message(WARNING "Shared system libraries requested, and static Gromacs libraries requested.")
endif()
else()
- message(FATAL_ERROR "BUILD_SHARED_LIBS=ON not yet working for Windows in the master branch")
+ if(MINGW)
+ set(CMAKE_SHARED_LINKER_FLAGS "-Wl,--export-all-symbols ${CMAKE_SHARED_LINKER_FLAGS}")
+ else()
+ message(FATAL_ERROR "BUILD_SHARED_LIBS=ON not yet working for Windows in the master branch")
+ endif()
if(GMX_PREFER_STATIC_LIBS)
#this combination segfaults (illegal passing of file handles)
message(FATAL_ERROR "Static system libraries requested, and shared Gromacs libraries requested.")
endif()
- add_definitions(-DUSE_VISIBILITY -DTMPI_USE_VISIBILITY)
- set(PKG_CFLAGS "$PKG_CFLAGS -DUSE_VISIBILITY -DTMPI_USE_VISIBILITY")
+ # Visibility not yet implemented
+ # add_definitions(-DUSE_VISIBILITY -DTMPI_USE_VISIBILITY)
+ # set(PKG_CFLAGS "$PKG_CFLAGS -DUSE_VISIBILITY -DTMPI_USE_VISIBILITY")
endif()
IF (GMX_PREFER_STATIC_LIBS)
# does not support AVX, so we need to tell the linker to use the clang
# compilers assembler instead - and this has to happen before we detect AVX
# flags.
- if(APPLE AND ${CMAKE_C_COMPILER_ID} STREQUAL "GNU")
+ if(APPLE AND "${CMAKE_C_COMPILER_ID}" STREQUAL "GNU")
gmx_test_cflag(GNU_C_USE_CLANG_AS "-Wa,-q" SIMD_C_FLAGS)
endif()
- if(APPLE AND ${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU")
+ if(APPLE AND "${CMAKE_CXX_COMPILER_ID}" STREQUAL "GNU")
gmx_test_cxxflag(GNU_CXX_USE_CLANG_AS "-Wa,-q" SIMD_CXX_FLAGS)
endif()
endmacro()
# We don't have the full compiler version string yet (BUILD_C_COMPILER),
# so we can't distinguish vanilla from Apple clang versions, but catering for a few rare AMD
# hackintoshes is not worth the effort.
- if (APPLE AND (${CMAKE_C_COMPILER_ID} STREQUAL "Clang" OR
- ${CMAKE_CXX_COMPILER_ID} STREQUAL "Clang"))
+ if (APPLE AND ("${CMAKE_C_COMPILER_ID}" STREQUAL "Clang" OR
+ "${CMAKE_CXX_COMPILER_ID}" STREQUAL "Clang"))
message(WARNING "Due to a known compiler bug, Clang up to version 3.2 (and Apple Clang up to version 4.1) produces incorrect code with AVX_128_FMA SIMD. As we cannot work around this bug on OS X, you will have to select a different compiler or SIMD instruction set.")
endif()
set(GMX_SIMD_X86_AVX2_256 1)
set(SIMD_STATUS_MESSAGE "Enabling 256-bit AVX2 SIMD instructions")
+elseif(${GMX_SIMD} STREQUAL "ARM_NEON")
+
+ gmx_find_cflag_for_source(CFLAGS_ARM_NEON "C compiler 32-bit ARM NEON flag"
+ "#include<arm_neon.h>
+ int main(){float32x4_t x=vdupq_n_f32(0.5);x=vmlaq_f32(x,x,x);return vgetq_lane_f32(x,0)>0;}"
+ SIMD_C_FLAGS
+ "-mfpu=neon" "")
+ gmx_find_cxxflag_for_source(CXXFLAGS_ARM_NEON "C++ compiler 32-bit ARM NEON flag"
+ "#include<arm_neon.h>
+ int main(){float32x4_t x=vdupq_n_f32(0.5);x=vmlaq_f32(x,x,x);return vgetq_lane_f32(x,0)>0;}"
+ SIMD_CXX_FLAGS
+ "-mfpu=neon" "-D__STDC_CONSTANT_MACROS" "")
+
+ if(NOT CFLAGS_ARM_NEON OR NOT CXXFLAGS_ARM_NEON)
+ message(FATAL_ERROR "Cannot find ARM 32-bit NEON compiler flag. Use a newer compiler, or disable NEON SIMD.")
+ endif()
+
+ set(GMX_SIMD_ARM_NEON 1)
+ set(SIMD_STATUS_MESSAGE "Enabling 32-bit ARM NEON SIMD instructions")
+
+elseif(${GMX_SIMD} STREQUAL "ARM_NEON_ASIMD")
+ # Gcc-4.8.1 appears to have a bug where the c++ compiler requires
+ # -D__STDC_CONSTANT_MACROS if we include arm_neon.h
+
+ gmx_find_cflag_for_source(CFLAGS_ARM_NEON_ASIMD "C compiler ARM NEON Advanced SIMD flag"
+ "#include<arm_neon.h>
+ int main(){float64x2_t x=vdupq_n_f64(0.5);x=vfmaq_f64(x,x,x);return vgetq_lane_f64(x,0)>0;}"
+ SIMD_C_FLAGS
+ "")
+ gmx_find_cxxflag_for_source(CXXFLAGS_ARM_NEON_ASIMD "C++ compiler ARM NEON Advanced SIMD flag"
+ "#include<arm_neon.h>
+ int main(){float64x2_t x=vdupq_n_f64(0.5);x=vfmaq_f64(x,x,x);return vgetq_lane_f64(x,0)>0;}"
+ SIMD_CXX_FLAGS
+ "-D__STDC_CONSTANT_MACROS" "")
+
+ if(NOT CFLAGS_ARM_NEON_ASIMD OR NOT CXXFLAGS_ARM_NEON_ASIMD)
+ message(FATAL_ERROR "Cannot find ARM (AArch64) NEON Advanced SIMD compiler flag. Use a newer compiler, or disable SIMD.")
+ endif()
+
+ if(CMAKE_C_COMPILER_ID MATCHES "GNU" AND CMAKE_C_COMPILER_VERSION VERSION_LESS "4.9")
+ message(WARNING "At least gcc-4.8.1 has many bugs for ARM (AArch64) NEON Advanced SIMD compilation. You might need gcc version 4.9 or later.")
+ endif()
+
+ if(CMAKE_C_COMPILER_ID MATCHES "Clang" AND CMAKE_C_COMPILER_VERSION VERSION_LESS "3.4")
+ message(FATAL_ERROR "Clang version 3.4 or later is required for ARM (AArch64) NEON Advanced SIMD.")
+ endif()
+
+ set(GMX_SIMD_ARM_NEON_ASIMD 1)
+ set(SIMD_STATUS_MESSAGE "Enabling ARM (AArch64) NEON Advanced SIMD instructions")
+
elseif(${GMX_SIMD} STREQUAL "IBM_QPX")
try_compile(TEST_QPX ${CMAKE_BINARY_DIR}
message(FATAL_ERROR "Cannot compile the requested IBM QPX intrinsics. If you are compiling for BlueGene/Q with the XL compilers, use 'cmake .. -DCMAKE_TOOLCHAIN_FILE=Platform/BlueGeneQ-static-XL-C' to set up the tool chain.")
endif()
+elseif(${GMX_SIMD} STREQUAL "IBM_VMX")
+
+ gmx_find_cflag_for_source(CFLAGS_IBM_VMX "C compiler IBM VMX SIMD flag"
+ "#include<altivec.h>
+ int main(){vector float x,y=vec_ctf(vec_splat_s32(1),0);x=vec_madd(y,y,y);return vec_all_ge(y,x);}"
+ SIMD_C_FLAGS
+ "-maltivec -mabi=altivec" "-qarch=auto -qaltivec")
+ gmx_find_cxxflag_for_source(CXXFLAGS_IBM_VMX "C++ compiler IBM VMX SIMD flag"
+ "#include<altivec.h>
+ int main(){vector float x,y=vec_ctf(vec_splat_s32(1),0);x=vec_madd(y,y,y);return vec_all_ge(y,x);}"
+ SIMD_CXX_FLAGS
+ "-maltivec -mabi=altivec" "-qarch=auto -qaltivec")
+
+ if(NOT CFLAGS_IBM_VMX OR NOT CXXFLAGS_IBM_VMX)
+ message(FATAL_ERROR "Cannot find IBM VMX SIMD compiler flag. Use a newer compiler, or disable VMX SIMD.")
+ endif()
+
+ set(GMX_SIMD_IBM_VMX 1)
+ set(SIMD_STATUS_MESSAGE "Enabling IBM VMX SIMD instructions")
+
elseif(${GMX_SIMD} STREQUAL "SPARC64_HPC_ACE")
# Note that GMX_RELAXED_DOUBLE_PRECISION is enabled by default in the top-level CMakeLists.txt
add_subdirectory(gmxlib)
add_subdirectory(mdlib)
add_subdirectory(gmxpreprocess)
+add_subdirectory(bonded)
add_subdirectory(commandline)
add_subdirectory(fft)
add_subdirectory(linearalgebra)
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)
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)
+set(LIBGROMACS_HEADERS
+ analysisdata.h
+ commandline.h
+ options.h
+ selection.h
+ trajectoryanalysis.h
+ utility.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()
+# 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("gmxlib/bondfree.c")
+ gmx_apply_gcc44_bug_workaround("bonded/bonded.cpp")
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)
+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
target_link_libraries(libgromacs
${EXTRAE_LIBRARIES}
- ${GMX_GPU_LIBRARIES}
${GMX_EXTRA_LIBRARIES}
${TNG_IO_LIBRARIES}
${FFT_LIBRARIES} ${LINEAR_ALGEBRA_LIBRARIES}
# for the binary
if (NOT GMX_BUILD_MDRUN_ONLY OR BUILD_SHARED_LIBS)
install(TARGETS libgromacs
- LIBRARY DESTINATION ${LIB_INSTALL_DIR}
- RUNTIME DESTINATION ${BIN_INSTALL_DIR}
- ARCHIVE DESTINATION ${LIB_INSTALL_DIR}
- COMPONENT libraries)
+ EXPORT libgromacs
- DESTINATION ${LIB_INSTALL_DIR}
++ LIBRARY DESTINATION ${LIB_INSTALL_DIR}
++ RUNTIME DESTINATION ${BIN_INSTALL_DIR}
++ ARCHIVE 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)
+ include(InstallLibInfo.cmake)
endif()
if (INSTALL_CUDART_LIB) #can be set manual by user
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "nbnxn_cuda_data_mgmt.h"
+
+#include "config.h"
#include <assert.h>
#include <stdarg.h>
-#include <stdlib.h>
#include <stdio.h>
+#include <stdlib.h>
#include <cuda.h>
-#include "gmx_fatal.h"
+#include "gromacs/gmxlib/cuda_tools/cudautils.cuh"
+#include "gromacs/legacyheaders/gmx_detect_hardware.h"
+#include "gromacs/legacyheaders/gpu_utils.h"
+#include "gromacs/legacyheaders/pmalloc_cuda.h"
+#include "gromacs/legacyheaders/tables.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/enums.h"
+#include "gromacs/legacyheaders/types/force_flags.h"
+#include "gromacs/legacyheaders/types/interaction_const.h"
+#include "gromacs/mdlib/nb_verlet.h"
+#include "gromacs/mdlib/nbnxn_consts.h"
+#include "gromacs/pbcutil/ishift.h"
+#include "gromacs/utility/common.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"
-#include "tables.h"
-#include "typedefs.h"
-#include "types/enums.h"
-#include "types/nb_verlet.h"
-#include "types/interaction_const.h"
-#include "types/force_flags.h"
-#include "../nbnxn_consts.h"
-#include "gmx_detect_hardware.h"
#include "nbnxn_cuda_types.h"
-#include "../../gmxlib/cuda_tools/cudautils.cuh"
-#include "nbnxn_cuda_data_mgmt.h"
-#include "pmalloc_cuda.h"
-#include "gpu_utils.h"
-
-#include "gromacs/utility/common.h"
static bool bUseCudaEventBlockingSync = false; /* makes the CPU thread block */
/*! Re-generate the GPU Ewald force table, resets rlist, and update the
* electrostatic type switching to twin cut-off (or back) if needed. */
-void nbnxn_cuda_pme_loadbal_update_param(nbnxn_cuda_ptr_t cu_nb,
- const interaction_const_t *ic)
+void nbnxn_cuda_pme_loadbal_update_param(const nonbonded_verlet_t *nbv,
+ const interaction_const_t *ic)
{
- cu_nbparam_t *nbp = cu_nb->nbparam;
+ if (!nbv || nbv->grp[0].kernel_type != nbnxnk8x8x8_CUDA)
+ {
+ return;
+ }
+ nbnxn_cuda_ptr_t cu_nb = nbv->cu_nbv;
+ cu_nbparam_t *nbp = cu_nb->nbparam;
set_cutoff_parameters(nbp, ic);
* priorities, because we are querying the priority range which in this
* case will be a single value.
*/
- #if CUDA_VERSION >= 5500
+ #if CUDA_VERSION >= 5050
{
int highest_priority;
stat = cudaDeviceGetStreamPriorityRange(NULL, &highest_priority);
return (cu_nb != NULL && cu_nb->bDoTime) ? cu_nb->timings : NULL;
}
-void nbnxn_cuda_reset_timings(nbnxn_cuda_ptr_t cu_nb)
+void nbnxn_cuda_reset_timings(nonbonded_verlet_t* nbv)
{
- if (cu_nb->bDoTime)
+ if (nbv->cu_nbv && nbv->cu_nbv->bDoTime)
{
- init_timings(cu_nb->timings);
+ init_timings(nbv->cu_nbv->timings);
}
}
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff