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Thu, 28 Apr 2022 03:39:25 GMT (envelope-from git) Date: Thu, 28 Apr 2022 03:39:25 GMT Message-Id: <202204280339.23S3dPaY010492@gitrepo.freebsd.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org From: Yuri Victorovich Subject: git: ffecb9942256 - main - science/gromacs: Update 2021.5 -> 2022.1 List-Id: Commit messages for all branches of the ports repository List-Archive: https://lists.freebsd.org/archives/dev-commits-ports-all List-Help: List-Post: List-Subscribe: List-Unsubscribe: Sender: owner-dev-commits-ports-all@freebsd.org X-BeenThere: dev-commits-ports-all@freebsd.org MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-Git-Committer: yuri X-Git-Repository: ports X-Git-Refname: refs/heads/main X-Git-Reftype: branch X-Git-Commit: ffecb994225660a18261a51e4847606f0973d62d Auto-Submitted: auto-generated ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1651117166; 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mx1.freebsd.org; none X-ThisMailContainsUnwantedMimeParts: N The branch main has been updated by yuri: URL: https://cgit.FreeBSD.org/ports/commit/?id=ffecb994225660a18261a51e4847606f0973d62d commit ffecb994225660a18261a51e4847606f0973d62d Author: Yuri Victorovich AuthorDate: 2022-04-28 03:06:20 +0000 Commit: Yuri Victorovich CommitDate: 2022-04-28 03:39:22 +0000 science/gromacs: Update 2021.5 -> 2022.1 Reported by: portscout --- science/gromacs/Makefile | 7 +- science/gromacs/distinfo | 6 +- .../patch-cmake_gmxManageSharedLibraries.cmake | 11 - science/gromacs/pkg-plist | 259 +++++++++++---------- 4 files changed, 145 insertions(+), 138 deletions(-) diff --git a/science/gromacs/Makefile b/science/gromacs/Makefile index e0f23553aa1c..28a7df372742 100644 --- a/science/gromacs/Makefile +++ b/science/gromacs/Makefile @@ -1,8 +1,7 @@ # Created by: Stephen Montgomery-Smith PORTNAME= gromacs -DISTVERSION= 2021.5 -PORTREVISION= 2 +DISTVERSION= 2022.1 CATEGORIES= science MASTER_SITES= ftp://ftp.gromacs.org/pub/gromacs/ @@ -12,12 +11,12 @@ COMMENT= Compute molecular dynamics LICENSE= LGPL21 LICENSE_FILE= ${WRKSRC}/COPYING -BROKEN_i386= undefined reference to `__atomic_load' and `__atomic_compare_exchange' +BROKEN_i386= undefined reference to `__atomic_load' and `__atomic_compare_exchange' #` BUILD_DEPENDS= boost-libs>=1.44:devel/boost-libs LIB_DEPENDS= libhwloc.so:devel/hwloc2 -USES= cmake compiler:c++14-lang fortran gnome perl5 pkgconfig shebangfix xorg +USES= cmake compiler:c++17-lang fortran gnome perl5 pkgconfig shebangfix xorg SHEBANG_FILES= admin/*.sh scripts/*.pl scripts/*.sh src/gromacs/selection/*.sh bash_CMD= ${SH} USE_GNOME= libxml2 diff --git a/science/gromacs/distinfo b/science/gromacs/distinfo index 42ab8fafcea0..fadfb2f4ed37 100644 --- a/science/gromacs/distinfo +++ b/science/gromacs/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1642283496 -SHA256 (gromacs-2021.5.tar.gz) = eba63fe6106812f72711ef7f76447b12dd1ee6c81b3d8d4d0e3098cd9ea009b6 -SIZE (gromacs-2021.5.tar.gz) = 38023772 +TIMESTAMP = 1651109042 +SHA256 (gromacs-2022.1.tar.gz) = 85ddab5197d79524a702c4959c2c43be875e0fc471df3a35224939dce8512450 +SIZE (gromacs-2022.1.tar.gz) = 40375423 diff --git a/science/gromacs/files/patch-cmake_gmxManageSharedLibraries.cmake b/science/gromacs/files/patch-cmake_gmxManageSharedLibraries.cmake deleted file mode 100644 index cb366e776b08..000000000000 --- a/science/gromacs/files/patch-cmake_gmxManageSharedLibraries.cmake +++ /dev/null @@ -1,11 +0,0 @@ ---- cmake/gmxManageSharedLibraries.cmake.orig 2015-07-27 14:11:45 UTC -+++ cmake/gmxManageSharedLibraries.cmake -@@ -39,7 +39,7 @@ - ######################################################################## - # Determine the defaults (this block has no effect if the variables have - # already been set) --if((APPLE OR CYGWIN OR ${CMAKE_SYSTEM_NAME} MATCHES "Linux|.*BSD|GNU") AND NOT GMX_BUILD_MDRUN_ONLY) -+if((APPLE OR CYGWIN OR ${CMAKE_SYSTEM_NAME} MATCHES "Linux|.*BSD|DragonFly") AND NOT GMX_BUILD_MDRUN_ONLY) - # Maybe Solaris should be here? Patch this if you know! - SET(SHARED_LIBS_DEFAULT ON) - elseif(WIN32 OR ${CMAKE_SYSTEM_NAME} MATCHES "BlueGene") diff --git a/science/gromacs/pkg-plist b/science/gromacs/pkg-plist index 6c35ed2eebf8..38d4889e21b2 100644 --- a/science/gromacs/pkg-plist +++ b/science/gromacs/pkg-plist @@ -3,9 +3,9 @@ bin/GMXRC.bash bin/GMXRC.csh bin/GMXRC.zsh bin/demux.pl -bin/gmx%%SUFFIX_MPI%%%%SUFFIX_D%% -bin/gmx-completion-gmx%%SUFFIX_MPI%%%%SUFFIX_D%%.bash +bin/gmx-completion-gmx%%SUFFIX_D%%.bash bin/gmx-completion.bash +bin/gmx%%SUFFIX_D%% bin/xplor2gmx.pl include/gmxapi/compat/mdparams.h include/gmxapi/compat/tpr.h @@ -94,8 +94,8 @@ include/gromacs/restraint/restraintpotential.h %%LEGACY%%include/gromacs/trajectoryanalysis/topologyinformation.h %%LEGACY%%include/gromacs/utility/arrayref.h include/gromacs/utility/basedefinitions.h -%%LEGACY%%%%LEGACY%%include/gromacs/utility/baseversion.h -%%LEGACY%%%%LEGACY%%include/gromacs/utility/classhelpers.h +%%LEGACY%%include/gromacs/utility/baseversion.h +%%LEGACY%%include/gromacs/utility/classhelpers.h include/gromacs/utility/current_function.h %%LEGACY%%include/gromacs/utility/enumerationhelpers.h %%LEGACY%%include/gromacs/utility/exceptions.h @@ -112,10 +112,23 @@ include/gromacs/utility/real.h %%LEGACY%%include/gromacs/utility/stringutil.h %%LEGACY%%include/gromacs/utility/unique_cptr.h %%LEGACY%%include/gromacs/version.h +include/muParser.h +include/muParserBase.h +include/muParserBytecode.h +include/muParserCallback.h +include/muParserDLL.h +include/muParserDef.h +include/muParserError.h +include/muParserFixes.h +include/muParserInt.h +include/muParserTemplateMagic.h +include/muParserTest.h +include/muParserToken.h +include/muParserTokenReader.h include/nblib/basicdefinitions.h include/nblib/box.h include/nblib/exception.h -include/nblib/forcecalculator.h +include/nblib/gmxcalculatorcpu.h include/nblib/integrator.h include/nblib/interactions.h include/nblib/kerneloptions.h @@ -124,33 +137,139 @@ include/nblib/listed_forces/calculator.h include/nblib/listed_forces/definitions.h include/nblib/molecules.h include/nblib/nblib.h +include/nblib/nbnxmsetuphelpers.h include/nblib/particlesequencer.h include/nblib/particletype.h include/nblib/simulationstate.h include/nblib/topology.h +include/nblib/tpr.h include/nblib/util/setup.h include/nblib/util/traits.hpp include/nblib/util/util.hpp include/nblib/vector.h -lib/libgmxapi%%SUFFIX_MPI%%%%SUFFIX_D%%.so -lib/libgmxapi%%SUFFIX_MPI%%%%SUFFIX_D%%.so.0 -lib/libgmxapi%%SUFFIX_MPI%%%%SUFFIX_D%%.so.0.2.1 -lib/libgromacs%%SUFFIX_MPI%%%%SUFFIX_D%%.so -lib/libgromacs%%SUFFIX_MPI%%%%SUFFIX_D%%.so.6 -lib/libgromacs%%SUFFIX_MPI%%%%SUFFIX_D%%.so.6.0.0 -lib/libnblib.so -lib/libnblib.so.0 -lib/libnblib.so.0.1.0 -libdata/pkgconfig/libgromacs%%SUFFIX_MPI%%%%SUFFIX_D%%.pc +lib/libgmxapi%%SUFFIX_D%%.so +lib/libgmxapi%%SUFFIX_D%%.so.0 +lib/libgmxapi%%SUFFIX_D%%.so.0.3.1 +lib/libgromacs%%SUFFIX_D%%.so +lib/libgromacs%%SUFFIX_D%%.so.7 +lib/libgromacs%%SUFFIX_D%%.so.7.0.0 +lib/libmuparser.so +lib/libmuparser.so.2 +lib/libmuparser.so.2.3.2 +lib/libnblib_gmx.so +lib/libnblib_gmx.so.0 +lib/libnblib_gmx.so.0.1.0 +libdata/pkgconfig/libgromacs%%SUFFIX_D%%.pc +libdata/pkgconfig/muparser.pc +man/man1/gmx-anaeig.1.gz +man/man1/gmx-analyze.1.gz +man/man1/gmx-angle.1.gz +man/man1/gmx-awh.1.gz +man/man1/gmx-bar.1.gz +man/man1/gmx-bundle.1.gz +man/man1/gmx-check.1.gz +man/man1/gmx-chi.1.gz +man/man1/gmx-cluster.1.gz +man/man1/gmx-clustsize.1.gz +man/man1/gmx-confrms.1.gz +man/man1/gmx-convert-tpr.1.gz +man/man1/gmx-convert-trj.1.gz +man/man1/gmx-covar.1.gz +man/man1/gmx-current.1.gz +man/man1/gmx-density.1.gz +man/man1/gmx-densmap.1.gz +man/man1/gmx-densorder.1.gz +man/man1/gmx-dielectric.1.gz +man/man1/gmx-dipoles.1.gz +man/man1/gmx-disre.1.gz +man/man1/gmx-distance.1.gz +man/man1/gmx-do%%SUFFIX_D%%ssp.1.gz +man/man1/gmx-dos.1.gz +man/man1/gmx-dump.1.gz +man/man1/gmx-dyecoupl.1.gz +man/man1/gmx-editconf.1.gz +man/man1/gmx-eneconv.1.gz +man/man1/gmx-enemat.1.gz +man/man1/gmx-energy.1.gz +man/man1/gmx-extract-cluster.1.gz +man/man1/gmx-filter.1.gz +man/man1/gmx-freevolume.1.gz +man/man1/gmx-gangle.1.gz +man/man1/gmx-genconf.1.gz +man/man1/gmx-genion.1.gz +man/man1/gmx-genrestr.1.gz +man/man1/gmx-grompp.1.gz +man/man1/gmx-gyrate.1.gz +man/man1/gmx-h2order.1.gz +man/man1/gmx-hbond.1.gz +man/man1/gmx-helix.1.gz +man/man1/gmx-helixorient.1.gz +man/man1/gmx-help.1.gz +man/man1/gmx-hydorder.1.gz +man/man1/gmx-insert-molecules.1.gz +man/man1/gmx-lie.1.gz +man/man1/gmx-make_edi.1.gz +man/man1/gmx-make_ndx.1.gz +man/man1/gmx-mdmat.1.gz +man/man1/gmx-mdrun.1.gz +man/man1/gmx-mindist.1.gz +man/man1/gmx-mk_angndx.1.gz +man/man1/gmx-msd.1.gz +man/man1/gmx-nmeig.1.gz +man/man1/gmx-nmens.1.gz +man/man1/gmx-nmr.1.gz +man/man1/gmx-nmtraj.1.gz +man/man1/gmx-nonbonded-benchmark.1.gz +man/man1/gmx-order.1.gz +man/man1/gmx-pairdist.1.gz +man/man1/gmx-pdb2gmx.1.gz +man/man1/gmx-pme_error.1.gz +man/man1/gmx-polystat.1.gz +man/man1/gmx-potential.1.gz +man/man1/gmx-principal.1.gz +man/man1/gmx-rama.1.gz +man/man1/gmx-rdf.1.gz +man/man1/gmx-report-methods.1.gz +man/man1/gmx-rms.1.gz +man/man1/gmx-rmsdist.1.gz +man/man1/gmx-rmsf.1.gz +man/man1/gmx-rotacf.1.gz +man/man1/gmx-rotmat.1.gz +man/man1/gmx-saltbr.1.gz +man/man1/gmx-sans.1.gz +man/man1/gmx-sasa.1.gz +man/man1/gmx-saxs.1.gz +man/man1/gmx-select.1.gz +man/man1/gmx-sham.1.gz +man/man1/gmx-sigeps.1.gz +man/man1/gmx-solvate.1.gz +man/man1/gmx-sorient.1.gz +man/man1/gmx-spatial.1.gz +man/man1/gmx-spol.1.gz +man/man1/gmx-tcaf.1.gz +man/man1/gmx-traj.1.gz +man/man1/gmx-trajectory.1.gz +man/man1/gmx-trjcat.1.gz +man/man1/gmx-trjconv.1.gz +man/man1/gmx-trjorder.1.gz +man/man1/gmx-tune_pme.1.gz +man/man1/gmx-vanhove.1.gz +man/man1/gmx-velacc.1.gz +man/man1/gmx-view.1.gz +man/man1/gmx-wham.1.gz +man/man1/gmx-wheel.1.gz +man/man1/gmx-x2top.1.gz +man/man1/gmx-xpm2ps.1.gz +man/man1/gmx.1.gz share/cmake/gmxapi/gmxapi-config-version.cmake share/cmake/gmxapi/gmxapi-config.cmake share/cmake/gmxapi/gmxapi-%%CMAKE_BUILD_TYPE%%.cmake share/cmake/gmxapi/gmxapi.cmake -share/cmake/gromacs%%SUFFIX_MPI%%%%SUFFIX_D%%/gromacs%%SUFFIX_MPI%%%%SUFFIX_D%%-config-version.cmake -share/cmake/gromacs%%SUFFIX_MPI%%%%SUFFIX_D%%/gromacs%%SUFFIX_MPI%%%%SUFFIX_D%%-config.cmake -share/cmake/gromacs%%SUFFIX_MPI%%%%SUFFIX_D%%/gromacs-toolchain%%SUFFIX_MPI%%%%SUFFIX_D%%.cmake -share/cmake/gromacs%%SUFFIX_MPI%%%%SUFFIX_D%%/libgromacs-%%CMAKE_BUILD_TYPE%%.cmake -share/cmake/gromacs%%SUFFIX_MPI%%%%SUFFIX_D%%/libgromacs.cmake +share/cmake/gromacs%%SUFFIX_D%%/gromacs-hints%%SUFFIX_D%%.cmake +share/cmake/gromacs%%SUFFIX_D%%/gromacs%%SUFFIX_D%%-config-version.cmake +share/cmake/gromacs%%SUFFIX_D%%/gromacs%%SUFFIX_D%%-config.cmake +share/cmake/gromacs%%SUFFIX_D%%/libgromacs-%%CMAKE_BUILD_TYPE%%.cmake +share/cmake/gromacs%%SUFFIX_D%%/libgromacs.cmake %%DATADIR%%/COPYING %%DATADIR%%/README.tutor %%DATADIR%%/README_FreeEnergyModifications.txt @@ -599,103 +718,3 @@ share/cmake/gromacs%%SUFFIX_MPI%%%%SUFFIX_D%%/libgromacs.cmake %%DATADIR%%/top/vdw-msms.dat %%DATADIR%%/top/vdwradii.dat %%DATADIR%%/top/xlateat.dat -man/man1/gmx-anaeig.1.gz -man/man1/gmx-analyze.1.gz -man/man1/gmx-angle.1.gz -man/man1/gmx-awh.1.gz -man/man1/gmx-bar.1.gz -man/man1/gmx-bundle.1.gz -man/man1/gmx-check.1.gz -man/man1/gmx-chi.1.gz -man/man1/gmx-cluster.1.gz -man/man1/gmx-clustsize.1.gz -man/man1/gmx-confrms.1.gz -man/man1/gmx-convert-tpr.1.gz -man/man1/gmx-convert-trj.1.gz -man/man1/gmx-covar.1.gz -man/man1/gmx-current.1.gz -man/man1/gmx-density.1.gz -man/man1/gmx-densmap.1.gz -man/man1/gmx-densorder.1.gz -man/man1/gmx-dielectric.1.gz -man/man1/gmx-dipoles.1.gz -man/man1/gmx-disre.1.gz -man/man1/gmx-distance.1.gz -man/man1/gmx-do_dssp.1.gz -man/man1/gmx-dos.1.gz -man/man1/gmx-dump.1.gz -man/man1/gmx-dyecoupl.1.gz -man/man1/gmx-editconf.1.gz -man/man1/gmx-eneconv.1.gz -man/man1/gmx-enemat.1.gz -man/man1/gmx-energy.1.gz -man/man1/gmx-extract-cluster.1.gz -man/man1/gmx-filter.1.gz -man/man1/gmx-freevolume.1.gz -man/man1/gmx-gangle.1.gz -man/man1/gmx-genconf.1.gz -man/man1/gmx-genion.1.gz -man/man1/gmx-genrestr.1.gz -man/man1/gmx-grompp.1.gz -man/man1/gmx-gyrate.1.gz -man/man1/gmx-h2order.1.gz -man/man1/gmx-hbond.1.gz -man/man1/gmx-helix.1.gz -man/man1/gmx-helixorient.1.gz -man/man1/gmx-help.1.gz -man/man1/gmx-hydorder.1.gz -man/man1/gmx-insert-molecules.1.gz -man/man1/gmx-lie.1.gz -man/man1/gmx-make_edi.1.gz -man/man1/gmx-make_ndx.1.gz -man/man1/gmx-mdmat.1.gz -man/man1/gmx-mdrun.1.gz -man/man1/gmx-mindist.1.gz -man/man1/gmx-mk_angndx.1.gz -man/man1/gmx-msd.1.gz -man/man1/gmx-nmeig.1.gz -man/man1/gmx-nmens.1.gz -man/man1/gmx-nmr.1.gz -man/man1/gmx-nmtraj.1.gz -man/man1/gmx-nonbonded-benchmark.1.gz -man/man1/gmx-order.1.gz -man/man1/gmx-pairdist.1.gz -man/man1/gmx-pdb2gmx.1.gz -man/man1/gmx-pme_error.1.gz -man/man1/gmx-polystat.1.gz -man/man1/gmx-potential.1.gz -man/man1/gmx-principal.1.gz -man/man1/gmx-rama.1.gz -man/man1/gmx-rdf.1.gz -man/man1/gmx-report-methods.1.gz -man/man1/gmx-rms.1.gz -man/man1/gmx-rmsdist.1.gz -man/man1/gmx-rmsf.1.gz -man/man1/gmx-rotacf.1.gz -man/man1/gmx-rotmat.1.gz -man/man1/gmx-saltbr.1.gz -man/man1/gmx-sans.1.gz -man/man1/gmx-sasa.1.gz -man/man1/gmx-saxs.1.gz -man/man1/gmx-select.1.gz -man/man1/gmx-sham.1.gz -man/man1/gmx-sigeps.1.gz -man/man1/gmx-solvate.1.gz -man/man1/gmx-sorient.1.gz -man/man1/gmx-spatial.1.gz -man/man1/gmx-spol.1.gz -man/man1/gmx-tcaf.1.gz -man/man1/gmx-traj.1.gz -man/man1/gmx-trajectory.1.gz -man/man1/gmx-trjcat.1.gz -man/man1/gmx-trjconv.1.gz -man/man1/gmx-trjorder.1.gz -man/man1/gmx-tune_pme.1.gz -man/man1/gmx-vanhove.1.gz -man/man1/gmx-velacc.1.gz -man/man1/gmx-view.1.gz -man/man1/gmx-wham.1.gz -man/man1/gmx-wheel.1.gz -man/man1/gmx-x2top.1.gz -man/man1/gmx-xpm2ps.1.gz -man/man1/gmx.1.gz