gromacs 5.0: patch

it should works, but more tests are needed

patches/gromacs-5.0.config

+
+
+function plumed_preliminary_test(){
+# check if the README contains the word GROMACS and if gromacs has been already configured
+  grep -q GROMACS README 1>/dev/null 2>/dev/null
+}
+
+function plumed_patch_info(){
+  echo ""
+  echo "PLUMED can be incorporated into gromacs using a simple patching procedure."
+  echo "Patching must be done _before_ the cmake command is invoked"
+  echo
+  echo "For more information on gromacs you should visit http://www.gromacs.org"
+}

patches/gromacs-5.0.diff/src/gromacs/CMakeLists.txt

+#
+# This file is part of the GROMACS molecular simulation package.
+#
+# Copyright (c) 2010,2011,2012,2013,2014, by the GROMACS development team, led by
+# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+# and including many others, as listed in the AUTHORS file in the
+# top-level source directory and at http://www.gromacs.org.
+#
+# GROMACS is free software; you can redistribute it and/or
+# modify it under the terms of the GNU Lesser General Public License
+# as published by the Free Software Foundation; either version 2.1
+# of the License, or (at your option) any later version.
+#
+# GROMACS is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+# Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with GROMACS; if not, see
+# http://www.gnu.org/licenses, or write to the Free Software Foundation,
+# Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
+#
+# If you want to redistribute modifications to GROMACS, please
+# consider that scientific software is very special. Version
+# control is crucial - bugs must be traceable. We will be happy to
+# consider code for inclusion in the official distribution, but
+# derived work must not be called official GROMACS. Details are found
+# in the README & COPYING files - if they are missing, get the
+# official version at http://www.gromacs.org.
+#
+# To help us fund GROMACS development, we humbly ask that you cite
+# the research papers on the package. Check out http://www.gromacs.org.
+
+include(${CMAKE_SOURCE_DIR}/Plumed.cmake)
+
+set(LIBGROMACS_SOURCES)
+
+function (gmx_install_headers DESTINATION)
+    if (NOT GMX_BUILD_MDRUN_ONLY)
+        if (DESTINATION)
+            set(DESTINATION ${INCL_INSTALL_DIR}/gromacs/${DESTINATION})
+        else()
+            set(DESTINATION ${INCL_INSTALL_DIR}/gromacs)
+        endif()
+        install(FILES ${ARGN} DESTINATION ${DESTINATION} COMPONENT development)
+    endif()
+endfunction ()
+
+if(GMX_USE_TNG)
+    option(GMX_EXTERNAL_TNG "Use external TNG instead of compiling the version shipped with GROMACS."
+           OFF)
+    # Detect TNG if GMX_EXTERNAL_TNG is explicitly ON
+    if(GMX_EXTERNAL_TNG)
+        find_package(TNG_IO 1.6.0)
+        if(NOT TNG_IO_FOUND)
+            message(FATAL_ERROR
+                "TNG >= 1.6.0 not found. "
+                "You can set GMX_EXTERNAL_TNG=OFF to compile TNG.")
+        endif()
+        include_directories(${TNG_IO_INCLUDE_DIRS})
+    endif()
+    if(NOT GMX_EXTERNAL_TNG)
+        # TNG wants zlib if it is available
+        find_package(ZLIB QUIET)
+        include(gmxTestZLib)
+        gmx_test_zlib(HAVE_ZLIB)
+
+        include(${CMAKE_SOURCE_DIR}/src/external/tng_io/BuildTNG.cmake)
+        tng_get_source_list(TNG_SOURCES TNG_IO_DEFINITIONS)
+        list(APPEND LIBGROMACS_SOURCES ${TNG_SOURCES})
+        tng_set_source_properties(WITH_ZLIB ${HAVE_ZLIB})
+
+        if (HAVE_ZLIB)
+            list(APPEND GMX_EXTRA_LIBRARIES ${ZLIB_LIBRARIES})
+        endif()
+    endif()
+else()
+    # We still need to get tng/tng_io_fwd.h from somewhere!
+    include_directories(${CMAKE_SOURCE_DIR}/src/external/tng_io/include)
+endif()
+
+add_subdirectory(gmxlib)
+add_subdirectory(mdlib)
+add_subdirectory(gmxpreprocess)
+add_subdirectory(commandline)
+add_subdirectory(fft)
+add_subdirectory(linearalgebra)
+add_subdirectory(math)
+add_subdirectory(random)
+add_subdirectory(onlinehelp)
+add_subdirectory(options)
+add_subdirectory(timing)
+add_subdirectory(utility)
+add_subdirectory(fileio)
+add_subdirectory(swap)
+add_subdirectory(essentialdynamics)
+add_subdirectory(pulling)
+add_subdirectory(simd)
+add_subdirectory(imd)
+if (NOT GMX_BUILD_MDRUN_ONLY)
+    add_subdirectory(legacyheaders)
+    add_subdirectory(gmxana)
+    add_subdirectory(statistics)
+    add_subdirectory(analysisdata)
+    add_subdirectory(selection)
+    add_subdirectory(trajectoryanalysis)
+    add_subdirectory(tools)
+endif()
+
+list(APPEND LIBGROMACS_SOURCES ${GMXLIB_SOURCES} ${MDLIB_SOURCES})
+
+# This would be the standard way to include thread_mpi, but
+# we want libgromacs to link the functions directly
+#if(GMX_THREAD_MPI)
+#    add_subdirectory(thread_mpi)
+#endif()
+#target_link_libraries(gmx ${GMX_EXTRA_LIBRARIES} ${THREAD_MPI_LIB})
+
+tmpi_get_source_list(THREAD_MPI_SOURCES ${CMAKE_SOURCE_DIR}/src/external/thread_mpi/src)
+list(APPEND LIBGROMACS_SOURCES ${THREAD_MPI_SOURCES})
+
+file(GLOB LIBGROMACS_HEADERS *.h)
+configure_file(version.h.cmakein version.h)
+gmx_install_headers("" ${LIBGROMACS_HEADERS})
+gmx_install_headers("" ${CMAKE_CURRENT_BINARY_DIR}/version.h)
+
+# Add target that generates baseversion-gen.c every time make is run
+# if git version info is requested, or create it statically.
+# This code is here instead of utility/CMakeLists.txt because CMake
+# ignores set_source_file_properties from subdirectories.
+set(GENERATED_VERSION_FILE
+    ${CMAKE_CURRENT_BINARY_DIR}/utility/baseversion-gen.c)
+set(GENERATED_VERSION_FILE_SOURCE
+    ${CMAKE_CURRENT_SOURCE_DIR}/utility/baseversion-gen.c.cmakein)
+if (GMX_GIT_VERSION_INFO)
+    add_custom_target(gmx-version ALL
+            COMMAND ${CMAKE_COMMAND}
+                -D GIT_EXECUTABLE="${GIT_EXECUTABLE}"
+                -D PROJECT_VERSION="${PROJECT_VERSION}"
+                -D PROJECT_SOURCE_DIR="${PROJECT_SOURCE_DIR}"
+                -D VERSION_CMAKEIN=${GENERATED_VERSION_FILE_SOURCE}
+                -D VERSION_OUT=${GENERATED_VERSION_FILE}
+                -P ${CMAKE_SOURCE_DIR}/cmake/gmxGenerateVersionInfo.cmake
+            WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
+            DEPENDS ${GENERATED_VERSION_FILE_SOURCE}
+            COMMENT "Generating git version information")
+    set_source_files_properties(${GENERATED_VERSION_FILE}
+                                PROPERTIES GENERATED true)
+else()
+    set(GMX_PROJECT_VERSION_STR ${PROJECT_VERSION})
+    configure_file(${GENERATED_VERSION_FILE_SOURCE} ${GENERATED_VERSION_FILE})
+endif()
+list(APPEND LIBGROMACS_SOURCES ${GENERATED_VERSION_FILE})
+
+# apply gcc 4.4.x bug workaround
+if(GMX_USE_GCC44_BUG_WORKAROUND)
+   include(gmxGCC44O3BugWorkaround)
+   gmx_apply_gcc44_bug_workaround("gmxlib/bondfree.c")
+   gmx_apply_gcc44_bug_workaround("mdlib/force.c")
+   gmx_apply_gcc44_bug_workaround("mdlib/constr.c")
+endif()
+
+add_library(libgromacs ${LIBGROMACS_SOURCES})
+if (GMX_GIT_VERSION_INFO)
+    add_dependencies(libgromacs gmx-version)
+endif()
+
+# Recent versions of gcc and clang give warnings on scanner.cpp, which
+# is a generated source file. These are awkward to suppress inline, so
+# we do it in the compilation command (after testing that the compiler
+# supports the suppressions). Setting the properties only works after
+# the related target has been created, e.g. after when the file is
+# used with add_library().
+include(CheckCXXCompilerFlag)
+check_cxx_compiler_flag(-Wno-unused-parameter HAS_NO_UNUSED_PARAMETER)
+if (HAS_NO_UNUSED_PARAMETER)
+    set(_scanner_cpp_compiler_flags "${_scanner_cpp_compiler_flags} -Wno-unused-parameter")
+endif()
+check_cxx_compiler_flag(-Wno-deprecated-register HAS_NO_DEPRECATED_REGISTER)
+if (HAS_NO_DEPRECATED_REGISTER)
+    set(_scanner_cpp_compiler_flags "${_scanner_cpp_compiler_flags} -Wno-deprecated-register")
+else()
+    check_cxx_compiler_flag(-Wno-deprecated HAS_NO_DEPRECATED)
+    if (HAS_NO_DEPRECATED)
+        set(_scanner_cpp_compiler_flags "${_scanner_cpp_compiler_flags} -Wno-deprecated")
+    endif()
+endif()
+set_source_files_properties(selection/scanner.cpp PROPERTIES COMPILE_FLAGS "${_scanner_cpp_compiler_flags}")
+
+target_link_libraries(libgromacs
+                      ${EXTRAE_LIBRARIES}
+                      ${GMX_GPU_LIBRARIES}
+                      ${GMX_EXTRA_LIBRARIES}
+                      ${TNG_IO_LIBRARIES}
+                      ${FFT_LIBRARIES} ${LINEAR_ALGEBRA_LIBRARIES}
+                      ${XML_LIBRARIES}
+                      ${THREAD_LIB} ${GMX_SHARED_LINKER_FLAGS} ${PLUMED_LOAD})
+set_target_properties(libgromacs PROPERTIES
+                      OUTPUT_NAME "gromacs${GMX_LIBS_SUFFIX}"
+                      SOVERSION ${LIBRARY_SOVERSION}
+                      VERSION ${LIBRARY_VERSION}
+                      COMPILE_FLAGS "${OpenMP_C_FLAGS}")
+
+# Only install the library in mdrun-only mode if it is actually necessary
+# for the binary
+if (NOT GMX_BUILD_MDRUN_ONLY OR BUILD_SHARED_LIBS)
+    install(TARGETS libgromacs DESTINATION ${LIB_INSTALL_DIR} COMPONENT libraries)
+endif()
+
+if (NOT GMX_BUILD_MDRUN_ONLY)
+    configure_file(${CMAKE_CURRENT_SOURCE_DIR}/libgromacs.pc.cmakein
+                   ${CMAKE_CURRENT_BINARY_DIR}/libgromacs.pc @ONLY)
+    install(FILES ${CMAKE_CURRENT_BINARY_DIR}/libgromacs.pc
+            DESTINATION ${LIB_INSTALL_DIR}/pkgconfig
+            RENAME "libgromacs${GMX_LIBS_SUFFIX}.pc"
+            COMPONENT development)
+endif()
+
+if (INSTALL_CUDART_LIB) #can be set manual by user
+    if (GMX_GPU)
+        foreach(CUDA_LIB ${CUDA_LIBRARIES})
+            string(REGEX MATCH "cudart" IS_CUDART ${CUDA_LIB})
+            if(IS_CUDART) #libcuda should not be installed
+                #install also name-links (linker uses those)
+                file(GLOB CUDA_LIBS ${CUDA_LIB}*)
+                install(FILES ${CUDA_LIBS} DESTINATION
+                    ${LIB_INSTALL_DIR} COMPONENT libraries)
+            endif()
+        endforeach()
+    else()
+        message(WARNING "INSTALL_CUDART_LIB only makes sense with GMX_GPU")
+    endif()
+endif()

patches/gromacs-5.0.diff/src/gromacs/CMakeLists.txt.preplumed

+#
+# This file is part of the GROMACS molecular simulation package.
+#
+# Copyright (c) 2010,2011,2012,2013,2014, by the GROMACS development team, led by
+# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+# and including many others, as listed in the AUTHORS file in the
+# top-level source directory and at http://www.gromacs.org.
+#
+# GROMACS is free software; you can redistribute it and/or
+# modify it under the terms of the GNU Lesser General Public License
+# as published by the Free Software Foundation; either version 2.1
+# of the License, or (at your option) any later version.
+#
+# GROMACS is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+# Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with GROMACS; if not, see
+# http://www.gnu.org/licenses, or write to the Free Software Foundation,
+# Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
+#
+# If you want to redistribute modifications to GROMACS, please
+# consider that scientific software is very special. Version
+# control is crucial - bugs must be traceable. We will be happy to
+# consider code for inclusion in the official distribution, but
+# derived work must not be called official GROMACS. Details are found
+# in the README & COPYING files - if they are missing, get the
+# official version at http://www.gromacs.org.
+#
+# To help us fund GROMACS development, we humbly ask that you cite
+# the research papers on the package. Check out http://www.gromacs.org.
+
+set(LIBGROMACS_SOURCES)
+
+function (gmx_install_headers DESTINATION)
+    if (NOT GMX_BUILD_MDRUN_ONLY)
+        if (DESTINATION)
+            set(DESTINATION ${INCL_INSTALL_DIR}/gromacs/${DESTINATION})
+        else()
+            set(DESTINATION ${INCL_INSTALL_DIR}/gromacs)
+        endif()
+        install(FILES ${ARGN} DESTINATION ${DESTINATION} COMPONENT development)
+    endif()
+endfunction ()
+
+if(GMX_USE_TNG)
+    option(GMX_EXTERNAL_TNG "Use external TNG instead of compiling the version shipped with GROMACS."
+           OFF)
+    # Detect TNG if GMX_EXTERNAL_TNG is explicitly ON
+    if(GMX_EXTERNAL_TNG)
+        find_package(TNG_IO 1.6.0)
+        if(NOT TNG_IO_FOUND)
+            message(FATAL_ERROR
+                "TNG >= 1.6.0 not found. "
+                "You can set GMX_EXTERNAL_TNG=OFF to compile TNG.")
+        endif()
+        include_directories(${TNG_IO_INCLUDE_DIRS})
+    endif()
+    if(NOT GMX_EXTERNAL_TNG)
+        # TNG wants zlib if it is available
+        find_package(ZLIB QUIET)
+        include(gmxTestZLib)
+        gmx_test_zlib(HAVE_ZLIB)
+
+        include(${CMAKE_SOURCE_DIR}/src/external/tng_io/BuildTNG.cmake)
+        tng_get_source_list(TNG_SOURCES TNG_IO_DEFINITIONS)
+        list(APPEND LIBGROMACS_SOURCES ${TNG_SOURCES})
+        tng_set_source_properties(WITH_ZLIB ${HAVE_ZLIB})
+
+        if (HAVE_ZLIB)
+            list(APPEND GMX_EXTRA_LIBRARIES ${ZLIB_LIBRARIES})
+        endif()
+    endif()
+else()
+    # We still need to get tng/tng_io_fwd.h from somewhere!
+    include_directories(${CMAKE_SOURCE_DIR}/src/external/tng_io/include)
+endif()
+
+add_subdirectory(gmxlib)
+add_subdirectory(mdlib)
+add_subdirectory(gmxpreprocess)
+add_subdirectory(commandline)
+add_subdirectory(fft)
+add_subdirectory(linearalgebra)
+add_subdirectory(math)
+add_subdirectory(random)
+add_subdirectory(onlinehelp)
+add_subdirectory(options)
+add_subdirectory(timing)
+add_subdirectory(utility)
+add_subdirectory(fileio)
+add_subdirectory(swap)
+add_subdirectory(essentialdynamics)
+add_subdirectory(pulling)
+add_subdirectory(simd)
+add_subdirectory(imd)
+if (NOT GMX_BUILD_MDRUN_ONLY)
+    add_subdirectory(legacyheaders)
+    add_subdirectory(gmxana)
+    add_subdirectory(statistics)
+    add_subdirectory(analysisdata)
+    add_subdirectory(selection)
+    add_subdirectory(trajectoryanalysis)
+    add_subdirectory(tools)
+endif()
+
+list(APPEND LIBGROMACS_SOURCES ${GMXLIB_SOURCES} ${MDLIB_SOURCES})
+
+# This would be the standard way to include thread_mpi, but
+# we want libgromacs to link the functions directly
+#if(GMX_THREAD_MPI)
+#    add_subdirectory(thread_mpi)
+#endif()
+#target_link_libraries(gmx ${GMX_EXTRA_LIBRARIES} ${THREAD_MPI_LIB})
+
+tmpi_get_source_list(THREAD_MPI_SOURCES ${CMAKE_SOURCE_DIR}/src/external/thread_mpi/src)
+list(APPEND LIBGROMACS_SOURCES ${THREAD_MPI_SOURCES})
+
+file(GLOB LIBGROMACS_HEADERS *.h)
+configure_file(version.h.cmakein version.h)
+gmx_install_headers("" ${LIBGROMACS_HEADERS})
+gmx_install_headers("" ${CMAKE_CURRENT_BINARY_DIR}/version.h)
+
+# Add target that generates baseversion-gen.c every time make is run
+# if git version info is requested, or create it statically.
+# This code is here instead of utility/CMakeLists.txt because CMake
+# ignores set_source_file_properties from subdirectories.
+set(GENERATED_VERSION_FILE
+    ${CMAKE_CURRENT_BINARY_DIR}/utility/baseversion-gen.c)
+set(GENERATED_VERSION_FILE_SOURCE
+    ${CMAKE_CURRENT_SOURCE_DIR}/utility/baseversion-gen.c.cmakein)
+if (GMX_GIT_VERSION_INFO)
+    add_custom_target(gmx-version ALL
+            COMMAND ${CMAKE_COMMAND}
+                -D GIT_EXECUTABLE="${GIT_EXECUTABLE}"
+                -D PROJECT_VERSION="${PROJECT_VERSION}"
+                -D PROJECT_SOURCE_DIR="${PROJECT_SOURCE_DIR}"
+                -D VERSION_CMAKEIN=${GENERATED_VERSION_FILE_SOURCE}
+                -D VERSION_OUT=${GENERATED_VERSION_FILE}
+                -P ${CMAKE_SOURCE_DIR}/cmake/gmxGenerateVersionInfo.cmake
+            WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
+            DEPENDS ${GENERATED_VERSION_FILE_SOURCE}
+            COMMENT "Generating git version information")
+    set_source_files_properties(${GENERATED_VERSION_FILE}
+                                PROPERTIES GENERATED true)
+else()
+    set(GMX_PROJECT_VERSION_STR ${PROJECT_VERSION})
+    configure_file(${GENERATED_VERSION_FILE_SOURCE} ${GENERATED_VERSION_FILE})
+endif()
+list(APPEND LIBGROMACS_SOURCES ${GENERATED_VERSION_FILE})
+
+# apply gcc 4.4.x bug workaround
+if(GMX_USE_GCC44_BUG_WORKAROUND)
+   include(gmxGCC44O3BugWorkaround)
+   gmx_apply_gcc44_bug_workaround("gmxlib/bondfree.c")
+   gmx_apply_gcc44_bug_workaround("mdlib/force.c")
+   gmx_apply_gcc44_bug_workaround("mdlib/constr.c")
+endif()
+
+add_library(libgromacs ${LIBGROMACS_SOURCES})
+if (GMX_GIT_VERSION_INFO)
+    add_dependencies(libgromacs gmx-version)
+endif()
+
+# Recent versions of gcc and clang give warnings on scanner.cpp, which
+# is a generated source file. These are awkward to suppress inline, so
+# we do it in the compilation command (after testing that the compiler
+# supports the suppressions). Setting the properties only works after
+# the related target has been created, e.g. after when the file is
+# used with add_library().
+include(CheckCXXCompilerFlag)
+check_cxx_compiler_flag(-Wno-unused-parameter HAS_NO_UNUSED_PARAMETER)
+if (HAS_NO_UNUSED_PARAMETER)
+    set(_scanner_cpp_compiler_flags "${_scanner_cpp_compiler_flags} -Wno-unused-parameter")
+endif()
+check_cxx_compiler_flag(-Wno-deprecated-register HAS_NO_DEPRECATED_REGISTER)
+if (HAS_NO_DEPRECATED_REGISTER)
+    set(_scanner_cpp_compiler_flags "${_scanner_cpp_compiler_flags} -Wno-deprecated-register")
+else()
+    check_cxx_compiler_flag(-Wno-deprecated HAS_NO_DEPRECATED)
+    if (HAS_NO_DEPRECATED)
+        set(_scanner_cpp_compiler_flags "${_scanner_cpp_compiler_flags} -Wno-deprecated")
+    endif()
+endif()
+set_source_files_properties(selection/scanner.cpp PROPERTIES COMPILE_FLAGS "${_scanner_cpp_compiler_flags}")
+
+target_link_libraries(libgromacs
+                      ${EXTRAE_LIBRARIES}
+                      ${GMX_GPU_LIBRARIES}
+                      ${GMX_EXTRA_LIBRARIES}
+                      ${TNG_IO_LIBRARIES}
+                      ${FFT_LIBRARIES} ${LINEAR_ALGEBRA_LIBRARIES}
+                      ${XML_LIBRARIES}
+                      ${THREAD_LIB} ${GMX_SHARED_LINKER_FLAGS})
+set_target_properties(libgromacs PROPERTIES
+                      OUTPUT_NAME "gromacs${GMX_LIBS_SUFFIX}"
+                      SOVERSION ${LIBRARY_SOVERSION}
+                      VERSION ${LIBRARY_VERSION}
+                      COMPILE_FLAGS "${OpenMP_C_FLAGS}")
+
+# Only install the library in mdrun-only mode if it is actually necessary
+# for the binary
+if (NOT GMX_BUILD_MDRUN_ONLY OR BUILD_SHARED_LIBS)
+    install(TARGETS libgromacs DESTINATION ${LIB_INSTALL_DIR} COMPONENT libraries)
+endif()
+
+if (NOT GMX_BUILD_MDRUN_ONLY)
+    configure_file(${CMAKE_CURRENT_SOURCE_DIR}/libgromacs.pc.cmakein
+                   ${CMAKE_CURRENT_BINARY_DIR}/libgromacs.pc @ONLY)
+    install(FILES ${CMAKE_CURRENT_BINARY_DIR}/libgromacs.pc
+            DESTINATION ${LIB_INSTALL_DIR}/pkgconfig
+            RENAME "libgromacs${GMX_LIBS_SUFFIX}.pc"
+            COMPONENT development)
+endif()
+
+if (INSTALL_CUDART_LIB) #can be set manual by user
+    if (GMX_GPU)
+        foreach(CUDA_LIB ${CUDA_LIBRARIES})
+            string(REGEX MATCH "cudart" IS_CUDART ${CUDA_LIB})
+            if(IS_CUDART) #libcuda should not be installed
+                #install also name-links (linker uses those)
+                file(GLOB CUDA_LIBS ${CUDA_LIB}*)
+                install(FILES ${CUDA_LIBS} DESTINATION
+                    ${LIB_INSTALL_DIR} COMPONENT libraries)
+            endif()
+        endforeach()
+    else()
+        message(WARNING "INSTALL_CUDART_LIB only makes sense with GMX_GPU")
+    endif()
+endif()