#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2009,2010,2011,2012,2013,2014, The GROMACS development team.
-# Copyright (c) 2015,2016,2017,2018,2019,2020, by the GROMACS development team, led by
+# Copyright (c) 2009,2010,2011,2012,2013 by the GROMACS development team.
+# Copyright (c) 2014,2015,2016,2017,2018 by the GROMACS development team.
+# Copyright (c) 2019,2020, 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.
# To help us fund GROMACS development, we humbly ask that you cite
# the research papers on the package. Check out http://www.gromacs.org.
-cmake_minimum_required(VERSION 3.9.6)
-if(POLICY CMP0074) #3.12
- cmake_policy(SET CMP0074 NEW)
-endif()
+cmake_minimum_required(VERSION 3.13)
+cmake_policy(SET CMP0074 NEW) # From CMake 3.12
cmake_policy(SET CMP0068 NEW) # From CMake-3.9
# CMake modules/macros are in a subdirectory to keep this file cleaner
list(APPEND CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/cmake ${CMAKE_CURRENT_SOURCE_DIR}/cmake/Platform)
if(CMAKE_SYSTEM_NAME STREQUAL "Darwin")
- # Providing a default value >=10.9 helps to find modern C++ compatibility,
+ # Providing a default value >=10.14 helps to find modern C++ compatibility,
# such as by defaulting to the Clang libc++ instead of libstdc++.
- set(CMAKE_OSX_DEPLOYMENT_TARGET 10.9 CACHE STRING
- "OS X deployment target affects default SDK version and compiler flags."
- FORCE)
+ set(CMAKE_OSX_DEPLOYMENT_TARGET 10.14 CACHE STRING
+ "OS X deployment target affects default SDK version and compiler flags.")
# By default, limit the binary architecture to a single 64-bit build.
set(CMAKE_OSX_ARCHITECTURES x86_64 CACHE STRING
"OS X architecture affects the compatibility of the (potentially fat) binaries produced."
project(Gromacs)
-set(CMAKE_CXX_STANDARD 14)
+set(CMAKE_CXX_STANDARD 17)
set(CMAKE_CXX_STANDARD_REQUIRED ON)
set(CMAKE_CXX_EXTENSIONS OFF)
find_package(LibStdCpp)
+# Python is first referenced in gmxVersionInfo, so we perform the search early
+# to find a suitable installation for all components.
+include(gmxPythonDiscovery)
# Set up common version variables, as well as general information about
# the build tree (whether the build is from a source package or from a git
# repository). Also declares a few functions that will be used for generating
include(gmxBuildTypeTSAN)
include(gmxBuildTypeASAN)
include(gmxBuildTypeMSAN)
+include(gmxBuildTypeUBSAN)
include(gmxBuildTypeReleaseWithAssert)
if(NOT CMAKE_BUILD_TYPE)
- set(CMAKE_BUILD_TYPE "Release" CACHE STRING "Choose the type of build, options are: Debug Release RelWithDebInfo MinSizeRel Reference RelWithAssert Profile TSAN ASAN MSAN." FORCE)
+ set(CMAKE_BUILD_TYPE "Release" CACHE STRING "Choose the type of build, options are: Debug Release RelWithDebInfo MinSizeRel Reference RelWithAssert Profile TSAN ASAN MSAN UBSAN." FORCE)
# Set the possible values of build type for cmake-gui
set_property(CACHE CMAKE_BUILD_TYPE PROPERTY STRINGS "Debug" "Release"
- "MinSizeRel" "RelWithDebInfo" "Reference" "RelWithAssert" "Profile" "TSAN" "ASAN" "MSAN")
+ "MinSizeRel" "RelWithDebInfo" "Reference" "RelWithAssert" "Profile" "TSAN" "ASAN" "MSAN" "UBSAN")
endif()
if(CMAKE_CONFIGURATION_TYPES)
# Add appropriate GROMACS-specific build types for the Visual
mark_as_advanced(GMX_COOL_QUOTES)
gmx_add_cache_dependency(GMX_COOL_QUOTES BOOL "NOT GMX_FAHCORE" OFF)
-option(GMX_USE_OPENCL "Enable OpenCL acceleration" OFF)
-
option(GMX_INSTALL_LEGACY_API "Install legacy headers" OFF)
-# The earliest version of the CUDA toolkit that supports c++14 is 9.0
-set(REQUIRED_CUDA_VERSION 9.0)
-set(REQUIRED_CUDA_COMPUTE_CAPABILITY 3.0)
-
-# OpenCL required version: 1.2 or newer
-set(REQUIRED_OPENCL_MIN_VERSION_MAJOR 1)
-set(REQUIRED_OPENCL_MIN_VERSION_MINOR 2)
-set(REQUIRED_OPENCL_MIN_VERSION ${REQUIRED_OPENCL_MIN_VERSION_MAJOR}.${REQUIRED_OPENCL_MIN_VERSION_MINOR})
-
-if(NOT GMX_USE_OPENCL)
- # CUDA detection is done only if GMX_USE_OPENCL is OFF.
- include(gmxManageGPU)
- set(GMX_USE_CUDA ${GMX_GPU})
- if(GMX_GPU)
- set(GMX_GPU_ACCELERATION_FRAMEWORK "GMX_GPU_CUDA")
- else()
- set(GMX_GPU_ACCELERATION_FRAMEWORK "GMX_GPU_NONE")
- endif()
-else()
- #Now the OpenCL path (for both AMD and NVIDIA)
- if(GMX_GPU)
- include(gmxManageOpenCL)
- set(GMX_GPU_ACCELERATION_FRAMEWORK "GMX_GPU_OPENCL")
- else()
- message(FATAL_ERROR "OpenCL requested but GPU option is not enabled (try -DGMX_GPU=on) ")
- endif()
-endif()
+gmx_option_multichoice(
+ GMX_GPU
+ "Framework for GPU acceleration"
+ OFF
+ OFF CUDA OpenCL SYCL)
gmx_option_multichoice(
GMX_SIMD
"SIMD instruction set for CPU kernels and compiler optimization"
"AUTO"
- AUTO None SSE2 SSE4.1 AVX_128_FMA AVX_256 AVX2_256 AVX2_128 AVX_512 AVX_512_KNL MIC ARM_NEON ARM_NEON_ASIMD IBM_VMX IBM_VSX Sparc64_HPC_ACE Reference)
+ AUTO None SSE2 SSE4.1 AVX_128_FMA AVX_256 AVX2_256 AVX2_128 AVX_512 AVX_512_KNL MIC ARM_NEON ARM_NEON_ASIMD ARM_SVE IBM_VMX IBM_VSX Sparc64_HPC_ACE Reference)
if(GMX_TARGET_MIC)
set(GMX_FFT_LIBRARY_DEFAULT "mkl")
mark_as_advanced(GMX_BUILD_OWN_FFTW)
mark_as_advanced(GMX_DISABLE_FFTW_MEASURE)
-gmx_option_multichoice(
- GMX_QMMM_PROGRAM
- "QM package for QM/MM"
- None
- none gaussian mopac gamess orca)
-
gmx_dependent_cache_variable(GMX_SIMD_REF_FLOAT_WIDTH "Reference SIMD single precision width" STRING "4" "GMX_SIMD STREQUAL REFERENCE")
gmx_dependent_cache_variable(GMX_SIMD_REF_DOUBLE_WIDTH "Reference SIMD double precision width" STRING "2" "GMX_SIMD STREQUAL REFERENCE")
check_cxx_source_compiles("int main(){ return __builtin_clzll(1);}" HAVE_BUILTIN_CLZLL)
if(MSVC)
check_cxx_source_compiles("#include <intrin.h>\n int main(){unsigned long r;unsigned long i=1;_BitScanReverse(&r,i);return r;}" HAVE_BITSCANREVERSE)
- check_cxx_source_compiles("#include <intrin.h>\n int main(){unsigned long r;unsigned __int64 i=1;_BitScanReverse(&r,i);return r;}" HAVE_BITSCANREVERSE64)
+ check_cxx_source_compiles("#include <intrin.h>\n int main(){unsigned long r;unsigned __int64 i=1;_BitScanReverse64(&r,i);return r;}" HAVE_BITSCANREVERSE64)
elseif(CMAKE_CXX_COMPILER_ID MATCHES "XL")
check_cxx_source_compiles("int main(){ return __cntlz4(1);}" HAVE_CNTLZ4)
check_cxx_source_compiles("int main(){ return __cntlz8(1);}" HAVE_CNTLZ8)
include(gmxManageSharedLibraries)
+########################################################################
+# Specify install locations
+########################################################################
+# Use GNUInstallDirs to set paths on multiarch systems.
+include(GNUInstallDirs)
+
+set(GMX_INSTALL_DATASUBDIR "gromacs" CACHE STRING "Subdirectory for GROMACS data under CMAKE_INSTALL_DATADIR")
+mark_as_advanced(GMX_INSTALL_DATASUBDIR)
+
+# Internal convenience so we do not have to join two path segments in the code
+set(GMX_INSTALL_GMXDATADIR ${CMAKE_INSTALL_DATADIR}/${GMX_INSTALL_DATASUBDIR})
+
+# If the nesting level wrt. the installation root is changed,
+# gromacs-config.cmake.cmakein needs to be adapted.
+set(GMX_INSTALL_CMAKEDIR ${CMAKE_INSTALL_DATAROOTDIR}/cmake)
+
+# TODO: Make GMXRC adapt if this is changed
+set(GMX_INSTALL_PKGCONFIGDIR ${CMAKE_INSTALL_LIBDIR}/pkgconfig)
+
+list(APPEND INSTALLED_HEADER_INCLUDE_DIRS ${CMAKE_INSTALL_INCLUDEDIR})
+
+# Binary and library suffix options
+include(gmxManageSuffixes)
+
+
########################################################################
# Find external packages #
########################################################################
# set(XML_LIBRARIES ${LIBXML2_LIBRARIES})
#endif()
-gmx_option_trivalue(
- GMX_HWLOC
- "Use hwloc portable hardware locality library"
- "AUTO")
+option(GMX_HWLOC "Use hwloc portable hardware locality library" OFF)
if (GMX_HWLOC)
# Find quietly the second time.
include(gmxManageLmfit)
+include(gmxManageMuparser)
+
if(GMX_GPU)
- # now that we have detected the dependencies, do the second configure pass
- gmx_gpu_setup()
- if (GMX_CLANG_CUDA)
- list(APPEND GMX_EXTRA_LIBRARIES ${GMX_CUDA_CLANG_LINK_LIBS})
- link_directories("${GMX_CUDA_CLANG_LINK_DIRS}")
+
+ string(TOUPPER "${GMX_GPU}" _gmx_gpu_uppercase)
+ if(${_gmx_gpu_uppercase} STREQUAL "CUDA")
+ include(gmxManageCuda)
+ elseif(${_gmx_gpu_uppercase} STREQUAL "OPENCL")
+ include(gmxManageOpenCL)
+ elseif(${_gmx_gpu_uppercase} STREQUAL "SYCL")
+ include(gmxManageSYCL)
endif()
+ if(NOT GMX_OPENMP)
+ message(WARNING "To use GPU acceleration efficiently, mdrun requires OpenMP multi-threading, which is currently not enabled.")
+ endif()
+
endif()
if(CYGWIN)
########################################################################
include_directories(BEFORE ${CMAKE_SOURCE_DIR}/src)
+include_directories(SYSTEM ${CMAKE_SOURCE_DIR}/src/external)
# Required for config.h, maybe should only be set in src/CMakeLists.txt
include_directories(BEFORE ${CMAKE_BINARY_DIR}/src)
include(gmxSetBuildInformation)
gmx_set_build_information()
-gmx_option_multichoice(
- GMX_USE_RDTSCP
- "Use low-latency RDTSCP instruction for CPU-based timers for mdrun execution; might need to be off when compiling for heterogeneous environments)"
- "AUTO"
- OFF ON AUTO DETECT)
+# Anything but truly ancient x86 hardware should support rdtscp, so we enable it by default.
+# The inline assembly calling it is only ever compiled on x86, so defaulting to ON is OK.
+option(GMX_USE_RDTSCP "Use low-latency RDTSCP instruction for x86 CPU-based timers for mdrun execution; might need to be off when compiling for heterogeneous environments" ON)
mark_as_advanced(GMX_USE_RDTSCP)
-macro(gmx_check_rdtscp)
- if (CPU_DETECTION_FEATURES MATCHES "rdtscp")
- set(HAVE_RDTSCP 1)
- set(RDTSCP_DETECTION_MESSAGE " - detected on the build host")
- else()
- set(RDTSCP_DETECTION_MESSAGE " - not detected on the build host")
- endif()
-endmacro()
-
-set(HAVE_RDTSCP 0)
-if (GMX_USE_RDTSCP STREQUAL "ON")
- set(HAVE_RDTSCP 1)
-elseif(GMX_USE_RDTSCP STREQUAL "DETECT")
- gmx_check_rdtscp()
-elseif(GMX_USE_RDTSCP STREQUAL "AUTO")
- # If the user specified automated SIMD selection, that the choice
- # is made based on detection on the build host. If so, then RDTSCP
- # should be chosen the same way.
- #
- # If the user specified an AVX SIMD level (e.g. when
- # cross-compiling GROMACS) then they will get our best guess, ie
- # that in practice AVX mostly correlates with rdtscp (and anyway
- # is only relevant in rather old x86 hardware).
- if (GMX_SIMD STREQUAL "AUTO")
- gmx_check_rdtscp()
- elseif (GMX_SIMD MATCHES "AVX")
- set(HAVE_RDTSCP 1)
- endif()
-endif()
-gmx_check_if_changed(HAVE_RDTSCP_CHANGED HAVE_RDTSCP)
-if (HAVE_RDTSCP_CHANGED)
- if (HAVE_RDTSCP)
- message(STATUS "Enabling RDTSCP support${RDTSCP_DETECTION_MESSAGE}")
- else()
- message(STATUS "Disabling RDTSCP support${RDTSCP_DETECTION_MESSAGE}")
- endif()
-endif()
-
include(gmxTestLargeFiles)
gmx_test_large_files(GMX_LARGEFILES)
include(gmxManageSimd)
gmx_manage_simd()
-include(gmxManageCycleCounters)
-gmx_manage_cycle_counters()
-
-# Process QM/MM Settings
-if(${GMX_QMMM_PROGRAM} STREQUAL "GAUSSIAN")
- set(GMX_QMMM_GAUSSIAN 1)
-elseif(${GMX_QMMM_PROGRAM} STREQUAL "MOPAC")
- set(GMX_QMMM_MOPAC 1)
-elseif(${GMX_QMMM_PROGRAM} STREQUAL "GAMESS")
- set(GMX_QMMM_GAMESS 1)
-elseif(${GMX_QMMM_PROGRAM} STREQUAL "ORCA")
- set(GMX_QMMM_ORCA 1)
-elseif(${GMX_QMMM_PROGRAM} STREQUAL "NONE")
- # nothing to do
-else()
- gmx_invalid_option_value(GMX_QMMM_PROGRAM)
-endif()
-
-
##################################################
# Process FFT library settings
##################################################
include(gmxManageLinearAlgebraLibraries)
include(gmxManagePluginSupport)
+gmx_manage_plugin_support()
-if (GMX_USE_PLUGINS)
+if(GMX_USE_PLUGINS)
if(NOT GMX_VMD_PLUGIN_PATH)
find_package(VMD)
endif()
include_directories(${COREWRAP_INCLUDE_DIR})
endif()
-# Value of GMX_BUILD_HELP=AUTO tries to generate things, but will only
-# produce warnings if that fails.
-set(build_help_default AUTO)
-if (SOURCE_IS_SOURCE_DISTRIBUTION OR CMAKE_CROSSCOMPILING)
- set(build_help_default OFF)
-endif()
-gmx_option_trivalue(GMX_BUILD_HELP "Build completions automatically (requires that compiled binaries can be executed on the build host) and install man pages if built (requires building the 'man' target manually)" ${build_help_default})
+option(GMX_BUILD_HELP "Build completions (requires that compiled binaries can be executed on build host) and install man pages if built (requires building the 'man' target manually)" OFF)
mark_as_advanced(GMX_BUILD_HELP)
if (GMX_BUILD_HELP AND SOURCE_IS_SOURCE_DISTRIBUTION AND BUILD_IS_INSOURCE)
message(FATAL_ERROR
# # # # # # # # # # NO MORE TESTS AFTER THIS LINE! # # # # # # # # # # #
# these are set after everything else
if (NOT GMX_SKIP_DEFAULT_CFLAGS)
- set(CMAKE_EXE_LINKER_FLAGS "${FFT_LINKER_FLAGS} ${MPI_LINKER_FLAGS} ${CMAKE_EXE_LINKER_FLAGS}")
- set(CMAKE_SHARED_LINKER_FLAGS "${FFT_LINKER_FLAGS} ${MPI_LINKER_FLAGS} ${CMAKE_SHARED_LINKER_FLAGS}")
+ set(CMAKE_EXE_LINKER_FLAGS "${FFT_LINKER_FLAGS} ${MPI_LINKER_FLAGS} ${CMAKE_EXE_LINKER_FLAGS} ${DISABLE_SYCL_CXX_FLAGS}")
+ set(CMAKE_SHARED_LINKER_FLAGS "${FFT_LINKER_FLAGS} ${MPI_LINKER_FLAGS} ${CMAKE_SHARED_LINKER_FLAGS} ${DISABLE_SYCL_CXX_FLAGS}")
else()
message("Recommended flags which are not added because GMX_SKIP_DEFAULT_CFLAGS=yes:")
message("CMAKE_C_FLAGS: ${SIMD_C_FLAGS};${MPI_COMPILE_FLAGS};${EXTRA_C_FLAGS};${GMXC_CFLAGS}")
message("CMAKE_EXE_LINKER_FLAGS: ${FFT_LINKER_FLAGS} ${MPI_LINKER_FLAGS}")
message("CMAKE_SHARED_LINKER_FLAGS: ${FFT_LINKER_FLAGS} ${MPI_LINKER_FLAGS}")
endif()
-
-########################################################################
-# Specify install locations
-########################################################################
-# Use GNUInstallDirs to set paths on multiarch systems.
-include(GNUInstallDirs)
-
-set(GMX_INSTALL_DATASUBDIR "gromacs" CACHE STRING "Subdirectory for GROMACS data under CMAKE_INSTALL_DATADIR")
-mark_as_advanced(GMX_INSTALL_DATASUBDIR)
-
-# Internal convenience so we do not have to join two path segments in the code
-set(GMX_INSTALL_GMXDATADIR ${CMAKE_INSTALL_DATADIR}/${GMX_INSTALL_DATASUBDIR})
-
-# If the nesting level wrt. the installation root is changed,
-# gromacs-config.cmake.cmakein needs to be adapted.
-set(GMX_INSTALL_CMAKEDIR ${CMAKE_INSTALL_DATAROOTDIR}/cmake)
-
-# TODO: Make GMXRC adapt if this is changed
-set(GMX_INSTALL_PKGCONFIGDIR ${CMAKE_INSTALL_LIBDIR}/pkgconfig)
-set(GMX_INSTALL_OCLDIR ${GMX_INSTALL_GMXDATADIR}/opencl)
-
-list(APPEND INSTALLED_HEADER_INCLUDE_DIRS ${CMAKE_INSTALL_INCLUDEDIR})
-
-# Binary and library suffix options
-include(gmxManageSuffixes)
+# Allow `admin` directory to be easily conveyed to nested CMake commands.
+set(GMX_ADMIN_DIR ${CMAKE_SOURCE_DIR}/admin)
################################################################
# Shared library load path settings
endif()
# TODO: Determine control flow and defaults for package installation and testing use cases.
-# Ref: http://redmine.gromacs.org/issues/2896
+# Ref: https://gitlab.com/gromacs/gromacs/-/issues/2896
option(GMX_PYTHON_PACKAGE "Configure gmxapi Python package" OFF)
mark_as_advanced(GMX_PYTHON_PACKAGE)
if (NOT GMX_BUILD_MDRUN_ONLY)
- # Note: Though only documented as an output variable, PYTHON_EXECUTABLE is
- # also effective as a CMake input variable to effectively hint the location
- # of the Python interpreter. This may be helpful in environments with both
- # Python 2 and Python 3 on the default PATH.
- # Ref: https://cmake.org/cmake/help/latest/module/FindPythonInterp.html
- if(FIND_PACKAGE_MESSAGE_DETAILS_PythonInterp)
- # Keep quiet on subsequent runs of cmake
- set(PythonInterp_FIND_QUIETLY ON)
- endif()
- # Older CMake versions might not search for Python newer than 3.7.
- set(Python_ADDITIONAL_VERSIONS 3.8)
- if(GMX_PYTHON_PACKAGE)
- find_package(PythonInterp 3.5 REQUIRED)
- # Note: PythonLibs will be found later by pybind11.
- # TODO: (issue #2998) When CMake >= 3.12 is required, update detection.
- # I.e. find_package(Python3 3.5 COMPONENTS Interpreter Development REQUIRED)
- else()
- find_package(PythonInterp 3.5)
- endif()
find_package(ImageMagick QUIET COMPONENTS convert)
include(gmxTestImageMagick)
GMX_TEST_IMAGEMAGICK(IMAGE_CONVERT_POSSIBLE)
add_subdirectory(share)
add_subdirectory(scripts)
endif()
+add_subdirectory(api)
add_subdirectory(src)
if (BUILD_TESTING)
gmx_cpack_write_config()
-# Issue a warning if NVIDIA GPUs were detected, but CUDA was not found.
-# Don't bother the user after the first configure pass.
-if ((CUDA_NOTFOUND_AUTO AND GMX_DETECT_GPU_AVAILABLE) AND NOT GMX_GPU_DETECTION_DONE)
- message(WARNING "${CUDA_NOTFOUND_MESSAGE}")
-endif()
-set(GMX_GPU_DETECTION_DONE TRUE CACHE INTERNAL "Whether GPU detection has already been done")
-
#######################
## uninstall target
#######################
variables:
KUBERNETES_CPU_LIMIT: 8
KUBERNETES_CPU_REQUEST: 4
- KUBERNETES_MEMORY_REQUEST: 8Gi
+ KUBERNETES_MEMORY_REQUEST: 4Gi
+ KUBERNETES_MEMORY_LIMIT: 8Gi
KUBERNETES_EXTENDED_RESOURCE_NAME: ""
KUBERNETES_EXTENDED_RESOURCE_LIMIT: 0
- CACHE_FALLBACK_KEY: "$CI_JOB_NAME-$CI_JOB_STAGE-release-2020"
+ CACHE_FALLBACK_KEY: "$CI_JOB_NAME-$CI_JOB_STAGE-master"
BUILD_DIR: build
INSTALL_DIR: install
CMAKE_GMXAPI_OPTIONS: ""
.use-cuda:
variables:
CMAKE_PRECISION_OPTIONS: "-DGMX_DOUBLE=OFF"
- CMAKE_GPU_OPTIONS: -DGMX_GPU=ON -DGMX_USE_CUDA=ON
+ CMAKE_GPU_OPTIONS: -DGMX_GPU=CUDA
.use-mpi:
variables:
.use-opencl:
variables:
CMAKE_PRECISION_OPTIONS: "-DGMX_DOUBLE=OFF"
- CMAKE_GPU_OPTIONS: -DGMX_GPU=ON -DGMX_USE_OPENCL=ON
+ CMAKE_GPU_OPTIONS: -DGMX_GPU=OpenCL
# Base definition for using gcc.
.use-gcc:base:
- export CCACHE_DIR=${PWD}/ccache
- export ASAN_SYMBOLIZER_PATH=/usr/local/bin/llvm-symbolizer
+# Base definition for using oneAPI.
+.use-oneapi:base:
+ variables:
+ # Use the HPC variants of icc and icpc so that OpenMP is active
+ CMAKE_COMPILER_SCRIPT: -DCMAKE_C_COMPILER=icx -DCMAKE_CXX_COMPILER=icpx -DCMAKE_INCLUDE_PATH=/opt/intel/oneapi/compiler/latest/linux/include/sycl -DCMAKE_PREFIX_PATH=/opt/intel/oneapi/compiler/latest/linux
+ CMAKE_EXTRA_OPTIONS: -DGMX_FFT_LIBRARY=mkl
+ before_script:
+ # Necessary to override gitlab default 'set -e' which breaks Intel's
+ # setvar.sh script
+ - set +e
+ - source /opt/intel/oneapi/setvars.sh
+ - mkdir -p ccache
+ - export CCACHE_BASEDIR=${PWD}
+ - export CCACHE_DIR=${PWD}/ccache
.rules-element:if-post-merge-acceptance-or-mr-then-always: &if-post-merge-acceptance-or-mr-then-always
if: '$CI_PIPELINE_SOURCE == "merge_request_event" ||
($CI_PIPELINE_SOURCE == "push" &&
- ($CI_COMMIT_REF_NAME == "master" || $CI_COMMIT_REF_NAME == "release-*"))'
- $CI_COMMIT_REF_NAME == "release-2020")'
++ $CI_COMMIT_REF_NAME == "master")'
when: always
# Include job only for post submit push
.rules-element:if-post-merge-acceptance-then-always: &if-post-merge-acceptance-then-always
if: '$CI_PIPELINE_SOURCE == "push" &&
- ($CI_COMMIT_REF_NAME == "master" || $CI_COMMIT_REF_NAME == "release-*")'
- $CI_COMMIT_REF_NAME == "release-2020"'
++ $CI_COMMIT_REF_NAME == "master"'
when: always
# When composing a rule set, note that the first matching rule is applied.
#
# This file is part of the GROMACS molecular simulation package.
#
--# Copyright (c) 2018,2019, by the GROMACS development team, led by
++# Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
else()
set(type_ "STATUS")
endif()
- MESSAGE(${type_} "Could not convert sample image, ImageMagick convert can not be used. A possible way to fix it can be found here: https://alexvanderbist.com/posts/2018/fixing-imagick-error-unauthorized")
+ MESSAGE(${type_} "Could not convert sample image, ImageMagick convert can not be used. A possible way to fix it can be found here: https://alexvanderbist.com/2018/fixing-imagick-error-unauthorized")
set(value_ OFF)
endif()
FILE(REMOVE_RECURSE ${TEMPDIR})
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2014,2015,2016,2017,2018,2019,2020, by the GROMACS development team, led by
+# Copyright (c) 2014,2015,2016,2017,2018 by the GROMACS development team.
+# Copyright (c) 2019,2020, 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.
# of configure time, because 1) some of the version variables are only
# available during build time, and 2) we don't want to do all the Sphinx setup
# during configuration to save some time when not building the content.
-# All the generated values get put into conf-vars.py (generated from
-# conf-vars.py.cmakein), which in turn is included by the Sphinx configuration
-# file conf.py.
+# All of the generated values get put into conf.py (generated from
+# conf.cmakein.py).
set(SOURCE_MD5SUM "unknown" CACHE STRING
"MD5 sum of the source tarball, normally used only for the pre-release webpage build")
set(SPHINX_SOURCE_FILES
index.rst
download.rst
- conf.py
links.dat
dev-manual/build-system.rst
dev-manual/change-management.rst
dev-manual/commitstyle.rst
+ dev-manual/containers.rst
dev-manual/documentation-generation.rst
dev-manual/contribute.rst
dev-manual/doxygen.rst
dev-manual/error-handling.rst
dev-manual/formatting.rst
+ dev-manual/gitlab.rst
dev-manual/gmxtree.rst
dev-manual/includestyle.rst
dev-manual/index.rst
+ dev-manual/infrastructure.rst
dev-manual/jenkins.rst
dev-manual/known-issues.rst
dev-manual/language-features.rst
how-to/visualize.rst
install-guide/index.rst
release-notes/index.rst
+ release-notes/2021/major/highlights.rst
+ release-notes/2021/major/features.rst
+ release-notes/2021/major/performance.rst
+ release-notes/2021/major/tools.rst
+ release-notes/2021/major/bugs-fixed.rst
+ release-notes/2021/major/removed-functionality.rst
+ release-notes/2021/major/deprecated-functionality.rst
+ release-notes/2021/major/portability.rst
+ release-notes/2021/major/miscellaneous.rst
release-notes/2020/2020.1.rst
release-notes/2020/2020.2.rst
release-notes/2020/2020.3.rst
release-notes/2020/2020.4.rst
+ release-notes/2020/2020.5.rst
release-notes/2020/major/highlights.rst
release-notes/2020/major/features.rst
release-notes/2020/major/performance.rst
set(IMAGE_CONVERT_STRING "impossible")
endif()
- set(SPHINX_CONFIG_VARS_FILE ${SPHINX_INPUT_DIR}/conf-vars.py)
+ set(SPHINX_CONFIG_FILE ${SPHINX_INPUT_DIR}/conf.py)
if (GMX_PYTHON_PACKAGE)
set(GMXAPI_PYTHON_STAGING_DIR ${CMAKE_BINARY_DIR}/python_packaging/src/gmxapi_staging)
# TODO: Resolve circular reference. We would like to get the CMake build-time directory for
# in this context?
endif ()
- gmx_configure_version_file(conf-vars.py.cmakein ${SPHINX_CONFIG_VARS_FILE}
+ gmx_configure_version_file(
+ conf.cmakein.py ${SPHINX_CONFIG_FILE}
EXTRA_VARS
- SPHINX_EXTENSION_PATH RELENG_PATH
- IMAGE_CONVERT_STRING
+ CMAKE_MINIMUM_REQUIRED_VERSION
EXPECTED_DOXYGEN_VERSION
EXPECTED_SPHINX_VERSION
- CMAKE_MINIMUM_REQUIRED_VERSION REQUIRED_CUDA_VERSION
- REQUIRED_OPENCL_MIN_VERSION
- REQUIRED_CUDA_COMPUTE_CAPABILITY REGRESSIONTEST_VERSION
- SOURCE_MD5SUM REGRESSIONTEST_MD5SUM_STRING
- GMX_TNG_MINIMUM_REQUIRED_VERSION
+ GMX_ADMIN_DIR
GMX_LMFIT_REQUIRED_VERSION
GMX_MANUAL_DOI_STRING
+ GMX_TNG_MINIMUM_REQUIRED_VERSION
GMX_SOURCE_DOI_STRING
GMXAPI_PYTHON_STAGING_DIR
+ IMAGE_CONVERT_STRING
+ REGRESSIONTEST_VERSION
+ REQUIRED_CUDA_COMPUTE_CAPABILITY
+ REQUIRED_CUDA_VERSION
+ REQUIRED_OPENCL_MIN_VERSION
+ REGRESSIONTEST_MD5SUM_STRING
+ RELENG_PATH
+ SOURCE_MD5SUM
+ SPHINX_EXTENSION_PATH
COMMENT "Configuring Sphinx configuration file")
- gmx_add_sphinx_input_file(${SPHINX_CONFIG_VARS_FILE})
+ gmx_add_sphinx_input_file(${SPHINX_CONFIG_FILE})
gmx_add_sphinx_source_files(FILES ${SPHINX_SOURCE_FILES})
if (EXISTS ${RELENG_PATH}/docs/FileList.cmake)
include(${RELENG_PATH}/docs/FileList.cmake)
)
endif ()
+ gmx_add_sphinx_source_files(
+ FILES
+ nblib/index.rst
+ nblib/guide-to-writing-MD-programs.rst
+ )
+
gmx_add_sphinx_source_files(
FILES
${REFERENCEMANUAL_SPHINX_FILES_GENERAL})
# Sphinx cache with pickled ReST documents
set(SPHINX_CACHE_DIR "${CMAKE_CURRENT_BINARY_DIR}/_doctrees")
+ set(SPHINX_CONFIG_OVERRIDES "")
+ if (GMX_DEVELOPER_BUILD)
+ set(SPHINX_CONFIG_OVERRIDES "-Dtodo_include_todos=1")
+ endif()
add_custom_target(webpage-sphinx
DEPENDS sphinx-programs
DEPENDS sphinx-input
-q -b html
-w sphinx-html.log
-d "${SPHINX_CACHE_DIR}"
+ ${SPHINX_CONFIG_OVERRIDES}
"${SPHINX_INPUT_DIR}"
"${HTML_OUTPUT_DIR}"
WORKING_DIRECTORY
set(HTML_BUILD_WARNINGS)
# Next, turn it off if any of the preconditions are unsatisified
-if (NOT PythonInterp_FOUND)
+if (NOT Python3_Interpreter_FOUND)
set(HTML_BUILD_IS_POSSIBLE OFF)
set(HTML_BUILD_NOT_POSSIBLE_REASON "Python is required")
elseif (NOT SPHINX_FOUND)
src/gromacs/nbnxm/kernels_simd_2xmm/kernel_common.h: warning: should include "nbnxm_simd.h"
src/gromacs/nbnxm/kernels_simd_4xm/kernel_common.h: warning: should include "nbnxm_simd.h"
+# This seems to be a false positive
+src/gromacs/nbnxm/cuda/nbnxm_cuda_types.h: error: NbnxmGpu: is in internal file(s), but appears in public documentation
+
# Temporary while we change the SIMD implementation
src/gromacs/simd/impl_sparc64_hpc_ace/impl_sparc64_hpc_ace_common.h: warning: should include "simd.h"
src/gromacs/tables/quadraticsplinetable.h: warning: includes "simd.h" unnecessarily
# These are specific to Folding@Home, and easiest to suppress here
- *: warning: includes non-local file as "corewrap.h"
src/gmxpre.h: warning: includes non-local file as "swindirect.h"
-# New external API (see https://redmine.gromacs.org/issues/2586) has some unresolved
+# New external API (see https://gitlab.com/gromacs/gromacs/-/issues/2586) has some unresolved
# conflicts with previous definitions of public API, installed API, and other things
# described or implemented in check-source.py, gmxtree.py, gmxtree.rst, and others
# TODO: resolve definitions, update testing heuristics, and activate policy checks
functionality supported, whereas patch releases contain only fixes for
issues identified in the corresponding major releases.
-Two versions of |Gromacs| are under active maintenance, the 2020
-series and the 2019 series. In the latter, only highly conservative
+Two versions of |Gromacs| are under active maintenance, the 2021
+series and the 2020 series. In the latter, only highly conservative
fixes will be made, and only to address issues that affect scientific
correctness. Naturally, some of those releases will be made after the
-year 2019 ends, but we keep 2019 in the name so users understand how
+year 2020 ends, but we keep 2019 in the name so users understand how
up to date their version is. Such fixes will also be incorporated into
-the 2020 release series, as appropriate. Around the time the 2021
-release is made, the 2019 series will no longer be maintained.
+the 2021 release series, as appropriate. Around the time the 2022
+release is made, the 2020 series will no longer be maintained.
Where issue numbers are reported in these release notes, more details
-can be found at https://redmine.gromacs.org at that issue number.
+can be found at https://gitlab.com/gromacs/gromacs/-/issues at that issue number.
+
+|Gromacs| 2021 series
+---------------------
+
+.. todolist::
+
+Major release
+^^^^^^^^^^^^^
+
+.. toctree::
+ :maxdepth: 1
+
+ 2021/major/highlights
+ 2021/major/features
+ 2021/major/performance
+ 2021/major/tools
+ 2021/major/bugs-fixed
+ 2021/major/deprecated-functionality
+ 2021/major/removed-functionality
+ 2021/major/portability
+ 2021/major/miscellaneous
+
|Gromacs| 2020 series
---------------------
.. toctree::
:maxdepth: 1
+ 2020/2020.5
2020/2020.4
2020/2020.3
2020/2020.2
#include "checkpoint.h"
-#include "config.h"
-
#include <cerrno>
#include <cstdlib>
#include <cstring>
#include "gromacs/math/vectypes.h"
#include "gromacs/mdtypes/awh_correlation_history.h"
#include "gromacs/mdtypes/awh_history.h"
+#include "gromacs/mdtypes/checkpointdata.h"
#include "gromacs/mdtypes/commrec.h"
#include "gromacs/mdtypes/df_history.h"
#include "gromacs/mdtypes/edsamhistory.h"
#include "gromacs/utility/sysinfo.h"
#include "gromacs/utility/txtdump.h"
- #if GMX_FAHCORE
- # include "corewrap.h"
- #endif
-
#define CPT_MAGIC1 171817
#define CPT_MAGIC2 171819
+namespace gmx
+{
+
+template<typename ValueType>
+void readKvtCheckpointValue(compat::not_null<ValueType*> value,
+ const std::string& name,
+ const std::string& identifier,
+ const KeyValueTreeObject& kvt)
+{
+ const std::string key = identifier + "-" + name;
+ if (!kvt.keyExists(key))
+ {
+ std::string errorMessage = "Cannot read requested checkpoint value " + key + " .";
+ GMX_THROW(InternalError(errorMessage));
+ }
+ *value = kvt[key].cast<ValueType>();
+}
+
+template void readKvtCheckpointValue(compat::not_null<std::int64_t*> value,
+ const std::string& name,
+ const std::string& identifier,
+ const KeyValueTreeObject& kvt);
+template void readKvtCheckpointValue(compat::not_null<real*> value,
+ const std::string& name,
+ const std::string& identifier,
+ const KeyValueTreeObject& kvt);
+
+template<typename ValueType>
+void writeKvtCheckpointValue(const ValueType& value,
+ const std::string& name,
+ const std::string& identifier,
+ KeyValueTreeObjectBuilder kvtBuilder)
+{
+ kvtBuilder.addValue<ValueType>(identifier + "-" + name, value);
+}
+
+template void writeKvtCheckpointValue(const std::int64_t& value,
+ const std::string& name,
+ const std::string& identifier,
+ KeyValueTreeObjectBuilder kvtBuilder);
+template void writeKvtCheckpointValue(const real& value,
+ const std::string& name,
+ const std::string& identifier,
+ KeyValueTreeObjectBuilder kvtBuilder);
+
+
+} // namespace gmx
+
/*! \brief Enum of values that describe the contents of a cpt file
* whose format matches a version number
*
cptv_Unknown = 17, /**< Version before numbering scheme */
cptv_RemoveBuildMachineInformation, /**< remove functionality that makes mdrun builds non-reproducible */
cptv_ComPrevStepAsPullGroupReference, /**< Allow using COM of previous step as pull group PBC reference */
- cptv_PullAverage, /**< Added possibility to output average pull force and position */
- cptv_MdModules, /**< Added checkpointing for MdModules */
- cptv_Count /**< the total number of cptv versions */
+ cptv_PullAverage, /**< Added possibility to output average pull force and position */
+ cptv_MdModules, /**< Added checkpointing for MdModules */
+ cptv_ModularSimulator, /**< Added checkpointing for modular simulator */
+ cptv_Count /**< the total number of cptv versions */
};
/*! \brief Version number of the file format written to checkpoint
{
contents->flagsPullHistory = 0;
}
+
+ if (contents->file_version >= cptv_ModularSimulator)
+ {
+ do_cpt_bool_err(xd, "Is modular simulator checkpoint",
+ &contents->isModularSimulatorCheckpoint, list);
+ }
+ else
+ {
+ contents->isModularSimulatorCheckpoint = false;
+ }
}
static int do_cpt_footer(XDR* xd, int file_version)
break;
/* The RNG entries are no longer written,
* the next 4 lines are only for reading old files.
+ * It's OK that three case statements fall through.
*/
case estLD_RNG_NOTSUPPORTED:
- ret = do_cpte_ints(xd, part, i, sflags, 0, nullptr, list);
- break;
case estLD_RNGI_NOTSUPPORTED:
- ret = do_cpte_ints(xd, part, i, sflags, 0, nullptr, list);
- break;
case estMC_RNG_NOTSUPPORTED:
- ret = do_cpte_ints(xd, part, i, sflags, 0, nullptr, list);
- break;
case estMC_RNGI_NOTSUPPORTED:
ret = do_cpte_ints(xd, part, i, sflags, 0, nullptr, list);
break;
gmx::MdModulesCheckpointReadingDataOnMaster mdModuleCheckpointReadingDataOnMaster = {
mdModuleCheckpointParameterTree, fileVersion
};
- mdModulesNotifier.notifier_.notify(mdModuleCheckpointReadingDataOnMaster);
+ mdModulesNotifier.checkpointingNotifications_.notify(mdModuleCheckpointReadingDataOnMaster);
}
}
return 0;
}
-static void mpiBarrierBeforeRename(const bool applyMpiBarrierBeforeRename, MPI_Comm mpiBarrierCommunicator)
-{
- if (applyMpiBarrierBeforeRename)
- {
-#if GMX_MPI
- MPI_Barrier(mpiBarrierCommunicator);
-#else
- GMX_RELEASE_ASSERT(false, "Should not request a barrier without MPI");
- GMX_UNUSED_VALUE(mpiBarrierCommunicator);
-#endif
- }
-}
-
-void write_checkpoint(const char* fn,
- gmx_bool bNumberAndKeep,
- FILE* fplog,
- const t_commrec* cr,
- ivec domdecCells,
- int nppnodes,
- int eIntegrator,
- int simulation_part,
- gmx_bool bExpanded,
- int elamstats,
- int64_t step,
- double t,
- t_state* state,
- ObservablesHistory* observablesHistory,
- const gmx::MdModulesNotifier& mdModulesNotifier,
- bool applyMpiBarrierBeforeRename,
- MPI_Comm mpiBarrierCommunicator)
-{
- t_fileio* fp;
- char* fntemp; /* the temporary checkpoint file name */
- int npmenodes;
- char buf[1024], suffix[5 + STEPSTRSIZE], sbuf[STEPSTRSIZE];
- t_fileio* ret;
-
- if (DOMAINDECOMP(cr))
- {
- npmenodes = cr->npmenodes;
- }
- else
- {
- npmenodes = 0;
- }
-
-#if !GMX_NO_RENAME
- /* make the new temporary filename */
- snew(fntemp, std::strlen(fn) + 5 + STEPSTRSIZE);
- std::strcpy(fntemp, fn);
- fntemp[std::strlen(fn) - std::strlen(ftp2ext(fn2ftp(fn))) - 1] = '\0';
- sprintf(suffix, "_%s%s", "step", gmx_step_str(step, sbuf));
- std::strcat(fntemp, suffix);
- std::strcat(fntemp, fn + std::strlen(fn) - std::strlen(ftp2ext(fn2ftp(fn))) - 1);
-#else
- /* if we can't rename, we just overwrite the cpt file.
- * dangerous if interrupted.
- */
- snew(fntemp, std::strlen(fn));
- std::strcpy(fntemp, fn);
-#endif
- std::string timebuf = gmx_format_current_time();
-
- if (fplog)
- {
- fprintf(fplog, "Writing checkpoint, step %s at %s\n\n", gmx_step_str(step, buf), timebuf.c_str());
- }
-
- /* Get offsets for open files */
- auto outputfiles = gmx_fio_get_output_file_positions();
-
- fp = gmx_fio_open(fntemp, "w");
-
- int flags_eks;
+void write_checkpoint_data(t_fileio* fp,
+ CheckpointHeaderContents headerContents,
+ gmx_bool bExpanded,
+ int elamstats,
+ t_state* state,
+ ObservablesHistory* observablesHistory,
+ const gmx::MdModulesNotifier& mdModulesNotifier,
+ std::vector<gmx_file_position_t>* outputfiles,
+ gmx::WriteCheckpointDataHolder* modularSimulatorCheckpointData)
+{
+ headerContents.flags_eks = 0;
if (state->ekinstate.bUpToDate)
{
- flags_eks = ((1 << eeksEKIN_N) | (1 << eeksEKINH) | (1 << eeksEKINF) | (1 << eeksEKINO)
- | (1 << eeksEKINSCALEF) | (1 << eeksEKINSCALEH) | (1 << eeksVSCALE)
- | (1 << eeksDEKINDL) | (1 << eeksMVCOS));
- }
- else
- {
- flags_eks = 0;
+ headerContents.flags_eks = ((1 << eeksEKIN_N) | (1 << eeksEKINH) | (1 << eeksEKINF)
+ | (1 << eeksEKINO) | (1 << eeksEKINSCALEF) | (1 << eeksEKINSCALEH)
+ | (1 << eeksVSCALE) | (1 << eeksDEKINDL) | (1 << eeksMVCOS));
}
+ headerContents.isModularSimulatorCheckpoint = !modularSimulatorCheckpointData->empty();
- energyhistory_t* enerhist = observablesHistory->energyHistory.get();
- int flags_enh = 0;
+ energyhistory_t* enerhist = observablesHistory->energyHistory.get();
+ headerContents.flags_enh = 0;
if (enerhist != nullptr && (enerhist->nsum > 0 || enerhist->nsum_sim > 0))
{
- flags_enh |= (1 << eenhENERGY_N) | (1 << eenhENERGY_NSTEPS) | (1 << eenhENERGY_NSTEPS_SIM);
+ headerContents.flags_enh |=
+ (1 << eenhENERGY_N) | (1 << eenhENERGY_NSTEPS) | (1 << eenhENERGY_NSTEPS_SIM);
if (enerhist->nsum > 0)
{
- flags_enh |= ((1 << eenhENERGY_AVER) | (1 << eenhENERGY_SUM) | (1 << eenhENERGY_NSUM));
+ headerContents.flags_enh |=
+ ((1 << eenhENERGY_AVER) | (1 << eenhENERGY_SUM) | (1 << eenhENERGY_NSUM));
}
if (enerhist->nsum_sim > 0)
{
- flags_enh |= ((1 << eenhENERGY_SUM_SIM) | (1 << eenhENERGY_NSUM_SIM));
+ headerContents.flags_enh |= ((1 << eenhENERGY_SUM_SIM) | (1 << eenhENERGY_NSUM_SIM));
}
if (enerhist->deltaHForeignLambdas != nullptr)
{
- flags_enh |= ((1 << eenhENERGY_DELTA_H_NN) | (1 << eenhENERGY_DELTA_H_LIST)
- | (1 << eenhENERGY_DELTA_H_STARTTIME) | (1 << eenhENERGY_DELTA_H_STARTLAMBDA));
+ headerContents.flags_enh |=
+ ((1 << eenhENERGY_DELTA_H_NN) | (1 << eenhENERGY_DELTA_H_LIST)
+ | (1 << eenhENERGY_DELTA_H_STARTTIME) | (1 << eenhENERGY_DELTA_H_STARTLAMBDA));
}
}
- PullHistory* pullHist = observablesHistory->pullHistory.get();
- int flagsPullHistory = 0;
+ PullHistory* pullHist = observablesHistory->pullHistory.get();
+ headerContents.flagsPullHistory = 0;
if (pullHist != nullptr && (pullHist->numValuesInXSum > 0 || pullHist->numValuesInFSum > 0))
{
- flagsPullHistory |= (1 << epullhPULL_NUMCOORDINATES);
- flagsPullHistory |= ((1 << epullhPULL_NUMGROUPS) | (1 << epullhPULL_NUMVALUESINXSUM)
- | (1 << epullhPULL_NUMVALUESINFSUM));
+ headerContents.flagsPullHistory |= (1 << epullhPULL_NUMCOORDINATES);
+ headerContents.flagsPullHistory |= ((1 << epullhPULL_NUMGROUPS) | (1 << epullhPULL_NUMVALUESINXSUM)
+ | (1 << epullhPULL_NUMVALUESINFSUM));
}
- int flags_dfh;
+ headerContents.flags_dfh = 0;
if (bExpanded)
{
- flags_dfh = ((1 << edfhBEQUIL) | (1 << edfhNATLAMBDA) | (1 << edfhSUMWEIGHTS)
- | (1 << edfhSUMDG) | (1 << edfhTIJ) | (1 << edfhTIJEMP));
+ headerContents.flags_dfh = ((1 << edfhBEQUIL) | (1 << edfhNATLAMBDA) | (1 << edfhSUMWEIGHTS)
+ | (1 << edfhSUMDG) | (1 << edfhTIJ) | (1 << edfhTIJEMP));
if (EWL(elamstats))
{
- flags_dfh |= ((1 << edfhWLDELTA) | (1 << edfhWLHISTO));
+ headerContents.flags_dfh |= ((1 << edfhWLDELTA) | (1 << edfhWLHISTO));
}
if ((elamstats == elamstatsMINVAR) || (elamstats == elamstatsBARKER)
|| (elamstats == elamstatsMETROPOLIS))
{
- flags_dfh |= ((1 << edfhACCUMP) | (1 << edfhACCUMM) | (1 << edfhACCUMP2)
- | (1 << edfhACCUMM2) | (1 << edfhSUMMINVAR) | (1 << edfhSUMVAR));
+ headerContents.flags_dfh |= ((1 << edfhACCUMP) | (1 << edfhACCUMM) | (1 << edfhACCUMP2)
+ | (1 << edfhACCUMM2) | (1 << edfhSUMMINVAR) | (1 << edfhSUMVAR));
}
}
- else
- {
- flags_dfh = 0;
- }
- int flags_awhh = 0;
+ headerContents.flags_awhh = 0;
if (state->awhHistory != nullptr && !state->awhHistory->bias.empty())
{
- flags_awhh |= ((1 << eawhhIN_INITIAL) | (1 << eawhhEQUILIBRATEHISTOGRAM) | (1 << eawhhHISTSIZE)
- | (1 << eawhhNPOINTS) | (1 << eawhhCOORDPOINT) | (1 << eawhhUMBRELLAGRIDPOINT)
- | (1 << eawhhUPDATELIST) | (1 << eawhhLOGSCALEDSAMPLEWEIGHT)
- | (1 << eawhhNUMUPDATES) | (1 << eawhhFORCECORRELATIONGRID));
- }
-
- /* We can check many more things now (CPU, acceleration, etc), but
- * it is highly unlikely to have two separate builds with exactly
- * the same version, user, time, and build host!
- */
-
- int nlambda = (state->dfhist ? state->dfhist->nlambda : 0);
-
- edsamhistory_t* edsamhist = observablesHistory->edsamHistory.get();
- int nED = (edsamhist ? edsamhist->nED : 0);
-
- swaphistory_t* swaphist = observablesHistory->swapHistory.get();
- int eSwapCoords = (swaphist ? swaphist->eSwapCoords : eswapNO);
-
- CheckpointHeaderContents headerContents = { 0,
- { 0 },
- { 0 },
- { 0 },
- { 0 },
- GMX_DOUBLE,
- { 0 },
- { 0 },
- eIntegrator,
- simulation_part,
- step,
- t,
- nppnodes,
- { 0 },
- npmenodes,
- state->natoms,
- state->ngtc,
- state->nnhpres,
- state->nhchainlength,
- nlambda,
- state->flags,
- flags_eks,
- flags_enh,
- flagsPullHistory,
- flags_dfh,
- flags_awhh,
- nED,
- eSwapCoords };
- std::strcpy(headerContents.version, gmx_version());
- std::strcpy(headerContents.fprog, gmx::getProgramContext().fullBinaryPath());
- std::strcpy(headerContents.ftime, timebuf.c_str());
- if (DOMAINDECOMP(cr))
- {
- copy_ivec(domdecCells, headerContents.dd_nc);
+ headerContents.flags_awhh |=
+ ((1 << eawhhIN_INITIAL) | (1 << eawhhEQUILIBRATEHISTOGRAM) | (1 << eawhhHISTSIZE)
+ | (1 << eawhhNPOINTS) | (1 << eawhhCOORDPOINT) | (1 << eawhhUMBRELLAGRIDPOINT)
+ | (1 << eawhhUPDATELIST) | (1 << eawhhLOGSCALEDSAMPLEWEIGHT)
+ | (1 << eawhhNUMUPDATES) | (1 << eawhhFORCECORRELATIONGRID));
}
do_cpt_header(gmx_fio_getxdr(fp), FALSE, nullptr, &headerContents);
if ((do_cpt_state(gmx_fio_getxdr(fp), state->flags, state, nullptr) < 0)
- || (do_cpt_ekinstate(gmx_fio_getxdr(fp), flags_eks, &state->ekinstate, nullptr) < 0)
- || (do_cpt_enerhist(gmx_fio_getxdr(fp), FALSE, flags_enh, enerhist, nullptr) < 0)
- || (doCptPullHist(gmx_fio_getxdr(fp), FALSE, flagsPullHistory, pullHist, StatePart::pullHistory, nullptr)
+ || (do_cpt_ekinstate(gmx_fio_getxdr(fp), headerContents.flags_eks, &state->ekinstate, nullptr) < 0)
+ || (do_cpt_enerhist(gmx_fio_getxdr(fp), FALSE, headerContents.flags_enh, enerhist, nullptr) < 0)
+ || (doCptPullHist(gmx_fio_getxdr(fp), FALSE, headerContents.flagsPullHistory, pullHist,
+ StatePart::pullHistory, nullptr)
+ < 0)
+ || (do_cpt_df_hist(gmx_fio_getxdr(fp), headerContents.flags_dfh, headerContents.nlambda,
+ &state->dfhist, nullptr)
+ < 0)
+ || (do_cpt_EDstate(gmx_fio_getxdr(fp), FALSE, headerContents.nED,
+ observablesHistory->edsamHistory.get(), nullptr)
+ < 0)
+ || (do_cpt_awh(gmx_fio_getxdr(fp), FALSE, headerContents.flags_awhh, state->awhHistory.get(), nullptr) < 0)
+ || (do_cpt_swapstate(gmx_fio_getxdr(fp), FALSE, headerContents.eSwapCoords,
+ observablesHistory->swapHistory.get(), nullptr)
< 0)
- || (do_cpt_df_hist(gmx_fio_getxdr(fp), flags_dfh, nlambda, &state->dfhist, nullptr) < 0)
- || (do_cpt_EDstate(gmx_fio_getxdr(fp), FALSE, nED, edsamhist, nullptr) < 0)
- || (do_cpt_awh(gmx_fio_getxdr(fp), FALSE, flags_awhh, state->awhHistory.get(), nullptr) < 0)
- || (do_cpt_swapstate(gmx_fio_getxdr(fp), FALSE, eSwapCoords, swaphist, nullptr) < 0)
- || (do_cpt_files(gmx_fio_getxdr(fp), FALSE, &outputfiles, nullptr, headerContents.file_version) < 0))
+ || (do_cpt_files(gmx_fio_getxdr(fp), FALSE, outputfiles, nullptr, headerContents.file_version) < 0))
{
gmx_file("Cannot read/write checkpoint; corrupt file, or maybe you are out of disk space?");
}
gmx::KeyValueTreeBuilder builder;
gmx::MdModulesWriteCheckpointData mdModulesWriteCheckpoint = { builder.rootObject(),
headerContents.file_version };
- mdModulesNotifier.notifier_.notify(mdModulesWriteCheckpoint);
+ mdModulesNotifier.checkpointingNotifications_.notify(mdModulesWriteCheckpoint);
auto tree = builder.build();
gmx::FileIOXdrSerializer serializer(fp);
gmx::serializeKeyValueTree(tree, &serializer);
}
- do_cpt_footer(gmx_fio_getxdr(fp), headerContents.file_version);
-
- /* we really, REALLY, want to make sure to physically write the checkpoint,
- and all the files it depends on, out to disk. Because we've
- opened the checkpoint with gmx_fio_open(), it's in our list
- of open files. */
- ret = gmx_fio_all_output_fsync();
-
- if (ret)
+ // Checkpointing modular simulator
{
- char buf[STRLEN];
- sprintf(buf, "Cannot fsync '%s'; maybe you are out of disk space?", gmx_fio_getname(ret));
-
- if (getenv(GMX_IGNORE_FSYNC_FAILURE_ENV) == nullptr)
- {
- gmx_file(buf);
- }
- else
- {
- gmx_warning("%s", buf);
- }
- }
-
- if (gmx_fio_close(fp) != 0)
- {
- gmx_file("Cannot read/write checkpoint; corrupt file, or maybe you are out of disk space?");
- }
-
- /* we don't move the checkpoint if the user specified they didn't want it,
- or if the fsyncs failed */
-#if !GMX_NO_RENAME
- if (!bNumberAndKeep && !ret)
- {
- if (gmx_fexist(fn))
- {
- /* Rename the previous checkpoint file */
- mpiBarrierBeforeRename(applyMpiBarrierBeforeRename, mpiBarrierCommunicator);
-
- std::strcpy(buf, fn);
- buf[std::strlen(fn) - std::strlen(ftp2ext(fn2ftp(fn))) - 1] = '\0';
- std::strcat(buf, "_prev");
- std::strcat(buf, fn + std::strlen(fn) - std::strlen(ftp2ext(fn2ftp(fn))) - 1);
- if (!GMX_FAHCORE)
- {
- /* we copy here so that if something goes wrong between now and
- * the rename below, there's always a state.cpt.
- * If renames are atomic (such as in POSIX systems),
- * this copying should be unneccesary.
- */
- gmx_file_copy(fn, buf, FALSE);
- /* We don't really care if this fails:
- * there's already a new checkpoint.
- */
- }
- else
- {
- gmx_file_rename(fn, buf);
- }
- }
-
- /* Rename the checkpoint file from the temporary to the final name */
- mpiBarrierBeforeRename(applyMpiBarrierBeforeRename, mpiBarrierCommunicator);
-
- if (gmx_file_rename(fntemp, fn) != 0)
- {
- gmx_file("Cannot rename checkpoint file; maybe you are out of disk space?");
- }
+ gmx::FileIOXdrSerializer serializer(fp);
+ modularSimulatorCheckpointData->serialize(&serializer);
}
-#endif /* GMX_NO_RENAME */
-
- sfree(fntemp);
+ do_cpt_footer(gmx_fio_getxdr(fp), headerContents.file_version);
+ #if GMX_FAHCORE
+ /* Always FAH checkpoint immediately after a Gromacs checkpoint.
+ *
+ * Note that it is critical that we save a FAH checkpoint directly
+ * after writing a Gromacs checkpoint. If the program dies, either
+ * by the machine powering off suddenly or the process being,
+ * killed, FAH can recover files that have only appended data by
+ * truncating them to the last recorded length. The Gromacs
+ * checkpoint does not just append data, it is fully rewritten each
+ * time so a crash between moving the new Gromacs checkpoint file in
+ * to place and writing a FAH checkpoint is not recoverable. Thus
+ * the time between these operations must be kept as short a
+ * possible.
+ */
+ fcCheckpoint();
+ #endif
}
static void check_int(FILE* fplog, const char* type, int p, int f, gmx_bool* mm)
check_int(fplog, "#ranks", cr->nnodes, headerContents.nnodes, &mm);
}
- if (cr->nnodes > 1 && reproducibilityRequested)
+ if (cr->sizeOfDefaultCommunicator > 1 && reproducibilityRequested)
{
+ // TODO: These checks are incorrect (see redmine #3309)
check_int(fplog, "#PME-ranks", cr->npmenodes, headerContents.npme, &mm);
- int npp = cr->nnodes;
+ int npp = cr->sizeOfDefaultCommunicator;
if (cr->npmenodes >= 0)
{
npp -= cr->npmenodes;
}
}
-static void read_checkpoint(const char* fn,
- t_fileio* logfio,
- const t_commrec* cr,
- const ivec dd_nc,
- int eIntegrator,
- int* init_fep_state,
- CheckpointHeaderContents* headerContents,
- t_state* state,
- ObservablesHistory* observablesHistory,
- gmx_bool reproducibilityRequested,
- const gmx::MdModulesNotifier& mdModulesNotifier)
+static void read_checkpoint(const char* fn,
+ t_fileio* logfio,
+ const t_commrec* cr,
+ const ivec dd_nc,
+ int eIntegrator,
+ int* init_fep_state,
+ CheckpointHeaderContents* headerContents,
+ t_state* state,
+ ObservablesHistory* observablesHistory,
+ gmx_bool reproducibilityRequested,
+ const gmx::MdModulesNotifier& mdModulesNotifier,
+ gmx::ReadCheckpointDataHolder* modularSimulatorCheckpointData,
+ bool useModularSimulator)
{
t_fileio* fp;
char buf[STEPSTRSIZE];
fn);
}
- if (headerContents->flags_state != state->flags)
+ // For modular simulator, no state object is populated, so we cannot do this check here!
+ if (headerContents->flags_state != state->flags && !useModularSimulator)
{
gmx_fatal(FARGS,
"Cannot change a simulation algorithm during a checkpoint restart. Perhaps you "
fn);
}
+ GMX_ASSERT(!(headerContents->isModularSimulatorCheckpoint && !useModularSimulator),
+ "Checkpoint file was written by modular simulator, but the current simulation uses "
+ "the legacy simulator.");
+ GMX_ASSERT(!(!headerContents->isModularSimulatorCheckpoint && useModularSimulator),
+ "Checkpoint file was written by legacy simulator, but the current simulation uses "
+ "the modular simulator.");
+
if (MASTER(cr))
{
check_match(fplog, cr, dd_nc, *headerContents, reproducibilityRequested);
cp_error();
}
do_cpt_mdmodules(headerContents->file_version, fp, mdModulesNotifier);
+ if (headerContents->file_version >= cptv_ModularSimulator)
+ {
+ gmx::FileIOXdrSerializer serializer(fp);
+ modularSimulatorCheckpointData->deserialize(&serializer);
+ }
ret = do_cpt_footer(gmx_fio_getxdr(fp), headerContents->file_version);
if (ret)
{
}
-void load_checkpoint(const char* fn,
- t_fileio* logfio,
- const t_commrec* cr,
- const ivec dd_nc,
- t_inputrec* ir,
- t_state* state,
- ObservablesHistory* observablesHistory,
- gmx_bool reproducibilityRequested,
- const gmx::MdModulesNotifier& mdModulesNotifier)
+void load_checkpoint(const char* fn,
+ t_fileio* logfio,
+ const t_commrec* cr,
+ const ivec dd_nc,
+ t_inputrec* ir,
+ t_state* state,
+ ObservablesHistory* observablesHistory,
+ gmx_bool reproducibilityRequested,
+ const gmx::MdModulesNotifier& mdModulesNotifier,
+ gmx::ReadCheckpointDataHolder* modularSimulatorCheckpointData,
+ bool useModularSimulator)
{
CheckpointHeaderContents headerContents;
if (SIMMASTER(cr))
{
/* Read the state from the checkpoint file */
- read_checkpoint(fn, logfio, cr, dd_nc, ir->eI, &(ir->fepvals->init_fep_state), &headerContents,
- state, observablesHistory, reproducibilityRequested, mdModulesNotifier);
+ read_checkpoint(fn, logfio, cr, dd_nc, ir->eI, &(ir->fepvals->init_fep_state),
+ &headerContents, state, observablesHistory, reproducibilityRequested,
+ mdModulesNotifier, modularSimulatorCheckpointData, useModularSimulator);
}
if (PAR(cr))
{
- gmx_bcast(sizeof(headerContents.step), &headerContents.step, cr);
- gmx::MdModulesCheckpointReadingBroadcast broadcastCheckPointData = { *cr, headerContents.file_version };
- mdModulesNotifier.notifier_.notify(broadcastCheckPointData);
+ gmx_bcast(sizeof(headerContents.step), &headerContents.step, cr->mpiDefaultCommunicator);
+ gmx::MdModulesCheckpointReadingBroadcast broadcastCheckPointData = {
+ cr->mpiDefaultCommunicator, PAR(cr), headerContents.file_version
+ };
+ mdModulesNotifier.checkpointingNotifications_.notify(broadcastCheckPointData);
}
ir->bContinuation = TRUE;
if (ir->nsteps >= 0)
}
gmx::MdModulesNotifier mdModuleNotifier;
do_cpt_mdmodules(headerContents.file_version, fp, mdModuleNotifier);
+ if (headerContents.file_version >= cptv_ModularSimulator)
+ {
+ // In the scope of the current function, we can just throw away the content
+ // of the modular checkpoint, but we need to read it to move the file pointer
+ gmx::FileIOXdrSerializer serializer(fp);
+ gmx::ReadCheckpointDataHolder modularSimulatorCheckpointData;
+ modularSimulatorCheckpointData.deserialize(&serializer);
+ }
ret = do_cpt_footer(gmx_fio_getxdr(fp), headerContents.file_version);
if (ret)
{
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013-2020, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, The GROMACS development team.
+ * Copyright (c) 2018,2019,2020, 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.
#include <algorithm>
#include <string>
-#include "gromacs/awh/read_params.h"
+#include "gromacs/applied_forces/awh/read_params.h"
#include "gromacs/fileio/readinp.h"
#include "gromacs/fileio/warninp.h"
#include "gromacs/gmxlib/network.h"
#include "gromacs/mdrun/mdmodules.h"
#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/mdtypes/md_enums.h"
+#include "gromacs/mdtypes/multipletimestepping.h"
#include "gromacs/mdtypes/pull_params.h"
#include "gromacs/options/options.h"
#include "gromacs/options/treesupport.h"
* message.
*/
-typedef struct t_inputrec_strings
+struct gmx_inputrec_strings
{
char tcgrps[STRLEN], tau_t[STRLEN], ref_t[STRLEN], acc[STRLEN], accgrps[STRLEN], freeze[STRLEN],
frdim[STRLEN], energy[STRLEN], user1[STRLEN], user2[STRLEN], vcm[STRLEN],
x_compressed_groups[STRLEN], couple_moltype[STRLEN], orirefitgrp[STRLEN],
egptable[STRLEN], egpexcl[STRLEN], wall_atomtype[STRLEN], wall_density[STRLEN],
deform[STRLEN], QMMM[STRLEN], imd_grp[STRLEN];
- char fep_lambda[efptNR][STRLEN];
- char lambda_weights[STRLEN];
- char** pull_grp;
- char** rot_grp;
- char anneal[STRLEN], anneal_npoints[STRLEN], anneal_time[STRLEN], anneal_temp[STRLEN];
- char QMmethod[STRLEN], QMbasis[STRLEN], QMcharge[STRLEN], QMmult[STRLEN], bSH[STRLEN],
+ char fep_lambda[efptNR][STRLEN];
+ char lambda_weights[STRLEN];
+ std::vector<std::string> pullGroupNames;
+ std::vector<std::string> rotateGroupNames;
+ char anneal[STRLEN], anneal_npoints[STRLEN], anneal_time[STRLEN], anneal_temp[STRLEN];
+ char QMmethod[STRLEN], QMbasis[STRLEN], QMcharge[STRLEN], QMmult[STRLEN], bSH[STRLEN],
CASorbitals[STRLEN], CASelectrons[STRLEN], SAon[STRLEN], SAoff[STRLEN], SAsteps[STRLEN];
+};
-} gmx_inputrec_strings;
-
-static gmx_inputrec_strings* is = nullptr;
+static gmx_inputrec_strings* inputrecStrings = nullptr;
void init_inputrec_strings()
{
- if (is)
+ if (inputrecStrings)
{
gmx_incons(
"Attempted to call init_inputrec_strings before calling done_inputrec_strings. "
"Only one inputrec (i.e. .mdp file) can be parsed at a time.");
}
- snew(is, 1);
+ inputrecStrings = new gmx_inputrec_strings();
}
void done_inputrec_strings()
{
- sfree(is);
- is = nullptr;
+ delete inputrecStrings;
+ inputrecStrings = nullptr;
}
}
}
+static void checkMtsRequirement(const t_inputrec& ir, const char* param, const int nstValue, warninp_t wi)
+{
+ GMX_RELEASE_ASSERT(ir.mtsLevels.size() >= 2, "Need at least two levels for MTS");
+ const int mtsFactor = ir.mtsLevels.back().stepFactor;
+ if (nstValue % mtsFactor != 0)
+ {
+ auto message = gmx::formatString(
+ "With MTS, %s = %d should be a multiple of mts-factor = %d", param, nstValue, mtsFactor);
+ warning_error(wi, message.c_str());
+ }
+}
+
+static void setupMtsLevels(gmx::ArrayRef<gmx::MtsLevel> mtsLevels,
+ const t_inputrec& ir,
+ const t_gromppopts& opts,
+ warninp_t wi)
+{
+ if (!(ir.eI == eiMD || ir.eI == eiSD1))
+ {
+ auto message = gmx::formatString(
+ "Multiple time stepping is only supported with integrators %s and %s",
+ ei_names[eiMD], ei_names[eiSD1]);
+ warning_error(wi, message.c_str());
+ }
+ if (opts.numMtsLevels != 2)
+ {
+ warning_error(wi, "Only mts-levels = 2 is supported");
+ }
+ else
+ {
+ const std::vector<std::string> inputForceGroups = gmx::splitString(opts.mtsLevel2Forces);
+ auto& forceGroups = mtsLevels[1].forceGroups;
+ for (const auto& inputForceGroup : inputForceGroups)
+ {
+ bool found = false;
+ int nameIndex = 0;
+ for (const auto& forceGroupName : gmx::mtsForceGroupNames)
+ {
+ if (gmx::equalCaseInsensitive(inputForceGroup, forceGroupName))
+ {
+ forceGroups.set(nameIndex);
+ found = true;
+ }
+ nameIndex++;
+ }
+ if (!found)
+ {
+ auto message =
+ gmx::formatString("Unknown MTS force group '%s'", inputForceGroup.c_str());
+ warning_error(wi, message.c_str());
+ }
+ }
+
+ if (mtsLevels[1].stepFactor <= 1)
+ {
+ gmx_fatal(FARGS, "mts-factor should be larger than 1");
+ }
+
+ // Make the level 0 use the complement of the force groups of group 1
+ mtsLevels[0].forceGroups = ~mtsLevels[1].forceGroups;
+ mtsLevels[0].stepFactor = 1;
+
+ if ((EEL_FULL(ir.coulombtype) || EVDW_PME(ir.vdwtype))
+ && !mtsLevels[1].forceGroups[static_cast<int>(gmx::MtsForceGroups::LongrangeNonbonded)])
+ {
+ warning_error(wi,
+ "With long-range electrostatics and/or LJ treatment, the long-range part "
+ "has to be part of the mts-level2-forces");
+ }
+
+ if (ir.nstcalcenergy > 0)
+ {
+ checkMtsRequirement(ir, "nstcalcenergy", ir.nstcalcenergy, wi);
+ }
+ checkMtsRequirement(ir, "nstenergy", ir.nstenergy, wi);
+ checkMtsRequirement(ir, "nstlog", ir.nstlog, wi);
+ if (ir.efep != efepNO)
+ {
+ checkMtsRequirement(ir, "nstdhdl", ir.fepvals->nstdhdl, wi);
+ }
+ }
+}
+
void check_ir(const char* mdparin,
const gmx::MdModulesNotifier& mdModulesNotifier,
t_inputrec* ir,
{
ir->nstpcouple = ir_optimal_nstpcouple(ir);
}
+ if (ir->useMts && ir->nstpcouple % ir->mtsLevels.back().stepFactor != 0)
+ {
+ warning_error(wi,
+ "With multiple time stepping, nstpcouple should be a mutiple of "
+ "mts-factor");
+ }
}
if (ir->nstcalcenergy > 0)
// Inquire all MdModules, if their parameters match with the energy
// calculation frequency
gmx::EnergyCalculationFrequencyErrors energyCalculationFrequencyErrors(ir->nstcalcenergy);
- mdModulesNotifier.notifier_.notify(&energyCalculationFrequencyErrors);
+ mdModulesNotifier.preProcessingNotifications_.notify(&energyCalculationFrequencyErrors);
// Emit all errors from the energy calculation frequency checks
for (const std::string& energyFrequencyErrorMessage :
/* TPI STUFF */
if (EI_TPI(ir->eI))
{
- sprintf(err_buf, "TPI only works with pbc = %s", epbc_names[epbcXYZ]);
- CHECK(ir->ePBC != epbcXYZ);
+ sprintf(err_buf, "TPI only works with pbc = %s", c_pbcTypeNames[PbcType::Xyz].c_str());
+ CHECK(ir->pbcType != PbcType::Xyz);
sprintf(err_buf, "with TPI nstlist should be larger than zero");
CHECK(ir->nstlist <= 0);
sprintf(err_buf, "TPI does not work with full electrostatics other than PME");
sprintf(err_buf, "The soft-core power is %d and can only be 1 or 2", fep->sc_power);
CHECK(fep->sc_alpha != 0 && fep->sc_power != 1 && fep->sc_power != 2);
- sprintf(err_buf, "The soft-core sc-r-power is %d and can only be 6 or 48",
+ sprintf(err_buf,
+ "The soft-core sc-r-power is %d and can only be 6. (sc-r-power 48 is no longer "
+ "supported.)",
static_cast<int>(fep->sc_r_power));
- CHECK(fep->sc_alpha != 0 && fep->sc_r_power != 6.0 && fep->sc_r_power != 48.0);
+ CHECK(fep->sc_alpha != 0 && fep->sc_r_power != 6.0);
sprintf(err_buf,
"Can't use positive delta-lambda (%g) if initial state/lambda does not start at "
}
/* PBC/WALLS */
- sprintf(err_buf, "walls only work with pbc=%s", epbc_names[epbcXY]);
- CHECK(ir->nwall && ir->ePBC != epbcXY);
+ sprintf(err_buf, "walls only work with pbc=%s", c_pbcTypeNames[PbcType::XY].c_str());
+ CHECK(ir->nwall && ir->pbcType != PbcType::XY);
/* VACUUM STUFF */
- if (ir->ePBC != epbcXYZ && ir->nwall != 2)
+ if (ir->pbcType != PbcType::Xyz && ir->nwall != 2)
{
- if (ir->ePBC == epbcNONE)
+ if (ir->pbcType == PbcType::No)
{
if (ir->epc != epcNO)
{
}
else
{
- sprintf(err_buf, "Can not have pressure coupling with pbc=%s", epbc_names[ir->ePBC]);
+ sprintf(err_buf, "Can not have pressure coupling with pbc=%s",
+ c_pbcTypeNames[ir->pbcType].c_str());
CHECK(ir->epc != epcNO);
}
- sprintf(err_buf, "Can not have Ewald with pbc=%s", epbc_names[ir->ePBC]);
+ sprintf(err_buf, "Can not have Ewald with pbc=%s", c_pbcTypeNames[ir->pbcType].c_str());
CHECK(EEL_FULL(ir->coulombtype));
- sprintf(err_buf, "Can not have dispersion correction with pbc=%s", epbc_names[ir->ePBC]);
+ sprintf(err_buf, "Can not have dispersion correction with pbc=%s",
+ c_pbcTypeNames[ir->pbcType].c_str());
CHECK(ir->eDispCorr != edispcNO);
}
"with coulombtype = %s or coulombtype = %s\n"
"without periodic boundary conditions (pbc = %s) and\n"
"rcoulomb and rvdw set to zero",
- eel_names[eelCUT], eel_names[eelUSER], epbc_names[epbcNONE]);
+ eel_names[eelCUT], eel_names[eelUSER], c_pbcTypeNames[PbcType::No].c_str());
CHECK(((ir->coulombtype != eelCUT) && (ir->coulombtype != eelUSER))
- || (ir->ePBC != epbcNONE) || (ir->rcoulomb != 0.0) || (ir->rvdw != 0.0));
+ || (ir->pbcType != PbcType::No) || (ir->rcoulomb != 0.0) || (ir->rvdw != 0.0));
if (ir->nstlist > 0)
{
"Can not remove the rotation around the center of mass with periodic "
"molecules");
CHECK(ir->bPeriodicMols);
- if (ir->ePBC != epbcNONE)
+ if (ir->pbcType != PbcType::No)
{
warning(wi,
"Removing the rotation around the center of mass in a periodic system, "
}
}
- if (EI_STATE_VELOCITY(ir->eI) && !EI_SD(ir->eI) && ir->ePBC == epbcNONE && ir->comm_mode != ecmANGULAR)
+ if (EI_STATE_VELOCITY(ir->eI) && !EI_SD(ir->eI) && ir->pbcType == PbcType::No && ir->comm_mode != ecmANGULAR)
{
sprintf(warn_buf,
"Tumbling and flying ice-cubes: We are not removing rotation around center of mass "
{
if (ir->ewald_geometry == eewg3D)
{
- sprintf(warn_buf, "With pbc=%s you should use ewald-geometry=%s", epbc_names[ir->ePBC],
- eewg_names[eewg3DC]);
+ sprintf(warn_buf, "With pbc=%s you should use ewald-geometry=%s",
+ c_pbcTypeNames[ir->pbcType].c_str(), eewg_names[eewg3DC]);
warning(wi, warn_buf);
}
/* This check avoids extra pbc coding for exclusion corrections */
sprintf(err_buf, "wall-ewald-zfac should be >= 2");
CHECK(ir->wall_ewald_zfac < 2);
}
- if ((ir->ewald_geometry == eewg3DC) && (ir->ePBC != epbcXY) && EEL_FULL(ir->coulombtype))
+ if ((ir->ewald_geometry == eewg3DC) && (ir->pbcType != PbcType::XY) && EEL_FULL(ir->coulombtype))
{
sprintf(warn_buf, "With %s and ewald_geometry = %s you should use pbc = %s",
- eel_names[ir->coulombtype], eewg_names[eewg3DC], epbc_names[epbcXY]);
+ eel_names[ir->coulombtype], eewg_names[eewg3DC], c_pbcTypeNames[PbcType::XY].c_str());
warning(wi, warn_buf);
}
if ((ir->epsilon_surface != 0) && EEL_FULL(ir->coulombtype))
if (ir->bQMMM)
{
- warning_error(wi, "QMMM is currently not supported");
- if (!EI_DYNAMICS(ir->eI))
- {
- char buf[STRLEN];
- sprintf(buf, "QMMM is only supported with dynamics, not with integrator %s", ei_names[ir->eI]);
- warning_error(wi, buf);
- }
+ warning_error(wi, "The QMMM integration you are trying to use is no longer supported");
}
if (ir->bAdress)
}
- /* make it easier if sc_r_power = 48 by increasing it to the 4th power, to be in the right scale. */
- if (fep->sc_r_power == 48)
- {
- if (fep->sc_alpha > 0.1)
- {
- gmx_fatal(FARGS,
- "sc_alpha (%f) for sc_r_power = 48 should usually be between 0.001 and 0.004",
- fep->sc_alpha);
- }
- }
-
/* now read in the weights */
parse_n_real(weights, &nweights, &(expand->init_lambda_weights), wi);
if (nweights == 0)
GetSimTemps(ir->fepvals->n_lambda, ir->simtempvals, ir->fepvals->all_lambda[efptTEMPERATURE]);
}
-static void convertYesNos(warninp_t /*wi*/,
- gmx::ArrayRef<const std::string> inputs,
- const char* /*name*/,
- gmx_bool* outputs)
-{
- int i = 0;
- for (const auto& input : inputs)
- {
- outputs[i] = gmx::equalCaseInsensitive(input, "Y", 1);
- ++i;
- }
-}
-
template<typename T>
void convertInts(warninp_t wi, gmx::ArrayRef<const std::string> inputs, const char* name, T* outputs)
{
gmx_fatal(FARGS, "Expected %d elements for wall_atomtype, found %zu", ir->nwall,
wallAtomTypes.size());
}
+ GMX_RELEASE_ASSERT(ir->nwall < 3, "Invalid number of walls");
for (int i = 0; i < ir->nwall; i++)
{
opts->wall_atomtype[i] = gmx_strdup(wallAtomTypes[i].c_str());
printStringNoNewline(
&inp, "Part index is updated automatically on checkpointing (keeps files separate)");
ir->simulation_part = get_eint(&inp, "simulation-part", 1, wi);
+ printStringNoNewline(&inp, "Multiple time-stepping");
+ ir->useMts = (get_eeenum(&inp, "mts", yesno_names, wi) != 0);
+ if (ir->useMts)
+ {
+ opts->numMtsLevels = get_eint(&inp, "mts-levels", 2, wi);
+ ir->mtsLevels.resize(2);
+ gmx::MtsLevel& mtsLevel = ir->mtsLevels[1];
+ opts->mtsLevel2Forces = setStringEntry(&inp, "mts-level2-forces",
+ "longrange-nonbonded nonbonded pair dihedral");
+ mtsLevel.stepFactor = get_eint(&inp, "mts-level2-factor", 2, wi);
+
+ // We clear after reading without dynamics to not force the user to remove MTS mdp options
+ if (!EI_DYNAMICS(ir->eI))
+ {
+ ir->useMts = false;
+ ir->mtsLevels.clear();
+ }
+ }
printStringNoNewline(&inp, "mode for center of mass motion removal");
ir->comm_mode = get_eeenum(&inp, "comm-mode", ecm_names, wi);
printStringNoNewline(&inp, "number of steps for center of mass motion removal");
ir->nstcomm = get_eint(&inp, "nstcomm", 100, wi);
printStringNoNewline(&inp, "group(s) for center of mass motion removal");
- setStringEntry(&inp, "comm-grps", is->vcm, nullptr);
+ setStringEntry(&inp, "comm-grps", inputrecStrings->vcm, nullptr);
printStringNewline(&inp, "LANGEVIN DYNAMICS OPTIONS");
printStringNoNewline(&inp, "Friction coefficient (amu/ps) and random seed");
printStringNoNewline(&inp, "This selects the subset of atoms for the compressed");
printStringNoNewline(&inp, "trajectory file. You can select multiple groups. By");
printStringNoNewline(&inp, "default, all atoms will be written.");
- setStringEntry(&inp, "compressed-x-grps", is->x_compressed_groups, nullptr);
+ setStringEntry(&inp, "compressed-x-grps", inputrecStrings->x_compressed_groups, nullptr);
printStringNoNewline(&inp, "Selection of energy groups");
- setStringEntry(&inp, "energygrps", is->energy, nullptr);
+ setStringEntry(&inp, "energygrps", inputrecStrings->energy, nullptr);
/* Neighbor searching */
printStringNewline(&inp, "NEIGHBORSEARCHING PARAMETERS");
printStringNoNewline(&inp, "nblist update frequency");
ir->nstlist = get_eint(&inp, "nstlist", 10, wi);
printStringNoNewline(&inp, "Periodic boundary conditions: xyz, no, xy");
- ir->ePBC = get_eeenum(&inp, "pbc", epbc_names, wi);
+ // TODO This conversion should be removed when proper std:string handling will be added to get_eeenum(...), etc.
+ std::vector<const char*> pbcTypesNamesChar;
+ for (const auto& pbcTypeName : c_pbcTypeNames)
+ {
+ pbcTypesNamesChar.push_back(pbcTypeName.c_str());
+ }
+ ir->pbcType = static_cast<PbcType>(get_eeenum(&inp, "pbc", pbcTypesNamesChar.data(), wi));
ir->bPeriodicMols = get_eeenum(&inp, "periodic-molecules", yesno_names, wi) != 0;
printStringNoNewline(&inp,
"Allowed energy error due to the Verlet buffer in kJ/mol/ps per atom,");
printStringNoNewline(&inp, "Extension of the potential lookup tables beyond the cut-off");
ir->tabext = get_ereal(&inp, "table-extension", 1.0, wi);
printStringNoNewline(&inp, "Separate tables between energy group pairs");
- setStringEntry(&inp, "energygrp-table", is->egptable, nullptr);
+ setStringEntry(&inp, "energygrp-table", inputrecStrings->egptable, nullptr);
printStringNoNewline(&inp, "Spacing for the PME/PPPM FFT grid");
ir->fourier_spacing = get_ereal(&inp, "fourierspacing", 0.12, wi);
printStringNoNewline(&inp, "FFT grid size, when a value is 0 fourierspacing will be used");
ir->opts.nhchainlength = get_eint(&inp, "nh-chain-length", 10, wi);
ir->bPrintNHChains = (get_eeenum(&inp, "print-nose-hoover-chain-variables", yesno_names, wi) != 0);
printStringNoNewline(&inp, "Groups to couple separately");
- setStringEntry(&inp, "tc-grps", is->tcgrps, nullptr);
+ setStringEntry(&inp, "tc-grps", inputrecStrings->tcgrps, nullptr);
printStringNoNewline(&inp, "Time constant (ps) and reference temperature (K)");
- setStringEntry(&inp, "tau-t", is->tau_t, nullptr);
- setStringEntry(&inp, "ref-t", is->ref_t, nullptr);
+ setStringEntry(&inp, "tau-t", inputrecStrings->tau_t, nullptr);
+ setStringEntry(&inp, "ref-t", inputrecStrings->ref_t, nullptr);
printStringNoNewline(&inp, "pressure coupling");
ir->epc = get_eeenum(&inp, "pcoupl", epcoupl_names, wi);
ir->epct = get_eeenum(&inp, "pcoupltype", epcoupltype_names, wi);
printStringNewline(&inp, "OPTIONS FOR QMMM calculations");
ir->bQMMM = (get_eeenum(&inp, "QMMM", yesno_names, wi) != 0);
printStringNoNewline(&inp, "Groups treated Quantum Mechanically");
- setStringEntry(&inp, "QMMM-grps", is->QMMM, nullptr);
+ setStringEntry(&inp, "QMMM-grps", inputrecStrings->QMMM, nullptr);
printStringNoNewline(&inp, "QM method");
- setStringEntry(&inp, "QMmethod", is->QMmethod, nullptr);
+ setStringEntry(&inp, "QMmethod", inputrecStrings->QMmethod, nullptr);
printStringNoNewline(&inp, "QMMM scheme");
- ir->QMMMscheme = get_eeenum(&inp, "QMMMscheme", eQMMMscheme_names, wi);
+ const char* noQMMMSchemeName = "normal";
+ get_eeenum(&inp, "QMMMscheme", &noQMMMSchemeName, wi);
printStringNoNewline(&inp, "QM basisset");
- setStringEntry(&inp, "QMbasis", is->QMbasis, nullptr);
+ setStringEntry(&inp, "QMbasis", inputrecStrings->QMbasis, nullptr);
printStringNoNewline(&inp, "QM charge");
- setStringEntry(&inp, "QMcharge", is->QMcharge, nullptr);
+ setStringEntry(&inp, "QMcharge", inputrecStrings->QMcharge, nullptr);
printStringNoNewline(&inp, "QM multiplicity");
- setStringEntry(&inp, "QMmult", is->QMmult, nullptr);
+ setStringEntry(&inp, "QMmult", inputrecStrings->QMmult, nullptr);
printStringNoNewline(&inp, "Surface Hopping");
- setStringEntry(&inp, "SH", is->bSH, nullptr);
+ setStringEntry(&inp, "SH", inputrecStrings->bSH, nullptr);
printStringNoNewline(&inp, "CAS space options");
- setStringEntry(&inp, "CASorbitals", is->CASorbitals, nullptr);
- setStringEntry(&inp, "CASelectrons", is->CASelectrons, nullptr);
- setStringEntry(&inp, "SAon", is->SAon, nullptr);
- setStringEntry(&inp, "SAoff", is->SAoff, nullptr);
- setStringEntry(&inp, "SAsteps", is->SAsteps, nullptr);
+ setStringEntry(&inp, "CASorbitals", inputrecStrings->CASorbitals, nullptr);
+ setStringEntry(&inp, "CASelectrons", inputrecStrings->CASelectrons, nullptr);
+ setStringEntry(&inp, "SAon", inputrecStrings->SAon, nullptr);
+ setStringEntry(&inp, "SAoff", inputrecStrings->SAoff, nullptr);
+ setStringEntry(&inp, "SAsteps", inputrecStrings->SAsteps, nullptr);
printStringNoNewline(&inp, "Scale factor for MM charges");
- ir->scalefactor = get_ereal(&inp, "MMChargeScaleFactor", 1.0, wi);
+ get_ereal(&inp, "MMChargeScaleFactor", 1.0, wi);
/* Simulated annealing */
printStringNewline(&inp, "SIMULATED ANNEALING");
printStringNoNewline(&inp, "Type of annealing for each temperature group (no/single/periodic)");
- setStringEntry(&inp, "annealing", is->anneal, nullptr);
+ setStringEntry(&inp, "annealing", inputrecStrings->anneal, nullptr);
printStringNoNewline(&inp,
"Number of time points to use for specifying annealing in each group");
- setStringEntry(&inp, "annealing-npoints", is->anneal_npoints, nullptr);
+ setStringEntry(&inp, "annealing-npoints", inputrecStrings->anneal_npoints, nullptr);
printStringNoNewline(&inp, "List of times at the annealing points for each group");
- setStringEntry(&inp, "annealing-time", is->anneal_time, nullptr);
+ setStringEntry(&inp, "annealing-time", inputrecStrings->anneal_time, nullptr);
printStringNoNewline(&inp, "Temp. at each annealing point, for each group.");
- setStringEntry(&inp, "annealing-temp", is->anneal_temp, nullptr);
+ setStringEntry(&inp, "annealing-temp", inputrecStrings->anneal_temp, nullptr);
/* Startup run */
printStringNewline(&inp, "GENERATE VELOCITIES FOR STARTUP RUN");
printStringNewline(&inp, "ENERGY GROUP EXCLUSIONS");
printStringNoNewline(
&inp, "Pairs of energy groups for which all non-bonded interactions are excluded");
- setStringEntry(&inp, "energygrp-excl", is->egpexcl, nullptr);
+ setStringEntry(&inp, "energygrp-excl", inputrecStrings->egpexcl, nullptr);
/* Walls */
printStringNewline(&inp, "WALLS");
ir->nwall = get_eint(&inp, "nwall", 0, wi);
ir->wall_type = get_eeenum(&inp, "wall-type", ewt_names, wi);
ir->wall_r_linpot = get_ereal(&inp, "wall-r-linpot", -1, wi);
- setStringEntry(&inp, "wall-atomtype", is->wall_atomtype, nullptr);
- setStringEntry(&inp, "wall-density", is->wall_density, nullptr);
+ setStringEntry(&inp, "wall-atomtype", inputrecStrings->wall_atomtype, nullptr);
+ setStringEntry(&inp, "wall-density", inputrecStrings->wall_density, nullptr);
ir->wall_ewald_zfac = get_ereal(&inp, "wall-ewald-zfac", 3, wi);
/* COM pulling */
if (ir->bPull)
{
snew(ir->pull, 1);
- is->pull_grp = read_pullparams(&inp, ir->pull, wi);
+ inputrecStrings->pullGroupNames = read_pullparams(&inp, ir->pull, wi);
+
+ if (ir->useMts)
+ {
+ for (int c = 0; c < ir->pull->ncoord; c++)
+ {
+ if (ir->pull->coord[c].eType == epullCONSTRAINT)
+ {
+ warning_error(wi,
+ "Constraint COM pulling is not supported in combination with "
+ "multiple time stepping");
+ break;
+ }
+ }
+ }
}
/* AWH biasing
- NOTE: needs COM pulling input */
+ NOTE: needs COM pulling or free energy input */
printStringNewline(&inp, "AWH biasing");
ir->bDoAwh = (get_eeenum(&inp, "awh", yesno_names, wi) != 0);
if (ir->bDoAwh)
{
- if (ir->bPull)
- {
- ir->awhParams = gmx::readAndCheckAwhParams(&inp, ir, wi);
- }
- else
- {
- gmx_fatal(FARGS, "AWH biasing is only compatible with COM pulling turned on");
- }
+ ir->awhParams = gmx::readAwhParams(&inp, wi);
}
/* Enforced rotation */
if (ir->bRot)
{
snew(ir->rot, 1);
- is->rot_grp = read_rotparams(&inp, ir->rot, wi);
+ inputrecStrings->rotateGroupNames = read_rotparams(&inp, ir->rot, wi);
}
/* Interactive MD */
ir->bIMD = FALSE;
printStringNewline(&inp, "Group to display and/or manipulate in interactive MD session");
- setStringEntry(&inp, "IMD-group", is->imd_grp, nullptr);
- if (is->imd_grp[0] != '\0')
+ setStringEntry(&inp, "IMD-group", inputrecStrings->imd_grp, nullptr);
+ if (inputrecStrings->imd_grp[0] != '\0')
{
snew(ir->imd, 1);
ir->bIMD = TRUE;
printStringNoNewline(&inp, "Orientation restraints force constant and tau for time averaging");
ir->orires_fc = get_ereal(&inp, "orire-fc", 0.0, wi);
ir->orires_tau = get_ereal(&inp, "orire-tau", 0.0, wi);
- setStringEntry(&inp, "orire-fitgrp", is->orirefitgrp, nullptr);
+ setStringEntry(&inp, "orire-fitgrp", inputrecStrings->orirefitgrp, nullptr);
printStringNoNewline(&inp, "Output frequency for trace(SD) and S to energy file");
ir->nstorireout = get_eint(&inp, "nstorireout", 100, wi);
/* free energy variables */
printStringNewline(&inp, "Free energy variables");
ir->efep = get_eeenum(&inp, "free-energy", efep_names, wi);
- setStringEntry(&inp, "couple-moltype", is->couple_moltype, nullptr);
+ setStringEntry(&inp, "couple-moltype", inputrecStrings->couple_moltype, nullptr);
opts->couple_lam0 = get_eeenum(&inp, "couple-lambda0", couple_lam, wi);
opts->couple_lam1 = get_eeenum(&inp, "couple-lambda1", couple_lam, wi);
opts->bCoupleIntra = (get_eeenum(&inp, "couple-intramol", yesno_names, wi) != 0);
fep->init_fep_state = get_eint(&inp, "init-lambda-state", -1, wi);
fep->delta_lambda = get_ereal(&inp, "delta-lambda", 0.0, wi);
fep->nstdhdl = get_eint(&inp, "nstdhdl", 50, wi);
- setStringEntry(&inp, "fep-lambdas", is->fep_lambda[efptFEP], nullptr);
- setStringEntry(&inp, "mass-lambdas", is->fep_lambda[efptMASS], nullptr);
- setStringEntry(&inp, "coul-lambdas", is->fep_lambda[efptCOUL], nullptr);
- setStringEntry(&inp, "vdw-lambdas", is->fep_lambda[efptVDW], nullptr);
- setStringEntry(&inp, "bonded-lambdas", is->fep_lambda[efptBONDED], nullptr);
- setStringEntry(&inp, "restraint-lambdas", is->fep_lambda[efptRESTRAINT], nullptr);
- setStringEntry(&inp, "temperature-lambdas", is->fep_lambda[efptTEMPERATURE], nullptr);
+ setStringEntry(&inp, "fep-lambdas", inputrecStrings->fep_lambda[efptFEP], nullptr);
+ setStringEntry(&inp, "mass-lambdas", inputrecStrings->fep_lambda[efptMASS], nullptr);
+ setStringEntry(&inp, "coul-lambdas", inputrecStrings->fep_lambda[efptCOUL], nullptr);
+ setStringEntry(&inp, "vdw-lambdas", inputrecStrings->fep_lambda[efptVDW], nullptr);
+ setStringEntry(&inp, "bonded-lambdas", inputrecStrings->fep_lambda[efptBONDED], nullptr);
+ setStringEntry(&inp, "restraint-lambdas", inputrecStrings->fep_lambda[efptRESTRAINT], nullptr);
+ setStringEntry(&inp, "temperature-lambdas", inputrecStrings->fep_lambda[efptTEMPERATURE], nullptr);
fep->lambda_neighbors = get_eint(&inp, "calc-lambda-neighbors", 1, wi);
- setStringEntry(&inp, "init-lambda-weights", is->lambda_weights, nullptr);
+ setStringEntry(&inp, "init-lambda-weights", inputrecStrings->lambda_weights, nullptr);
fep->edHdLPrintEnergy = get_eeenum(&inp, "dhdl-print-energy", edHdLPrintEnergy_names, wi);
fep->sc_alpha = get_ereal(&inp, "sc-alpha", 0.0, wi);
fep->sc_power = get_eint(&inp, "sc-power", 1, wi);
/* Non-equilibrium MD stuff */
printStringNewline(&inp, "Non-equilibrium MD stuff");
- setStringEntry(&inp, "acc-grps", is->accgrps, nullptr);
- setStringEntry(&inp, "accelerate", is->acc, nullptr);
- setStringEntry(&inp, "freezegrps", is->freeze, nullptr);
- setStringEntry(&inp, "freezedim", is->frdim, nullptr);
+ setStringEntry(&inp, "acc-grps", inputrecStrings->accgrps, nullptr);
+ setStringEntry(&inp, "accelerate", inputrecStrings->acc, nullptr);
+ setStringEntry(&inp, "freezegrps", inputrecStrings->freeze, nullptr);
+ setStringEntry(&inp, "freezedim", inputrecStrings->frdim, nullptr);
ir->cos_accel = get_ereal(&inp, "cos-acceleration", 0, wi);
- setStringEntry(&inp, "deform", is->deform, nullptr);
+ setStringEntry(&inp, "deform", inputrecStrings->deform, nullptr);
/* simulated tempering variables */
printStringNewline(&inp, "simulated tempering variables");
/* User defined thingies */
printStringNewline(&inp, "User defined thingies");
- setStringEntry(&inp, "user1-grps", is->user1, nullptr);
- setStringEntry(&inp, "user2-grps", is->user2, nullptr);
+ setStringEntry(&inp, "user1-grps", inputrecStrings->user1, nullptr);
+ setStringEntry(&inp, "user2-grps", inputrecStrings->user2, nullptr);
ir->userint1 = get_eint(&inp, "userint1", 0, wi);
ir->userint2 = get_eint(&inp, "userint2", 0, wi);
ir->userint3 = get_eint(&inp, "userint3", 0, wi);
}
opts->couple_moltype = nullptr;
- if (strlen(is->couple_moltype) > 0)
+ if (strlen(inputrecStrings->couple_moltype) > 0)
{
if (ir->efep != efepNO)
{
- opts->couple_moltype = gmx_strdup(is->couple_moltype);
+ opts->couple_moltype = gmx_strdup(inputrecStrings->couple_moltype);
if (opts->couple_lam0 == opts->couple_lam1)
{
warning(wi, "The lambda=0 and lambda=1 states for coupling are identical");
/* FREE ENERGY AND EXPANDED ENSEMBLE OPTIONS */
if (ir->efep != efepNO)
{
- if (fep->delta_lambda > 0)
+ if (fep->delta_lambda != 0)
{
ir->efep = efepSLOWGROWTH;
}
{
ir->bExpanded = TRUE;
}
- do_fep_params(ir, is->fep_lambda, is->lambda_weights, wi);
+ do_fep_params(ir, inputrecStrings->fep_lambda, inputrecStrings->lambda_weights, wi);
if (ir->bSimTemp) /* done after fep params */
{
do_simtemp_params(ir);
/* WALL PARAMETERS */
- do_wall_params(ir, is->wall_atomtype, is->wall_density, opts, wi);
+ do_wall_params(ir, inputrecStrings->wall_atomtype, inputrecStrings->wall_density, opts, wi);
/* ORIENTATION RESTRAINT PARAMETERS */
- if (opts->bOrire && gmx::splitString(is->orirefitgrp).size() != 1)
+ if (opts->bOrire && gmx::splitString(inputrecStrings->orirefitgrp).size() != 1)
{
warning_error(wi, "ERROR: Need one orientation restraint fit group\n");
}
}
double gmx_unused canary;
- int ndeform = sscanf(is->deform, "%lf %lf %lf %lf %lf %lf %lf", &(dumdub[0][0]), &(dumdub[0][1]),
- &(dumdub[0][2]), &(dumdub[0][3]), &(dumdub[0][4]), &(dumdub[0][5]), &canary);
+ int ndeform = sscanf(inputrecStrings->deform, "%lf %lf %lf %lf %lf %lf %lf", &(dumdub[0][0]),
+ &(dumdub[0][1]), &(dumdub[0][2]), &(dumdub[0][3]), &(dumdub[0][4]),
+ &(dumdub[0][5]), &canary);
- if (strlen(is->deform) > 0 && ndeform != 6)
+ if (strlen(inputrecStrings->deform) > 0 && ndeform != 6)
{
- warning_error(
- wi, gmx::formatString(
- "Cannot parse exactly 6 box deformation velocities from string '%s'", is->deform)
- .c_str());
+ warning_error(wi,
+ gmx::formatString(
+ "Cannot parse exactly 6 box deformation velocities from string '%s'",
+ inputrecStrings->deform)
+ .c_str());
}
for (i = 0; i < 3; i++)
{
}
}
- sfree(dumstr[0]);
- sfree(dumstr[1]);
-}
-
-static int search_QMstring(const char* s, int ng, const char* gn[])
-{
- /* same as normal search_string, but this one searches QM strings */
- int i;
+ /* Set up MTS levels, this needs to happen before checking AWH parameters */
+ if (ir->useMts)
+ {
+ setupMtsLevels(ir->mtsLevels, *ir, *opts, wi);
+ }
- for (i = 0; (i < ng); i++)
+ if (ir->bDoAwh)
{
- if (gmx_strcasecmp(s, gn[i]) == 0)
- {
- return i;
- }
+ gmx::checkAwhParams(ir->awhParams, ir, wi);
}
- gmx_fatal(FARGS, "this QM method or basisset (%s) is not implemented\n!", s);
-} /* search_QMstring */
+ sfree(dumstr[0]);
+ sfree(dumstr[1]);
+}
/* We would like gn to be const as well, but C doesn't allow this */
/* TODO this is utility functionality (search for the index of a
if (numFrozenDims == DIM)
{
/* Do not remove COM motion for this fully frozen atom */
- if (groups->groups[SimulationAtomGroupType::MassCenterVelocityRemoval].empty())
+ if (groups->groupNumbers[SimulationAtomGroupType::MassCenterVelocityRemoval].empty())
{
- groups->groups[SimulationAtomGroupType::MassCenterVelocityRemoval].resize(numAtoms, 0);
+ groups->groupNumbers[SimulationAtomGroupType::MassCenterVelocityRemoval].resize(
+ numAtoms, 0);
}
- groups->groups[SimulationAtomGroupType::MassCenterVelocityRemoval][a] = vcmRestGroup;
+ groups->groupNumbers[SimulationAtomGroupType::MassCenterVelocityRemoval][a] = vcmRestGroup;
numFullyFrozenVcmAtoms++;
}
else if (numFrozenDims > 0)
set_warning_line(wi, mdparin, -1);
- auto temperatureCouplingTauValues = gmx::splitString(is->tau_t);
- auto temperatureCouplingReferenceValues = gmx::splitString(is->ref_t);
- auto temperatureCouplingGroupNames = gmx::splitString(is->tcgrps);
+ auto temperatureCouplingTauValues = gmx::splitString(inputrecStrings->tau_t);
+ auto temperatureCouplingReferenceValues = gmx::splitString(inputrecStrings->ref_t);
+ auto temperatureCouplingGroupNames = gmx::splitString(inputrecStrings->tcgrps);
if (temperatureCouplingTauValues.size() != temperatureCouplingGroupNames.size()
|| temperatureCouplingReferenceValues.size() != temperatureCouplingGroupNames.size())
{
}
/* Simulated annealing for each group. There are nr groups */
- auto simulatedAnnealingGroupNames = gmx::splitString(is->anneal);
+ auto simulatedAnnealingGroupNames = gmx::splitString(inputrecStrings->anneal);
if (simulatedAnnealingGroupNames.size() == 1
&& gmx::equalCaseInsensitive(simulatedAnnealingGroupNames[0], "N", 1))
{
if (bAnneal)
{
/* Read the other fields too */
- auto simulatedAnnealingPoints = gmx::splitString(is->anneal_npoints);
+ auto simulatedAnnealingPoints = gmx::splitString(inputrecStrings->anneal_npoints);
if (simulatedAnnealingPoints.size() != simulatedAnnealingGroupNames.size())
{
gmx_fatal(FARGS, "Found %zu annealing-npoints values for %zu groups\n",
numSimulatedAnnealingFields += ir->opts.anneal_npoints[i];
}
- auto simulatedAnnealingTimes = gmx::splitString(is->anneal_time);
+ auto simulatedAnnealingTimes = gmx::splitString(inputrecStrings->anneal_time);
if (simulatedAnnealingTimes.size() != numSimulatedAnnealingFields)
{
gmx_fatal(FARGS, "Found %zu annealing-time values, wanted %zu\n",
simulatedAnnealingTimes.size(), numSimulatedAnnealingFields);
}
- auto simulatedAnnealingTemperatures = gmx::splitString(is->anneal_temp);
+ auto simulatedAnnealingTemperatures = gmx::splitString(inputrecStrings->anneal_temp);
if (simulatedAnnealingTemperatures.size() != numSimulatedAnnealingFields)
{
gmx_fatal(FARGS, "Found %zu annealing-temp values, wanted %zu\n",
if (ir->bPull)
{
- make_pull_groups(ir->pull, is->pull_grp, defaultIndexGroups, gnames);
+ make_pull_groups(ir->pull, inputrecStrings->pullGroupNames, defaultIndexGroups, gnames);
make_pull_coords(ir->pull);
}
if (ir->bRot)
{
- make_rotation_groups(ir->rot, is->rot_grp, defaultIndexGroups, gnames);
+ make_rotation_groups(ir->rot, inputrecStrings->rotateGroupNames, defaultIndexGroups, gnames);
}
if (ir->eSwapCoords != eswapNO)
/* Make indices for IMD session */
if (ir->bIMD)
{
- make_IMD_group(ir->imd, is->imd_grp, defaultIndexGroups, gnames);
+ make_IMD_group(ir->imd, inputrecStrings->imd_grp, defaultIndexGroups, gnames);
}
gmx::IndexGroupsAndNames defaultIndexGroupsAndNames(
*defaultIndexGroups, gmx::arrayRefFromArray(gnames, defaultIndexGroups->nr));
- notifier.notifier_.notify(defaultIndexGroupsAndNames);
+ notifier.preProcessingNotifications_.notify(defaultIndexGroupsAndNames);
- auto accelerations = gmx::splitString(is->acc);
- auto accelerationGroupNames = gmx::splitString(is->accgrps);
+ auto accelerations = gmx::splitString(inputrecStrings->acc);
+ auto accelerationGroupNames = gmx::splitString(inputrecStrings->accgrps);
if (accelerationGroupNames.size() * DIM != accelerations.size())
{
gmx_fatal(FARGS, "Invalid Acceleration input: %zu groups and %zu acc. values",
convertRvecs(wi, accelerations, "anneal-time", ir->opts.acc);
- auto freezeDims = gmx::splitString(is->frdim);
- auto freezeGroupNames = gmx::splitString(is->freeze);
+ auto freezeDims = gmx::splitString(inputrecStrings->frdim);
+ auto freezeGroupNames = gmx::splitString(inputrecStrings->freeze);
if (freezeDims.size() != DIM * freezeGroupNames.size())
{
gmx_fatal(FARGS, "Invalid Freezing input: %zu groups and %zu freeze values",
}
}
- auto energyGroupNames = gmx::splitString(is->energy);
+ auto energyGroupNames = gmx::splitString(inputrecStrings->energy);
do_numbering(natoms, groups, energyGroupNames, defaultIndexGroups, gnames,
SimulationAtomGroupType::EnergyOutput, restnm, egrptpALL_GENREST, bVerbose, wi);
add_wall_energrps(groups, ir->nwall, symtab);
ir->opts.ngener = groups->groups[SimulationAtomGroupType::EnergyOutput].size();
- auto vcmGroupNames = gmx::splitString(is->vcm);
+ auto vcmGroupNames = gmx::splitString(inputrecStrings->vcm);
do_numbering(natoms, groups, vcmGroupNames, defaultIndexGroups, gnames,
SimulationAtomGroupType::MassCenterVelocityRemoval, restnm,
vcmGroupNames.empty() ? egrptpALL_GENREST : egrptpPART, bVerbose, wi);
/* Now we have filled the freeze struct, so we can calculate NRDF */
calc_nrdf(mtop, ir, gnames);
- auto user1GroupNames = gmx::splitString(is->user1);
+ auto user1GroupNames = gmx::splitString(inputrecStrings->user1);
do_numbering(natoms, groups, user1GroupNames, defaultIndexGroups, gnames,
SimulationAtomGroupType::User1, restnm, egrptpALL_GENREST, bVerbose, wi);
- auto user2GroupNames = gmx::splitString(is->user2);
+ auto user2GroupNames = gmx::splitString(inputrecStrings->user2);
do_numbering(natoms, groups, user2GroupNames, defaultIndexGroups, gnames,
SimulationAtomGroupType::User2, restnm, egrptpALL_GENREST, bVerbose, wi);
- auto compressedXGroupNames = gmx::splitString(is->x_compressed_groups);
+ auto compressedXGroupNames = gmx::splitString(inputrecStrings->x_compressed_groups);
do_numbering(natoms, groups, compressedXGroupNames, defaultIndexGroups, gnames,
SimulationAtomGroupType::CompressedPositionOutput, restnm, egrptpONE, bVerbose, wi);
- auto orirefFitGroupNames = gmx::splitString(is->orirefitgrp);
+ auto orirefFitGroupNames = gmx::splitString(inputrecStrings->orirefitgrp);
do_numbering(natoms, groups, orirefFitGroupNames, defaultIndexGroups, gnames,
SimulationAtomGroupType::OrientationRestraintsFit, restnm, egrptpALL_GENREST,
bVerbose, wi);
- /* QMMM input processing */
- auto qmGroupNames = gmx::splitString(is->QMMM);
- auto qmMethods = gmx::splitString(is->QMmethod);
- auto qmBasisSets = gmx::splitString(is->QMbasis);
- if (ir->eI != eiMimic)
+ /* MiMiC QMMM input processing */
+ auto qmGroupNames = gmx::splitString(inputrecStrings->QMMM);
+ if (qmGroupNames.size() > 1)
{
- if (qmMethods.size() != qmGroupNames.size() || qmBasisSets.size() != qmGroupNames.size())
- {
- gmx_fatal(FARGS,
- "Invalid QMMM input: %zu groups %zu basissets"
- " and %zu methods\n",
- qmGroupNames.size(), qmBasisSets.size(), qmMethods.size());
- }
- /* group rest, if any, is always MM! */
- do_numbering(natoms, groups, qmGroupNames, defaultIndexGroups, gnames,
- SimulationAtomGroupType::QuantumMechanics, restnm, egrptpALL_GENREST, bVerbose, wi);
- nr = qmGroupNames.size(); /*atoms->grps[egcQMMM].nr;*/
- ir->opts.ngQM = qmGroupNames.size();
- snew(ir->opts.QMmethod, nr);
- snew(ir->opts.QMbasis, nr);
- for (i = 0; i < nr; i++)
- {
- /* input consists of strings: RHF CASSCF PM3 .. These need to be
- * converted to the corresponding enum in names.c
- */
- ir->opts.QMmethod[i] = search_QMstring(qmMethods[i].c_str(), eQMmethodNR, eQMmethod_names);
- ir->opts.QMbasis[i] = search_QMstring(qmBasisSets[i].c_str(), eQMbasisNR, eQMbasis_names);
- }
- auto qmMultiplicities = gmx::splitString(is->QMmult);
- auto qmCharges = gmx::splitString(is->QMcharge);
- auto qmbSH = gmx::splitString(is->bSH);
- snew(ir->opts.QMmult, nr);
- snew(ir->opts.QMcharge, nr);
- snew(ir->opts.bSH, nr);
- convertInts(wi, qmMultiplicities, "QMmult", ir->opts.QMmult);
- convertInts(wi, qmCharges, "QMcharge", ir->opts.QMcharge);
- convertYesNos(wi, qmbSH, "bSH", ir->opts.bSH);
-
- auto CASelectrons = gmx::splitString(is->CASelectrons);
- auto CASorbitals = gmx::splitString(is->CASorbitals);
- snew(ir->opts.CASelectrons, nr);
- snew(ir->opts.CASorbitals, nr);
- convertInts(wi, CASelectrons, "CASelectrons", ir->opts.CASelectrons);
- convertInts(wi, CASorbitals, "CASOrbitals", ir->opts.CASorbitals);
-
- auto SAon = gmx::splitString(is->SAon);
- auto SAoff = gmx::splitString(is->SAoff);
- auto SAsteps = gmx::splitString(is->SAsteps);
- snew(ir->opts.SAon, nr);
- snew(ir->opts.SAoff, nr);
- snew(ir->opts.SAsteps, nr);
- convertInts(wi, SAon, "SAon", ir->opts.SAon);
- convertInts(wi, SAoff, "SAoff", ir->opts.SAoff);
- convertInts(wi, SAsteps, "SAsteps", ir->opts.SAsteps);
+ gmx_fatal(FARGS, "Currently, having more than one QM group in MiMiC is not supported");
}
- else
- {
- /* MiMiC */
- if (qmGroupNames.size() > 1)
- {
- gmx_fatal(FARGS, "Currently, having more than one QM group in MiMiC is not supported");
- }
- /* group rest, if any, is always MM! */
- do_numbering(natoms, groups, qmGroupNames, defaultIndexGroups, gnames,
- SimulationAtomGroupType::QuantumMechanics, restnm, egrptpALL_GENREST, bVerbose, wi);
+ /* group rest, if any, is always MM! */
+ do_numbering(natoms, groups, qmGroupNames, defaultIndexGroups, gnames,
+ SimulationAtomGroupType::QuantumMechanics, restnm, egrptpALL_GENREST, bVerbose, wi);
+ ir->opts.ngQM = qmGroupNames.size();
- ir->opts.ngQM = qmGroupNames.size();
- }
-
- /* end of QMMM input */
+ /* end of MiMiC QMMM input */
if (bVerbose)
{
nr = groups->groups[SimulationAtomGroupType::EnergyOutput].size();
snew(ir->opts.egp_flags, nr * nr);
- bExcl = do_egp_flag(ir, groups, "energygrp-excl", is->egpexcl, EGP_EXCL);
+ bExcl = do_egp_flag(ir, groups, "energygrp-excl", inputrecStrings->egpexcl, EGP_EXCL);
if (bExcl && ir->cutoff_scheme == ecutsVERLET)
{
warning_error(wi, "Energy group exclusions are currently not supported");
warning(wi, "Can not exclude the lattice Coulomb energy between energy groups");
}
- bTable = do_egp_flag(ir, groups, "energygrp-table", is->egptable, EGP_TABLE);
+ bTable = do_egp_flag(ir, groups, "energygrp-table", inputrecStrings->egptable, EGP_TABLE);
if (bTable && !(ir->vdwtype == evdwUSER) && !(ir->coulombtype == eelUSER)
&& !(ir->coulombtype == eelPMEUSER) && !(ir->coulombtype == eelPMEUSERSWITCH))
{
void triple_check(const char* mdparin, t_inputrec* ir, gmx_mtop_t* sys, warninp_t wi)
{
+ // Not meeting MTS requirements should have resulted in a fatal error, so we can assert here
+ gmx::assertMtsRequirements(*ir);
+
char err_buf[STRLEN];
int i, m, c, nmol;
bool bCharge, bAcc;
char warn_buf[STRLEN];
const char* ptr;
- ptr = check_box(ir->ePBC, box);
+ ptr = check_box(ir->pbcType, box);
if (ptr)
{
warning_error(wi, ptr);
ir->LincsWarnAngle = 90.0;
}
- if (ir->ePBC != epbcNONE)
+ if (ir->pbcType != PbcType::No)
{
if (ir->nstlist == 0)
{
"With nstlist=0 atoms are only put into the box at step 0, therefore drifting "
"atoms might cause the simulation to crash.");
}
- if (gmx::square(ir->rlist) >= max_cutoff2(ir->ePBC, box))
+ if (gmx::square(ir->rlist) >= max_cutoff2(ir->pbcType, box))
{
sprintf(warn_buf,
"ERROR: The cut-off length is longer than half the shortest box vector or "
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015,2016 by the GROMACS development team.
+ * Copyright (c) 2012,2013,2014,2015,2016, The GROMACS development team.
* Copyright (c) 2017,2018,2019,2020, 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
#include <string>
#include <vector>
-#include "gromacs/gpu_utils/gpu_utils.h"
#include "gromacs/hardware/cpuinfo.h"
+#include "gromacs/hardware/device_management.h"
#include "gromacs/hardware/hardwaretopology.h"
#include "gromacs/hardware/hw_info.h"
#include "gromacs/hardware/identifyavx512fmaunits.h"
#include "gromacs/utility/stringutil.h"
#include "gromacs/utility/sysinfo.h"
+ #include "architecture.h"
+
//! Constant used to help minimize preprocessed code
-static const bool bGPUBinary = GMX_GPU != GMX_GPU_NONE;
+static constexpr bool bGPUBinary = (GMX_GPU != 0);
/*! \internal \brief
* Returns the GPU information text, one GPU per line.
*/
-static std::string sprint_gpus(const gmx_gpu_info_t& gpu_info)
+static std::string sprint_gpus(const std::vector<std::unique_ptr<DeviceInformation>>& deviceInfoList)
{
- char stmp[STRLEN];
- std::vector<std::string> gpuStrings;
- for (int i = 0; i < gpu_info.n_dev; i++)
+ std::vector<std::string> gpuStrings(0);
+ for (const auto& deviceInfo : deviceInfoList)
{
- get_gpu_device_info_string(stmp, gpu_info, i);
- gpuStrings.push_back(gmx::formatString(" %s", stmp));
+ gpuStrings.emplace_back(" " + getDeviceInformationString(*deviceInfo));
}
return gmx::joinStrings(gpuStrings, "\n");
}
and runtime CPU do not match. */
static void check_use_of_rdtscp_on_this_cpu(const gmx::MDLogger& mdlog, const gmx::CpuInfo& cpuInfo)
{
- bool binaryUsesRdtscp = HAVE_RDTSCP;
+ bool binaryUsesRdtscp = GMX_USE_RDTSCP;
const char* programName = gmx::getProgramContext().displayName();
s += gmx::formatString(" %d cores,", hwinfo->ncore_tot);
}
s += gmx::formatString(" %d logical cores", hwinfo->nhwthread_tot);
- if (hwinfo->gpu_info.bDetectGPUs)
+ if (canPerformDeviceDetection(nullptr))
{
s += gmx::formatString(", %d compatible GPU%s", hwinfo->ngpu_compatible_tot,
hwinfo->ngpu_compatible_tot == 1 ? "" : "s");
}
else if (bGPUBinary)
{
- s += gmx::formatString(" (GPU detection deactivated)");
+ if (isDeviceDetectionEnabled())
+ {
+ s += gmx::formatString(" (GPU detection failed)");
+ }
+ else
+ {
+ s += gmx::formatString(" (GPU detection deactivated)");
+ }
}
s += gmx::formatString("\n");
}
}
- if (bGPUBinary && hwinfo->gpu_info.n_dev > 0)
+ if (bGPUBinary && !hwinfo->deviceInfoList.empty())
{
s += gmx::formatString(" GPU info:\n");
- s += gmx::formatString(" Number of GPUs detected: %d\n", hwinfo->gpu_info.n_dev);
- s += sprint_gpus(hwinfo->gpu_info) + "\n";
+ s += gmx::formatString(" Number of GPUs detected: %d\n",
+ static_cast<int>(hwinfo->deviceInfoList.size()));
+ s += sprint_gpus(hwinfo->deviceInfoList) + "\n";
}
return s;
}
gmx::simdCheck(static_cast<gmx::SimdType>(hwinfo->simd_suggest_min), fplog, warnToStdErr);
}
- /* For RDTSCP we only check on our local node and skip the MPI reduction */
- check_use_of_rdtscp_on_this_cpu(mdlog, cpuInfo);
+ /* For RDTSCP we only check on our local node and skip the MPI reduction, only on x86 */
+ if (gmx::c_architecture == gmx::Architecture::X86)
+ {
+ check_use_of_rdtscp_on_this_cpu(mdlog, cpuInfo);
+ }
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2013,2014,2015,2016,2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017 The GROMACS development team.
+ * Copyright (c) 2018,2019,2020, 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.
#include "mdoutf.h"
+#include "config.h"
+
#include "gromacs/commandline/filenm.h"
#include "gromacs/domdec/collect.h"
#include "gromacs/domdec/domdec_struct.h"
#include "gromacs/mdlib/trajectory_writing.h"
#include "gromacs/mdrunutility/handlerestart.h"
#include "gromacs/mdrunutility/multisim.h"
+#include "gromacs/mdtypes/awh_history.h"
#include "gromacs/mdtypes/commrec.h"
+#include "gromacs/mdtypes/df_history.h"
+#include "gromacs/mdtypes/edsamhistory.h"
+#include "gromacs/mdtypes/energyhistory.h"
#include "gromacs/mdtypes/imdoutputprovider.h"
#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/mdtypes/md_enums.h"
#include "gromacs/mdtypes/mdrunoptions.h"
+#include "gromacs/mdtypes/observableshistory.h"
#include "gromacs/mdtypes/state.h"
+#include "gromacs/mdtypes/swaphistory.h"
#include "gromacs/timing/wallcycle.h"
#include "gromacs/topology/topology.h"
+#include "gromacs/utility/baseversion.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/pleasecite.h"
+#include "gromacs/utility/programcontext.h"
#include "gromacs/utility/smalloc.h"
+#include "gromacs/utility/sysinfo.h"
struct gmx_mdoutf
{
FILE* fp_dhdl;
int natoms_global;
int natoms_x_compressed;
- SimulationGroups* groups; /* for compressed position writing */
+ const SimulationGroups* groups; /* for compressed position writing */
gmx_wallcycle_t wcycle;
rvec* f_global;
gmx::IMDOutputProvider* outputProvider;
const gmx::MdModulesNotifier* mdModulesNotifier;
bool simulationsShareState;
- MPI_Comm mpiCommMasters;
+ MPI_Comm mastersComm;
};
gmx::IMDOutputProvider* outputProvider,
const gmx::MdModulesNotifier& mdModulesNotifier,
const t_inputrec* ir,
- gmx_mtop_t* top_global,
+ const gmx_mtop_t* top_global,
const gmx_output_env_t* oenv,
gmx_wallcycle_t wcycle,
const gmx::StartingBehavior startingBehavior,
of->simulationsShareState = simulationsShareState;
if (of->simulationsShareState)
{
- of->mpiCommMasters = ms->mpi_comm_masters;
+ of->mastersComm = ms->mastersComm_;
}
if (MASTER(cr))
return of->wcycle;
}
-void mdoutf_write_to_trajectory_files(FILE* fplog,
- const t_commrec* cr,
- gmx_mdoutf_t of,
- int mdof_flags,
- int natoms,
- int64_t step,
- double t,
- t_state* state_local,
- t_state* state_global,
- ObservablesHistory* observablesHistory,
- gmx::ArrayRef<gmx::RVec> f_local)
+static void mpiBarrierBeforeRename(const bool applyMpiBarrierBeforeRename, MPI_Comm mpiBarrierCommunicator)
+{
+ if (applyMpiBarrierBeforeRename)
+ {
+#if GMX_MPI
+ MPI_Barrier(mpiBarrierCommunicator);
+#else
+ GMX_RELEASE_ASSERT(false, "Should not request a barrier without MPI");
+ GMX_UNUSED_VALUE(mpiBarrierCommunicator);
+#endif
+ }
+}
+/*! \brief Write a checkpoint to the filename
+ *
+ * Appends the _step<step>.cpt with bNumberAndKeep, otherwise moves
+ * the previous checkpoint filename with suffix _prev.cpt.
+ */
+static void write_checkpoint(const char* fn,
+ gmx_bool bNumberAndKeep,
+ FILE* fplog,
+ const t_commrec* cr,
+ ivec domdecCells,
+ int nppnodes,
+ int eIntegrator,
+ int simulation_part,
+ gmx_bool bExpanded,
+ int elamstats,
+ int64_t step,
+ double t,
+ t_state* state,
+ ObservablesHistory* observablesHistory,
+ const gmx::MdModulesNotifier& mdModulesNotifier,
+ gmx::WriteCheckpointDataHolder* modularSimulatorCheckpointData,
+ bool applyMpiBarrierBeforeRename,
+ MPI_Comm mpiBarrierCommunicator)
+{
+ t_fileio* fp;
+ char* fntemp; /* the temporary checkpoint file name */
+ int npmenodes;
+ char buf[1024], suffix[5 + STEPSTRSIZE], sbuf[STEPSTRSIZE];
+ t_fileio* ret;
+
+ if (DOMAINDECOMP(cr))
+ {
+ npmenodes = cr->npmenodes;
+ }
+ else
+ {
+ npmenodes = 0;
+ }
+
+#if !GMX_NO_RENAME
+ /* make the new temporary filename */
+ snew(fntemp, std::strlen(fn) + 5 + STEPSTRSIZE);
+ std::strcpy(fntemp, fn);
+ fntemp[std::strlen(fn) - std::strlen(ftp2ext(fn2ftp(fn))) - 1] = '\0';
+ sprintf(suffix, "_%s%s", "step", gmx_step_str(step, sbuf));
+ std::strcat(fntemp, suffix);
+ std::strcat(fntemp, fn + std::strlen(fn) - std::strlen(ftp2ext(fn2ftp(fn))) - 1);
+#else
+ /* if we can't rename, we just overwrite the cpt file.
+ * dangerous if interrupted.
+ */
+ snew(fntemp, std::strlen(fn));
+ std::strcpy(fntemp, fn);
+#endif
+ std::string timebuf = gmx_format_current_time();
+
+ if (fplog)
+ {
+ fprintf(fplog, "Writing checkpoint, step %s at %s\n\n", gmx_step_str(step, buf), timebuf.c_str());
+ }
+
+ /* Get offsets for open files */
+ auto outputfiles = gmx_fio_get_output_file_positions();
+
+ fp = gmx_fio_open(fntemp, "w");
+
+ /* We can check many more things now (CPU, acceleration, etc), but
+ * it is highly unlikely to have two separate builds with exactly
+ * the same version, user, time, and build host!
+ */
+
+ int nlambda = (state->dfhist ? state->dfhist->nlambda : 0);
+
+ edsamhistory_t* edsamhist = observablesHistory->edsamHistory.get();
+ int nED = (edsamhist ? edsamhist->nED : 0);
+
+ swaphistory_t* swaphist = observablesHistory->swapHistory.get();
+ int eSwapCoords = (swaphist ? swaphist->eSwapCoords : eswapNO);
+
+ CheckpointHeaderContents headerContents = { 0,
+ { 0 },
+ { 0 },
+ { 0 },
+ { 0 },
+ GMX_DOUBLE,
+ { 0 },
+ { 0 },
+ eIntegrator,
+ simulation_part,
+ step,
+ t,
+ nppnodes,
+ { 0 },
+ npmenodes,
+ state->natoms,
+ state->ngtc,
+ state->nnhpres,
+ state->nhchainlength,
+ nlambda,
+ state->flags,
+ 0,
+ 0,
+ 0,
+ 0,
+ 0,
+ nED,
+ eSwapCoords,
+ false };
+ std::strcpy(headerContents.version, gmx_version());
+ std::strcpy(headerContents.fprog, gmx::getProgramContext().fullBinaryPath());
+ std::strcpy(headerContents.ftime, timebuf.c_str());
+ if (DOMAINDECOMP(cr))
+ {
+ copy_ivec(domdecCells, headerContents.dd_nc);
+ }
+
+ write_checkpoint_data(fp, headerContents, bExpanded, elamstats, state, observablesHistory,
+ mdModulesNotifier, &outputfiles, modularSimulatorCheckpointData);
+
+ /* we really, REALLY, want to make sure to physically write the checkpoint,
+ and all the files it depends on, out to disk. Because we've
+ opened the checkpoint with gmx_fio_open(), it's in our list
+ of open files. */
+ ret = gmx_fio_all_output_fsync();
+
+ if (ret)
+ {
+ char buf[STRLEN];
+ sprintf(buf, "Cannot fsync '%s'; maybe you are out of disk space?", gmx_fio_getname(ret));
+
+ if (getenv(GMX_IGNORE_FSYNC_FAILURE_ENV) == nullptr)
+ {
+ gmx_file(buf);
+ }
+ else
+ {
+ gmx_warning("%s", buf);
+ }
+ }
+
+ if (gmx_fio_close(fp) != 0)
+ {
+ gmx_file("Cannot read/write checkpoint; corrupt file, or maybe you are out of disk space?");
+ }
+
+ /* we don't move the checkpoint if the user specified they didn't want it,
+ or if the fsyncs failed */
+#if !GMX_NO_RENAME
+ if (!bNumberAndKeep && !ret)
+ {
+ if (gmx_fexist(fn))
+ {
+ /* Rename the previous checkpoint file */
+ mpiBarrierBeforeRename(applyMpiBarrierBeforeRename, mpiBarrierCommunicator);
+
+ std::strcpy(buf, fn);
+ buf[std::strlen(fn) - std::strlen(ftp2ext(fn2ftp(fn))) - 1] = '\0';
+ std::strcat(buf, "_prev");
+ std::strcat(buf, fn + std::strlen(fn) - std::strlen(ftp2ext(fn2ftp(fn))) - 1);
+ if (!GMX_FAHCORE)
+ {
+ /* we copy here so that if something goes wrong between now and
+ * the rename below, there's always a state.cpt.
+ * If renames are atomic (such as in POSIX systems),
+ * this copying should be unneccesary.
+ */
+ gmx_file_copy(fn, buf, FALSE);
+ /* We don't really care if this fails:
+ * there's already a new checkpoint.
+ */
+ }
+ else
+ {
+ gmx_file_rename(fn, buf);
+ }
+ }
+
+ /* Rename the checkpoint file from the temporary to the final name */
+ mpiBarrierBeforeRename(applyMpiBarrierBeforeRename, mpiBarrierCommunicator);
+
+ if (gmx_file_rename(fntemp, fn) != 0)
+ {
+ gmx_file("Cannot rename checkpoint file; maybe you are out of disk space?");
+ }
+ }
+#endif /* GMX_NO_RENAME */
+
+ sfree(fntemp);
+
+#if GMX_FAHCORE
+ /*code for alternate checkpointing scheme. moved from top of loop over
+ steps */
+ fcRequestCheckPoint();
+ if (fcCheckPointParallel(cr->nodeid, NULL, 0) == 0)
+ {
+ gmx_fatal(3, __FILE__, __LINE__, "Checkpoint error on step %d\n", step);
+ }
+#endif /* end GMX_FAHCORE block */
+}
+
+void mdoutf_write_checkpoint(gmx_mdoutf_t of,
+ FILE* fplog,
+ const t_commrec* cr,
+ int64_t step,
+ double t,
+ t_state* state_global,
+ ObservablesHistory* observablesHistory,
+ gmx::WriteCheckpointDataHolder* modularSimulatorCheckpointData)
+{
+ fflush_tng(of->tng);
+ fflush_tng(of->tng_low_prec);
+ /* Write the checkpoint file.
+ * When simulations share the state, an MPI barrier is applied before
+ * renaming old and new checkpoint files to minimize the risk of
+ * checkpoint files getting out of sync.
+ */
+ ivec one_ivec = { 1, 1, 1 };
+ write_checkpoint(of->fn_cpt, of->bKeepAndNumCPT, fplog, cr,
+ DOMAINDECOMP(cr) ? cr->dd->numCells : one_ivec,
+ DOMAINDECOMP(cr) ? cr->dd->nnodes : cr->nnodes, of->eIntegrator,
+ of->simulation_part, of->bExpanded, of->elamstats, step, t, state_global,
+ observablesHistory, *(of->mdModulesNotifier), modularSimulatorCheckpointData,
+ of->simulationsShareState, of->mastersComm);
+}
+
+void mdoutf_write_to_trajectory_files(FILE* fplog,
+ const t_commrec* cr,
+ gmx_mdoutf_t of,
+ int mdof_flags,
+ int natoms,
+ int64_t step,
+ double t,
+ t_state* state_local,
+ t_state* state_global,
+ ObservablesHistory* observablesHistory,
+ gmx::ArrayRef<const gmx::RVec> f_local,
+ gmx::WriteCheckpointDataHolder* modularSimulatorCheckpointData)
{
- rvec* f_global;
+ const rvec* f_global;
if (DOMAINDECOMP(cr))
{
if (mdof_flags & (MDOF_X | MDOF_X_COMPRESSED))
{
auto globalXRef = MASTER(cr) ? state_global->x : gmx::ArrayRef<gmx::RVec>();
- dd_collect_vec(cr->dd, state_local, state_local->x, globalXRef);
+ dd_collect_vec(cr->dd, state_local->ddp_count, state_local->ddp_count_cg_gl,
+ state_local->cg_gl, state_local->x, globalXRef);
}
if (mdof_flags & MDOF_V)
{
auto globalVRef = MASTER(cr) ? state_global->v : gmx::ArrayRef<gmx::RVec>();
- dd_collect_vec(cr->dd, state_local, state_local->v, globalVRef);
+ dd_collect_vec(cr->dd, state_local->ddp_count, state_local->ddp_count_cg_gl,
+ state_local->cg_gl, state_local->v, globalVRef);
}
}
f_global = of->f_global;
if (mdof_flags & MDOF_F)
{
- dd_collect_vec(cr->dd, state_local, f_local,
- gmx::arrayRefFromArray(reinterpret_cast<gmx::RVec*>(f_global), f_local.size()));
+ dd_collect_vec(
+ cr->dd, state_local->ddp_count, state_local->ddp_count_cg_gl, state_local->cg_gl, f_local,
+ gmx::arrayRefFromArray(reinterpret_cast<gmx::RVec*>(of->f_global), f_local.size()));
}
}
else
{
if (mdof_flags & MDOF_CPT)
{
- fflush_tng(of->tng);
- fflush_tng(of->tng_low_prec);
- /* Write the checkpoint file.
- * When simulations share the state, an MPI barrier is applied before
- * renaming old and new checkpoint files to minimize the risk of
- * checkpoint files getting out of sync.
- */
- ivec one_ivec = { 1, 1, 1 };
- write_checkpoint(of->fn_cpt, of->bKeepAndNumCPT, fplog, cr,
- DOMAINDECOMP(cr) ? cr->dd->nc : one_ivec,
- DOMAINDECOMP(cr) ? cr->dd->nnodes : cr->nnodes, of->eIntegrator,
- of->simulation_part, of->bExpanded, of->elamstats, step, t,
- state_global, observablesHistory, *(of->mdModulesNotifier),
- of->simulationsShareState, of->mpiCommMasters);
+ mdoutf_write_checkpoint(of, fplog, cr, step, t, state_global, observablesHistory,
+ modularSimulatorCheckpointData);
}
if (mdof_flags & (MDOF_X | MDOF_V | MDOF_F))
nullptr, nullptr);
}
}
+
+ #if GMX_FAHCORE
+ /* Write a FAH checkpoint after writing any other data. We may end up
+ checkpointing twice but it's fast so it's ok. */
+ if ((mdof_flags & ~MDOF_CPT))
+ {
+ fcCheckpoint();
+ }
+ #endif
}
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017,2018,2019,2020, by the GROMACS development team, led by
++ * Copyright (c) 2013,2014,2015,2016,2017, The GROMACS development team.
+ * Copyright (c) 2018,2019,2020, 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.
#include "gromacs/mdlib/mdoutf.h"
#include "gromacs/mdlib/stat.h"
#include "gromacs/mdlib/update.h"
+#include "gromacs/mdtypes/checkpointdata.h"
#include "gromacs/mdtypes/commrec.h"
#include "gromacs/mdtypes/forcerec.h"
#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/topology/topology.h"
#include "gromacs/utility/smalloc.h"
-void do_md_trajectory_writing(FILE* fplog,
- t_commrec* cr,
- int nfile,
- const t_filenm fnm[],
- int64_t step,
- int64_t step_rel,
- double t,
- t_inputrec* ir,
- t_state* state,
- t_state* state_global,
- ObservablesHistory* observablesHistory,
- const gmx_mtop_t* top_global,
- t_forcerec* fr,
- gmx_mdoutf_t outf,
- const gmx::EnergyOutput& energyOutput,
- gmx_ekindata_t* ekind,
- gmx::ArrayRef<gmx::RVec> f,
- gmx_bool bCPT,
- gmx_bool bRerunMD,
- gmx_bool bLastStep,
- gmx_bool bDoConfOut,
- gmx_bool bSumEkinhOld)
+void do_md_trajectory_writing(FILE* fplog,
+ t_commrec* cr,
+ int nfile,
+ const t_filenm fnm[],
+ int64_t step,
+ int64_t step_rel,
+ double t,
+ t_inputrec* ir,
+ t_state* state,
+ t_state* state_global,
+ ObservablesHistory* observablesHistory,
+ const gmx_mtop_t* top_global,
+ t_forcerec* fr,
+ gmx_mdoutf_t outf,
+ const gmx::EnergyOutput& energyOutput,
+ gmx_ekindata_t* ekind,
+ gmx::ArrayRef<const gmx::RVec> f,
+ gmx_bool bCPT,
+ gmx_bool bRerunMD,
+ gmx_bool bLastStep,
+ gmx_bool bDoConfOut,
+ gmx_bool bSumEkinhOld)
{
int mdof_flags;
rvec* x_for_confout = nullptr;
mdof_flags |= MDOF_LAMBDA_COMPRESSED;
}
- #if GMX_FAHCORE
- if (bLastStep)
- {
- /* Enforce writing positions and velocities at end of run */
- mdof_flags |= (MDOF_X | MDOF_V);
- }
- if (MASTER(cr))
- {
- fcReportProgress(ir->nsteps, step);
- }
-
- # if defined(__native_client__)
- fcCheckin(MASTER(cr));
- # endif
-
- /* sync bCPT and fc record-keeping */
- if (bCPT && MASTER(cr))
- {
- fcRequestCheckPoint();
- }
- #endif
-
if (mdof_flags != 0)
{
wallcycle_start(mdoutf_get_wcycle(outf), ewcTRAJ);
energyOutput.fillEnergyHistory(observablesHistory->energyHistory.get());
}
}
+ // The current function is only called by legacy code, while
+ // mdoutf_write_to_trajectory_files is also called from modular simulator. Create a dummy
+ // modular simulator checkpointing object for compatibility.
+ gmx::WriteCheckpointDataHolder checkpointDataHolder;
// Note that part of the following code is duplicated in StatePropagatorData::trajectoryWriterTeardown.
// This duplication is needed while both legacy and modular code paths are in use.
// TODO: Remove duplication asap, make sure to keep in sync in the meantime.
- mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags, top_global->natoms, step, t,
- state, state_global, observablesHistory, f);
+ mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags, top_global->natoms, step, t, state,
+ state_global, observablesHistory, f, &checkpointDataHolder);
if (bLastStep && step_rel == ir->nsteps && bDoConfOut && MASTER(cr) && !bRerunMD)
{
if (fr->bMolPBC && state == state_global)
if (fr->bMolPBC && !ir->bPeriodicMols)
{
/* Make molecules whole only for confout writing */
- do_pbc_mtop(ir->ePBC, state->box, top_global, x_for_confout);
+ do_pbc_mtop(ir->pbcType, state->box, top_global, x_for_confout);
}
write_sto_conf_mtop(ftp2fn(efSTO, nfile, fnm), *top_global->name, top_global,
- x_for_confout, state_global->v.rvec_array(), ir->ePBC, state->box);
+ x_for_confout, state_global->v.rvec_array(), ir->pbcType, state->box);
if (fr->bMolPBC && state == state_global)
{
sfree(x_for_confout);
}
wallcycle_stop(mdoutf_get_wcycle(outf), ewcTRAJ);
}
+ #if GMX_FAHCORE
+ if (MASTER(cr))
+ {
+ fcWriteVisFrame(ir->ePBC, state_global->box, top_global, state_global->x.rvec_array());
+ }
+ #endif
}
#include <algorithm>
#include <memory>
+#include <numeric>
-#include "gromacs/awh/awh.h"
+#include "gromacs/applied_forces/awh/awh.h"
#include "gromacs/commandline/filenm.h"
#include "gromacs/domdec/collect.h"
#include "gromacs/domdec/dlbtiming.h"
#include "gromacs/domdec/domdec.h"
#include "gromacs/domdec/domdec_network.h"
#include "gromacs/domdec/domdec_struct.h"
+#include "gromacs/domdec/gpuhaloexchange.h"
#include "gromacs/domdec/mdsetup.h"
#include "gromacs/domdec/partition.h"
#include "gromacs/essentialdynamics/edsam.h"
-#include "gromacs/ewald/pme.h"
#include "gromacs/ewald/pme_load_balancing.h"
+#include "gromacs/ewald/pme_pp.h"
#include "gromacs/fileio/trxio.h"
#include "gromacs/gmxlib/network.h"
#include "gromacs/gmxlib/nrnb.h"
+#include "gromacs/gpu_utils/device_stream_manager.h"
#include "gromacs/gpu_utils/gpu_utils.h"
#include "gromacs/imd/imd.h"
-#include "gromacs/listed_forces/manage_threading.h"
+#include "gromacs/listed_forces/listed_forces.h"
#include "gromacs/math/functions.h"
-#include "gromacs/math/utilities.h"
+#include "gromacs/math/invertmatrix.h"
#include "gromacs/math/vec.h"
#include "gromacs/math/vectypes.h"
#include "gromacs/mdlib/checkpointhandler.h"
#include "gromacs/mdlib/compute_io.h"
#include "gromacs/mdlib/constr.h"
+#include "gromacs/mdlib/coupling.h"
#include "gromacs/mdlib/ebin.h"
#include "gromacs/mdlib/enerdata_utils.h"
#include "gromacs/mdlib/energyoutput.h"
#include "gromacs/mdlib/force.h"
#include "gromacs/mdlib/force_flags.h"
#include "gromacs/mdlib/forcerec.h"
+#include "gromacs/mdlib/freeenergyparameters.h"
#include "gromacs/mdlib/md_support.h"
#include "gromacs/mdlib/mdatoms.h"
#include "gromacs/mdlib/mdoutf.h"
#include "gromacs/mdlib/tgroup.h"
#include "gromacs/mdlib/trajectory_writing.h"
#include "gromacs/mdlib/update.h"
-#include "gromacs/mdlib/update_constrain_cuda.h"
+#include "gromacs/mdlib/update_constrain_gpu.h"
#include "gromacs/mdlib/vcm.h"
#include "gromacs/mdlib/vsite.h"
#include "gromacs/mdrunutility/handlerestart.h"
#include "gromacs/mdtypes/df_history.h"
#include "gromacs/mdtypes/energyhistory.h"
#include "gromacs/mdtypes/fcdata.h"
+#include "gromacs/mdtypes/forcebuffers.h"
#include "gromacs/mdtypes/forcerec.h"
#include "gromacs/mdtypes/group.h"
#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/mdtypes/md_enums.h"
#include "gromacs/mdtypes/mdatom.h"
#include "gromacs/mdtypes/mdrunoptions.h"
+#include "gromacs/mdtypes/multipletimestepping.h"
#include "gromacs/mdtypes/observableshistory.h"
#include "gromacs/mdtypes/pullhistory.h"
#include "gromacs/mdtypes/simulation_workload.h"
#include "gromacs/mdtypes/state.h"
#include "gromacs/mdtypes/state_propagator_data_gpu.h"
-#include "gromacs/modularsimulator/energyelement.h"
+#include "gromacs/modularsimulator/energydata.h"
#include "gromacs/nbnxm/gpu_data_mgmt.h"
#include "gromacs/nbnxm/nbnxm.h"
-#include "gromacs/pbcutil/mshift.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/pulling/output.h"
#include "gromacs/pulling/pull.h"
#include "replicaexchange.h"
#include "shellfc.h"
- #if GMX_FAHCORE
- # include "corewrap.h"
- #endif
-
using gmx::SimulationSignaller;
void gmx::LegacySimulator::do_md()
// will go away eventually.
t_inputrec* ir = inputrec;
int64_t step, step_rel;
- double t, t0 = ir->init_t, lam0[efptNR];
+ double t, t0 = ir->init_t;
gmx_bool bGStatEveryStep, bGStat, bCalcVir, bCalcEnerStep, bCalcEner;
- gmx_bool bNS, bNStList, bStopCM, bFirstStep, bInitStep, bLastStep = FALSE;
+ gmx_bool bNS = FALSE, bNStList, bStopCM, bFirstStep, bInitStep, bLastStep = FALSE;
gmx_bool bDoDHDL = FALSE, bDoFEP = FALSE, bDoExpanded = FALSE;
gmx_bool do_ene, do_log, do_verbose;
gmx_bool bMasterState;
unsigned int force_flags;
- tensor force_vir = { { 0 } }, shake_vir = { { 0 } }, total_vir = { { 0 } }, tmp_vir = { { 0 } },
- pres = { { 0 } };
- int i, m;
- rvec mu_tot;
- matrix pressureCouplingMu, M;
- gmx_repl_ex_t repl_ex = nullptr;
- gmx_localtop_t top;
- PaddedHostVector<gmx::RVec> f{};
- gmx_global_stat_t gstat;
- t_graph* graph = nullptr;
- gmx_shellfc_t* shellfc;
- gmx_bool bSumEkinhOld, bDoReplEx, bExchanged, bNeedRepartition;
- gmx_bool bTemp, bPres, bTrotter;
- real dvdl_constr;
- std::vector<RVec> cbuf;
- matrix lastbox;
- int lamnew = 0;
+ tensor force_vir = { { 0 } }, shake_vir = { { 0 } }, total_vir = { { 0 } }, pres = { { 0 } };
+ int i, m;
+ rvec mu_tot;
+ matrix pressureCouplingMu, M;
+ gmx_repl_ex_t repl_ex = nullptr;
+ gmx_global_stat_t gstat;
+ gmx_shellfc_t* shellfc;
+ gmx_bool bSumEkinhOld, bDoReplEx, bExchanged, bNeedRepartition;
+ gmx_bool bTemp, bPres, bTrotter;
+ real dvdl_constr;
+ std::vector<RVec> cbuf;
+ matrix lastbox;
+ int lamnew = 0;
/* for FEP */
int nstfep = 0;
double cycles;
int nstglobalcomm = computeGlobalCommunicationPeriod(mdlog, ir, cr);
bGStatEveryStep = (nstglobalcomm == 1);
- SimulationGroups* groups = &top_global->groups;
+ const SimulationGroups* groups = &top_global->groups;
std::unique_ptr<EssentialDynamics> ed = nullptr;
if (opt2bSet("-ei", nfile, fnm))
"Either specify the -ei option to mdrun, or do not use this checkpoint file.");
}
- initialize_lambdas(fplog, *ir, MASTER(cr), &state_global->fep_state, state_global->lambda, lam0);
- Update upd(ir, deform);
+ int* fep_state = MASTER(cr) ? &state_global->fep_state : nullptr;
+ gmx::ArrayRef<real> lambda = MASTER(cr) ? state_global->lambda : gmx::ArrayRef<real>();
+ initialize_lambdas(fplog, *ir, MASTER(cr), fep_state, lambda);
+ Update upd(*ir, deform);
const bool doSimulatedAnnealing = initSimulatedAnnealing(ir, &upd);
const bool useReplicaExchange = (replExParams.exchangeInterval > 0);
+ const t_fcdata& fcdata = *fr->fcdata;
+
bool simulationsShareState = false;
int nstSignalComm = nstglobalcomm;
{
// TODO This implementation of ensemble orientation restraints is nasty because
// a user can't just do multi-sim with single-sim orientation restraints.
bool usingEnsembleRestraints =
- (fcd->disres.nsystems > 1) || ((ms != nullptr) && (fcd->orires.nr != 0));
+ (fcdata.disres->nsystems > 1) || ((ms != nullptr) && (fcdata.orires->nr != 0));
bool awhUsesMultiSim = (ir->bDoAwh && ir->awhParams->shareBiasMultisim && (ms != nullptr));
// Replica exchange, ensemble restraints and AWH need all
t_state* state;
+ gmx_localtop_t top(top_global->ffparams);
+
auto mdatoms = mdAtoms->mdatoms();
- std::unique_ptr<UpdateConstrainCuda> integrator;
+ const auto& simulationWork = runScheduleWork->simulationWork;
+ const bool useGpuForPme = simulationWork.useGpuPme;
+ const bool useGpuForNonbonded = simulationWork.useGpuNonbonded;
+ const bool useGpuForBufferOps = simulationWork.useGpuBufferOps;
+ const bool useGpuForUpdate = simulationWork.useGpuUpdate;
+ ForceBuffers f(fr->useMts, ((useGpuForNonbonded && useGpuForBufferOps) || useGpuForUpdate)
+ ? PinningPolicy::PinnedIfSupported
+ : PinningPolicy::CannotBePinned);
if (DOMAINDECOMP(cr))
{
- dd_init_local_top(*top_global, &top);
-
stateInstance = std::make_unique<t_state>();
state = stateInstance.get();
dd_init_local_state(cr->dd, state_global, state);
else
{
state_change_natoms(state_global, state_global->natoms);
- f.resizeWithPadding(state_global->natoms);
/* Copy the pointer to the global state */
state = state_global;
/* Generate and initialize new topology */
- mdAlgorithmsSetupAtomData(cr, ir, *top_global, &top, fr, &graph, mdAtoms, constr, vsite, shellfc);
+ mdAlgorithmsSetupAtomData(cr, ir, *top_global, &top, fr, &f, mdAtoms, constr, vsite, shellfc);
upd.setNumAtoms(state->natoms);
}
- const auto& simulationWork = runScheduleWork->simulationWork;
- const bool useGpuForPme = simulationWork.useGpuPme;
- const bool useGpuForNonbonded = simulationWork.useGpuNonbonded;
- const bool useGpuForBufferOps = simulationWork.useGpuBufferOps;
- const bool useGpuForUpdate = simulationWork.useGpuUpdate;
+ std::unique_ptr<UpdateConstrainGpu> integrator;
StatePropagatorDataGpu* stateGpu = fr->stateGpu;
+ // TODO: the assertions below should be handled by UpdateConstraintsBuilder.
if (useGpuForUpdate)
{
GMX_RELEASE_ASSERT(!DOMAINDECOMP(cr) || ddUsesUpdateGroups(*cr->dd) || constr == nullptr
GMX_RELEASE_ASSERT(
ir->etc != etcNOSEHOOVER,
"Nose-Hoover temperature coupling is not supported with the GPU update.\n");
- GMX_RELEASE_ASSERT(ir->epc == epcNO || ir->epc == epcPARRINELLORAHMAN || ir->epc == epcBERENDSEN,
- "Only Parrinello-Rahman and Berendsen pressure coupling are supported "
- "with the GPU update.\n");
+ GMX_RELEASE_ASSERT(
+ ir->epc == epcNO || ir->epc == epcPARRINELLORAHMAN || ir->epc == epcBERENDSEN
+ || ir->epc == epcCRESCALE,
+ "Only Parrinello-Rahman, Berendsen, and C-rescale pressure coupling are supported "
+ "with the GPU update.\n");
GMX_RELEASE_ASSERT(!mdatoms->haveVsites,
"Virtual sites are not supported with the GPU update.\n");
GMX_RELEASE_ASSERT(ed == nullptr,
"Essential dynamics is not supported with the GPU update.\n");
GMX_RELEASE_ASSERT(!ir->bPull || !pull_have_constraint(ir->pull),
"Constraints pulling is not supported with the GPU update.\n");
- GMX_RELEASE_ASSERT(fcd->orires.nr == 0,
+ GMX_RELEASE_ASSERT(fcdata.orires->nr == 0,
"Orientation restraints are not supported with the GPU update.\n");
- GMX_RELEASE_ASSERT(ir->efep == efepNO,
- "Free energy perturbations are not supported with the GPU update.");
- GMX_RELEASE_ASSERT(graph == nullptr, "The graph is not supported with GPU update.");
+ GMX_RELEASE_ASSERT(
+ ir->efep == efepNO
+ || (!haveFreeEnergyType(*ir, efptBONDED) && !haveFreeEnergyType(*ir, efptMASS)),
+ "Free energy perturbation of masses and constraints are not supported with the GPU "
+ "update.");
if (constr != nullptr && constr->numConstraintsTotal() > 0)
{
{
GMX_LOG(mdlog.info).asParagraph().appendText("Updating coordinates on the GPU.");
}
- integrator = std::make_unique<UpdateConstrainCuda>(
- *ir, *top_global, stateGpu->getUpdateStream(), stateGpu->xUpdatedOnDevice());
-
- t_pbc pbc;
- set_pbc(&pbc, epbcXYZ, state->box);
- integrator->setPbc(&pbc);
+ GMX_RELEASE_ASSERT(fr->deviceStreamManager != nullptr,
+ "Device stream manager should be initialized in order to use GPU "
+ "update-constraints.");
+ GMX_RELEASE_ASSERT(
+ fr->deviceStreamManager->streamIsValid(gmx::DeviceStreamType::UpdateAndConstraints),
+ "Update stream should be initialized in order to use GPU "
+ "update-constraints.");
+ integrator = std::make_unique<UpdateConstrainGpu>(
+ *ir, *top_global, fr->deviceStreamManager->context(),
+ fr->deviceStreamManager->stream(gmx::DeviceStreamType::UpdateAndConstraints),
+ stateGpu->xUpdatedOnDevice());
+
+ integrator->setPbc(PbcType::Xyz, state->box);
}
if (useGpuForPme || (useGpuForNonbonded && useGpuForBufferOps) || useGpuForUpdate)
{
changePinningPolicy(&state->x, PinningPolicy::PinnedIfSupported);
}
- if ((useGpuForNonbonded && useGpuForBufferOps) || useGpuForUpdate)
- {
- changePinningPolicy(&f, PinningPolicy::PinnedIfSupported);
- }
if (useGpuForUpdate)
{
changePinningPolicy(&state->v, PinningPolicy::PinnedIfSupported);
if (MASTER(cr))
{
- EnergyElement::initializeEnergyHistory(startingBehavior, observablesHistory, &energyOutput);
+ EnergyData::initializeEnergyHistory(startingBehavior, observablesHistory, &energyOutput);
}
- preparePrevStepPullCom(ir, pull_work, mdatoms, state, state_global, cr,
+ preparePrevStepPullCom(ir, pull_work, mdatoms->massT, state, state_global, cr,
startingBehavior != StartingBehavior::NewSimulation);
// TODO: Remove this by converting AWH into a ForceProvider
if (constr)
{
/* Constrain the initial coordinates and velocities */
- do_constrain_first(fplog, constr, ir, mdatoms, state->natoms, state->x.arrayRefWithPadding(),
- state->v.arrayRefWithPadding(), state->box, state->lambda[efptBONDED]);
+ do_constrain_first(fplog, constr, ir, mdatoms->nr, mdatoms->homenr,
+ state->x.arrayRefWithPadding(), state->v.arrayRefWithPadding(),
+ state->box, state->lambda[efptBONDED]);
}
if (vsite)
{
/* Construct the virtual sites for the initial configuration */
- construct_vsites(vsite, state->x.rvec_array(), ir->delta_t, nullptr, top.idef.iparams,
- top.idef.il, fr->ePBC, fr->bMolPBC, cr, state->box);
+ vsite->construct(state->x, ir->delta_t, {}, state->box);
}
}
nstfep = ir->fepvals->nstdhdl;
if (ir->bExpanded)
{
- nstfep = gmx_greatest_common_divisor(ir->expandedvals->nstexpanded, nstfep);
+ nstfep = std::gcd(ir->expandedvals->nstexpanded, nstfep);
}
if (useReplicaExchange)
{
- nstfep = gmx_greatest_common_divisor(replExParams.exchangeInterval, nstfep);
+ nstfep = std::gcd(replExParams.exchangeInterval, nstfep);
+ }
+ if (ir->bDoAwh)
+ {
+ nstfep = std::gcd(ir->awhParams->nstSampleCoord, nstfep);
}
}
bool hasReadEkinState = MASTER(cr) ? state_global->ekinstate.hasReadEkinState : false;
if (PAR(cr))
{
- gmx_bcast(sizeof(hasReadEkinState), &hasReadEkinState, cr);
+ gmx_bcast(sizeof(hasReadEkinState), &hasReadEkinState, cr->mpi_comm_mygroup);
}
if (hasReadEkinState)
{
cglo_flags_iteration |= CGLO_STOPCM;
cglo_flags_iteration &= ~CGLO_TEMPERATURE;
}
- compute_globals(gstat, cr, ir, fr, ekind, state->x.rvec_array(), state->v.rvec_array(),
- state->box, state->lambda[efptVDW], mdatoms, nrnb, &vcm, nullptr, enerd,
- force_vir, shake_vir, total_vir, pres, mu_tot, constr, &nullSignaller,
+ compute_globals(gstat, cr, ir, fr, ekind, makeConstArrayRef(state->x),
+ makeConstArrayRef(state->v), state->box, mdatoms, nrnb, &vcm, nullptr,
+ enerd, force_vir, shake_vir, total_vir, pres, constr, &nullSignaller,
state->box, &totalNumberOfBondedInteractions, &bSumEkinhOld,
cglo_flags_iteration
| (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS
/* At initialization, do not pass x with acceleration-correction mode
* to avoid (incorrect) correction of the initial coordinates.
*/
- rvec* xPtr = nullptr;
- if (vcm.mode != ecmLINEAR_ACCELERATION_CORRECTION)
- {
- xPtr = state->x.rvec_array();
- }
- process_and_stopcm_grp(fplog, &vcm, *mdatoms, xPtr, state->v.rvec_array());
+ auto x = (vcm.mode == ecmLINEAR_ACCELERATION_CORRECTION) ? ArrayRef<RVec>()
+ : makeArrayRef(state->x);
+ process_and_stopcm_grp(fplog, &vcm, *mdatoms, x, makeArrayRef(state->v));
inc_nrnb(nrnb, eNR_STOPCM, mdatoms->homenr);
}
}
checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions, top_global, &top,
- state->x.rvec_array(), state->box,
+ makeConstArrayRef(state->x), state->box,
&shouldCheckNumberOfBondedInteractions);
if (ir->eI == eiVVAK)
{
kinetic energy calculation. This minimized excess variables, but
perhaps loses some logic?*/
- compute_globals(gstat, cr, ir, fr, ekind, state->x.rvec_array(), state->v.rvec_array(),
- state->box, state->lambda[efptVDW], mdatoms, nrnb, &vcm, nullptr, enerd,
- force_vir, shake_vir, total_vir, pres, mu_tot, constr, &nullSignaller,
+ compute_globals(gstat, cr, ir, fr, ekind, makeConstArrayRef(state->x),
+ makeConstArrayRef(state->v), state->box, mdatoms, nrnb, &vcm, nullptr,
+ enerd, force_vir, shake_vir, total_vir, pres, constr, &nullSignaller,
state->box, nullptr, &bSumEkinhOld, cglo_flags & ~CGLO_PRESSURE);
}
wallcycle_start(wcycle, ewcRUN);
print_start(fplog, cr, walltime_accounting, "mdrun");
- #if GMX_FAHCORE
- /* safest point to do file checkpointing is here. More general point would be immediately before integrator call */
- int chkpt_ret = fcCheckPointParallel(cr->nodeid, NULL, 0);
- if (chkpt_ret == 0)
- {
- gmx_fatal(3, __FILE__, __LINE__, "Checkpoint error on step %d\n", 0);
- }
- #endif
-
/***********************************************************
*
* Loop over MD steps
bExchanged = FALSE;
bNeedRepartition = FALSE;
+ step = ir->init_step;
+ step_rel = 0;
+
auto stopHandler = stopHandlerBuilder->getStopHandlerMD(
compat::not_null<SimulationSignal*>(&signals[eglsSTOPCOND]), simulationsShareState,
MASTER(cr), ir->nstlist, mdrunOptions.reproducible, nstSignalComm,
const DDBalanceRegionHandler ddBalanceRegionHandler(cr);
- step = ir->init_step;
- step_rel = 0;
-
- // TODO extract this to new multi-simulation module
if (MASTER(cr) && isMultiSim(ms) && !useReplicaExchange)
{
- if (!multisim_int_all_are_equal(ms, ir->nsteps))
- {
- GMX_LOG(mdlog.warning)
- .appendText(
- "Note: The number of steps is not consistent across multi "
- "simulations,\n"
- "but we are proceeding anyway!");
- }
- if (!multisim_int_all_are_equal(ms, ir->init_step))
- {
- if (simulationsShareState)
- {
- if (MASTER(cr))
- {
- gmx_fatal(FARGS,
- "The initial step is not consistent across multi simulations which "
- "share the state");
- }
- gmx_barrier(cr);
- }
- else
- {
- GMX_LOG(mdlog.warning)
- .appendText(
- "Note: The initial step is not consistent across multi "
- "simulations,\n"
- "but we are proceeding anyway!");
- }
- }
+ logInitialMultisimStatus(ms, cr, mdlog, simulationsShareState, ir->nsteps, ir->init_step);
}
/* and stop now if we should */
if (ir->efep != efepNO || ir->bSimTemp)
{
/* find and set the current lambdas */
- setCurrentLambdasLocal(step, ir->fepvals, lam0, state->lambda, state->fep_state);
+ state->lambda = currentLambdas(step, *(ir->fepvals), state->fep_state);
bDoDHDL = do_per_step(step, ir->fepvals->nstdhdl);
bDoFEP = ((ir->efep != efepNO) && do_per_step(step, nstfep));
/* Correct the new box if it is too skewed */
if (inputrecDynamicBox(ir))
{
- if (correct_box(fplog, step, state->box, graph))
+ if (correct_box(fplog, step, state->box))
{
bMasterState = TRUE;
// If update is offloaded, it should be informed about the box size change
if (useGpuForUpdate)
{
- t_pbc pbc;
- set_pbc(&pbc, epbcXYZ, state->box);
- integrator->setPbc(&pbc);
+ integrator->setPbc(PbcType::Xyz, state->box);
}
}
}
}
}
+ // Allocate or re-size GPU halo exchange object, if necessary
+ if (bNS && havePPDomainDecomposition(cr) && simulationWork.useGpuHaloExchange)
+ {
+ GMX_RELEASE_ASSERT(fr->deviceStreamManager != nullptr,
+ "GPU device manager has to be initialized to use GPU "
+ "version of halo exchange.");
+ constructGpuHaloExchange(mdlog, *cr, *fr->deviceStreamManager, wcycle);
+ }
+
if (MASTER(cr) && do_log)
{
- energyOutput.printHeader(fplog, step, t); /* can we improve the information printed here? */
+ gmx::EnergyOutput::printHeader(fplog, step,
+ t); /* can we improve the information printed here? */
}
if (ir->efep != efepNO)
/* We need the kinetic energy at minus the half step for determining
* the full step kinetic energy and possibly for T-coupling.*/
/* This may not be quite working correctly yet . . . . */
- compute_globals(gstat, cr, ir, fr, ekind, state->x.rvec_array(), state->v.rvec_array(),
- state->box, state->lambda[efptVDW], mdatoms, nrnb, &vcm, wcycle, enerd,
- nullptr, nullptr, nullptr, nullptr, mu_tot, constr, &nullSignaller,
+ compute_globals(gstat, cr, ir, fr, ekind, makeConstArrayRef(state->x),
+ makeConstArrayRef(state->v), state->box, mdatoms, nrnb, &vcm, wcycle,
+ enerd, nullptr, nullptr, nullptr, nullptr, constr, &nullSignaller,
state->box, &totalNumberOfBondedInteractions, &bSumEkinhOld,
CGLO_GSTAT | CGLO_TEMPERATURE | CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS);
checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions, top_global,
- &top, state->x.rvec_array(), state->box,
+ &top, makeConstArrayRef(state->x), state->box,
&shouldCheckNumberOfBondedInteractions);
}
clear_mat(force_vir);
force_flags = (GMX_FORCE_STATECHANGED | ((inputrecDynamicBox(ir)) ? GMX_FORCE_DYNAMICBOX : 0)
| GMX_FORCE_ALLFORCES | (bCalcVir ? GMX_FORCE_VIRIAL : 0)
| (bCalcEner ? GMX_FORCE_ENERGY : 0) | (bDoFEP ? GMX_FORCE_DHDL : 0));
+ if (fr->useMts && !do_per_step(step, ir->nstfout))
+ {
+ force_flags |= GMX_FORCE_DO_NOT_NEED_NORMAL_FORCE;
+ }
if (shellfc)
{
/* Now is the time to relax the shells */
relax_shell_flexcon(fplog, cr, ms, mdrunOptions.verbose, enforcedRotation, step, ir,
- imdSession, pull_work, bNS, force_flags, &top, constr, enerd, fcd,
+ imdSession, pull_work, bNS, force_flags, &top, constr, enerd,
state->natoms, state->x.arrayRefWithPadding(),
- state->v.arrayRefWithPadding(), state->box, state->lambda, &state->hist,
- f.arrayRefWithPadding(), force_vir, mdatoms, nrnb, wcycle, graph,
- shellfc, fr, runScheduleWork, t, mu_tot, vsite, ddBalanceRegionHandler);
+ state->v.arrayRefWithPadding(), state->box, state->lambda,
+ &state->hist, &f.view(), force_vir, mdatoms, nrnb, wcycle, shellfc,
+ fr, runScheduleWork, t, mu_tot, vsite, ddBalanceRegionHandler);
}
else
{
*/
do_force(fplog, cr, ms, ir, awh.get(), enforcedRotation, imdSession, pull_work, step,
nrnb, wcycle, &top, state->box, state->x.arrayRefWithPadding(), &state->hist,
- f.arrayRefWithPadding(), force_vir, mdatoms, enerd, fcd, state->lambda, graph,
- fr, runScheduleWork, vsite, mu_tot, t, ed ? ed->getLegacyED() : nullptr,
+ &f.view(), force_vir, mdatoms, enerd, state->lambda, fr, runScheduleWork,
+ vsite, mu_tot, t, ed ? ed->getLegacyED() : nullptr,
(bNS ? GMX_FORCE_NS : 0) | force_flags, ddBalanceRegionHandler);
}
trotter_seq, ettTSEQ1);
}
- update_coords(step, ir, mdatoms, state, f.arrayRefWithPadding(), fcd, ekind, M, &upd,
- etrtVELOCITY1, cr, constr);
+ upd.update_coords(*ir, step, mdatoms, state, f.view().forceWithPadding(), fcdata, ekind,
+ M, etrtVELOCITY1, cr, constr != nullptr);
wallcycle_stop(wcycle, ewcUPDATE);
- constrain_velocities(step, nullptr, state, shake_vir, constr, bCalcVir, do_log, do_ene);
+ constrain_velocities(constr, do_log, do_ene, step, state, nullptr, bCalcVir, shake_vir);
wallcycle_start(wcycle, ewcUPDATE);
/* if VV, compute the pressure and constraints */
/* For VV2, we strictly only need this if using pressure
if (bGStat || do_per_step(step - 1, nstglobalcomm))
{
wallcycle_stop(wcycle, ewcUPDATE);
- compute_globals(gstat, cr, ir, fr, ekind, state->x.rvec_array(), state->v.rvec_array(),
- state->box, state->lambda[efptVDW], mdatoms, nrnb, &vcm, wcycle, enerd,
- force_vir, shake_vir, total_vir, pres, mu_tot, constr, &nullSignaller,
+ compute_globals(gstat, cr, ir, fr, ekind, makeConstArrayRef(state->x),
+ makeConstArrayRef(state->v), state->box, mdatoms, nrnb, &vcm, wcycle,
+ enerd, force_vir, shake_vir, total_vir, pres, constr, &nullSignaller,
state->box, &totalNumberOfBondedInteractions, &bSumEkinhOld,
(bGStat ? CGLO_GSTAT : 0) | (bCalcEner ? CGLO_ENERGY : 0)
| (bTemp ? CGLO_TEMPERATURE : 0) | (bPres ? CGLO_PRESSURE : 0)
b) If we are using EkinAveEkin for the kinetic energy for the temperature control, we still feed in
EkinAveVel because it's needed for the pressure */
checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions,
- top_global, &top, state->x.rvec_array(), state->box,
- &shouldCheckNumberOfBondedInteractions);
+ top_global, &top, makeConstArrayRef(state->x),
+ state->box, &shouldCheckNumberOfBondedInteractions);
if (bStopCM)
{
- process_and_stopcm_grp(fplog, &vcm, *mdatoms, state->x.rvec_array(),
- state->v.rvec_array());
+ process_and_stopcm_grp(fplog, &vcm, *mdatoms, makeArrayRef(state->x),
+ makeArrayRef(state->v));
inc_nrnb(nrnb, eNR_STOPCM, mdatoms->homenr);
}
wallcycle_start(wcycle, ewcUPDATE);
/* We need the kinetic energy at minus the half step for determining
* the full step kinetic energy and possibly for T-coupling.*/
/* This may not be quite working correctly yet . . . . */
- compute_globals(gstat, cr, ir, fr, ekind, state->x.rvec_array(),
- state->v.rvec_array(), state->box, state->lambda[efptVDW],
- mdatoms, nrnb, &vcm, wcycle, enerd, nullptr, nullptr, nullptr,
- nullptr, mu_tot, constr, &nullSignaller, state->box, nullptr,
- &bSumEkinhOld, CGLO_GSTAT | CGLO_TEMPERATURE);
+ compute_globals(gstat, cr, ir, fr, ekind, makeConstArrayRef(state->x),
+ makeConstArrayRef(state->v), state->box, mdatoms, nrnb, &vcm, wcycle,
+ enerd, nullptr, nullptr, nullptr, nullptr, constr, &nullSignaller,
+ state->box, nullptr, &bSumEkinhOld, CGLO_GSTAT | CGLO_TEMPERATURE);
wallcycle_start(wcycle, ewcUPDATE);
}
}
{
saved_conserved_quantity -= enerd->term[F_DISPCORR];
}
- /* sum up the foreign energy and dhdl terms for vv. currently done every step so that dhdl is correct in the .edr */
+ /* sum up the foreign kinetic energy and dK/dl terms for vv. currently done every step so that dhdl is correct in the .edr */
if (ir->efep != efepNO)
{
- sum_dhdl(enerd, state->lambda, *ir->fepvals);
+ accumulateKineticLambdaComponents(enerd, state->lambda, *ir->fepvals);
}
}
if (runScheduleWork->stepWork.useGpuFBufferOps && (simulationWork.useGpuUpdate && !vsite)
&& do_per_step(step, ir->nstfout))
{
- stateGpu->copyForcesFromGpu(ArrayRef<RVec>(f), AtomLocality::Local);
+ stateGpu->copyForcesFromGpu(f.view().force(), AtomLocality::Local);
stateGpu->waitForcesReadyOnHost(AtomLocality::Local);
}
/* Now we have the energies and forces corresponding to the
* the update.
*/
do_md_trajectory_writing(fplog, cr, nfile, fnm, step, step_rel, t, ir, state, state_global,
- observablesHistory, top_global, fr, outf, energyOutput, ekind, f,
- checkpointHandler->isCheckpointingStep(), bRerunMD, bLastStep,
- mdrunOptions.writeConfout, bSumEkinhOld);
+ observablesHistory, top_global, fr, outf, energyOutput, ekind,
+ f.view().force(), checkpointHandler->isCheckpointingStep(),
+ bRerunMD, bLastStep, mdrunOptions.writeConfout, bSumEkinhOld);
/* Check if IMD step and do IMD communication, if bIMD is TRUE. */
bInteractiveMDstep = imdSession->run(step, bNS, state->box, state->x.rvec_array(), t);
/* if we have constraints, we have to remove the kinetic energy parallel to the bonds */
if (constr && bIfRandomize)
{
- constrain_velocities(step, nullptr, state, tmp_vir, constr, bCalcVir, do_log, do_ene);
+ constrain_velocities(constr, do_log, do_ene, step, state, nullptr, false, nullptr);
}
}
/* Box is changed in update() when we do pressure coupling,
if (EI_VV(ir->eI))
{
/* velocity half-step update */
- update_coords(step, ir, mdatoms, state, f.arrayRefWithPadding(), fcd, ekind, M, &upd,
- etrtVELOCITY2, cr, constr);
+ upd.update_coords(*ir, step, mdatoms, state, f.view().forceWithPadding(), fcdata, ekind,
+ M, etrtVELOCITY2, cr, constr != nullptr);
}
/* Above, initialize just copies ekinh into ekin,
// If the buffer ops were not offloaded this step, the forces are on the host and have to be copied
if (!runScheduleWork->stepWork.useGpuFBufferOps)
{
- stateGpu->copyForcesToGpu(ArrayRef<RVec>(f), AtomLocality::Local);
+ stateGpu->copyForcesToGpu(f.view().force(), AtomLocality::Local);
}
const bool doTemperatureScaling =
}
else
{
- update_coords(step, ir, mdatoms, state, f.arrayRefWithPadding(), fcd, ekind, M, &upd,
- etrtPOSITION, cr, constr);
+ /* With multiple time stepping we need to do an additional normal
+ * update step to obtain the virial, as the actual MTS integration
+ * using an acceleration where the slow forces are multiplied by mtsFactor.
+ * Using that acceleration would result in a virial with the slow
+ * force contribution would be a factor mtsFactor too large.
+ */
+ if (fr->useMts && bCalcVir && constr != nullptr)
+ {
+ upd.update_for_constraint_virial(*ir, *mdatoms, *state, f.view().forceWithPadding(), *ekind);
+
+ constrain_coordinates(constr, do_log, do_ene, step, state,
+ upd.xp()->arrayRefWithPadding(), &dvdl_constr, bCalcVir, shake_vir);
+ }
+
+ ArrayRefWithPadding<const RVec> forceCombined =
+ (fr->useMts && step % ir->mtsLevels[1].stepFactor == 0)
+ ? f.view().forceMtsCombinedWithPadding()
+ : f.view().forceWithPadding();
+ upd.update_coords(*ir, step, mdatoms, state, forceCombined, fcdata, ekind, M,
+ etrtPOSITION, cr, constr != nullptr);
wallcycle_stop(wcycle, ewcUPDATE);
- constrain_coordinates(step, &dvdl_constr, state, shake_vir, &upd, constr, bCalcVir,
- do_log, do_ene);
+ constrain_coordinates(constr, do_log, do_ene, step, state, upd.xp()->arrayRefWithPadding(),
+ &dvdl_constr, bCalcVir && !fr->useMts, shake_vir);
- update_sd_second_half(step, &dvdl_constr, ir, mdatoms, state, cr, nrnb, wcycle, &upd,
- constr, do_log, do_ene);
- finish_update(ir, mdatoms, state, graph, nrnb, wcycle, &upd, constr);
+ upd.update_sd_second_half(*ir, step, &dvdl_constr, mdatoms, state, cr, nrnb, wcycle,
+ constr, do_log, do_ene);
+ upd.finish_update(*ir, mdatoms, state, wcycle, constr != nullptr);
}
if (ir->bPull && ir->pull->bSetPbcRefToPrevStepCOM)
{
/* erase F_EKIN and F_TEMP here? */
/* just compute the kinetic energy at the half step to perform a trotter step */
- compute_globals(gstat, cr, ir, fr, ekind, state->x.rvec_array(), state->v.rvec_array(),
- state->box, state->lambda[efptVDW], mdatoms, nrnb, &vcm, wcycle, enerd,
- force_vir, shake_vir, total_vir, pres, mu_tot, constr, &nullSignaller, lastbox,
+ compute_globals(gstat, cr, ir, fr, ekind, makeConstArrayRef(state->x),
+ makeConstArrayRef(state->v), state->box, mdatoms, nrnb, &vcm, wcycle, enerd,
+ force_vir, shake_vir, total_vir, pres, constr, &nullSignaller, lastbox,
nullptr, &bSumEkinhOld, (bGStat ? CGLO_GSTAT : 0) | CGLO_TEMPERATURE);
wallcycle_start(wcycle, ewcUPDATE);
trotter_update(ir, step, ekind, enerd, state, total_vir, mdatoms, &MassQ, trotter_seq, ettTSEQ4);
/* now we know the scaling, we can compute the positions again */
std::copy(cbuf.begin(), cbuf.end(), state->x.begin());
- update_coords(step, ir, mdatoms, state, f.arrayRefWithPadding(), fcd, ekind, M, &upd,
- etrtPOSITION, cr, constr);
+ upd.update_coords(*ir, step, mdatoms, state, f.view().forceWithPadding(), fcdata, ekind,
+ M, etrtPOSITION, cr, constr != nullptr);
wallcycle_stop(wcycle, ewcUPDATE);
/* do we need an extra constraint here? just need to copy out of as_rvec_array(state->v.data()) to upd->xp? */
* to numerical errors, or are they important
* physically? I'm thinking they are just errors, but not completely sure.
* For now, will call without actually constraining, constr=NULL*/
- finish_update(ir, mdatoms, state, graph, nrnb, wcycle, &upd, nullptr);
+ upd.finish_update(*ir, mdatoms, state, wcycle, false);
}
if (EI_VV(ir->eI))
{
/* this factor or 2 correction is necessary
because half of the constraint force is removed
in the vv step, so we have to double it. See
- the Redmine issue #1255. It is not yet clear
+ the Issue #1255. It is not yet clear
if the factor of 2 is exact, or just a very
good approximation, and this will be
investigated. The next step is to see if this
if (vsite != nullptr)
{
wallcycle_start(wcycle, ewcVSITECONSTR);
- if (graph != nullptr)
- {
- shift_self(graph, state->box, state->x.rvec_array());
- }
- construct_vsites(vsite, state->x.rvec_array(), ir->delta_t, state->v.rvec_array(),
- top.idef.iparams, top.idef.il, fr->ePBC, fr->bMolPBC, cr, state->box);
-
- if (graph != nullptr)
- {
- unshift_self(graph, state->box, state->x.rvec_array());
- }
+ vsite->construct(state->x, ir->delta_t, state->v, state->box);
wallcycle_stop(wcycle, ewcVSITECONSTR);
}
bool doIntraSimSignal = true;
SimulationSignaller signaller(&signals, cr, ms, doInterSimSignal, doIntraSimSignal);
- compute_globals(
- gstat, cr, ir, fr, ekind, state->x.rvec_array(), state->v.rvec_array(),
- state->box, state->lambda[efptVDW], mdatoms, nrnb, &vcm, wcycle, enerd,
- force_vir, shake_vir, total_vir, pres, mu_tot, constr, &signaller, lastbox,
- &totalNumberOfBondedInteractions, &bSumEkinhOld,
- (bGStat ? CGLO_GSTAT : 0) | (!EI_VV(ir->eI) && bCalcEner ? CGLO_ENERGY : 0)
- | (!EI_VV(ir->eI) && bStopCM ? CGLO_STOPCM : 0)
- | (!EI_VV(ir->eI) ? CGLO_TEMPERATURE : 0)
- | (!EI_VV(ir->eI) ? CGLO_PRESSURE : 0) | CGLO_CONSTRAINT
- | (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS
- : 0));
+ compute_globals(gstat, cr, ir, fr, ekind, makeConstArrayRef(state->x),
+ makeConstArrayRef(state->v), state->box, mdatoms, nrnb, &vcm,
+ wcycle, enerd, force_vir, shake_vir, total_vir, pres, constr,
+ &signaller, lastbox, &totalNumberOfBondedInteractions, &bSumEkinhOld,
+ (bGStat ? CGLO_GSTAT : 0) | (!EI_VV(ir->eI) && bCalcEner ? CGLO_ENERGY : 0)
+ | (!EI_VV(ir->eI) && bStopCM ? CGLO_STOPCM : 0)
+ | (!EI_VV(ir->eI) ? CGLO_TEMPERATURE : 0)
+ | (!EI_VV(ir->eI) ? CGLO_PRESSURE : 0) | CGLO_CONSTRAINT
+ | (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS
+ : 0));
checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions,
- top_global, &top, state->x.rvec_array(), state->box,
- &shouldCheckNumberOfBondedInteractions);
+ top_global, &top, makeConstArrayRef(state->x),
+ state->box, &shouldCheckNumberOfBondedInteractions);
if (!EI_VV(ir->eI) && bStopCM)
{
- process_and_stopcm_grp(fplog, &vcm, *mdatoms, state->x.rvec_array(),
- state->v.rvec_array());
+ process_and_stopcm_grp(fplog, &vcm, *mdatoms, makeArrayRef(state->x),
+ makeArrayRef(state->v));
inc_nrnb(nrnb, eNR_STOPCM, mdatoms->homenr);
// TODO: The special case of removing CM motion should be dealt more gracefully
if (ir->efep != efepNO && !EI_VV(ir->eI))
{
- /* Sum up the foreign energy and dhdl terms for md and sd.
- Currently done every step so that dhdl is correct in the .edr */
- sum_dhdl(enerd, state->lambda, *ir->fepvals);
+ /* Sum up the foreign energy and dK/dl terms for md and sd.
+ Currently done every step so that dH/dl is correct in the .edr */
+ accumulateKineticLambdaComponents(enerd, state->lambda, *ir->fepvals);
}
update_pcouple_after_coordinates(fplog, step, ir, mdatoms, pres, force_vir, shake_vir,
- pressureCouplingMu, state, nrnb, &upd, !useGpuForUpdate);
+ pressureCouplingMu, state, nrnb, upd.deform(), !useGpuForUpdate);
const bool doBerendsenPressureCoupling =
(inputrec->epc == epcBERENDSEN && do_per_step(step, inputrec->nstpcouple));
- if (useGpuForUpdate && (doBerendsenPressureCoupling || doParrinelloRahman))
+ const bool doCRescalePressureCoupling =
+ (inputrec->epc == epcCRESCALE && do_per_step(step, inputrec->nstpcouple));
+ if (useGpuForUpdate
+ && (doBerendsenPressureCoupling || doCRescalePressureCoupling || doParrinelloRahman))
{
integrator->scaleCoordinates(pressureCouplingMu);
- t_pbc pbc;
- set_pbc(&pbc, epbcXYZ, state->box);
- integrator->setPbc(&pbc);
+ if (doCRescalePressureCoupling)
+ {
+ matrix pressureCouplingInvMu;
+ gmx::invertBoxMatrix(pressureCouplingMu, pressureCouplingInvMu);
+ integrator->scaleVelocities(pressureCouplingInvMu);
+ }
+ integrator->setPbc(PbcType::Xyz, state->box);
}
/* ################# END UPDATE STEP 2 ################# */
}
if (bCalcEner)
{
- energyOutput.addDataAtEnergyStep(bDoDHDL, bCalcEnerStep, t, mdatoms->tmass, enerd, state,
- ir->fepvals, ir->expandedvals, lastbox, shake_vir,
- force_vir, total_vir, pres, ekind, mu_tot, constr);
+ energyOutput.addDataAtEnergyStep(
+ bDoDHDL, bCalcEnerStep, t, mdatoms->tmass, enerd, ir->fepvals,
+ ir->expandedvals, lastbox,
+ PTCouplingArrays{ state->boxv, state->nosehoover_xi, state->nosehoover_vxi,
+ state->nhpres_xi, state->nhpres_vxi },
+ state->fep_state, shake_vir, force_vir, total_vir, pres, ekind, mu_tot, constr);
}
else
{
if (doSimulatedAnnealing)
{
- energyOutput.printAnnealingTemperatures(do_log ? fplog : nullptr, groups, &(ir->opts));
+ gmx::EnergyOutput::printAnnealingTemperatures(do_log ? fplog : nullptr, groups,
+ &(ir->opts));
}
if (do_log || do_ene || do_dr || do_or)
{
energyOutput.printStepToEnergyFile(mdoutf_get_fp_ene(outf), do_ene, do_dr, do_or,
- do_log ? fplog : nullptr, step, t, fcd, awh.get());
+ do_log ? fplog : nullptr, step, t,
+ fr->fcdata.get(), awh.get());
+ }
+ if (do_log && ir->bDoAwh && awh->hasFepLambdaDimension())
+ {
+ const bool isInitialOutput = false;
+ printLambdaStateToLog(fplog, state->lambda, isInitialOutput);
}
if (ir->bPull)
/* Gets written into the state at the beginning of next loop*/
state->fep_state = lamnew;
}
+ else if (ir->bDoAwh && awh->needForeignEnergyDifferences(step))
+ {
+ state->fep_state = awh->fepLambdaState();
+ }
/* Print the remaining wall clock time for the run */
if (isMasterSimMasterRank(ms, MASTER(cr)) && (do_verbose || gmx_got_usr_signal()) && !bPMETunePrinting)
{
step++;
step_rel++;
+ #if GMX_FAHCORE
+ if (MASTER(cr))
+ {
+ fcReportProgress(ir->nsteps + ir->init_step, step);
+ }
+ #endif
+
resetHandler->resetCounters(step, step_rel, mdlog, fplog, cr, fr->nbv.get(), nrnb,
fr->pmedata, pme_loadbal, wcycle, walltime_accounting);
{
if (ir->nstcalcenergy > 0)
{
- energyOutput.printAnnealingTemperatures(fplog, groups, &(ir->opts));
+ gmx::EnergyOutput::printAnnealingTemperatures(fplog, groups, &(ir->opts));
energyOutput.printAverages(fplog, groups);
}
}
#include "gromacs/domdec/localatomsetmanager.h"
#include "gromacs/domdec/partition.h"
#include "gromacs/ewald/ewald_utils.h"
-#include "gromacs/ewald/pme.h"
#include "gromacs/ewald/pme_gpu_program.h"
+#include "gromacs/ewald/pme_only.h"
#include "gromacs/ewald/pme_pp_comm_gpu.h"
#include "gromacs/fileio/checkpoint.h"
#include "gromacs/fileio/gmxfio.h"
#include "gromacs/fileio/tpxio.h"
#include "gromacs/gmxlib/network.h"
#include "gromacs/gmxlib/nrnb.h"
-#include "gromacs/gpu_utils/gpu_utils.h"
+#include "gromacs/gpu_utils/device_stream_manager.h"
#include "gromacs/hardware/cpuinfo.h"
#include "gromacs/hardware/detecthardware.h"
+#include "gromacs/hardware/device_management.h"
#include "gromacs/hardware/printhardware.h"
#include "gromacs/imd/imd.h"
#include "gromacs/listed_forces/disre.h"
#include "gromacs/listed_forces/gpubonded.h"
+#include "gromacs/listed_forces/listed_forces.h"
#include "gromacs/listed_forces/orires.h"
#include "gromacs/math/functions.h"
#include "gromacs/math/utilities.h"
#include "gromacs/mdlib/force.h"
#include "gromacs/mdlib/forcerec.h"
#include "gromacs/mdlib/gmx_omp_nthreads.h"
+#include "gromacs/mdlib/gpuforcereduction.h"
#include "gromacs/mdlib/makeconstraints.h"
#include "gromacs/mdlib/md_support.h"
#include "gromacs/mdlib/mdatoms.h"
-#include "gromacs/mdlib/membed.h"
-#include "gromacs/mdlib/qmmm.h"
#include "gromacs/mdlib/sighandler.h"
#include "gromacs/mdlib/stophandler.h"
+#include "gromacs/mdlib/tgroup.h"
#include "gromacs/mdlib/updategroups.h"
+#include "gromacs/mdlib/vsite.h"
#include "gromacs/mdrun/mdmodules.h"
#include "gromacs/mdrun/simulationcontext.h"
+#include "gromacs/mdrun/simulationinput.h"
+#include "gromacs/mdrun/simulationinputhandle.h"
#include "gromacs/mdrunutility/handlerestart.h"
#include "gromacs/mdrunutility/logging.h"
#include "gromacs/mdrunutility/multisim.h"
#include "gromacs/mdrunutility/printtime.h"
#include "gromacs/mdrunutility/threadaffinity.h"
+#include "gromacs/mdtypes/checkpointdata.h"
#include "gromacs/mdtypes/commrec.h"
#include "gromacs/mdtypes/enerdata.h"
#include "gromacs/mdtypes/fcdata.h"
+#include "gromacs/mdtypes/forcerec.h"
#include "gromacs/mdtypes/group.h"
#include "gromacs/mdtypes/inputrec.h"
+#include "gromacs/mdtypes/interaction_const.h"
#include "gromacs/mdtypes/md_enums.h"
+#include "gromacs/mdtypes/mdatom.h"
#include "gromacs/mdtypes/mdrunoptions.h"
#include "gromacs/mdtypes/observableshistory.h"
#include "gromacs/mdtypes/simulation_workload.h"
#include "gromacs/mdtypes/state.h"
#include "gromacs/mdtypes/state_propagator_data_gpu.h"
+#include "gromacs/modularsimulator/modularsimulator.h"
#include "gromacs/nbnxm/gpu_data_mgmt.h"
#include "gromacs/nbnxm/nbnxm.h"
#include "gromacs/nbnxm/pairlist_tuning.h"
#include "gromacs/utility/stringutil.h"
#include "isimulator.h"
+#include "membedholder.h"
#include "replicaexchange.h"
#include "simulatorbuilder.h"
- #if GMX_FAHCORE
- # include "corewrap.h"
- #endif
-
namespace gmx
{
// getenv results are ignored when clearly they are used.
#pragma GCC diagnostic push
#pragma GCC diagnostic ignored "-Wunused-result"
- devFlags.enableGpuBufferOps = (getenv("GMX_USE_GPU_BUFFER_OPS") != nullptr)
- && (GMX_GPU == GMX_GPU_CUDA) && useGpuForNonbonded;
+
+ devFlags.enableGpuBufferOps =
+ GMX_GPU_CUDA && useGpuForNonbonded && (getenv("GMX_USE_GPU_BUFFER_OPS") != nullptr);
+ devFlags.enableGpuHaloExchange = GMX_GPU_CUDA && GMX_THREAD_MPI && getenv("GMX_GPU_DD_COMMS") != nullptr;
- devFlags.forceGpuUpdateDefault = (getenv("GMX_FORCE_UPDATE_DEFAULT_GPU") != nullptr);
+ devFlags.forceGpuUpdateDefault = (getenv("GMX_FORCE_UPDATE_DEFAULT_GPU") != nullptr) || GMX_FAHCORE;
- devFlags.enableGpuHaloExchange =
- (getenv("GMX_GPU_DD_COMMS") != nullptr && GMX_THREAD_MPI && (GMX_GPU == GMX_GPU_CUDA));
devFlags.enableGpuPmePPComm =
- (getenv("GMX_GPU_PME_PP_COMMS") != nullptr && GMX_THREAD_MPI && (GMX_GPU == GMX_GPU_CUDA));
+ GMX_GPU_CUDA && GMX_THREAD_MPI && getenv("GMX_GPU_PME_PP_COMMS") != nullptr;
+
#pragma GCC diagnostic pop
if (devFlags.enableGpuBufferOps)
GMX_LOG(mdlog.warning)
.asParagraph()
.appendTextFormatted(
- "This run uses the 'GPU halo exchange' feature, enabled by the "
+ "This run has requested the 'GPU halo exchange' feature, enabled by "
+ "the "
"GMX_GPU_DD_COMMS environment variable.");
}
else
{
if (pmeRunMode == PmeRunMode::GPU)
{
+ if (!devFlags.enableGpuBufferOps)
+ {
+ GMX_LOG(mdlog.warning)
+ .asParagraph()
+ .appendTextFormatted(
+ "Enabling GPU buffer operations required by GMX_GPU_PME_PP_COMMS "
+ "(equivalent with GMX_USE_GPU_BUFFER_OPS=1).");
+ devFlags.enableGpuBufferOps = true;
+ }
GMX_LOG(mdlog.warning)
.asParagraph()
.appendTextFormatted(
// Copy members of master runner.
// \todo Replace with builder when Simulation context and/or runner phases are better defined.
- // Ref https://redmine.gromacs.org/issues/2587 and https://redmine.gromacs.org/issues/2375
+ // Ref https://gitlab.com/gromacs/gromacs/-/issues/2587 and https://gitlab.com/gromacs/gromacs/-/issues/2375
newRunner.hw_opt = hw_opt;
newRunner.filenames = filenames;
newRunner.pforce = pforce;
// Give the spawned thread the newly created valid communicator
// for the simulation.
- newRunner.communicator = MPI_COMM_WORLD;
- newRunner.ms = ms;
- newRunner.startingBehavior = startingBehavior;
- newRunner.stopHandlerBuilder_ = std::make_unique<StopHandlerBuilder>(*stopHandlerBuilder_);
+ newRunner.libraryWorldCommunicator = MPI_COMM_WORLD;
+ newRunner.simulationCommunicator = MPI_COMM_WORLD;
+ newRunner.ms = ms;
+ newRunner.startingBehavior = startingBehavior;
+ newRunner.stopHandlerBuilder_ = std::make_unique<StopHandlerBuilder>(*stopHandlerBuilder_);
+ newRunner.inputHolder_ = inputHolder_;
threadMpiMdrunnerAccessBarrier();
// Give the master thread the newly created valid communicator for
// the simulation.
- communicator = MPI_COMM_WORLD;
+ libraryWorldCommunicator = MPI_COMM_WORLD;
+ simulationCommunicator = MPI_COMM_WORLD;
threadMpiMdrunnerAccessBarrier();
#else
GMX_UNUSED_VALUE(numThreadsToLaunch);
bool makeGpuPairList,
const gmx::CpuInfo& cpuinfo)
{
+ // We checked the cut-offs in grompp, but double-check here.
+ // We have PME+LJcutoff kernels for rcoulomb>rvdw.
+ if (EEL_PME_EWALD(ir->coulombtype) && ir->vdwtype == eelCUT)
+ {
+ GMX_RELEASE_ASSERT(ir->rcoulomb >= ir->rvdw,
+ "With Verlet lists and PME we should have rcoulomb>=rvdw");
+ }
+ else
+ {
+ GMX_RELEASE_ASSERT(ir->rcoulomb == ir->rvdw,
+ "With Verlet lists and no PME rcoulomb and rvdw should be identical");
+ }
/* For NVE simulations, we will retain the initial list buffer */
if (EI_DYNAMICS(ir->eI) && ir->verletbuf_tol > 0 && !(EI_MD(ir->eI) && ir->etc == etcNO))
{
{
matrix box;
t_forcerec* fr = nullptr;
- t_fcdata* fcd = nullptr;
real ewaldcoeff_q = 0;
real ewaldcoeff_lj = 0;
int nChargePerturbed = -1, nTypePerturbed = 0;
gmx_wallcycle_t wcycle;
gmx_walltime_accounting_t walltime_accounting = nullptr;
- gmx_membed_t* membed = nullptr;
- gmx_hw_info_t* hwinfo = nullptr;
+ MembedHolder membedHolder(filenames.size(), filenames.data());
+ gmx_hw_info_t* hwinfo = nullptr;
/* CAUTION: threads may be started later on in this function, so
cr doesn't reflect the final parallel state right now */
/* TODO: inputrec should tell us whether we use an algorithm, not a file option */
const bool doEssentialDynamics = opt2bSet("-ei", filenames.size(), filenames.data());
- const bool doMembed = opt2bSet("-membed", filenames.size(), filenames.data());
const bool doRerun = mdrunOptions.rerun;
// Handle task-assignment related user options.
{
fplog = gmx_fio_getfp(logFileHandle);
}
- const bool isSimulationMasterRank = findIsSimulationMasterRank(ms, communicator);
+ const bool isSimulationMasterRank = findIsSimulationMasterRank(ms, simulationCommunicator);
gmx::LoggerOwner logOwner(buildLogger(fplog, isSimulationMasterRank));
gmx::MDLogger mdlog(logOwner.logger());
// this is expressed, e.g. by expressly running detection only the
// master rank for thread-MPI, rather than relying on the mutex
// and reference count.
- PhysicalNodeCommunicator physicalNodeComm(communicator, gmx_physicalnode_id_hash());
+ PhysicalNodeCommunicator physicalNodeComm(libraryWorldCommunicator, gmx_physicalnode_id_hash());
hwinfo = gmx_detect_hardware(mdlog, physicalNodeComm);
gmx_print_detected_hardware(fplog, isSimulationMasterRank && isMasterSim(ms), mdlog, hwinfo);
- std::vector<int> gpuIdsToUse = makeGpuIdsToUse(hwinfo->gpu_info, hw_opt.gpuIdsAvailable);
+ std::vector<int> gpuIdsToUse = makeGpuIdsToUse(hwinfo->deviceInfoList, hw_opt.gpuIdsAvailable);
+ const int numDevicesToUse = gmx::ssize(gpuIdsToUse);
// Print citation requests after all software/hardware printing
pleaseCiteGromacs(fplog);
- // TODO Replace this by unique_ptr once t_inputrec is C++
- t_inputrec inputrecInstance;
- t_inputrec* inputrec = nullptr;
- std::unique_ptr<t_state> globalState;
+ // Note: legacy program logic relies on checking whether these pointers are assigned.
+ // Objects may or may not be allocated later.
+ std::unique_ptr<t_inputrec> inputrec;
+ std::unique_ptr<t_state> globalState;
auto partialDeserializedTpr = std::make_unique<PartialDeserializedTprFile>();
if (isSimulationMasterRank)
{
+ // Allocate objects to be initialized by later function calls.
/* Only the master rank has the global state */
globalState = std::make_unique<t_state>();
+ inputrec = std::make_unique<t_inputrec>();
/* Read (nearly) all data required for the simulation
* and keep the partly serialized tpr contents to send to other ranks later
*/
- *partialDeserializedTpr = read_tpx_state(ftp2fn(efTPR, filenames.size(), filenames.data()),
- &inputrecInstance, globalState.get(), &mtop);
- inputrec = &inputrecInstance;
+ applyGlobalSimulationState(*inputHolder_.get(), partialDeserializedTpr.get(),
+ globalState.get(), inputrec.get(), &mtop);
}
/* Check and update the hardware options for internal consistency */
checkAndUpdateHardwareOptions(mdlog, &hw_opt, isSimulationMasterRank, domdecOptions.numPmeRanks,
- inputrec);
+ inputrec.get());
if (GMX_THREAD_MPI && isSimulationMasterRank)
{
// the number of GPUs to choose the number of ranks.
auto canUseGpuForNonbonded = buildSupportsNonbondedOnGpu(nullptr);
useGpuForNonbonded = decideWhetherToUseGpusForNonbondedWithThreadMpi(
- nonbondedTarget, gpuIdsToUse, userGpuTaskAssignment, emulateGpuNonbonded,
+ nonbondedTarget, numDevicesToUse, userGpuTaskAssignment, emulateGpuNonbonded,
canUseGpuForNonbonded,
gpuAccelerationOfNonbondedIsUseful(mdlog, *inputrec, GMX_THREAD_MPI),
hw_opt.nthreads_tmpi);
useGpuForPme = decideWhetherToUseGpusForPmeWithThreadMpi(
- useGpuForNonbonded, pmeTarget, gpuIdsToUse, userGpuTaskAssignment, *hwinfo,
- *inputrec, mtop, hw_opt.nthreads_tmpi, domdecOptions.numPmeRanks);
+ useGpuForNonbonded, pmeTarget, numDevicesToUse, userGpuTaskAssignment, *hwinfo,
+ *inputrec, hw_opt.nthreads_tmpi, domdecOptions.numPmeRanks);
}
GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
* TODO Over-writing the user-supplied value here does
* prevent any possible subsequent checks from working
* correctly. */
- hw_opt.nthreads_tmpi = get_nthreads_mpi(hwinfo, &hw_opt, gpuIdsToUse, useGpuForNonbonded,
- useGpuForPme, inputrec, &mtop, mdlog, doMembed);
+ hw_opt.nthreads_tmpi =
+ get_nthreads_mpi(hwinfo, &hw_opt, numDevicesToUse, useGpuForNonbonded, useGpuForPme,
+ inputrec.get(), &mtop, mdlog, membedHolder.doMembed());
// Now start the threads for thread MPI.
spawnThreads(hw_opt.nthreads_tmpi);
// The spawned threads enter mdrunner() and execution of
// master and spawned threads joins at the end of this block.
- physicalNodeComm = PhysicalNodeCommunicator(communicator, gmx_physicalnode_id_hash());
+ physicalNodeComm =
+ PhysicalNodeCommunicator(libraryWorldCommunicator, gmx_physicalnode_id_hash());
}
- GMX_RELEASE_ASSERT(communicator == MPI_COMM_WORLD, "Must have valid world communicator");
- CommrecHandle crHandle = init_commrec(communicator, ms);
+ GMX_RELEASE_ASSERT(ms || simulationCommunicator != MPI_COMM_NULL,
+ "Must have valid communicator unless running a multi-simulation");
+ CommrecHandle crHandle = init_commrec(simulationCommunicator);
t_commrec* cr = crHandle.get();
GMX_RELEASE_ASSERT(cr != nullptr, "Must have valid commrec");
/* now broadcast everything to the non-master nodes/threads: */
if (!isSimulationMasterRank)
{
- inputrec = &inputrecInstance;
+ // Until now, only the master rank has a non-null pointer.
+ // On non-master ranks, allocate the object that will receive data in the following call.
+ inputrec = std::make_unique<t_inputrec>();
}
- init_parallel(cr, inputrec, &mtop, partialDeserializedTpr.get());
+ init_parallel(cr->mpiDefaultCommunicator, MASTER(cr), inputrec.get(), &mtop,
+ partialDeserializedTpr.get());
}
GMX_RELEASE_ASSERT(inputrec != nullptr, "All ranks should have a valid inputrec now");
partialDeserializedTpr.reset(nullptr);
// the inputrec read by the master rank. The ranks can now all run
// the task-deciding functions and will agree on the result
// without needing to communicate.
- //
- // TODO Should we do the communication in debug mode to support
- // having an assertion?
const bool useDomainDecomposition = (PAR(cr) && !(EI_TPI(inputrec->eI) || inputrec->eI == eiNM));
// Note that these variables describe only their own node.
nonbondedTarget, userGpuTaskAssignment, emulateGpuNonbonded, canUseGpuForNonbonded,
gpuAccelerationOfNonbondedIsUseful(mdlog, *inputrec, !GMX_THREAD_MPI), gpusWereDetected);
useGpuForPme = decideWhetherToUseGpusForPme(
- useGpuForNonbonded, pmeTarget, userGpuTaskAssignment, *hwinfo, *inputrec, mtop,
- cr->nnodes, domdecOptions.numPmeRanks, gpusWereDetected);
+ useGpuForNonbonded, pmeTarget, userGpuTaskAssignment, *hwinfo, *inputrec,
+ cr->sizeOfDefaultCommunicator, domdecOptions.numPmeRanks, gpusWereDetected);
auto canUseGpuForBonded = buildSupportsGpuBondeds(nullptr)
&& inputSupportsGpuBondeds(*inputrec, mtop, nullptr);
useGpuForBonded = decideWhetherToUseGpusForBonded(
const DevelopmentFeatureFlags devFlags =
manageDevelopmentFeatures(mdlog, useGpuForNonbonded, pmeRunMode);
- const bool inputIsCompatibleWithModularSimulator = ModularSimulator::isInputCompatible(
- false, inputrec, doRerun, mtop, ms, replExParams, nullptr, doEssentialDynamics, doMembed);
- const bool useModularSimulator = inputIsCompatibleWithModularSimulator
- && !(getenv("GMX_DISABLE_MODULAR_SIMULATOR") != nullptr);
+ const bool useModularSimulator =
+ checkUseModularSimulator(false, inputrec.get(), doRerun, mtop, ms, replExParams,
+ nullptr, doEssentialDynamics, membedHolder.doMembed());
// Build restraints.
// TODO: hide restraint implementation details from Mdrunner.
// TODO: Error handling
mdModules_->assignOptionsToModules(*inputrec->params, nullptr);
- const auto& mdModulesNotifier = mdModules_->notifier().notifier_;
+ // now that the MdModules know their options, they know which callbacks to sign up to
+ mdModules_->subscribeToSimulationSetupNotifications();
+ const auto& mdModulesNotifier = mdModules_->notifier().simulationSetupNotifications_;
if (inputrec->internalParameters != nullptr)
{
if (fplog != nullptr)
{
- pr_inputrec(fplog, 0, "Input Parameters", inputrec, FALSE);
+ pr_inputrec(fplog, 0, "Input Parameters", inputrec.get(), FALSE);
fprintf(fplog, "\n");
}
}
/* now make sure the state is initialized and propagated */
- set_state_entries(globalState.get(), inputrec, useModularSimulator);
+ set_state_entries(globalState.get(), inputrec.get(), useModularSimulator);
}
/* NM and TPI parallelize over force/energy calculations, not atoms,
{
globalState = std::make_unique<t_state>();
}
- broadcastStateWithoutDynamics(cr, globalState.get());
+ broadcastStateWithoutDynamics(cr->mpiDefaultCommunicator, DOMAINDECOMP(cr), PAR(cr),
+ globalState.get());
}
/* A parallel command line option consistency check that we can
{
if (domdecOptions.numPmeRanks > 0)
{
- gmx_fatal_collective(FARGS, cr->mpi_comm_mysim, MASTER(cr),
+ gmx_fatal_collective(FARGS, cr->mpiDefaultCommunicator, MASTER(cr),
"PME-only ranks are requested, but the system does not use PME "
"for electrostatics or LJ");
}
}
}
- #if GMX_FAHCORE
- if (MASTER(cr))
- {
- fcRegisterSteps(inputrec->nsteps, inputrec->init_step);
- }
- #endif
-
/* NMR restraints must be initialized before load_checkpoint,
* since with time averaging the history is added to t_state.
* For proper consistency check we therefore need to extend
* So the PME-only nodes (if present) will also initialize
* the distance restraints.
*/
- snew(fcd, 1);
/* This needs to be called before read_checkpoint to extend the state */
- init_disres(fplog, &mtop, inputrec, cr, ms, fcd, globalState.get(), replExParams.exchangeInterval > 0);
+ t_disresdata* disresdata;
+ snew(disresdata, 1);
+ init_disres(fplog, &mtop, inputrec.get(), DisResRunMode::MDRun,
+ MASTER(cr) ? DDRole::Master : DDRole::Agent,
+ PAR(cr) ? NumRanks::Multiple : NumRanks::Single, cr->mpi_comm_mysim, ms, disresdata,
+ globalState.get(), replExParams.exchangeInterval > 0);
- init_orires(fplog, &mtop, inputrec, cr, ms, globalState.get(), &(fcd->orires));
+ t_oriresdata* oriresdata;
+ snew(oriresdata, 1);
+ init_orires(fplog, &mtop, inputrec.get(), cr, ms, globalState.get(), oriresdata);
- auto deform = prepareBoxDeformation(globalState->box, cr, *inputrec);
+ auto deform = prepareBoxDeformation(
+ globalState != nullptr ? globalState->box : box, MASTER(cr) ? DDRole::Master : DDRole::Agent,
+ PAR(cr) ? NumRanks::Multiple : NumRanks::Single, cr->mpi_comm_mygroup, *inputrec);
+ #if GMX_FAHCORE
+ /* We have to remember the generation's first step before reading checkpoint.
+ This way, we can report to the F@H core both the generation's first step
+ and the restored first step, thus making it able to distinguish between
+ an interruption/resume and start of the n-th generation simulation.
+ Having this information, the F@H core can correctly calculate and report
+ the progress.
+ */
+ int gen_first_step = 0;
+ if (MASTER(cr))
+ {
+ gen_first_step = inputrec->init_step;
+ }
+ #endif
+
ObservablesHistory observablesHistory = {};
+ auto modularSimulatorCheckpointData = std::make_unique<ReadCheckpointDataHolder>();
if (startingBehavior != StartingBehavior::NewSimulation)
{
/* Check if checkpoint file exists before doing continuation.
inputrec->nsteps = -1;
}
- load_checkpoint(opt2fn_master("-cpi", filenames.size(), filenames.data(), cr),
- logFileHandle, cr, domdecOptions.numCells, inputrec, globalState.get(),
- &observablesHistory, mdrunOptions.reproducible, mdModules_->notifier());
+ // Finish applying initial simulation state information from external sources on all ranks.
+ // Reconcile checkpoint file data with Mdrunner state established up to this point.
+ applyLocalState(*inputHolder_.get(), logFileHandle, cr, domdecOptions.numCells,
+ inputrec.get(), globalState.get(), &observablesHistory,
+ mdrunOptions.reproducible, mdModules_->notifier(),
+ modularSimulatorCheckpointData.get(), useModularSimulator);
+ // TODO: (#3652) Synchronize filesystem state, SimulationInput contents, and program
+ // invariants
+ // on all code paths.
+ // Write checkpoint or provide hook to update SimulationInput.
+ // If there was a checkpoint file, SimulationInput contains more information
+ // than if there wasn't. At this point, we have synchronized the in-memory
+ // state with the filesystem state only for restarted simulations. We should
+ // be calling applyLocalState unconditionally and expect that the completeness
+ // of SimulationInput is not dependent on its creation method.
if (startingBehavior == StartingBehavior::RestartWithAppending && logFileHandle)
{
}
}
+ #if GMX_FAHCORE
+ if (MASTER(cr))
+ {
+ fcRegisterSteps(inputrec->nsteps + inputrec->init_step, gen_first_step);
+ }
+ #endif
+
if (mdrunOptions.numStepsCommandline > -2)
{
GMX_LOG(mdlog.info)
"file field.");
}
/* override nsteps with value set on the commandline */
- override_nsteps_cmdline(mdlog, mdrunOptions.numStepsCommandline, inputrec);
+ override_nsteps_cmdline(mdlog, mdrunOptions.numStepsCommandline, inputrec.get());
- if (SIMMASTER(cr))
+ if (isSimulationMasterRank)
{
copy_mat(globalState->box, box);
}
if (PAR(cr))
{
- gmx_bcast(sizeof(box), box, cr);
+ gmx_bcast(sizeof(box), box, cr->mpiDefaultCommunicator);
}
if (inputrec->cutoff_scheme != ecutsVERLET)
"Verlet scheme, or use an earlier version of GROMACS if necessary.");
}
/* Update rlist and nstlist. */
- prepare_verlet_scheme(fplog, cr, inputrec, nstlist_cmdline, &mtop, box,
+ /* Note: prepare_verlet_scheme is calling increaseNstlist(...), which (while attempting to
+ * increase rlist) tries to check if the newly chosen value fits with the DD scheme. As this is
+ * run before any DD scheme is set up, this check is never executed. See #3334 for more details.
+ */
+ prepare_verlet_scheme(fplog, cr, inputrec.get(), nstlist_cmdline, &mtop, box,
useGpuForNonbonded || (emulateGpuNonbonded == EmulateGpuNonbonded::Yes),
*hwinfo->cpuInfo);
- const bool prefer1DAnd1PulseDD = (devFlags.enableGpuHaloExchange && useGpuForNonbonded);
// This builder is necessary while we have multi-part construction
// of DD. Before DD is constructed, we use the existence of
// the builder object to indicate that further construction of DD
if (useDomainDecomposition)
{
ddBuilder = std::make_unique<DomainDecompositionBuilder>(
- mdlog, cr, domdecOptions, mdrunOptions, prefer1DAnd1PulseDD, mtop, *inputrec, box,
+ mdlog, cr, domdecOptions, mdrunOptions, mtop, *inputrec, box,
positionsFromStatePointer(globalState.get()));
}
else
{
/* PME, if used, is done on all nodes with 1D decomposition */
- cr->npmenodes = 0;
- cr->duty = (DUTY_PP | DUTY_PME);
+ cr->nnodes = cr->sizeOfDefaultCommunicator;
+ cr->sim_nodeid = cr->rankInDefaultCommunicator;
+ cr->nodeid = cr->rankInDefaultCommunicator;
+ cr->npmenodes = 0;
+ cr->duty = (DUTY_PP | DUTY_PME);
- if (inputrec->ePBC == epbcSCREW)
+ if (inputrec->pbcType == PbcType::Screw)
{
gmx_fatal(FARGS, "pbc=screw is only implemented with domain decomposition");
}
}
- // Produce the task assignment for this rank.
- GpuTaskAssignmentsBuilder gpuTaskAssignmentsBuilder;
- GpuTaskAssignments gpuTaskAssignments = gpuTaskAssignmentsBuilder.build(
- gpuIdsToUse, userGpuTaskAssignment, *hwinfo, communicator, physicalNodeComm,
+ // Produce the task assignment for this rank - done after DD is constructed
+ GpuTaskAssignments gpuTaskAssignments = GpuTaskAssignmentsBuilder::build(
+ gpuIdsToUse, userGpuTaskAssignment, *hwinfo, simulationCommunicator, physicalNodeComm,
nonbondedTarget, pmeTarget, bondedTarget, updateTarget, useGpuForNonbonded,
useGpuForPme, thisRankHasDuty(cr, DUTY_PP),
// TODO cr->duty & DUTY_PME should imply that a PME
EEL_PME(inputrec->coulombtype) && thisRankHasDuty(cr, DUTY_PME));
// Get the device handles for the modules, nullptr when no task is assigned.
- gmx_device_info_t* nonbondedDeviceInfo = gpuTaskAssignments.initNonbondedDevice(cr);
- gmx_device_info_t* pmeDeviceInfo = gpuTaskAssignments.initPmeDevice();
+ int deviceId = -1;
+ DeviceInformation* deviceInfo = gpuTaskAssignments.initDevice(&deviceId);
+
+ // timing enabling - TODO put this in gpu_utils (even though generally this is just option handling?)
+ bool useTiming = true;
- // TODO Initialize GPU streams here.
+ if (GMX_GPU_CUDA)
+ {
+ /* WARNING: CUDA timings are incorrect with multiple streams.
+ * This is the main reason why they are disabled by default.
+ */
+ // TODO: Consider turning on by default when we can detect nr of streams.
+ useTiming = (getenv("GMX_ENABLE_GPU_TIMING") != nullptr);
+ }
+ else if (GMX_GPU_OPENCL)
+ {
+ useTiming = (getenv("GMX_DISABLE_GPU_TIMING") == nullptr);
+ }
// TODO Currently this is always built, yet DD partition code
// checks if it is built before using it. Probably it should
const bool printHostName = (cr->nnodes > 1);
gpuTaskAssignments.reportGpuUsage(mdlog, printHostName, useGpuForBonded, pmeRunMode, useGpuForUpdate);
+ const bool disableNonbondedCalculation = (getenv("GMX_NO_NONBONDED") != nullptr);
+ if (disableNonbondedCalculation)
+ {
+ /* turn off non-bonded calculations */
+ GMX_LOG(mdlog.warning)
+ .asParagraph()
+ .appendText(
+ "Found environment variable GMX_NO_NONBONDED.\n"
+ "Disabling nonbonded calculations.");
+ }
+
+ MdrunScheduleWorkload runScheduleWork;
+
+ bool useGpuDirectHalo = decideWhetherToUseGpuForHalo(
+ devFlags, havePPDomainDecomposition(cr), useGpuForNonbonded, useModularSimulator,
+ doRerun, EI_ENERGY_MINIMIZATION(inputrec->eI));
+
+ // Also populates the simulation constant workload description.
+ runScheduleWork.simulationWork = createSimulationWorkload(
+ *inputrec, disableNonbondedCalculation, devFlags, useGpuForNonbonded, pmeRunMode,
+ useGpuForBonded, useGpuForUpdate, useGpuDirectHalo);
+
+ std::unique_ptr<DeviceStreamManager> deviceStreamManager = nullptr;
+
+ if (deviceInfo != nullptr)
+ {
+ if (DOMAINDECOMP(cr) && thisRankHasDuty(cr, DUTY_PP))
+ {
+ dd_setup_dlb_resource_sharing(cr, deviceId);
+ }
+ deviceStreamManager = std::make_unique<DeviceStreamManager>(
+ *deviceInfo, havePPDomainDecomposition(cr), runScheduleWork.simulationWork, useTiming);
+ }
+
// If the user chose a task assignment, give them some hints
// where appropriate.
if (!userGpuTaskAssignment.empty())
{
- gpuTaskAssignments.logPerformanceHints(mdlog, ssize(gpuIdsToUse));
+ gpuTaskAssignments.logPerformanceHints(mdlog, numDevicesToUse);
}
if (PAR(cr))
.appendTextFormatted(
"This is simulation %d out of %d running as a composite GROMACS\n"
"multi-simulation job. Setup for this simulation:\n",
- ms->sim, ms->nsim);
+ ms->simulationIndex_, ms->numSimulations_);
}
GMX_LOG(mdlog.warning)
.appendTextFormatted("Using %d MPI %s\n", cr->nnodes,
// Only for DD, only master PP rank needs to perform setup, and only if thread MPI plus
// any of the GPU communication features are active.
if (DOMAINDECOMP(cr) && MASTER(cr) && thisRankHasDuty(cr, DUTY_PP) && GMX_THREAD_MPI
- && (devFlags.enableGpuHaloExchange || devFlags.enableGpuPmePPComm))
+ && (runScheduleWork.simulationWork.useGpuHaloExchange
+ || runScheduleWork.simulationWork.useGpuPmePpCommunication))
{
setupGpuDevicePeerAccess(gpuIdsToUse, mdlog);
}
/* Master synchronizes its value of reset_counters with all nodes
* including PME only nodes */
int64_t reset_counters = wcycle_get_reset_counters(wcycle);
- gmx_bcast_sim(sizeof(reset_counters), &reset_counters, cr);
+ gmx_bcast(sizeof(reset_counters), &reset_counters, cr->mpi_comm_mysim);
wcycle_set_reset_counters(wcycle, reset_counters);
}
// Membrane embedding must be initialized before we call init_forcerec()
- if (doMembed)
- {
- if (MASTER(cr))
- {
- fprintf(stderr, "Initializing membed");
- }
- /* Note that membed cannot work in parallel because mtop is
- * changed here. Fix this if we ever want to make it run with
- * multiple ranks. */
- membed = init_membed(fplog, filenames.size(), filenames.data(), &mtop, inputrec,
- globalState.get(), cr, &mdrunOptions.checkpointOptions.period);
- }
+ membedHolder.initializeMembed(fplog, filenames.size(), filenames.data(), &mtop, inputrec.get(),
+ globalState.get(), cr, &mdrunOptions.checkpointOptions.period);
- const bool thisRankHasPmeGpuTask = gpuTaskAssignments.thisRankHasPmeGpuTask();
- std::unique_ptr<MDAtoms> mdAtoms;
- std::unique_ptr<gmx_vsite_t> vsite;
+ const bool thisRankHasPmeGpuTask = gpuTaskAssignments.thisRankHasPmeGpuTask();
+ std::unique_ptr<MDAtoms> mdAtoms;
+ std::unique_ptr<VirtualSitesHandler> vsite;
+ std::unique_ptr<GpuBonded> gpuBonded;
t_nrnb nrnb;
if (thisRankHasDuty(cr, DUTY_PP))
{
mdModulesNotifier.notify(*cr);
mdModulesNotifier.notify(&atomSets);
- mdModulesNotifier.notify(PeriodicBoundaryConditionType{ inputrec->ePBC });
+ mdModulesNotifier.notify(inputrec->pbcType);
mdModulesNotifier.notify(SimulationTimeStep{ inputrec->delta_t });
/* Initiate forcerecord */
fr = new t_forcerec;
fr->forceProviders = mdModules_->initForceProviders();
- init_forcerec(fplog, mdlog, fr, fcd, inputrec, &mtop, cr, box,
+ init_forcerec(fplog, mdlog, fr, inputrec.get(), &mtop, cr, box,
opt2fn("-table", filenames.size(), filenames.data()),
opt2fn("-tablep", filenames.size(), filenames.data()),
- opt2fns("-tableb", filenames.size(), filenames.data()), *hwinfo,
- nonbondedDeviceInfo, useGpuForBonded,
- pmeRunMode == PmeRunMode::GPU && !thisRankHasDuty(cr, DUTY_PME), pforce, wcycle);
-
- // TODO Move this to happen during domain decomposition setup,
- // once stream and event handling works well with that.
- // TODO remove need to pass local stream into GPU halo exchange - Redmine #3093
- if (havePPDomainDecomposition(cr) && prefer1DAnd1PulseDD && is1DAnd1PulseDD(*cr->dd))
+ opt2fns("-tableb", filenames.size(), filenames.data()), pforce);
+ // Dirty hack, for fixing disres and orires should be made mdmodules
+ fr->fcdata->disres = disresdata;
+ fr->fcdata->orires = oriresdata;
+
+ // Save a handle to device stream manager to use elsewhere in the code
+ // TODO: Forcerec is not a correct place to store it.
+ fr->deviceStreamManager = deviceStreamManager.get();
+
+ if (runScheduleWork.simulationWork.useGpuPmePpCommunication && !thisRankHasDuty(cr, DUTY_PME))
{
- GMX_RELEASE_ASSERT(devFlags.enableGpuBufferOps,
- "Must use GMX_USE_GPU_BUFFER_OPS=1 to use GMX_GPU_DD_COMMS=1");
- void* streamLocal =
- Nbnxm::gpu_get_command_stream(fr->nbv->gpu_nbv, InteractionLocality::Local);
- void* streamNonLocal =
- Nbnxm::gpu_get_command_stream(fr->nbv->gpu_nbv, InteractionLocality::NonLocal);
- GMX_LOG(mdlog.warning)
- .asParagraph()
- .appendTextFormatted(
- "NOTE: This run uses the 'GPU halo exchange' feature, enabled by the "
- "GMX_GPU_DD_COMMS environment variable.");
- cr->dd->gpuHaloExchange = std::make_unique<GpuHaloExchange>(
- cr->dd, cr->mpi_comm_mysim, streamLocal, streamNonLocal);
+ GMX_RELEASE_ASSERT(
+ deviceStreamManager != nullptr,
+ "GPU device stream manager should be valid in order to use PME-PP direct "
+ "communications.");
+ GMX_RELEASE_ASSERT(
+ deviceStreamManager->streamIsValid(DeviceStreamType::PmePpTransfer),
+ "GPU PP-PME stream should be valid in order to use GPU PME-PP direct "
+ "communications.");
+ fr->pmePpCommGpu = std::make_unique<gmx::PmePpCommGpu>(
+ cr->mpi_comm_mysim, cr->dd->pme_nodeid, deviceStreamManager->context(),
+ deviceStreamManager->stream(DeviceStreamType::PmePpTransfer));
+ }
+
+ fr->nbv = Nbnxm::init_nb_verlet(mdlog, inputrec.get(), fr, cr, *hwinfo,
+ runScheduleWork.simulationWork.useGpuNonbonded,
+ deviceStreamManager.get(), &mtop, box, wcycle);
+ // TODO: Move the logic below to a GPU bonded builder
+ if (runScheduleWork.simulationWork.useGpuBonded)
+ {
+ GMX_RELEASE_ASSERT(deviceStreamManager != nullptr,
+ "GPU device stream manager should be valid in order to use GPU "
+ "version of bonded forces.");
+ gpuBonded = std::make_unique<GpuBonded>(
+ mtop.ffparams, fr->ic->epsfac * fr->fudgeQQ, deviceStreamManager->context(),
+ deviceStreamManager->bondedStream(havePPDomainDecomposition(cr)), wcycle);
+ fr->gpuBonded = gpuBonded.get();
}
/* Initialize the mdAtoms structure.
}
/* Initialize the virtual site communication */
- vsite = initVsite(mtop, cr);
+ vsite = makeVirtualSitesHandler(mtop, cr, fr->pbcType);
calc_shifts(box, fr->shift_vec);
/* With periodic molecules the charge groups should be whole at start up
* and the virtual sites should not be far from their proper positions.
*/
- if (!inputrec->bContinuation && MASTER(cr) && !(inputrec->ePBC != epbcNONE && inputrec->bPeriodicMols))
+ if (!inputrec->bContinuation && MASTER(cr)
+ && !(inputrec->pbcType != PbcType::No && inputrec->bPeriodicMols))
{
/* Make molecules whole at start of run */
- if (fr->ePBC != epbcNONE)
+ if (fr->pbcType != PbcType::No)
{
- do_pbc_first_mtop(fplog, inputrec->ePBC, box, &mtop, globalState->x.rvec_array());
+ do_pbc_first_mtop(fplog, inputrec->pbcType, box, &mtop, globalState->x.rvec_array());
}
if (vsite)
{
* for the initial distribution in the domain decomposition
* and for the initial shell prediction.
*/
- constructVsitesGlobal(mtop, globalState->x);
+ constructVirtualSitesGlobal(mtop, globalState->x);
}
}
PmeGpuProgramStorage pmeGpuProgram;
if (thisRankHasPmeGpuTask)
{
- pmeGpuProgram = buildPmeGpuProgram(pmeDeviceInfo);
+ GMX_RELEASE_ASSERT(
+ (deviceStreamManager != nullptr),
+ "GPU device stream manager should be initialized in order to use GPU for PME.");
+ GMX_RELEASE_ASSERT((deviceInfo != nullptr),
+ "GPU device should be initialized in order to use GPU for PME.");
+ pmeGpuProgram = buildPmeGpuProgram(deviceStreamManager->context());
}
/* Initiate PME if necessary,
if (cr->npmenodes > 0)
{
/* The PME only nodes need to know nChargePerturbed(FEP on Q) and nTypePerturbed(FEP on LJ)*/
- gmx_bcast_sim(sizeof(nChargePerturbed), &nChargePerturbed, cr);
- gmx_bcast_sim(sizeof(nTypePerturbed), &nTypePerturbed, cr);
+ gmx_bcast(sizeof(nChargePerturbed), &nChargePerturbed, cr->mpi_comm_mysim);
+ gmx_bcast(sizeof(nTypePerturbed), &nTypePerturbed, cr->mpi_comm_mysim);
}
if (thisRankHasDuty(cr, DUTY_PME))
{
try
{
- pmedata = gmx_pme_init(cr, getNumPmeDomains(cr->dd), inputrec, nChargePerturbed != 0,
- nTypePerturbed != 0, mdrunOptions.reproducible, ewaldcoeff_q,
- ewaldcoeff_lj, gmx_omp_nthreads_get(emntPME), pmeRunMode,
- nullptr, pmeDeviceInfo, pmeGpuProgram.get(), mdlog);
+ // TODO: This should be in the builder.
+ GMX_RELEASE_ASSERT(!runScheduleWork.simulationWork.useGpuPme
+ || (deviceStreamManager != nullptr),
+ "Device stream manager should be valid in order to use GPU "
+ "version of PME.");
+ GMX_RELEASE_ASSERT(
+ !runScheduleWork.simulationWork.useGpuPme
+ || deviceStreamManager->streamIsValid(DeviceStreamType::Pme),
+ "GPU PME stream should be valid in order to use GPU version of PME.");
+
+ const DeviceContext* deviceContext = runScheduleWork.simulationWork.useGpuPme
+ ? &deviceStreamManager->context()
+ : nullptr;
+ const DeviceStream* pmeStream =
+ runScheduleWork.simulationWork.useGpuPme
+ ? &deviceStreamManager->stream(DeviceStreamType::Pme)
+ : nullptr;
+
+ pmedata = gmx_pme_init(cr, getNumPmeDomains(cr->dd), inputrec.get(),
+ nChargePerturbed != 0, nTypePerturbed != 0,
+ mdrunOptions.reproducible, ewaldcoeff_q, ewaldcoeff_lj,
+ gmx_omp_nthreads_get(emntPME), pmeRunMode, nullptr,
+ deviceContext, pmeStream, pmeGpuProgram.get(), mdlog);
}
GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
}
if (inputrec->bPull)
{
/* Initialize pull code */
- pull_work = init_pull(fplog, inputrec->pull, inputrec, &mtop, cr, &atomSets,
+ pull_work = init_pull(fplog, inputrec->pull, inputrec.get(), &mtop, cr, &atomSets,
inputrec->fepvals->init_lambda);
if (inputrec->pull->bXOutAverage || inputrec->pull->bFOutAverage)
{
if (inputrec->bRot)
{
/* Initialize enforced rotation code */
- enforcedRotation =
- init_rot(fplog, inputrec, filenames.size(), filenames.data(), cr, &atomSets,
- globalState.get(), &mtop, oenv, mdrunOptions, startingBehavior);
+ enforcedRotation = init_rot(fplog, inputrec.get(), filenames.size(), filenames.data(),
+ cr, &atomSets, globalState.get(), &mtop, oenv, mdrunOptions,
+ startingBehavior);
}
t_swap* swap = nullptr;
if (inputrec->eSwapCoords != eswapNO)
{
/* Initialize ion swapping code */
- swap = init_swapcoords(fplog, inputrec,
+ swap = init_swapcoords(fplog, inputrec.get(),
opt2fn_master("-swap", filenames.size(), filenames.data(), cr),
&mtop, globalState.get(), &observablesHistory, cr, &atomSets,
oenv, mdrunOptions, startingBehavior);
}
/* Let makeConstraints know whether we have essential dynamics constraints. */
- auto constr = makeConstraints(mtop, *inputrec, pull_work, doEssentialDynamics, fplog,
- *mdAtoms->mdatoms(), cr, ms, &nrnb, wcycle, fr->bMolPBC);
+ auto constr = makeConstraints(mtop, *inputrec, pull_work, doEssentialDynamics, fplog, cr,
+ ms, &nrnb, wcycle, fr->bMolPBC);
/* Energy terms and groups */
gmx_enerdata_t enerd(mtop.groups.groups[SimulationAtomGroupType::EnergyOutput].size(),
/* Set up interactive MD (IMD) */
auto imdSession =
- makeImdSession(inputrec, cr, wcycle, &enerd, ms, &mtop, mdlog,
+ makeImdSession(inputrec.get(), cr, wcycle, &enerd, ms, &mtop, mdlog,
MASTER(cr) ? globalState->x.rvec_array() : nullptr, filenames.size(),
filenames.data(), oenv, mdrunOptions.imdOptions, startingBehavior);
/* This call is not included in init_domain_decomposition mainly
* because fr->cginfo_mb is set later.
*/
- dd_init_bondeds(fplog, cr->dd, &mtop, vsite.get(), inputrec,
+ dd_init_bondeds(fplog, cr->dd, mtop, vsite.get(), inputrec.get(),
domdecOptions.checkBondedInteractions, fr->cginfo_mb);
}
- // TODO This is not the right place to manage the lifetime of
- // this data structure, but currently it's the easiest way to
- // make it work.
- MdrunScheduleWorkload runScheduleWork;
- // Also populates the simulation constant workload description.
- runScheduleWork.simulationWork = createSimulationWorkload(
- useGpuForNonbonded, pmeRunMode, useGpuForBonded, useGpuForUpdate,
- devFlags.enableGpuBufferOps, devFlags.enableGpuHaloExchange,
- devFlags.enableGpuPmePPComm, haveEwaldSurfaceContribution(*inputrec));
+ if (runScheduleWork.simulationWork.useGpuBufferOps)
+ {
+ fr->gpuForceReduction[gmx::AtomLocality::Local] = std::make_unique<gmx::GpuForceReduction>(
+ deviceStreamManager->context(),
+ deviceStreamManager->stream(gmx::DeviceStreamType::NonBondedLocal));
+ fr->gpuForceReduction[gmx::AtomLocality::NonLocal] = std::make_unique<gmx::GpuForceReduction>(
+ deviceStreamManager->context(),
+ deviceStreamManager->stream(gmx::DeviceStreamType::NonBondedNonLocal));
+ }
std::unique_ptr<gmx::StatePropagatorDataGpu> stateGpu;
if (gpusWereDetected
- && ((useGpuForPme && thisRankHasDuty(cr, DUTY_PME))
+ && ((runScheduleWork.simulationWork.useGpuPme && thisRankHasDuty(cr, DUTY_PME))
|| runScheduleWork.simulationWork.useGpuBufferOps))
{
- const void* pmeStream = pme_gpu_get_device_stream(fr->pmedata);
- const void* localStream =
- fr->nbv->gpu_nbv != nullptr
- ? Nbnxm::gpu_get_command_stream(fr->nbv->gpu_nbv, InteractionLocality::Local)
- : nullptr;
- const void* nonLocalStream =
- fr->nbv->gpu_nbv != nullptr
- ? Nbnxm::gpu_get_command_stream(fr->nbv->gpu_nbv, InteractionLocality::NonLocal)
- : nullptr;
- const void* deviceContext = pme_gpu_get_device_context(fr->pmedata);
- const int paddingSize = pme_gpu_get_padding_size(fr->pmedata);
GpuApiCallBehavior transferKind = (inputrec->eI == eiMD && !doRerun && !useModularSimulator)
? GpuApiCallBehavior::Async
: GpuApiCallBehavior::Sync;
-
+ GMX_RELEASE_ASSERT(deviceStreamManager != nullptr,
+ "GPU device stream manager should be initialized to use GPU.");
stateGpu = std::make_unique<gmx::StatePropagatorDataGpu>(
- pmeStream, localStream, nonLocalStream, deviceContext, transferKind, paddingSize, wcycle);
+ *deviceStreamManager, transferKind, pme_gpu_get_block_size(fr->pmedata), wcycle);
fr->stateGpu = stateGpu.get();
}
GMX_ASSERT(stopHandlerBuilder_, "Runner must provide StopHandlerBuilder to simulator.");
SimulatorBuilder simulatorBuilder;
+ simulatorBuilder.add(SimulatorStateData(globalState.get(), &observablesHistory, &enerd, &ekind));
+ simulatorBuilder.add(std::move(membedHolder));
+ simulatorBuilder.add(std::move(stopHandlerBuilder_));
+ simulatorBuilder.add(SimulatorConfig(mdrunOptions, startingBehavior, &runScheduleWork));
+
+
+ simulatorBuilder.add(SimulatorEnv(fplog, cr, ms, mdlog, oenv));
+ simulatorBuilder.add(Profiling(&nrnb, walltime_accounting, wcycle));
+ simulatorBuilder.add(ConstraintsParam(
+ constr.get(), enforcedRotation ? enforcedRotation->getLegacyEnfrot() : nullptr,
+ vsite.get()));
+ // TODO: Separate `fr` to a separate add, and make the `build` handle the coupling sensibly.
+ simulatorBuilder.add(LegacyInput(static_cast<int>(filenames.size()), filenames.data(),
+ inputrec.get(), fr));
+ simulatorBuilder.add(ReplicaExchangeParameters(replExParams));
+ simulatorBuilder.add(InteractiveMD(imdSession.get()));
+ simulatorBuilder.add(SimulatorModules(mdModules_->outputProvider(), mdModules_->notifier()));
+ simulatorBuilder.add(CenterOfMassPulling(pull_work));
+ // Todo move to an MDModule
+ simulatorBuilder.add(IonSwapping(swap));
+ simulatorBuilder.add(TopologyData(&mtop, mdAtoms.get()));
+ simulatorBuilder.add(BoxDeformationHandle(deform.get()));
+ simulatorBuilder.add(std::move(modularSimulatorCheckpointData));
+
// build and run simulator object based on user-input
- auto simulator = simulatorBuilder.build(
- inputIsCompatibleWithModularSimulator, fplog, cr, ms, mdlog,
- static_cast<int>(filenames.size()), filenames.data(), oenv, mdrunOptions,
- startingBehavior, vsite.get(), constr.get(),
- enforcedRotation ? enforcedRotation->getLegacyEnfrot() : nullptr, deform.get(),
- mdModules_->outputProvider(), mdModules_->notifier(), inputrec, imdSession.get(),
- pull_work, swap, &mtop, fcd, globalState.get(), &observablesHistory, mdAtoms.get(),
- &nrnb, wcycle, fr, &enerd, &ekind, &runScheduleWork, replExParams, membed,
- walltime_accounting, std::move(stopHandlerBuilder_), doRerun);
+ auto simulator = simulatorBuilder.build(useModularSimulator);
simulator->run();
if (fr->pmePpCommGpu)
GMX_RELEASE_ASSERT(pmedata, "pmedata was NULL while cr->duty was not DUTY_PP");
/* do PME only */
walltime_accounting = walltime_accounting_init(gmx_omp_nthreads_get(emntPME));
- gmx_pmeonly(pmedata, cr, &nrnb, wcycle, walltime_accounting, inputrec, pmeRunMode);
+ gmx_pmeonly(pmedata, cr, &nrnb, wcycle, walltime_accounting, inputrec.get(), pmeRunMode,
+ deviceStreamManager.get());
}
wallcycle_stop(wcycle, ewcRUN);
/* Finish up, write some stuff
* if rerunMD, don't write last frame again
*/
- finish_run(fplog, mdlog, cr, inputrec, &nrnb, wcycle, walltime_accounting,
+ finish_run(fplog, mdlog, cr, inputrec.get(), &nrnb, wcycle, walltime_accounting,
fr ? fr->nbv.get() : nullptr, pmedata, EI_DYNAMICS(inputrec->eI) && !isMultiSim(ms));
// clean up cycle counter
wallcycle_destroy(wcycle);
+ deviceStreamManager.reset(nullptr);
// Free PME data
if (pmedata)
{
}
// FIXME: this is only here to manually unpin mdAtoms->chargeA_ and state->x,
- // before we destroy the GPU context(s) in free_gpu_resources().
+ // before we destroy the GPU context(s)
// Pinned buffers are associated with contexts in CUDA.
// As soon as we destroy GPU contexts after mdrunner() exits, these lines should go.
mdAtoms.reset(nullptr);
globalState.reset(nullptr);
mdModules_.reset(nullptr); // destruct force providers here as they might also use the GPU
+ gpuBonded.reset(nullptr);
+ /* Free pinned buffers in *fr */
+ delete fr;
+ fr = nullptr;
+ // TODO convert to C++ so we can get rid of these frees
+ sfree(disresdata);
+ sfree(oriresdata);
- /* Free GPU memory and set a physical node tMPI barrier (which should eventually go away) */
- free_gpu_resources(fr, physicalNodeComm, hwinfo->gpu_info);
- free_gpu(nonbondedDeviceInfo);
- free_gpu(pmeDeviceInfo);
- done_forcerec(fr, mtop.molblock.size());
- sfree(fcd);
+ if (!hwinfo->deviceInfoList.empty())
+ {
+ /* stop the GPU profiler (only CUDA) */
+ stopGpuProfiler();
+ }
- if (doMembed)
+ /* With tMPI we need to wait for all ranks to finish deallocation before
+ * destroying the CUDA context as some tMPI ranks may be sharing
+ * GPU and context.
+ *
+ * This is not a concern in OpenCL where we use one context per rank.
+ *
+ * Note: it is safe to not call the barrier on the ranks which do not use GPU,
+ * but it is easier and more futureproof to call it on the whole node.
+ *
+ * Note that this function needs to be called even if GPUs are not used
+ * in this run because the PME ranks have no knowledge of whether GPUs
+ * are used or not, but all ranks need to enter the barrier below.
+ * \todo Remove this physical node barrier after making sure
+ * that it's not needed anymore (with a shared GPU run).
+ */
+ if (GMX_THREAD_MPI)
{
- free_membed(membed);
+ physicalNodeComm.barrier();
}
+ releaseDevice(deviceInfo);
/* Does what it says */
print_date_and_time(fplog, cr->nodeid, "Finished mdrun", gmx_gettime());
/* we need to join all threads. The sub-threads join when they
exit this function, but the master thread needs to be told to
wait for that. */
- if (PAR(cr) && MASTER(cr))
+ if (MASTER(cr))
{
tMPI_Finalize();
}
#endif
return rc;
-}
+} // namespace gmx
Mdrunner::~Mdrunner()
{
Mdrunner::Mdrunner(Mdrunner&&) noexcept = default;
-//NOLINTNEXTLINE(performance-noexcept-move-constructor) working around GCC bug 58265
-Mdrunner& Mdrunner::operator=(Mdrunner&& /*handle*/) noexcept(BUGFREE_NOEXCEPT_STRING) = default;
+Mdrunner& Mdrunner::operator=(Mdrunner&& /*handle*/) noexcept = default;
class Mdrunner::BuilderImplementation
{
void addDomdec(const DomdecOptions& options);
+ void addInput(SimulationInputHandle inputHolder);
+
void addVerletList(int nstlist);
void addReplicaExchange(const ReplicaExchangeParameters& params);
//! Command-line override for the duration of a neighbor list with the Verlet scheme.
int nstlist_ = 0;
+ //! World communicator, used for hardware detection and task assignment
+ MPI_Comm libraryWorldCommunicator_ = MPI_COMM_NULL;
+
//! Multisim communicator handle.
gmx_multisim_t* multiSimulation_;
//! mdrun communicator
- MPI_Comm communicator_ = MPI_COMM_NULL;
+ MPI_Comm simulationCommunicator_ = MPI_COMM_NULL;
//! Print a warning if any force is larger than this (in kJ/mol nm).
real forceWarningThreshold_ = -1;
* \brief Builder for simulation stop signal handler.
*/
std::unique_ptr<StopHandlerBuilder> stopHandlerBuilder_ = nullptr;
+
+ /*!
+ * \brief Sources for initial simulation state.
+ *
+ * See issue #3652 for near-term refinements to the SimulationInput interface.
+ *
+ * See issue #3379 for broader discussion on API aspects of simulation inputs and outputs.
+ */
+ SimulationInputHandle inputHolder_;
};
Mdrunner::BuilderImplementation::BuilderImplementation(std::unique_ptr<MDModules> mdModules,
compat::not_null<SimulationContext*> context) :
mdModules_(std::move(mdModules))
{
- communicator_ = context->communicator_;
- multiSimulation_ = context->multiSimulation_.get();
+ libraryWorldCommunicator_ = context->libraryWorldCommunicator_;
+ simulationCommunicator_ = context->simulationCommunicator_;
+ multiSimulation_ = context->multiSimulation_.get();
}
Mdrunner::BuilderImplementation::~BuilderImplementation() = default;
newRunner.filenames = filenames_;
- newRunner.communicator = communicator_;
+ newRunner.libraryWorldCommunicator = libraryWorldCommunicator_;
+
+ newRunner.simulationCommunicator = simulationCommunicator_;
// nullptr is a valid value for the multisim handle
newRunner.ms = multiSimulation_;
+ if (inputHolder_)
+ {
+ newRunner.inputHolder_ = std::move(inputHolder_);
+ }
+ else
+ {
+ GMX_THROW(gmx::APIError("MdrunnerBuilder::addInput() is required before build()."));
+ }
+
// \todo Clarify ownership and lifetime management for gmx_output_env_t
// \todo Update sanity checking when output environment has clearly specified invariants.
// Initialization and default values for oenv are not well specified in the current version.
stopHandlerBuilder_ = std::move(builder);
}
+void Mdrunner::BuilderImplementation::addInput(SimulationInputHandle inputHolder)
+{
+ inputHolder_ = std::move(inputHolder);
+}
+
MdrunnerBuilder::MdrunnerBuilder(std::unique_ptr<MDModules> mdModules,
compat::not_null<SimulationContext*> context) :
impl_{ std::make_unique<Mdrunner::BuilderImplementation>(std::move(mdModules), context) }
return *this;
}
+MdrunnerBuilder& MdrunnerBuilder::addInput(SimulationInputHandle input)
+{
+ impl_->addInput(std::move(input));
+ return *this;
+}
+
MdrunnerBuilder::MdrunnerBuilder(MdrunnerBuilder&&) noexcept = default;
MdrunnerBuilder& MdrunnerBuilder::operator=(MdrunnerBuilder&&) noexcept = default;
#ifndef GMX_MDTYPES_STATE_PROPAGATOR_DATA_GPU_H
#define GMX_MDTYPES_STATE_PROPAGATOR_DATA_GPU_H
+ #include <tuple>
+
#include "gromacs/gpu_utils/devicebuffer_datatype.h"
#include "gromacs/gpu_utils/gpu_utils.h"
#include "gromacs/math/vectypes.h"
#include "locality.h"
+class DeviceContext;
+class DeviceStream;
class GpuEventSynchronizer;
struct gmx_wallcycle;
namespace gmx
{
+class DeviceStreamManager;
class StatePropagatorDataGpu
{
* ops are offloaded. This feature is currently not available in OpenCL and
* hence these streams are not set in these builds.
*
- * \note In CUDA, the update stream is created in the constructor as a temporary
- * solution, in place until the stream manager is introduced.
- * Note that this makes it impossible to construct this object in CUDA
- * builds executing on a host without any CUDA-capable device available.
- *
- * \note In CUDA, \p deviceContext is unused, hence always nullptr;
- * all stream arguments can also be nullptr in runs where the
- * respective streams are not required.
- * In OpenCL, \p deviceContext needs to be a valid device context.
- * In OpenCL runs StatePropagatorDataGpu is currently only used
- * with PME offload, and only on ranks with PME duty. Hence, the
- * \p pmeStream argument needs to be a valid OpenCL queue object
- * which must have been created in \p deviceContext.
- *
- * \todo Make a \p CommandStream visible in the CPU parts of the code so we
- * will not have to pass a void*.
- * \todo Make a \p DeviceContext object visible in CPU parts of the code so we
- * will not have to pass a void*.
- *
- * \param[in] pmeStream Device PME stream, nullptr allowed.
- * \param[in] localStream Device NBNXM local stream, nullptr allowed.
- * \param[in] nonLocalStream Device NBNXM non-local stream, nullptr allowed.
- * \param[in] deviceContext Device context, nullptr allowed.
- * \param[in] transferKind H2D/D2H transfer call behavior (synchronous or not).
- * \param[in] paddingSize Padding size for coordinates buffer.
- * \param[in] wcycle Wall cycle counter data.
+ * \param[in] deviceStreamManager Object that owns the DeviceContext and DeviceStreams.
+ * \param[in] transferKind H2D/D2H transfer call behavior (synchronous or not).
+ * \param[in] allocationBlockSizeDivisor Deterines padding size for coordinates buffer.
+ * \param[in] wcycle Wall cycle counter data.
*/
- StatePropagatorDataGpu(const void* pmeStream,
- const void* localStream,
- const void* nonLocalStream,
- const void* deviceContext,
- GpuApiCallBehavior transferKind,
- int paddingSize,
- gmx_wallcycle* wcycle);
+ StatePropagatorDataGpu(const DeviceStreamManager& deviceStreamManager,
+ GpuApiCallBehavior transferKind,
+ int allocationBlockSizeDivisor,
+ gmx_wallcycle* wcycle);
/*! \brief Constructor to use in PME-only rank and in tests.
*
* \param[in] pmeStream Device PME stream, nullptr is not allowed.
* \param[in] deviceContext Device context, nullptr allowed for non-OpenCL builds.
* \param[in] transferKind H2D/D2H transfer call behavior (synchronous or not).
- * \param[in] paddingSize Padding size for coordinates buffer.
+ * \param[in] allocationBlockSizeDivisor Determines padding size for coordinates buffer.
* \param[in] wcycle Wall cycle counter data.
*/
- StatePropagatorDataGpu(const void* pmeStream,
- const void* deviceContext,
- GpuApiCallBehavior transferKind,
- int paddingSize,
- gmx_wallcycle* wcycle);
+ StatePropagatorDataGpu(const DeviceStream* pmeStream,
+ const DeviceContext& deviceContext,
+ GpuApiCallBehavior transferKind,
+ int allocationBlockSizeDivisor,
+ gmx_wallcycle* wcycle);
//! Move constructor
StatePropagatorDataGpu(StatePropagatorDataGpu&& other) noexcept;
*
* \returns GPU positions buffer.
*/
- DeviceBuffer<float> getCoordinates();
+ DeviceBuffer<RVec> getCoordinates();
/*! \brief Copy positions to the GPU memory.
*
*
* \returns GPU velocities buffer.
*/
- DeviceBuffer<float> getVelocities();
+ DeviceBuffer<RVec> getVelocities();
/*! \brief Copy velocities to the GPU memory.
*
*
* \returns GPU force buffer.
*/
- DeviceBuffer<float> getForces();
+ DeviceBuffer<RVec> getForces();
/*! \brief Copy forces to the GPU memory.
*
*
* \returns The device command stream to use in update-constraints.
*/
- void* getUpdateStream();
+ const DeviceStream* getUpdateStream();
/*! \brief Getter for the number of local atoms.
*
#include "gromacs/fileio/xvgr.h"
#include "gromacs/math/functions.h"
+#include "gromacs/math/multidimarray.h"
#include "gromacs/math/units.h"
#include "gromacs/math/utilities.h"
#include "gromacs/math/vec.h"
+#include "gromacs/mdspan/extensions.h"
#include "gromacs/mdtypes/fcdata.h"
+#include "gromacs/mdtypes/interaction_const.h"
#include "gromacs/mdtypes/md_enums.h"
#include "gromacs/mdtypes/nblist.h"
#include "gromacs/utility/arrayref.h"
etabLJ6Switch,
etabLJ12Switch,
etabCOULSwitch,
- etabLJ6Encad,
- etabLJ12Encad,
- etabCOULEncad,
etabEXPMIN,
etabUSER,
etabNR
/* This structure holds name and a flag that tells whether
this is a Coulomb type funtion */
static const t_tab_props tprops[etabNR] = {
- { "LJ6", FALSE },
- { "LJ12", FALSE },
- { "LJ6Shift", FALSE },
- { "LJ12Shift", FALSE },
- { "Shift", TRUE },
- { "RF", TRUE },
- { "RF-zero", TRUE },
- { "COUL", TRUE },
- { "Ewald", TRUE },
- { "Ewald-Switch", TRUE },
- { "Ewald-User", TRUE },
- { "Ewald-User-Switch", TRUE },
- { "LJ6Ewald", FALSE },
- { "LJ6Switch", FALSE },
- { "LJ12Switch", FALSE },
- { "COULSwitch", TRUE },
- { "LJ6-Encad shift", FALSE },
- { "LJ12-Encad shift", FALSE },
- { "COUL-Encad shift", TRUE },
- { "EXPMIN", FALSE },
- { "USER", FALSE },
+ { "LJ6", FALSE }, { "LJ12", FALSE }, { "LJ6Shift", FALSE },
+ { "LJ12Shift", FALSE }, { "Shift", TRUE }, { "RF", TRUE },
+ { "RF-zero", TRUE }, { "COUL", TRUE }, { "Ewald", TRUE },
+ { "Ewald-Switch", TRUE }, { "Ewald-User", TRUE }, { "Ewald-User-Switch", TRUE },
+ { "LJ6Ewald", FALSE }, { "LJ6Switch", FALSE }, { "LJ12Switch", FALSE },
+ { "COULSwitch", TRUE }, { "EXPMIN", FALSE }, { "USER", FALSE },
};
typedef struct
static void read_tables(FILE* fp, const char* filename, int ntab, int angle, t_tabledata td[])
{
char buf[STRLEN];
- double **yy = nullptr, start, end, dx0, dx1, ssd, vm, vp, f, numf;
- int k, i, nx, nx0 = 0, ny, nny, ns;
+ double start, end, dx0, dx1, ssd, vm, vp, f, numf;
+ int k, i, nx0 = 0, nny, ns;
gmx_bool bAllZero, bZeroV, bZeroF;
double tabscale;
nny = 2 * ntab + 1;
std::string libfn = gmx::findLibraryFile(filename);
- nx = read_xvg(libfn.c_str(), &yy, &ny);
- if (ny != nny)
+ gmx::MultiDimArray<std::vector<double>, gmx::dynamicExtents2D> xvgData = readXvgData(libfn);
+ int numColumns = xvgData.extent(0);
+ if (numColumns != nny)
{
gmx_fatal(FARGS, "Trying to read file %s, but nr columns = %d, should be %d", libfn.c_str(),
- ny, nny);
+ numColumns, nny);
}
+ int numRows = xvgData.extent(1);
+
+ const auto& yy = xvgData.asView();
if (angle == 0)
{
if (yy[0][0] != 0.0)
start = -180.0;
}
end = 180.0;
- if (yy[0][0] != start || yy[0][nx - 1] != end)
+ if (yy[0][0] != start || yy[0][numRows - 1] != end)
{
gmx_fatal(FARGS, "The angles in file %s should go from %f to %f instead of %f to %f\n",
- libfn.c_str(), start, end, yy[0][0], yy[0][nx - 1]);
+ libfn.c_str(), start, end, yy[0][0], yy[0][numRows - 1]);
}
}
- tabscale = (nx - 1) / (yy[0][nx - 1] - yy[0][0]);
+ tabscale = (numRows - 1) / (yy[0][numRows - 1] - yy[0][0]);
if (fp)
{
- fprintf(fp, "Read user tables from %s with %d data points.\n", libfn.c_str(), nx);
+ fprintf(fp, "Read user tables from %s with %d data points.\n", libfn.c_str(), numRows);
if (angle == 0)
{
fprintf(fp, "Tabscale = %g points/nm\n", tabscale);
{
bZeroV = TRUE;
bZeroF = TRUE;
- for (i = 0; (i < nx); i++)
+ for (i = 0; (i < numRows); i++)
{
if (i >= 2)
{
if (!bZeroV && bZeroF)
{
- set_forces(fp, angle, nx, 1 / tabscale, yy[1 + k * 2], yy[1 + k * 2 + 1], k);
+ set_forces(fp, angle, numRows, 1 / tabscale, yy[1 + k * 2].data(),
+ yy[1 + k * 2 + 1].data(), k);
}
else
{
*/
ssd = 0;
ns = 0;
- for (i = 1; (i < nx - 1); i++)
+ for (i = 1; (i < numRows - 1); i++)
{
vm = yy[1 + 2 * k][i - 1];
vp = yy[1 + 2 * k][i + 1];
for (k = 0; (k < ntab); k++)
{
- init_table(nx, nx0, tabscale, &(td[k]), TRUE);
- for (i = 0; (i < nx); i++)
+ init_table(numRows, nx0, tabscale, &(td[k]), TRUE);
+ for (i = 0; (i < numRows); i++)
{
td[k].x[i] = yy[0][i];
td[k].v[i] = yy[2 * k + 1][i];
td[k].f[i] = yy[2 * k + 2][i];
}
}
- for (i = 0; (i < ny); i++)
- {
- sfree(yy[i]);
- }
- sfree(yy);
}
static void done_tabledata(t_tabledata* td)
int i;
double reppow, p;
double r1, rc, r12, r13;
- double r, r2, r6, rc2, rc6, rc12;
+ double r, r2, r6, rc2;
double expr, Vtab, Ftab;
/* Parameters for David's function */
double A = 0, B = 0, C = 0, A_3 = 0, B_4 = 0;
if (bPotentialShift)
{
- rc2 = rc * rc;
- rc6 = 1.0 / (rc2 * rc2 * rc2);
+ rc2 = rc * rc;
+ double rc6 = 1.0 / (rc2 * rc2 * rc2);
+ double rc12;
if (gmx_within_tol(reppow, 12.0, 10 * GMX_DOUBLE_EPS))
{
rc12 = rc6 * rc6;
swi1 = 0.0;
}
- rc6 = rc * rc * rc;
- rc6 = 1.0 / (rc6 * rc6);
-
switch (tp)
{
case etabLJ6:
Ftab = reppow * Vtab / r;
}
break;
- case etabLJ6Encad:
- if (r < rc)
- {
- Vtab = -(r6 - 6.0 * (rc - r) * rc6 / rc - rc6);
- Ftab = -(6.0 * r6 / r - 6.0 * rc6 / rc);
- }
- else /* r>rc */
- {
- Vtab = 0;
- Ftab = 0;
- }
- break;
- case etabLJ12Encad:
- if (r < rc)
- {
- Vtab = -(r6 - 6.0 * (rc - r) * rc6 / rc - rc6);
- Ftab = -(6.0 * r6 / r - 6.0 * rc6 / rc);
- }
- else /* r>rc */
- {
- Vtab = 0;
- Ftab = 0;
- }
- break;
case etabCOUL:
Vtab = 1.0 / r;
Ftab = 1.0 / r2;
Vtab = expr;
Ftab = expr;
break;
- case etabCOULEncad:
- if (r < rc)
- {
- Vtab = 1.0 / r - (rc - r) / (rc * rc) - 1.0 / rc;
- Ftab = 1.0 / r2 - 1.0 / (rc * rc);
- }
- else /* r>rc */
- {
- Vtab = 0;
- Ftab = 0;
- }
- break;
default:
gmx_fatal(FARGS, "Table type %d not implemented yet. (%s,%d)", tp, __FILE__, __LINE__);
}
case eelRF_ZERO: tabsel[etiCOUL] = etabRF_ZERO; break;
case eelSWITCH: tabsel[etiCOUL] = etabCOULSwitch; break;
case eelUSER: tabsel[etiCOUL] = etabUSER; break;
- case eelENCADSHIFT: tabsel[etiCOUL] = etabCOULEncad; break;
default: gmx_fatal(FARGS, "Invalid eeltype %d", eltype);
}
tabsel[etiLJ6] = etabLJ6;
tabsel[etiLJ12] = etabLJ12;
break;
- case evdwENCADSHIFT:
- tabsel[etiLJ6] = etabLJ6Encad;
- tabsel[etiLJ12] = etabLJ12Encad;
- break;
case evdwPME:
tabsel[etiLJ6] = etabLJ6Ewald;
tabsel[etiLJ12] = etabLJ12;
/* Each table type (e.g. coul,lj6,lj12) requires four
* numbers per table->n+1 data points. For performance reasons we want
- * the table data to be aligned to a 32-byte boundary.
+ * the table data to be aligned to (at least) a 32-byte boundary.
*/
- snew_aligned(table->data, table->stride * (table->n + 1) * sizeof(real), 32);
+ table->data.resize(table->stride * (table->n + 1) * sizeof(real));
for (int k = 0; (k < etiNR); k++)
{
}
copy2table(table->n, k * table->formatsize, table->stride, td[k].x, td[k].v, td[k].f,
- scalefactor, table->data);
+ scalefactor, table->data.data());
done_tabledata(&(td[k]));
}
}
tab.n = td.nx;
tab.scale = td.tabscale;
- snew(tab.data, tab.n * stride);
- copy2table(tab.n, 0, stride, td.x, td.v, td.f, 1.0, tab.data);
+ tab.data.resize(tab.n * stride);
+ copy2table(tab.n, 0, stride, td.x, td.v, td.f, 1.0, tab.data.data());
done_tabledata(&td);
return tab;
GMX_RELEASE_ASSERT(ic->vdwtype != evdwUSER || tabfn,
"With VdW user tables we need a table file name");
- if (tabfn == nullptr)
- {
- return std::unique_ptr<t_forcetable>(nullptr);
- }
-
t_forcetable* fullTable = make_tables(fp, ic, tabfn, rtab, 0);
/* Copy the contents of the table to one that has just dispersion
* and repulsion, to improve cache performance. We want the table
dispersionCorrectionTable->ninteractions = 2;
dispersionCorrectionTable->stride =
dispersionCorrectionTable->formatsize * dispersionCorrectionTable->ninteractions;
- snew_aligned(dispersionCorrectionTable->data,
- dispersionCorrectionTable->stride * (dispersionCorrectionTable->n + 1), 32);
+ dispersionCorrectionTable->data.resize(dispersionCorrectionTable->stride
+ * (dispersionCorrectionTable->n + 1));
for (int i = 0; i <= fullTable->n; i++)
{
r(0),
n(0),
scale(0),
- data(nullptr),
formatsize(0),
ninteractions(0),
stride(0)
{
}
-
-t_forcetable::~t_forcetable()
-{
- sfree_aligned(data);
-}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017,2018,2019,2020, by the GROMACS development team, led by
++ * Copyright (c) 2013,2014,2015,2016,2017, The GROMACS development team.
+ * Copyright (c) 2018,2019,2020, 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.
outFilesDemux.resize(nset);
for (i = 0; (i < nset); i++)
{
- outFilesDemux[0] = gmx::formatString("%d_%s", i, name.c_str());
+ outFilesDemux[i] = gmx::formatString("%d_%s", i, name.c_str());
}
}
do_demux(inFiles, outFilesDemux, n, val, t, dt_remd, isize, index, dt, oenv);
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2011,2014,2015,2016,2018 by the GROMACS development team.
- * Copyright (c) 2011,2014,2015,2016,2018,2019,2020, by the GROMACS development team, led by
++ * Copyright (c) 2011,2014,2015,2016,2018, The GROMACS development team.
+ * Copyright (c) 2019,2020, 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.
#include "gromacs/topology/idef.h"
#include "gromacs/topology/symtab.h"
#include "gromacs/utility/enumerationhelpers.h"
+#include "gromacs/utility/listoflists.h"
#include "gromacs/utility/unique_cptr.h"
enum class SimulationAtomGroupType : int
/*! \brief Default copy constructor */
gmx_moltype_t(const gmx_moltype_t&) = default;
- char** name; /**< Name of the molecule type */
- t_atoms atoms; /**< The atoms in this molecule */
- InteractionLists ilist; /**< Interaction list with local indices */
- t_blocka excls; /**< The exclusions */
+ char** name; /**< Name of the molecule type */
+ t_atoms atoms; /**< The atoms in this molecule */
+ InteractionLists ilist; /**< Interaction list with local indices */
+ gmx::ListOfLists<int> excls; /**< The exclusions */
};
/*! \brief Block of molecules of the same type, used in gmx_mtop_t */
*/
struct SimulationGroups
{
- //! Groups of particles
+ // TODO: collect groups and groupNumbers in a struct for each group type
+ //! Group numbers for each of the different SimulationAtomGroupType groups.
gmx::EnumerationArray<SimulationAtomGroupType, AtomGroupIndices> groups;
//! Names of groups, stored as pointer to the entries in the symbol table.
std::vector<char**> groupNames;
- //! Group numbers for the different SimulationAtomGroupType groups.
+ //! Indices into groups for each atom for each of the different SimulationAtomGroupType groups.
gmx::EnumerationArray<SimulationAtomGroupType, std::vector<unsigned char>> groupNumbers;
/*! \brief
- * Number of group numbers for a single SimulationGroup.
+ * Number of atoms for which group numbers are stored for a single SimulationGroup.
*
- * \param[in] group Integer value for the group type.
+ * \param[in] group The group type.
*/
int numberOfGroupNumbers(SimulationAtomGroupType group) const
{
- return gmx::ssize(groupNumbers[group]);
+ return static_cast<int>(groupNumbers[group].size());
}
};
std::unique_ptr<InteractionLists> intermolecular_ilist = nullptr;
//! Number of global atoms.
int natoms = 0;
- //! Parameter for residue numbering.
- int maxres_renum = 0;
- //! The maximum residue number in moltype
- int maxresnr = -1;
//! Atomtype properties
t_atomtypes atomtypes;
//! Groups of atoms for different purposes
SimulationGroups groups;
- //! The symbol table
+ //! The legacy symbol table
t_symtab symtab;
//! Tells whether we have valid molecule indices
bool haveMoleculeIndices = false;
*/
std::vector<int> intermolecularExclusionGroup;
- /* Derived data below */
+ //! Maximum number of residues in molecule to trigger renumbering of residues
+ int maxResiduesPerMoleculeToTriggerRenumber() const
+ {
+ return maxResiduesPerMoleculeToTriggerRenumber_;
+ }
+ //! Maximum residue number that is not renumbered.
+ int maxResNumberNotRenumbered() const { return maxResNumberNotRenumbered_; }
+ /*! \brief Finalize this data structure.
+ *
+ * Should be called after generating or reading mtop, to set some compute
+ * intesive variables to avoid N^2 operations later on.
+ *
+ * \todo Move into a builder class, once available.
+ */
+ void finalize();
+
+ /* Derived data below */
//! Indices for each molblock entry for fast lookup of atom properties
std::vector<MoleculeBlockIndices> moleculeBlockIndices;
+
+private:
+ //! Build the molblock indices
+ void buildMolblockIndices();
+ //! Maximum number of residues in molecule to trigger renumbering of residues
+ int maxResiduesPerMoleculeToTriggerRenumber_ = 0;
+ //! The maximum residue number in moltype that is not renumbered
+ int maxResNumberNotRenumbered_ = -1;
};
/*! \brief
struct gmx_localtop_t
{
//! Constructor used for normal operation, manages own resources.
- gmx_localtop_t();
-
- ~gmx_localtop_t();
+ gmx_localtop_t(const gmx_ffparams_t& ffparams);
//! The interaction function definition
- t_idef idef;
- //! Atomtype properties
- t_atomtypes atomtypes;
+ InteractionDefinitions idef;
//! The exclusions
- t_blocka excls;
- //! Flag for domain decomposition so we don't free already freed memory.
- bool useInDomainDecomp_ = false;
+ gmx::ListOfLists<int> excls;
};
/* The old topology struct, completely written out, used in analysis tools */
t_atomtypes atomtypes; /* Atomtype properties */
t_block mols; /* The molecules */
gmx_bool bIntermolecularInteractions; /* Inter.mol. int. ? */
- t_blocka excls; /* The exclusions */
- t_symtab symtab; /* The symbol table */
+ /* Note that the exclusions are not stored in t_topology */
+ t_symtab symtab; /* The symbol table */
} t_topology;
void init_top(t_topology* top);
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017,2018,2019,2020, by the GROMACS development team, led by
++ * Copyright (c) 2013,2014,2015,2016,2017, The GROMACS development team.
+ * Copyright (c) 2018,2019,2020, 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.
#include "errorformat.h"
-static bool bDebug = false;
-static gmx::Mutex where_mutex;
+static bool bDebug = false;
FILE* debug = nullptr;
gmx_bool gmx_debug_at = FALSE;
}
#endif
- if (exitType == ExitType_CleanExit)
+ if (!GMX_FAHCORE)
{
- std::exit(returnValue);
+ if (exitType == ExitType_CleanExit)
+ {
+ std::exit(returnValue);
+ }
+ // We cannot use std::exit() if other threads may still be executing, since that would cause
+ // destructors to be called for global objects that may still be in use elsewhere.
+ std::_Exit(returnValue);
}
- // We cannot use std::exit() if other threads may still be executing, since that would cause
- // destructors to be called for global objects that may still be in use elsewhere.
- std::_Exit(returnValue);
}
void gmx_fatal_mpi_va(int /*f_errno*/,
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017,2018,2019,2020, by the GROMACS development team, led by
++ * Copyright (c) 2013,2014,2015,2016,2017, The GROMACS development team.
+ * Copyright (c) 2018,2019,2020, 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.
}
#if GMX_FAHCORE
- /* don't use pipes!*/
- # define popen fah_fopen
- # define pclose fah_fclose
- # define SKIP_FFOPS 1
- #else
# ifdef gmx_ffclose
# undef gmx_ffclose
# endif
- # if (!HAVE_PIPES && !defined(__native_client__))
+ #endif
+ #if (!HAVE_PIPES && !defined(__native_client__))
-static FILE* popen(const char* nm, const char* mode)
+static FILE* popen(const char* /* nm */, const char* /* mode */)
{
gmx_impl("Sorry no pipes...");
return NULL;
}
-static int pclose(FILE* fp)
+static int pclose(FILE* /* fp */)
{
gmx_impl("Sorry no pipes...");
return 0;
}
- # endif /* !HAVE_PIPES && !defined(__native_client__) */
- #endif /* GMX_FAHCORE */
+ #endif /* !HAVE_PIPES && !defined(__native_client__) */
int gmx_ffclose(FILE* fp)
{
- #ifdef SKIP_FFOPS
- return fclose(fp);
- #else
t_pstack *ps, *tmp;
int ret = 0;
}
return ret;
- #endif
}
int gmx_truncate(const std::string& filename, gmx_off_t length)
{
- #if GMX_NATIVE_WINDOWS
+ #if GMX_NATIVE_WINDOWS && !GMX_FAHCORE
FILE* fp = fopen(filename.c_str(), "rb+");
if (fp == NULL)
{
FILE* gmx_ffopen(const std::string& file, const char* mode)
{
- #ifdef SKIP_FFOPS
- return fopen(file, mode);
- #else
FILE* ff = nullptr;
gmx_bool bRead;
int bs;
}
}
return ff;
- #endif
}
namespace gmx
#else
if (MoveFileEx(oldname, newname, MOVEFILE_REPLACE_EXISTING | MOVEFILE_WRITE_THROUGH))
{
+ # if GMX_FAHCORE
+ /* This just lets the F@H checksumming system know about the rename */
+ fcRename(oldname, newname);
+ # endif
return 0;
}
else
{
int rc = 0;
- #if GMX_FAHCORE
- /* the fahcore defines its own os-independent fsync */
- rc = fah_fsync(fp);
- #else /* GMX_FAHCORE */
{
int fn;
/* get the file number */
- # if HAVE_FILENO
+ #if HAVE_FILENO
fn = fileno(fp);
- # elif HAVE__FILENO
+ #elif HAVE__FILENO
fn = _fileno(fp);
- # else
+ #else
+ GMX_UNUSED_VALUE(fp);
fn = -1;
- # endif
+ #endif
/* do the actual fsync */
if (fn >= 0)
{
- # if HAVE_FSYNC
+ #if HAVE_FSYNC
rc = fsync(fn);
- # elif HAVE__COMMIT
+ #elif HAVE__COMMIT
rc = _commit(fn);
- # endif
+ #endif
}
}
- #endif /* GMX_FAHCORE */
/* We check for these error codes this way because POSIX requires them
to be defined, and using anything other than macros is unlikely: */
#endif
if (rc != 0)
{
- gmx_fatal(FARGS, "Cannot change directory to '%s'. Reason: %s", directory, strerror(errno));
+ auto message = gmx::formatString("Cannot change directory to '%s'. Reason: %s", directory,
+ strerror(errno));
+ GMX_THROW(gmx::FileIOError(message));
}
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2013,2014,2015,2016,2018 by the GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2018,2019,2020, by the GROMACS development team, led by
++ * Copyright (c) 2013,2014,2015,2016,2018, The GROMACS development team.
+ * Copyright (c) 2019,2020, 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.
}
else
{
- # if GMX_FAHCORE
- fah_MPI_Init(argc, argv);
- # else
- # if GMX_OPENMP
+ # if GMX_OPENMP
/* Formally we need to use MPI_Init_thread and ask for MPI_THREAD_FUNNELED
* level of thread support when using OpenMP. However, in practice we
* have never seen any problems with just using MPI_Init(), and some MPI
"the MPI library. Keep your fingers crossed.");
MPI_Init(argc, argv);
}
- # else
+ # else
MPI_Init(argc, argv);
- # endif
# endif
}
// Bump the counter to record this initialization event
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2013,2014,2015,2016,2017,2018,2019,2020, by the GROMACS development team, led by
+# Copyright (c) 2013,2014,2015,2016,2017 The GROMACS development team.
+# Copyright (c) 2018,2019,2020, 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.
energyreader.cpp
energycomparison.cpp
moduletest.cpp
- mdmodulenotification.cpp
+ simulatorcomparison.cpp
terminationhelper.cpp
trajectorycomparison.cpp
trajectoryreader.cpp
+ # pseudo-library for code for mdrun
+ $<TARGET_OBJECTS:mdrun_objlib>
)
+target_include_directories(mdrun_test_infrastructure SYSTEM PRIVATE ${PROJECT_SOURCE_DIR}/src/external)
# To avoid running into test timeouts, some end-to-end tests of mdrun
# functionality are split off. This can be rearranged in future as we
set(testname "MdrunOutputTests")
set(exename "mdrun-output-test")
-gmx_add_gtest_executable(
- ${exename}
- # files with code for tests
- compressed_x_output.cpp
- helpwriting.cpp
- outputfiles.cpp
- trajectory_writing.cpp
- # pseudo-library for code for mdrun
- $<TARGET_OBJECTS:mdrun_objlib>
+gmx_add_gtest_executable(${exename}
+ CPP_SOURCE_FILES
+ compressed_x_output.cpp
+ helpwriting.cpp
+ outputfiles.cpp
+ trajectory_writing.cpp
+ # pseudo-library for code for mdrun
+ $<TARGET_OBJECTS:mdrun_objlib>
)
target_link_libraries(${exename} PRIVATE mdrun_test_infrastructure)
gmx_register_gtest_test(${testname} ${exename} OPENMP_THREADS 2 INTEGRATION_TEST IGNORE_LEAKS)
set(testname "MdrunModulesTests")
set(exename "mdrun-modules-test")
-gmx_add_gtest_executable(
- ${exename}
- densityfittingmodule.cpp
- interactiveMD.cpp
- mimic.cpp
- # pseudo-library for code for mdrun
- $<TARGET_OBJECTS:mdrun_objlib>
+gmx_add_gtest_executable(${exename}
+ CPP_SOURCE_FILES
+ densityfittingmodule.cpp
+ interactiveMD.cpp
+ mimic.cpp
+ # pseudo-library for code for mdrun
+ $<TARGET_OBJECTS:mdrun_objlib>
)
target_link_libraries(${exename} PRIVATE mdrun_test_infrastructure)
gmx_register_gtest_test(${testname} ${exename} OPENMP_THREADS 2 INTEGRATION_TEST IGNORE_LEAKS)
set(testname "MdrunIOTests")
set(exename "mdrun-io-test")
-gmx_add_gtest_executable(
- ${exename}
- exactcontinuation.cpp
- grompp.cpp
- initialconstraints.cpp
- termination.cpp
- # pseudo-library for code for mdrun
- $<TARGET_OBJECTS:mdrun_objlib>
+gmx_add_gtest_executable(${exename}
+ CPP_SOURCE_FILES
+ exactcontinuation.cpp
+ grompp.cpp
+ initialconstraints.cpp
+ termination.cpp
+ # pseudo-library for code for mdrun
+ $<TARGET_OBJECTS:mdrun_objlib>
)
target_link_libraries(${exename} PRIVATE mdrun_test_infrastructure)
gmx_register_gtest_test(${testname} ${exename} OPENMP_THREADS 2 INTEGRATION_TEST IGNORE_LEAKS)
++# To avoid running into test timeouts, some end-to-end tests of mdrun
++# functionality are split off. This can be rearranged in future as we
++# see fit.
set(testname "MdrunTests")
set(exename "mdrun-test")
-gmx_add_gtest_executable(
- ${exename}
- dispersion_correction.cpp
- orires.cpp
- pmetest.cpp
- simulator.cpp
- swapcoords.cpp
- tabulated_bonded_interactions.cpp
- # pseudo-library for code for mdrun
- $<TARGET_OBJECTS:mdrun_objlib>
+gmx_add_gtest_executable(${exename}
+ CPP_SOURCE_FILES
+ ewaldsurfaceterm.cpp
+ multiple_time_stepping.cpp
+ orires.cpp
+ simulator.cpp
+ swapcoords.cpp
+ tabulated_bonded_interactions.cpp
+ # pseudo-library for code for mdrun
+ $<TARGET_OBJECTS:mdrun_objlib>
+ )
+target_link_libraries(${exename} PRIVATE mdrun_test_infrastructure)
+gmx_register_gtest_test(${testname} ${exename} OPENMP_THREADS 2 INTEGRATION_TEST IGNORE_LEAKS)
+
+
+set(testname "MdrunPmeTests")
+set(exename "mdrun-pme-test")
+
+gmx_add_gtest_executable(${exename}
+ CPP_SOURCE_FILES
+ pmetest.cpp
+ # pseudo-library for code for mdrun
+ $<TARGET_OBJECTS:mdrun_objlib>
)
target_link_libraries(${exename} PRIVATE mdrun_test_infrastructure)
-gmx_register_gtest_test(${testname} ${exename} OPENMP_THREADS 2 INTEGRATION_TEST)
+gmx_register_gtest_test(${testname} ${exename} OPENMP_THREADS 2 INTEGRATION_TEST IGNORE_LEAKS)
+
set(testname "MdrunNonIntegratorTests")
set(exename "mdrun-non-integrator-test")
-gmx_add_gtest_executable(
- ${exename}
- # files with code for tests
- minimize.cpp
- nonbonded_bench.cpp
- normalmodes.cpp
- rerun.cpp
- simple_mdrun.cpp
- # pseudo-library for code for mdrun
- $<TARGET_OBJECTS:mdrun_objlib>
- )
+gmx_add_gtest_executable(${exename}
+ CPP_SOURCE_FILES
+ # files with code for tests
+ minimize.cpp
+ nonbonded_bench.cpp
+ normalmodes.cpp
+ rerun.cpp
+ simple_mdrun.cpp
+ # pseudo-library for code for mdrun
+ $<TARGET_OBJECTS:mdrun_objlib>
+ )
target_link_libraries(${exename} PRIVATE mdrun_test_infrastructure)
-gmx_register_gtest_test(${testname} ${exename} OPENMP_THREADS 2 INTEGRATION_TEST)
+gmx_register_gtest_test(${testname} ${exename} OPENMP_THREADS 2 INTEGRATION_TEST IGNORE_LEAKS)
# TPI does not support OpenMP, so we need a separate test binary
set(testname "MdrunTpiTests")
set(exename "mdrun-tpi-test")
-gmx_add_gtest_executable(
- ${exename}
- # files with code for tests
- tpitest.cpp
- # pseudo-library for code for mdrun
- $<TARGET_OBJECTS:mdrun_objlib>
- )
+gmx_add_gtest_executable(${exename}
+ CPP_SOURCE_FILES
+ # files with code for tests
+ tpitest.cpp
+ # pseudo-library for code for mdrun
+ $<TARGET_OBJECTS:mdrun_objlib>
+ )
target_link_libraries(${exename} PRIVATE mdrun_test_infrastructure)
-gmx_register_gtest_test(${testname} ${exename} INTEGRATION_TEST)
+gmx_register_gtest_test(${testname} ${exename} INTEGRATION_TEST IGNORE_LEAKS)
# Tests that only make sense to run with multiple ranks and/or real
# MPI are implemented here.
set(testname "MdrunMpiTests")
set(exename "mdrun-mpi-test")
-gmx_add_gtest_executable(
- ${exename} MPI
- # files with code for tests
- domain_decomposition.cpp
- minimize.cpp
- mimic.cpp
- multisim.cpp
- multisimtest.cpp
- pmetest.cpp
- replicaexchange.cpp
- # pseudo-library for code for mdrun
- $<TARGET_OBJECTS:mdrun_objlib>
- )
+gmx_add_gtest_executable(${exename} MPI
+ CPP_SOURCE_FILES
+ # files with code for tests
+ domain_decomposition.cpp
+ minimize.cpp
+ mimic.cpp
+ multisim.cpp
+ multisimtest.cpp
+ replicaexchange.cpp
+ pmetest.cpp
+ # pseudo-library for code for mdrun
+ $<TARGET_OBJECTS:mdrun_objlib>
+ )
target_link_libraries(${exename} PRIVATE mdrun_test_infrastructure)
-gmx_register_gtest_test(${testname} ${exename} MPI_RANKS 2 OPENMP_THREADS 2 INTEGRATION_TEST)
+gmx_register_gtest_test(${testname} ${exename} MPI_RANKS 2 OPENMP_THREADS 2 INTEGRATION_TEST IGNORE_LEAKS)
+
+# Tests that only make sense to run with multiple ranks and/or real
+# MPI are implemented here. Special case for slow PME tests
+set(testname "MdrunMpiPmeTests")
+set(exename "mdrun-mpi-pme-test")
+
+gmx_add_gtest_executable(${exename} MPI
+ CPP_SOURCE_FILES
+ # files with code for tests
+ pmetest.cpp
+ # pseudo-library for code for mdrun
+ $<TARGET_OBJECTS:mdrun_objlib>
+ )
+target_link_libraries(${exename} PRIVATE mdrun_test_infrastructure)
+gmx_register_gtest_test(${testname} ${exename} MPI_RANKS 2 OPENMP_THREADS 2 INTEGRATION_TEST IGNORE_LEAKS)
# Slow-running tests that target testing multiple-rank coordination behaviors
set(exename "mdrun-mpi-coordination-test")
-gmx_add_gtest_executable(
- ${exename} MPI
- # files with code for tests
- periodicactions.cpp
- # pseudo-library for code for mdrun
- $<TARGET_OBJECTS:mdrun_objlib>
- )
+gmx_add_gtest_executable(${exename} MPI
+ CPP_SOURCE_FILES
+ # files with code for tests
+ periodicactions.cpp
+ # pseudo-library for code for mdrun
+ $<TARGET_OBJECTS:mdrun_objlib>
+ )
target_link_libraries(${exename} PRIVATE mdrun_test_infrastructure)
# These tests are extremely slow without optimization or OpenMP, so only run them for
# with OpenMP enabled.
if (CMAKE_BUILD_TYPE MATCHES "Rel" AND GMX_OPENMP)
set(testname "MdrunMpiCoordinationTestsOneRank")
- gmx_register_gtest_test(${testname} ${exename} MPI_RANKS 1 SLOW_TEST)
+ gmx_register_gtest_test(${testname} ${exename} MPI_RANKS 1 SLOW_TEST IGNORE_LEAKS)
set(testname "MdrunMpiCoordinationTestsTwoRanks")
- gmx_register_gtest_test(${testname} ${exename} MPI_RANKS 2 SLOW_TEST)
+ gmx_register_gtest_test(${testname} ${exename} MPI_RANKS 2 SLOW_TEST IGNORE_LEAKS)
endif()
+
+# Keeping the FEP tests separate for now to be able to judge runtime more easily
+# Can be included in mdrun tests later
+set(testname "MdrunFEPTests")
+set(exename "mdrunfep-test")
+
+gmx_add_gtest_executable(${exename}
+ CPP_SOURCE_FILES
+ # files with code for tests
+ freeenergy.cpp
+ # pseudo-library for code for mdrun
+ $<TARGET_OBJECTS:mdrun_objlib>
+)
+target_link_libraries(${exename} PRIVATE mdrun_test_infrastructure)
+gmx_register_gtest_test(${testname} ${exename} OPENMP_THREADS 2 INTEGRATION_TEST IGNORE_LEAKS)
#
# This file is part of the GROMACS molecular simulation package.
#
- # Copyright (c) 2012,2013,2014,2015,2016 by the GROMACS development team.
+ # Copyright (c) 2012,2013,2014,2015,2016, The GROMACS development team.
# Copyright (c) 2017,2018,2019,2020, 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
# End copied from regression tests.
#
- if (NOT PYTHONINTERP_FOUND)
+ if (NOT Python3_Interpreter_FOUND)
message(FATAL_ERROR
"Python not found. Physical validation requires python. \
- Install python, set PYTHON_EXECUTABLE to a valid python location, \
+ Install python, set Python3_ROOT_DIR or PYTHON_EXECUTABLE to a valid location, \
or set GMX_PHYSICAL_VALIDATION=OFF to disable the physical validation tests.")
endif()
#
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff