diff options
| -rw-r--r-- | sci-chemistry/gromacs/ChangeLog | 8 | ||||
| -rw-r--r-- | sci-chemistry/gromacs/files/gromacs-4.6.1-openmm.patch | 151 | ||||
| -rw-r--r-- | sci-chemistry/gromacs/gromacs-4.6.2.ebuild (renamed from sci-chemistry/gromacs/gromacs-4.6.1.ebuild) | 13 |
3 files changed, 15 insertions, 157 deletions
diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog index faf9b633eb6e..3b411f1bee22 100644 --- a/sci-chemistry/gromacs/ChangeLog +++ b/sci-chemistry/gromacs/ChangeLog @@ -1,6 +1,12 @@ # ChangeLog for sci-chemistry/gromacs # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.125 2013/05/28 03:28:04 ottxor Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.126 2013/06/01 21:36:28 ottxor Exp $ + +*gromacs-4.6.2 (01 Jun 2013) + + 01 Jun 2013; Christoph Junghans <ottxor@gentoo.org> +gromacs-4.6.2.ebuild, + -files/gromacs-4.6.1-openmm.patch, -gromacs-4.6.1.ebuild: + version bump 28 May 2013; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.1.ebuild: fixed a typo, which prevented cuda build diff --git a/sci-chemistry/gromacs/files/gromacs-4.6.1-openmm.patch b/sci-chemistry/gromacs/files/gromacs-4.6.1-openmm.patch deleted file mode 100644 index dd4214af0513..000000000000 --- a/sci-chemistry/gromacs/files/gromacs-4.6.1-openmm.patch +++ /dev/null @@ -1,151 +0,0 @@ -From e96c29f92e6cd1dd05945ef80e6a78d55747cf2e Mon Sep 17 00:00:00 2001 -From: Christoph Junghans <junghans@votca.org> -Date: Thu, 17 Jan 2013 20:30:30 -0700 -Subject: [PATCH] fix out of source build for OpenMM - -* introduced in e508a07b6e127fa1cf31d263bcbd33e4040066cb - -Change-Id: I6ad45fd2d5766d1c4a91ef2e0c442ff030fc1296 ---- - CMakeLists.txt | 2 +- - src/contrib/BuildMdrunOpenMM.cmake | 6 +++--- - src/contrib/CMakeLists.txt | 3 --- - src/contrib/mdrun_openmm.c | 12 +++++++----- - src/contrib/openmm_wrapper.cpp | 1 + - src/kernel/CMakeLists.txt | 5 ++++- - 6 files changed, 16 insertions(+), 13 deletions(-) - -diff --git a/CMakeLists.txt b/CMakeLists.txt -index df12172..4c11a29 100644 ---- a/CMakeLists.txt -+++ b/CMakeLists.txt -@@ -153,7 +153,7 @@ mark_as_advanced(GMX_FORCE_CXX) - option(GMX_COOL_QUOTES "Enable Gromacs cool quotes" ON) - mark_as_advanced(GMX_COOL_QUOTES) - --if(GMX_GPU OR GMX_FORCE_CXX) -+if(GMX_GPU OR GMX_FORCE_CXX OR GMX_OPENMM) - enable_language(CXX) - endif() - set(CMAKE_PREFIX_PATH "" CACHE STRING "Extra locations to search for external libraries and tools (give directory without lib, bin, or include)") -diff --git a/src/contrib/BuildMdrunOpenMM.cmake b/src/contrib/BuildMdrunOpenMM.cmake -index bc954d6..6d04958 100644 ---- a/src/contrib/BuildMdrunOpenMM.cmake -+++ b/src/contrib/BuildMdrunOpenMM.cmake -@@ -39,14 +39,14 @@ link_directories(${OpenMM_LIBRARY_DIR}) - # if the same OpenMM installation is used for running and building - add_definitions( -DOPENMM_PLUGIN_DIR="${OpenMM_PLUGIN_DIR}" ) - file(TO_CMAKE_PATH ${OpenMM_PLUGIN_DIR} _path) --add_library(openmm_api_wrapper STATIC openmm_wrapper.cpp) -+add_library(openmm_api_wrapper STATIC ${CMAKE_SOURCE_DIR}/src/contrib/openmm_wrapper.cpp) - target_link_libraries(openmm_api_wrapper ${OpenMM_LIBRARIES}) - list(APPEND GMX_EXTRA_LIBRARIES openmm_api_wrapper ${OpenMM_LIBRARIES}) - - list(REMOVE_ITEM MDRUN_SOURCES mdrun.c) - list(APPEND MDRUN_SOURCES -- ${CMAKE_CURRENT_SOURCE_DIR}/src/contrib/md_openmm.c -- ${CMAKE_CURRENT_SOURCE_DIR}/src/contrib/mdrun_openmm.c) -+ ${CMAKE_SOURCE_DIR}/src/contrib/md_openmm.c -+ ${CMAKE_SOURCE_DIR}/src/contrib/mdrun_openmm.c) - - # this is to circumvent the following MSVC error: - # warning LNK4098: defaultlib 'LIBCMT' conflicts with use of other libs -diff --git a/src/contrib/CMakeLists.txt b/src/contrib/CMakeLists.txt -index 7c5bb83..7725210 100644 ---- a/src/contrib/CMakeLists.txt -+++ b/src/contrib/CMakeLists.txt -@@ -49,7 +49,6 @@ if(GMX_OPENMM) - message(FATAL_ERROR "The OpenMM build is not compatible with the native GPU build") - endif() - -- enable_language(CXX) - set (GMX_BINARY_SUFFIX "-openmm") - set (GMX_LIBS_SUFFIX "_openmm") - -@@ -99,8 +98,6 @@ if(GMX_OPENMM) - if(CMAKE_BUILD_TYPE STREQUAL "DEBUG") - set(CUDA_VERBOSE_BUILD ON) - endif() -- list(APPEND CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/src/contrib) -- find_package(OpenMM) - - # mark as advanced the unused variables - mark_as_advanced(FORCE GMX_CPU_ACCELERATION GMX_MPI GMX_FFT_LIBRARY -diff --git a/src/contrib/mdrun_openmm.c b/src/contrib/mdrun_openmm.c -index 7771dcd..aeedeb4 100644 ---- a/src/contrib/mdrun_openmm.c -+++ b/src/contrib/mdrun_openmm.c -@@ -153,7 +153,7 @@ int cmain(int argc,char *argv[]) - { efXVG, "-tpi", "tpi", ffOPTWR }, - { efXVG, "-tpid", "tpidist", ffOPTWR }, - { efEDI, "-ei", "sam", ffOPTRD }, -- { efEDO, "-eo", "sam", ffOPTWR }, -+ { efXVG, "-eo", "sam", ffOPTWR }, - { efGCT, "-j", "wham", ffOPTRD }, - { efGCT, "-jo", "bam", ffOPTWR }, - { efXVG, "-ffout", "gct", ffOPTWR }, -@@ -205,6 +205,8 @@ int cmain(int argc,char *argv[]) - { NULL, "interleave", "pp_pme", "cartesian", NULL }; - const char *dddlb_opt[] = - { NULL, "auto", "no", "yes", NULL }; -+ const char *thread_aff_opt[threadaffNR+1] = -+ { NULL, "auto", "no", "yes", NULL }; - const char *nbpu_opt[] = - { NULL, "auto", "cpu", "gpu", "gpu_cpu", NULL }; - real rdd=0.0,rconstr=0.0,dlb_scale=0.8,pforce=-1; -@@ -236,12 +238,12 @@ int cmain(int argc,char *argv[]) - "Number of OpenMP threads per MPI process/thread to start (0 is guess)" }, - { "-ntomp_pme", FALSE, etINT, {&hw_opt.nthreads_omp_pme}, - "Number of OpenMP threads per MPI process/thread to start (0 is -ntomp)" }, -- { "-pin", FALSE, etBOOL, {&hw_opt.bThreadPinning}, -+ { "-pin", FALSE, etBOOL, {thread_aff_opt}, - "Pin OpenMP threads to cores" }, -- { "-pinht", FALSE, etBOOL, {&hw_opt.bPinHyperthreading}, -- "Always pin threads to Hyper-Threading cores" }, - { "-pinoffset", FALSE, etINT, {&hw_opt.core_pinning_offset}, - "Core offset for pinning (for running multiple mdrun processes on a single physical node)" }, -+ { "-pinstride", FALSE, etINT, {&hw_opt.core_pinning_stride}, -+ "Pinning distance in logical cores for threads, use 0 to minimize the number of threads per physical core" }, - { "-gpu_id", FALSE, etSTR, {&hw_opt.gpu_id}, - "List of GPU id's to use" }, - { "-ddcheck", FALSE, etBOOL, {&bDDBondCheck}, -@@ -413,7 +415,7 @@ int cmain(int argc,char *argv[]) - - if (MULTISIM(cr) && MASTER(cr)) - { -- check_multi_int(stdout,cr->ms,sim_part,"simulation part"); -+ check_multi_int(stdout,cr->ms,sim_part,"simulation part", TRUE); - } - } - else -diff --git a/src/contrib/openmm_wrapper.cpp b/src/contrib/openmm_wrapper.cpp -index 07f0eca..05c3210 100644 ---- a/src/contrib/openmm_wrapper.cpp -+++ b/src/contrib/openmm_wrapper.cpp -@@ -63,6 +63,7 @@ using namespace std; - #include "mdrun.h" - #include "physics.h" - #include "string2.h" -+#include "openmm_gpu_utils.h" - #include "gpu_utils.h" - #include "mtop_util.h" - -diff --git a/src/kernel/CMakeLists.txt b/src/kernel/CMakeLists.txt -index 01e290c..3f95d33 100644 ---- a/src/kernel/CMakeLists.txt -+++ b/src/kernel/CMakeLists.txt -@@ -88,7 +88,10 @@ if(GMX_OPENMM) - # Even though the OpenMM build has "moved to contrib", many things - # have be be done from within the scope of the CMakeLists.txt that - # builds its mdrun, and that is here -- include(../contrib/BuildMdrunOpenMM) -+ list(APPEND CMAKE_MODULE_PATH ${CMAKE_SOURCE_DIR}/src/contrib) -+ find_package(OpenMM) -+ include_directories(${CMAKE_CURRENT_SOURCE_DIR}) -+ include(${CMAKE_SOURCE_DIR}/src/contrib/BuildMdrunOpenMM.cmake) - endif(GMX_OPENMM) - - if(GMX_GPU OR GMX_FORCE_CXX) --- -1.8.1.5 - diff --git a/sci-chemistry/gromacs/gromacs-4.6.1.ebuild b/sci-chemistry/gromacs/gromacs-4.6.2.ebuild index a277b67824d5..be02e1d0463d 100644 --- a/sci-chemistry/gromacs/gromacs-4.6.1.ebuild +++ b/sci-chemistry/gromacs/gromacs-4.6.2.ebuild @@ -1,11 +1,11 @@ # Copyright 1999-2013 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-4.6.1.ebuild,v 1.3 2013/05/28 03:28:04 ottxor Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-4.6.2.ebuild,v 1.1 2013/06/01 21:36:28 ottxor Exp $ EAPI=5 -TEST_PV="4.6.1" -MANUAL_PV="4.6.1" +TEST_PV="4.6.2" +MANUAL_PV="4.6.2" CMAKE_MAKEFILE_GENERATOR="ninja" @@ -20,6 +20,7 @@ if [[ $PV = *9999* ]]; then inherit git-2 LIVE_DEPEND="doc? ( dev-texlive/texlive-latex + dev-texlive/texlive-latexextra media-gfx/imagemagick sys-apps/coreutils )" @@ -27,7 +28,6 @@ else SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${P}.tar.gz doc? ( ftp://ftp.gromacs.org/pub/manual/manual-${MANUAL_PV}.pdf -> ${PN}-manual-${MANUAL_PV}.pdf ) test? ( http://${PN}.googlecode.com/files/regressiontests-${TEST_PV}.tar.gz )" - PATCHES=( "${FILESDIR}/${P}-openmm.patch" ) LIVE_DEPEND="" fi @@ -182,7 +182,7 @@ src_configure() { [[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF" local cuda=( "-DGMX_GPU=OFF" ) [[ ${x} = "float" ]] && use cuda && \ - cuda=( -DGMX_GPU=ON -DCUDA_HOST_COMPILER_OPTIONS="${NVCCFLAGS}" ) + cuda=( -DGMX_GPU=ON ) mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_MPI=OFF $(cmake-utils_use threads GMX_THREAD_MPI) "${cuda[@]}" -DGMX_OPENMM=OFF "$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")" @@ -243,7 +243,10 @@ src_install() { mycmakeargs=( -DGMXBIN="${ED}"/usr/bin -DGMXSRC="${WORKDIR}/${P}" ) BUILD_DIR="${WORKDIR}"/manual_build \ CMAKE_USE_DIR="${WORKDIR}/manual" cmake-utils_src_configure + [[ ${CHOST} = *-darwin* ]] && \ + export DYLD_LIBRARY_PATH="${DYLD_LIBRARY_PATH}${DYLD_LIBRARY_PATH:+:}${ED}/usr/$(get_libdir)" BUILD_DIR="${WORKDIR}"/manual_build cmake-utils_src_make + [[ ${CHOST} = *-darwin* ]] && DYLD_LIBRARY_PATH="${ED}/usr/$(get_libdir)" newdoc "${WORKDIR}"/manual_build/gromacs.pdf "${PN}-manual-${PV}.pdf" fi use mpi || continue |