patch: gmx466

patches/gromacs-4.6.6.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-4.6.6.diff/src/kernel/CMakeLists.txt

+#
+# This file is part of the GROMACS molecular simulation package.
+#
+# Copyright (c) 2012,2013, by the GROMACS development team, led by
+# David van der Spoel, Berk Hess, 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(GMXPREPROCESS_SOURCES 
+    add_par.c       
+    calc_verletbuf.c
+    compute_io.c    
+    convparm.c      
+    gen_ad.c        
+    gen_vsite.c     
+    genhydro.c   
+    gpp_atomtype.c  
+    gpp_bond_atomtype.c     
+    h_db.c          
+    hackblock.c             
+    hizzie.c        
+    nm2type.c
+    pdb2top.c       
+    pgutil.c        
+    readir.c        
+    readpull.c      
+    readadress.c      
+    readrot.c
+    resall.c        
+    sorting.c       
+    specbond.c      
+    ter_db.c        
+    tomorse.c       
+    topdirs.c       
+    topexcl.c       
+    topio.c         
+    toppush.c       
+    topshake.c      
+    toputil.c       
+    tpbcmp.c        
+    vsite_parm.c    
+    fflibutil.c
+    xlate.c)
+
+set(MDRUN_SOURCES 
+    gctio.c    ionize.c runner.c
+    do_gct.c     repl_ex.c  xutils.c pme_loadbal.c
+    md.c         mdrun.c    genalg.c membed.c)
+
+add_library(gmxpreprocess ${GMXPREPROCESS_SOURCES})
+target_link_libraries(gmxpreprocess md)
+set_target_properties(gmxpreprocess PROPERTIES OUTPUT_NAME "gmxpreprocess${GMX_LIBS_SUFFIX}" SOVERSION ${SOVERSION}
+    COMPILE_FLAGS "${OpenMP_C_FLAGS}")
+
+
+if(GMX_GPU)
+    include_directories(${CMAKE_SOURCE_DIR}/src/gmxlib/gpu_utils)
+endif()
+
+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
+    list(APPEND CMAKE_MODULE_PATH ${CMAKE_SOURCE_DIR}/src/contrib)
+    find_package(OpenMM)
+    include_directories(${CMAKE_CURRENT_SOURCE_DIR})
+    include(${CMAKE_SOURCE_DIR}/src/contrib/BuildMdrunOpenMM.cmake)
+endif(GMX_OPENMM)
+
+if(GMX_GPU OR GMX_FORCE_CXX)
+    set_source_files_properties(main.c PROPERTIES LANGUAGE CXX)
+    if ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Clang")
+        set_source_files_properties(main.c PROPERTIES COMPILE_FLAGS "-x c++")
+    endif()
+endif()
+
+if(GMX_FAHCORE)
+  add_library(fahcore ${MDRUN_SOURCES})
+else(GMX_FAHCORE)
+
+set(GMX_KERNEL_PROGRAMS
+    grompp tpbconv pdb2gmx g_protonate gmxdump g_x2top gmxcheck)
+if (NOT GMX_NO_QUOTES)
+  set(GMX_KERNEL_PROGRAMS ${GMX_KERNEL_PROGRAMS} g_luck)
+endif (NOT GMX_NO_QUOTES)
+
+
+foreach(PROGRAM ${GMX_KERNEL_PROGRAMS})
+    add_executable(${PROGRAM} ${PROGRAM}.c main.c)
+    if (NOT ${PROGRAM} STREQUAL "g_luck")
+        gmx_add_man_page(${PROGRAM})
+    endif()
+    target_link_libraries(${PROGRAM} gmxpreprocess md gmx ${OpenMP_LINKER_FLAGS})
+    set_target_properties(${PROGRAM} PROPERTIES OUTPUT_NAME "${PROGRAM}${GMX_BINARY_SUFFIX}")
+endforeach()
+
+add_executable(mdrun ${MDRUN_SOURCES} main.c)
+gmx_add_man_page(mdrun)
+target_link_libraries(mdrun gmxpreprocess md gmx ${OpenMP_LINKER_FLAGS} ${PLUMED_LOAD})
+set_target_properties(mdrun PROPERTIES OUTPUT_NAME "mdrun${GMX_BINARY_SUFFIX}" COMPILE_FLAGS "${OpenMP_C_FLAGS}")
+
+if(GMX_OPENMM)
+    target_link_libraries(mdrun openmm_api_wrapper)
+endif()
+
+# Construct component groups for installation; note that a component may
+# belong to only one group
+foreach(PROGRAM ${GMX_KERNEL_PROGRAMS})
+    set(CPACK_COMPONENT_${PROGRAM}_GROUP tools)
+endforeach()
+set(CPACK_COMPONENT_MDRUN_GROUP mdrun)
+
+foreach(PROGRAM ${GMX_KERNEL_PROGRAMS} mdrun)
+    # Manage CPack component dependencies
+    set(CPACK_COMPONENT_${PROGRAM}_DEPENDS libraries libraries-gmxpreprocess)
+
+    # Create custom install-xxxx target
+    if (BUILD_SHARED_LIBS)
+    # If shared libraries are used, we need to install the libraries in
+    # addition to the mdrun binary.
+       add_custom_target(install-${PROGRAM}
+           COMMAND ${CMAKE_COMMAND} -DCOMPONENT=libraries
+                   -P ${CMAKE_BINARY_DIR}/cmake_install.cmake
+           COMMAND ${CMAKE_COMMAND} -DCOMPONENT=libraries-gmxpreprocess
+                   -P ${CMAKE_BINARY_DIR}/cmake_install.cmake
+           COMMAND ${CMAKE_COMMAND} -DCOMPONENT=${PROGRAM}
+                   -P ${CMAKE_BINARY_DIR}/cmake_install.cmake
+           COMMENT "Installing ${PROGRAM}")
+    else()
+       add_custom_target(install-${PROGRAM}
+           COMMAND ${CMAKE_COMMAND} -DCOMPONENT=${PROGRAM}
+                   -P ${CMAKE_BINARY_DIR}/cmake_install.cmake
+           COMMENT "Installing ${PROGRAM}")
+    endif()
+    add_dependencies(install-${PROGRAM} ${PROGRAM})
+
+    # Finally, trigger installation
+    install(
+      TARGETS ${PROGRAM}
+      COMPONENT ${PROGRAM}
+      DESTINATION ${BIN_INSTALL_DIR}
+      )
+endforeach()
+
+install(TARGETS gmxpreprocess DESTINATION ${LIB_INSTALL_DIR} COMPONENT libraries-gmxpreprocess)
+
+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
+                    ${LIB_INSTALL_DIR} COMPONENT libraries)
+            endif()
+        endforeach()
+    else()
+        message(WARNING "INSTALL_CUDART_LIB only makes sense with GMX_GPU")
+    endif()
+endif ()
+endif(GMX_FAHCORE)
+
+configure_file(${CMAKE_CURRENT_SOURCE_DIR}/libgmxpreprocess.pc.cmakein ${CMAKE_CURRENT_BINARY_DIR}/libgmxpreprocess.pc @ONLY)
+install(FILES ${CMAKE_CURRENT_BINARY_DIR}/libgmxpreprocess.pc
+        DESTINATION ${LIB_INSTALL_DIR}/pkgconfig
+        RENAME "libgmxpreprocess${GMX_LIBS_SUFFIX}.pc"
+        COMPONENT development)

patches/gromacs-4.6.6.diff/src/kernel/CMakeLists.txt.preplumed

+#
+# This file is part of the GROMACS molecular simulation package.
+#
+# Copyright (c) 2012,2013, by the GROMACS development team, led by
+# David van der Spoel, Berk Hess, 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(GMXPREPROCESS_SOURCES 
+    add_par.c       
+    calc_verletbuf.c
+    compute_io.c    
+    convparm.c      
+    gen_ad.c        
+    gen_vsite.c     
+    genhydro.c   
+    gpp_atomtype.c  
+    gpp_bond_atomtype.c     
+    h_db.c          
+    hackblock.c             
+    hizzie.c        
+    nm2type.c
+    pdb2top.c       
+    pgutil.c        
+    readir.c        
+    readpull.c      
+    readadress.c      
+    readrot.c
+    resall.c        
+    sorting.c       
+    specbond.c      
+    ter_db.c        
+    tomorse.c       
+    topdirs.c       
+    topexcl.c       
+    topio.c         
+    toppush.c       
+    topshake.c      
+    toputil.c       
+    tpbcmp.c        
+    vsite_parm.c    
+    fflibutil.c
+    xlate.c)
+
+set(MDRUN_SOURCES 
+    gctio.c    ionize.c runner.c
+    do_gct.c     repl_ex.c  xutils.c pme_loadbal.c
+    md.c         mdrun.c    genalg.c membed.c)
+
+add_library(gmxpreprocess ${GMXPREPROCESS_SOURCES})
+target_link_libraries(gmxpreprocess md)
+set_target_properties(gmxpreprocess PROPERTIES OUTPUT_NAME "gmxpreprocess${GMX_LIBS_SUFFIX}" SOVERSION ${SOVERSION}
+    COMPILE_FLAGS "${OpenMP_C_FLAGS}")
+
+
+if(GMX_GPU)
+    include_directories(${CMAKE_SOURCE_DIR}/src/gmxlib/gpu_utils)
+endif()
+
+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
+    list(APPEND CMAKE_MODULE_PATH ${CMAKE_SOURCE_DIR}/src/contrib)
+    find_package(OpenMM)
+    include_directories(${CMAKE_CURRENT_SOURCE_DIR})
+    include(${CMAKE_SOURCE_DIR}/src/contrib/BuildMdrunOpenMM.cmake)
+endif(GMX_OPENMM)
+
+if(GMX_GPU OR GMX_FORCE_CXX)
+    set_source_files_properties(main.c PROPERTIES LANGUAGE CXX)
+    if ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Clang")
+        set_source_files_properties(main.c PROPERTIES COMPILE_FLAGS "-x c++")
+    endif()
+endif()
+
+if(GMX_FAHCORE)
+  add_library(fahcore ${MDRUN_SOURCES})
+else(GMX_FAHCORE)
+
+set(GMX_KERNEL_PROGRAMS
+    grompp tpbconv pdb2gmx g_protonate gmxdump g_x2top gmxcheck)
+if (NOT GMX_NO_QUOTES)
+  set(GMX_KERNEL_PROGRAMS ${GMX_KERNEL_PROGRAMS} g_luck)
+endif (NOT GMX_NO_QUOTES)
+
+
+foreach(PROGRAM ${GMX_KERNEL_PROGRAMS})
+    add_executable(${PROGRAM} ${PROGRAM}.c main.c)
+    if (NOT ${PROGRAM} STREQUAL "g_luck")
+        gmx_add_man_page(${PROGRAM})
+    endif()
+    target_link_libraries(${PROGRAM} gmxpreprocess md gmx ${OpenMP_LINKER_FLAGS})
+    set_target_properties(${PROGRAM} PROPERTIES OUTPUT_NAME "${PROGRAM}${GMX_BINARY_SUFFIX}")
+endforeach()
+
+add_executable(mdrun ${MDRUN_SOURCES} main.c)
+gmx_add_man_page(mdrun)
+target_link_libraries(mdrun gmxpreprocess md gmx ${OpenMP_LINKER_FLAGS})
+set_target_properties(mdrun PROPERTIES OUTPUT_NAME "mdrun${GMX_BINARY_SUFFIX}" COMPILE_FLAGS "${OpenMP_C_FLAGS}")
+
+if(GMX_OPENMM)
+    target_link_libraries(mdrun openmm_api_wrapper)
+endif()
+
+# Construct component groups for installation; note that a component may
+# belong to only one group
+foreach(PROGRAM ${GMX_KERNEL_PROGRAMS})
+    set(CPACK_COMPONENT_${PROGRAM}_GROUP tools)
+endforeach()
+set(CPACK_COMPONENT_MDRUN_GROUP mdrun)
+
+foreach(PROGRAM ${GMX_KERNEL_PROGRAMS} mdrun)
+    # Manage CPack component dependencies
+    set(CPACK_COMPONENT_${PROGRAM}_DEPENDS libraries libraries-gmxpreprocess)
+
+    # Create custom install-xxxx target
+    if (BUILD_SHARED_LIBS)
+    # If shared libraries are used, we need to install the libraries in
+    # addition to the mdrun binary.
+       add_custom_target(install-${PROGRAM}
+           COMMAND ${CMAKE_COMMAND} -DCOMPONENT=libraries
+                   -P ${CMAKE_BINARY_DIR}/cmake_install.cmake
+           COMMAND ${CMAKE_COMMAND} -DCOMPONENT=libraries-gmxpreprocess
+                   -P ${CMAKE_BINARY_DIR}/cmake_install.cmake
+           COMMAND ${CMAKE_COMMAND} -DCOMPONENT=${PROGRAM}
+                   -P ${CMAKE_BINARY_DIR}/cmake_install.cmake
+           COMMENT "Installing ${PROGRAM}")
+    else()
+       add_custom_target(install-${PROGRAM}
+           COMMAND ${CMAKE_COMMAND} -DCOMPONENT=${PROGRAM}
+                   -P ${CMAKE_BINARY_DIR}/cmake_install.cmake
+           COMMENT "Installing ${PROGRAM}")
+    endif()
+    add_dependencies(install-${PROGRAM} ${PROGRAM})
+
+    # Finally, trigger installation
+    install(
+      TARGETS ${PROGRAM}
+      COMPONENT ${PROGRAM}
+      DESTINATION ${BIN_INSTALL_DIR}
+      )
+endforeach()
+
+install(TARGETS gmxpreprocess DESTINATION ${LIB_INSTALL_DIR} COMPONENT libraries-gmxpreprocess)
+
+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
+                    ${LIB_INSTALL_DIR} COMPONENT libraries)
+            endif()
+        endforeach()
+    else()
+        message(WARNING "INSTALL_CUDART_LIB only makes sense with GMX_GPU")
+    endif()
+endif ()
+endif(GMX_FAHCORE)
+
+configure_file(${CMAKE_CURRENT_SOURCE_DIR}/libgmxpreprocess.pc.cmakein ${CMAKE_CURRENT_BINARY_DIR}/libgmxpreprocess.pc @ONLY)
+install(FILES ${CMAKE_CURRENT_BINARY_DIR}/libgmxpreprocess.pc
+        DESTINATION ${LIB_INSTALL_DIR}/pkgconfig
+        RENAME "libgmxpreprocess${GMX_LIBS_SUFFIX}.pc"
+        COMPONENT development)