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Merge branch 'develop' of github.com:lammps/lammps into local-composition

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This commit is contained in:
Stan Gerald Moore
2023-08-04 13:23:53 -06:00
parent 3657ed6beb 4851f30634
commit 376b83df52
1477 changed files with 64329 additions and 90451 deletions
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2
.github/CONTRIBUTING.md vendored
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@ -1,6 +1,6 @@
# Contributing to LAMMPS via GitHub
Thank your for considering to contribute to the LAMMPS software project.
Thank you for considering to contribute to the LAMMPS software project.
The following is a set of guidelines as well as explanations of policies and work flows for contributing to the LAMMPS molecular dynamics software project. These guidelines focus on submitting issues or pull requests on the LAMMPS GitHub project.

3
.gitignore vendored
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@ -57,3 +57,6 @@ out/x86
out/x64
src/Makefile.package-e
src/Makefile.package.settings-e
/cmake/build/x64-Debug-Clang
/install/x64-GUI-MSVC
/install

31
cmake/CMakeLists.txt
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@ -136,15 +136,15 @@ if((PKG_KOKKOS) AND (Kokkos_ENABLE_CUDA) AND NOT (CMAKE_CXX_COMPILER_ID STREQUAL
set(CMAKE_TUNE_DEFAULT "${CMAKE_TUNE_DEFAULT} -Xcudafe --diag_suppress=unrecognized_pragma")
endif()
# we require C++11 without extensions. Kokkos requires at least C++14 (currently)
# we require C++11 without extensions. Kokkos requires at least C++17 (currently)
if(NOT CMAKE_CXX_STANDARD)
set(CMAKE_CXX_STANDARD 11)
endif()
if(CMAKE_CXX_STANDARD LESS 11)
message(FATAL_ERROR "C++ standard must be set to at least 11")
endif()
if(PKG_KOKKOS AND (CMAKE_CXX_STANDARD LESS 14))
set(CMAKE_CXX_STANDARD 14)
if(PKG_KOKKOS AND (CMAKE_CXX_STANDARD LESS 17))
set(CMAKE_CXX_STANDARD 17)
endif()
set(CMAKE_CXX_STANDARD_REQUIRED ON)
set(CMAKE_CXX_EXTENSIONS OFF CACHE BOOL "Use compiler extensions")
@ -192,6 +192,7 @@ option(BUILD_SHARED_LIBS "Build shared library" OFF)
option(CMAKE_POSITION_INDEPENDENT_CODE "Create object compatible with shared libraries" ON)
option(BUILD_TOOLS "Build and install LAMMPS tools (msi2lmp, binary2txt, chain)" OFF)
option(BUILD_LAMMPS_SHELL "Build and install the LAMMPS shell" OFF)
option(BUILD_LAMMPS_GUI "Build and install the LAMMPS GUI" OFF)
# Support using clang-tidy for C++ files with selected options
set(ENABLE_CLANG_TIDY OFF CACHE BOOL "Include clang-tidy processing when compiling")
@ -278,7 +279,6 @@ set(STANDARD_PACKAGES
MOLECULE
MOLFILE
MPIIO
MSCG
NETCDF
ORIENT
PERI
@ -384,11 +384,6 @@ if(NOT ${LAMMPS_MEMALIGN} STREQUAL "0")
target_compile_definitions(lammps PRIVATE -DLAMMPS_MEMALIGN=${LAMMPS_MEMALIGN})
endif()
option(LAMMPS_EXCEPTIONS "enable the use of C++ exceptions for error messages (useful for library interface)" ${ENABLE_TESTING})
if(LAMMPS_EXCEPTIONS)
target_compile_definitions(lammps PUBLIC -DLAMMPS_EXCEPTIONS)
endif()
# "hard" dependencies between packages resulting
# in an error instead of skipping over files
pkg_depends(ML-IAP ML-SNAP)
@ -440,7 +435,7 @@ if(BUILD_OMP)
target_link_libraries(lmp PRIVATE OpenMP::OpenMP_CXX)
endif()
if(PKG_MSCG OR PKG_ATC OR PKG_AWPMD OR PKG_ML-QUIP OR PKG_ML-POD OR PKG_ELECTRODE OR BUILD_TOOLS)
if(PKG_ATC OR PKG_AWPMD OR PKG_ML-QUIP OR PKG_ML-POD OR PKG_ELECTRODE OR BUILD_TOOLS)
enable_language(C)
if (NOT USE_INTERNAL_LINALG)
find_package(LAPACK)
@ -520,7 +515,7 @@ else()
endif()
foreach(PKG_WITH_INCL KSPACE PYTHON ML-IAP VORONOI COLVARS ML-HDNNP MDI MOLFILE NETCDF
PLUMED QMMM ML-QUIP SCAFACOS MACHDYN VTK KIM MSCG COMPRESS ML-PACE LEPTON)
PLUMED QMMM ML-QUIP SCAFACOS MACHDYN VTK KIM COMPRESS ML-PACE LEPTON)
if(PKG_${PKG_WITH_INCL})
include(Packages/${PKG_WITH_INCL})
endif()
@ -795,9 +790,11 @@ include(Tools)
include(Documentation)
###############################################################################
# Install potential and force field files in data directory
# Install bench, potential and force field files in data directory
###############################################################################
set(LAMMPS_INSTALL_DATADIR ${CMAKE_INSTALL_FULL_DATADIR}/lammps)
set(LAMMPS_INSTALL_DATADIR ${CMAKE_INSTALL_DATADIR}/lammps)
install(DIRECTORY ${LAMMPS_DIR}/bench DESTINATION ${LAMMPS_INSTALL_DATADIR})
install(DIRECTORY ${LAMMPS_POTENTIALS_DIR} DESTINATION ${LAMMPS_INSTALL_DATADIR})
if(BUILD_TOOLS)
install(DIRECTORY ${LAMMPS_TOOLS_DIR}/msi2lmp/frc_files DESTINATION ${LAMMPS_INSTALL_DATADIR})
@ -1025,6 +1022,14 @@ endif()
if(BUILD_LAMMPS_SHELL)
message(STATUS "<<< Building LAMMPS Shell >>>")
endif()
if(BUILD_LAMMPS_GUI)
message(STATUS "<<< Building LAMMPS GUI >>>")
if(LAMMPS_GUI_USE_PLUGIN)
message(STATUS "Loading LAMMPS library as plugin at run time")
else()
message(STATUS "Linking LAMMPS library at compile time")
endif()
endif()
if(ENABLE_TESTING)
message(STATUS "<<< Building Unit Tests >>>")
if(ENABLE_COVERAGE)

53
cmake/CMakeSettings.json
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@ -63,6 +63,11 @@
"name": "ENABLE_TESTING",
"value": "True",
"type": "BOOL"
},
{
"name": "BUILD_LAMMPS_GUI",
"value": "False",
"type": "BOOL"
}
]
},
@ -303,6 +308,54 @@
"type": "STRING"
}
]
},
{
"name": "x64-GUI-MSVC",
"generator": "Ninja",
"configurationType": "Release",
"buildRoot": "${workspaceRoot}\\build\\${name}",
"installRoot": "${workspaceRoot}\\install\\${name}",
"cmakeCommandArgs": "-C ${workspaceRoot}\\cmake\\presets\\windows.cmake -D QT_DIR=C:\\Qt\\5.15.2\\msvc2019_64\\lib\\cmake\\Qt5 -D Qt5_DIR=C:\\Qt\\5.15.2\\msvc2019_64\\lib\\cmake\\Qt5",
"buildCommandArgs": "",
"ctestCommandArgs": "-V",
"inheritEnvironments": [ "msvc_x64_x64" ],
"variables": [
{
"name": "BUILD_SHARED_LIBS",
"value": "True",
"type": "BOOL"
},
{
"name": "BUILD_TOOLS",
"value": "True",
"type": "BOOL"
},
{
"name": "LAMMPS_EXCEPTIONS",
"value": "True",
"type": "BOOL"
},
{
"name": "ENABLE_TESTING",
"value": "False",
"type": "BOOL"
},
{
"name": "BUILD_MPI",
"value": "False",
"type": "BOOL"
},
{
"name": "WITH_PNG",
"value": "False",
"type": "BOOL"
},
{
"name": "BUILD_LAMMPS_GUI",
"value": "True",
"type": "BOOL"
}
]
}
]
}

4
cmake/Modules/LAMMPSInterfacePlugin.cmake
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@ -28,9 +28,7 @@ if(MSVC)
add_compile_options(/Zc:__cplusplus)
add_compile_options(/wd4244)
add_compile_options(/wd4267)
if(LAMMPS_EXCEPTIONS)
add_compile_options(/EHsc)
endif()
add_compile_options(/EHsc)
endif()
add_compile_definitions(_CRT_SECURE_NO_WARNINGS)
endif()

104
cmake/Modules/Packages/GPU.cmake
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@ -64,6 +64,8 @@ if(GPU_API STREQUAL "CUDA")
endif()
set(GPU_CUDA_MPS_FLAGS "-DCUDA_MPS_SUPPORT")
endif()
option(CUDA_BUILD_MULTIARCH "Enable building CUDA kernels for all supported GPU architectures" ON)
mark_as_advanced(GPU_BUILD_MULTIARCH)
set(GPU_ARCH "sm_50" CACHE STRING "LAMMPS GPU CUDA SM primary architecture (e.g. sm_60)")
@ -93,56 +95,58 @@ if(GPU_API STREQUAL "CUDA")
# --arch translates directly instead of JIT, so this should be for the preferred or most common architecture
set(GPU_CUDA_GENCODE "-arch=${GPU_ARCH}")
# apply the following to build "fat" CUDA binaries only for known CUDA toolkits since version 8.0
# only the Kepler achitecture and beyond is supported
# comparison chart according to: https://en.wikipedia.org/wiki/CUDA#GPUs_supported
if(CUDA_VERSION VERSION_LESS 8.0)
message(FATAL_ERROR "CUDA Toolkit version 8.0 or later is required")
elseif(CUDA_VERSION VERSION_GREATER_EQUAL "13.0")
message(WARNING "Untested CUDA Toolkit version ${CUDA_VERSION}. Use at your own risk")
set(GPU_CUDA_GENCODE "-arch=all")
elseif(CUDA_VERSION VERSION_GREATER_EQUAL "12.0")
set(GPU_CUDA_GENCODE "-arch=all")
else()
# Kepler (GPU Arch 3.0) is supported by CUDA 5 to CUDA 10.2
if((CUDA_VERSION VERSION_GREATER_EQUAL "5.0") AND (CUDA_VERSION VERSION_LESS "11.0"))
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_30,code=[sm_30,compute_30] ")
endif()
# Kepler (GPU Arch 3.5) is supported by CUDA 5 to CUDA 11
if((CUDA_VERSION VERSION_GREATER_EQUAL "5.0") AND (CUDA_VERSION VERSION_LESS "12.0"))
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_35,code=[sm_35,compute_35]")
endif()
# Maxwell (GPU Arch 5.x) is supported by CUDA 6 and later
if(CUDA_VERSION VERSION_GREATER_EQUAL "6.0")
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_50,code=[sm_50,compute_50] -gencode arch=compute_52,code=[sm_52,compute_52]")
endif()
# Pascal (GPU Arch 6.x) is supported by CUDA 8 and later
if(CUDA_VERSION VERSION_GREATER_EQUAL "8.0")
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_60,code=[sm_60,compute_60] -gencode arch=compute_61,code=[sm_61,compute_61]")
endif()
# Volta (GPU Arch 7.0) is supported by CUDA 9 and later
if(CUDA_VERSION VERSION_GREATER_EQUAL "9.0")
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_70,code=[sm_70,compute_70]")
endif()
# Turing (GPU Arch 7.5) is supported by CUDA 10 and later
if(CUDA_VERSION VERSION_GREATER_EQUAL "10.0")
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_75,code=[sm_75,compute_75]")
endif()
# Ampere (GPU Arch 8.0) is supported by CUDA 11 and later
if(CUDA_VERSION VERSION_GREATER_EQUAL "11.0")
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_80,code=[sm_80,compute_80]")
endif()
# Ampere (GPU Arch 8.6) is supported by CUDA 11.1 and later
if(CUDA_VERSION VERSION_GREATER_EQUAL "11.1")
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_86,code=[sm_86,compute_86]")
endif()
# Lovelace (GPU Arch 8.9) is supported by CUDA 11.8 and later
if(CUDA_VERSION VERSION_GREATER_EQUAL "11.8")
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_90,code=[sm_90,compute_90]")
endif()
# Hopper (GPU Arch 9.0) is supported by CUDA 12.0 and later
if(CUDA_VERSION VERSION_GREATER_EQUAL "12.0")
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_90,code=[sm_90,compute_90]")
if(CUDA_BUILD_MULTIARCH)
# apply the following to build "fat" CUDA binaries only for known CUDA toolkits since version 8.0
# only the Kepler achitecture and beyond is supported
# comparison chart according to: https://en.wikipedia.org/wiki/CUDA#GPUs_supported
if(CUDA_VERSION VERSION_LESS 8.0)
message(FATAL_ERROR "CUDA Toolkit version 8.0 or later is required")
elseif(CUDA_VERSION VERSION_GREATER_EQUAL "13.0")
message(WARNING "Untested CUDA Toolkit version ${CUDA_VERSION}. Use at your own risk")
set(GPU_CUDA_GENCODE "-arch=all")
elseif(CUDA_VERSION VERSION_GREATER_EQUAL "12.0")
set(GPU_CUDA_GENCODE "-arch=all")
else()
# Kepler (GPU Arch 3.0) is supported by CUDA 5 to CUDA 10.2
if((CUDA_VERSION VERSION_GREATER_EQUAL "5.0") AND (CUDA_VERSION VERSION_LESS "11.0"))
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_30,code=[sm_30,compute_30] ")
endif()
# Kepler (GPU Arch 3.5) is supported by CUDA 5 to CUDA 11
if((CUDA_VERSION VERSION_GREATER_EQUAL "5.0") AND (CUDA_VERSION VERSION_LESS "12.0"))
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_35,code=[sm_35,compute_35]")
endif()
# Maxwell (GPU Arch 5.x) is supported by CUDA 6 and later
if(CUDA_VERSION VERSION_GREATER_EQUAL "6.0")
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_50,code=[sm_50,compute_50] -gencode arch=compute_52,code=[sm_52,compute_52]")
endif()
# Pascal (GPU Arch 6.x) is supported by CUDA 8 and later
if(CUDA_VERSION VERSION_GREATER_EQUAL "8.0")
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_60,code=[sm_60,compute_60] -gencode arch=compute_61,code=[sm_61,compute_61]")
endif()
# Volta (GPU Arch 7.0) is supported by CUDA 9 and later
if(CUDA_VERSION VERSION_GREATER_EQUAL "9.0")
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_70,code=[sm_70,compute_70]")
endif()
# Turing (GPU Arch 7.5) is supported by CUDA 10 and later
if(CUDA_VERSION VERSION_GREATER_EQUAL "10.0")
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_75,code=[sm_75,compute_75]")
endif()
# Ampere (GPU Arch 8.0) is supported by CUDA 11 and later
if(CUDA_VERSION VERSION_GREATER_EQUAL "11.0")
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_80,code=[sm_80,compute_80]")
endif()
# Ampere (GPU Arch 8.6) is supported by CUDA 11.1 and later
if(CUDA_VERSION VERSION_GREATER_EQUAL "11.1")
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_86,code=[sm_86,compute_86]")
endif()
# Lovelace (GPU Arch 8.9) is supported by CUDA 11.8 and later
if(CUDA_VERSION VERSION_GREATER_EQUAL "11.8")
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_90,code=[sm_90,compute_90]")
endif()
# Hopper (GPU Arch 9.0) is supported by CUDA 12.0 and later
if(CUDA_VERSION VERSION_GREATER_EQUAL "12.0")
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_90,code=[sm_90,compute_90]")
endif()
endif()
endif()

13
cmake/Modules/Packages/KOKKOS.cmake
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@ -1,7 +1,8 @@
########################################################################
# As of version 3.3.0 Kokkos requires C++14
if(CMAKE_CXX_STANDARD LESS 14)
message(FATAL_ERROR "The KOKKOS package requires the C++ standard to be set to at least C++14")
# As of version 4.0.0 Kokkos requires C++17
if(CMAKE_CXX_STANDARD LESS 17)
message(FATAL_ERROR "The KOKKOS package requires the C++ standard to
be set to at least C++17")
endif()
########################################################################
@ -49,8 +50,8 @@ if(DOWNLOAD_KOKKOS)
list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_CXX_EXTENSIONS=${CMAKE_CXX_EXTENSIONS}")
list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}")
include(ExternalProject)
set(KOKKOS_URL "https://github.com/kokkos/kokkos/archive/3.7.02.tar.gz" CACHE STRING "URL for KOKKOS tarball")
set(KOKKOS_MD5 "34d7860d548c06a4040236d959c9f99a" CACHE STRING "MD5 checksum of KOKKOS tarball")
set(KOKKOS_URL "https://github.com/kokkos/kokkos/archive/4.1.00.tar.gz" CACHE STRING "URL for KOKKOS tarball")
set(KOKKOS_MD5 "a5f096bd8ad01b97fdc7a32583b17a33" CACHE STRING "MD5 checksum of KOKKOS tarball")
mark_as_advanced(KOKKOS_URL)
mark_as_advanced(KOKKOS_MD5)
GetFallbackURL(KOKKOS_URL KOKKOS_FALLBACK)
@ -75,7 +76,7 @@ if(DOWNLOAD_KOKKOS)
add_dependencies(LAMMPS::KOKKOSCORE kokkos_build)
add_dependencies(LAMMPS::KOKKOSCONTAINERS kokkos_build)
elseif(EXTERNAL_KOKKOS)
find_package(Kokkos 3.7.02 REQUIRED CONFIG)
find_package(Kokkos 4.1.00 REQUIRED CONFIG)
target_link_libraries(lammps PRIVATE Kokkos::kokkos)
else()
set(LAMMPS_LIB_KOKKOS_SRC_DIR ${LAMMPS_LIB_SOURCE_DIR}/kokkos)

28
cmake/Modules/Packages/MSCG.cmake
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@ -1,28 +0,0 @@
find_package(GSL REQUIRED)
find_package(MSCG QUIET)
if(MSGC_FOUND)
set(DOWNLOAD_MSCG_DEFAULT OFF)
else()
set(DOWNLOAD_MSCG_DEFAULT ON)
endif()
option(DOWNLOAD_MSCG "Download MSCG library instead of using an already installed one)" ${DOWNLOAD_MSCG_DEFAULT})
if(DOWNLOAD_MSCG)
set(MSCG_URL "https://github.com/uchicago-voth/MSCG-release/archive/491270a73539e3f6951e76f7dbe84e258b3ebb45.tar.gz" CACHE STRING "URL for MSCG tarball")
set(MSCG_MD5 "7ea50748fba5c3a372e0266bd31d2f11" CACHE STRING "MD5 checksum of MSCG tarball")
mark_as_advanced(MSCG_URL)
mark_as_advanced(MSCG_MD5)
include(ExternalCMakeProject)
ExternalCMakeProject(mscg ${MSCG_URL} ${MSCG_MD5} MSCG-release src/CMake "")
# set include and link library
target_include_directories(lammps PRIVATE "${CMAKE_BINARY_DIR}/_deps/mscg-src/src")
target_link_libraries(lammps PRIVATE mscg)
else()
find_package(MSCG)
if(NOT MSCG_FOUND)
message(FATAL_ERROR "MSCG not found, help CMake to find it by setting MSCG_LIBRARY and MSCG_INCLUDE_DIR, or set DOWNLOAD_MSCG=ON to download it")
endif()
target_link_libraries(lammps PRIVATE MSCG::MSCG)
endif()
target_link_libraries(lammps PRIVATE GSL::gsl ${LAPACK_LIBRARIES})

13
cmake/Modules/Tools.cmake
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@ -37,12 +37,13 @@ if(BUILD_TOOLS)
add_subdirectory(${LAMMPS_TOOLS_DIR}/phonon ${CMAKE_BINARY_DIR}/phana_build)
endif()
find_package(PkgConfig QUIET)
if(BUILD_LAMMPS_SHELL)
if(NOT PkgConfig_FOUND)
message(FATAL_ERROR "Must have pkg-config installed for building LAMMPS shell")
endif()
find_package(PkgConfig REQUIRED)
pkg_check_modules(READLINE IMPORTED_TARGET REQUIRED readline)
if(NOT LAMMPS_EXCEPTIONS)
message(WARNING "The LAMMPS shell needs LAMMPS_EXCEPTIONS enabled for full functionality")
endif()
# include resource compiler to embed icons into the executable on Windows
if(CMAKE_SYSTEM_NAME STREQUAL "Windows")
@ -67,4 +68,8 @@ if(BUILD_LAMMPS_SHELL)
install(FILES ${LAMMPS_TOOLS_DIR}/lammps-shell/lammps-shell.desktop DESTINATION ${CMAKE_INSTALL_DATAROOTDIR}/applications/)
endif()
if(BUILD_LAMMPS_GUI)
get_filename_component(LAMMPS_GUI_DIR ${LAMMPS_SOURCE_DIR}/../tools/lammps-gui ABSOLUTE)
get_filename_component(LAMMPS_GUI_BIN ${CMAKE_BINARY_DIR}/lammps-gui-build ABSOLUTE)
add_subdirectory(${LAMMPS_GUI_DIR} ${LAMMPS_GUI_BIN})
endif()

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34
cmake/packaging/MacOSXBundleInfo.plist.in Normal file
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@ -0,0 +1,34 @@
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE plist PUBLIC "-//Apple Computer//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd">
<plist version="1.0">
<dict>
<key>CFBundleDevelopmentRegion</key>
<string>en-US</string>
<key>CFBundleExecutable</key>
<string>${MACOSX_BUNDLE_EXECUTABLE_NAME}</string>
<key>CFBundleDisplayName</key>
<string>The LAMMPS Molecular Dynamics Software</string>
<key>CFBundleIconFile</key>
<string>lammps</string>
<key>CFBundleIdentifier</key>
<string>org.lammps.gui</string>
<key>CFBundleInfoDictionaryVersion</key>
<string>6.0</string>
<key>CFBundleLongVersionString</key>
<string>${MACOSX_BUNDLE_LONG_VERSION_STRING}</string>
<key>CFBundleName</key>
<string>LAMMPS</string>
<key>CFBundlePackageType</key>
<string>APPL</string>
<key>CFBundleShortVersionString</key>
<string>${MACOSX_BUNDLE_SHORT_VERSION_STRING}</string>
<key>CFBundleSignature</key>
<string>????</string>
<key>CFBundleVersion</key>
<string>${MACOSX_BUNDLE_BUNDLE_VERSION}</string>
<key>CSResourcesFileMapped</key>
<true/>
<key>NSHumanReadableCopyright</key>
<string>${MACOSX_BUNDLE_COPYRIGHT}</string>
</dict>
</plist>

69
cmake/packaging/README.macos Normal file
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@ -0,0 +1,69 @@
LAMMPS and LAMMPS GUI universal binaries for macOS (arm64/x86_64)
=================================================================
This package provides universal binaries of LAMMPS and LAMMPS GUI that should
run on macOS systems running running macOS version 11 (Big Sur) or newer. Note
the binaries are compiled without MPI support and contain a compatible subset
of the available packages.
The following individual commands are included:
binary2txt lammps-gui lmp msi2lmp phana stl_bin2txt
After copying the lammps-gui folder into your Applications folder, please follow
these steps:
1. Open the Terminal app
2. Type the following command and press ENTER:
open ~/.zprofile
This will open a text editor for modifying the .zprofile file in your home
directory.
3. Add the following lines to the end of the file, save it, and close the editor
LAMMPS_INSTALL_DIR=/Applications/LAMMPS.app/Contents
LAMMPS_POTENTIALS=${LAMMPS_INSTALL_DIR}/share/lammps/potentials
LAMMPS_BENCH_DIR=${LAMMPS_INSTALL_DIR}/share/lammps/bench
MSI2LMP_LIBRARY=${LAMMPS_INSTALL_DIR}/share/lammps/frc_files
PATH=${LAMMPS_INSTALL_DIR}/bin:$PATH
export LAMMPS_POTENTIALS LAMMPS_BENCH_DIR PATH
4. In your existing terminal, type the following command make the settings active
source ~/.zprofile
Note, you don't have to type this in new terminals, since they will apply
the changes from .zprofile automatically.
Note: the above assumes you use the default shell (zsh) that comes with
MacOS. If you customized MacOS to use a different shell, you'll need to modify
that shell's init file (.cshrc, .bashrc, etc.) instead with appropiate commands
to modify the same environment variables.
5. Try running LAMMPS (which might fail, see step 7)
lmp -in ${LAMMPS_BENCH_DIR}/in.lj
6. Try running the LAMMPS GUI
lammps-gui ${LAMMPS_BENCH_DIR}/in.rhodo
Depending on the size and resolution of your screen, the fonts may
be too small to read. This can be adjusted by setting the environment
variable QT_FONT_DPI. The default value would be 72, so to increase
the fonts by a third one can add to the .zprofile file the line
export QT_FONT_DPI=96
and reload as shown above.
7. Give permission to execute the commands (lmp, lammps-gui, msi2lmp, binary2txt, phana, stl_bin2txt)
MacOS will likely block the initial run of the executables, since they
were downloaded from the internet and are missing a known signature from an
identified developer. Go to "Settings" and search for "Security settings". It
should display a message that an executable like "lmp" was blocked. Press
"Open anyway", which might prompt you for your admin credentials. Afterwards
"lmp" and the other executables should work as expected.

77
cmake/packaging/build_linux_tgz.sh Executable file
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@ -0,0 +1,77 @@
#!/bin/bash
APP_NAME=lammps-gui
DESTDIR=${PWD}/../LAMMPS_GUI
echo "Delete old files, if they exist"
rm -rf ${DESTDIR} ../LAMMPS-Linux-amd64.tar.gz
echo "Create staging area for deployment and populate"
DESTDIR=${DESTDIR} cmake --install . --prefix "/"
echo "Remove debug info"
for s in ${DESTDIR}/bin/* ${DESTDIR}/lib/liblammps*
do \
test -f $s && strip --strip-debug $s
done
echo "Remove libc, gcc, and X11 related shared libs"
rm -f ${DESTDIR}/lib/ld*.so ${DESTDIR}/lib/ld*.so.[0-9]
rm -f ${DESTDIR}/lib/lib{c,dl,rt,m,pthread}.so.?
rm -f ${DESTDIR}/lib/lib{c,dl,rt,m,pthread}-[0-9].[0-9]*.so
rm -f ${DESTDIR}/lib/libX* ${DESTDIR}/lib/libxcb*
rm -f ${DESTDIR}/lib/libgcc_s*
rm -f ${DESTDIR}/lib/libstdc++*
# get qt dir
QTDIR=$(ldd ${DESTDIR}/bin/lammps-gui | grep libQt5Core | sed -e 's/^.*=> *//' -e 's/libQt5Core.so.*$/qt5/')
cat > ${DESTDIR}/bin/qt.conf <<EOF
[Paths]
Plugins = ../qt5plugins
EOF
# platform plugin
mkdir -p ${DESTDIR}/qt5plugins/platforms
cp ${QTDIR}/plugins/platforms/libqxcb.so ${DESTDIR}/qt5plugins/platforms
# get platform plugin dependencies
QTDEPS=$(LD_LIBRARY_PATH=${DESTDIR}/lib ldd ${QTDIR}/plugins/platforms/libqxcb.so | grep -v ${DESTDIR} | grep libQt5 | sed -e 's/^.*=> *//' -e 's/\(libQt5.*.so.*\) .*$/\1/')
for dep in ${QTDEPS}
do \
cp ${dep} ${DESTDIR}/lib
done
echo "Add additional plugins for Qt"
for dir in styles imageformats
do \
cp -r ${QTDIR}/plugins/${dir} ${DESTDIR}/qt5plugins/
done
# get imageplugin dependencies
for s in ${DESTDIR}/qt5plugins/imageformats/*.so
do \
QTDEPS=$(LD_LIBRARY_PATH=${DESTDIR}/lib ldd $s | grep -v ${DESTDIR} | grep -E '(libQt5|jpeg)' | sed -e 's/^.*=> *//' -e 's/\(lib.*.so.*\) .*$/\1/')
for dep in ${QTDEPS}
do \
cp ${dep} ${DESTDIR}/lib
done
done
echo "Set up wrapper script"
MYDIR=$(dirname "$0")
cp ${MYDIR}/linux_wrapper.sh ${DESTDIR}/bin
for s in ${DESTDIR}/bin/*
do \
EXE=$(basename $s)
test ${EXE} = linux_wrapper.sh && continue
test ${EXE} = qt.conf && continue
ln -s bin/linux_wrapper.sh ${DESTDIR}/${EXE}
done
pushd ..
tar -czvvf LAMMPS-Linux-amd64.tar.gz LAMMPS_GUI
popd
echo "Cleanup dir"
rm -r ${DESTDIR}
exit 0

111
cmake/packaging/build_macos_dmg.sh Executable file
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@ -0,0 +1,111 @@
#!/bin/bash
APP_NAME=lammps-gui
echo "Delete old files, if they exist"
rm -f ${APP_NAME}.dmg ${APP_NAME}-rw.dmg LAMMPS-macOS-multiarch.dmg
echo "Create initial dmg file with macdeployqt"
macdeployqt lammps-gui.app -dmg
echo "Create writable dmg file"
hdiutil convert ${APP_NAME}.dmg -format UDRW -o ${APP_NAME}-rw.dmg
echo "Mount writeable DMG file in read-write mode. Keep track of device and volume names"
DEVICE=$(hdiutil attach -readwrite -noverify ${APP_NAME}-rw.dmg | grep '^/dev/' | sed 1q | awk '{print $1}')
VOLUME=$(df | grep ${DEVICE} | sed -e 's/^.*\(\/Volumes\/\)/\1/')
sleep 2
echo "Create link to Application folder and move README and background image files"
pushd "${VOLUME}"
ln -s /Applications .
mv ${APP_NAME}.app/Contents/Resources/README.txt .
mkdir .background
mv ${APP_NAME}.app/Contents/Resources/LAMMPS_DMG_Background.png .background/background.png
mv ${APP_NAME}.app LAMMPS.app
cd LAMMPS.app/Contents
echo "Attach icons to LAMMPS console and GUI executables"
echo "read 'icns' (-16455) \"Resources/lammps.icns\";" > icon.rsrc
Rez -a icon.rsrc -o bin/lmp
SetFile -a C bin/lmp
Rez -a icon.rsrc -o MacOS/lammps-gui
SetFile -a C MacOS/lammps-gui
rm icon.rsrc
popd
echo 'Tell the Finder to resize the window, set the background,'
echo 'change the icon size, place the icons in the right position, etc.'
echo '
tell application "Finder"
tell disk "'${APP_NAME}'"
-- wait for the image to finish mounting
set open_attempts to 0
repeat while open_attempts < 4
try
open
delay 1
set open_attempts to 5
close
on error errStr number errorNumber
set open_attempts to open_attempts + 1
delay 10
end try
end repeat
delay 5
-- open the image the first time and save a .DS_Store
-- just the background and icon setup
open
set current view of container window to icon view
set theViewOptions to the icon view options of container window
set background picture of theViewOptions to file ".background:background.png"
set arrangement of theViewOptions to not arranged
set icon size of theViewOptions to 64
delay 5
close
-- next set up the position of the app and Applications symlink
-- plus hide all window decorations
open
update without registering applications
tell container window
set sidebar width to 0
set statusbar visible to false
set toolbar visible to false
set the bounds to { 100, 40, 868, 640 }
set position of item "'LAMMPS'.app" to { 190, 216 }
set position of item "Applications" to { 576, 216 }
set position of item "README.txt" to { 190, 400 }
end tell
update without registering applications
delay 5
close
-- one last open and close to check the results
open
delay 5
close
end tell
delay 1
end tell
' | osascript
sync
echo "Unmount modified disk image and convert to compressed read-only image"
hdiutil detach "${DEVICE}"
hdiutil convert "${APP_NAME}-rw.dmg" -format UDZO -o "LAMMPS-macOS-multiarch.dmg"
echo "Attach icon to .dmg file"
echo "read 'icns' (-16455) \"lammps-gui.app/Contents/Resources/lammps.icns\";" > icon.rsrc
Rez -a icon.rsrc -o LAMMPS-macOS-multiarch.dmg
SetFile -a C LAMMPS-macOS-multiarch.dmg
rm icon.rsrc
echo "Delete temporary disk images"
rm -f "${APP_NAME}-rw.dmg"
rm -f "${APP_NAME}.dmg"
exit 0

64
cmake/packaging/build_windows_cross_zip.sh Executable file
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@ -0,0 +1,64 @@
#!/bin/bash
APP_NAME=lammps-gui
DESTDIR=${PWD}/LAMMPS_GUI
SYSROOT="$1"
echo "Delete old files, if they exist"
rm -rvf ${DESTDIR}/LAMMPS_GUI ${DESTDIR}/LAMMPS-Win10-amd64.zip
echo "Create staging area for deployment and populate"
DESTDIR=${DESTDIR} cmake --install . --prefix "/"
# no static libs needed
rm -rvf ${DESTDIR}/lib
# but the LAMMPS lib
echo "Copying required DLL files"
for dll in $(objdump -p *.exe *.dll | sed -n -e '/DLL Name:/s/^.*DLL Name: *//p' | sort | uniq)
do \
doskip=0
for skip in ADVAPI32 CFGMGR32 GDI32 KERNEL32 MPR NETAPI32 PSAPI SHELL32 USER32 USERENV UxTheme VERSION WS2_32 WSOCK32 d3d11 dwmapi liblammps msvcrt_ole32
do \
test ${dll} = ${skip}.dll && doskip=1
done
test ${doskip} -eq 1 && continue
test -f ${DESTDIR}/bin/${dll} || cp -v ${SYSROOT}/bin/${dll} ${DESTDIR}/bin
done
echo "Copy required Qt plugins"
mkdir -p ${DESTDIR}/qt5plugins
for plugin in imageformats platforms styles
do \
cp -r ${SYSROOT}/lib/qt5/plugins/${plugin} ${DESTDIR}/qt5plugins/
done
echo "Check dependencies of DLL files"
for dll in $(objdump -p ${DESTDIR}/bin/*.dll ${DESTDIR}/qt5plugins/*/*.dll | sed -n -e '/DLL Name:/s/^.*DLL Name: *//p' | sort | uniq)
do \
doskip=0
for skip in ADVAPI32 CFGMGR32 GDI32 KERNEL32 MPR NETAPI32 PSAPI SHELL32 USER32 USERENV UxTheme VERSION WS2_32 WSOCK32 d3d11 dwmapi liblammps msvcrt_ole32
do \
test ${dll} = ${skip}.dll && doskip=1
done
test ${doskip} -eq 1 && continue
test -f ${DESTDIR}/bin/${dll} || cp -v ${SYSROOT}/bin/${dll} ${DESTDIR}/bin
done
for dll in $(objdump -p ${DESTDIR}/bin/*.dll ${DESTDIR}/qt5plugins/*/*.dll | sed -n -e '/DLL Name:/s/^.*DLL Name: *//p' | sort | uniq)
do \
doskip=0
for skip in ADVAPI32 CFGMGR32 GDI32 KERNEL32 MPR NETAPI32 PSAPI SHELL32 USER32 USERENV UxTheme VERSION WS2_32 WSOCK32 d3d11 dwmapi liblammps msvcrt_ole32
do \
test ${dll} = ${skip}.dll && doskip=1
done
test ${doskip} -eq 1 && continue
test -f ${DESTDIR}/bin/${dll} || cp -v ${SYSROOT}/bin/${dll} ${DESTDIR}/bin
done
cat > ${DESTDIR}/bin/qt.conf <<EOF
[Paths]
Plugins = ../qt5plugins
EOF
zip -9rvD LAMMPS-Win10-amd64.zip LAMMPS_GUI

28
cmake/packaging/build_windows_vs.cmake Normal file
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@ -0,0 +1,28 @@
# CMake script to be run post installation to build zipped package
# clean up old zipfile and deployment tree
file(REMOVE LAMMPS-Win10-amd64.zip)
file(REMOVE_RECURSE LAMMPS_GUI)
file(RENAME ${INSTNAME} LAMMPS_GUI)
# move all executables and dlls to main folder and delete bin folder
file(GLOB BINFILES LIST_DIRECTORIES FALSE LAMMPS_GUI/bin/*.exe LAMMPS_GUI/bin/*.dll)
foreach(bin ${BINFILES})
get_filename_component(exe ${bin} NAME)
file(RENAME ${bin} LAMMPS_GUI/${exe})
endforeach()
file(REMOVE_RECURSE LAMMPS_GUI/bin)
# create qt.conf so Qt will find its plugins
file(WRITE LAMMPS_GUI/qt.conf "[Paths]\r\nPlugins = qt5plugins\r\n")
# initialize environment and then run windeployqt to populate folder with missing dependencies and Qt plugins
file(WRITE qtdeploy.bat "@ECHO OFF\r\nset VSCMD_DEBUG=0\r\nCALL ${VC_INIT} x64\r\nset PATH=${QT5_BIN_DIR};%PATH%\r\nwindeployqt --plugindir LAMMPS_GUI/qt5plugins --release LAMMPS_GUI/lammps-gui.exe --no-quick-import --no-webkit2 --no-translations --no-system-d3d-compiler --no-angle --no-opengl-sw\r\n")
execute_process(COMMAND cmd.exe /c qtdeploy.bat COMMAND_ECHO STDERR)
file(REMOVE qtdeploy.bat)
# create zip archive
file(WRITE makearchive.ps1 "Compress-Archive -Path LAMMPS_GUI -CompressionLevel Optimal -DestinationPath LAMMPS-Win10-amd64.zip")
execute_process(COMMAND powershell -ExecutionPolicy Bypass -File makearchive.ps1)
file(REMOVE makearchive.ps1)
file(REMOVE_RECURSE LAMMPS_GUI)

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15
cmake/packaging/linux_wrapper.sh Executable file
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@ -0,0 +1,15 @@
#!/bin/sh
# wrapper for bundled executables
BASEDIR=$(dirname "$0")
EXENAME=$(basename "$0")
# append to LD_LIBRARY_PATH to prefer local (newer) libs
LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${BASEDIR}/lib
# set some environment variables for LAMMPS etc.
LAMMPS_POTENTIALS=${BASEDIR}/share/lammps/potentials
MSI2LMP_LIBRARY=${BASEDIR}/share/lammps/frc_files
export LD_LIBRARY_PATH LAMMPS_POTENTIALS MSI2LMP_LIBRARY
exec "${BASEDIR}/bin/${EXENAME}" "$@"

30
cmake/packaging/png2iconset.sh Executable file
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@ -0,0 +1,30 @@
#!/bin/sh
if [ $# != 2 ]
then
echo "usage: $0 <pngfile> <iconset name>"
exit 1
fi
png="$1"
ico="$2"
if [ ! -f ${png} ]
then
echo "PNG Image $1 not found"
fi
rm -rf ${ico}.iconset
mkdir ${ico}.iconset
sips -z 16 16 ${png} --out ${ico}.iconset/icon_16x16.png
sips -z 32 32 ${png} --out ${ico}.iconset/icon_16x16@2x.png
sips -z 32 32 ${png} --out ${ico}.iconset/icon_32x32.png
sips -z 64 64 ${png} --out ${ico}.iconset/icon_32x32@2x.png
sips -z 128 128 ${png} --out ${ico}.iconset/icon_128x128.png
sips -z 256 256 ${png} --out ${ico}.iconset/icon_128x128@2x.png
sips -z 256 256 ${png} --out ${ico}.iconset/icon_256x256.png
sips -z 512 512 ${png} --out ${ico}.iconset/icon_256x256@2x.png
sips -z 512 512 ${png} --out ${ico}.iconset/icon_512x512.png
sips -z 1024 1024 ${png} --out ${ico}.iconset/icon_512x512@2x.png
iconutil -c icns ${ico}.iconset
rm -rf ${ico}.iconset

1
cmake/presets/all_off.cmake
View File

@ -64,7 +64,6 @@ set(ALL_PACKAGES
MOLECULE
MOLFILE
MPIIO
MSCG
NETCDF
OPENMP
OPT

1
cmake/presets/all_on.cmake
View File

@ -66,7 +66,6 @@ set(ALL_PACKAGES
MOLECULE
MOLFILE
MPIIO
MSCG
NETCDF
OPENMP
OPT

1
cmake/presets/download.cmake
View File

@ -9,7 +9,6 @@ endforeach()
set(DOWNLOAD_KIM ON CACHE BOOL "" FORCE)
set(DOWNLOAD_MDI ON CACHE BOOL "" FORCE)
set(DOWNLOAD_MSCG ON CACHE BOOL "" FORCE)
set(DOWNLOAD_VORO ON CACHE BOOL "" FORCE)
set(DOWNLOAD_EIGEN3 ON CACHE BOOL "" FORCE)
set(DOWNLOAD_PACE ON CACHE BOOL "" FORCE)

14
cmake/presets/macos-multiarch.cmake Normal file
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@ -0,0 +1,14 @@
# preset that will build portable multi-arch binaries on macOS without MPI
set(CMAKE_OSX_ARCHITECTURES "arm64;x86_64" CACHE STRING "" FORCE)
set(CMAKE_OSX_DEPLOYMENT_TARGET 11.0 CACHE STRING "" FORCE)
set(CMAKE_BUILD_TYPE Release CACHE STRING "" FORCE)
set(CMAKE_CXX_COMPILER "clang++" CACHE STRING "" FORCE)
set(CMAKE_C_COMPILER "clang" CACHE STRING "" FORCE)
set(CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_C_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
set(BUILD_MPI FALSE CACHE BOOL "" FORCE)
set(BUILD_SHARED_LIBS FALSE CACHE BOOL "" FORCE)
set(LAMMPS_EXCEPTIONS TRUE CACHE BOOL "" FORCE)

2
cmake/presets/most.cmake
View File

@ -24,8 +24,8 @@ set(ALL_PACKAGES
DPD-REACT
DPD-SMOOTH
DRUDE
ELECTRODE
EFF
ELECTRODE
EXTRA-COMPUTE
EXTRA-DUMP
EXTRA-FIX

1
cmake/presets/nolib.cmake
View File

@ -20,7 +20,6 @@ set(PACKAGES_WITH_LIB
ML-QUIP
MOLFILE
MPIIO
MSCG
NETCDF
PLUMED
PYTHON

2
cmake/presets/windows.cmake
View File

@ -32,6 +32,7 @@ set(WIN_PACKAGES
INTERLAYER
KSPACE
LEPTON
MACHDYN
MANIFOLD
MANYBODY
MC
@ -45,6 +46,7 @@ set(WIN_PACKAGES
MOLECULE
MOLFILE
OPENMP
OPT
ORIENT
PERI
PHONON

4
doc/lammps.1
View File

@ -1,7 +1,7 @@
.TH LAMMPS "1" "15 June 2023" "2023-06-15"
.TH LAMMPS "1" "2 August 2023" "2023-08-2"
.SH NAME
.B LAMMPS
\- Molecular Dynamics Simulator. Version 15 June 2023
\- Molecular Dynamics Simulator. Version 2 August 2023
.SH SYNOPSIS
.B lmp

130
doc/src/Build_extras.rst
View File

@ -52,7 +52,6 @@ This is the list of packages that may require additional steps.
* :ref:`ML-POD <ml-pod>`
* :ref:`ML-QUIP <ml-quip>`
* :ref:`MOLFILE <molfile>`
* :ref:`MSCG <mscg>`
* :ref:`NETCDF <netcdf>`
* :ref:`OPENMP <openmp>`
* :ref:`OPT <opt>`
@ -140,6 +139,8 @@ CMake build
# value = yes or no (default)
-D CUDA_MPS_SUPPORT=value # enables some tweaks required to run with active nvidia-cuda-mps daemon
# value = yes or no (default)
-D CUDA_BUILD_MULTIARCH=value # enables building CUDA kernels for all supported GPU architectures
# value = yes (default) or no
-D USE_STATIC_OPENCL_LOADER=value # downloads/includes OpenCL ICD loader library, no local OpenCL headers/libs needed
# value = yes (default) or no
@ -158,41 +159,49 @@ CMake build
A more detailed list can be found, for example,
at `Wikipedia's CUDA article <https://en.wikipedia.org/wiki/CUDA#GPUs_supported>`_
CMake can detect which version of the CUDA toolkit is used and thus will try
to include support for **all** major GPU architectures supported by this toolkit.
Thus the GPU_ARCH setting is merely an optimization, to have code for
the preferred GPU architecture directly included rather than having to wait
for the JIT compiler of the CUDA driver to translate it.
CMake can detect which version of the CUDA toolkit is used and thus will
try to include support for **all** major GPU architectures supported by
this toolkit. Thus the GPU_ARCH setting is merely an optimization, to
have code for the preferred GPU architecture directly included rather
than having to wait for the JIT compiler of the CUDA driver to translate
it. This behavior can be turned off (e.g. to speed up compilation) by
setting :code:`CUDA_ENABLE_MULTIARCH` to :code:`no`.
When compiling for CUDA or HIP with CUDA, version 8.0 or later of the CUDA toolkit
is required and a GPU architecture of Kepler or later, which must *also* be
supported by the CUDA toolkit in use **and** the CUDA driver in use.
When compiling for OpenCL, OpenCL version 1.2 or later is required and the
GPU must be supported by the GPU driver and OpenCL runtime bundled with the driver.
When compiling for CUDA or HIP with CUDA, version 8.0 or later of the
CUDA toolkit is required and a GPU architecture of Kepler or later,
which must *also* be supported by the CUDA toolkit in use **and** the
CUDA driver in use. When compiling for OpenCL, OpenCL version 1.2 or
later is required and the GPU must be supported by the GPU driver and
OpenCL runtime bundled with the driver.
When building with CMake, you **must NOT** build the GPU library in ``lib/gpu``
using the traditional build procedure. CMake will detect files generated by that
process and will terminate with an error and a suggestion for how to remove them.
When building with CMake, you **must NOT** build the GPU library in
``lib/gpu`` using the traditional build procedure. CMake will detect
files generated by that process and will terminate with an error and a
suggestion for how to remove them.
If you are compiling for OpenCL, the default setting is to download, build, and
link with a static OpenCL ICD loader library and standard OpenCL headers. This
way no local OpenCL development headers or library needs to be present and only
OpenCL compatible drivers need to be installed to use OpenCL. If this is not
desired, you can set :code:`USE_STATIC_OPENCL_LOADER` to :code:`no`.
If you are compiling for OpenCL, the default setting is to download,
build, and link with a static OpenCL ICD loader library and standard
OpenCL headers. This way no local OpenCL development headers or library
needs to be present and only OpenCL compatible drivers need to be
installed to use OpenCL. If this is not desired, you can set
:code:`USE_STATIC_OPENCL_LOADER` to :code:`no`.
The GPU library has some multi-thread support using OpenMP. If LAMMPS is built
with ``-D BUILD_OMP=on`` this will also be enabled.
The GPU library has some multi-thread support using OpenMP. If LAMMPS
is built with ``-D BUILD_OMP=on`` this will also be enabled.
If you are compiling with HIP, note that before running CMake you will have to
set appropriate environment variables. Some variables such as
:code:`HCC_AMDGPU_TARGET` (for ROCm <= 4.0) or :code:`CUDA_PATH` are necessary for :code:`hipcc`
and the linker to work correctly.
If you are compiling with HIP, note that before running CMake you will
have to set appropriate environment variables. Some variables such as
:code:`HCC_AMDGPU_TARGET` (for ROCm <= 4.0) or :code:`CUDA_PATH` are
necessary for :code:`hipcc` and the linker to work correctly.
Using CHIP-SPV implementation of HIP is now supported. It allows one to run HIP
code on Intel GPUs via the OpenCL or Level Zero backends. To use CHIP-SPV, you must
set :code:`-DHIP_USE_DEVICE_SORT=OFF` in your CMake command line as CHIP-SPV does not
yet support hipCUB. The use of HIP for Intel GPUs is still experimental so you
should only use this option in preparations to run on Aurora system at ANL.
.. versionadded:: 3Aug2022
Using the CHIP-SPV implementation of HIP is supported. It allows one to
run HIP code on Intel GPUs via the OpenCL or Level Zero backends. To use
CHIP-SPV, you must set :code:`-DHIP_USE_DEVICE_SORT=OFF` in your CMake
command line as CHIP-SPV does not yet support hipCUB. As of Summer 2022,
the use of HIP for Intel GPUs is experimental. You should only use this
option in preparations to run on Aurora system at Argonne.
.. code:: bash
@ -629,6 +638,12 @@ They must be specified in uppercase.
* - VEGA90A
- GPU
- AMD GPU MI200 GFX90A
* - NAVI1030
- GPU
- AMD GPU V620/W6800
* - NAVI1100
- GPU
- AMD GPU RX7900XTX
* - INTEL_GEN
- GPU
- SPIR64-based devices, e.g. Intel GPUs, using JIT
@ -651,7 +666,7 @@ They must be specified in uppercase.
- GPU
- Intel GPU Ponte Vecchio
This list was last updated for version 3.7.1 of the Kokkos library.
This list was last updated for version 4.0.1 of the Kokkos library.
.. tabs::
@ -921,59 +936,6 @@ Python version 3.6 or later.
----------
.. _mscg:
MSCG package
-----------------------
To build with this package, you must download and build the MS-CG
library. Building the MS-CG library requires that the GSL
(GNU Scientific Library) headers and libraries are installed on your
machine. See the ``lib/mscg/README`` and ``MSCG/Install`` files for
more details.
.. tabs::
.. tab:: CMake build
.. code-block:: bash
-D DOWNLOAD_MSCG=value # download MSCG for build, value = no (default) or yes
-D MSCG_LIBRARY=path # MSCG library file (only needed if a custom location)
-D MSCG_INCLUDE_DIR=path # MSCG include directory (only needed if a custom location)
If ``DOWNLOAD_MSCG`` is set, the MSCG library will be downloaded
and built inside the CMake build directory. If the MSCG library
is already on your system (in a location CMake cannot find it),
``MSCG_LIBRARY`` is the filename (plus path) of the MSCG library
file, not the directory the library file is in.
``MSCG_INCLUDE_DIR`` is the directory the MSCG include file is in.
.. tab:: Traditional make
You can download and build the MS-CG library manually if you
prefer; follow the instructions in ``lib/mscg/README``\ . You can
also do it in one step from the ``lammps/src`` dir, using a
command like these, which simply invokes the
``lib/mscg/Install.py`` script with the specified args:
.. code-block:: bash
make lib-mscg # print help message
make lib-mscg args="-b -m serial" # download and build in lib/mscg/MSCG-release-master
# with the settings compatible with "make serial"
make lib-mscg args="-b -m mpi" # download and build in lib/mscg/MSCG-release-master
# with the settings compatible with "make mpi"
make lib-mscg args="-p /usr/local/mscg-release" # use the existing MS-CG installation in /usr/local/mscg-release
Note that 2 symbolic (soft) links, ``includelink`` and ``liblink``,
will be created in ``lib/mscg`` to point to the MS-CG
``src/installation`` dir. When LAMMPS is built in src it will use
these links. You should not need to edit the
``lib/mscg/Makefile.lammps`` file.
----------
.. _opt:
OPT package

1
doc/src/Build_package.rst
View File

@ -55,7 +55,6 @@ packages:
* :ref:`ML-POD <ml-pod>`
* :ref:`ML-QUIP <ml-quip>`
* :ref:`MOLFILE <molfile>`
* :ref:`MSCG <mscg>`
* :ref:`NETCDF <netcdf>`
* :ref:`OPENMP <openmp>`
* :ref:`OPT <opt>`

26
doc/src/Build_settings.rst
View File

@ -459,27 +459,13 @@ those systems:
.. _exceptions:
Exception handling when using LAMMPS as a library
------------------------------------------------------------------
-------------------------------------------------
This setting is useful when external codes drive LAMMPS as a library.
With this option enabled, LAMMPS errors do not kill the calling code.
Instead, the call stack is unwound and control returns to the caller,
e.g. to Python. Of course, the calling code has to be set up to
*catch* exceptions thrown from within LAMMPS.
.. tabs::
.. tab:: CMake build
.. code-block:: bash
-D LAMMPS_EXCEPTIONS=value # yes or no (default)
.. tab:: Traditional make
.. code-block:: make
LMP_INC = -DLAMMPS_EXCEPTIONS <other LMP_INC settings>
LAMMPS errors do not kill the calling code, but throw an exception. In
the C-library interface, the call stack is unwound and control returns
to the caller, e.g. to Python or a code that is coupled to LAMMPS and
the error status can be queried. When using C++ directly, the calling
code has to be set up to *catch* exceptions thrown from within LAMMPS.
.. note::

1
doc/src/Commands_fix.rst
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@ -116,7 +116,6 @@ OPT.
* :doc:`momentum (k) <fix_momentum>`
* :doc:`momentum/chunk <fix_momentum>`
* :doc:`move <fix_move>`
* :doc:`mscg <fix_mscg>`
* :doc:`msst <fix_msst>`
* :doc:`mvv/dpd <fix_mvv_dpd>`
* :doc:`mvv/edpd <fix_mvv_dpd>`

10
doc/src/Commands_removed.rst
View File

@ -85,6 +85,16 @@ The same functionality is available through
:doc:`bond style mesocnt <bond_mesocnt>` and
:doc:`angle style mesocnt <angle_mesocnt>`.
MSCG package
------------
.. deprecated:: TBD
The MSCG package has been removed from LAMMPS since it was unmaintained
for many years and instead superseded by the `OpenMSCG software
<https://software.rcc.uchicago.edu/mscg/>`_ of the Voth group at the
University of Chicago, which can be used independent from LAMMPS.
REAX package
------------

4
doc/src/Developer_grid.rst
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@ -92,8 +92,8 @@ Arguments for these methods can be values returned by the
*setup_grid()* method (described below), which define the extent of
the grid cells (owned+ghost) the processor owns. These 4 methods
allocate memory for 2d (first two) and 3d (second two) grid data. The
two methods that end in "_one" allocate an array which stores a single
value per grid cell. The two that end in "_multi" allocate an array
two methods that end in "_offset" allocate an array which stores a single
value per grid cell. The two that end in "_last" allocate an array
which stores *Nvalues* per grid cell.
.. code-block:: c++

2
doc/src/Examples.rst
View File

@ -104,8 +104,6 @@ Lowercase directories
+-------------+------------------------------------------------------------------+
| min | energy minimization of 2d LJ melt |
+-------------+------------------------------------------------------------------+
| mscg | parameterize a multi-scale coarse-graining (MSCG) model |
+-------------+------------------------------------------------------------------+
| msst | MSST shock dynamics |
+-------------+------------------------------------------------------------------+
| multi | multi neighboring for systems with large interaction disparities |

20
doc/src/Fortran.rst
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@ -2278,19 +2278,13 @@ Procedures Bound to the :f:type:`lammps` Derived Type
.. versionadded:: 3Nov2022
In case of an error, LAMMPS will either abort or throw a C++ exception.
The latter has to be :ref:`enabled at compile time <exceptions>`.
This function checks if exceptions were enabled.
When using the library interface with C++ exceptions enabled, the library
interface functions will "catch" them, and the error status can then be
checked by calling :f:func:`has_error`. The most recent error message can be
retrieved via :f:func:`get_last_error_message`.
This can allow one to restart a calculation or delete and recreate
the LAMMPS instance when a C++ exception occurs. One application
of using exceptions this way is the :ref:`lammps_shell`. If C++
exceptions are disabled and an error happens during a call to
LAMMPS or the Fortran API, the application will terminate.
When using the library interface, the library interface functions
will "catch" exceptions, and then the error status can be checked by
calling :f:func:`has_error`. The most recent error message can be
retrieved via :f:func:`get_last_error_message`. This allows to
restart a calculation or delete and recreate the LAMMPS instance when
a C++ exception occurs. One application of using exceptions this way
is the :ref:`lammps_shell`.
:to: :cpp:func:`lammps_config_has_exceptions`
:r has_exceptions:

8
doc/src/Howto_cmake.rst
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@ -338,8 +338,6 @@ Some common LAMMPS specific variables
- common compiler flags, for optimization or instrumentation (default:)
* - ``LAMMPS_MACHINE``
- when set to ``name`` the LAMMPS executable and library will be called ``lmp_name`` and ``liblammps_name.a``
* - ``LAMMPS_EXCEPTIONS``
- when set to ``on`` errors will throw a C++ exception instead of aborting (default: ``off``)
* - ``FFT``
- select which FFT library to use: ``FFTW3``, ``MKL``, ``KISS`` (default, unless FFTW3 is found)
* - ``FFT_SINGLE``
@ -412,9 +410,9 @@ interface (``ccmake`` or ``cmake-gui``).
Using a preset to select a compiler package (``clang.cmake``,
``gcc.cmake``, ``intel.cmake``, ``oneapi.cmake``, or ``pgi.cmake``)
are an exception to the mechanism of updating the configuration incrementally,
as they will trigger a reset of cached internal CMake settings and thus
reset settings to their default values.
are an exception to the mechanism of updating the configuration
incrementally, as they will trigger a reset of cached internal CMake
settings and thus reset settings to their default values.
Compilation and build targets
-----------------------------

26
doc/src/Howto_pylammps.rst
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@ -53,10 +53,10 @@ System-wide Installation
Step 1: Building LAMMPS as a shared library
"""""""""""""""""""""""""""""""""""""""""""
To use LAMMPS inside of Python it has to be compiled as shared library. This
library is then loaded by the Python interface. In this example we enable the
MOLECULE package and compile LAMMPS with C++ exceptions, PNG, JPEG and FFMPEG
output support enabled.
To use LAMMPS inside of Python it has to be compiled as shared
library. This library is then loaded by the Python interface. In this
example we enable the MOLECULE package and compile LAMMPS with PNG, JPEG
and FFMPEG output support enabled.
Step 1a: For the CMake based build system, the steps are:
@ -66,7 +66,7 @@ Step 1a: For the CMake based build system, the steps are:
cd $LAMMPS_DIR/build-shared
# MPI, PNG, Jpeg, FFMPEG are auto-detected
cmake ../cmake -DPKG_MOLECULE=yes -DLAMMPS_EXCEPTIONS=yes -DBUILD_LIB=yes -DBUILD_SHARED_LIBS=yes
cmake ../cmake -DPKG_MOLECULE=yes -DBUILD_LIB=yes -DBUILD_SHARED_LIBS=yes
make
Step 1b: For the legacy, make based build system, the steps are:
@ -79,7 +79,7 @@ Step 1b: For the legacy, make based build system, the steps are:
make yes-MOLECULE
# compile shared library using Makefile
make mpi mode=shlib LMP_INC="-DLAMMPS_PNG -DLAMMPS_JPEG -DLAMMPS_FFMPEG -DLAMMPS_EXCEPTIONS" JPG_LIB="-lpng -ljpeg"
make mpi mode=shlib LMP_INC="-DLAMMPS_PNG -DLAMMPS_JPEG -DLAMMPS_FFMPEG" JPG_LIB="-lpng -ljpeg"
Step 2: Installing the LAMMPS Python package
""""""""""""""""""""""""""""""""""""""""""""
@ -356,18 +356,16 @@ Together with matplotlib plotting data out of LAMMPS becomes simple:
Error handling with PyLammps
----------------------------
Compiling the shared library with C++ exception support provides a better error
handling experience. Without exceptions the LAMMPS code will terminate the
current Python process with an error message. C++ exceptions allow capturing
them on the C++ side and rethrowing them on the Python side. This way you
can handle LAMMPS errors through the Python exception handling mechanism.
Using C++ exceptions in LAMMPS for errors allows capturing them on the
C++ side and rethrowing them on the Python side. This way you can handle
LAMMPS errors through the Python exception handling mechanism.
.. warning::
Capturing a LAMMPS exception in Python can still mean that the
current LAMMPS process is in an illegal state and must be terminated. It is
advised to save your data and terminate the Python instance as quickly as
possible.
current LAMMPS process is in an illegal state and must be
terminated. It is advised to save your data and terminate the Python
instance as quickly as possible.
Using PyLammps in IPython notebooks and Jupyter
-----------------------------------------------

2
doc/src/Intro_portability.rst
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@ -12,7 +12,7 @@ Programming language standards
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Most of the C++ code currently requires a compiler compatible with the
C++11 standard, the KOKKOS package currently requires C++14. Most of
C++11 standard, the KOKKOS package currently requires C++17. Most of
the Python code is written to be compatible with Python 3.5 or later or
Python 2.7. Some Python scripts *require* Python 3 and a few others
still need to be ported from Python 2 to Python 3.

42
doc/src/Modify_style.rst
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@ -28,20 +28,34 @@ Include files (varied)
packages and hard-to-find bugs have regularly manifested in the
past.
- Header files, especially those defining a "style", should only use
the absolute minimum number of include files and **must not**
contain any ``using`` statements. Typically, that would only be the
header for the base class. Instead, any include statements should
be put in the corresponding implementation files and forward
declarations be used. For implementation files, the "include what
you use" principle should be employed. However, there is the
notable exception that when the ``pointers.h`` header is included
(or one of the base classes derived from it) certain headers will
always be included and thus do not need to be explicitly specified.
These are: `mpi.h`, `cstddef`, `cstdio`, `cstdlib`, `string`,
`utils.h`, `vector`, `fmt/format.h`, `climits`, `cinttypes`. This
also means any such file can assume that `FILE`, `NULL`, and
`INT_MAX` are defined.
- Header files, especially those defining a "style", should only use the
absolute minimum number of include files and **must not** contain any
``using`` statements. Typically, that would only be the header for the
base class. Instead, any include statements should be put in the
corresponding implementation files and forward declarations be used.
For implementation files, the "include what you use" principle should
be employed. However, there is the notable exception that when the
``pointers.h`` header is included (or the header of one of the classes
derived from it), certain headers will *always* be included and thus
do not need to be explicitly specified. These are: `mpi.h`,
`cstddef`, `cstdio`, `cstdlib`, `string`, `utils.h`, `vector`,
`fmt/format.h`, `climits`, `cinttypes`. This also means any such file
can assume that `FILE`, `NULL`, and `INT_MAX` are defined.
- Class members variables should not be initialized in the header file,
but instead should be initialized either in the initializer list of
the constructor or explicitly assigned in the body of the constructor.
If the member variable is relevant to the functionality of a class
(for example when it stores a value from a command line argument), the
member variable declaration is followed by a brief comment explaining
its purpose and what its values can be. Class members that are
pointers should always be initialized to ``nullptr`` in the
initializer list of the constructor. This reduces clutter in the
header and avoids accessing uninitialized pointers, which leads to
hard to debug issues, class members are often implicitly initialized
to ``NULL`` on the first use (but *not* after a :doc:`clear command
<clear>`). Please see the files ``reset_atoms_mol.h`` and
``reset_atoms_mol.cpp`` as an example.
- System headers or headers from installed libraries are included with
angular brackets (example: ``#include <vector>``), while local

35
doc/src/Packages_details.rst
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@ -88,7 +88,6 @@ page gives those details.
* :ref:`MOLECULE <PKG-MOLECULE>`
* :ref:`MOLFILE <PKG-MOLFILE>`
* :ref:`MPIIO <PKG-MPIIO>`
* :ref:`MSCG <PKG-MSCG>`
* :ref:`NETCDF <PKG-NETCDF>`
* :ref:`OPENMP <PKG-OPENMP>`
* :ref:`OPT <PKG-OPT>`
@ -1257,7 +1256,7 @@ Also see the :ref:`GPU <PKG-GPU>`, :ref:`OPT <PKG-OPT>`, :ref:`INTEL
<PKG-INTEL>`, and :ref:`OPENMP <PKG-OPENMP>` packages, which have styles
optimized for CPUs, KNLs, and GPUs.
You must have a C++14 compatible compiler to use this package.
You must have a C++17 compatible compiler to use this package.
KOKKOS makes extensive use of advanced C++ features, which can
expose compiler bugs, especially when compiling for maximum
performance at high optimization levels. Please see the file
@ -2066,38 +2065,6 @@ The MPIIO package requires that LAMMPS is build in :ref:`MPI parallel mode <seri
----------
.. _PKG-MSCG:
MSCG package
------------
**Contents:**
A :doc:`fix mscg <fix_mscg>` command which can parameterize a
Multi-Scale Coarse-Graining (MSCG) model using the open-source `MS-CG library <mscg-home_>`_.
.. _mscg-home: https://github.com/uchicago-voth/MSCG-release
To use this package you must have the MS-CG library available on your
system.
**Authors:** The fix was written by Lauren Abbott (Sandia). The MS-CG
library was developed by Jacob Wagner in Greg Voth's group at the
University of Chicago.
**Install:**
This package has :ref:`specific installation instructions <mscg>` on the :doc:`Build extras <Build_extras>` page.
**Supporting info:**
* src/MSCG: filenames -> commands
* src/MSCG/README
* lib/mscg/README
* examples/mscg
----------
.. _PKG-NETCDF:
NETCDF package

5
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@ -338,11 +338,6 @@ whether an extra library is needed to build and use the package:
- :doc:`dump <dump>`
- n/a
- no
* - :ref:`MSCG <PKG-MSCG>`
- multi-scale coarse-graining wrapper
- :doc:`fix mscg <fix_mscg>`
- mscg
- ext
* - :ref:`NETCDF <PKG-NETCDF>`
- dump output via NetCDF
- :doc:`dump netcdf <dump_netcdf>`

18
doc/src/Python_error.rst
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@ -1,11 +1,11 @@
Handling LAMMPS errors
*******************************
**********************
Compiling the shared library with :ref:`C++ exception support <exceptions>` provides a better error
handling experience. Without exceptions the LAMMPS code will terminate the
current Python process with an error message. C++ exceptions allow capturing
them on the C++ side and rethrowing them on the Python side. This way
LAMMPS errors can be handled through the Python exception handling mechanism.
The shared library is compiled with :ref:`C++ exception support
<exceptions>` to provide a better error handling experience. C++
exceptions allow capturing errors on the C++ side and rethrowing them on
the Python side. This way LAMMPS errors can be handled through the
Python exception handling mechanism.
.. code-block:: python
@ -31,6 +31,6 @@ LAMMPS errors can be handled through the Python exception handling mechanism.
.. warning::
Capturing a LAMMPS exception in Python can still mean that the
current LAMMPS process is in an illegal state and must be terminated. It is
advised to save your data and terminate the Python instance as quickly as
possible.
current LAMMPS process is in an illegal state and must be
terminated. It is advised to save your data and terminate the Python
instance as quickly as possible when running in parallel with MPI.

18
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@ -26,23 +26,29 @@ task). These are Serial (MPI-only for CPUs and Intel Phi), OpenMP
GPUs) and HIP (for AMD GPUs). You choose the mode at build time to
produce an executable compatible with a specific hardware.
.. admonition:: C++14 support
.. admonition:: C++17 support
:class: note
Kokkos requires using a compiler that supports the c++14 standard. For
some compilers, it may be necessary to add a flag to enable c++14 support.
For example, the GNU compiler uses the -std=c++14 flag. For a list of
Kokkos requires using a compiler that supports the c++17 standard. For
some compilers, it may be necessary to add a flag to enable c++17 support.
For example, the GNU compiler uses the -std=c++17 flag. For a list of
compilers that have been tested with the Kokkos library, see the Kokkos
`README <https://github.com/kokkos/kokkos/blob/master/README.md>`_.
`Wiki <https://kokkos.github.io/kokkos-core-wiki/requirements.html>`_.
.. admonition:: NVIDIA CUDA support
:class: note
To build with Kokkos support for NVIDIA GPUs, the NVIDIA CUDA toolkit
software version 9.0 or later must be installed on your system. See
software version 11.0 or later must be installed on your system. See
the discussion for the :doc:`GPU package <Speed_gpu>` for details of
how to check and do this.
.. admonition:: AMD ROCm (HIP) support
:class: note
To build with Kokkos support for AMD GPUs, the AMD ROCm toolkit
software version 5.2.0 or later must be installed on your system.
.. admonition:: CUDA and MPI library compatibility
:class: note

224
doc/src/Tools.rst
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@ -93,6 +93,7 @@ Miscellaneous tools
* :ref:`i-pi <ipi>`
* :ref:`kate <kate>`
* :ref:`LAMMPS shell <lammps_shell>`
* :ref:`LAMMPS GUI <lammps_gui>`
* :ref:`LAMMPS magic patterns for file(1) <magic>`
* :ref:`Offline build tool <offline>`
* :ref:`singularity/apptainer <singularity_tool>`
@ -634,6 +635,229 @@ you first need to use the :doc:`clear` command.
----------
.. _lammps_gui:
LAMMPS GUI
----------
.. versionadded:: 2Aug2023
Overview
^^^^^^^^
LAMMPS GUI is essentially a small graphical text editor that is linked
to the :ref:`LAMMPS C-library interface <lammps_c_api>` and thus can run
LAMMPS directly using the contents of the editor's text buffer as input.
This is similar to what people usually would do using a text editor to
edit the input and then a command line terminal window to run the input
commands. The main benefit is that this integrates very well with
graphical desktop environments and that it is easier to use for
beginners in running computations and thus very suitable for tutorials
on LAMMPS. A small difference is that for the LAMMPS GUI it is not
require to first commit its buffer of the text editor to a file.
Features
^^^^^^^^
The main window of the LAMMPS GUI is a generic text editor window with
line numbers and syntax highlighting set up for LAMMPS input files. It
can be used to edit any kind of text file, though. The output of a run
is captured and displayed in a separate dialog window and *not* sent to
the console or a log file (unless the :doc:`log command <log>` is used
in the input. The log window is regularly updated during the run and a
progress bar for the run command shown at the bottom of the main window.
Starting a new run will open another log windows. The state of LAMMPS
will be reset between two runs. After the simulation is finished, an
image of the simulated system can be created and shown in an image
viewer window. Ongoing runs can be stopped at the next iteration via
triggering a timeout.
When opening a file, the editor will determine the directory where the
file resides and switch its current working directory to the folder of
that file. Many LAMMPS inputs contain commands that read other files,
typically from the folder of the input file. The GUI will always show
the current working directory in the bottom. The editor window can also
receive (entire) files via drag-n-drop from a file manager GUI or a
desktop environment. When exiting the GUI with a modified buffer, a
dialog asking to either cancel, ignore the modifications, or save the
file with show up. Same when attempting to load a new file into a
modified buffer.
Hotkeys
^^^^^^^
Almost all functionality is accessible from the menu or via hotkeys.
The following hotkeys are available (On macOS use the Command key
instead of Ctrl (aka Control)).
.. list-table::
:header-rows: 1
:widths: auto
* - Hotkey
- Function
- Hotkey
- Function
- Hotkey
- Function
- Hotkey
- Function
* - Ctrl+N
- New File
- Ctrl+Z
- Undo edit
- Ctrl+V
- Paste text
- Ctrl+Q
- Quit (Main Window only)
* - Ctrl+O
- Open File
- Ctrl+Shift+Z
- Redo edit
- Ctrl+Enter
- Run LAMMPS
- Ctrl+W
- Close (Log and Image Window only)
* - CTRL+S
- Save File
- Ctrl+C
- Copy text
- Ctrl+/
- Stop Active Run
- Ctrl+P
- Preferences
* - Ctrl+Shift+S
- Save File As
- Ctrl+X
- Cut text
- Ctrl+I
- Create Snapshot Image
- Ctrl+Shift+/
- Quick Help
Further editing keybindings `are documented with the Qt documentation
<https://doc.qt.io/qt-5/qplaintextedit.html#editing-key-bindings>`_. In
case of conflicts the list above takes precedence.
Parallelization
^^^^^^^^^^^^^^^
Due to its nature as a graphical application, it is not possible to use
the LAMMPS GUI in parallel with MPI, but OpenMP multi-threading is
available and enabled by default.
Prerequisites and portability
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
LAMMPS GUI is programmed in C++ based on the C++11 standard and using
the `Qt GUI framework <https://www.qt.io/product/framework>`_.
Currently, Qt version 5.12 or later is required; Qt 5.15LTS is
recommended Qt 6.x not (yet) supported. Furthermore, CMake version 3.16
is required and LAMMPS must be configured with ``-D
LAMMPS_EXCETIONS=on`` and ``-D BUILD_MPI=off``. It has been successfully
compiled and tested on:
- Ubuntu Linux 20.04LTS x86_64 using GCC 9, Qt version 5.12
- Fedora Linux 38 x86\_64 using GCC 13 and Clang 16, Qt version 5.15LTS
- Apple macOS 12 (Monterey) and macOS 13 (Ventura) with Xcode on arm64 and x86\_64, Qt version 5.15LTS
- Windows 10 and 11 x86_64 with Visual Studio 2022 and Visual C++ 14.36, Qt version 5.15LTS
Pre-compiled executables
^^^^^^^^^^^^^^^^^^^^^^^^
Pre-compiled LAMMPS executables including the GUI are currently
available from https://download.lammps.org/static. You can unpack the
archive (or mount the macOS disk image) and run the GUI directly in
place. The folder may also be moved around and added to the ``PATH``
environment variable so the executables will be found automatically. The
LAMMPS GUI executable is called ``lammps-gui`` and takes no arguments or
will interpret the first argument as filename to load.
Compilation
^^^^^^^^^^^
The source for the LAMMPS GUI is included with the LAMMPS source code
distribution in the folder `tools/lammps-gui` and thus it can be can be
built as part of a regular LAMMPS compilation.
:doc:`Using CMake <Howto_cmake>` is required.
To enable its compilation the CMake variable ``-D BUILD_LAMMPS_GUI=on``
must be set when creating the CMake configuration. All other settings
(compiler, flags, compile type) for LAMMPS GUI are then inherited from
the regular LAMMPS build. If the Qt library is packaged for Linux
distributions, then its location is typically auto-detected since the
required CMake configuration files are stored in a location where CMake
can find them without additional help. Otherwise, the location of the
Qt library installation must be indicated by setting
``-D Qt5_DIR=/path/to/qt5/lib/cmake/Qt5``, which is a path to a folder inside
the Qt installation that contains the file ``Qt5Config.cmake``.
It is also possible to build the LAMMPS GUI as a standalone executable
(e.g. when LAMMPS has been compiled with traditional make), then the
CMake configuration needs to be told where to find the LAMMPS headers
and the LAMMPS library, via `-D LAMMPS_SOURCE_DIR=/path/to/lammps/src`.
CMake will try to guess a build folder with the LAMMPS library from that
path, but it can also be set with `-D LAMMPS_LIB_DIR=/path/to/lammps/lib`.
Rather than linking to the LAMMPS library during compilation, it is also
possible to compile the GUI with a plugin loader library that will load
the LAMMPS library dynamically at runtime during the start of the GUI
from a shared library; e.g. `liblammps.so` or `liblammps.dylib` or
`liblammps.dll` (depending on the operating system). This has the
advantage that the LAMMPS library can be updated LAMMPS without having
to recompile the GUI. The ABI of the LAMMPS C-library interface is very
stable and generally backward compatible. This feature is enabled by
setting ``-D LAMMPS_GUI_USE_PLUGIN=on`` and then
``-D LAMMPS_PLUGINLIB_DIR=/path/to/lammps/plugin/loader``. Typically, this
would be the ``examples/COUPLE/plugin`` folder of the LAMMPS distribution.
Platform notes
^^^^^^^^^^^^^^
macOS
"""""
When building on macOS, the build procedure will try to manufacture a
drag-n-drop installer, LAMMPS-macOS-multiarch.dmg, when using the 'dmg'
target (i.e. `cmake --build <build dir> --target dmg` or `make dmg`.
To build multi-arch executables that will run on both, arm64 and x86_64
architectures natively, it is necessary to set the CMake variable ``-D
CMAKE_OSX_ARCHITECTURES=arm64;x86_64``. To achieve wide compatibility
with different macOS versions, you can also set ``-D
CMAKE_OSX_DEPLOYMENT_TARGET=11.0`` which will set compatibility to macOS
11 (Big Sur) and later, even if you are compiling on a more recent macOS
version.
Windows
"""""""
On Windows currently only compilation from within Visual Studio 2022 is
supported and tested. Using CMake and Ninja as build system is
required. Qt needs to be installed, tested was a package downloaded from
https://www.qt.io, into the ``C:\\Qt`` folder. There is a custom
`x64-GUI-MSVC` build configuration provided that will activate building
the `lammps-gui.exe` executable in addition to LAMMPS. When requesting
an installation from the `Build` menu, it will create a compressed zip
file with the executables and required dependent .dll files. This zip
file can be uncompressed and ``lammps-gui.exe`` run directly from there.
The uncompressed folder can be added to the ``PATH`` environment and
LAMMPS and LAMMPS GUI can be launched from anywhere from the command
line.
Linux
"""""
Version 5.12 or later of the Qt library and CMake version 3.16 are
required and those are provided by, e.g., Ubuntu 20.04LTS. Thus older
Linux distributions are not likely to be supported, while more recent
ones will work, even for pre-compiled executables (see above). After
compiling with ``cmake --build <build folder>``, use
``cmake --build <build folder> --target tgz`` or ``make tgz`` to build
a ``LAMMPS-Linux-amd64.tar.gz`` file with the executables and their
support libraries.
----------
.. _arc:
lmp2arc tool

1
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@ -268,7 +268,6 @@ accelerated styles exist.
* :doc:`momentum <fix_momentum>` - zero the linear and/or angular momentum of a group of atoms
* :doc:`momentum/chunk <fix_momentum>` - zero the linear and/or angular momentum of a chunk of atoms
* :doc:`move <fix_move>` - move atoms in a prescribed fashion
* :doc:`mscg <fix_mscg>` - apply MSCG method for force-matching to generate coarse grain models
* :doc:`msst <fix_msst>` - multi-scale shock technique (MSST) integration
* :doc:`mvv/dpd <fix_mvv_dpd>` - DPD using the modified velocity-Verlet integration algorithm
* :doc:`mvv/edpd <fix_mvv_dpd>` - constant energy DPD using the modified velocity-Verlet algorithm

141
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@ -1,141 +0,0 @@
.. index:: fix mscg
fix mscg command
================
Syntax
""""""
.. code-block:: LAMMPS
fix ID group-ID mscg N keyword args ...
* ID, group-ID are documented in :doc:`fix <fix>` command
* mscg = style name of this fix command
* N = envoke this fix every this many timesteps
* zero or more keyword/value pairs may be appended
* keyword = *range* or *name* or *max*
.. parsed-literal::
*range* arg = *on* or *off*
*on* = range finding functionality is performed
*off* = force matching functionality is performed
*name* args = name1 ... nameN
name1,...,nameN = string names for each atom type (1-Ntype)
*max* args = maxb maxa maxd
maxb,maxa,maxd = maximum bonds/angles/dihedrals per atom
Examples
""""""""
.. code-block:: LAMMPS
fix 1 all mscg 1
fix 1 all mscg 1 range name A B
fix 1 all mscg 1 max 4 8 20
Description
"""""""""""
This fix applies the Multi-Scale Coarse-Graining (MSCG) method to
snapshots from a dump file to generate potentials for coarse-grained
simulations from all-atom simulations, using a force-matching technique
(:ref:`Izvekov <Izvekov>`, :ref:`Noid <Noid>`).
It makes use of the MS-CG library, written and maintained by Greg Voth's
group at the University of Chicago, which is freely available on their
`MS-CG GitHub site <https://github.com/uchicago-voth/MSCG-release>`_.
See instructions on obtaining and installing the MS-CG library in the
src/MSCG/README file, which must be done before you build LAMMPS with
this fix command and use the command in a LAMMPS input script.
An example script using this fix is provided the examples/mscg
directory.
The general workflow for using LAMMPS in conjunction with the MS-CG
library to create a coarse-grained model and run coarse-grained
simulations is as follows:
1. Perform all-atom simulations on the system to be coarse grained.
2. Generate a trajectory mapped to the coarse-grained model.
3. Create input files for the MS-CG library.
4. Run the range finder functionality of the MS-CG library.
5. Run the force matching functionality of the MS-CG library.
6. Check the results of the force matching.
7. Run coarse-grained simulations using the new coarse-grained potentials.
This fix can perform the range finding and force matching steps 4 and 5
of the above workflow when used in conjunction with the :doc:`rerun
<rerun>` command. It does not perform steps 1-3 and 6-7.
Step 2 can be performed using a Python script (cgmap), which defines the
coarse-grained model and converts a standard LAMMPS dump file for an
all-atom simulation (step 1) into a LAMMPS dump file which has the
positions of and forces on the coarse-grained beads. To use cgmap the
following repositories need to be downloaded and installed.
#. The custom lammpsdata branch of mdtraj from https://github.com/hockyg/mdtraj/tree/lammpsdata
#. The master branch of cgmap from https://github.com/uchicago-voth/cgmap
In step 3, an input file named "control.in" is needed by the MS-CG
library which sets parameters for the range finding and force matching
functionalities. See the examples/mscg/control.in file as an example.
And see the documentation provided with the MS-CG library for more
info on this file.
When this fix is used to perform steps 4 and 5, the MS-CG library also
produces additional output files. The range finder functionality
(step 4) outputs files defining pair and bonded interaction ranges. The
force matching functionality (step 5) outputs tabulated force files for
every interaction in the system. Other diagnostic files can also be
output depending on the parameters in the MS-CG library input script.
Again, see the documentation provided with the MS-CG library for more
info.
----------
The *range* keyword specifies which MS-CG library functionality should
be invoked. If *on*, the step 4 range finder functionality is invoked.
*off*, the step 5 force matching functionality is invoked.
If the *name* keyword is used, string names are defined to associate
with the integer atom types in LAMMPS. *Ntype* names must be provided,
one for each atom type (1-Ntype).
The *max* keyword specifies the maximum number of bonds, angles, and
dihedrals a bead can have in the coarse-grained model.
Restrictions
""""""""""""
This fix is part of the MSCG package. It is only enabled if LAMMPS was
built with that package. Building the MSCG package also requires
external libraries. See the :doc:`Build_package` and :doc:`Build_extras`
pages for more info.
Currently, the MS-CG library is not set up to run in parallel with MPI,
so this fix can only be used in a serial LAMMPS build and run on a
single processor.
Related commands
""""""""""""""""
none
Default
"""""""
The default keyword settings are range off, max 4 12 36.
----------
.. _Izvekov:
**(Izvekov)** Izvekov, Voth, J Chem Phys 123, 134105 (2005).
.. _Noid:
**(Noid)** Noid, Chu, Ayton, Krishna, Izvekov, Voth, Das, Andersen, J
Chem Phys 128, 134105 (2008).

2
doc/utils/requirements.txt
View File

@ -1,4 +1,4 @@
Sphinx >= 5.3.0, <7.1.0
Sphinx >= 5.3.0, <7.2.0
sphinxcontrib-spelling
sphinxcontrib-jquery
git+https://github.com/akohlmey/sphinx-fortran@parallel-read

3
doc/utils/sphinx-config/false_positives.txt
View File

@ -1528,6 +1528,7 @@ inhomogeneous
init
initialdelay
initialisms
initializer
initializations
InitiatorIDs
initio
@ -3488,6 +3489,7 @@ supercell
superset
supersphere
Supinski
Sur
Surblys
surfactant
surfactants
@ -3834,6 +3836,7 @@ vectorized
Vegt
vel
Velázquez
Ventura
venv
Verlag
verlet

4
examples/COUPLE/plugin/CMakeLists.txt
View File

@ -23,9 +23,7 @@ endif()
# and prints lots of pointless warnings about "unsafe" functions
if(MSVC)
if(CMAKE_C_COMPILER_ID STREQUAL "MSVC")
if(LAMMPS_EXCEPTIONS)
add_compile_options(/EHsc)
endif()
add_compile_options(/EHsc)
endif()
add_compile_definitions(_CRT_SECURE_NO_WARNINGS)
endif()

2
examples/COUPLE/plugin/liblammpsplugin.h
View File

@ -239,7 +239,7 @@ struct _liblammpsplugin {
void (*free)(void *);
void (*is_running)(void *);
int (*is_running)(void *);
void (*force_timeout)(void *);
int (*has_error)(void *);

4
examples/COUPLE/simple/CMakeLists.txt
View File

@ -18,9 +18,7 @@ endif()
# and prints lots of pointless warnings about "unsafe" functions
if(MSVC)
if(CMAKE_C_COMPILER_ID STREQUAL "MSVC")
if(LAMMPS_EXCEPTIONS)
add_compile_options(/EHsc)
endif()
add_compile_options(/EHsc)
endif()
add_compile_definitions(_CRT_SECURE_NO_WARNINGS)
endif()

1
examples/README
View File

@ -91,7 +91,6 @@ mesh: create_atoms mesh command
micelle: self-assembly of small lipid-like molecules into 2d bilayers
min: energy minimization of 2d LJ melt
mliap: examples for using several bundled MLIAP potentials
mscg: parameterize a multi-scale coarse-graining (MSCG) model
msst: MSST shock dynamics
nb3b: use of nonbonded 3-body harmonic pair style
neb: nudged elastic band (NEB) calculation for barrier finding

10
examples/mscg/README
View File

@ -1,10 +0,0 @@
Running this example requires that LAMMPS be built with the MSCG
package and its fix mscg command. The fix uses the Multi-Scale
Coarse-Graining (MS-CG) library, freely available at
https://github.com/uchicago-voth/MSCG-release, to compute optimized
coarse-grained force field parameters. The MS-CG library was
developed by Jacob Wagner in Greg Voth's group at the University of
Chicago.
See the lib/mscg/README file for instructions on how to download and
install the MS-CG library for use with LAMMPS.

12
examples/mscg/control.in
View File

@ -1,12 +0,0 @@
block_size 1
start_frame 1
n_frames 19
nonbonded_cutoff 10.0
basis_type 0
primary_output_style 0
output_solution_flag 1
output_spline_coeffs_flag 1
pair_nonbonded_bspline_basis_order 6
pair_nonbonded_basis_set_resolution 0.7
pair_nonbonded_output_binwidth 0.1
matrix_type 0

1015
examples/mscg/data.meoh
View File

File diff suppressed because it is too large Load Diff

20180
examples/mscg/dump.meoh
View File

File diff suppressed because it is too large Load Diff

22
examples/mscg/in.mscg
View File

@ -1,22 +0,0 @@
units real
atom_style full
pair_style zero 10.0
read_data data.meoh
pair_coeff * *
thermo 1
thermo_style custom step
# Test 1a: range finder functionality
fix 1 all mscg 1 range on
rerun dump.meoh first 0 last 4500 every 250 dump x y z fx fy fz
print "TEST_1a mscg range finder"
unfix 1
# Test 1b: force matching functionality
fix 1 all mscg 1
rerun dump.meoh first 0 last 4500 every 250 dump x y z fx fy fz
print "TEST_1b mscg force matching"
print TEST_DONE

105
examples/mscg/log.16Mar23.g++.1
View File

@ -1,105 +0,0 @@
LAMMPS (8 Feb 2023)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
units real
atom_style full
pair_style zero 10.0
read_data data.meoh
Reading data file ...
orthogonal box = (-20.6917 -20.6917 -20.6917) to (20.6917 20.6917 20.6917)
1 by 1 by 1 MPI processor grid
reading atoms ...
1000 atoms
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.007 seconds
pair_coeff * *
thermo 1
thermo_style custom step
# Test 1a: range finder functionality
fix 1 all mscg 1 range on
rerun dump.meoh first 0 last 4500 every 250 dump x y z fx fy fz
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 7 7 7
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 6.045 | 6.045 | 6.045 Mbytes
Step
0
250
500
750
1000
1250
1500
1750
2000
2250
2500
2750
3000
3250
3500
3750
4000
4250
4500
Loop time of 0.245891 on 1 procs for 19 steps with 1000 atoms
print "TEST_1a mscg range finder"
TEST_1a mscg range finder
unfix 1
# Test 1b: force matching functionality
fix 1 all mscg 1
rerun dump.meoh first 0 last 4500 every 250 dump x y z fx fy fz
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 6.045 | 6.045 | 6.045 Mbytes
Step
0
250
500
750
1000
1250
1500
1750
2000
2250
2500
2750
3000
3250
3500
3750
4000
4250
4500
Loop time of 0.433986 on 1 procs for 19 steps with 1000 atoms
print "TEST_1b mscg force matching"
TEST_1b mscg force matching
print TEST_DONE
TEST_DONE
Total wall time: 0:00:00

71
examples/mscg/output_16Mar23/1_1.dat
View File

@ -1,71 +0,0 @@
3.000000 9.109433117503674e+00
3.100000 6.562933520937051e+00
3.200000 3.803570347770783e+00
3.300000 1.524835163098694e+00
3.400000 3.680752991750511e-02
3.500000 -6.369395346711866e-01
3.600000 -6.624341032589213e-01
3.700000 -2.983998819283989e-01
3.800000 1.996942072449469e-01
3.900000 6.507540486137935e-01
4.000000 9.561503221901252e-01
4.100000 1.082978861799261e+00
4.200000 1.046366050930359e+00
4.300000 8.917742185869113e-01
4.400000 6.773070351372578e-01
4.500000 4.561974686292022e-01
4.600000 2.640422255436971e-01
4.700000 1.180848207166380e-01
4.800000 2.124502216672507e-02
4.900000 -3.366915456585443e-02
5.000000 -5.974945208074427e-02
5.100000 -7.177537677873873e-02
5.200000 -8.204929079011507e-02
5.300000 -9.745573177789707e-02
5.400000 -1.196283642109915e-01
5.500000 -1.463411396781238e-01
5.600000 -1.729465415853768e-01
5.700000 -1.938138298537278e-01
5.800000 -2.037672856165882e-01
5.900000 -1.995060297815394e-01
6.000000 -1.805447650094144e-01
6.100000 -1.489384048916932e-01
6.200000 -1.085276302304308e-01
6.300000 -6.416601955090541e-02
6.400000 -2.094717961426480e-02
6.500000 1.656812406982645e-02
6.600000 4.511482523443927e-02
6.700000 6.322611594801032e-02
6.800000 7.107524696431811e-02
6.900000 7.005702917383723e-02
7.000000 6.235932355899154e-02
7.100000 5.053453114940768e-02
7.200000 3.707108297716843e-02
7.300000 2.397003518601587e-02
7.400000 1.245439896007831e-02
7.500000 3.015413982707119e-03
7.600000 -4.408442264121739e-03
7.700000 -1.024733994435217e-02
7.800000 -1.511598231239246e-02
7.900000 -1.962949115765983e-02
8.000000 -2.422153184874873e-02
8.100000 -2.902066868449916e-02
8.200000 -3.387453677654857e-02
8.300000 -3.843224513464188e-02
8.400000 -4.222901944115068e-02
8.500000 -4.477084482559266e-02
8.600000 -4.561910863915099e-02
8.700000 -4.447439067652353e-02
8.800000 -4.123808661911404e-02
8.900000 -3.601776131390161e-02
9.000000 -2.911033476210515e-02
9.100000 -2.098441550402311e-02
9.200000 -1.226263400387303e-02
9.300000 -3.703976034631109e-03
9.400000 3.815231963949414e-03
9.500000 9.355387087425532e-03
9.600000 1.205664749783030e-02
9.700000 1.131702059340882e-02
9.800000 6.971799313021964e-03
9.900000 -5.270015594498346e-04
10.000000 -9.931209090702869e-03

104
examples/mscg/output_16Mar23/1_1.table
View File

@ -1,104 +0,0 @@
# Header information on force file
1_1
N 99 R 0.200000 10.000000
1 0.200000 127.263594 80.411422
2 0.300000 119.349776 77.864922
3 0.400000 111.690609 75.318423
4 0.500000 104.286092 72.771923
5 0.600000 97.136225 70.225423
6 0.700000 90.241007 67.678924
7 0.800000 83.600440 65.132424
8 0.900000 77.214522 62.585925
9 1.000000 71.083255 60.039425
10 1.100000 65.206637 57.492925
11 1.200000 59.584670 54.946426
12 1.300000 54.217352 52.399926
13 1.400000 49.104684 49.853427
14 1.500000 44.246667 47.306927
15 1.600000 39.643299 44.760427
16 1.700000 35.294581 42.213928
17 1.800000 31.200513 39.667428
18 1.900000 27.361096 37.120929
19 2.000000 23.776328 34.574429
20 2.100000 20.446210 32.027929
21 2.200000 17.370742 29.481430
22 2.300000 14.549924 26.934930
23 2.400000 11.983756 24.388431
24 2.500000 9.672238 21.841931
25 2.600000 7.615370 19.295432
26 2.700000 5.813151 16.748932
27 2.800000 4.265583 14.202432
28 2.900000 2.972665 11.655933
29 3.000000 1.934397 9.109433
30 3.100000 1.150778 6.562934
31 3.200000 0.632453 3.803570
32 3.300000 0.366033 1.524835
33 3.400000 0.287951 0.036808
34 3.500000 0.317957 -0.636940
35 3.600000 0.382926 -0.662434
36 3.700000 0.430968 -0.298400
37 3.800000 0.435903 0.199694
38 3.900000 0.393381 0.650754
39 4.000000 0.313035 0.956150
40 4.100000 0.211079 1.082979
41 4.200000 0.104612 1.046366
42 4.300000 0.007705 0.891774
43 4.400000 -0.070749 0.677307
44 4.500000 -0.127425 0.456197
45 4.600000 -0.163437 0.264042
46 4.700000 -0.182543 0.118085
47 4.800000 -0.189509 0.021245
48 4.900000 -0.188888 -0.033669
49 5.000000 -0.184217 -0.059749
50 5.100000 -0.177641 -0.071775
51 5.200000 -0.169950 -0.082049
52 5.300000 -0.160975 -0.097456
53 5.400000 -0.150120 -0.119628
54 5.500000 -0.136822 -0.146341
55 5.600000 -0.120858 -0.172947
56 5.700000 -0.102520 -0.193814
57 5.800000 -0.082640 -0.203767
58 5.900000 -0.062477 -0.199506
59 6.000000 -0.043474 -0.180545
60 6.100000 -0.027000 -0.148938
61 6.200000 -0.014127 -0.108528
62 6.300000 -0.005492 -0.064166
63 6.400000 -0.001236 -0.020947
64 6.500000 -0.001018 0.016568
65 6.600000 -0.004102 0.045115
66 6.700000 -0.009519 0.063226
67 6.800000 -0.016234 0.071075
68 6.900000 -0.023290 0.070057
69 7.000000 -0.029911 0.062359
70 7.100000 -0.035556 0.050535
71 7.200000 -0.039936 0.037071
72 7.300000 -0.042988 0.023970
73 7.400000 -0.044809 0.012454
74 7.500000 -0.045583 0.003015
75 7.600000 -0.045513 -0.004408
76 7.700000 -0.044781 -0.010247
77 7.800000 -0.043512 -0.015116
78 7.900000 -0.041775 -0.019629
79 8.000000 -0.039583 -0.024222
80 8.100000 -0.036920 -0.029021
81 8.200000 -0.033776 -0.033875
82 8.300000 -0.030160 -0.038432
83 8.400000 -0.026127 -0.042229
84 8.500000 -0.021777 -0.044771
85 8.600000 -0.017258 -0.045619
86 8.700000 -0.012753 -0.044474
87 8.800000 -0.008467 -0.041238
88 8.900000 -0.004605 -0.036018
89 9.000000 -0.001348 -0.029110
90 9.100000 0.001156 -0.020984
91 9.200000 0.002819 -0.012263
92 9.300000 0.003617 -0.003704
93 9.400000 0.003612 0.003815
94 9.500000 0.002953 0.009355
95 9.600000 0.001882 0.012057
96 9.700000 0.000714 0.011317
97 9.800000 -0.000201 0.006972
98 9.900000 -0.000523 -0.000527
99 10.000000 0.000000 -0.009931

2
examples/mscg/output_16Mar23/b-spline.out
View File

@ -1,2 +0,0 @@
n: 1 1 6 11 3.000000000000000e+00 1.000000000000000e+01
9.109454054135307e+00 6.178334150703818e+00 -6.242976259059743e+00 4.778144787445235e+00 -1.082885612852992e+00 4.521835893850554e-01 -6.477047196208028e-01 2.947887062333265e-01 -4.195609079009661e-02 1.111775827831465e-02 -8.823466147380592e-02 -1.696076806027540e-02 3.192205281984208e-02 3.656991607866288e-03 -9.931306149957592e-03

1
examples/mscg/output_16Mar23/rmin.in
View File

@ -1 +0,0 @@
1 1 2.852369 10.000000 fm

0
examples/mscg/output_16Mar23/rmin_b.in
View File

17
examples/mscg/output_16Mar23/sol_info.out
View File

@ -1,17 +0,0 @@
fm_matrix_rows:3000; fm_matrix_columns:15;
Singular vector:
2.307693e+00
1.998418e+00
1.400114e+00
1.183608e+00
9.718949e-01
7.471241e-01
5.277965e-01
5.084369e-01
3.510398e-01
2.997000e-01
2.142454e-01
1.201800e-01
7.143923e-02
3.077326e-02
1.835581e-02

2
examples/mscg/output_16Mar23/x.out
View File

@ -1,2 +0,0 @@
<EFBFBD>ٝ\
8"@<40>!D:<3A><>@<40>v<EFBFBD><76><EFBFBD><EFBFBD><18>H<EFBFBD><48><EFBFBD><EFBFBD>@H3H<33>S<7F><53>Ԗ p<><70><EFBFBD>??<3F><>俀% s<><73><EFBFBD>?:y<><79>D{<7B><><EFBFBD>z<EFBFBD>A<EFBFBD>Ć?#Tg<54><67><EFBFBD><EFBFBD><EFBFBD>l#<23><>)^<5E><><EFBFBD><EFBFBD><EFBFBD>YX<>?K<>pkD<6B>m?<3F>

4
examples/plugins/CMakeLists.txt
View File

@ -36,9 +36,7 @@ else()
add_compile_options(/Zc:__cplusplus)
add_compile_options(/wd4244)
add_compile_options(/wd4267)
if(LAMMPS_EXCEPTIONS)
add_compile_options(/EHsc)
endif()
add_compile_options(/EHsc)
endif()
add_compile_definitions(_CRT_SECURE_NO_WARNINGS)
endif()

2
lib/README
View File

@ -41,8 +41,6 @@ mdi hooks to the MDI library, used by MDI package
from Taylor Barnes (MolSSI at Virginia Tech)
molfile hooks to VMD molfile plugins, used by the MOLFILE package
from Axel Kohlmeyer (Temple U) and the VMD development team
mscg hooks to the MSCG library, used by fix_mscg command
from Jacob Wagner and Greg Voth group (U Chicago)
netcdf hooks to a NetCDF library installed on your system
from Lars Pastewka (Karlsruhe Institute of Technology)
plugin settings to load styles into LAMMPS from plugins

4
lib/awpmd/ivutils/include/wavepacket.h
View File

@ -23,7 +23,7 @@ class WavePacket;
///\en Template for v=der operation in \ref Wavepacket::int2phys_der()
template<class Type>
struct eq_second : public binary_function <Type, Type, Type> {
struct eq_second {
Type operator()(const Type& /* _Left */, const Type& _Right) const{
return _Right;
}
@ -31,7 +31,7 @@ struct eq_second : public binary_function <Type, Type, Type> {
///\en Template for v=-der operation in \ref Wavepacket::int2phys_der()
template<class Type>
struct eq_minus_second : public binary_function <Type, Type, Type> {
struct eq_minus_second {
Type operator()(const Type& /* _Left */, const Type& _Right) const{
return -_Right;
}

11
lib/gpu/lal_device.cpp
View File

@ -29,7 +29,7 @@
const char *ocl_prefetch_test =
" #if (NBOR_PREFETCH == 1) \n"\
" inline void ucl_prefetch(const __global int *p) { prefetch(p, 1); } \n"\
" #else \n"\
" #elif (NBOR_PREFETCH == 2) \n"\
" enum LSC_LDCC {LSC_LDCC_DEFAULT, LSC_LDCC_L1UC_L3UC, LSC_LDCC_L1UC_L3C, \n"\
" LSC_LDCC_L1C_L3UC, LSC_LDCC_L1C_L3C, LSC_LDCC_L1S_L3UC, \n"\
" LSC_LDCC_L1S_L3C, LSC_LDCC_L1IAR_L3C, }; \n"\
@ -745,7 +745,14 @@ void DeviceT::estimate_gpu_overhead(const int kernel_calls,
gpu_overhead=0.0;
gpu_driver_overhead=0.0;
for (int z=0; z<11; z++) {
// TODO: XXX
// The following estimation currently fails on Intel GPUs
// that do not support double precision with OpenCL error code -5.
// Until we have a better solution, we just skip this test in this case.
int zloops = 11;
if (!gpu->double_precision()) zloops = 0;
for (int z=0; z < zloops; z++) {
gpu->sync();
gpu_barrier();
over_timer.start();

2
lib/gpu/lal_pre_ocl_config.h
View File

@ -43,7 +43,7 @@ const char * ocl_config_strings[] =
"NVIDIA_GPU,203,32,32,1,1,4,8,2,256,256,128,64,128,8,128,11,128,8,0",
"AMD_GPU,403,64,64,0,1,4,8,2,256,256,128,64,128,8,128,11,128,8,0",
#ifdef _SINGLE_SINGLE
"INTEL_GPU,500,8,32,1,1,4,8,2,128,128,128,128,64,8,128,8,128,8,2",
"INTEL_GPU,500,8,32,1,1,4,8,2,128,128,128,128,64,8,128,8,128,8,0",
"APPLE_GPU,600,16,16,0,1,4,8,1,64,64,64,64,64,8,128,8,128,8,0",
#else
"INTEL_GPU,500,8,32,1,1,2,8,2,128,128,128,128,64,8,128,8,128,8,2",

6
lib/gpu/lal_preprocessor.h
View File

@ -333,12 +333,12 @@ inline void ucl_prefetch(const __global int *p) {
struct _lgpu_float3 {
float x; float y; float z;
};
struct _lgpu_double3 {
double x; double y; double z;
};
#ifdef _SINGLE_SINGLE
#define acctyp3 struct _lgpu_float3
#else
struct _lgpu_double3 {
double x; double y; double z;
};
#define acctyp3 struct _lgpu_double3
#endif

251
lib/kokkos/BUILD.md
View File

@ -52,6 +52,10 @@ There are numerous device backends, options, and architecture-specific optimizat
````
which activates the OpenMP backend. All of the options controlling device backends, options, architectures, and third-party libraries (TPLs) are given below.
Kokkos requires as a minimum C++17, however C++20 and C++23 are supported depending on the compiler.
The latest minimum compiler versions can be found in `cmake/kokkos_compiler_id.cmake`.
## Known Issues<a name="KnownIssues"></a>
### Cray
@ -107,249 +111,4 @@ For dev-build details, consult the kokkos-spack repository [README](https://gith
# Kokkos Keyword Listing
## Device Backends
Device backends can be enabled by specifying `-DKokkos_ENABLE_X`.
* Kokkos_ENABLE_CUDA
* Whether to build CUDA backend
* BOOL Default: OFF
* Kokkos_ENABLE_HPX
* Whether to build HPX backend (experimental)
* BOOL Default: OFF
* Kokkos_ENABLE_OPENMP
* Whether to build OpenMP backend
* BOOL Default: OFF
* Kokkos_ENABLE_THREADS
* Whether to build C++ thread backend
* BOOL Default: OFF
* Kokkos_ENABLE_SERIAL
* Whether to build serial backend
* BOOL Default: ON
* Kokkos_ENABLE_HIP (Experimental)
* Whether to build HIP backend
* BOOL Default: OFF
* Kokkos_ENABLE_OPENMPTARGET (Experimental)
* Whether to build the OpenMP target backend
* BOOL Default: OFF
## Enable Options
Options can be enabled by specifying `-DKokkos_ENABLE_X`.
* Kokkos_ENABLE_AGGRESSIVE_VECTORIZATION
* Whether to aggressively vectorize loops
* BOOL Default: OFF
* Kokkos_ENABLE_COMPILER_WARNINGS
* Whether to print all compiler warnings
* BOOL Default: OFF
* Kokkos_ENABLE_CUDA_CONSTEXPR
* Whether to activate experimental relaxed constexpr functions
* BOOL Default: OFF
* Kokkos_ENABLE_CUDA_LAMBDA
* Whether to activate experimental lambda features
* BOOL Default: OFF
* Kokkos_ENABLE_CUDA_LDG_INTRINSIC
* Whether to use CUDA LDG intrinsics
* BOOL Default: OFF
* Kokkos_ENABLE_CUDA_RELOCATABLE_DEVICE_CODE
* Whether to enable relocatable device code (RDC) for CUDA
* BOOL Default: OFF
* Kokkos_ENABLE_CUDA_UVM
* Whether to use unified memory (UM) by default for CUDA
* BOOL Default: OFF
* Kokkos_ENABLE_DEBUG
* Whether to activate extra debug features - may increase compile times
* BOOL Default: OFF
* Kokkos_ENABLE_DEBUG_BOUNDS_CHECK
* Whether to use bounds checking - will increase runtime
* BOOL Default: OFF
* Kokkos_ENABLE_DEBUG_DUALVIEW_MODIFY_CHECK
* Debug check on dual views
* BOOL Default: OFF
* Kokkos_ENABLE_EXAMPLES
* Whether to enable building examples
* BOOL Default: OFF
* Kokkos_ENABLE_HPX_ASYNC_DISPATCH
* Whether HPX supports asynchronous dispatch
* BOOL Default: OFF
* Kokkos_ENABLE_IMPL_CUDA_MALLOC_ASYNC
* Whether to enable CudaMallocAsync (requires CUDA Toolkit 11.2). This is an experimental performance feature and currently has issue when using with UCX. See https://github.com/kokkos/kokkos/issues/4228 for more details.
* BOOL Default: OFF
* Kokkos_ENABLE_LARGE_MEM_TESTS
* Whether to perform extra large memory tests
* BOOL_Default: OFF
* Kokkos_ENABLE_PROFILING_LOAD_PRINT
* Whether to print information about which profiling tools gotloaded
* BOOL Default: OFF
* Kokkos_ENABLE_TESTS
* Whether to enable test suite
* BOOL Default: OFF
## Other Options
* Kokkos_CXX_STANDARD
* The C++ standard for Kokkos to use: c++14, c++17, or c++20. This should be given in CMake style as 14, 17, or 20.
* STRING Default: 14
## Third-party Libraries (TPLs)
The following options control enabling TPLs:
* Kokkos_ENABLE_HPX
* Whether to enable the HPX library
* BOOL Default: OFF
* Kokkos_ENABLE_HWLOC
* Whether to enable the HWLOC library
* BOOL Default: Off
* Kokkos_ENABLE_LIBNUMA
* Whether to enable the LIBNUMA library
* BOOL Default: Off
* Kokkos_ENABLE_MEMKIND
* Whether to enable the MEMKIND library
* BOOL Default: Off
* Kokkos_ENABLE_LIBDL
* Whether to enable the LIBDL library
* BOOL Default: On
* Kokkos_ENABLE_LIBRT
* Whether to enable the LIBRT library
* BOOL Default: Off
The following options control finding and configuring non-CMake TPLs:
* Kokkos_CUDA_DIR or CUDA_ROOT
* Location of CUDA install prefix for libraries
* PATH Default:
* Kokkos_HWLOC_DIR or HWLOC_ROOT
* Location of HWLOC install prefix
* PATH Default:
* Kokkos_LIBNUMA_DIR or LIBNUMA_ROOT
* Location of LIBNUMA install prefix
* PATH Default:
* Kokkos_MEMKIND_DIR or MEMKIND_ROOT
* Location of MEMKIND install prefix
* PATH Default:
* Kokkos_LIBDL_DIR or LIBDL_ROOT
* Location of LIBDL install prefix
* PATH Default:
* Kokkos_LIBRT_DIR or LIBRT_ROOT
* Location of LIBRT install prefix
* PATH Default:
The following options control `find_package` paths for CMake-based TPLs:
* HPX_DIR or HPX_ROOT
* Location of HPX prefix (ROOT) or CMake config file (DIR)
* PATH Default:
## Architecture Keywords
Architecture-specific optimizations can be enabled by specifying `-DKokkos_ARCH_X`.
* Kokkos_ARCH_NATIVE
* Whether to optimize for the the local CPU architecture
* BOOL Default: OFF
* Kokkos_ARCH_AMDAVX
* Whether to optimize for the AMDAVX architecture
* BOOL Default: OFF
* Kokkos_ARCH_ARMV80
* Whether to optimize for the ARMV80 architecture
* BOOL Default: OFF
* Kokkos_ARCH_ARMV81
* Whether to optimize for the ARMV81 architecture
* BOOL Default: OFF
* Kokkos_ARCH_ARMV8_THUNDERX
* Whether to optimize for the ARMV8_THUNDERX architecture
* BOOL Default: OFF
* Kokkos_ARCH_ARMV8_TX2
* Whether to optimize for the ARMV8_TX2 architecture
* BOOL Default: OFF
* Kokkos_ARCH_BDW
* Whether to optimize for the BDW architecture
* BOOL Default: OFF
* Kokkos_ARCH_BGQ
* Whether to optimize for the BGQ architecture
* BOOL Default: OFF
* Kokkos_ARCH_ZEN
* Whether to optimize for the Zen architecture
* BOOL Default: OFF
* Kokkos_ARCH_ZEN2
* Whether to optimize for the Zen2 architecture
* BOOL Default: OFF
* Kokkos_ARCH_ZEN3
* Whether to optimize for the Zen3 architecture
* BOOL Default: OFF
* Kokkos_ARCH_HSW
* Whether to optimize for the HSW architecture
* BOOL Default: OFF
* Kokkos_ARCH_KEPLER30
* Whether to optimize for the KEPLER30 architecture
* BOOL Default: OFF
* Kokkos_ARCH_KEPLER32
* Whether to optimize for the KEPLER32 architecture
* BOOL Default: OFF
* Kokkos_ARCH_KEPLER35
* Whether to optimize for the KEPLER35 architecture
* BOOL Default: OFF
* Kokkos_ARCH_KEPLER37
* Whether to optimize for the KEPLER37 architecture
* BOOL Default: OFF
* Kokkos_ARCH_KNC
* Whether to optimize for the KNC architecture
* BOOL Default: OFF
* Kokkos_ARCH_KNL
* Whether to optimize for the KNL architecture
* BOOL Default: OFF
* Kokkos_ARCH_MAXWELL50
* Whether to optimize for the MAXWELL50 architecture
* BOOL Default: OFF
* Kokkos_ARCH_MAXWELL52
* Whether to optimize for the MAXWELL52 architecture
* BOOL Default: OFF
* Kokkos_ARCH_MAXWELL53
* Whether to optimize for the MAXWELL53 architecture
* BOOL Default: OFF
* Kokkos_ARCH_PASCAL60
* Whether to optimize for the PASCAL60 architecture
* BOOL Default: OFF
* Kokkos_ARCH_PASCAL61
* Whether to optimize for the PASCAL61 architecture
* BOOL Default: OFF
* Kokkos_ARCH_POWER7
* Whether to optimize for the POWER7 architecture
* BOOL Default: OFF
* Kokkos_ARCH_POWER8
* Whether to optimize for the POWER8 architecture
* BOOL Default: OFF
* Kokkos_ARCH_POWER9
* Whether to optimize for the POWER9 architecture
* BOOL Default: OFF
* Kokkos_ARCH_ICL
* Whether to optimize for the ICL architecture
* BOOL Default: OFF
* Kokkos_ARCH_ICX
* Whether to optimize for the ICX architecture
* BOOL Default: OFF
* Kokkos_ARCH_SKL
* Whether to optimize for the SKL architecture
* BOOL Default: OFF
* Kokkos_ARCH_SKX
* Whether to optimize for the SKX architecture
* BOOL Default: OFF
* Kokkos_ARCH_SNB
* Whether to optimize for the SNB architecture
* BOOL Default: OFF
* Kokkos_ARCH_SPR
* Whether to optimize for the SPR architecture
* BOOL Default: OFF
* Kokkos_ARCH_TURING75
* Whether to optimize for the TURING75 architecture
* BOOL Default: OFF
* Kokkos_ARCH_VOLTA70
* Whether to optimize for the VOLTA70 architecture
* BOOL Default: OFF
* Kokkos_ARCH_VOLTA72
* Whether to optimize for the VOLTA72 architecture
* BOOL Default: OFF
* Kokkos_ARCH_WSM
* Whether to optimize for the WSM architecture
* BOOL Default: OFF
##### [LICENSE](https://github.com/kokkos/kokkos/blob/devel/LICENSE)
[![License](https://img.shields.io/badge/License-BSD%203--Clause-blue.svg)](https://opensource.org/licenses/BSD-3-Clause)
Under the terms of Contract DE-NA0003525 with NTESS,
the U.S. Government retains certain rights in this software.
Please refer to our [wiki](https://kokkos.github.io/kokkos-core-wiki/keywords.html#cmake-keywords).

208
lib/kokkos/CHANGELOG.md
View File

@ -1,5 +1,213 @@
# CHANGELOG
## [4.1.00](https://github.com/kokkos/kokkos/tree/4.0.01) (2023-06-16)
[Full Changelog](https://github.com/kokkos/kokkos/compare/4.0.01...4.1.00)
### Features:
* Add `<Kokkos_BitManipulation.hpp>` header [\#4577](https://github.com/kokkos/kokkos/pull/4577) [\#5907](https://github.com/kokkos/kokkos/pull/5907) [\#5967](https://github.com/kokkos/kokkos/pull/5967) [\#6101](https://github.com/kokkos/kokkos/pull/6101)
* Add `UnorderedMapInsertOpTypes` [\#5877](https://github.com/kokkos/kokkos/pull/5877) and documentation [\#350](https://github.com/kokkos/kokkos-core-wiki/pull/350)
* Add multiple reducers support for team-level parallel reduce [\#5727](https://github.com/kokkos/kokkos/pull/5727)
### Backend and Architecture Enhancements:
#### CUDA:
* Allow NVCC 12 to compile using C++20 flag [\#5977](https://github.com/kokkos/kokkos/pull/5977)
* Remove ability to disable CMake option `Kokkos_ENABLE_CUDA_LAMBDA` and unconditionally enable CUDA extended lambda support. [\#5964](https://github.com/kokkos/kokkos/pull/5964)
* Drop unnecessary fences around the memory allocation when using `CudaUVMSpace` in views [\#6008](https://github.com/kokkos/kokkos/pull/6008)
#### HIP:
* Improve performance for `parallel_reduce`. Use different parameters for `LightWeight` kernels [\#6029](https://github.com/kokkos/kokkos/pull/6029) and [\#6160](https://github.com/kokkos/kokkos/pull/6160)
#### SYCL:
* Only pass one wrapper object in SYCL reductions [\#6047](https://github.com/kokkos/kokkos/pull/6047)
* Improve and simplify parallel_scan implementation [\#6064](https://github.com/kokkos/kokkos/pull/6064)
* Remove workaround for submit_barrier not being enqueued properly [\#5504](https://github.com/kokkos/kokkos/pull/5504)
* Fix guards for using scratch space with SYCL [\#6003](https://github.com/kokkos/kokkos/pull/6003)
* Fix compiling SYCL with KOKKOS_IMPL_DO_NOT_USE_PRINTF_USAGE [\#6219](https://github.com/kokkos/kokkos/pull/6219)
#### OpenMPTarget:
* Improve hierarchical parallelism for Intel architectures [\#6043](https://github.com/kokkos/kokkos/pull/6043)
* Enable Cray compiler for the OpenMPTarget backend. [\#5889](https://github.com/kokkos/kokkos/pull/5889)
#### HPX:
* Update HPX backend to use HPX's sender/receiver functionality [\#5628](https://github.com/kokkos/kokkos/pull/5628)
* Increase minimum required HPX version to 1.8.0 [\#6132](https://github.com/kokkos/kokkos/pull/6132)
* Implement HPX::in_parallel [\#6143](https://github.com/kokkos/kokkos/pull/6143)
### General Enhancements
* Export CMake `Kokkos_{CUDA,HIP}_ARCHITECTURES` variables [\#5919](https://github.com/kokkos/kokkos/pull/5919) [\#5925](https://github.com/kokkos/kokkos/pull/5925)
* Add `Kokkos::Profiling::ScopedRegion` [\#5959](https://github.com/kokkos/kokkos/pull/5959) [\#5972](https://github.com/kokkos/kokkos/pull/5972)
* Add support for `View::rank[_dynamic]()`[\#5870](https://github.com/kokkos/kokkos/pull/5870)
* Detect incompatible relocatable device code mode to prevent ODR violations [\#5991](https://github.com/kokkos/kokkos/pull/5991)
* Add (experimental) support for 32-bit Darwin and PPC [\#5916](https://github.com/kokkos/kokkos/pull/5916)
* Add missing half and bhalf specialization of the infinity numeric trait [\#6055](https://github.com/kokkos/kokkos/pull/6055)
* Add `is_dual_view` trait and align further with regular view [\#6120](https://github.com/kokkos/kokkos/pull/6120)
* Allow templated functors in parallel_for, parallel_reduce and parallel_scan [\#5976](https://github.com/kokkos/kokkos/pull/5976)
* Define KOKKOS_COMPILER_INTEL_LLVM and only define at most one KOKKOS_COMPILER* macro [\#5906](https://github.com/kokkos/kokkos/pull/5906)
* Allow linking against build tree [\#6078](https://github.com/kokkos/kokkos/pull/6078)
* Allow passing a temporary std::vector to partition_space [\#6167](https://github.com/kokkos/kokkos/pull/6167)
* `Kokkos` can be used as an external dependency in `Trilinos` [\#6142](https://github.com/kokkos/kokkos/pull/6142), [\#6157](https://github.com/kokkos/kokkos/pull/6157) [\#6163](https://github.com/kokkos/kokkos/pull/6163)
* Left align demangled stacktrace output [\#6191](https://github.com/kokkos/kokkos/pull/6191)
* Improve OpenMP affinity warning to include MPI concerns [\#6185](https://github.com/kokkos/kokkos/pull/6185)
### Build System Changes
* Drop `Kokkos_ENABLE_LAUNCH_COMPILER` option which had no effect [\#6148](https://github.com/kokkos/kokkos/pull/6148)
* Export variables for relevant Kokkos options with cmake[\#6142](https://github.com/kokkos/kokkos/pull/6142)
### Incompatibilities (i.e. breaking changes)
* Desul atomics always enabled [\#5801](https://github.com/kokkos/kokkos/pull/5801)
* Drop `KOKKOS_ENABLE_CUDA_ASM*` and `KOKKOS_ENABLE_*_ATOMICS` macros [\#5940](https://github.com/kokkos/kokkos/pull/5940)
* Drop `KOKKOS_ENABLE_RFO_PREFETCH` macro [\#5944](https://github.com/kokkos/kokkos/pull/5944)
* Deprecate `Kokkos_ENABLE_CUDA_LAMBDA` configuration option and force it to `ON` [\#5964](https://github.com/kokkos/kokkos/pull/5964)
* Remove TriBITS Kokkos subpackages [\#6104](https://github.com/kokkos/kokkos/pull/6104)
* Cuda: Remove unused attach_texture_object [\#6129](https://github.com/kokkos/kokkos/pull/6129)
* Drop Kokkos_ENABLE_PROFILING_LOAD_PRINT configuration option [\#6150](https://github.com/kokkos/kokkos/pull/6150)
* Drop pointless Kokkos{Algorithms,Containers}_config.h files [\#6108](https://github.com/kokkos/kokkos/pull/6108)
### Deprecations
* Deprecate `BinSort`, `BinOp1D`, and `BinOp3D` default constructors [\#6131](https://github.com/kokkos/kokkos/pull/6131)
### Bug Fixes
* Fix `SYCLTeamMember` to take arguments for scratch sizes as `std::size_t` [\#5981](https://github.com/kokkos/kokkos/pull/5981)
* Fix Kokkos_SIMD with AVX2 on 64-bit architectures [\#6075](https://github.com/kokkos/kokkos/pull/6075)
* Fix an incorrectly returning size for SIMD uint64_t in AVX2 [\#6004](https://github.com/kokkos/kokkos/pull/6004)
* Fix missing avx512 header file with gcc versions before 10 [\#6183](https://github.com/kokkos/kokkos/pull/6183)
* Fix incorrect results of `parallel_reduce` of types smaller than `int` on CUDA and HIP: [\#5745](https://github.com/kokkos/kokkos/pull/5745)
* CMake: update package compatibility mode when building within Trilinos [\#6012](https://github.com/kokkos/kokkos/pull/6012)
* Fix warnings generated from internal uses of `ALL_t` rather than `Kokkos::ALL_t` [\#6028](https://github.com/kokkos/kokkos/pull/6028)
* Fix bug in `hpcbind` script: check for correct Slurm variable [\#6116](https://github.com/kokkos/kokkos/pull/6116)
* KokkosTools: Don't call callbacks before backends are initialized [\#6114](https://github.com/kokkos/kokkos/pull/6114)
* Fix global fence in Kokkos::resize(DynRankView) [\#6184](https://github.com/kokkos/kokkos/pull/6184)
* Fix `BinSort` support for strided views [\#6081](https://github.com/kokkos/kokkos/pull/6184)
* Fix missing `is_*_view` traits in containers [\#6195](https://github.com/kokkos/kokkos/pull/6195)
* Fix broken OpenMP target on NVHPC [\#6171](https://github.com/kokkos/kokkos/pull/6171)
* Sorting an empty view should exit early and not fail [\#6130](https://github.com/kokkos/kokkos/pull/6130)
## [4.0.01](https://github.com/kokkos/kokkos/tree/4.0.01) (2023-04-14)
[Full Changelog](https://github.com/kokkos/kokkos/compare/4.0.00...4.0.01)
### Backend and Architecture Enhancements:
#### CUDA:
- Allow NVCC 12 to compile using C++20 flag [\#6020](https://github.com/kokkos/kokkos/pull/6020)
- Add CUDA Ada architecture support [\#6022](https://github.com/kokkos/kokkos/pull/6022)
#### HIP:
- Add support for AMDGPU target NAVI31 / RX 7900 XT(X): gfx1100 [\#6021](https://github.com/kokkos/kokkos/pull/6021)
- HIP: Fix warning from `std::memcpy` [\#6019](https://github.com/kokkos/kokkos/pull/6019)
#### SYCL:
- Fix `SYCLTeamMember` to take arguments for scratch sizes as `std::size_t` [\#5986](https://github.com/kokkos/kokkos/pull/5986)
### General Enhancements
- Fixup 4.0 change log [\#6023](https://github.com/kokkos/kokkos/pull/6023)
### Build System Changes
- Cherry-pick TriBITS update from Trilinos [\#6037](https://github.com/kokkos/kokkos/pull/6037)
- CMake: update package compatibility mode when building within Trilinos [\#6013](https://github.com/kokkos/kokkos/pull/6013)
### Bug Fixes
- Fix an incorrectly returning size for SIMD uint64_t in AVX2 [\#6011](https://github.com/kokkos/kokkos/pull/6011)
- Desul atomics: wrong value for `desul::Impl::numeric_limits_max<uint64_t>` [\#6018](https://github.com/kokkos/kokkos/pull/6018)
- Fix warning in some user code when using std::memcpy [\#6000](https://github.com/kokkos/kokkos/pull/6000)
- Fix excessive build times using Makefile.kokkos [\#6068](https://github.com/kokkos/kokkos/pull/6068)
## [4.0.0](https://github.com/kokkos/kokkos/tree/4.0.00) (2023-02-21)
[Full Changelog](https://github.com/kokkos/kokkos/compare/3.7.01...4.0.00)
### Features:
- Allow value types without default constructor in `Kokkos::View` with `Kokkos::WithoutInitializing` [\#5307](https://github.com/kokkos/kokkos/pull/5307)
- `parallel_scan` with `View` as result type. [\#5146](https://github.com/kokkos/kokkos/pull/5146)
- Introduced `SharedSpace`, an alias for a `MemorySpace` that is accessible by every `ExecutionSpace`. The memory is moved and then accessed locally. [\#5289](https://github.com/kokkos/kokkos/pull/5289)
- Introduced `SharedHostPinnedSpace`, an alias for a `MemorySpace` that is accessible by every `ExecutionSpace`. The memory is pinned to the host and accessed via zero-copy access. [\#5405](https://github.com/kokkos/kokkos/pull/5405)
- Add team- and thread-level `sort`, `sort_by_key` algorithms. [\#5317](https://github.com/kokkos/kokkos/pull/5317)
- Groundwork for `MDSpan` integration. [\#4973](https://github.com/kokkos/kokkos/pull/4973) and [\#5304](https://github.com/kokkos/kokkos/pull/5304)
- Introduced MD version of hierarchical parallelism: `TeamThreadMDRange`, `ThreadVectorMDRange` and `TeamVectorMDRange`. [\#5238](https://github.com/kokkos/kokkos/pull/5238)
### Backend and Architecture Enhancements:
#### CUDA:
- Allow CUDA PTX forward compatibility [\#3612](https://github.com/kokkos/kokkos/pull/3612) [\#5536](https://github.com/kokkos/kokkos/pull/5536) [\#5527](https://github.com/kokkos/kokkos/pull/5527)
- Add support for NVIDIA Hopper GPU architecture [\#5538](https://github.com/kokkos/kokkos/pull/5538)
- Don't rely on synchronization behavior of default stream in CUDA and HIP [\#5391](https://github.com/kokkos/kokkos/pull/5391)
- Improve CUDA cache config settings [\#5706](https://github.com/kokkos/kokkos/pull/5706)
#### HIP:
- Move `HIP`, `HIPSpace`, `HIPHostPinnedSpace`, and `HIPManagedSpace` out of the `Experimental` namespace [\#5383](https://github.com/kokkos/kokkos/pull/5383)
- Don't rely on synchronization behavior of default stream in CUDA and HIP [\#5391](https://github.com/kokkos/kokkos/pull/5391)
- Export AMD architecture flag when using Trilinos [\#5528](https://github.com/kokkos/kokkos/pull/5528)
- Fix linking error (see [OLCF issue](https://docs.olcf.ornl.gov/systems/crusher_quick_start_guide.html#olcfdev-1167-kokkos-build-failures-with-prgenv-amd)) when using `amdclang`: [\#5539](https://github.com/kokkos/kokkos/pull/5539)
- Remove support for MI25 and added support for Navi 1030 [\#5522](https://github.com/kokkos/kokkos/pull/5522)
- Fix race condition when using `HSA_XNACK=1` [\#5755](https://github.com/kokkos/kokkos/pull/5755)
- Add parameter to force using GlobalMemory launch mechanism. This can be used when encountering compiler bugs with ROCm 5.3 and 5.4 [\#5796](https://github.com/kokkos/kokkos/pull/5796)
#### SYCL:
- Delegate choice of workgroup size for `parallel_reduce` with `RangePolicy` to the compiler. [\#5227](https://github.com/kokkos/kokkos/pull/5227)
- SYCL `RangePolicy`: manually specify workgroup size through chunk size [\#4875](https://github.com/kokkos/kokkos/pull/4875)
#### OpenMPTarget:
- Select the right device [\#5492](https://github.com/kokkos/kokkos/pull/5492)
#### OpenMP:
- Add `partition_space` [\#5105](https://github.com/kokkos/kokkos/pull/5105)
### General Enhancements
- Implement `OffsetView` constructor taking `pair`s and `ViewCtorProp` [\#5303](https://github.com/kokkos/kokkos/pull/5303)
- Promote math constants to `Kokkos::numbers` namespace [\#5434](https://github.com/kokkos/kokkos/pull/5434)
- Add overloads of `hypot` math function that take 3 arguments [\#5341](https://github.com/kokkos/kokkos/pull/5341)
- Add `fma` fused multiply-add math function [\#5428](https://github.com/kokkos/kokkos/pull/5428)
- Views using `MemoryTraits::Atomic` don't need `volatile` overloads for the value type anymore. [\#5455](https://github.com/kokkos/kokkos/pull/5455)
- Added `is_team_handle` trait [\#5375](https://github.com/kokkos/kokkos/pull/5375)
- Refactor desul atomics to support compiling CUDA with NVC++ [\#5431](https://github.com/kokkos/kokkos/pull/5431) [\#5497](https://github.com/kokkos/kokkos/pull/5497) [\#5498](https://github.com/kokkos/kokkos/pull/5498)
- Support finding `libquadmath` with native compiler support [\#5286](https://github.com/kokkos/kokkos/pull/5286)
- Add architecture flags for MSVC [\#5673](https://github.com/kokkos/kokkos/pull/5673)
- SIMD backend for ARM NEON [\#5829](https://github.com/kokkos/kokkos/pull/5829)
### Build System Changes
- Let CMake determine OpenMP flags. [\#4105](https://github.com/kokkos/kokkos/pull/4105)
- Update minimum compiler versions. [\#5323](https://github.com/kokkos/kokkos/pull/5323)
- Makefile and CMake support for C++23 [\#5283](https://github.com/kokkos/kokkos/pull/5283)
- Do not add `-cuda` to the link line with NVHPC compiler when the CUDA backend is not actually enabled [\#5485](https://github.com/kokkos/kokkos/pull/5485)
- Only add `-latomic` in generated GNU makefiles when OpenMPTarget backend is enabled [\#5501](https://github.com/kokkos/kokkos/pull/5501) [\#5537](https://github.com/kokkos/kokkos/pull/5537) (3.7 patch release candidate)
- `Kokkos_ENABLE_CUDA_LAMBDA` now `ON` by default with NVCC [\#5580](https://github.com/kokkos/kokkos/pull/5580)
- Fix enabling of relocatable device code when using CUDA as CMake language [\#5564](https://github.com/kokkos/kokkos/pull/5564)
- Fix cmake configuration with CUDA 12 [\#5691](https://github.com/kokkos/kokkos/pull/5691)
### Incompatibilities (i.e. breaking changes)
- ***Require C++17*** [\#5277](https://github.com/kokkos/kokkos/pull/5277)
- Turn setting `Kokkos_CXX_STANDARD` into an error [\#5293](https://github.com/kokkos/kokkos/pull/5293)
- Remove all deprecations in Kokkos 3 [\#5297](https://github.com/kokkos/kokkos/pull/5297)
- Remove `KOKKOS_COMPILER_CUDA_VERSION` [\#5430](https://github.com/kokkos/kokkos/pull/5430)
- Drop `reciprocal_overflow_threshold` numeric trait [\#5326](https://github.com/kokkos/kokkos/pull/5326)
- Move `reduction_identity` out of `<Kokkos_NumericTraits.hpp>` into a new `<Kokkos_ReductionIdentity.hpp>` header [\#5450](https://github.com/kokkos/kokkos/pull/5450)
- Reduction and scan routines will report an error if the `join()` operator they would use takes `volatile`-qualified parameters [\#5409](https://github.com/kokkos/kokkos/pull/5409)
- `ENABLE_CUDA_UVM` is dropped in favor of using `SharedSpace` as `MemorySpace` explicitly [\#5608](https://github.com/kokkos/kokkos/pull/5608)
- Remove Kokkos_ENABLE_CUDA_LDG_INTRINSIC option [\#5623](https://github.com/kokkos/kokkos/pull/5623)
- Don't rely on synchronization behavior of default stream in CUDA and HIP - this potentially will break unintended implicit synchronization with other libraries such as MPI [\#5391](https://github.com/kokkos/kokkos/pull/5391)
- Make ExecutionSpace::concurrency() a non-static member function [\#5655](https://github.com/kokkos/kokkos/pull/5655) and related PRs
- Remove code guarded by `KOKKOS_ENABLE_DEPRECATED_CODE_3`
### Deprecations
- Deprecate `CudaUVMSpace::available()` which always returned `true` [\#5614](https://github.com/kokkos/kokkos/pull/5614)
- Deprecate `volatile`-qualified members from `Kokkos::pair` and `Kokkos::complex` [\#5412](https://github.com/kokkos/kokkos/pull/5412)
- Deprecate `KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_*` macros [\#5824](https://github.com/kokkos/kokkos/pull/5824) (oversight in 3.6)
### Bug Fixes
- Avoid allocating memory for `UniqueToken` [\#5300](https://github.com/kokkos/kokkos/pull/5300)
- Fix `pragma ivdep` in `Kokkos_OpenMP_Parallel.hpp` [\#5356](https://github.com/kokkos/kokkos/pull/5356)
- Fix configuring with Threads support when rerunning CMake [\#5486](https://github.com/kokkos/kokkos/pull/5486)
- Fix View assignment between `LayoutLeft` and `LayoutRight` with static extents [\#5535](https://github.com/kokkos/kokkos/pull/5535) (3.7 patch release candidate)
- Add `fence()` calls to sorting routine overloads that don't take an execution space parameter [\#5389](https://github.com/kokkos/kokkos/pull/5389)
- `ClockTic` changed to 64 bit to fix overflow on Power [\#5577](https://github.com/kokkos/kokkos/pull/5577) (incl. in 3.7.01 patch release)
- Fix incorrect offset in CUDA and HIP `parallel_scan` for < 4 byte types [\#5555](https://github.com/kokkos/kokkos/pull/5555) (3.7 patch release candidate)
- Fix incorrect alignment behavior of scratch allocations in some corner cases (e.g. very small allocations) [\#5687](https://github.com/kokkos/kokkos/pull/5687) (3.7 patch release candidate)
- Add missing `ReductionIdentity<char>` specialization [\#5798](https://github.com/kokkos/kokkos/pull/5798)
- Don't install standard algorithms headers multiple times [\#5670](https://github.com/kokkos/kokkos/pull/5670)
- Fix max scratch size calculation for level 0 scratch in CUDA and HIP [\#5718](https://github.com/kokkos/kokkos/pull/5718)
## [3.7.02](https://github.com/kokkos/kokkos/tree/3.7.02) (2023-05-17)
[Full Changelog](https://github.com/kokkos/kokkos/compare/3.7.01...3.7.02)

66
lib/kokkos/CMakeLists.txt
View File

@ -5,13 +5,16 @@ if( "${CMAKE_SOURCE_DIR}" STREQUAL "${CMAKE_BINARY_DIR}" )
message( FATAL_ERROR "FATAL: In-source builds are not allowed. You should create a separate directory for build files and delete CMakeCache.txt." )
endif()
if (COMMAND TRIBITS_PACKAGE)
TRIBITS_PACKAGE(Kokkos)
endif()
# We want to determine if options are given with the wrong case
# In order to detect which arguments are given to compare against
# the list of valid arguments, at the beginning here we need to
# form a list of all the given variables. If it begins with any
# case of KoKkOS, we add it to the list.
GET_CMAKE_PROPERTY(_variableNames VARIABLES)
SET(KOKKOS_GIVEN_VARIABLES)
FOREACH (var ${_variableNames})
@ -34,6 +37,8 @@ IF(COMMAND TRIBITS_PACKAGE_DECL)
SET(KOKKOS_HAS_TRILINOS ON)
ELSE()
SET(KOKKOS_HAS_TRILINOS OFF)
SET(PACKAGE_NAME Kokkos)
SET(PACKAGE_SOURCE_DIR "${CMAKE_CURRENT_SOURCE_DIR}")
ENDIF()
# Is this build a subdirectory of another project
GET_DIRECTORY_PROPERTY(HAS_PARENT PARENT_DIRECTORY)
@ -87,6 +92,16 @@ IF(NOT KOKKOS_HAS_TRILINOS)
SET(KOKKOS_COMPILE_LANGUAGE CUDA)
ENDIF()
# use lower case here since we haven't parsed options yet
IF (Kokkos_ENABLE_COMPILE_AS_CMAKE_LANGUAGE AND Kokkos_ENABLE_HIP)
# Without this as a language for the package we would get a C++ compiler enabled.
# but we still need a C++ compiler even if we build all our cpp files as HIP only
# because otherwise the C++ features don't work etc.
SET(KOKKOS_INTERNAL_EXTRA_COMPILE_LANGUAGE CXX)
SET(KOKKOS_COMPILE_LANGUAGE HIP)
ENDIF()
IF (Spack_WORKAROUND)
IF (Kokkos_ENABLE_COMPILE_AS_CMAKE_LANGUAGE)
@ -113,6 +128,8 @@ IF(NOT KOKKOS_HAS_TRILINOS)
FORCE)
ENDIF()
ENDIF()
ELSE()
SET(KOKKOS_COMPILE_LANGUAGE CXX)
ENDIF()
IF (NOT CMAKE_SIZEOF_VOID_P)
@ -123,15 +140,27 @@ IF (NOT CMAKE_SIZEOF_VOID_P)
MESSAGE(FATAL_ERROR "Kokkos did not configure correctly and failed to validate compiler. The most likely cause is linkage errors during CMake compiler validation. Please consult the CMake error log shown below for the exact error during compiler validation")
ENDIF()
ELSEIF (NOT CMAKE_SIZEOF_VOID_P EQUAL 8)
MESSAGE(FATAL_ERROR "Kokkos assumes a 64-bit build; i.e., 8-byte pointers, but found ${CMAKE_SIZEOF_VOID_P}-byte pointers instead")
IF(CMAKE_SIZEOF_VOID_P EQUAL 4)
MESSAGE(WARNING "32-bit builds are experimental and not officially supported.")
SET(KOKKOS_IMPL_32BIT ON)
ELSE()
MESSAGE(FATAL_ERROR "Kokkos assumes a 64-bit build, i.e., 8-byte pointers, but found ${CMAKE_SIZEOF_VOID_P}-byte pointers instead;")
ENDIF()
ENDIF()
set(Kokkos_VERSION_MAJOR 3)
set(Kokkos_VERSION_MINOR 7)
set(Kokkos_VERSION_PATCH 02)
set(Kokkos_VERSION_MAJOR 4)
set(Kokkos_VERSION_MINOR 1)
set(Kokkos_VERSION_PATCH 00)
set(Kokkos_VERSION "${Kokkos_VERSION_MAJOR}.${Kokkos_VERSION_MINOR}.${Kokkos_VERSION_PATCH}")
message(STATUS "Kokkos version: ${Kokkos_VERSION}")
math(EXPR KOKKOS_VERSION "${Kokkos_VERSION_MAJOR} * 10000 + ${Kokkos_VERSION_MINOR} * 100 + ${Kokkos_VERSION_PATCH}")
# mathematical expressions below are not stricly necessary but they eliminate
# the rather aggravating leading 0 in the releases patch version number, and,
# in some way, are a sanity check for our arithmetic
math(EXPR KOKKOS_VERSION_MAJOR "${KOKKOS_VERSION} / 10000")
math(EXPR KOKKOS_VERSION_MINOR "${KOKKOS_VERSION} / 100 % 100")
math(EXPR KOKKOS_VERSION_PATCH "${KOKKOS_VERSION} % 100")
# Load either the real TriBITS or a TriBITS wrapper
# for certain utility functions that are universal (like GLOBAL_SET)
@ -167,7 +196,7 @@ IF(NOT MSVC)
ENDIF()
IF(Kokkos_ENABLE_TESTS AND NOT KOKKOS_HAS_TRILINOS)
find_package(GTest)
find_package(GTest QUIET)
ENDIF()
# Include a set of Kokkos-specific wrapper functions that
@ -180,6 +209,14 @@ INCLUDE(${KOKKOS_SRC_PATH}/cmake/kokkos_tribits.cmake)
# to allow platform-specific checks
INCLUDE(${KOKKOS_SRC_PATH}/cmake/kokkos_check_env.cmake)
IF(NOT KOKKOS_HAS_TRILINOS)
# This does not work in Trilinos and we simply don't care
# to fix it for Trilinos
# Gather information about the runtime environment
INCLUDE(${KOKKOS_SRC_PATH}/cmake/build_env_info.cmake)
check_git_setup()
ENDIF()
# The build environment setup goes in the following steps
# 1) Check all the enable options. This includes checking Kokkos_DEVICES
# 2) Check the compiler ID (type and version)
@ -194,14 +231,8 @@ KOKKOS_SETUP_BUILD_ENVIRONMENT()
OPTION(BUILD_SHARED_LIBS "Build shared libraries" OFF)
SET(KOKKOS_EXT_LIBRARIES Kokkos::kokkos Kokkos::kokkoscore Kokkos::kokkoscontainers Kokkos::kokkosalgorithms)
SET(KOKKOS_SUB_LIBRARIES kokkoscore kokkoscontainers kokkosalgorithms)
IF (KOKKOS_CXX_STANDARD GREATER_EQUAL 17)
LIST(APPEND KOKKOS_EXT_LIBRARIES Kokkos::kokkossimd)
LIST(APPEND KOKKOS_SUB_LIBRARIES kokkossimd)
ENDIF()
SET(KOKKOS_INT_LIBRARIES kokkos ${KOKKOS_SUB_LIBRARIES})
SET_PROPERTY(GLOBAL PROPERTY KOKKOS_INT_LIBRARIES ${KOKKOS_INT_LIBRARIES})
SET(KOKKOS_COMPONENT_LIBRARIES kokkoscore kokkoscontainers kokkosalgorithms kokkossimd)
SET_PROPERTY(GLOBAL PROPERTY KOKKOS_INT_LIBRARIES kokkos ${KOKKOS_COMPONENT_LIBRARIES})
IF (KOKKOS_HAS_TRILINOS)
SET(TRILINOS_INCDIR ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR})
@ -270,8 +301,6 @@ IF (KOKKOS_HAS_TRILINOS)
$<$<COMPILE_LANGUAGE:CXX>:${KOKKOS_ALL_COMPILE_OPTIONS}>)
ENDIF()
KOKKOS_PACKAGE_DECL()
#------------------------------------------------------------------------------
#
@ -285,7 +314,6 @@ KOKKOS_PROCESS_SUBPACKAGES()
# E) If Kokkos itself is enabled, process the Kokkos package
#
KOKKOS_PACKAGE_DEF()
KOKKOS_EXCLUDE_AUTOTOOLS_FILES()
KOKKOS_PACKAGE_POSTPROCESS()
KOKKOS_CONFIGURE_CORE()
@ -295,7 +323,9 @@ IF (NOT KOKKOS_HAS_TRILINOS AND NOT Kokkos_INSTALL_TESTING)
#Make sure in-tree projects can reference this as Kokkos::
#to match the installed target names
ADD_LIBRARY(Kokkos::kokkos ALIAS kokkos)
TARGET_LINK_LIBRARIES(kokkos INTERFACE ${KOKKOS_SUB_LIBRARIES})
# all_libs target is required for TriBITS-compliance
ADD_LIBRARY(Kokkos::all_libs ALIAS kokkos)
TARGET_LINK_LIBRARIES(kokkos INTERFACE ${KOKKOS_COMPONENT_LIBRARIES})
KOKKOS_INTERNAL_ADD_LIBRARY_INSTALL(kokkos)
ENDIF()
INCLUDE(${KOKKOS_SRC_PATH}/cmake/kokkos_install.cmake)

281
lib/kokkos/LICENSE
View File

@ -1,43 +1,238 @@
//@HEADER
// ************************************************************************
//
// Kokkos v. 3.0
// Copyright (2020) National Technology & Engineering
// Solutions of Sandia, LLC (NTESS).
//
// Under the terms of Contract DE-NA0003525 with NTESS,
// the U.S. Government retains certain rights in this software.
//
// Kokkos is licensed under 3-clause BSD terms of use:
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are
// met:
//
// 1. Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
//
// 2. Redistributions in binary form must reproduce the above copyright
// notice, this list of conditions and the following disclaimer in the
// documentation and/or other materials provided with the distribution.
//
// 3. Neither the name of the Corporation nor the names of the
// contributors may be used to endorse or promote products derived from
// this software without specific prior written permission.
//
// THIS SOFTWARE IS PROVIDED BY NTESS "AS IS" AND ANY
// EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL NTESS OR THE
// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
// NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
// Questions? Contact Christian R. Trott (crtrott@sandia.gov)
//
// ************************************************************************
//@HEADER
************************************************************************
Kokkos v. 4.0
Copyright (2022) National Technology & Engineering
Solutions of Sandia, LLC (NTESS).
Under the terms of Contract DE-NA0003525 with NTESS,
the U.S. Government retains certain rights in this software.
==============================================================================
Kokkos is under the Apache License v2.0 with LLVM Exceptions:
==============================================================================
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---- LLVM Exceptions to the Apache 2.0 License ----
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==============================================================================
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************************************************************************

15
lib/kokkos/LICENSE_FILE_HEADER Normal file
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@ -0,0 +1,15 @@
//@HEADER
// ************************************************************************
//
// Kokkos v. 4.0
// Copyright (2022) National Technology & Engineering
// Solutions of Sandia, LLC (NTESS).
//
// Under the terms of Contract DE-NA0003525 with NTESS,
// the U.S. Government retains certain rights in this software.
//
// Part of Kokkos, under the Apache License v2.0 with LLVM Exceptions.
// See https://kokkos.org/LICENSE for license information.
// SPDX-License-Identifier: Apache-2.0 WITH LLVM-exception
//
//@HEADER

792
lib/kokkos/Makefile.kokkos
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23
lib/kokkos/Makefile.targets
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@ -51,8 +51,6 @@ Kokkos_CudaSpace.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/Cuda/Kokkos_Cu
$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/Cuda/Kokkos_CudaSpace.cpp
Kokkos_Cuda_Task.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/Cuda/Kokkos_Cuda_Task.cpp
$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/Cuda/Kokkos_Cuda_Task.cpp
Kokkos_Cuda_Locks.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/Cuda/Kokkos_Cuda_Locks.cpp
$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/Cuda/Kokkos_Cuda_Locks.cpp
Lock_Array_CUDA.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/tpls/desul/src/Lock_Array_CUDA.cpp
$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/tpls/desul/src/Lock_Array_CUDA.cpp
endif
@ -67,12 +65,16 @@ Kokkos_SYCL_Instance.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/SYCL/Kokko
endif
ifeq ($(KOKKOS_INTERNAL_USE_HIP), 1)
Kokkos_HIP.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/HIP/Kokkos_HIP.cpp
$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/HIP/Kokkos_HIP.cpp
Kokkos_HIP_SharedAllocationRecord.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/HIP/Kokkos_HIP_SharedAllocationRecord.cpp
$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/HIP/Kokkos_HIP_SharedAllocationRecord.cpp
Kokkos_HIP_DeepCopy.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/HIP/Kokkos_HIP_DeepCopy.cpp
$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/HIP/Kokkos_HIP_DeepCopy.cpp
Kokkos_HIP_Space.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/HIP/Kokkos_HIP_Space.cpp
$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/HIP/Kokkos_HIP_Space.cpp
Kokkos_HIP_Instance.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/HIP/Kokkos_HIP_Instance.cpp
$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/HIP/Kokkos_HIP_Instance.cpp
Kokkos_HIP_Locks.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/HIP/Kokkos_HIP_Locks.cpp
$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/HIP/Kokkos_HIP_Locks.cpp
Lock_Array_HIP.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/tpls/desul/src/Lock_Array_HIP.cpp
$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/tpls/desul/src/Lock_Array_HIP.cpp
endif
@ -83,6 +85,8 @@ Kokkos_ThreadsExec.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/Threads/Kokk
endif
ifeq ($(KOKKOS_INTERNAL_USE_OPENMP), 1)
Kokkos_OpenMP.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/OpenMP/Kokkos_OpenMP.cpp
$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/OpenMP/Kokkos_OpenMP.cpp
Kokkos_OpenMP_Instance.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/OpenMP/Kokkos_OpenMP_Instance.cpp
$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/OpenMP/Kokkos_OpenMP_Instance.cpp
Kokkos_OpenMP_Task.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/OpenMP/Kokkos_OpenMP_Task.cpp
@ -107,5 +111,16 @@ Kokkos_OpenMPTarget_Task.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/OpenMP
$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/OpenMPTarget/Kokkos_OpenMPTarget_Task.cpp
endif
ifeq ($(KOKKOS_INTERNAL_USE_OPENACC), 1)
Kokkos_OpenACC.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/OpenACC/Kokkos_OpenACC.cpp
$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/OpenACC/Kokkos_OpenACC.cpp
Kokkos_OpenACCSpace.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/OpenACC/Kokkos_OpenACCSpace.cpp
$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/OpenACC/Kokkos_OpenACCSpace.cpp
Kokkos_OpenACC_Instance.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/OpenACC/Kokkos_OpenACC_Instance.cpp
$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/OpenACC/Kokkos_OpenACC_Instance.cpp
Kokkos_OpenACC_SharedAllocationRecord.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/OpenACC/Kokkos_OpenACC_SharedAllocationRecord.cpp
$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/OpenACC/Kokkos_OpenACC_SharedAllocationRecord.cpp
endif
Kokkos_HBWSpace.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/impl/Kokkos_HBWSpace.cpp
$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/impl/Kokkos_HBWSpace.cpp

11
lib/kokkos/algorithms/CMakeLists.txt
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@ -1,14 +1,7 @@
KOKKOS_SUBPACKAGE(Algorithms)
IF (NOT Kokkos_INSTALL_TESTING)
ADD_SUBDIRECTORY(src)
ENDIF()
IF(NOT (KOKKOS_ENABLE_OPENMPTARGET AND KOKKOS_CXX_COMPILER_ID STREQUAL NVHPC))
# FIXME_OPENACC: temporarily disabled due to unimplemented features
IF(NOT ((KOKKOS_ENABLE_OPENMPTARGET OR KOKKOS_ENABLE_OPENACC) AND KOKKOS_CXX_COMPILER_ID STREQUAL NVHPC))
KOKKOS_ADD_TEST_DIRECTORIES(unit_tests)
ENDIF()
KOKKOS_SUBPACKAGE_POSTPROCESS()

5
lib/kokkos/algorithms/cmake/Dependencies.cmake
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@ -1,5 +0,0 @@
TRIBITS_PACKAGE_DEFINE_DEPENDENCIES(
LIB_REQUIRED_PACKAGES KokkosCore KokkosContainers
LIB_OPTIONAL_TPLS Pthread CUDA HWLOC
TEST_OPTIONAL_TPLS CUSPARSE
)

4
lib/kokkos/algorithms/cmake/KokkosAlgorithms_config.h.in
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@ -1,4 +0,0 @@
#ifndef KOKKOS_ALGORITHMS_CONFIG_H
#define KOKKOS_ALGORITHMS_CONFIG_H
#endif

4
lib/kokkos/algorithms/src/CMakeLists.txt
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@ -1,6 +1,3 @@
KOKKOS_CONFIGURE_FILE(${PACKAGE_NAME}_config.h)
#I have to leave these here for tribits
KOKKOS_INCLUDE_DIRECTORIES(${CMAKE_CURRENT_BINARY_DIR})
KOKKOS_INCLUDE_DIRECTORIES(${CMAKE_CURRENT_SOURCE_DIR})
@ -9,7 +6,6 @@ KOKKOS_INCLUDE_DIRECTORIES(${CMAKE_CURRENT_SOURCE_DIR})
FILE(GLOB ALGO_HEADERS *.hpp)
FILE(GLOB ALGO_SOURCES *.cpp)
LIST(APPEND ALGO_HEADERS ${CMAKE_CURRENT_BINARY_DIR}/${PACKAGE_NAME}_config.h)
APPEND_GLOB(ALGO_HEADERS ${CMAKE_CURRENT_SOURCE_DIR}/std_algorithms/*.hpp)
APPEND_GLOB(ALGO_HEADERS ${CMAKE_CURRENT_SOURCE_DIR}/std_algorithms/impl/*.hpp)

16
lib/kokkos/algorithms/src/KokkosAlgorithms_dummy.cpp
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@ -1 +1,17 @@
//@HEADER
// ************************************************************************
//
// Kokkos v. 4.0
// Copyright (2022) National Technology & Engineering
// Solutions of Sandia, LLC (NTESS).
//
// Under the terms of Contract DE-NA0003525 with NTESS,
// the U.S. Government retains certain rights in this software.
//
// Part of Kokkos, under the Apache License v2.0 with LLVM Exceptions.
// See https://kokkos.org/LICENSE for license information.
// SPDX-License-Identifier: Apache-2.0 WITH LLVM-exception
//
//@HEADER
void KOKKOS_ALGORITHMS_SRC_DUMMY_PREVENT_LINK_ERROR() {}

188
lib/kokkos/algorithms/src/Kokkos_NestedSort.hpp Normal file
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@ -0,0 +1,188 @@
//@HEADER
// ************************************************************************
//
// Kokkos v. 4.0
// Copyright (2022) National Technology & Engineering
// Solutions of Sandia, LLC (NTESS).
//
// Under the terms of Contract DE-NA0003525 with NTESS,
// the U.S. Government retains certain rights in this software.
//
// Part of Kokkos, under the Apache License v2.0 with LLVM Exceptions.
// See https://kokkos.org/LICENSE for license information.
// SPDX-License-Identifier: Apache-2.0 WITH LLVM-exception
//
//@HEADER
#ifndef KOKKOS_NESTEDSORT_HPP_
#define KOKKOS_NESTEDSORT_HPP_
#include <Kokkos_Core.hpp>
#include <std_algorithms/impl/Kokkos_HelperPredicates.hpp>
#include <std_algorithms/Kokkos_Swap.hpp>
namespace Kokkos {
namespace Experimental {
namespace Impl {
// true for TeamVectorRange, false for ThreadVectorRange
template <bool teamLevel>
struct NestedRange {};
// Specialization for team-level
template <>
struct NestedRange<true> {
template <typename TeamMember, typename SizeType>
KOKKOS_FUNCTION static auto create(const TeamMember& t, SizeType len) {
return Kokkos::TeamVectorRange(t, len);
}
template <typename TeamMember>
KOKKOS_FUNCTION static void barrier(const TeamMember& t) {
t.team_barrier();
}
};
// Specialization for thread-level
template <>
struct NestedRange<false> {
template <typename TeamMember, typename SizeType>
KOKKOS_FUNCTION static auto create(const TeamMember& t, SizeType len) {
return Kokkos::ThreadVectorRange(t, len);
}
// Barrier is no-op, as vector lanes of a thread are implicitly synchronized
// after parallel region
template <typename TeamMember>
KOKKOS_FUNCTION static void barrier(const TeamMember&) {}
};
// When just doing sort (not sort_by_key), use nullptr_t for ValueViewType.
// This only takes the NestedRange instance for template arg deduction.
template <class TeamMember, class KeyViewType, class ValueViewType,
class Comparator, bool useTeamLevel>
KOKKOS_INLINE_FUNCTION void sort_nested_impl(
const TeamMember& t, const KeyViewType& keyView,
[[maybe_unused]] const ValueViewType& valueView, const Comparator& comp,
const NestedRange<useTeamLevel>) {
using SizeType = typename KeyViewType::size_type;
using KeyType = typename KeyViewType::non_const_value_type;
using Range = NestedRange<useTeamLevel>;
SizeType n = keyView.extent(0);
SizeType npot = 1;
SizeType levels = 0;
// FIXME: ceiling power-of-two is a common thing to need - make it a utility
while (npot < n) {
levels++;
npot <<= 1;
}
for (SizeType i = 0; i < levels; i++) {
for (SizeType j = 0; j <= i; j++) {
// n/2 pairs of items are compared in parallel
Kokkos::parallel_for(Range::create(t, npot / 2), [=](const SizeType k) {
// How big are the brown/pink boxes?
// (Terminology comes from Wikipedia diagram)
// https://commons.wikimedia.org/wiki/File:BitonicSort.svg#/media/File:BitonicSort.svg
SizeType boxSize = SizeType(2) << (i - j);
// Which box contains this thread?
SizeType boxID = k >> (i - j); // k * 2 / boxSize;
SizeType boxStart = boxID << (1 + i - j); // boxID * boxSize
SizeType boxOffset = k - (boxStart >> 1); // k - boxID * boxSize / 2;
SizeType elem1 = boxStart + boxOffset;
// In first phase (j == 0, brown box): within a box, compare with the
// opposite value in the box.
// In later phases (j > 0, pink box): within a box, compare with fixed
// distance (boxSize / 2) apart.
SizeType elem2 = (j == 0) ? (boxStart + boxSize - 1 - boxOffset)
: (elem1 + boxSize / 2);
if (elem2 < n) {
KeyType key1 = keyView(elem1);
KeyType key2 = keyView(elem2);
if (comp(key2, key1)) {
keyView(elem1) = key2;
keyView(elem2) = key1;
if constexpr (!std::is_same_v<ValueViewType, std::nullptr_t>) {
Kokkos::Experimental::swap(valueView(elem1), valueView(elem2));
}
}
}
});
Range::barrier(t);
}
}
}
} // namespace Impl
template <class TeamMember, class ViewType>
KOKKOS_INLINE_FUNCTION void sort_team(const TeamMember& t,
const ViewType& view) {
Impl::sort_nested_impl(t, view, nullptr,
Experimental::Impl::StdAlgoLessThanBinaryPredicate<
typename ViewType::non_const_value_type>(),
Impl::NestedRange<true>());
}
template <class TeamMember, class ViewType, class Comparator>
KOKKOS_INLINE_FUNCTION void sort_team(const TeamMember& t, const ViewType& view,
const Comparator& comp) {
Impl::sort_nested_impl(t, view, nullptr, comp, Impl::NestedRange<true>());
}
template <class TeamMember, class KeyViewType, class ValueViewType>
KOKKOS_INLINE_FUNCTION void sort_by_key_team(const TeamMember& t,
const KeyViewType& keyView,
const ValueViewType& valueView) {
Impl::sort_nested_impl(t, keyView, valueView,
Experimental::Impl::StdAlgoLessThanBinaryPredicate<
typename KeyViewType::non_const_value_type>(),
Impl::NestedRange<true>());
}
template <class TeamMember, class KeyViewType, class ValueViewType,
class Comparator>
KOKKOS_INLINE_FUNCTION void sort_by_key_team(const TeamMember& t,
const KeyViewType& keyView,
const ValueViewType& valueView,
const Comparator& comp) {
Impl::sort_nested_impl(t, keyView, valueView, comp,
Impl::NestedRange<true>());
}
template <class TeamMember, class ViewType>
KOKKOS_INLINE_FUNCTION void sort_thread(const TeamMember& t,
const ViewType& view) {
Impl::sort_nested_impl(t, view, nullptr,
Experimental::Impl::StdAlgoLessThanBinaryPredicate<
typename ViewType::non_const_value_type>(),
Impl::NestedRange<false>());
}
template <class TeamMember, class ViewType, class Comparator>
KOKKOS_INLINE_FUNCTION void sort_thread(const TeamMember& t,
const ViewType& view,
const Comparator& comp) {
Impl::sort_nested_impl(t, view, nullptr, comp, Impl::NestedRange<false>());
}
template <class TeamMember, class KeyViewType, class ValueViewType>
KOKKOS_INLINE_FUNCTION void sort_by_key_thread(const TeamMember& t,
const KeyViewType& keyView,
const ValueViewType& valueView) {
Impl::sort_nested_impl(t, keyView, valueView,
Experimental::Impl::StdAlgoLessThanBinaryPredicate<
typename KeyViewType::non_const_value_type>(),
Impl::NestedRange<false>());
}
template <class TeamMember, class KeyViewType, class ValueViewType,
class Comparator>
KOKKOS_INLINE_FUNCTION void sort_by_key_thread(const TeamMember& t,
const KeyViewType& keyView,
const ValueViewType& valueView,
const Comparator& comp) {
Impl::sort_nested_impl(t, keyView, valueView, comp,
Impl::NestedRange<false>());
}
} // namespace Experimental
} // namespace Kokkos
#endif

132
lib/kokkos/algorithms/src/Kokkos_Random.hpp
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@ -1,46 +1,18 @@
/*
//@HEADER
// ************************************************************************
//
// Kokkos v. 3.0
// Copyright (2020) National Technology & Engineering
// Kokkos v. 4.0
// Copyright (2022) National Technology & Engineering
// Solutions of Sandia, LLC (NTESS).
//
// Under the terms of Contract DE-NA0003525 with NTESS,
// the U.S. Government retains certain rights in this software.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are
// met:
// Part of Kokkos, under the Apache License v2.0 with LLVM Exceptions.
// See https://kokkos.org/LICENSE for license information.
// SPDX-License-Identifier: Apache-2.0 WITH LLVM-exception
//
// 1. Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
//
// 2. Redistributions in binary form must reproduce the above copyright
// notice, this list of conditions and the following disclaimer in the
// documentation and/or other materials provided with the distribution.
//
// 3. Neither the name of the Corporation nor the names of the
// contributors may be used to endorse or promote products derived from
// this software without specific prior written permission.
//
// THIS SOFTWARE IS PROVIDED BY NTESS "AS IS" AND ANY
// EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL NTESS OR THE
// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
// NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
// Questions? Contact Christian R. Trott (crtrott@sandia.gov)
//
// ************************************************************************
//@HEADER
*/
#ifndef KOKKOS_RANDOM_HPP
#define KOKKOS_RANDOM_HPP
@ -631,8 +603,7 @@ struct Random_XorShift1024_UseCArrayState<Kokkos::Cuda> : std::false_type {};
#endif
#ifdef KOKKOS_ENABLE_HIP
template <>
struct Random_XorShift1024_UseCArrayState<Kokkos::Experimental::HIP>
: std::false_type {};
struct Random_XorShift1024_UseCArrayState<Kokkos::HIP> : std::false_type {};
#endif
#ifdef KOKKOS_ENABLE_OPENMPTARGET
template <>
@ -657,7 +628,7 @@ struct Random_UniqueIndex {
#if defined(KOKKOS_ENABLE_CUDA)
#define KOKKOS_IMPL_EXECUTION_SPACE_CUDA_OR_HIP Kokkos::Cuda
#elif defined(KOKKOS_ENABLE_HIP)
#define KOKKOS_IMPL_EXECUTION_SPACE_CUDA_OR_HIP Kokkos::Experimental::HIP
#define KOKKOS_IMPL_EXECUTION_SPACE_CUDA_OR_HIP Kokkos::HIP
#endif
template <class MemorySpace>
@ -907,38 +878,32 @@ class Random_XorShift64_Pool {
using execution_space = typename device_type::execution_space;
using locks_type = View<int**, device_type>;
using state_data_type = View<uint64_t**, device_type>;
locks_type locks_;
state_data_type state_;
int num_states_;
int padding_;
locks_type locks_ = {};
state_data_type state_ = {};
int num_states_ = {};
int padding_ = {};
public:
using generator_type = Random_XorShift64<DeviceType>;
KOKKOS_INLINE_FUNCTION
Random_XorShift64_Pool() {
num_states_ = 0;
padding_ = 0;
}
#ifdef KOKKOS_ENABLE_DEPRECATED_CODE_4
KOKKOS_DEFAULTED_FUNCTION Random_XorShift64_Pool() = default;
KOKKOS_DEFAULTED_FUNCTION Random_XorShift64_Pool(
Random_XorShift64_Pool const&) = default;
KOKKOS_DEFAULTED_FUNCTION Random_XorShift64_Pool& operator=(
Random_XorShift64_Pool const&) = default;
#else
Random_XorShift64_Pool() = default;
#endif
Random_XorShift64_Pool(uint64_t seed) {
num_states_ = 0;
init(seed, execution_space().concurrency());
}
KOKKOS_INLINE_FUNCTION
Random_XorShift64_Pool(const Random_XorShift64_Pool& src)
: locks_(src.locks_), state_(src.state_), num_states_(src.num_states_) {}
KOKKOS_INLINE_FUNCTION
Random_XorShift64_Pool operator=(const Random_XorShift64_Pool& src) {
locks_ = src.locks_;
state_ = src.state_;
num_states_ = src.num_states_;
padding_ = src.padding_;
return *this;
}
void init(uint64_t seed, int num_states) {
if (seed == 0) seed = uint64_t(1318319);
// I only want to pad on CPU like archs (less than 1000 threads). 64 is a
@ -976,8 +941,8 @@ class Random_XorShift64_Pool {
deep_copy(locks_, h_lock);
}
KOKKOS_INLINE_FUNCTION
Random_XorShift64<DeviceType> get_state() const {
KOKKOS_INLINE_FUNCTION Random_XorShift64<DeviceType> get_state() const {
KOKKOS_EXPECTS(num_states_ > 0);
const int i = Impl::Random_UniqueIndex<device_type>::get_state_idx(locks_);
return Random_XorShift64<DeviceType>(state_(i, 0), i);
}
@ -1158,43 +1123,35 @@ class Random_XorShift1024_Pool {
using int_view_type = View<int**, device_type>;
using state_data_type = View<uint64_t * [16], device_type>;
locks_type locks_;
state_data_type state_;
int_view_type p_;
int num_states_;
int padding_;
locks_type locks_ = {};
state_data_type state_ = {};
int_view_type p_ = {};
int num_states_ = {};
int padding_ = {};
friend class Random_XorShift1024<DeviceType>;
public:
using generator_type = Random_XorShift1024<DeviceType>;
KOKKOS_INLINE_FUNCTION
Random_XorShift1024_Pool() { num_states_ = 0; }
#ifdef KOKKOS_ENABLE_DEPRECATED_CODE_4
KOKKOS_DEFAULTED_FUNCTION Random_XorShift1024_Pool() = default;
inline Random_XorShift1024_Pool(uint64_t seed) {
KOKKOS_DEFAULTED_FUNCTION Random_XorShift1024_Pool(
Random_XorShift1024_Pool const&) = default;
KOKKOS_DEFAULTED_FUNCTION Random_XorShift1024_Pool& operator=(
Random_XorShift1024_Pool const&) = default;
#else
Random_XorShift1024_Pool() = default;
#endif
Random_XorShift1024_Pool(uint64_t seed) {
num_states_ = 0;
init(seed, execution_space().concurrency());
}
KOKKOS_INLINE_FUNCTION
Random_XorShift1024_Pool(const Random_XorShift1024_Pool& src)
: locks_(src.locks_),
state_(src.state_),
p_(src.p_),
num_states_(src.num_states_) {}
KOKKOS_INLINE_FUNCTION
Random_XorShift1024_Pool operator=(const Random_XorShift1024_Pool& src) {
locks_ = src.locks_;
state_ = src.state_;
p_ = src.p_;
num_states_ = src.num_states_;
padding_ = src.padding_;
return *this;
}
inline void init(uint64_t seed, int num_states) {
void init(uint64_t seed, int num_states) {
if (seed == 0) seed = uint64_t(1318319);
// I only want to pad on CPU like archs (less than 1000 threads). 64 is a
// magic number, or random number I just wanted something not too large and
@ -1237,6 +1194,7 @@ class Random_XorShift1024_Pool {
KOKKOS_INLINE_FUNCTION
Random_XorShift1024<DeviceType> get_state() const {
KOKKOS_EXPECTS(num_states_ > 0);
const int i = Impl::Random_UniqueIndex<device_type>::get_state_idx(locks_);
return Random_XorShift1024<DeviceType>(state_, p_(i, 0), i);
};
@ -1556,7 +1514,7 @@ void fill_random(const ExecutionSpace& exec, ViewType a, RandomPool g,
"Kokkos::fill_random",
Kokkos::RangePolicy<ExecutionSpace>(exec, 0, (LDA + 127) / 128),
Impl::fill_random_functor_begin_end<ViewType, RandomPool, 128,
ViewType::Rank, IndexType>(
ViewType::rank, IndexType>(
a, g, begin, end));
}

285
lib/kokkos/algorithms/src/Kokkos_Sort.hpp
View File

@ -1,46 +1,18 @@
/*
//@HEADER
// ************************************************************************
//
// Kokkos v. 3.0
// Copyright (2020) National Technology & Engineering
// Kokkos v. 4.0
// Copyright (2022) National Technology & Engineering
// Solutions of Sandia, LLC (NTESS).
//
// Under the terms of Contract DE-NA0003525 with NTESS,
// the U.S. Government retains certain rights in this software.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are
// met:
// Part of Kokkos, under the Apache License v2.0 with LLVM Exceptions.
// See https://kokkos.org/LICENSE for license information.
// SPDX-License-Identifier: Apache-2.0 WITH LLVM-exception
//
// 1. Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
//
// 2. Redistributions in binary form must reproduce the above copyright
// notice, this list of conditions and the following disclaimer in the
// documentation and/or other materials provided with the distribution.
//
// 3. Neither the name of the Corporation nor the names of the
// contributors may be used to endorse or promote products derived from
// this software without specific prior written permission.
//
// THIS SOFTWARE IS PROVIDED BY NTESS "AS IS" AND ANY
// EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL NTESS OR THE
// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
// NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
// Questions? Contact Christian R. Trott (crtrott@sandia.gov)
//
// ************************************************************************
//@HEADER
*/
#ifndef KOKKOS_SORT_HPP_
#define KOKKOS_SORT_HPP_
@ -50,14 +22,60 @@
#endif
#include <Kokkos_Core.hpp>
#include <Kokkos_NestedSort.hpp>
#include <std_algorithms/Kokkos_BeginEnd.hpp>
#include <algorithm>
#if defined(KOKKOS_ENABLE_CUDA)
// Workaround for `Instruction 'shfl' without '.sync' is not supported on
// .target sm_70 and higher from PTX ISA version 6.4`.
// Also see https://github.com/NVIDIA/cub/pull/170.
#if !defined(CUB_USE_COOPERATIVE_GROUPS)
#define CUB_USE_COOPERATIVE_GROUPS
#endif
#pragma GCC diagnostic push
#pragma GCC diagnostic ignored "-Wshadow"
#if defined(KOKKOS_COMPILER_CLANG)
// Some versions of Clang fail to compile Thrust, failing with errors like
// this:
// <snip>/thrust/system/cuda/detail/core/agent_launcher.h:557:11:
// error: use of undeclared identifier 'va_printf'
// The exact combination of versions for Clang and Thrust (or CUDA) for this
// failure was not investigated, however even very recent version combination
// (Clang 10.0.0 and Cuda 10.0) demonstrated failure.
//
// Defining _CubLog here locally allows us to avoid that code path, however
// disabling some debugging diagnostics
#pragma push_macro("_CubLog")
#ifdef _CubLog
#undef _CubLog
#endif
#define _CubLog
#include <thrust/device_ptr.h>
#include <thrust/sort.h>
#pragma pop_macro("_CubLog")
#else
#include <thrust/device_ptr.h>
#include <thrust/sort.h>
#endif
#pragma GCC diagnostic pop
#endif
#if defined(KOKKOS_ENABLE_ONEDPL)
#include <oneapi/dpl/execution>
#include <oneapi/dpl/algorithm>
#endif
namespace Kokkos {
namespace Impl {
template <class DstViewType, class SrcViewType, int Rank = DstViewType::Rank>
template <class DstViewType, class SrcViewType, int Rank = DstViewType::rank>
struct CopyOp;
template <class DstViewType, class SrcViewType>
@ -128,8 +146,12 @@ class BinSort {
Kokkos::is_view<SrcViewType>::value,
Kokkos::View<typename SrcViewType::const_data_type,
typename SrcViewType::array_layout,
typename SrcViewType::device_type,
Kokkos::MemoryTraits<Kokkos::RandomAccess> >,
typename SrcViewType::device_type
#if !defined(KOKKOS_COMPILER_NVHPC) // FIXME_NVHPC
,
Kokkos::MemoryTraits<Kokkos::RandomAccess>
#endif
>,
typename SrcViewType::const_type>;
using perm_view_type = typename PermuteViewType::const_type;
@ -208,7 +230,11 @@ class BinSort {
bool sort_within_bins;
public:
BinSort() = default;
#ifdef KOKKOS_ENABLE_DEPRECATED_CODE_4
KOKKOS_DEPRECATED BinSort() = default;
#else
BinSort() = delete;
#endif
//----------------------------------------
// Constructor: takes the keys, the binning_operator and optionally whether to
@ -311,6 +337,10 @@ class BinSort {
template <class ExecutionSpace, class ValuesViewType>
void sort(const ExecutionSpace& exec, ValuesViewType const& values,
int values_range_begin, int values_range_end) const {
if (values.extent(0) == 0) {
return;
}
static_assert(
Kokkos::SpaceAccessibility<ExecutionSpace,
typename Space::memory_space>::accessible,
@ -322,11 +352,6 @@ class BinSort {
"The provided execution space must be able to access the memory space "
"of the View argument!");
using scratch_view_type =
Kokkos::View<typename ValuesViewType::data_type,
typename ValuesViewType::array_layout,
typename ValuesViewType::device_type>;
const size_t len = range_end - range_begin;
const size_t values_len = values_range_end - values_range_begin;
if (len != values_len) {
@ -334,6 +359,9 @@ class BinSort {
"BinSort::sort: values range length != permutation vector length");
}
using scratch_view_type =
Kokkos::View<typename ValuesViewType::data_type,
typename ValuesViewType::device_type>;
scratch_view_type sorted_values(
view_alloc(exec, WithoutInitializing,
"Kokkos::SortImpl::BinSortFunctor::sorted_values"),
@ -438,24 +466,29 @@ class BinSort {
void operator()(const bin_sort_bins_tag& /*tag*/, const int i) const {
auto bin_size = bin_count_const(i);
if (bin_size <= 1) return;
int upper_bound = bin_offsets(i) + bin_size;
bool sorted = false;
while (!sorted) {
sorted = true;
int old_idx = sort_order(bin_offsets(i));
int new_idx = 0;
for (int k = bin_offsets(i) + 1; k < upper_bound; k++) {
new_idx = sort_order(k);
if (!bin_op(keys_rnd, old_idx, new_idx)) {
sort_order(k - 1) = new_idx;
sort_order(k) = old_idx;
sorted = false;
} else {
old_idx = new_idx;
}
constexpr bool use_std_sort =
std::is_same_v<typename exec_space::memory_space, HostSpace>;
int lower_bound = bin_offsets(i);
int upper_bound = lower_bound + bin_size;
// Switching to std::sort for more than 10 elements has been found
// reasonable experimentally.
if (use_std_sort && bin_size > 10) {
if constexpr (use_std_sort) {
std::sort(&sort_order(lower_bound), &sort_order(upper_bound),
[this](int p, int q) { return bin_op(keys_rnd, p, q); });
}
} else {
for (int k = lower_bound + 1; k < upper_bound; ++k) {
int old_idx = sort_order(k);
int j = k - 1;
while (j >= lower_bound) {
int new_idx = sort_order(j);
if (!bin_op(keys_rnd, old_idx, new_idx)) break;
sort_order(j + 1) = new_idx;
--j;
}
sort_order(j + 1) = old_idx;
}
upper_bound--;
}
}
};
@ -468,7 +501,11 @@ struct BinOp1D {
double mul_ = {};
double min_ = {};
BinOp1D() = default;
#ifdef KOKKOS_ENABLE_DEPRECATED_CODE_4
KOKKOS_DEPRECATED BinOp1D() = default;
#else
BinOp1D() = delete;
#endif
// Construct BinOp with number of bins, minimum value and maximum value
BinOp1D(int max_bins__, typename KeyViewType::const_value_type min,
@ -512,7 +549,11 @@ struct BinOp3D {
double mul_[3] = {};
double min_[3] = {};
BinOp3D() = default;
#ifdef KOKKOS_ENABLE_DEPRECATED_CODE_4
KOKKOS_DEPRECATED BinOp3D() = default;
#else
BinOp3D() = delete;
#endif
BinOp3D(int max_bins__[], typename KeyViewType::const_value_type min[],
typename KeyViewType::const_value_type max[]) {
@ -559,24 +600,6 @@ struct BinOp3D {
namespace Impl {
template <class ViewType, class ExecutionSpace>
bool try_std_sort(ViewType view, const ExecutionSpace& exec) {
bool possible = true;
size_t stride[8] = {view.stride_0(), view.stride_1(), view.stride_2(),
view.stride_3(), view.stride_4(), view.stride_5(),
view.stride_6(), view.stride_7()};
possible = possible &&
SpaceAccessibility<HostSpace,
typename ViewType::memory_space>::accessible;
possible = possible && (ViewType::Rank == 1);
possible = possible && (stride[0] == 1);
if (possible) {
exec.fence("Kokkos::sort: Fence before sorting on the host");
std::sort(view.data(), view.data() + view.extent(0));
}
return possible;
}
template <class ViewType>
struct min_max_functor {
using minmax_scalar =
@ -594,9 +617,18 @@ struct min_max_functor {
} // namespace Impl
template <class ExecutionSpace, class ViewType>
std::enable_if_t<Kokkos::is_execution_space<ExecutionSpace>::value> sort(
const ExecutionSpace& exec, ViewType const& view) {
template <class ExecutionSpace, class DataType, class... Properties>
std::enable_if_t<(Kokkos::is_execution_space<ExecutionSpace>::value) &&
(!SpaceAccessibility<
HostSpace, typename Kokkos::View<DataType, Properties...>::
memory_space>::accessible)>
sort(const ExecutionSpace& exec,
const Kokkos::View<DataType, Properties...>& view) {
if (view.extent(0) == 0) {
return;
}
using ViewType = Kokkos::View<DataType, Properties...>;
using CompType = BinOp1D<ViewType>;
Kokkos::MinMaxScalar<typename ViewType::non_const_value_type> result;
@ -634,44 +666,84 @@ std::enable_if_t<Kokkos::is_execution_space<ExecutionSpace>::value> sort(
bin_sort.sort(exec, view);
}
#ifdef KOKKOS_ENABLE_DEPRECATED_CODE_3
template <class ExecutionSpace, class ViewType>
KOKKOS_DEPRECATED_WITH_COMMENT(
"Use the overload not taking bool always_use_kokkos_sort")
std::enable_if_t<Kokkos::is_execution_space<ExecutionSpace>::value> sort(
const ExecutionSpace& exec, ViewType const& view,
bool const always_use_kokkos_sort) {
if (!always_use_kokkos_sort && Impl::try_std_sort(view, exec)) {
#if defined(KOKKOS_ENABLE_ONEDPL)
template <class DataType, class... Properties>
void sort(const Experimental::SYCL& space,
const Kokkos::View<DataType, Properties...>& view) {
if (view.extent(0) == 0) {
return;
} else {
sort(exec, view);
}
using ViewType = Kokkos::View<DataType, Properties...>;
static_assert(SpaceAccessibility<Experimental::SYCL,
typename ViewType::memory_space>::accessible,
"SYCL execution space is not able to access the memory space "
"of the View argument!");
auto queue = space.sycl_queue();
auto policy = oneapi::dpl::execution::make_device_policy(queue);
// Can't use Experimental::begin/end here since the oneDPL then assumes that
// the data is on the host.
static_assert(
ViewType::rank == 1 &&
(std::is_same<typename ViewType::array_layout, LayoutRight>::value ||
std::is_same<typename ViewType::array_layout, LayoutLeft>::value),
"SYCL sort only supports contiguous 1D Views.");
const int n = view.extent(0);
oneapi::dpl::sort(policy, view.data(), view.data() + n);
}
#endif
template <class ExecutionSpace, class DataType, class... Properties>
std::enable_if_t<(Kokkos::is_execution_space<ExecutionSpace>::value) &&
(SpaceAccessibility<
HostSpace, typename Kokkos::View<DataType, Properties...>::
memory_space>::accessible)>
sort(const ExecutionSpace&, const Kokkos::View<DataType, Properties...>& view) {
if (view.extent(0) == 0) {
return;
}
auto first = Experimental::begin(view);
auto last = Experimental::end(view);
std::sort(first, last);
}
#if defined(KOKKOS_ENABLE_CUDA)
template <class DataType, class... Properties>
void sort(const Cuda& space,
const Kokkos::View<DataType, Properties...>& view) {
if (view.extent(0) == 0) {
return;
}
const auto exec = thrust::cuda::par.on(space.cuda_stream());
auto first = Experimental::begin(view);
auto last = Experimental::end(view);
thrust::sort(exec, first, last);
}
#endif
template <class ViewType>
void sort(ViewType const& view) {
Kokkos::fence("Kokkos::sort: before");
if (view.extent(0) == 0) {
return;
}
typename ViewType::execution_space exec;
sort(exec, view);
exec.fence("Kokkos::sort: fence after sorting");
}
#ifdef KOKKOS_ENABLE_DEPRECATED_CODE_3
template <class ViewType>
KOKKOS_DEPRECATED_WITH_COMMENT(
"Use the overload not taking bool always_use_kokkos_sort")
void sort(ViewType const& view, bool const always_use_kokkos_sort) {
typename ViewType::execution_space exec;
sort(exec, view, always_use_kokkos_sort);
exec.fence("Kokkos::Sort: fence after sorting");
}
#endif
template <class ExecutionSpace, class ViewType>
std::enable_if_t<Kokkos::is_execution_space<ExecutionSpace>::value> sort(
const ExecutionSpace& exec, ViewType view, size_t const begin,
size_t const end) {
if (view.extent(0) == 0) {
return;
}
using range_policy = Kokkos::RangePolicy<typename ViewType::execution_space>;
using CompType = BinOp1D<ViewType>;
@ -694,6 +766,11 @@ std::enable_if_t<Kokkos::is_execution_space<ExecutionSpace>::value> sort(
template <class ViewType>
void sort(ViewType view, size_t const begin, size_t const end) {
Kokkos::fence("Kokkos::sort: before");
if (view.extent(0) == 0) {
return;
}
typename ViewType::execution_space exec;
sort(exec, view, begin, end);
exec.fence("Kokkos::Sort: fence after sorting");

38
lib/kokkos/algorithms/src/Kokkos_StdAlgorithms.hpp
View File

@ -1,46 +1,18 @@
/*
//@HEADER
// ************************************************************************
//
// Kokkos v. 3.0
// Copyright (2020) National Technology & Engineering
// Kokkos v. 4.0
// Copyright (2022) National Technology & Engineering
// Solutions of Sandia, LLC (NTESS).
//
// Under the terms of Contract DE-NA0003525 with NTESS,
// the U.S. Government retains certain rights in this software.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are
// met:
// Part of Kokkos, under the Apache License v2.0 with LLVM Exceptions.
// See https://kokkos.org/LICENSE for license information.
// SPDX-License-Identifier: Apache-2.0 WITH LLVM-exception
//
// 1. Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
//
// 2. Redistributions in binary form must reproduce the above copyright
// notice, this list of conditions and the following disclaimer in the
// documentation and/or other materials provided with the distribution.
//
// 3. Neither the name of the Corporation nor the names of the
// contributors may be used to endorse or promote products derived from
// this software without specific prior written permission.
//
// THIS SOFTWARE IS PROVIDED BY NTESS "AS IS" AND ANY
// EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL NTESS OR THE
// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
// NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
// Questions? Contact Christian R. Trott (crtrott@sandia.gov)
//
// ************************************************************************
//@HEADER
*/
#ifndef KOKKOS_STD_ALGORITHMS_HPP
#define KOKKOS_STD_ALGORITHMS_HPP

38
lib/kokkos/algorithms/src/std_algorithms/Kokkos_AdjacentDifference.hpp
View File

@ -1,46 +1,18 @@
/*
//@HEADER
// ************************************************************************
//
// Kokkos v. 3.0
// Copyright (2020) National Technology & Engineering
// Kokkos v. 4.0
// Copyright (2022) National Technology & Engineering
// Solutions of Sandia, LLC (NTESS).
//
// Under the terms of Contract DE-NA0003525 with NTESS,
// the U.S. Government retains certain rights in this software.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are
// met:
// Part of Kokkos, under the Apache License v2.0 with LLVM Exceptions.
// See https://kokkos.org/LICENSE for license information.
// SPDX-License-Identifier: Apache-2.0 WITH LLVM-exception
//
// 1. Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
//
// 2. Redistributions in binary form must reproduce the above copyright
// notice, this list of conditions and the following disclaimer in the
// documentation and/or other materials provided with the distribution.
//
// 3. Neither the name of the Corporation nor the names of the
// contributors may be used to endorse or promote products derived from
// this software without specific prior written permission.
//
// THIS SOFTWARE IS PROVIDED BY NTESS "AS IS" AND ANY
// EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL NTESS OR THE
// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
// NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
// Questions? Contact Christian R. Trott (crtrott@sandia.gov)
//
// ************************************************************************
//@HEADER
*/
#ifndef KOKKOS_STD_ALGORITHMS_ADJACENT_DIFFERENCE_HPP
#define KOKKOS_STD_ALGORITHMS_ADJACENT_DIFFERENCE_HPP

38
lib/kokkos/algorithms/src/std_algorithms/Kokkos_AdjacentFind.hpp
View File

@ -1,46 +1,18 @@
/*
//@HEADER
// ************************************************************************
//
// Kokkos v. 3.0
// Copyright (2020) National Technology & Engineering
// Kokkos v. 4.0
// Copyright (2022) National Technology & Engineering
// Solutions of Sandia, LLC (NTESS).
//
// Under the terms of Contract DE-NA0003525 with NTESS,
// the U.S. Government retains certain rights in this software.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are
// met:
// Part of Kokkos, under the Apache License v2.0 with LLVM Exceptions.
// See https://kokkos.org/LICENSE for license information.
// SPDX-License-Identifier: Apache-2.0 WITH LLVM-exception
//
// 1. Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
//
// 2. Redistributions in binary form must reproduce the above copyright
// notice, this list of conditions and the following disclaimer in the
// documentation and/or other materials provided with the distribution.
//
// 3. Neither the name of the Corporation nor the names of the
// contributors may be used to endorse or promote products derived from
// this software without specific prior written permission.
//
// THIS SOFTWARE IS PROVIDED BY NTESS "AS IS" AND ANY
// EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL NTESS OR THE
// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
// NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
// Questions? Contact Christian R. Trott (crtrott@sandia.gov)
//
// ************************************************************************
//@HEADER
*/
#ifndef KOKKOS_STD_ALGORITHMS_ADJACENT_FIND_HPP
#define KOKKOS_STD_ALGORITHMS_ADJACENT_FIND_HPP

38
lib/kokkos/algorithms/src/std_algorithms/Kokkos_AllOf.hpp
View File

@ -1,46 +1,18 @@
/*
//@HEADER
// ************************************************************************
//
// Kokkos v. 3.0
// Copyright (2020) National Technology & Engineering
// Kokkos v. 4.0
// Copyright (2022) National Technology & Engineering
// Solutions of Sandia, LLC (NTESS).
//
// Under the terms of Contract DE-NA0003525 with NTESS,
// the U.S. Government retains certain rights in this software.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are
// met:
// Part of Kokkos, under the Apache License v2.0 with LLVM Exceptions.
// See https://kokkos.org/LICENSE for license information.
// SPDX-License-Identifier: Apache-2.0 WITH LLVM-exception
//
// 1. Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
//
// 2. Redistributions in binary form must reproduce the above copyright
// notice, this list of conditions and the following disclaimer in the
// documentation and/or other materials provided with the distribution.
//
// 3. Neither the name of the Corporation nor the names of the
// contributors may be used to endorse or promote products derived from
// this software without specific prior written permission.
//
// THIS SOFTWARE IS PROVIDED BY NTESS "AS IS" AND ANY
// EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL NTESS OR THE
// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
// NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
// Questions? Contact Christian R. Trott (crtrott@sandia.gov)
//
// ************************************************************************
//@HEADER
*/
#ifndef KOKKOS_STD_ALGORITHMS_ALL_OF_HPP
#define KOKKOS_STD_ALGORITHMS_ALL_OF_HPP

38
lib/kokkos/algorithms/src/std_algorithms/Kokkos_AnyOf.hpp
View File

@ -1,46 +1,18 @@
/*
//@HEADER
// ************************************************************************
//
// Kokkos v. 3.0
// Copyright (2020) National Technology & Engineering
// Kokkos v. 4.0
// Copyright (2022) National Technology & Engineering
// Solutions of Sandia, LLC (NTESS).
//
// Under the terms of Contract DE-NA0003525 with NTESS,
// the U.S. Government retains certain rights in this software.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are
// met:
// Part of Kokkos, under the Apache License v2.0 with LLVM Exceptions.
// See https://kokkos.org/LICENSE for license information.
// SPDX-License-Identifier: Apache-2.0 WITH LLVM-exception
//
// 1. Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
//
// 2. Redistributions in binary form must reproduce the above copyright
// notice, this list of conditions and the following disclaimer in the
// documentation and/or other materials provided with the distribution.
//
// 3. Neither the name of the Corporation nor the names of the
// contributors may be used to endorse or promote products derived from
// this software without specific prior written permission.
//
// THIS SOFTWARE IS PROVIDED BY NTESS "AS IS" AND ANY
// EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL NTESS OR THE
// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
// NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
// Questions? Contact Christian R. Trott (crtrott@sandia.gov)
//
// ************************************************************************
//@HEADER
*/
#ifndef KOKKOS_STD_ALGORITHMS_ANY_OF_HPP
#define KOKKOS_STD_ALGORITHMS_ANY_OF_HPP

38
lib/kokkos/algorithms/src/std_algorithms/Kokkos_BeginEnd.hpp
View File

@ -1,46 +1,18 @@
/*
//@HEADER
// ************************************************************************
//
// Kokkos v. 3.0
// Copyright (2020) National Technology & Engineering
// Kokkos v. 4.0
// Copyright (2022) National Technology & Engineering
// Solutions of Sandia, LLC (NTESS).
//
// Under the terms of Contract DE-NA0003525 with NTESS,
// the U.S. Government retains certain rights in this software.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are
// met:
// Part of Kokkos, under the Apache License v2.0 with LLVM Exceptions.
// See https://kokkos.org/LICENSE for license information.
// SPDX-License-Identifier: Apache-2.0 WITH LLVM-exception
//
// 1. Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
//
// 2. Redistributions in binary form must reproduce the above copyright
// notice, this list of conditions and the following disclaimer in the
// documentation and/or other materials provided with the distribution.
//
// 3. Neither the name of the Corporation nor the names of the
// contributors may be used to endorse or promote products derived from
// this software without specific prior written permission.
//
// THIS SOFTWARE IS PROVIDED BY NTESS "AS IS" AND ANY
// EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL NTESS OR THE
// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
// NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
// Questions? Contact Christian R. Trott (crtrott@sandia.gov)
//
// ************************************************************************
//@HEADER
*/
#ifndef KOKKOS_BEGIN_END_HPP
#define KOKKOS_BEGIN_END_HPP

38
lib/kokkos/algorithms/src/std_algorithms/Kokkos_Copy.hpp
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@ -1,46 +1,18 @@
/*
//@HEADER
// ************************************************************************
//
// Kokkos v. 3.0
// Copyright (2020) National Technology & Engineering
// Kokkos v. 4.0
// Copyright (2022) National Technology & Engineering
// Solutions of Sandia, LLC (NTESS).
//
// Under the terms of Contract DE-NA0003525 with NTESS,
// the U.S. Government retains certain rights in this software.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are
// met:
// Part of Kokkos, under the Apache License v2.0 with LLVM Exceptions.
// See https://kokkos.org/LICENSE for license information.
// SPDX-License-Identifier: Apache-2.0 WITH LLVM-exception
//
// 1. Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
//
// 2. Redistributions in binary form must reproduce the above copyright
// notice, this list of conditions and the following disclaimer in the
// documentation and/or other materials provided with the distribution.
//
// 3. Neither the name of the Corporation nor the names of the
// contributors may be used to endorse or promote products derived from
// this software without specific prior written permission.
//
// THIS SOFTWARE IS PROVIDED BY NTESS "AS IS" AND ANY
// EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL NTESS OR THE
// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
// NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
// Questions? Contact Christian R. Trott (crtrott@sandia.gov)
//
// ************************************************************************
//@HEADER
*/
#ifndef KOKKOS_STD_ALGORITHMS_COPY_HPP
#define KOKKOS_STD_ALGORITHMS_COPY_HPP

38
lib/kokkos/algorithms/src/std_algorithms/Kokkos_CopyBackward.hpp
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@ -1,46 +1,18 @@
/*
//@HEADER
// ************************************************************************
//
// Kokkos v. 3.0
// Copyright (2020) National Technology & Engineering
// Kokkos v. 4.0
// Copyright (2022) National Technology & Engineering
// Solutions of Sandia, LLC (NTESS).
//
// Under the terms of Contract DE-NA0003525 with NTESS,
// the U.S. Government retains certain rights in this software.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are
// met:
// Part of Kokkos, under the Apache License v2.0 with LLVM Exceptions.
// See https://kokkos.org/LICENSE for license information.
// SPDX-License-Identifier: Apache-2.0 WITH LLVM-exception
//
// 1. Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
//
// 2. Redistributions in binary form must reproduce the above copyright
// notice, this list of conditions and the following disclaimer in the
// documentation and/or other materials provided with the distribution.
//
// 3. Neither the name of the Corporation nor the names of the
// contributors may be used to endorse or promote products derived from
// this software without specific prior written permission.
//
// THIS SOFTWARE IS PROVIDED BY NTESS "AS IS" AND ANY
// EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL NTESS OR THE
// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
// NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
// Questions? Contact Christian R. Trott (crtrott@sandia.gov)
//
// ************************************************************************
//@HEADER
*/
#ifndef KOKKOS_STD_ALGORITHMS_COPY_BACKWARD_HPP
#define KOKKOS_STD_ALGORITHMS_COPY_BACKWARD_HPP

38
lib/kokkos/algorithms/src/std_algorithms/Kokkos_CopyIf.hpp
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@ -1,46 +1,18 @@
/*
//@HEADER
// ************************************************************************
//
// Kokkos v. 3.0
// Copyright (2020) National Technology & Engineering
// Kokkos v. 4.0
// Copyright (2022) National Technology & Engineering
// Solutions of Sandia, LLC (NTESS).
//
// Under the terms of Contract DE-NA0003525 with NTESS,
// the U.S. Government retains certain rights in this software.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are
// met:
// Part of Kokkos, under the Apache License v2.0 with LLVM Exceptions.
// See https://kokkos.org/LICENSE for license information.
// SPDX-License-Identifier: Apache-2.0 WITH LLVM-exception
//
// 1. Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
//
// 2. Redistributions in binary form must reproduce the above copyright
// notice, this list of conditions and the following disclaimer in the
// documentation and/or other materials provided with the distribution.
//
// 3. Neither the name of the Corporation nor the names of the
// contributors may be used to endorse or promote products derived from
// this software without specific prior written permission.
//
// THIS SOFTWARE IS PROVIDED BY NTESS "AS IS" AND ANY
// EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL NTESS OR THE
// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
// NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
// Questions? Contact Christian R. Trott (crtrott@sandia.gov)
//
// ************************************************************************
//@HEADER
*/
#ifndef KOKKOS_STD_ALGORITHMS_COPY_IF_HPP
#define KOKKOS_STD_ALGORITHMS_COPY_IF_HPP

38
lib/kokkos/algorithms/src/std_algorithms/Kokkos_CopyN.hpp
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@ -1,46 +1,18 @@
/*
//@HEADER
// ************************************************************************
//
// Kokkos v. 3.0
// Copyright (2020) National Technology & Engineering
// Kokkos v. 4.0
// Copyright (2022) National Technology & Engineering
// Solutions of Sandia, LLC (NTESS).
//
// Under the terms of Contract DE-NA0003525 with NTESS,
// the U.S. Government retains certain rights in this software.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are
// met:
// Part of Kokkos, under the Apache License v2.0 with LLVM Exceptions.
// See https://kokkos.org/LICENSE for license information.
// SPDX-License-Identifier: Apache-2.0 WITH LLVM-exception
//
// 1. Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
//
// 2. Redistributions in binary form must reproduce the above copyright
// notice, this list of conditions and the following disclaimer in the
// documentation and/or other materials provided with the distribution.
//
// 3. Neither the name of the Corporation nor the names of the
// contributors may be used to endorse or promote products derived from
// this software without specific prior written permission.
//
// THIS SOFTWARE IS PROVIDED BY NTESS "AS IS" AND ANY
// EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL NTESS OR THE
// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
// NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
// Questions? Contact Christian R. Trott (crtrott@sandia.gov)
//
// ************************************************************************
//@HEADER
*/
#ifndef KOKKOS_STD_ALGORITHMS_COPY_N_HPP
#define KOKKOS_STD_ALGORITHMS_COPY_N_HPP

38
lib/kokkos/algorithms/src/std_algorithms/Kokkos_Count.hpp
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@ -1,46 +1,18 @@
/*
//@HEADER
// ************************************************************************
//
// Kokkos v. 3.0
// Copyright (2020) National Technology & Engineering
// Kokkos v. 4.0
// Copyright (2022) National Technology & Engineering
// Solutions of Sandia, LLC (NTESS).
//
// Under the terms of Contract DE-NA0003525 with NTESS,
// the U.S. Government retains certain rights in this software.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are
// met:
// Part of Kokkos, under the Apache License v2.0 with LLVM Exceptions.
// See https://kokkos.org/LICENSE for license information.
// SPDX-License-Identifier: Apache-2.0 WITH LLVM-exception
//
// 1. Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
//
// 2. Redistributions in binary form must reproduce the above copyright
// notice, this list of conditions and the following disclaimer in the
// documentation and/or other materials provided with the distribution.
//
// 3. Neither the name of the Corporation nor the names of the
// contributors may be used to endorse or promote products derived from
// this software without specific prior written permission.
//
// THIS SOFTWARE IS PROVIDED BY NTESS "AS IS" AND ANY
// EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL NTESS OR THE
// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
// NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
// Questions? Contact Christian R. Trott (crtrott@sandia.gov)
//
// ************************************************************************
//@HEADER
*/
#ifndef KOKKOS_STD_ALGORITHMS_COUNT_HPP
#define KOKKOS_STD_ALGORITHMS_COUNT_HPP

38
lib/kokkos/algorithms/src/std_algorithms/Kokkos_CountIf.hpp
View File

@ -1,46 +1,18 @@
/*
//@HEADER
// ************************************************************************
//
// Kokkos v. 3.0
// Copyright (2020) National Technology & Engineering
// Kokkos v. 4.0
// Copyright (2022) National Technology & Engineering
// Solutions of Sandia, LLC (NTESS).
//
// Under the terms of Contract DE-NA0003525 with NTESS,
// the U.S. Government retains certain rights in this software.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are
// met:
// Part of Kokkos, under the Apache License v2.0 with LLVM Exceptions.
// See https://kokkos.org/LICENSE for license information.
// SPDX-License-Identifier: Apache-2.0 WITH LLVM-exception
//
// 1. Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
//
// 2. Redistributions in binary form must reproduce the above copyright
// notice, this list of conditions and the following disclaimer in the
// documentation and/or other materials provided with the distribution.
//
// 3. Neither the name of the Corporation nor the names of the
// contributors may be used to endorse or promote products derived from
// this software without specific prior written permission.
//
// THIS SOFTWARE IS PROVIDED BY NTESS "AS IS" AND ANY
// EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL NTESS OR THE
// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
// NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
// Questions? Contact Christian R. Trott (crtrott@sandia.gov)
//
// ************************************************************************
//@HEADER
*/
#ifndef KOKKOS_STD_ALGORITHMS_COUNT_IF_HPP
#define KOKKOS_STD_ALGORITHMS_COUNT_IF_HPP

38
lib/kokkos/algorithms/src/std_algorithms/Kokkos_Distance.hpp
View File

@ -1,46 +1,18 @@
/*
//@HEADER
// ************************************************************************
//
// Kokkos v. 3.0
// Copyright (2020) National Technology & Engineering
// Kokkos v. 4.0
// Copyright (2022) National Technology & Engineering
// Solutions of Sandia, LLC (NTESS).
//
// Under the terms of Contract DE-NA0003525 with NTESS,
// the U.S. Government retains certain rights in this software.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are
// met:
// Part of Kokkos, under the Apache License v2.0 with LLVM Exceptions.
// See https://kokkos.org/LICENSE for license information.
// SPDX-License-Identifier: Apache-2.0 WITH LLVM-exception
//
// 1. Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
//
// 2. Redistributions in binary form must reproduce the above copyright
// notice, this list of conditions and the following disclaimer in the
// documentation and/or other materials provided with the distribution.
//
// 3. Neither the name of the Corporation nor the names of the
// contributors may be used to endorse or promote products derived from
// this software without specific prior written permission.
//
// THIS SOFTWARE IS PROVIDED BY NTESS "AS IS" AND ANY
// EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL NTESS OR THE
// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
// NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
// Questions? Contact Christian R. Trott (crtrott@sandia.gov)
//
// ************************************************************************
//@HEADER
*/
#ifndef KOKKOS_STD_ALGORITHMS_DISTANCE_HPP
#define KOKKOS_STD_ALGORITHMS_DISTANCE_HPP

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