFEM MPI OPTIONS_SINGLE_MPI= NOMPI MPICH OPENMPI OPTIONS_DEFAULT= MPICH OPENMP OPTIONS_SUB= yes MFEM_DESC= Build with MFEM mesh library MFEM_CMAKE_ON= -DMFEM_DIR=${WRKSRC_mfem} MFEM_BROKEN= see https://github.com/LLNL/cardioid/issues/15 NOMPI_DESC= Build without parallel processing support NOMPI_BROKEN= https://github.com/LLNL/axom/issues/913 MPICH_USES= mpi:mpich MPICH_CMAKE_ON= -DENABLE_MPI=ON OPENMPI_USES= mpi:openmpi OPENMPI_CMAKE_ON= -DENABLE_MPI=ON OPENMP_CMAKE_BOOL= ENABLE_OPENMP OPENMP_BROKEN_OFF= https://github.com/LLNL/cardioid/issues/14 .include .if (!exists(/usr/include/omp.h) && ${PORT_OPTIONS:MOPENMP}) USES+= compiler:gcc-c++11-lib .else USES+= compiler:c++11-lang .endif .include diff --git a/science/chrono/Makefile b/science/chrono/Makefile index 1ecabb5fcbbf..529910d60e26 100644 --- a/science/chrono/Makefile +++ b/science/chrono/Makefile @@ -1,127 +1,127 @@ PORTNAME= chrono DISTVERSION= 9.0.1 -PORTREVISION= 4 +PORTREVISION= 5 CATEGORIES= science devel PKGNAMESUFFIX= -physics-simulation-engine MAINTAINER= yuri@FreeBSD.org COMMENT= C++ library for multi-physics simulation WWW= https://projectchrono.org/ \ https://github.com/projectchrono/chrono LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE BROKEN_i386= use of overloaded operator '[]' is ambiguous (with operand types 'chrono::quaternion' and 'int'): https://github.com/projectchrono/chrono/issues/158 BROKEN_aarch64= cannot find -lFALSE, see https://github.com/projectchrono/chrono/issues/389 BUILD_DEPENDS= openmpi>0:net/openmpi LIB_DEPENDS= libblas.so:math/blas \ libepoll-shim.so:devel/libepoll-shim \ libfabric.so:net/libfabric \ libhwloc.so:devel/hwloc2 \ libjson-c.so:devel/json-c \ libmetis.so:math/metis \ libpciaccess.so:devel/libpciaccess \ libpng16.so:graphics/png \ libscotch.so:cad/scotch \ libze_loader.so:devel/level-zero USES= cmake compiler:c++14-lang eigen:3 fortran gnome jpeg xorg USE_LDCONFIG= yes USE_GNOME= libxml2 USE_XORG= x11 xau xcb xdmcp xext xxf86vm USE_GITHUB= yes GH_ACCOUNT= project${PORTNAME} ALL_MODULES= Cascade Cosimulation Distributed FSI Irrlicht Multicore MUMPS OpenGL Pardiso_Project Postprocess Sensor SynChrono Vehicle # module names in a human readable case; for the list of available modules: grep -r "option(ENABLE_MODULE" work OPTIONS_DEFINE= HDF5 DEMOS OPTIONS_GROUP= MODULES OPTIONS_GROUP_MODULES= ${ALL_MODULES:tu} MODULES_DESC= Enable modules: OPTIONS_DEFAULT= HDF5 OPTIONS_SUB= yes HDF5_CMAKE_BOOL= ENABLE_HDF5 HDF5_LIB_DEPENDS= libhdf5.so:science/hdf5 DEMOS_DESC= Build and install demo programs DEMOS_CMAKE_BOOL= BUILD_DEMOS DEMOS_BROKEN= /usr/local/lib/libdmumps.so: undefined reference to `mpi_pack_' # ' CASCADE_CMAKE_ON= -DCASCADE_INCLUDE_DIR:STRING=${LOCALBASE}/include/OpenCASCADE -DCASCADE_LIBDIR:STRING=${LOCALBASE}/lib CASCADE_LIB_DEPENDS= libTKernel.so:cad/opencascade740 DISTRIBUTED_BROKEN= requires cuda_runtime_api.h in thrust package which is missing for some reason DISTRIBUTED_IMPLIES= MULTICORE FSI_BROKEN= requires CUDA IRRLICHT_LIB_DEPENDS= libIrrlicht.so:x11-toolkits/irrlicht MULTICORE_BUILD_DEPENDS= blaze>0:math/blaze \ thrust>0:devel/thrust MUMPS_CMAKE_ON= -DMUMPS_ROOT:STRING=${LOCALBASE} MUMPS_LIB_DEPENDS= libdmumps.so:math/mumps \ libopenblas.so:math/openblas PARDISO_PROJECT_BROKEN= Not available for FreeBSD; License is restrictive SENSOR_BROKEN= requires CUDA SYNCHRONO_USES= localbase SYNCHRONO_BUILD_DEPENDS= flatc:devel/flatbuffers # until https://github.com/projectchrono/chrono/issues/391 is fixed SYNCHRONO_LIB_DEPENDS= libmpi.so:net/mpich SYNCHRONO_IMPLIES= VEHICLE SYNCHRONO_BROKEN= fails with the modern flatbuffers versions, see https://github.com/projectchrono/chrono/issues/391 OPENGL_USES= gl OPENGL_USE= GL=gl,glu,glew OPENGL_BUILD_DEPENDS= ${LOCALBASE}/include/glm/glm.hpp:math/glm OPENGL_LIB_DEPENDS= libglfw.so:graphics/glfw VEHICLE_LIB_DEPENDS= libsz.so:science/libaec \ libmpi.so:net/openmpi .for module in ${ALL_MODULES} ${module:tu}_DESC= Chrono ${module} module ${module:tu}_CMAKE_BOOL= ENABLE_MODULE_${module:tu} .if "${${module:tu}_BROKEN}" == "" OPTIONS_DEFAULT+= ${module:tu} .endif .endfor #.include .include .if ${PORT_OPTIONS:MVEHICLE} && ${PORT_OPTIONS:MIRRLICHT} PLIST_FILES+= lib/libChronoEngine_vehicle_irrlicht.so .endif .if ${PORT_OPTIONS:MVEHICLE} && ${PORT_OPTIONS:MOPENGL} PLIST_FILES+= lib/libChronoEngine_vehicle_opengl.so .endif #.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|' do-test: @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} && \ ctest -C ${CMAKE_BUILD_TYPE} ${_MAKE_JOBS} .include diff --git a/science/code_saturne/Makefile b/science/code_saturne/Makefile index 3431d8506e0c..df0c580f7cb3 100644 --- a/science/code_saturne/Makefile +++ b/science/code_saturne/Makefile @@ -1,119 +1,119 @@ PORTNAME= code_saturne PORTVERSION= 8.1.1 -PORTREVISION= 5 +PORTREVISION= 6 CATEGORIES= science parallel MASTER_SITES= https://www.code-saturne.org/releases/ MAINTAINER= thierry@FreeBSD.org COMMENT= EDF's general purpose Computational Fluid Dynamics (CFD) software WWW= https://www.code-saturne.org/ LICENSE= GPLv2 LICENSE_FILE= ${WRKSRC}/COPYING BUILD_DEPENDS= ${MPI4PY} \ gsed:textproc/gsed LIB_DEPENDS= libsysinfo.so:devel/libsysinfo \ libcgns.so:science/cgnslib \ libpetsc.so:science/PETSc \ libHYPRE.so:science/hypre \ libhdf5.so:science/hdf5 \ libscotch.so:cad/scotch \ libsmumps.so:math/mumps \ libcblas.so:math/cblas \ libmedC.so:french/med RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}matplotlib>0:math/py-matplotlib@${PY_FLAVOR} \ ${MPI4PY} \ xmgrace:math/grace \ bash:shells/bash \ xterm:x11/xterm USES= autoreconf bison blaslapack compiler:c11 fortran gettext gnome gmake \ iconv localbase libtool mpi pyqt:5 python shebangfix xorg USE_GNOME= libxml2 USE_PYQT= pyqt5 USE_XORG= x11 SHEBANG_FILES= install_saturne.py tests/unittests.py build-aux/*.py CFLAGS+= -D__XSI_VISIBLE -Wno-error=incompatible-function-pointer-types CPPFLAGS+= -I${LOCALBASE}/include -I${LOCALBASE}/include/libxml2 GNU_CONFIGURE= yes CONFIGURE_ARGS= --without-salome --without-salome-yacs --without-salome-kernel \ --without-salome-gui --enable-python \ --with-blas=yes --with-blas-type=BLAS \ --with-blas-include=${LOCALBASE}/include/cblas \ --with-blas-lib=${LOCALBASE}/lib \ --with-hypre="${LOCALBASE}" --with-mpi \ --with-mumps="${LOCALBASE}" --with-petsc="${LOCALBASE}" \ --with-scotch-include="${LOCALBASE}/include" CONFIGURE_ENV= ac_cv_path_SED=${LOCALBASE}/bin/gsed ldflags_rpath="-R" \ MUMPS_LIBS="-lmpiseq -llapack" GNU_CONFIGURE_MANPREFIX=${PREFIX}/share USE_LDCONFIG= yes INSTALL_TARGET= install-strip BINARY_ALIAS= python=${PYTHON_CMD} \ pyrcc5=pyrcc5-${PYTHON_VER} \ pyuic5=pyuic5-${PYTHON_VER} OPTIONS_DEFINE= DOCS OPTIONS_DEFAULT= METIS OPTIONS_RADIO= METIS OPTIONS_RADIO_METIS= METIS PARMETIS OPTIONS_SUB= yes METIS_DESC= Support of METIS METIS_LIB_DEPENDS= libmetis.so:math/metis METIS_CONFIGURE_ON= --with-metis-include="${LOCALBASE}/include" PARMETIS_DESC= Support of ParMETIS PARMETIS_LIB_DEPENDS= libparmetis.so:math/parmetis PARMETIS_CONFIGURE_ON= --with-metis-include="${LOCALBASE}/include/parmetis" \ --with-metis-lib="${LOCALBASE}/lib" PARMETIS_CONFIGURE_ENV= LIBS=-lexecinfo TEST_TARGET= check .if defined(PACKAGE_BUILDING) TERM= vt100 # Force for pointyhat to override su .else TERM?= vt100 # Default value needed for tput in jail or tinderbox .endif .include .if ${ARCH} == "i386" # /wrkdirs/usr/ports/science/code_saturne/work/code_saturne-5.3.0/src/apps/.libs # /libsaturne.so: # undefined reference to `__atomic_compare_exchange' CONFIGURE_ARGS+= --disable-openmp .else CONFIGURE_ARGS+= --enable-openmp .endif .if ${PORT_OPTIONS:MDOCS} USES+= tex USE_TEX= tex:build BUILD_DEPENDS+= fig2dev:print/fig2dev \ doxygen:devel/doxygen \ dot:graphics/graphviz \ dvips:print/tex-dvipsk \ ${PYTHON_PKGNAMEPREFIX}sphinx>=0,1:textproc/py-sphinx@${PY_FLAVOR} BINARY_ALIAS+= sphinx-build=sphinx-build-${PYTHON_VER} ALL_TARGET= all pdf DOCS= AUTHORS ChangeLog README PORTDOCS= * .endif pre-configure: ${REINPLACE_CMD} -e 's|/usr/bin/env python|${PYTHON_CMD}|' \ ${WRKSRC}/Makefile.am ${REINPLACE_CMD} -e 's|make -s|${GMAKE} -s|' ${WRKSRC}/m4/cs_petsc.m4 .for cs in config/cs_auto_flags.sh libple/config/ple_auto_flags.sh ${REINPLACE_CMD} -e 's|fopenmp=libomp|fopenmp|' ${WRKSRC}/${cs} .endfor post-install: ${STRIP_CMD} ${STAGEDIR}${PREFIX}/libexec/code_saturne/cs_solver post-install-DOCS-on: @${MKDIR} ${STAGEDIR}${DOCSDIR} ${INSTALL_DATA} ${DOCS:C|^|${WRKSRC}/|} ${STAGEDIR}${DOCSDIR} .include diff --git a/science/conduit/Makefile b/science/conduit/Makefile index 5f2c3994456b..c12aadfbdc46 100644 --- a/science/conduit/Makefile +++ b/science/conduit/Makefile @@ -1,51 +1,51 @@ PORTNAME= conduit DISTVERSIONPREFIX= v DISTVERSION= 0.9.5 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org COMMENT= Simplified data exchange for HPC simulations WWW= https://github.com/LLNL/conduit LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/../LICENSE LIB_DEPENDS= libhdf5.so:science/hdf5 \ libsiloh5.so:science/silo USES= cmake:testing compiler:c++11-lang fortran USE_LDCONFIG= yes USE_GITHUB= yes GH_ACCOUNT= LLNL GH_TUPLE= LLNL:blt:058b312:blt/blt \ Alpine-DAV:spack_configs:26a5d10:spack_configs/../scripts/uberenv_configs/spack_configs \ LLNL:uberenv:5430066:LLNL_uberenv/../scripts/uberenv WRKSRC_SUBDIR= src CMAKE_ON= ENABLE_FORTRAN CMAKE_OFF= CONDUIT_ENABLE_TESTS ENABLE_DOCS ENABLE_EXAMPLES ENABLE_GIT ENABLE_TESTS ENABLE_VALGRIND CMAKE_ARGS= -DHDF5_DIR=${LOCALBASE} \ -DSILO_DIR=${LOCALBASE} \ -DFREEBSD_EXAMPLESDIR=${EXAMPLESDIR} # complete list of optional dependencies (enabled with *_DIR): https://llnl-conduit.readthedocs.io/en/latest/building.html #CMAKE_ARGS+= -DADIOS_DIR=${LOCALBASE} # broken, see https://github.com/LLNL/conduit/issues/841 CMAKE_TESTING_ON= ENABLE_TESTS OPTIONS_SINGLE= MPI OPTIONS_SINGLE_MPI= NOMPI MPICH OPENMPI OPTIONS_DEFAULT= MPICH OPTIONS_SUB= yes NOMPI_DESC= Build without parallel processing support MPICH_USES= mpi:mpich MPICH_CMAKE_ON= -DENABLE_MPI=ON OPENMPI_USES= mpi:openmpi OPENMPI_CMAKE_ON= -DENABLE_MPI=ON # tests as of 0.9.5: 100% tests passed, 0 tests failed out of 3 .include diff --git a/science/cp2k/Makefile b/science/cp2k/Makefile index d57c3e43a6a5..ef21041ed5a4 100644 --- a/science/cp2k/Makefile +++ b/science/cp2k/Makefile @@ -1,74 +1,75 @@ PORTNAME= cp2k DISTVERSIONPREFIX= v DISTVERSION= 2026.1 +PORTREVISION= 1 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org COMMENT= Quantum chemistry and solid state physics software package WWW= https://www.cp2k.org/ \ https://github.com/cp2k/cp2k LICENSE= GPLv2+ LICENSE_FILE= ${WRKSRC}/LICENSE .if !exists(/usr/include/omp.h) BROKEN= requires OpenMP support that is missing on this architecture .endif BUILD_DEPENDS= fypp:devel/py-fypp@${PY_FLAVOR} LIB_DEPENDS= libdbcsr.so:math/dbcsr \ libfftw3.so:math/fftw3 \ libopenblas.so:math/openblas RUN_DEPENDS= cp2k-data>0:science/cp2k-data TEST_DEPENDS= bash:shells/bash USES= cmake fortran localbase:ldflags python:build,test shebangfix tar:bz2 USE_GCC= yes # OpenMP is used from both Fortan and C code, therefore C code should be compiled with GCC, otherwise it fails at run-time (same in dbcsr) USE_GITHUB= yes SHEBANG_GLOB= *.py GCC_VERSION= ${GCC_DEFAULT} MAKE_ARGS= XARCH=FreeBSD-gfortran VERSION=${VERSION} FC=gfortran${GCC_VERSION} CC=${CC} LD=gfortran${GCC_VERSION} \ DATA_DIR=${DATADIR} FFLAGS+= -D__NO_STATM_ACCESS BINARY_ALIAS= python=${PYTHON_CMD} python3=${PYTHON_CMD} OPTIONS_DEFINE= LIBINT MPIX OPTIONS_DEFAULT= MPIX # LIBINT LIBINT_DESC= Use libint to evaluate integrals LIBINT_CMAKE_BOOL= CP2K_USE_LIBINT2 LIBINT_LIB_DEPENDS= libint2.so:science/libint2 LIBINT_BROKEN= missing fortran support MPIX_DESC= Enable MPI MPIX_CMAKE_BOOL= CP2K_USE_MPI MPIX_USES= mpi:mpich MPIX_LIB_DEPENDS= libscalapack.so:math/scalapack MPIX_VARS= EXE_VERSION=psmp MPIX_VARS_OFF= EXE_VERSION=ssmp PLIST_SUB= SUFFIX=.${EXE_VERSION} do-test: install @cd ${WRKSRC}/ && \ ${SETENV} ${MAKE_ENV} CP2K_STEM=${PREFIX}/bin/cp2k \ ./tests/do_regtest.py ${BUILD_WRKSRC}/bin ${EXE_VERSION} # build instructions: https://github.com/cp2k/cp2k/blob/master/INSTALL.md # tests as of 2026.1: # Number of FAILED tests 0 # Number of WRONG tests 0 # Number of CORRECT tests 3038 # Total number of tests 3038 # # Summary: correct: 3038 / 3038; 20min # Status: OK .include diff --git a/science/dftbplus/Makefile b/science/dftbplus/Makefile index f504de4af01a..3a409e022613 100644 --- a/science/dftbplus/Makefile +++ b/science/dftbplus/Makefile @@ -1,110 +1,110 @@ PORTNAME= dftbplus DISTVERSION= 24.1 -PORTREVISION= 5 +PORTREVISION= 6 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org COMMENT= DFTB+: Package for performing fast atomistic simulations WWW= https://dftbplus.org/ LICENSE= GPLv3 # main code is under LGPL3+, the bundled dftd3-lib is under GPLv1+, this makes the result GPLv3 (based on https://www.gnu.org/licenses/gpl-faq.html#AllCompatibility) BROKEN_aarch64= Lack of IEEE754 support in gcc causes "Cannot find an intrinsic module named 'ieee_arithmetic'", see bug\#255890 LIB_DEPENDS= libblas.so:math/blas \ liblapack.so:math/lapack \ libopenblas.so:math/openblas RUN_DEPENDS= ${PYNUMPY} TEST_DEPENDS= bash:shells/bash USES= cmake compiler:gcc-c++11-lib fortran pkgconfig python:build shebangfix USE_LDCONFIG= yes SHEBANG_FILES= tools/dptools/bin/* tools/misc/* utils/srcmanip/* utils/build/* external/fypp/bin/* utils/get_opt_externals \ external/fypp/bin/fypp utils/test/testlist_to_fypp SHEBANG_GLOB= *.py *.sh USE_GITHUB= yes GH_TUPLE= \ aradi:fytest:94e05ac:aradi_fytest/external/fytest/origin \ dftbplus:testparams:cd7536f:testparams/external/slakos/origin \ dftd4:dftd4:056491b:dftd4_dftd4/external/dftd4/origin TEST_TARGET= test BINARY_ALIAS= git=false CMAKE_ON= BLAS_DETECTION BUILD_SHARED_LIBS WITH_API ENABLE_DYNAMIC_LOADING CMAKE_ARGS= -DLAPACK_LIBRARY=lapack -DSCALAPACK_LIBRARY=scalapack BINARY_ALIAS= git=false python=${PYTHON_CMD} python3=${PYTHON_CMD} OPTIONS_DEFINE= ARPACK CHIMES DFTD3 MBD MPIX PLUMED POISSON PYTHON SOCKETS TBLITE TRANSPORT # see config.cmake for a complete list OPTIONS_DEFAULT= CHIMES DFTD3 MBD MPIX PLUMED POISSON TRANSPORT SOCKETS # PYTHON TBLITE OPTIONS_SUB= yes ARPACK_DESC= Build with ARPACK for large eigenvalue problems ARPACK_CMAKE_BOOL= WITH_ARPACK ARPACK_LIB_DEPENDS= libarpack.so:math/arpack-ng ARPACK_PREVENTS= MPIX # ARPACK is only used in a single-core application CHIMES_DESC= Build with ChIMES CHIMES_CMAKE_BOOL= WITH_CHIMES CHIMES_LIB_DEPENDS= libchimescalc.so:science/chimes-calculator DFTD3_DESC= Build with s-dft3 DFTD3_CMAKE_BOOL= WITH_SDFTD3 DFTD3_LIB_DEPENDS= libs-dftd3.so:science/simple-dftd3 \ libmctc-lib.so:science/mctc-lib \ libmstore.so:science/mstore \ libtoml-f.so:textproc/toml-f # binaries not linked with libtoml-f.so, see https://github.com/dftbplus/dftbplus/issues/1040 MBD_DESC= Build with many-body-dispersion support MBD_CMAKE_BOOL= WITH_MBD MBD_LIB_DEPENDS= libmbd.so:science/libmbd MPIX_DESC= MPI (Message Passing Interface) support # the MPI option name causes failure in MPI_USES=mpi:openmpi MPIX_CMAKE_BOOL= WITH_MPI MPIX_USES= mpi:mpich MPIX_LIB_DEPENDS= libmpich.so:net/mpich \ libmpifx.so:net/mpifx \ libscalapack.so:math/scalapack \ libscalapackfx.so:math/scalapackfx MPIX_LDFLAGS= ${LOCALBASE}/lib/libmpich.so ${LOCALBASE}/lib/libmpifort.so ${LOCALBASE}/lib/libmpi.so PLUMED_DESC= Do metadynamics via the PLUMED2 library PLUMED_CMAKE_BOOL= WITH_PLUMED PLUMED_LIB_DEPENDS= libplumed.so:science/plumed POISSON_DESC= Include Poisson-solver POISSON_CMAKE_BOOL= WITH_POISSON PYTHON_USES= python PYTHON_CMAKE_BOOL= WITH_PYTHON PYTHON_BROKEN= fails to install into stage directory: https://github.com/dftbplus/dftbplus/issues/931 SOCKETS_DESC= Build with sockets library SOCKETS_CMAKE_BOOL= WITH_SOCKETS SOCKETS_BINARY_ALIAS= gcc=${CC} TBLITE_DESC= Include xTB support via tblite TBLITE_CMAKE_BOOL= WITH_TBLITE TBLITE_BROKEN= fails to build, see https://github.com/dftbplus/dftbplus/issues/1041 TRANSPORT_DESC= Transport via libNEGF TRANSPORT_CMAKE_BOOL= WITH_TRANSPORT TRANSPORT_LIB_DEPENDS= libnegf.so:science/libnegf \ libmpi.so:net/mpich \ libmpifx.so:net/mpifx .include .if ${GCC_DEFAULT} >= 10 # workaround for Type mismatch between actual argument at (1) and actual argument at (2) (COMPLEX(8)/CHARACTER(*)). # in theory, this should set FCFLAGS, but the port does not conform FFLAGS+= -fallow-argument-mismatch .endif # 5 tests fail, see https://github.com/dftbplus/dftbplus/issues/1474 .include diff --git a/science/elk/Makefile b/science/elk/Makefile index 3901d4ab49f2..e6d760e394d3 100644 --- a/science/elk/Makefile +++ b/science/elk/Makefile @@ -1,85 +1,85 @@ PORTNAME= elk DISTVERSION= 10.3.12 -PORTREVISION= 3 +PORTREVISION= 4 CATEGORIES= science MASTER_SITES= SF/${PORTNAME} PKGNAMESUFFIX= -chemistry DIST_SUBDIR= ${PORTNAME}${PKGNAMESUFFIX} MAINTAINER= yuri@FreeBSD.org COMMENT= All-electron full-potential linearised augmented-planewave code WWW= http://elk.sourceforge.net/ LICENSE= GPLv3 LICENSE_FILE= ${WRKSRC}/COPYING LIB_DEPENDS= libblas.so:math/blas \ libblis.so:math/blis \ libfftw3.so:math/fftw3 \ libfftw3f.so:math/fftw3-float \ liblapack.so:math/lapack \ libopenblas.so:math/openblas \ libwannier.so:science/wannier90 \ libxc.so:science/libxc USES= fortran gmake tar:tgz BINARY_ALIAS= make=${GMAKE} LDFLAGS+= ${LOCALBASE}/lib/gcc${GCC_DEFAULT}/libgcc_s.so OPTIONS_DEFINE= DOCS EXAMPLES NATIVE OPENMP OPTIONS_RADIO= MPI OPTIONS_RADIO_MPI= MPICH OPENMPI OPTIONS_DEFAULT= OPENMP MPICH PARALLEL_DESC= Enable parallelizations: NATIVE_MAKE_ARGS= FFLAGS="${FFLAGS} -march=native -mtune=native" NATIVE_VARS= FFLAGS="-march=native -mtune=native" OPENMP_VARS= OPENMP_FLAGS=-fopenmp MPICH_USES= mpi:mpich MPICH_MAKE_ARGS= F90=${MPIF90} OPENMPI_USES= mpi:openmpi OPENMPI_MAKE_ARGS= F90=${MPIF90} PORTDOCS= * PORTEXAMPLES= * MAKE_JOBS_UNSAFE= yes PLIST_FILES= bin/${PORTNAME} .include .if ${GCC_DEFAULT} >= 10 # workaround for Type mismatch in argument 'cc' at (1); passed COMPLEX(8) to REAL(8) FCFLAGS+= -fallow-argument-mismatch .endif post-patch: @${SED} 's|%%GMAKE%%|${GMAKE}|; s|%%FC%%|${FC}|; \ s|%%FCFLAGS%%|${FCFLAGS}|; \ s|%%OPENMP_FLAGS%%|${OPENMP_FLAGS}|' \ < ${FILESDIR}/make.inc.in \ > ${WRKSRC}/make.inc do-install: ${INSTALL_PROGRAM} ${WRKSRC}/src/${PORTNAME} ${STAGEDIR}${PREFIX}/bin do-install-DOCS-on: @${MKDIR} ${STAGEDIR}${DOCSDIR} ${INSTALL_DATA} ${WRKSRC}/docs/*.pdf ${STAGEDIR}${DOCSDIR} do-install-EXAMPLES-on: @${MKDIR} ${STAGEDIR}${EXAMPLESDIR} cd ${WRKSRC}/examples && ${COPYTREE_SHARE} . ${STAGEDIR}${EXAMPLESDIR} do-test: # several tests fail, see https://sourceforge.net/p/elk/discussion/897822/thread/5d7862dd8b/ @cd ${WRKSRC}/tests && ./test.sh # 1 test (test_024) fails, reported to dewhurst@mpi-halle.mpg.de on 2026-06-26 (before was: see https://sourceforge.net/p/elk/discussion/897820/thread/f7b5859624/) .include diff --git a/science/elmerfem/Makefile b/science/elmerfem/Makefile index 32806a7ae7d4..17c560d80809 100644 --- a/science/elmerfem/Makefile +++ b/science/elmerfem/Makefile @@ -1,130 +1,130 @@ PORTNAME= elmerfem DISTVERSIONPREFIX= release- DISTVERSION= 26.1 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= science MAINTAINER= thierry@FreeBSD.org COMMENT= Multiphysical simulation software WWW= https://www.elmerfem.org/blog/ LICENSE= GPLv2 LIB_DEPENDS= libhdf5.so:science/hdf5 \ libmetis.so:math/metis \ libnetcdf.so:science/netcdf \ libparpack.so:math/arpack-ng \ libcholmod.so:math/suitesparse-cholmod \ libumfpack.so:math/suitesparse-umfpack USES= blaslapack:openblas cmake compiler:c++11-lang fortran localbase mpi USE_CXXSTD= c++14 USE_GITHUB= yes GH_ACCOUNT= ElmerCSC USE_LDCONFIG= ${PREFIX}/lib/elmersolver CMAKE_ARGS= -DELMER_FEM_REVISION:STRING=${GH_TAGNAME} ALL_TARGET= # empty CMAKE_ARGS+= -DHAVE_INTTYPES_H:BOOL=ON \ -DEXTERNAL_ARPACK:BOOL=ON \ -DEXTERNAL_PARPACK:BOOL=ON \ -DEXTERNAL_UMFPACK:BOOL=ON .if !defined(MAINTAINER_MODE) CMAKE_ARGS+= -Wno-dev .endif OPTIONS_DEFINE= DOCS GUI OCC OPTIONS_DEFAULT= GUI OCC OPTIONS_SUB= yes GUI_DESC= Build with ElmerGUI (Graphical User Interface) OCC_DESC= Use OpenCASCADE for CAD import in ElmerGUI DOCS_USES= tex DOCS_USE= tex=pdftex:build GUI_LIB_DEPENDS= libqwt.so:x11-toolkits/qwt6@qt5 GUI_USES= gl jpeg qt:5 xorg GUI_USE= gl=gl,glu xorg=ice,sm,x11,xext,xt qt=${_QT5_LIBS:ts,} GUI_CMAKE_BOOL= WITH_ELMERGUI WITH_PARAVIEW GUI_CMAKE_ON= -DQWT_LIBRARY=${QT_LIBDIR}/libqwt.so \ -DQWT_INCLUDE_DIR=${QT_INCDIR}/qwt6 \ -DDESIRED_QT_VERSION=5 \ -DWITH_QT5:BOOL=TRUE \ -DQT_FOUND:BOOL=TRUE OCC_IMPLIES= GUI OCC_LIB_DEPENDS= libexpat.so:textproc/expat2 \ libfreetype.so:print/freetype2 \ libpng.so:graphics/png \ libpython${_PYVERSION}.so:lang/python${PYTHON_SUFFIX} \ libboost_thread.so:devel/boost-libs \ libtiff.so:graphics/tiff \ libTKernel.so:cad/opencascade \ libvtksys-${VTK_VER}.so:math/vtk${VTK_VER:R} OCC_USES= python OCC_CMAKE_BOOL= WITH_OCC OCC_CMAKE_ON= -DVTK_DIR=${LOCALBASE}/lib/cmake/vtk-9.0 \ -DPython3_EXECUTABLE=${PYTHON_CMD} _LIBSTAGEDIR= ${STAGEDIR}/${PREFIX}/lib/elmersolver _PYVERSION= ${PYTHON_VER}${PYTHON_ABIVER} _QT5_LIBS= buildtools:build core declarative gui network opengl \ printsupport qmake:build script sql svg widgets xml .include <../../math/vtk9/Makefile.version> .include .if ${ARCH} == "amd64" CFLAGS_${ARCH}= -fPIC CXXFLAGS_${ARCH}= -fPIC FCFLAGS+= -fPIC FFLAGS+= -fPIC .endif PDFS= elmerice/Solvers/Documentation/m1qn3.pdf \ elmerice/Solvers/Documentation/poroussolver.pdf \ elmerice/Solvers/Documentation/siasolver.pdf \ elmerice/UserFunctions/Documentation/usf_damage.pdf \ fem/src/modules/contrib/ShellMultiSolver/ShellMutiSolverUserGuide.pdf PORTDOCS= * .if ${GCC_DEFAULT} >= 10 # workaround for Type mismatch between actual argument at (1) and actual argument at (2) (REAL(8)/COMPLEX(8)). # in theory, this should set FCFLAGS, but the port does not conform FFLAGS+= -fallow-argument-mismatch .endif pre-configure: ${RM} ${WRKSRC}/cmake/Modules/CMakeParseArguments.cmake ${RM} -r ${WRKSRC}/elmergrid/src/metis-5.1.0 ${REINPLACE_CMD} -e 's,"metis.*/metis\.h",,' \ ${WRKSRC}/elmergrid/src/egparallel.c pre-configure-DOCS-off: ${REINPLACE_CMD} -e '/doc/s|ADD_SUB|#ADD_SUB|' ${WRKSRC}/fhutiter/CMakeLists.txt pre-configure-OCC-on: ${REINPLACE_CMD} -e "s|\$${VERSION}|`${PKG_QUERY} '%v' opencascade`|" \ "${WRKSRC}/cmake/Modules/FindOCE.cmake" ${REINPLACE_CMD} -e 's|$${INCLUDE}|${LOCALBASE}/include/OpenCASCADE|' \ "${WRKSRC}/cmake/Modules/FindOCE.cmake" post-install: ${LN} -sf ElmerSolver_mpi ${STAGEDIR}${PREFIX}/bin/ElmerSolver ${LN} -sf libelmersolver.so ${_LIBSTAGEDIR}/libelmersolver.so.0 ${LN} -sf libfhuti.so ${_LIBSTAGEDIR}/libfhuti.so.0 ${LN} -sf libmatc.so ${_LIBSTAGEDIR}/libmatc.so.0 ${LN} -sf libmpi_stubs.so ${_LIBSTAGEDIR}/libmpi_stubs.so.0 @${STRIP_CMD} ${STAGEDIR}/${PREFIX}/bin/ElmerGrid post-install-DOCS-on: @${MKDIR} ${STAGEDIR}${DOCSDIR} ${INSTALL_DATA} ${PDFS:C|^|${WRKSRC}/|} ${STAGEDIR}${DOCSDIR} do-test: @cd ${TEST_WRKSRC} && ctest -C ${CMAKE_BUILD_TYPE} ${_MAKE_JOBS} .include diff --git a/science/fleur/Makefile b/science/fleur/Makefile index 062471209bd4..f1979c90b1e5 100644 --- a/science/fleur/Makefile +++ b/science/fleur/Makefile @@ -1,87 +1,87 @@ PORTNAME= fleur DISTVERSION= 7.2 -PORTREVISION= 4 +PORTREVISION= 5 CATEGORIES= science # chemistry MAINTAINER= yuri@FreeBSD.org COMMENT= FLAPW code for atomic computations in quantum chemistry and physics WWW= https://www.flapw.de/master/ LICENSE= MIT LICENSE_FILE= ${WRKSRC}/LICENSE BROKEN_aarch64= Fatal Error: Cannot find an intrinsic module named 'ieee_arithmetic' at (1) LIB_DEPENDS= libfftw3.so:math/fftw3 \ libhdf5.so:science/hdf5 \ liblapack.so:math/lapack \ libopenblas.so:math/openblas TEST_DEPENDS= ${PYTHON_PKGNAMEPREFIX}pytest>0:devel/py-pytest@${PY_FLAVOR} \ USES= cmake:noninja fortran gnome localbase:ldflags python:test tar:tgz USE_GNOME= libxml2 USE_GITLAB= yes GL_SITE= https://iffgit.fz-juelich.de GL_TAGNAME= 447eed3b7ec3de5fcdfbd232cd1eda4caefb51d3 FFLAGS= -I${LOCALBASE}/include LDFLAGS+= -llapack -lopenblas -lxml2 # to fix missing symbols, see https://iffgit.fz-juelich.de/fleur/fleur/-/issues/670 OPTIONS_DEFINE= HDF5 KPLIB MPI SCALAPACK ELPA LIBXC WANNIER OPTIONS_DEFAULT= MPI SCALAPACK ELPA WANNIER # HDF5 KPLIB LIBXC HDF5_CMAKE_BOOL= CLI_FLEUR_USE_HDF5 HDF5_CMAKE_ON= -DHDF5_INCLUDE_DIRS=${LOCALBASE}/include HDF5_LIB_DEPENDS= libhdf5.so:science/hdf5 HDF5_BROKEN= Missing hdf5.mod in hdf5 # hdf5 doesn't include Fortran binding KPLIB_DESC= Use kpLib library #KPLIB_CMAKE_BOOL= CLI_FLEUR_USE_KPLIB KPLIB_DEPENDS= libkplib.so:science/kplib KPLIB_BROKEN= Fails to find the pre-installed libkplib.so library, see https://iffgit.fz-juelich.de/fleur/fleur/-/issues/691 MPI_CMAKE_BOOL= CLI_FLEUR_USE_MPI MPI_LDFLAGS= -lmpich -lmpifort MPI_LIB_DEPENDS= libmpich.so:net/mpich MPI_VARS= SUFFIX=_MPI SCALAPACK_DESC= Use the ScaLAPACK Scalable LAPACK library SCALAPACK_CMAKE_BOOL= FLEUR_USE_SCALAPACK # no such variable, see https://iffgit.fz-juelich.de/fleur/fleur/-/issues/692, it works only through LDFLAGS set below SCALAPACK_VARS= FFLAGS+=-fallow-argument-mismatch SCALAPACK_LDFLAGS= -lscalapack SCALAPACK_LIB_DEPENDS= libscalapack.so:math/scalapack SCALAPACK_IMPLIES= MPI ELPA_DESC= Use libelpa, Eigenvalue SoLver for Petaflop Applications ELPA_CMAKE_BOOL= FLEUR_USE_ELPA # no such variable, see https://iffgit.fz-juelich.de/fleur/fleur/-/issues/689, it works only through FFLAGS set below ELPA_VARS= FFLAGS+=-I${LOCALBASE}/include/elpa-2021.11.001/modules ELPA_LDFLAGS= -lelpa ELPA_LIB_DEPENDS= libelpa.so:math/elpa LIBXC_DESC= Use libxc library LIBXC_CMAKE_BOOL= CLI_FLEUR_USE_LIBXC LIBXC_LIB_DEPENDS= libxc.so:science/libxc LIBXC_BROKEN= Silently links with libxc when CLI_FLEUR_USE_LIBXC=OFF, see https://iffgit.fz-juelich.de/fleur/fleur/-/issues/690 WANNIER_DESC= Use Wannier library WANNIER_CMAKE_BOOL= CLI_FLEUR_USE_WANNIER WANNIER_LIB_DEPENDS= libwannier.so:science/wannier90 EXECUTABLES= bin/fleur${SUFFIX} \ bin/inpgen PLIST_FILES= ${EXECUTABLES} CONFLICTS_BUILD= libxc # see https://iffgit.fz-juelich.de/fleur/fleur/-/issues/690 post-install: # strip @cd ${STAGEDIR}${PREFIX} && ${STRIP_CMD} ${EXECUTABLES} do-test: # now: some tests fail or freeze, possibly because of missing hdf5 and kplib dependencies # was: 9 testcases are known to fail, see https://iffgit.fz-juelich.de/fleur/fleur/-/issues/671 @cd ${WRKSRC}/testing && pytest tests --build_dir=${TEST_WRKSRC} # tests fail to run: INTERNALERROR> pluggy._manager.PluginValidationError: unknown hook 'pytest_html_report_title' in plugin .include diff --git a/science/frontistr/Makefile b/science/frontistr/Makefile index cc8be06a48af..d2185788d578 100644 --- a/science/frontistr/Makefile +++ b/science/frontistr/Makefile @@ -1,56 +1,56 @@ PORTNAME= FrontISTR PORTVERSION= 5.2 -PORTREVISION= 6 +PORTREVISION= 7 DISTVERSIONPREFIX= v CATEGORIES= science cad MAINTAINER= thierry@FreeBSD.org COMMENT= Large-Scale Parallel FEM Program for Nonlinear Structural Analysis WWW= https://gitlab.com/FrontISTR-Commons/FrontISTR LICENSE= MIT LIB_DEPENDS= libmetis.so:math/metis \ libscotch.so:cad/scotch \ libcmumps.so.5:math/mumps \ libscalapack.so:math/scalapack TEST_DEPENDS= bash:shells/bash \ gawk:lang/gawk USE_GITLAB= yes GL_ACCOUNT= ${PORTNAME}-Commons GL_TAGNAME= c66bdc397de319ca59a0565b3f3b1a3b33f0c50c USES= blaslapack:openblas cmake:testing fortran mpi shebangfix SHEBANG_GLOB= *.sh FFLAGS+= -fallow-argument-mismatch ALL_TARGET= all OPTIONS_DEFINE= DOCS EXAMPLES DOCS_USES= python:build DOCS_BUILD_DEPENDS= doxygen:devel/doxygen \ dot:graphics/graphviz \ ${PYTHON_PKGNAMEPREFIX}mkdocs>0:textproc/py-mkdocs@${PY_FLAVOR} DOCS_CMAKE_BOOL= WITH_DOC DOCS_ALL_TARGET= doc PORTDOCS= * PORTEXAMPLES= * pre-configure: ${REINPLACE_CMD} -e 's/awk/gawk/' ${WRKSRC}/tests/test.sh do-install-DOCS-on: ${FIND} ${BUILD_WRKSRC}/doc/html -type d -empty -delete ${MKDIR} ${STAGEDIR}${DOCSDIR} cd ${BUILD_WRKSRC}/doc/html && ${COPYTREE_SHARE} . ${STAGEDIR}${DOCSDIR} do-install-EXAMPLES-on: ${MKDIR} ${STAGEDIR}${EXAMPLESDIR} cd ${WRKSRC}/examples && ${COPYTREE_SHARE} . ${STAGEDIR}${EXAMPLESDIR} do-test: (cd ${TEST_WRKSRC} && ctest) .include diff --git a/science/hypre/Makefile b/science/hypre/Makefile index a439de1d4f3c..631946cb119a 100644 --- a/science/hypre/Makefile +++ b/science/hypre/Makefile @@ -1,74 +1,74 @@ PORTNAME= hypre DISTVERSIONPREFIX= v DISTVERSION= 2.33.0 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org COMMENT= Scalable Linear Solvers and Multigrid Methods WWW= https://computing.llnl.gov/projects/hypre-scalable-linear-solvers-multigrid-methods \ https://github.com/hypre-space/hypre LICENSE= APACHE20 MIT LICENSE_COMB= dual LICENSE_FILE_APACHE20= ${WRKSRC}/../LICENSE-APACHE LICENSE_FILE_MIT= ${WRKSRC}/../LICENSE-MIT .if !exists(/usr/include/omp.h) BROKEN= requires OpenMP support that is missing on this architecture .endif LIB_DEPENDS= libsuperlu.so:math/superlu USES= blaslapack:openblas cmake:testing fortran localbase USE_LDCONFIG= yes USE_GITHUB= yes GH_ACCOUNT= hypre-space WRKSRC_SUBDIR= src CMAKE_ON= BUILD_SHARED_LIBS HYPRE_ENABLE_OPENMP HYPRE_ENABLE_SUPERLU CMAKE_OFF= HYPRE_ENABLE_HYPRE_BLAS HYPRE_ENABLE_HYPRE_LAPACK CMAKE_ARGS= -DTPL_BLAS_LIBRARIES="${_BLASLIB}" \ -DTPL_SUPERLU_LIBRARIES="${LOCALBASE}/lib/libsuperlu.so" \ -DTPL_SUPERLU_INCLUDE_DIRS="${LOCALBASE}/include/superlu" CMAKE_TESTING_ON= HYPRE_BUILD_TESTS # tests are only built and not run, see https://github.com/hypre-space/hypre/issues/502 OPTIONS_DEFINE= DOCS OPTIONS_SINGLE= MPI OPTIONS_SINGLE_MPI= NOMPI MPICH OPENMPI OPTIONS_DEFAULT= MPICH NOMPI_DESC= Build without parallel processing support NOMPI_CMAKE_ON= -DHYPRE_ENABLE_MPI=OFF MPICH_USES= mpi:mpich MPICH_CMAKE_ON= -DHYPRE_ENABLE_MPI=ON OPENMPI_USES= mpi:openmpi OPENMPI_CMAKE_ON= -DHYPRE_ENABLE_MPI=ON OPENMPI_BROKEN= doesn't switch to openmpi in cmake build, see https://github.com/hypre-space/hypre/issues/720 PORTDOCS= * xpost-install: ${MV} ${STAGEDIR}${PREFIX}/lib/libHYPRE.so \ ${STAGEDIR}${PREFIX}/lib/libHYPRE.so.0 ${RLN} ${STAGEDIR}${PREFIX}/lib/libHYPRE.so.0 \ ${STAGEDIR}${PREFIX}/lib/libHYPRE.so post-install-DOCS-on: ${MKDIR} ${STAGEDIR}${DOCSDIR} cd ${WRKSRC}/docs && ${COPYTREE_SHARE} usr-manual ${STAGEDIR}${DOCSDIR} post-test: # run tests; unclear how to to run tests, see https://github.com/hypre-space/hypre/issues/502 .for t in ij ij_assembly ij_mv maxwell_unscaled @cd ${WRKSRC}/test && \ ${ECHO} "==> running test ${t}" && \ ${BUILD_WRKSRC}/test/${t} .endfor # the test ij_mv fails, see https://github.com/hypre-space/hypre/issues/1161 .include diff --git a/science/jdftx/Makefile b/science/jdftx/Makefile index 9fdbdf0b0370..96c88a2564c6 100644 --- a/science/jdftx/Makefile +++ b/science/jdftx/Makefile @@ -1,58 +1,58 @@ PORTNAME= jdftx DISTVERSIONPREFIX= v DISTVERSION= 1.7.0 -PORTREVISION= 7 +PORTREVISION= 8 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org COMMENT= Software for joint density functional theory in chemistry WWW= https://jdftx.org/ LICENSE= GPLv3+ LICENSE_FILE= ${WRKSRC}/COPYING BUILD_DEPENDS= bash:shells/bash LIB_DEPENDS= libblas.so:math/blas \ libcblas.so:math/cblas \ libfftw3.so:math/fftw3 \ libgsl.so:math/gsl \ liblapack.so:math/lapack RUN_DEPENDS= bash:shells/bash TEST_DEPENDS= bash:shells/bash USES= compiler:c++11-lang cmake fortran localbase:ldflags shebangfix SHEBANG_GLOB= *.sh SHEBANG_FILES= scripts/* SHEBANG_LANG= octave USE_GITHUB= yes GH_ACCOUNT= shankar1729 USE_LDCONFIG= yes TEST_TARGET= test WRKSRC_SUBDIR= ${PORTNAME} CMAKE_ARGS= -DLAPACK_LIBRARIES:STRING="-llapack -lblas" OPTIONS_DEFINE= MPI LIBXC HDF5 SCALAPACK OCTAVE OPTIONS_DEFAULT= MPI LIBXC MPI_CMAKE_BOOL= EnableMPI MPI_LIB_DEPENDS= libmpich.so:net/mpich LIBXC_DESC= Use LibXC for additional exchange-correlation functionals LIBXC_CMAKE_BOOL= EnableLibXC LIBXC_LIB_DEPENDS= libxc.so:science/libxc HDF5_CMAKE_BOOL= EnableHDF5 HDF5_LIB_DEPENDS= libhdf5.so:science/hdf5 HDF5_BROKEN= use of undeclared identifier 'H5Pset_dxpl_mpio' # https://github.com/shankar1729/jdftx/issues/37 SCALAPACK_DESC= Enable ScaLAPACK support SCALAPACK_CMAKE_BOOL= EnableScaLAPACK SCALAPACK_LIB_DEPENDS= libscalapack.so:math/scalapack OCTAVE_DESC= With Octave support (only for one script: dryRunToPDB) OCTAVE_RUN_DEPENDS= octave:math/octave .include diff --git a/science/libgridxc/Makefile b/science/libgridxc/Makefile index 0d6de425b923..c7e97295caf4 100644 --- a/science/libgridxc/Makefile +++ b/science/libgridxc/Makefile @@ -1,39 +1,40 @@ PORTNAME= libgridxc DISTVERSION= 2.0.2 +PORTREVISION= 1 CATEGORIES= science MASTER_SITES= https://gitlab.com/siesta-project/libraries/${PORTNAME}/-/archive/${DISTVERSION}/ MAINTAINER= yuri@FreeBSD.org COMMENT= Library to compute the exchange and correlation energy and potentials WWW= https://gitlab.com/siesta-project/libraries/libgridxc LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/COPYING USES= cmake fortran pkgconfig USE_LDCONFIG= yes CMAKE_ON= BUILD_SHARED_LIBS OPTIONS_SINGLE= MPI OPTIONS_SINGLE_MPI= NOMPI MPICH OPENMPI OPTIONS_DEFINE= LIBXC OPTIONS_DEFAULT= LIBXC MPICH OPTIONS_SUB= yes NOMPI_DESC= Build without parallel processing support MPICH_USES= mpi:mpich MPICH_CMAKE_ON= -DWITH_MPI=ON MPICH_VARS= FFLAGS+=-fallow-argument-mismatch OPENMPI_USES= mpi:openmpi OPENMPI_CMAKE_ON= -DWITH_MPI=ON OPENMPI_VARS= FFLAGS+=-fallow-argument-mismatch LIBXC_DESC= Use libxc for exchange-correlation functionals for DFT LIBXC_CMAKE_BOOL= WITH_LIBXC LIBXC_VARS= FCFLAGS+="-I${LOCALBASE}/include" LDFLAGS+="-L${LOCALBASE}/lib -lxcf90" LIBXC_LIB_DEPENDS= libxc.so:science/libxc .include diff --git a/science/libnegf/Makefile b/science/libnegf/Makefile index 0f74f9734203..b95541e1f75a 100644 --- a/science/libnegf/Makefile +++ b/science/libnegf/Makefile @@ -1,37 +1,37 @@ PORTNAME= libnegf DISTVERSIONPREFIX= v DISTVERSION= 1.1.3 -PORTREVISION= 4 +PORTREVISION= 5 CATEGORIES= science # chemistry MAINTAINER= yuri@FreeBSD.org COMMENT= Non Equilibrium Green's Functions library WWW= https://github.com/libnegf/libnegf LICENSE= GPLv3 .if !exists(/usr/include/omp.h) BROKEN= requires OpenMP support that is missing on this architecture .endif LIB_DEPENDS= libmpi.so:net/mpich \ libopenblas.so:math/openblas USES= cmake:testing fortran python:build USE_GITHUB= yes CMAKE_ON= BUILD_SHARED_LIBS BINARY_ALIAS= python=${PYTHON_CMD} python3=${PYTHON_CMD} OPTIONS_DEFINE= INELASTIC MPI OPTIONS_DEFAULT= MPI # MPI default has to be in sync with science/dftbplus INELASTIC_DESC= Build with inelastic scattering INELASTIC_CMAKE_BOOL= WITH_INELASTIC INELASTIC_BROKEN= Error: Can't open included file 'fftw3.f03', see https://github.com/libnegf/libnegf/issues/56 MPI_CMAKE_BOOL= WITH_MPI MPI_LIB_DEPENDS= libmpifx.so:net/mpifx .include diff --git a/science/liggghts/Makefile b/science/liggghts/Makefile index d088170996e3..d27aad15c63c 100644 --- a/science/liggghts/Makefile +++ b/science/liggghts/Makefile @@ -1,46 +1,46 @@ PORTNAME= liggghts DISTVERSION= 3.8.0-58 -PORTREVISION= 7 +PORTREVISION= 8 DISTVERSIONSUFFIX= -g6e28cfe3 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org COMMENT= Discrete element method particle simulation software WWW= https://www.cfdem.com/liggghts-open-source-discrete-element-method-particle-simulation-code LICENSE= GPLv2 LICENSE_FILE= ${WRKSRC}/../LICENSE BUILD_DEPENDS= gsed:textproc/gsed LIB_DEPENDS= libexpat.so:textproc/expat2 \ libfreetype.so:print/freetype2 \ libhdf5_hl.so:science/hdf5 \ libmpi.so:net/mpich \ libnetcdf.so:science/netcdf \ libpng.so:graphics/png \ libtiff.so:graphics/tiff \ libvtkViewsCore-${VTK_VER}.so:math/vtk${VTK_VER:R} USES= compiler:c++17-lang cmake fortran gl jpeg python qt:5 xorg USE_XORG= ice sm x11 xext xt USE_QT= core declarative gui network opengl sql widgets qmake:build buildtools:build USE_GL= gl USE_LDCONFIG= yes USE_GITHUB= yes GH_ACCOUNT= CFDEMproject GH_PROJECT= ${PORTNAME:tu}-PUBLIC CMAKE_ARGS= -DVTK_DIR=${LOCALBASE}/lib/cmake/vtk-${VTK_VER} \ -DPython3_EXECUTABLE=${PYTHON_CMD} WRKSRC_SUBDIR= src CFLAGS+= -fPIC CXXFLAGS+= -fPIC \ -I${LOCALBASE}/include/vtk-${VTK_VER} BINARY_ALIAS= sed=gsed .include <../../math/vtk9/Makefile.version> .include diff --git a/science/madness/Makefile b/science/madness/Makefile index 3fafb1124224..16b551ac2834 100644 --- a/science/madness/Makefile +++ b/science/madness/Makefile @@ -1,35 +1,35 @@ PORTNAME= madness DISTVERSION= 0.10.1.20180823 -PORTREVISION= 17 +PORTREVISION= 18 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org COMMENT= Multiresolution adaptive numeric environment for scientific simulation WWW= https://github.com/m-a-d-n-e-s-s/madness LICENSE= GPLv2 LICENSE_FILE= ${WRKSRC}/LICENSE BUILD_DEPENDS= libsysinfo>0:devel/libsysinfo LIB_DEPENDS= libblas.so:math/blas \ liblapack.so:math/lapack \ libmpich.so:net/mpich \ libtcmalloc.so:devel/google-perftools \ libxc.so:science/libxc USES= cmake compiler:c++14-lang fortran localbase:ldflags python:build USE_GITHUB= yes GH_ACCOUNT= m-a-d-n-e-s-s GH_TAGNAME= ebb3fd7 USE_LDCONFIG= yes CMAKE_ARGS= -DLAPACK_LIBRARIES:STRING="-L${LOCALBASE}/lib -llapack -lblas -L${LOCALBASE}/lib/gcc${GCC_DEFAULT} -lgcc_s" -DPYTHON_EXECUTABLE=${PYTHON_CMD} OPTIONS_DEFINE= TBB #OPTIONS_DEFAULT= TBB # oneTBB support needs to be fixed: https://github.com/m-a-d-n-e-s-s/madness/issues/366 TBB_DESC= Enables use of Intel Thread Building Blocks TBB_CMAKE_BOOL= ENABLE_TBB TBB_LIB_DEPENDS= libtbb.so:devel/tbb .include diff --git a/science/mdynamix/Makefile b/science/mdynamix/Makefile index fe71bb4d552c..9ae97ae8d1a2 100644 --- a/science/mdynamix/Makefile +++ b/science/mdynamix/Makefile @@ -1,37 +1,38 @@ PORTNAME= mdynamix DISTVERSION= 5.3.0 +PORTREVISION= 1 CATEGORIES= science MASTER_SITES= http://www.fos.su.se/~sasha/${PORTNAME}/versions/ DISTNAME= md${DISTVERSION:S/.//g} MAINTAINER= yuri@FreeBSD.org COMMENT= General purpose molecular dynamics code WWW= http://www.fos.su.se/~sasha/mdynamix/ LICENSE= GPLv2+ LIB_DEPENDS= libmpich.so:net/mpich USES= fortran gmake WRKSRC= ${WRKDIR}/mdynamix ALL_TARGET= default mpi MAKE_ARGS= FFLAGS="${FFLAGS} -ffast-math" LDFLAGS="${LDFLAGS}" BINARY_ALIAS= make=gmake gfortran=${FC} PLIST_FILES= bin/md bin/mdp do-install: ${INSTALL_PROGRAM} ${WRKSRC}/md ${STAGEDIR}${PREFIX}/bin ${INSTALL_PROGRAM} ${WRKSRC}/mdp ${STAGEDIR}${PREFIX}/bin .include .if ${FORTRAN_DEFAULT} == gfortran && ${GCC_DEFAULT} >= 10 # workaround for Type mismatch between actual argument at (1) and actual argument at (2) (INTEGER(4)/REAL(4)). # in theory, this should set FCFLAGS, but the port does not conform FFLAGS+= -fallow-argument-mismatch .endif .include diff --git a/science/mpqc/Makefile b/science/mpqc/Makefile index b7b5a293c010..b7e856b43113 100644 --- a/science/mpqc/Makefile +++ b/science/mpqc/Makefile @@ -1,114 +1,114 @@ PORTNAME= mpqc PORTVERSION= 2.3.1 -PORTREVISION= 52 +PORTREVISION= 53 CATEGORIES= science parallel MASTER_SITES= SF MAINTAINER= yuri@FreeBSD.org COMMENT= Massively Parallel Quantum Chemistry Program WWW= https://mpqc.org/ LICENSE= GPLv2 LICENSE_FILE= ${WRKSRC}/COPYING BUILD_DEPENDS= dot:graphics/graphviz LIB_DEPENDS= libint.so:science/libint RUN_DEPENDS= wish:x11-toolkits/tk-wrapper \ dot:graphics/graphviz USES= fortran gmake libtool localbase perl5 shebangfix tar:bzip2 CONFLICTS_BUILD= ga # devel/ga: it links to libarmci.so, has HAVE_ARMCI defined, and hits some bug GNU_CONFIGURE= yes CONFIGURE_ARGS= --enable-production \ --enable-shared \ --with-cc-optflags="${CFLAGS}" \ --with-cxx-optflags="${CXXFLAGS}" \ --with-sc-datadir=${DATADIR} ALL_TARGET= default INSTALL_TARGET= install install_devel DESTDIRNAME= installroot SHEBANG_FILES= src/bin/mpqc/ccarunproc src/bin/mpqc/mpqcrunproc USE_LDCONFIG= yes USE_CXXSTD= c++98 # workaround https://github.com/ValeevGroup/mpqc/issues/57 OPTIONS_DEFINE= ATLAS DOXYGEN EXAMPLES ICC MPI OPTIFLAGS OPTIONS_DEFAULT= DOXYGEN MPI OPTIONS_SUB= yes ICC_DESC= Build with ICC compiler instead ATLAS_DESC= Link with ATLAS instead of BLAS OPTIFLAGS_DESC= Build with optimized flags ATLAS_USES= blaslapack:atlas ATLAS_USES_OFF= blaslapack:netlib DOXYGEN_CONFIGURE_ENABLE= doxygen-man DOXYGEN_BUILD_DEPENDS= doxygen:devel/doxygen \ dot:graphics/graphviz DOXYGEN_USES= tex DOXYGEN_USE= TEX=base,dvipsk,pdftex ICC_BUILD_DEPENDS= ${LOCALBASE}/intel_cc_80/bin/icc:lang/icc MPI_CONFIGURE_ENABLE= parallel MPI_LIB_DEPENDS= libmpich.so:net/mpich MPI_LDFLAGS= -lmpich # build fails to supply libmpich.so to link OPTIFLAGS_CFLAGS= -ffast-math OPTIFLAGS_CXXFLAGS= -ffast-math .include .if ${PORT_OPTIONS:MICC} CC= ${LOCALBASE}/intel_cc_80/bin/icc CXX= ${LOCALBASE}/intel_cc_80/bin/icpc CFLAGS= -O3 -tpp7 -xMKW -Vaxlib CXXFLAGS= -O3 -tpp7 -xMKW -Vaxlib LIBS+= -lsvml .endif post-patch: @${REINPLACE_CMD} \ -e 's/-lblas/${BLASLIB}/' -e 's/-llapack/${LAPACKLIB}/' \ -e 's/pthread_join(0,0)/pthread_create(0,0,0,0)/' \ -e 's|/usr/bin/wish|${LOCALBASE}/bin/wish|' \ ${WRKSRC}/configure @${REINPLACE_CMD} \ 's|#include |#include <${WRKSRC}/src/lib/chemistry/qc/mbptr12/f77sym.h>|' \ ${WRKSRC}/src/lib/chemistry/qc/mbptr12/blas.h \ ${WRKSRC}/src/lib/chemistry/qc/mbptr12/lapack.h post-configure: # workaround: https://github.com/ValeevGroup/mpqc/issues/56 @${REINPLACE_CMD} -e ' \ s|/\* #undef USING_NAMESPACE_STD \*/|#define USING_NAMESPACE_STD 1|; \ s|/\* #undef HAVE_SGETN \*/|#define HAVE_SGETN 1|' \ ${WRKSRC}/src/lib/scconfig.h do-build-DOXYGEN-on: @(cd ${WRKSRC}/doc && ${SETENV} ${MAKE_ENV} ${MAKE_CMD} ${MAKE_ARGS}) ${RM} ${WRKSRC}/doc/man/man1/_* ${WRKSRC}/doc/man/man3/_* do-install-DOXYGEN-on: @(cd ${WRKSRC}/doc && ${SETENV} ${MAKE_ENV} ${MAKE_CMD} ${MAKE_ARGS} \ install install_man) ${MV} ${STAGEDIR}${PREFIX}/html ${STAGEDIR}${DOCSDIR} do-install-EXAMPLES-on: @(cd ${WRKSRC}/doc && ${SETENV} ${MAKE_ENV} ${MAKE_CMD} ${MAKE_ARGS} \ install_samples) ${MV} ${STAGEDIR}${PREFIX}/examples/mp2 ${STAGEDIR}${EXAMPLESDIR} ${RMDIR} ${STAGEDIR}${PREFIX}/examples post-install: (cd ${STAGEDIR}${PREFIX}/bin && ${STRIP_CMD} scpr molrender mpqc scls) ${STRIP_CMD} ${STAGEDIR}${PREFIX}/lib/*.so validate: (cd ${WRKSRC}/src/bin/mpqc/validate && \ ${MAKE_CMD} check0 && \ ${MAKE_CMD} check0_run && \ ${MAKE_CMD} check0_chk) .include diff --git a/science/mrchem/Makefile b/science/mrchem/Makefile index c4e674ba2355..b86dae4b4e17 100644 --- a/science/mrchem/Makefile +++ b/science/mrchem/Makefile @@ -1,58 +1,59 @@ PORTNAME= mrchem DISTVERSIONPREFIX= v DISTVERSION= 1.1.4 +PORTREVISION= 1 CATEGORIES= science # chemistry MAINTAINER= yuri@FreeBSD.org COMMENT= MultiResolution Chemistry WWW= https://github.com/MRChemSoft/mrchem LICENSE= GPLv3 LICENSE_FILE= ${WRKSRC}/LICENSE BUILD_DEPENDS= nlohmann-json>0:devel/nlohmann-json LIB_DEPENDS= libmrcpp.so:science/mrcpp \ libxcfun.so:science/xcfun USES= cmake:testing compiler:c++14-lang eigen:3 shebangfix USE_GITHUB= yes GH_ACCOUNT= MRChemSoft SHEBANG_FILES= python/mrchem.in tests/*/test OPTIONS_DEFINE= ARCH_FLAGS PYTHON # the Python module also exists in the separate port science/py-mrchem, so it should be off by default here OPTIONS_SINGLE= MPI OPTIONS_SINGLE_MPI= NOMPI MPICH OPENMPI OPTIONS_DEFAULT= MPICH OPTIONS_SUB= yes ARCH_FLAGS_DESC= Enable architecture-specific compiler flags ARCH_FLAGS_CMAKE_BOOL= ENABLE_ARCH_FLAGS NOMPI_DESC= Build without parallel processing support MPICH_USES= mpi:mpich MPICH_CMAKE_ON= -DENABLE_MPI=ON OPENMPI_USES= mpi:openmpi OPENMPI_CMAKE_ON= -DENABLE_MPI=ON OPENMPI_BROKEN= fails to compile with OpenMPI, see https://github.com/MRChemSoft/mrchem/issues/438 PYTHON_USES= python PYTHON_CMAKE_BOOL= BUILD_PYTHON PYTHON_CMAKE_ON= -DPython3_EXECUTABLE=${PYTHON_CMD} \ -DPYMOD_INSTALL_LIBDIR=${PYTHON_SITELIBDIR:S;${PREFIX}/lib/;;} post-install-PYTHON-on: @${RMDIR} ${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}/mrchem/input_parser/docs .include .if !${PORT_OPTIONS:MPYTHON} pre-test: @${ECHO} "tests require the port to be built with PYTHON=ON" && false .endif .include diff --git a/science/mrcpp/Makefile b/science/mrcpp/Makefile index 89254107290c..9837cf134504 100644 --- a/science/mrcpp/Makefile +++ b/science/mrcpp/Makefile @@ -1,42 +1,42 @@ PORTNAME= mrcpp DISTVERSIONPREFIX= v DISTVERSION= 1.5.0 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= science # chemistry MAINTAINER= yuri@FreeBSD.org COMMENT= MultiResolution Computation Program Package WWW= https://github.com/MRChemSoft/mrcpp LICENSE= GPLv3 LICENSE_FILE= ${WRKSRC}/LICENSE USES= cmake:testing compiler:c++14-lang eigen:3 USE_LDCONFIG= yes USE_GITHUB= yes GH_ACCOUNT= MRChemSoft GH_TAGNAME= e865a7e CMAKE_OFF= ENABLE_TESTS CMAKE_TESTING_ON= ENABLE_TESTS BINARY_ALIAS= git=false OPTIONS_DEFINE= ARCH_FLAGS OPTIONS_SINGLE= MPI OPTIONS_SINGLE_MPI= NOMPI MPICH OPENMPI OPTIONS_DEFAULT= MPICH # should be same default as in science/mrchem ARCH_FLAGS_DESC= Enable architecture-specific compiler flags ARCH_FLAGS_CMAKE_BOOL= ENABLE_ARCH_FLAGS NOMPI_DESC= Build without parallel processing support MPICH_USES= mpi:mpich MPICH_CMAKE_ON= -DENABLE_MPI=ON OPENMPI_USES= mpi:openmpi OPENMPI_CMAKE_ON= -DENABLE_MPI=ON .include diff --git a/science/nlcglib/Makefile b/science/nlcglib/Makefile index 208a28091b6a..3cd7617b52d5 100644 --- a/science/nlcglib/Makefile +++ b/science/nlcglib/Makefile @@ -1,44 +1,44 @@ PORTNAME= nlcglib DISTVERSIONPREFIX= v DISTVERSION= 1.1.0 -PORTREVISION= 3 +PORTREVISION= 4 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org COMMENT= Nonlinear CG methods for wave-function optimization in DFT WWW= https://github.com/simonpintarelli/nlcglib LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE BUILD_DEPENDS= nlohmann-json>0:devel/nlohmann-json LIB_DEPENDS= libkokkoscore.so:devel/kokkos \ libopenblas.so:math/openblas TEST_DEPENDS= googletest>0:devel/googletest USES= cmake:testing pkgconfig USE_LDCONFIG= yes USE_GITHUB= yes GH_ACCOUNT= simonpintarelli CMAKE_TESTING_ON= BUILD_TESTS # tests fail to compile, see https://github.com/simonpintarelli/nlcglib/issues/19 OPTIONS_DEFINE= OPENMP OPTIONS_SINGLE= MPI OPTIONS_SINGLE_MPI= MPICH OPENMPI OPTIONS_DEFAULT= MPICH .if exists(/usr/include/omp.h) OPTIONS_DEFAULT+= OPENMP .else OPENMP_BROKEN= requires OpenMP support that is missing on this architecture .endif MPICH_USES= mpi:mpich OPENMPI_USES= mpi:openmpi OPENMP_CMAKE_BOOL= USE_OPENMP # binaries are still linked with libomp when USE_OPENMP=OFF, see https://github.com/simonpintarelli/nlcglib/issues/13 .include diff --git a/science/nwchem/Makefile b/science/nwchem/Makefile index ea8db7bb6730..8674625c3f4d 100644 --- a/science/nwchem/Makefile +++ b/science/nwchem/Makefile @@ -1,121 +1,122 @@ PORTNAME= nwchem #DISTVERSIONPREFIX= v DISTVERSION= 7.3.1 +PORTREVISION= 1 DISTVERSIONSUFFIX= -release.revision-23c3b41b-src.2025-11-06 CATEGORIES= science MASTER_SITES= https://github.com/nwchemgit/nwchem/releases/download/v${DISTVERSION}-release/ \ https://www.chemie.uni-bonn.de/grimme/de/software/dft-d3/:dft3 \ https://gitlab.com/libxc/libxc/-/archive/${LIBXC_VERSION}/:libxc DISTFILES= ${PORTNAME}-${DISTVERSION}${DISTVERSIONSUFFIX}${EXTRACT_SUFX} \ dftd3.tgz:dft3 \ libxc-${LIBXC_VERSION}.tar.gz:libxc DIST_SUBDIR= ${PORTNAME}-${PORTVERSION} EXTRACT_ONLY= ${DISTNAME}.tar.gz MAINTAINER= yuri@FreeBSD.org COMMENT= High-performance computational chemistry software WWW= https://nwchemgit.github.io/ \ https://github.com/nwchemgit/nwchem LICENSE= ECL20 LICENSE_NAME= Educational Community License (ECL) 2.0 LICENSE_FILE= ${WRKSRC}/../LICENSE.TXT LICENSE_PERMS= dist-mirror dist-sell pkg-mirror pkg-sell auto-accept BROKEN_aarch64= fails to build: gfortran10: error: unrecognized command-line option '-m64' BUILD_DEPENDS= bash:shells/bash LIB_DEPENDS= libblas.so:math/blas \ libga.so:devel/ga \ libhwloc.so:devel/hwloc2 \ libscalapack.so:math/scalapack RUN_DEPENDS= nwchem-data>0:science/nwchem-data TEST_DEPENDS= bash:shells/bash USES= cmake:indirect fortran gettext-runtime gmake perl5 pkgconfig USE_PERL5= build #USE_GITHUB= yes #GH_ACCOUNT= nwchemgit WRKSRC= ${WRKDIR}/${PORTNAME}-${DISTVERSION} MAKEFILE= GNUmakefile ARCH_64BIT= ${ARCH:C/.*64.*/64/:S/${ARCH}//} MAKE_ARGS= NWCHEM_TOP=${WRKSRC}/.. NWCHEM_MODULES=all NWCHEM_LONG_PATHS=Y NWCHEM_TARGET=LINUX${ARCH_64BIT} USE_INTERNALBLAS=Y EXTERNAL_GA_PATH=${LOCALBASE} \ USE_64TO32=y SUB_FILES= nwchemrc WRKSRC_SUBDIR= src BINARY_ALIAS= gcc=${CC} gfortran=gfortran${GCC_DEFAULT} BINARY_ALIAS+= make=${GMAKE} # only for LIBXC PLIST_FILES= bin/nwchem etc/nwchemrc LIBXC_VERSION= 7.0.0 # from src/libext/libxc/build_libxc.sh MAKE_ENV+= SCALAPACK_LIB=${PREFIX}/lib/libscalapack.so \ SCALAPACK_SIZE=8 OPTIONS_DEFINE= LIBXC PYTHON # more potential optional dependencies are listed in src/libext/GNUmakefile OPTIONS_DEFAULT= LIBXC PYTHON BLAS_SIZE_4 MPICH # the MPI default should be the same as for the MPI option in math/scalapack and devel/ga OPTIONS_RADIO= BLAS_SIZE MPI OPTIONS_RADIO_BLAS_SIZE= BLAS_SIZE_4 BLAS_SIZE_8 # should be the same choice as in devel/ga and math/blas or math/openblasblas OPTIONS_RADIO_MPI= NOMPI MPICH OPENMPI BLAS_SIZE_DESC= BLAS_SIZE value to use during build (should be same as in devel/ga) BLAS_SIZE_4_DESC= BLAS_SIZE=4 BLAS_SIZE_4_MAKE_ARGS= BLAS_SIZE=4 BLAS_SIZE_8_BROKEN= SEGVs on many examples, possibly due to the need to compile blas or openblas with the 8-byte-integers option BLAS_SIZE_8_DESC= BLAS_SIZE=8 BLAS_SIZE_8_MAKE_ARGS= BLAS_SIZE=8 NOMPI_DESC= MPI isn't used NOMPI_BROKEN= Fails to build without MPI MPICH_MAKE_ENV= USE_MPI=Y MPICH_LIB_DEPENDS= libmpich.so:net/mpich OPENMPI_MAKE_ENV= USE_MPI=Y PATH=${LOCALBASE}/mpi/openmpi/bin:$${PATH} # mpif90 in path determines which MPI library to use, see https://www.nwchem-sw.org/index-php/Compiling_NWChem.html#MPI_variables OPENMPI_BUILD_DEPENDS= openmpi>0:net/openmpi OPENMPI_RUN_DEPENDS= openmpi>0:net/openmpi OPENMPI_VARS= CONFLICTS_BUILD=mpich LIBXC_DESC= Use libxc LIBXC_USES= cmake:indirect LIBXC_MAKE_ENV= USE_LIBXC=Y PYTHON_DESC= Enable Python syntax in input files PYTHON_USES= python PYTHON_MAKE_ENV= PYTHONVERSION=${PYTHON_VER} NWCHEM_MODULES="all python" post-extract: @${RM} ${WRKSRC}/atomscf/src.orig # symlink the downloaded dftd3.tgz @${LN} -s ${DISTDIR}/${DIST_SUBDIR}/dftd3.tgz ${WRKSRC}/nwpw/nwpwlib/nwpwxc/ post-extract-LIBXC-on: # symlink the downloaded libxc @${LN} -s ${DISTDIR}/${DIST_SUBDIR}/libxc-${LIBXC_VERSION}.tar.gz ${WRKSRC}/libext/libxc/ post-patch: @${REINPLACE_CMD} 's|nwchrc="/etc/nwchemrc"|nwchrc="${PREFIX}/etc/nwchemrc"|' ${WRKSRC}/util/util_nwchemrc.F pre-build: @cd ${WRKSRC} && \ ${SETENV} ${MAKE_ENV} ${MAKE_CMD} nwchem_config #pre-build-BLAS_SIZE_4-on: # this is already done in the tarball, but not in the repository # @cd ${WRKSRC} && \ # ${SETENV} ${MAKE_ENV} ${MAKE_CMD} 64_to_32 do-install: ${INSTALL_DATA} ${WRKDIR}/nwchemrc ${STAGEDIR}${PREFIX}/etc/nwchemrc ${INSTALL_PROGRAM} ${WRKSRC}/../bin/LINUX${ARCH_64BIT}/${PORTNAME} ${STAGEDIR}${PREFIX}/bin/${PORTNAME} do-test: @cd ${WRKSRC}/../QA && NWCHEM_TOP=${WRKSRC}/.. NWCHEM_TARGET=LINUX64 ./doqmtests.mpi .include diff --git a/science/openmx/Makefile b/science/openmx/Makefile index 4b1ef46ed92f..917e0e04a118 100644 --- a/science/openmx/Makefile +++ b/science/openmx/Makefile @@ -1,83 +1,83 @@ PORTNAME= openmx DISTVERSION= 3.9.9 # the 18June12 patch upgrades 3.9 -> 3.9.9 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= science MASTER_SITES= https://www.openmx-square.org/ \ https://www.openmx-square.org/bugfixed/21Oct17/:patch DISTFILES= ${PORTNAME}${DISTVERSION:R}${EXTRACT_SUFX} \ patch${DISTVERSION}${EXTRACT_SUFX}:patch # this patch isn't a patch, but a set of file updates DIST_SUBDIR= ${PORTNAME} EXTRACT_ONLY= ${PORTNAME}${DISTVERSION:R}${EXTRACT_SUFX} MAINTAINER= yuri@FreeBSD.org COMMENT= Nanoscale material simulations using density functional theories (DFT) WWW= https://www.openmx-square.org/ LICENSE= GPLv2 .if !exists(/usr/include/omp.h) BROKEN= requires OpenMP support that is missing on this architecture .endif BROKEN_i386= undefined reference to `__atomic_load', see bug#229605 and https://reviews.llvm.org/D42154 LIB_DEPENDS= libblas.so:math/blas \ libcblas.so:math/cblas \ libfftw3.so:math/fftw3 \ liblapack.so:math/lapack \ libmpich.so:net/mpich \ libscalapack.so:math/scalapack USES= dos2unix fortran gmake localbase:ldflags USE_CXXSTD= c++11 DOS2UNIX_FILES= openmx_common.h MAKEFILE= makefile WRKSRC= ${WRKDIR}/${PORTNAME}${DISTVERSION:R} CFLAGS+= -Dkcomp -fcommon LDFLAGS+= -lmpifort FFLAGS+= -fallow-argument-mismatch WRKSRC_SUBDIR= source MAKE_ENV= MPICH_CC=${CC} BINARY_ALIAS= gcc=${CXX} UTIL_PROGS= DosMain jx analysis_example esp polB bandgnu13 bin2txt cube2xsf intensity_map md2axsf PLIST_FILES= bin/${PORTNAME} ${UTIL_PROGS:C/^/bin\//} OPTIONS_DEFINE_amd64= SIMD OPTIONS_DEFINE_i386= SIMD OPTIONS_DEFAULT_amd64= SIMD OPTIONS_DEFAULT_i386= SIMD SIMD_CFLAGS= -msse -msse2 -mfpmath=sse SIMD_CFLAGS_OFF= -Dnosse CFLAGS+= ${ARCH:S/amd64//:S/i386//:S/${ARCH}/-Dnosse/} MAKE_JOBS_UNSAFE= yes pre-patch: # overlay files before patching @cd ${WRKSRC} && \ ${TAR} xzf ${DISTDIR}/${DIST_SUBDIR}/patch${DISTVERSION}${EXTRACT_SUFX} post-patch: @cd ${WRKSRC} && \ ${ECHO} "const char DFT_DATA_PATH[YOUSO10] = \"${DATADIR}/DFT_DATA19\";" >> ${WRKSRC}/Input_std.c do-install: ${INSTALL_PROGRAM} ${WRKSRC}/${PORTNAME} ${STAGEDIR}${PREFIX}/bin .for u in ${UTIL_PROGS} ${INSTALL_PROGRAM} ${WRKSRC}/${u} ${STAGEDIR}${PREFIX}/bin .endfor cd ${WRKSRC}/.. && ${COPYTREE_SHARE} DFT_DATA19 ${STAGEDIR}${DATADIR} # autoplist for potentials: about 500 files in DATADIR @cd ${STAGEDIR}${PREFIX} && \ ${FIND} ${DATADIR:S/^${PREFIX}\///} -type f >> ${TMPPLIST} .include diff --git a/science/parthenon/Makefile b/science/parthenon/Makefile index b09ecf9ad2ee..b080a999c667 100644 --- a/science/parthenon/Makefile +++ b/science/parthenon/Makefile @@ -1,54 +1,54 @@ PORTNAME= parthenon DISTVERSIONPREFIX= v DISTVERSION= 24.08 -PORTREVISION= 3 +PORTREVISION= 4 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org COMMENT= Portable block-structured Adaptive Mesh Refinement (AMR) framework WWW= https://parthenon-hpc-lab.github.io/parthenon/develop/index.html LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE BROKEN_armv7= compilation fails, see https://github.com/parthenon-hpc-lab/parthenon/issues/1226 BROKEN_i386= compilation fails, see https://github.com/parthenon-hpc-lab/parthenon/issues/1226 RUN_DEPENDS= bash:shells/bash LIB_DEPENDS= libkokkoscore.so:devel/kokkos USES= cmake:testing compiler:c++17-lang mpi:mpich python:test USE_GITHUB= yes GH_ACCOUNT= parthenon-hpc-lab GH_TUPLE= catchorg:Catch2:216713a:catch2/external/Catch2 CMAKE_ON= BUILD_SHARED_LIBS \ PARTHENON_IMPORT_KOKKOS \ PARTHENON_DISABLE_EXAMPLES CMAKE_OFF= PARTHENON_ENABLE_TESTING CMAKE_TESTING_ON= PARTHENON_ENABLE_TESTING \ PARTHENON_ENABLE_UNIT_TESTS \ PARTHENON_ENABLE_INTEGRATION_TESTS \ PARTHENON_ENABLE_REGRESSION_TESTS LDFLAGS+= -lexecinfo TEST_ENV= ${MAKE_ENV} PYTHONPATH=${WRKSRC}/scripts/python/packages/parthenon_tools/parthenon_tools OPTIONS_DEFINE= ASCENT HDF5 OPTIONS_DEFAULT= ASCENT ASCENT_DESC= Enable Ascent for in situ visualization and analysis ASCENT_CMAKE_BOOL= PARTHENON_ENABLE_ASCENT ASCENT_LIB_DEPENDS= libascent_mpi.so:science/ascent \ libconduit.so:science/conduit \ libhdf5.so:science/hdf5 \ libsiloh5.so:science/silo HDF5_CMAKE_OFF= -DPARTHENON_DISABLE_HDF5=ON HDF5_BROKEN= configure fails: Both MPI and HDF5 are enabled but only a serial version of HDF5 was found. # few tests don't find some test files .include diff --git a/science/pnetcdf/Makefile b/science/pnetcdf/Makefile index 8f20c0b5240c..a9c8a9fa816d 100644 --- a/science/pnetcdf/Makefile +++ b/science/pnetcdf/Makefile @@ -1,43 +1,44 @@ PORTNAME= pnetcdf PORTVERSION= 1.14.1 +PORTREVISION= 1 CATEGORIES= science parallel MASTER_SITES= https://parallel-netcdf.github.io/Release/ \ LOCAL/sunpoet MAINTAINER= sunpoet@FreeBSD.org COMMENT= Library providing high-performance I/O WWW= https://parallel-netcdf.github.io/ \ https://github.com/Parallel-NetCDF/PnetCDF LICENSE= NetCDF LICENSE_NAME= NetCDF License LICENSE_FILE= ${WRKSRC}/COPYRIGHT LICENSE_PERMS= auto-accept dist-mirror dist-sell pkg-mirror pkg-sell USES= fortran gmake libtool mpi:${FLAVOR} perl5 USE_PERL5= build CFLAGS+= -fPIC CONFIGURE_ARGS= --with-mpi=${MPI_HOME} ac_cv_fc_compiler_nag=no # Workaround for GCC 10+ for Type mismatch between actual argument at (1) and actual argument at (2) (INTEGER(8)/CHARACTER(*)). FCFLAGS+= -fallow-argument-mismatch GNU_CONFIGURE= yes INSTALL_TARGET= install-strip MAKE_JOBS_UNSAFE= yes USE_LDCONFIG= yes CONFLICTS_INSTALL= hdf-4.* pnetcdf-mpich pnetcdf-openmpi FLAVORS= mpich openmpi FLAVOR?= ${FLAVORS:[1]} mpich_PKGNAMESUFFIX= -mpich openmpi_PKGNAMESUFFIX= -openmpi .if ${FLAVOR} == openmpi # See https://github.com/open-mpi/ompi/issues/3195 for details. BROKEN_armv6= PnetCDF requires MPI_Offset >= 8 but Open MPI sets MPI_Offset to 4 on 32-bit architecture regardless of LFS BROKEN_armv7= PnetCDF requires MPI_Offset >= 8 but Open MPI sets MPI_Offset to 4 on 32-bit architecture regardless of LFS BROKEN_i386= PnetCDF requires MPI_Offset >= 8 but Open MPI sets MPI_Offset to 4 on 32-bit architecture regardless of LFS BROKEN_powerpc= PnetCDF requires MPI_Offset >= 8 but Open MPI sets MPI_Offset to 4 on 32-bit architecture regardless of LFS .endif .include diff --git a/science/py-asap3/Makefile b/science/py-asap3/Makefile index 421b77a892db..baeba537fdf7 100644 --- a/science/py-asap3/Makefile +++ b/science/py-asap3/Makefile @@ -1,26 +1,26 @@ PORTNAME= asap3 DISTVERSION= 3.12.8 -PORTREVISION= 4 +PORTREVISION= 5 CATEGORIES= science python # chemistry MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= yuri@FreeBSD.org COMMENT= Classical potentials for MD with ASE WWW= https://wiki.fysik.dtu.dk/asap LICENSE= GPLv3 LICENSE_FILE= ${WRKSRC}/LICENSE BUILD_DEPENDS= ${PYNUMPY} LIB_DEPENDS= libmpich.so:net/mpich # not sure if this is used RUN_DEPENDS= ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}ase>0:science/py-ase@${PY_FLAVOR} USES= localbase python USE_PYTHON= distutils concurrent autoplist pytest post-install: @${STRIP_CMD} ${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}/_asap.cpython-${PYTHON_SUFFIX}.so .include diff --git a/science/py-gpaw/Makefile b/science/py-gpaw/Makefile index d849a0d2021b..486020a01409 100644 --- a/science/py-gpaw/Makefile +++ b/science/py-gpaw/Makefile @@ -1,43 +1,43 @@ PORTNAME= gpaw DISTVERSION= 24.6.0 -PORTREVISION= 4 +PORTREVISION= 5 CATEGORIES= science python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= yuri@FreeBSD.org COMMENT= DFT and beyond within the projector-augmented wave method in chemistry WWW= https://wiki.fysik.dtu.dk/gpaw/ \ https://gitlab.com/gpaw/gpaw LICENSE= GPLv3+ LICENSE_FILE= ${WRKSRC}/LICENSE BUILD_DEPENDS= ${PYNUMPY} LIB_DEPENDS= libblas.so:math/blas \ libmpich.so:net/mpich \ libopenblas.so:math/openblas \ libxc.so:science/libxc RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}ase>0:science/py-ase@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}matplotlib>0:math/py-matplotlib@${PY_FLAVOR} \ ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}scipy>0:science/py-scipy@${PY_FLAVOR} \ gpaw-setups>0:science/gpaw-setups USES= gettext-runtime localbase python shebangfix USE_PYTHON= distutils concurrent autoplist SHEBANG_FILES= tools/* LDFLAGS= -lmpi # otherwise: ImportError: /usr/local/lib/python3.8/site-packages/_gpaw.cpython-38.so: Undefined symbol "MPI_Comm_rank" post-install: @${STRIP_CMD} ${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}/_gpaw*.so do-test: install # tests fail to run, see https://gitlab.com/gpaw/gpaw/-/issues/1273 @${ECHO} "== Performing a test calculation on one CPU ==" @gpaw test @${ECHO} "== Performing a test calculation on 8 CPUs ==" @gpaw -P 8 test .include diff --git a/science/py-hoomd-blue/Makefile b/science/py-hoomd-blue/Makefile index 5fb3d5f92d35..782792d9e514 100644 --- a/science/py-hoomd-blue/Makefile +++ b/science/py-hoomd-blue/Makefile @@ -1,74 +1,75 @@ PORTNAME= hoomd-blue DISTVERSIONPREFIX= v DISTVERSION= 6.0.0 +PORTREVISION= 1 CATEGORIES= science # physics PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= yuri@FreeBSD.org COMMENT= Molecular dynamics and Monte Carlo soft matter simulation WWW= https://glotzerlab.engin.umich.edu/hoomd-blue/ \ https://github.com/glotzerlab/hoomd-blue LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE BUILD_DEPENDS= pybind11>0:devel/pybind11 USES= cmake:testing compiler:c++17-lang eigen:3 localbase:ldflags python shebangfix # see https://github.com/glotzerlab/hoomd-blue/issues/1204 USE_GITHUB= yes GH_ACCOUNT= glotzerlab GH_TUPLE= glotzerlab:upp11:0c1fb8dfb4bcdc1c5c4eff9165539b15e70c4360:glotzerlab_upp11/hoomd/extern/upp11 \ glotzerlab:nano-signal-slot:8d13689:glotzerlab_nano_signal_slot/hoomd/extern/nano-signal-slot \ glotzerlab:quickhull:1ffbc6f884ea1da89e104a5996cf8a726db673d5:glotzerlab_quickhull/hoomd/extern/quickhull \ glotzerlab:HIP:db753e4:glotzerlab_HIP/hoomd/extern/HIP \ glotzerlab:hipCUB:64d8adf:glotzerlab_hipCUB/hoomd/extern/hipCUB \ mphowardlab:neighbor:ba0f06869b766066a7068852fa3b8c5fa746f71f:mphowardlab_neighbor/hoomd/extern/neighbor \ mphowardlab:hipper:076059b:mphowardlab_hipper/hoomd/extern/hipper \ glotzerlab:hoomd-examples:94a5b52d159bc7c07e2650e31b429cef55384542:glotzerlab_hoomd_examples/sphinx-doc/tutorial \ glotzerlab:OpenRAND:92dc12a:glotzerlab_OpenRAND/hoomd/extern/OpenRAND \ mphowardlab:hipper:b6da049a516ada03e4e1b66ca6b4c2c7c9668595:mphowardlab_hipper/hoomd/extern/hipper SHEBANG_GLOB= *.sh CMAKE_OFF= BUILD_TESTING LDFLAGS+= -lexecinfo OPTIONS_DEFINE= TBB OPTIONS_SINGLE= MPI OPTIONS_SINGLE_MPI= NOMPI MPICH OPENMPI OPTIONS_DEFAULT= MPICH TBB OPTIONS_SUB= yes NOMPI_DESC= Build without parallel processing support NOMPI_CMAKE_ON= -DENABLE_MPI=OFF MPICH_USES= mpi:mpich MPICH_CMAKE_ON= -DENABLE_MPI=ON MPICH_BUILD_DEPENDS= cereal>0:devel/cereal OPENMPI_USES= mpi:openmpi OPENMPI_CMAKE_ON= -DENABLE_MPI=ON OPENMPI_BUILD_DEPENDS= cereal>0:devel/cereal OPENMPI_BROKEN= see https://github.com/glotzerlab/hoomd-blue/issues/1397 TBB_DESC= Enable support for Threading Building Blocks (TBB) TBB_CMAKE_BOOL= ENABLE_TBB TBB_LIB_DEPENDS= libtbb.so:devel/onetbb # tests as of 6.0.0: 97% tests passed, 2 tests failed out of 67 # The following tests FAILED: # 18 - mpi-test_load_balancer (Failed) # 35 - mpi-test_communication (Failed) .include post-patch: .if ${COMPILER_TYPE} == clang @${REINPLACE_CMD} -e 's|std::unary_function|std::__unary_function|' \ ${WRKSRC}/hoomd/ParticleData.cc .endif .include diff --git a/science/py-pnetcdf/Makefile b/science/py-pnetcdf/Makefile index 6162f6f155ef..400a993c5118 100644 --- a/science/py-pnetcdf/Makefile +++ b/science/py-pnetcdf/Makefile @@ -1,31 +1,31 @@ PORTNAME= pnetcdf PORTVERSION= 1.0.0 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= science python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= sunpoet@FreeBSD.org COMMENT= Object-oriented python interface to the PnetCDF library WWW= https://github.com/Parallel-NetCDF/PnetCDF-Python LICENSE= MIT BUILD_DEPENDS= ${PYTHON_PKGNAMEPREFIX}mpi4py-mpich>=3.1.4:net/py-mpi4py-mpich@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}numpy>=0,1:math/py-numpy@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}packaging>=23.1:devel/py-packaging@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}setuptools>=61:devel/py-setuptools@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}wheel>=0:devel/py-wheel@${PY_FLAVOR} LIB_DEPENDS= libpnetcdf.so:science/pnetcdf@mpich RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}mpi4py-mpich>=3.1.4:net/py-mpi4py-mpich@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}numpy>=0,1:math/py-numpy@${PY_FLAVOR} USES= localbase mpi:mpich python USE_PYTHON= autoplist concurrent cython cython_run pep517 CFLAGS+= -I${MPI_HOME}/include post-install: ${FIND} ${STAGEDIR}${PYTHON_SITELIBDIR} -name '*.so' -exec ${STRIP_CMD} {} + .include diff --git a/science/qbox/Makefile b/science/qbox/Makefile index 6c76aa7980fe..7e134bc0aa22 100644 --- a/science/qbox/Makefile +++ b/science/qbox/Makefile @@ -1,47 +1,47 @@ PORTNAME= qbox DISTVERSIONPREFIX= rel DISTVERSION= 1_78_4 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org COMMENT= First-principles molecular dynamics code WWW= http://qboxcode.org/ LICENSE= GPLv2+ LICENSE_FILE= ${WRKSRC}/../COPYING LIB_DEPENDS= libblas.so:math/blas \ libcurl.so:ftp/curl \ libfftw3.so:math/fftw3 \ liblapack.so:math/lapack \ libmpicxx.so:net/mpich \ libscalapack.so:math/scalapack \ libuuid.so:misc/libuuid \ libxerces-c.so:textproc/xerces-c3 USES= compiler:c++11-lang gmake iconv:wchar_t localbase:ldflags USE_GITHUB= yes GH_ACCOUNT= qboxcode GH_PROJECT= qbox-public WRKSRC_SUBDIR= src MAKE_ARGS= TARGET=freebsd ALL_TARGET= qb TEST_TARGET= tests TESTING_UNSAFE= only builds tests, but doesn't run them: https://github.com/qboxcode/qbox-public/issues/6, tests fail to link, see https://github.com/qboxcode/qbox-public/issues/11 PLIST_FILES= bin/qb post-extract: @${SED} -e 's|%%LOCALBASE%%|${LOCALBASE}|; s|%%CXXFLAGS%%|${CXXFLAGS}|; s|%%LDFLAGS%%|${LDFLAGS}|' < ${FILESDIR}/freebsd.mk.in > ${WRKSRC}/freebsd.mk do-install: ${INSTALL_PROGRAM} ${WRKSRC}/qb ${STAGEDIR}${PREFIX}/bin # tests fail to compile, see https://github.com/qboxcode/qbox-public/issues/12 .include diff --git a/science/qmcpack/Makefile b/science/qmcpack/Makefile index 7bec4719c90a..3c5daa89e496 100644 --- a/science/qmcpack/Makefile +++ b/science/qmcpack/Makefile @@ -1,67 +1,68 @@ PORTNAME= qmcpack DISTVERSIONPREFIX= v DISTVERSION= 4.1.0 +PORTREVISION= 1 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org COMMENT= Many-body ab initio Quantum Monte Carlo code for quantum chemistry WWW= https://www.qmcpack.org/ \ https://github.com/QMCPACK/qmcpack LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE BROKEN_i386= undefined reference to `__atomic_load' .if !exists(/usr/include/omp.h) BROKEN= requires OpenMP support that is missing on this architecture .endif LIB_DEPENDS= libboost_thread.so:devel/boost-libs \ libfftw3.so:math/fftw3 \ libhdf5.so:science/hdf5 \ libmpich.so:net/mpich \ libopenblas.so:math/openblas \ libsz.so:science/libaec TEST_DEPENDS= bash:shells/bash USES= cmake:testing compiler:c++17-lang fortran gnome localbase:ldflags pkgconfig python shebangfix USE_GNOME= libxml2 USE_GITHUB= yes GH_ACCOUNT= ${PORTNAME:tu} SHEBANG_FILES= src/QMCTools/gpaw4qmcpack.py \ ${NEXUS_PLIST_FILES:C/^/nexus\//} SHEBANG_GLOB= check.sh CMAKE_OFF= BUILD_UNIT_TESTS CMAKE_ARGS= -DFREEBSD_PYTHON_VER=${PYTHON_VER} CMAKE_TESTING_ON= BUILD_UNIT_TESTS # many tests fail, see https://github.com/QMCPACK/qmcpack/issues/4274 PROGS= convert4qmc convertpw4qmc gpaw4qmcpack.py ppconvert qmc-check-affinity qmc-extract-eshdf-kvectors qmc-get-supercell qmcfinitesize qmcpack qmcpack.settings PLIST_FILES= ${PROGS:C/^/bin\//} BINARY_ALIAS= python=${PYTHON_CMD} python3=${PYTHON_CMD} OPTIONS_DEFINE= NEXUS OPTIONS_DEFAULT= NEXUS OPTIONS_SUB= yes NEXUS_DESC= Install Nexus (workflow utility) alongside QMCPACK NEXUS_CMAKE_BOOL= INSTALL_NEXUS NEXUS_PY_DEPENDS= ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}h5py>0:science/py-h5py@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pandas>0:math/py-pandas@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pyscf>0:science/py-pyscf@${PY_FLAVOR} NEXUS_BUILD_DEPENDS= ${NEXUS_PY_DEPENDS} NEXUS_RUN_DEPENDS= ${NEXUS_PY_DEPENDS} NEXUS_PLIST_FILES= bin/eshdf \ bin/nxs-redo \ bin/nxs-sim \ bin/nxs-test \ bin/qdens \ bin/qdens-radial \ bin/qmc-fit \ bin/qmca .include diff --git a/science/quantum-espresso/Makefile b/science/quantum-espresso/Makefile index 90d7bb73b6ca..904c63734a37 100644 --- a/science/quantum-espresso/Makefile +++ b/science/quantum-espresso/Makefile @@ -1,98 +1,99 @@ PORTNAME= quantum-espresso DISTVERSIONPREFIX= qe- DISTVERSION= 7.5 +PORTREVISION= 1 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org COMMENT= Package for research in electronic structure, simulation, optimization WWW= https://www.quantum-espresso.org \ https://gitlab.com/QEF/q-e \ https://github.com/QEF/q-e LICENSE= GPLv2 LICENSE_FILE= ${WRKSRC}/License ONLY_FOR_ARCHS= amd64 i386 ONLY_FOR_ARCHS_REASON= requires the intrinsic module 'ieee_arithmetic' which is not available on other architectures #BROKEN_aarch64= compilation fails: cannot find an intrinsic module named 'ieee_arithmetic', see https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=278942 #BROKEN_armv6= fails to build: gfortran8: error: iotk_base_tmp.f90: No such file or directory #BROKEN_armv7= fails to build: gfortran8: error: iotk_base_tmp.f90: No such file or directory #BUILD_DEPENDS= fox-xml>0:textproc/fox-xml \ bash:shells/bash LIB_DEPENDS= libblas.so:math/blas \ libfftw3.so:math/fftw3 \ liblapack.so:math/lapack \ libopenblas.so:math/openblas USES= cmake fortran localbase:ldflags python shebangfix GNU_CONFIGURE= yes USE_GITHUB= yes GH_ACCOUNT= QEF GH_PROJECT= q-e GH_TUPLE= anharmonic:d3q:6e5f978:anharmonic_d3q/external/d3q \ pietrodelugas:fox:3453648e6837658b747b895bb7bef4b1ed2eac40:pietrodelugas_fox/external/fox \ Reference-LAPACK:lapack:12d825396fcef1e0a1b27be9f119f9e554621e55:Reference_LAPACK_lapack/external/lapack \ libmbd:libmbd:89a3cc1:libmbd_libmbd/external/mbd \ QMCPACK:pw2qmcpack:f72ab25fa4ea755c1b4b230ae8074b47d5509c70:QMCPACK_pw2qmcpack/external/pw2qmcpack \ dceresoli:qe-gipaw:490046d:dceresoli_qe_gipaw/external/qe-gipaw \ wannier-developers:wannier90:1d6b187374a2d50b509e5e79e2cab01a79ff7ce1:wannier_developers_wannier90/external/wannier90 USE_GITLAB= nodefault GL_TUPLE= max-centre/components:devicexlib:a6b89ef:devxlib/external/devxlib SHEBANG_FILES= configure SHEBANG_GLOB= *.sh *.py #MAKE_ARGS= TOPDIR=${WRKSRC} #BINARY_ALIAS= make=gmake cpp=/usr/local/bin/cpp${GCC_DEFAULT} FFLAGS+= ${MPI_CFLAGS} LDFLAGS+= ${LOCALBASE}/lib/gcc${GCC_DEFAULT}/libgfortran.so -lm \ ${MPI_LIBS} BINARY_ALIAS= git=false wget=false curl=false OPTIONS_SINGLE= MPI OPTIONS_SINGLE_MPI= MPICH OPENMPI OPTIONS_DEFAULT= OPENMPI MPICH_USES= mpi:mpich OPENMPI_USES= mpi:mpich # SEGV with openmpi4 .include . if ${GCC_DEFAULT} >= 10 FFLAGS+= -fallow-argument-mismatch # workaround for https://github.com/QEF/q-e/issues/34 . endif post-extract: @${RM} \ ${WRKSRC}/archive/lapack-3.6.1.tgz \ ${WRKSRC}/PP/src/bgw2pw.f90.orig @cd ${WRKSRC} && ${MKDIR} FoX && ${LN} -s ${LOCALBASE}/include FoX/finclude post-install: # remove wannier90 binaries that come from the bundled wannier90 package (reported to the upstream vie e-mail on 2024-03-11) .for p in wannier90.x postw90.x w90chk2chk.x ${RM} ${STAGEDIR}${PREFIX}/bin/${p} .endfor # strip binaries @${STRIP_CMD} ${STAGEDIR}${PREFIX}/bin/*.x do-test: @cd ${WRKSRC}/test-suite && \ ${GMAKE} ESPRESSO_BUILD=${BUILD_WRKSRC} ESPRESSO_PSEUDO=${WRKSRC}/pseudo run-tests run-examples: build .for c in PP PW PWCOND PHonon @cd ${WRKSRC}/$c/examples && PREFIX=${STAGEDIR}${PREFIX} PSEUDO_DIR=/usr/local/share/quantum-espresso ./run_all_examples .endfor # tests as of QE 7.5: 243 out of 247 tests passed (5 skipped, 4 unknown) # many pseudopotentials that can be used with QE are listed in https://pseudopotentials.quantum-espresso.org/ # QE became so popular that many other parties develop and distribute pseudopotentials compatible with QE # ESPRESSO_PSEUDO is an env variable that can be set to point to a directory with pseudopotentials .include diff --git a/science/spheral/Makefile b/science/spheral/Makefile index d35d06393bf2..025f42fab8d0 100644 --- a/science/spheral/Makefile +++ b/science/spheral/Makefile @@ -1,81 +1,81 @@ PORTNAME= spheral DISTVERSIONPREFIX= v DISTVERSION= 2025.06.1 -PORTREVISION= 4 +PORTREVISION= 5 CATEGORIES= science # physics MAINTAINER= yuri@FreeBSD.org COMMENT= Environment for hydrodynamical & gravitational numerical simulations WWW= https://github.com/LLNL/spheral LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE BUILD_DEPENDS= ${LOCALBASE}/include/polyclipper2d.hh:math/polyclipper LIB_DEPENDS= libadiak.so:misc/adiak \ libaxom_core.so:science/axom \ libboost_filesystem.so:devel/boost-libs \ libcamp.so:devel/camp \ libchai.so:devel/chai \ libconduit.so:science/conduit \ libfmt.so:devel/libfmt \ libhdf5.so:science/hdf5 \ libmfem.so:math/mfem \ libosdCPU.so:graphics/opensubdiv \ libpolytope.so:science/polytope \ libqhull_r.so:math/qhull \ libRAJA.so:misc/raja \ libsiloh5.so:science/silo \ libsz.so:science/libaec \ libsundials_core.so:math/sundials \ libumpire.so:devel/umpire USES= cmake:testing compiler:c++14-lang eigen:3 fortran localbase:ldflags lua mpi:mpich python USE_LDCONFIG= yes USE_GITHUB= yes GH_ACCOUNT= LLNL GH_TUPLE= LLNL:PolyClipper:e1fe47c:PolyClipper/extern/PolyClipper \ LLNL:PYB11Generator:7160812:PYB11Generator/extern/PYB11Generator \ llnl:blt:29eecef:blt/cmake/blt \ llnl:uberenv:126f8de:uberenv/scripts/devtools/uberenv CMAKE_ARGS= -Daneos_DIR=${LOCALBASE} \ -Daxom_DIR=${LOCALBASE} \ -Dboost_DIR=${LOCALBASE} \ -Dconduit_DIR=${LOCALBASE} \ -Deigen_DIR=${LOCALBASE} \ -Dhdf5_DIR=${LOCALBASE} \ -Dopensubdiv_DIR=${LOCALBASE} \ -Dpython_DIR=${LOCALBASE} \ -Dpolyclipper_DIR=${LOCALBASE} \ -Dpolytope_DIR=${LOCALBASE} \ -Dpybind11_DIR=${LOCALBASE} \ -Dqhull_DIR=${LOCALBASE} \ -Dsilo_DIR=${LOCALBASE} \ -Dzlib_DIR=/usr CMAKE_ARGS+= -DPYTHON_EXECUTABLE=${PYTHON_CMD} \ -DPython_EXECUTABLE=${PYTHON_CMD} \ -DPython3_EXECUTABLE=${PYTHON_CMD} CMAKE_OFF= ENABLE_TESTS ENABLE_DOCS \ ENABLE_ANEOS \ ENABLE_CUDA CMAKE_ON= ENABLE_CXXONLY # disable Python support which is still for Python-2.7, see https://github.com/LLNL/spheral/issues/183 CMAKE_ON+= ENABLE_OPENMP \ USE_EXTERNAL_CHAI \ ENABLE_SUNDIALS CMAKE_TESTING_ON= ENABLE_TESTS # tests fail to build, see https://github.com/LLNL/spheral/issues/230 CXXFLAGS+= -I${LOCALBASE}/include/eigen3 BINARY_ALIAS= git=false python=${PYTHON_CMD} python3=${PYTHON_CMD} post-patch: @${REINPLACE_CMD} -e 's|\.a|.so|; s|qhullstatic|qhull_r|; s|python2\.7|python${PYTHON_VER}|g' ${WRKSRC}/cmake/tpl/*.cmake @${CHMOD} +x ${WRKSRC}/src/helpers/InstantiationGenerator.py post-install: # remove the stray file Spheral/mpi.py @${RM} -r ${STAGEDIR}${PREFIX}/Spheral .include