From owner-svn-ports-head@FreeBSD.ORG Sun Aug 10 00:03:10 2014 Return-Path: Delivered-To: svn-ports-head@freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2001:1900:2254:206a::19:1]) (using TLSv1 with cipher ADH-AES256-SHA (256/256 bits)) (No client certificate requested) by hub.freebsd.org (Postfix) with ESMTPS id 808D0117 for ; Sun, 10 Aug 2014 00:03:10 +0000 (UTC) Received: from svn.freebsd.org (svn.freebsd.org [IPv6:2001:1900:2254:2068::e6a:0]) (using TLSv1 with cipher ECDHE-RSA-AES256-SHA (256/256 bits)) (Client did not present a certificate) by mx1.freebsd.org (Postfix) with ESMTPS id 6D2762984 for ; Sun, 10 Aug 2014 00:03:10 +0000 (UTC) Received: from marino (uid 1323) (envelope-from marino@FreeBSD.org) id 2dcc by svn.freebsd.org (DragonFly Mail Agent v0.9+); Sun, 10 Aug 2014 00:03:09 +0000 From: John Marino Date: Sun, 10 Aug 2014 00:03:09 +0000 (UTC) To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r364488 - in head/science/gromacs: . files X-SVN-Group: ports-head MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Message-Id: <53e6b6bd.2dcc.de215ed@svn.freebsd.org> X-BeenThere: svn-ports-head@freebsd.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: SVN commit messages for the ports tree for head List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Sun, 10 Aug 2014 00:03:10 -0000 Author: marino Date: Sun Aug 10 00:03:09 2014 New Revision: 364488 URL: http://svnweb.freebsd.org/changeset/ports/364488 QAT: https://qat.redports.org/buildarchive/r364488/ Log: science/gromacs: Upgrade version 4.6.5 => 5.0 PR: 191826 Submitted by: Ports Fury Added: head/science/gromacs/files/patch-src__external__thread_mpi__src__atomic.c (contents, props changed) Deleted: head/science/gromacs/files/patch-CMakeLists.txt head/science/gromacs/files/patch-src__gmxlib__thread_mpi__atomic.c Modified: head/science/gromacs/Makefile head/science/gromacs/distinfo head/science/gromacs/pkg-descr head/science/gromacs/pkg-plist Modified: head/science/gromacs/Makefile ============================================================================== --- head/science/gromacs/Makefile Sat Aug 9 23:54:31 2014 (r364487) +++ head/science/gromacs/Makefile Sun Aug 10 00:03:09 2014 (r364488) @@ -2,8 +2,7 @@ # $FreeBSD$ PORTNAME= gromacs -PORTVERSION= 4.6.5 -PORTREVISION= 3 +PORTVERSION= 5.0 CATEGORIES= science MASTER_SITES= ftp://ftp.gromacs.org/pub/gromacs/ @@ -12,86 +11,68 @@ COMMENT= Compute molecular dynamics LICENSE= LGPL21 -OPTIONS_DEFINE= ATLAS FLOAT GSL SIMD X11 -OPTIONS_DEFAULT= FLOAT GSL X11 -OPTIONS_RADIO= MPI -OPTIONS_RADIO_MPI= MPICH OMPI - -OPTIONS_SUB= yes - -ATLAS_DESC= Use ATLAS for BLAS and LAPACK -FLOAT_DESC= Use single instead of double precision -GSL_DESC= Extra analysis using math/gsl -MPICH_DESC= MPI support using net/mpich2 -OMPI_DESC= MPI support using net/openmpi +BUILD_DEPENDS= boost-libs>=1.44:${PORTSDIR}/devel/boost-libs USES= cmake fortran perl5 pkgconfig shebangfix -SHEBANG_FILES= admin/*.pl scripts/*.pl scripts/*.sh src/gmxlib/selection/*.sh +SHEBANG_FILES= admin/*.sh scripts/*.pl scripts/*.sh src/gromacs/selection/*.sh bash_CMD= ${SH} -CMAKE_ARGS= -DBLAS_LIBRARIES:FILEPATH="${BLAS_LIBS}" \ - -DLAPACK_LIBRARIES:FILEPATH="${LAPACK_LIBS}" +USE_GNOME= libxml2 +CMAKE_ARGS= -DGMX_USE_RDTSCP:BOOL=OFF \ + -DUSE_PYTHON_SCRIPTS:BOOL=OFF USE_LDCONFIG= yes -GSL_LIB_DEPENDS= libgsl.so:${PORTSDIR}/math/gsl -GSL_CMAKE_ON= -DGMX_GSL:BOOL=ON -GSL_CMAKE_OFF= -DGMX_GSL:BOOL=OFF - -SIMD_CMAKE_OFF= -DGMX_CPU_ACCELERATION:STRING="None" +OPTIONS_DEFINE= ATLAS FLOAT SIMD X11 +OPTIONS_RADIO= MPI +OPTIONS_RADIO_MPI= MPICH OMPI +OPTIONS_DEFAULT= FLOAT X11 +OPTIONS_SUB= yes +ATLAS_DESC= Use ATLAS for BLAS and LAPACK +ATLAS_LIB_DEPENDS= libalapack.so:${PORTSDIR}/math/atlas +ATLAS_LIB_DEPENDS_OFF= libblas.so:${PORTSDIR}/math/blas \ + liblapack.so:${PORTSDIR}/math/lapack +ATLAS_CMAKE_ON= -DBLAS_LIBRARIES:FILEPATH="${LOCALBASE}/lib/libcblas.so;${LOCALBASE}/lib/libf77blas.so" \ + -DLAPACK_LIBRARIES:FILEPATH="${LOCALBASE}/lib/libalapack.so" +ATLAS_CMAKE_OFF= -DBLAS_LIBRARIES:FILEPATH="${LOCALBASE}/lib/libblas.so" \ + -DLAPACK_LIBRARIES:FILEPATH="${LOCALBASE}/lib/liblapack.so" +FLOAT_DESC= Use single instead of double precision +FLOAT_BUILD_DEPENDS= fftw3>0:${PORTSDIR}/math/fftw3 +FLOAT_LIB_DEPENDS= libfftw3f.so:${PORTSDIR}/math/fftw3-float +FLOAT_LIB_DEPENDS_OFF= libfftw3.so:${PORTSDIR}/math/fftw3 +FLOAT_CMAKE_ON= -DGMX_DOUBLE:BOOL=OFF +FLOAT_CMAKE_OFF= -DGMX_DOUBLE:BOOL=ON +MPICH_DESC= MPI support using net/mpich2 +MPICH_LIB_DEPENDS= libmpich.so:${PORTSDIR}/net/mpich2 +MPICH_CMAKE_ON= -DMPI_C_COMPILER:FILEPATH="${LOCALBASE}/bin/mpicc" +OMPI_DESC= MPI support using net/openmpi +OMPI_BUILD_DEPENDS= openmpi>0:${PORTSDIR}/net/openmpi +OMPI_RUN_DEPENDS= openmpi>0:${PORTSDIR}/net/openmpi +OMPI_CMAKE_ON= -DMPI_C_COMPILER:FILEPATH="${LOCALBASE}/mpi/openmpi/bin/mpicc" +SIMD_CMAKE_OFF= -DGMX_SIMD:STRING="None" X11_USE= XORG=xext,x11 X11_CMAKE_ON= -DGMX_X11:BOOL=ON X11_CMAKE_OFF= -DGMX_X11:BOOL=OFF .include -.if ${PORT_OPTIONS:MATLAS} -LIB_DEPENDS+= libalapack.so:${PORTSDIR}/math/atlas -BLAS_LIBS= ${LOCALBASE}/lib/libcblas.so;${LOCALBASE}/lib/libf77blas.so -LAPACK_LIBS= ${LOCALBASE}/lib/libalapack.so -.else -LIB_DEPENDS+= libblas.so:${PORTSDIR}/math/blas \ - liblapack.so:${PORTSDIR}/math/lapack -BLAS_LIBS= ${LOCALBASE}/lib/libblas.so -LAPACK_LIBS= ${LOCALBASE}/lib/liblapack.so -.endif - .if ${PORT_OPTIONS:MFLOAT} -BUILD_DEPENDS+= fftw3>0:${PORTSDIR}/math/fftw3 -LIB_DEPENDS+= libfftw3f.so:${PORTSDIR}/math/fftw3-float -CMAKE_ARGS+= -DGMX_DOUBLE:BOOL=OFF PLIST_SUB+= SUFFIX_D="" .else -LIB_DEPENDS+= libfftw3.so:${PORTSDIR}/math/fftw3 -CMAKE_ARGS+= -DGMX_DOUBLE:BOOL=ON PLIST_SUB+= SUFFIX_D="_d" .endif .if ${PORT_OPTIONS:MMPICH} || ${PORT_OPTIONS:MOMPI} -CMAKE_ARGS+= -DGMX_MPI:BOOL=ON \ - -DMPI_C_COMPILER:FILEPATH="${MPICC}" +CMAKE_ARGS+= -DGMX_MPI:BOOL=ON PLIST_SUB+= SUFFIX_MPI="_mpi" .else CMAKE_ARGS+= -DGMX_MPI:BOOL=OFF PLIST_SUB+= SUFFIX_MPI="" .endif -.if ${PORT_OPTIONS:MMPICH} -BUILD_DEPENDS+= ${LOCALBASE}/bin/mpicc:${PORTSDIR}/net/mpich2 -RUN_DEPENDS+= ${LOCALBASE}/bin/mpicc:${PORTSDIR}/net/mpich2 -MPICC= ${LOCALBASE}/bin/mpicc -.endif - -.if ${PORT_OPTIONS:MOMPI} -BUILD_DEPENDS+= ${LOCALBASE}/mpi/openmpi/bin/mpicc:${PORTSDIR}/net/openmpi -RUN_DEPENDS+= ${LOCALBASE}/mpi/openmpi/bin/mpicc:${PORTSDIR}/net/openmpi -MPICC= ${LOCALBASE}/mpi/openmpi/bin/mpicc -.endif - post-patch: @${FIND} ${WRKSRC} -name "CMakeLists.txt" | ${XARGS} \ ${REINPLACE_CMD} -e \ 's|share/man|man| ; \ - s|-lpthread|-pthread| ; \ /pkgconfig/s|LIB_INSTALL_DIR}|CMAKE_INSTALL_PREFIX}/libdata|' @${FIND} ${WRKSRC} -name "GMXRC.*" | ${XARGS} ${REINPLACE_CMD} -e \ 's|LDLIB/pkgconfig|LDLIB/../libdata/pkgconfig| ; \ Modified: head/science/gromacs/distinfo ============================================================================== --- head/science/gromacs/distinfo Sat Aug 9 23:54:31 2014 (r364487) +++ head/science/gromacs/distinfo Sun Aug 10 00:03:09 2014 (r364488) @@ -1,2 +1,2 @@ -SHA256 (gromacs-4.6.5.tar.gz) = a7242f315963a111e87fd28795696b1e818ac97479788356c4f73a04e9cdef09 -SIZE (gromacs-4.6.5.tar.gz) = 10991576 +SHA256 (gromacs-5.0.tar.gz) = c2c9b5e75e014785641f39fbbde9829ce200f963344b35fa942f041a0dcfeb20 +SIZE (gromacs-5.0.tar.gz) = 26862408 Added: head/science/gromacs/files/patch-src__external__thread_mpi__src__atomic.c ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/science/gromacs/files/patch-src__external__thread_mpi__src__atomic.c Sun Aug 10 00:03:09 2014 (r364488) @@ -0,0 +1,17 @@ +--- src/external/thread_mpi/src/atomic.c.orig ++++ src/external/thread_mpi/src/atomic.c +@@ -35,6 +35,14 @@ + files. + */ + ++#ifdef HAVE_TMPI_CONFIG_H ++#include "tmpi_config.h" ++#endif ++ ++#ifdef HAVE_CONFIG_H ++#include "config.h" ++#endif ++ + #include "impl.h" + + /* This file is only needed when no intrinsic atomic operations are present. */ Modified: head/science/gromacs/pkg-descr ============================================================================== --- head/science/gromacs/pkg-descr Sat Aug 9 23:54:31 2014 (r364487) +++ head/science/gromacs/pkg-descr Sun Aug 10 00:03:09 2014 (r364488) @@ -1,5 +1,5 @@ -GROMACS is a versatile package to perform molecular dynamics, i.e. simulate -the Newtonian equations of motion for systems with hundreds to millions of -particles. +GROMACS is a versatile package to perform molecular dynamics, i.e. +simulate the Newtonian equations of motion for systems with hundreds to +millions of particles. WWW: http://www.gromacs.org Modified: head/science/gromacs/pkg-plist ============================================================================== --- head/science/gromacs/pkg-plist Sat Aug 9 23:54:31 2014 (r364487) +++ head/science/gromacs/pkg-plist Sun Aug 10 00:03:09 2014 (r364488) @@ -2,9 +2,6 @@ bin/GMXRC bin/GMXRC.bash bin/GMXRC.csh bin/GMXRC.zsh -bin/completion.bash -bin/completion.csh -bin/completion.zsh bin/demux.pl bin/do_dssp%%SUFFIX_MPI%%%%SUFFIX_D%% bin/editconf%%SUFFIX_MPI%%%%SUFFIX_D%% @@ -41,11 +38,8 @@ bin/g_hbond%%SUFFIX_MPI%%%%SUFFIX_D%% bin/g_helix%%SUFFIX_MPI%%%%SUFFIX_D%% bin/g_helixorient%%SUFFIX_MPI%%%%SUFFIX_D%% bin/g_hydorder%%SUFFIX_MPI%%%%SUFFIX_D%% -bin/g_kinetics%%SUFFIX_MPI%%%%SUFFIX_D%% bin/g_lie%%SUFFIX_MPI%%%%SUFFIX_D%% -bin/g_luck%%SUFFIX_MPI%%%%SUFFIX_D%% bin/g_mdmat%%SUFFIX_MPI%%%%SUFFIX_D%% -bin/g_membed%%SUFFIX_MPI%%%%SUFFIX_D%% bin/g_mindist%%SUFFIX_MPI%%%%SUFFIX_D%% bin/g_morph%%SUFFIX_MPI%%%%SUFFIX_D%% bin/g_msd%%SUFFIX_MPI%%%%SUFFIX_D%% @@ -69,6 +63,7 @@ bin/g_rotmat%%SUFFIX_MPI%%%%SUFFIX_D%% bin/g_saltbr%%SUFFIX_MPI%%%%SUFFIX_D%% bin/g_sans%%SUFFIX_MPI%%%%SUFFIX_D%% bin/g_sas%%SUFFIX_MPI%%%%SUFFIX_D%% +bin/g_saxs%%SUFFIX_MPI%%%%SUFFIX_D%% bin/g_select%%SUFFIX_MPI%%%%SUFFIX_D%% bin/g_sgangle%%SUFFIX_MPI%%%%SUFFIX_D%% bin/g_sham%%SUFFIX_MPI%%%%SUFFIX_D%% @@ -84,11 +79,13 @@ bin/g_velacc%%SUFFIX_MPI%%%%SUFFIX_D%% bin/g_wham%%SUFFIX_MPI%%%%SUFFIX_D%% bin/g_wheel%%SUFFIX_MPI%%%%SUFFIX_D%% bin/g_x2top%%SUFFIX_MPI%%%%SUFFIX_D%% -%%X11%%bin/g_xrama%%SUFFIX_MPI%%%%SUFFIX_D%% bin/genbox%%SUFFIX_MPI%%%%SUFFIX_D%% bin/genconf%%SUFFIX_MPI%%%%SUFFIX_D%% bin/genion%%SUFFIX_MPI%%%%SUFFIX_D%% bin/genrestr%%SUFFIX_MPI%%%%SUFFIX_D%% +bin/gmx%%SUFFIX_MPI%%%%SUFFIX_D%% +bin/gmx-completion-gmx%%SUFFIX_MPI%%%%SUFFIX_D%%.bash +bin/gmx-completion.bash bin/gmxcheck%%SUFFIX_MPI%%%%SUFFIX_D%% bin/gmxdump%%SUFFIX_MPI%%%%SUFFIX_D%% bin/grompp%%SUFFIX_MPI%%%%SUFFIX_D%% @@ -96,7 +93,6 @@ bin/make_edi%%SUFFIX_MPI%%%%SUFFIX_D%% bin/make_ndx%%SUFFIX_MPI%%%%SUFFIX_D%% bin/mdrun%%SUFFIX_MPI%%%%SUFFIX_D%% bin/mk_angndx%%SUFFIX_MPI%%%%SUFFIX_D%% -%%X11%%bin/ngmx%%SUFFIX_MPI%%%%SUFFIX_D%% bin/pdb2gmx%%SUFFIX_MPI%%%%SUFFIX_D%% bin/tpbconv%%SUFFIX_MPI%%%%SUFFIX_D%% bin/trjcat%%SUFFIX_MPI%%%%SUFFIX_D%% @@ -104,360 +100,301 @@ bin/trjconv%%SUFFIX_MPI%%%%SUFFIX_D%% bin/trjorder%%SUFFIX_MPI%%%%SUFFIX_D%% bin/xplor2gmx.pl bin/xpm2ps%%SUFFIX_MPI%%%%SUFFIX_D%% -include/gromacs/3dview.h -include/gromacs/CTestTestfile.cmake -include/gromacs/assert.h -include/gromacs/atomprop.h -include/gromacs/bondf.h -include/gromacs/calcgrid.h -include/gromacs/calch.h -include/gromacs/calcmu.h -include/gromacs/centerofmass.h -include/gromacs/chargegroup.h -include/gromacs/checkpoint.h -include/gromacs/confio.h -include/gromacs/constr.h -include/gromacs/copyrite.h -include/gromacs/coulomb.h -include/gromacs/displacement.h -include/gromacs/disre.h -include/gromacs/do_fit.h -include/gromacs/domdec.h -include/gromacs/domdec_network.h -include/gromacs/ebin.h -include/gromacs/edsam.h -include/gromacs/enxio.h -include/gromacs/ffscanf.h -include/gromacs/filenm.h -include/gromacs/force.h -include/gromacs/futil.h -include/gromacs/gbutil.h -include/gromacs/gen_ad.h -include/gromacs/genborn.h -include/gromacs/gmx_ana.h -include/gromacs/gmx_avx_double.h -include/gromacs/gmx_avx_single.h -include/gromacs/gmx_cpuid.h -include/gromacs/gmx_cyclecounter.h -include/gromacs/gmx_detect_hardware.h -include/gromacs/gmx_fatal.h -include/gromacs/gmx_fatal_collective.h -include/gromacs/gmx_fft.h -include/gromacs/gmx_ga2la.h -include/gromacs/gmx_hash.h -include/gromacs/gmx_header_config.h -include/gromacs/gmx_math_x86_avx_128_fma_double.h -include/gromacs/gmx_math_x86_avx_128_fma_single.h -include/gromacs/gmx_math_x86_avx_256_double.h -include/gromacs/gmx_math_x86_avx_256_single.h -include/gromacs/gmx_math_x86_sse2_double.h -include/gromacs/gmx_math_x86_sse2_single.h -include/gromacs/gmx_math_x86_sse4_1_double.h -include/gromacs/gmx_math_x86_sse4_1_single.h -include/gromacs/gmx_matrix.h -include/gromacs/gmx_omp.h -include/gromacs/gmx_omp_nthreads.h -include/gromacs/gmx_parallel_3dfft.h -include/gromacs/gmx_random.h -include/gromacs/gmx_simd4_macros.h -include/gromacs/gmx_simd4_ref.h -include/gromacs/gmx_simd_macros.h -include/gromacs/gmx_simd_math_double.h -include/gromacs/gmx_simd_math_single.h -include/gromacs/gmx_simd_ref.h -include/gromacs/gmx_simd_vec.h -include/gromacs/gmx_sort.h -include/gromacs/gmx_statistics.h -include/gromacs/gmx_system_xdr.h -include/gromacs/gmx_thread_affinity.h -include/gromacs/gmx_wallcycle.h -include/gromacs/gmx_x86_avx_128_fma.h -include/gromacs/gmx_x86_avx_256.h -include/gromacs/gmx_x86_sse2.h -include/gromacs/gmx_x86_sse4_1.h -include/gromacs/gmxcomplex.h -include/gromacs/gmxcpp.h -include/gromacs/gmxfio.h -include/gromacs/gpp_atomtype.h -include/gromacs/gpp_nextnb.h -include/gromacs/gpu_utils.h -include/gromacs/grompp.h -include/gromacs/gstat.h -include/gromacs/hackblock.h -include/gromacs/histogram.h -include/gromacs/index.h -include/gromacs/indexutil.h -include/gromacs/inputrec.h -include/gromacs/invblock.h -include/gromacs/macros.h -include/gromacs/main.h -include/gromacs/mainpage.h -include/gromacs/maths.h -include/gromacs/matio.h -include/gromacs/md5.h -include/gromacs/md_logging.h -include/gromacs/md_support.h -include/gromacs/mdatoms.h -include/gromacs/mdebin.h -include/gromacs/mdrun.h -include/gromacs/mpelogging.h -include/gromacs/mshift.h -include/gromacs/mtop_util.h -include/gromacs/mtxio.h -include/gromacs/mvdata.h -include/gromacs/names.h -include/gromacs/nbnxn_cuda_data_mgmt.h -include/gromacs/nbsearch.h -include/gromacs/network.h -include/gromacs/nonbonded.h -include/gromacs/nrama.h -include/gromacs/nrjac.h -include/gromacs/nrnb.h -include/gromacs/ns.h -include/gromacs/nsgrid.h -include/gromacs/oenv.h -include/gromacs/orires.h -include/gromacs/partdec.h -include/gromacs/pbc.h -include/gromacs/pdb2top.h -include/gromacs/pdbio.h -include/gromacs/perf_est.h -include/gromacs/physics.h -include/gromacs/pmalloc_cuda.h -include/gromacs/pme.h -include/gromacs/poscalc.h -include/gromacs/position.h -include/gromacs/princ.h -include/gromacs/pull.h -include/gromacs/pull_rotation.h -include/gromacs/qmmm.h -include/gromacs/random.h -include/gromacs/rbin.h -include/gromacs/readinp.h -include/gromacs/resall.h -include/gromacs/rmpbc.h +include/gromacs/analysisdata.h +include/gromacs/analysisdata/abstractdata.h +include/gromacs/analysisdata/analysisdata.h +include/gromacs/analysisdata/arraydata.h +include/gromacs/analysisdata/dataframe.h +include/gromacs/analysisdata/datamodule.h +include/gromacs/analysisdata/modules/average.h +include/gromacs/analysisdata/modules/displacement.h +include/gromacs/analysisdata/modules/histogram.h +include/gromacs/analysisdata/modules/lifetime.h +include/gromacs/analysisdata/modules/plot.h +include/gromacs/commandline.h +include/gromacs/commandline/cmdlinehelpwriter.h +include/gromacs/commandline/cmdlineinit.h +include/gromacs/commandline/cmdlinemodule.h +include/gromacs/commandline/cmdlineparser.h +include/gromacs/commandline/cmdlineprogramcontext.h +include/gromacs/commandline/pargs.h +include/gromacs/fft/fft.h +include/gromacs/fileio/confio.h +include/gromacs/fileio/enxio.h +include/gromacs/fileio/filenm.h +include/gromacs/fileio/futil.h +include/gromacs/fileio/gmxfio.h +include/gromacs/fileio/matio.h +include/gromacs/fileio/mdoutf.h +include/gromacs/fileio/pdbio.h +include/gromacs/fileio/tpxio.h +include/gromacs/fileio/trajectory_writing.h +include/gromacs/fileio/trnio.h +include/gromacs/fileio/trx.h +include/gromacs/fileio/trxio.h +include/gromacs/fileio/xdr_datatype.h +include/gromacs/fileio/xtcio.h +include/gromacs/gmxana/gstat.h +include/gromacs/legacyheaders/atomprop.h +include/gromacs/legacyheaders/bondf.h +include/gromacs/legacyheaders/calcgrid.h +include/gromacs/legacyheaders/calch.h +include/gromacs/legacyheaders/calcmu.h +include/gromacs/legacyheaders/chargegroup.h +include/gromacs/legacyheaders/checkpoint.h +include/gromacs/legacyheaders/constr.h +include/gromacs/legacyheaders/copyrite.h +include/gromacs/legacyheaders/coulomb.h +include/gromacs/legacyheaders/disre.h +include/gromacs/legacyheaders/domdec.h +include/gromacs/legacyheaders/domdec_network.h +include/gromacs/legacyheaders/ebin.h +include/gromacs/legacyheaders/force.h +include/gromacs/legacyheaders/genborn.h +include/gromacs/legacyheaders/gmx_cpuid.h +include/gromacs/legacyheaders/gmx_detect_hardware.h +include/gromacs/legacyheaders/gmx_fatal.h +include/gromacs/legacyheaders/gmx_fatal_collective.h +include/gromacs/legacyheaders/gmx_omp_nthreads.h +include/gromacs/legacyheaders/gmx_thread_affinity.h +include/gromacs/legacyheaders/index.h +include/gromacs/legacyheaders/inputrec.h +include/gromacs/legacyheaders/invblock.h +include/gromacs/legacyheaders/macros.h +include/gromacs/legacyheaders/main.h +include/gromacs/legacyheaders/md_logging.h 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