gromacs-5.0.4 patch

gromacs-5.1.0 beta patch

patches/gromacs-5.1.0.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(){
+cat << EOF
+
+PLUMED can be incorporated into gromacs using the standard patching procedure.
+Patching must be done in the gromacs root directory  _before_ the cmake command is invoked.
+
+To enable PLUMED in a gromacs simulation one should use
+mdrun with an extra -plumed flag. The flag can be used to
+specify the name of the PLUMED input file, e.g.:
+
+gmx mdrun -plumed plumed.dat
+
+For more information on gromacs you should visit http://www.gromacs.org
+
+EOF
+}
+

patches/gromacs-5.1.0.diff/src/gromacs/CMakeLists.txt

+#
+# This file is part of the GROMACS molecular simulation package.
+#
+# Copyright (c) 2010,2011,2012,2013,2014,2015, 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)
+
+set_property(GLOBAL PROPERTY GMX_INSTALLED_HEADERS)
+
+function (gmx_install_headers)
+    if (NOT GMX_BUILD_MDRUN_ONLY)
+        file(RELATIVE_PATH _dest ${PROJECT_SOURCE_DIR}/src ${CMAKE_CURRENT_LIST_DIR})
+        install(FILES       ${ARGN}
+                DESTINATION "${INCL_INSTALL_DIR}/${_dest}"
+                COMPONENT   development)
+    endif()
+    foreach (_file ${ARGN})
+        if (IS_ABSOLUTE "${_file}")
+            set_property(GLOBAL APPEND PROPERTY GMX_INSTALLED_HEADERS ${_file})
+        else()
+            set_property(GLOBAL APPEND PROPERTY GMX_INSTALLED_HEADERS
+                         ${CMAKE_CURRENT_LIST_DIR}/${_file})
+        endif()
+    endforeach()
+endfunction ()
+
+function (gmx_write_installed_header_list)
+    get_property(_list GLOBAL PROPERTY GMX_INSTALLED_HEADERS)
+    string(REPLACE ";" "\n" _list "${_list}")
+    # TODO: Make this only update the file timestamp if the contents actually change.
+    file(WRITE ${CMAKE_CURRENT_BINARY_DIR}/installed-headers.txt "${_list}")
+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(${TNG_IO_INCLUDE_DIRS})
+    endif()
+    if(NOT GMX_EXTERNAL_TNG)
+        include(${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 ${ZLIB_LIBRARIES})
+            include_directories(${ZLIB_INCLUDE_DIRS})
+        endif()
+    endif()
+else()
+    # We still need to get tng/tng_io_fwd.h from somewhere!
+    include_directories(BEFORE ${CMAKE_SOURCE_DIR}/src/external/tng_io/include)
+endif()
+
+add_subdirectory(gmxlib)
+add_subdirectory(mdlib)
+add_subdirectory(listed-forces)
+add_subdirectory(commandline)
+add_subdirectory(domdec)
+add_subdirectory(ewald)
+add_subdirectory(fft)
+add_subdirectory(linearalgebra)
+add_subdirectory(math)
+add_subdirectory(random)
+add_subdirectory(onlinehelp)
+add_subdirectory(options)
+add_subdirectory(pbcutil)
+add_subdirectory(timing)
+add_subdirectory(topology)
+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(gmxpreprocess)
+    add_subdirectory(correlationfunctions)
+    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})
+
+configure_file(version.h.cmakein version.h)
+gmx_install_headers(
+    analysisdata.h
+    commandline.h
+    options.h
+    selection.h
+    trajectoryanalysis.h
+    utility.h
+    ${CMAKE_CURRENT_BINARY_DIR}/version.h
+    )
+
+# This code is here instead of utility/CMakeLists.txt, because CMake
+# custom commands and source file properties can only be set in the directory
+# that contains the target that uses them.
+# TODO: Generate a header instead that can be included from baseversion.c.
+# That probably simplifies things somewhat.
+set(GENERATED_VERSION_FILE utility/baseversion-gen.c)
+gmx_configure_version_file(
+    utility/baseversion-gen.c.cmakein ${GENERATED_VERSION_FILE}
+    REMOTE_HASH SOURCE_FILE)
+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("listed-forces/bonded.cpp")
+   gmx_apply_gcc44_bug_workaround("mdlib/force.c")
+   gmx_apply_gcc44_bug_workaround("mdlib/constr.c")
+endif()
+
+if (GMX_GPU)
+    cuda_add_library(libgromacs ${LIBGROMACS_SOURCES}
+            OPTIONS
+            RELWITHDEBINFO -g
+            DEBUG -g -D_DEBUG_=1)
+else()
+    add_library(libgromacs ${LIBGROMACS_SOURCES})
+endif()
+
+# Recent versions of gcc and clang give warnings on scanner.cpp, which
+# is a generated source file. These are awkward to suppress inline, so
+# we do it in the compilation command (after testing that the compiler
+# supports the suppressions). Setting the properties only works after
+# the related target has been created, e.g. after when the file is
+# used with add_library().
+include(CheckCXXCompilerFlag)
+check_cxx_compiler_flag(-Wno-unused-parameter HAS_NO_UNUSED_PARAMETER)
+if (HAS_NO_UNUSED_PARAMETER)
+    set(_scanner_cpp_compiler_flags "${_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_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_MAJOR}
+                      VERSION ${LIBRARY_VERSION}
+                      COMPILE_FLAGS "${OpenMP_C_FLAGS}")
+
+gmx_write_installed_header_list()
+
+# 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
+            EXPORT libgromacs
+            LIBRARY DESTINATION ${LIB_INSTALL_DIR}
+            RUNTIME DESTINATION ${BIN_INSTALL_DIR}
+            ARCHIVE DESTINATION ${LIB_INSTALL_DIR}
+            COMPONENT libraries)
+endif()
+
+if (NOT GMX_BUILD_MDRUN_ONLY)
+    include(InstallLibInfo.cmake)
+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-5.1.0.diff/src/gromacs/CMakeLists.txt.preplumed

+#
+# This file is part of the GROMACS molecular simulation package.
+#
+# Copyright (c) 2010,2011,2012,2013,2014,2015, 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)
+
+set_property(GLOBAL PROPERTY GMX_INSTALLED_HEADERS)
+
+function (gmx_install_headers)
+    if (NOT GMX_BUILD_MDRUN_ONLY)
+        file(RELATIVE_PATH _dest ${PROJECT_SOURCE_DIR}/src ${CMAKE_CURRENT_LIST_DIR})
+        install(FILES       ${ARGN}
+                DESTINATION "${INCL_INSTALL_DIR}/${_dest}"
+                COMPONENT   development)
+    endif()
+    foreach (_file ${ARGN})
+        if (IS_ABSOLUTE "${_file}")
+            set_property(GLOBAL APPEND PROPERTY GMX_INSTALLED_HEADERS ${_file})
+        else()
+            set_property(GLOBAL APPEND PROPERTY GMX_INSTALLED_HEADERS
+                         ${CMAKE_CURRENT_LIST_DIR}/${_file})
+        endif()
+    endforeach()
+endfunction ()
+
+function (gmx_write_installed_header_list)
+    get_property(_list GLOBAL PROPERTY GMX_INSTALLED_HEADERS)
+    string(REPLACE ";" "\n" _list "${_list}")
+    # TODO: Make this only update the file timestamp if the contents actually change.
+    file(WRITE ${CMAKE_CURRENT_BINARY_DIR}/installed-headers.txt "${_list}")
+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(${TNG_IO_INCLUDE_DIRS})
+    endif()
+    if(NOT GMX_EXTERNAL_TNG)
+        include(${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 ${ZLIB_LIBRARIES})
+            include_directories(${ZLIB_INCLUDE_DIRS})
+        endif()
+    endif()
+else()
+    # We still need to get tng/tng_io_fwd.h from somewhere!
+    include_directories(BEFORE ${CMAKE_SOURCE_DIR}/src/external/tng_io/include)
+endif()
+
+add_subdirectory(gmxlib)
+add_subdirectory(mdlib)
+add_subdirectory(listed-forces)
+add_subdirectory(commandline)
+add_subdirectory(domdec)
+add_subdirectory(ewald)
+add_subdirectory(fft)
+add_subdirectory(linearalgebra)
+add_subdirectory(math)
+add_subdirectory(random)
+add_subdirectory(onlinehelp)
+add_subdirectory(options)
+add_subdirectory(pbcutil)
+add_subdirectory(timing)
+add_subdirectory(topology)
+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(gmxpreprocess)
+    add_subdirectory(correlationfunctions)
+    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})
+
+configure_file(version.h.cmakein version.h)
+gmx_install_headers(
+    analysisdata.h
+    commandline.h
+    options.h
+    selection.h
+    trajectoryanalysis.h
+    utility.h
+    ${CMAKE_CURRENT_BINARY_DIR}/version.h
+    )
+
+# This code is here instead of utility/CMakeLists.txt, because CMake
+# custom commands and source file properties can only be set in the directory
+# that contains the target that uses them.
+# TODO: Generate a header instead that can be included from baseversion.c.
+# That probably simplifies things somewhat.
+set(GENERATED_VERSION_FILE utility/baseversion-gen.c)
+gmx_configure_version_file(
+    utility/baseversion-gen.c.cmakein ${GENERATED_VERSION_FILE}
+    REMOTE_HASH SOURCE_FILE)
+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("listed-forces/bonded.cpp")
+   gmx_apply_gcc44_bug_workaround("mdlib/force.c")
+   gmx_apply_gcc44_bug_workaround("mdlib/constr.c")
+endif()
+
+if (GMX_GPU)
+    cuda_add_library(libgromacs ${LIBGROMACS_SOURCES}
+            OPTIONS
+            RELWITHDEBINFO -g
+            DEBUG -g -D_DEBUG_=1)
+else()
+    add_library(libgromacs ${LIBGROMACS_SOURCES})
+endif()
+
+# Recent versions of gcc and clang give warnings on scanner.cpp, which
+# is a generated source file. These are awkward to suppress inline, so
+# we do it in the compilation command (after testing that the compiler
+# supports the suppressions). Setting the properties only works after
+# the related target has been created, e.g. after when the file is
+# used with add_library().
+include(CheckCXXCompilerFlag)
+check_cxx_compiler_flag(-Wno-unused-parameter HAS_NO_UNUSED_PARAMETER)
+if (HAS_NO_UNUSED_PARAMETER)
+    set(_scanner_cpp_compiler_flags "${_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_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_MAJOR}
+                      VERSION ${LIBRARY_VERSION}
+                      COMPILE_FLAGS "${OpenMP_C_FLAGS}")
+
+gmx_write_installed_header_list()
+
+# 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
+            EXPORT libgromacs
+            LIBRARY DESTINATION ${LIB_INSTALL_DIR}
+            RUNTIME DESTINATION ${BIN_INSTALL_DIR}
+            ARCHIVE DESTINATION ${LIB_INSTALL_DIR}
+            COMPONENT libraries)
+endif()
+
+if (NOT GMX_BUILD_MDRUN_ONLY)
+    include(InstallLibInfo.cmake)
+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()