Unverified Commit 921d3dad authored by Axel Kohlmeyer's avatar Axel Kohlmeyer Committed by GitHub
Browse files

Merge pull request #1400 from akohlmey/collected-small-changes 

Refactor USER-INTEL support in CMake and support Linux-2-Windows cross-compiling with CMake
parents 585403d6 bd923d8b

cmake/CMakeLists.txt

+110 −49
Original line number Diff line number Diff line
@@ -322,7 +322,7 @@ pkg_depends(USER-SCAFACOS MPI) 


find_package(OpenMP QUIET)

option(BUILD_OMP "Build with OpenMP support" ${OpenMP_FOUND})

if(BUILD_OMP OR PKG_KOKKOS OR PKG_USER-INTEL)

if(BUILD_OMP)

  find_package(OpenMP REQUIRED)

  set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}")

  set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")
@@ -560,6 +560,20 @@ if(PKG_USER-PLUMED) 


  option(DOWNLOAD_PLUMED "Download Plumed package instead of using an already installed one" OFF)

  if(DOWNLOAD_PLUMED)

    if(BUILD_MPI)

      set(PLUMED_CONFIG_MPI "--enable-mpi")

      set(PLUMED_CONFIG_CC  ${CMAKE_MPI_C_COMPILER})

      set(PLUMED_CONFIG_CXX  ${CMAKE_MPI_CXX_COMPILER})

    else()

      set(PLUMED_CONFIG_MPI "--disable-mpi")

      set(PLUMED_CONFIG_CC  ${CMAKE_C_COMPILER})

      set(PLUMED_CONFIG_CXX  ${CMAKE_CXX_COMPILER})

    endif()

    if(BUILD_OMP)

      set(PLUMED_CONFIG_OMP "--enable-openmp")

    else()

      set(PLUMED_CONFIG_OMP "--disable-openmp")

    endif()

    message(STATUS "PLUMED download requested - we will build our own")

    include(ExternalProject)

    ExternalProject_Add(plumed_build
@@ -569,8 +583,10 @@ if(PKG_USER-PLUMED) 
      CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR>

                                               ${CONFIGURE_REQUEST_PIC}

                                               --enable-modules=all

                                               CXX=${CMAKE_MPI_CXX_COMPILER}

                                               CC=${CMAKE_MPI_C_COMPILER}

                                               ${PLUMED_CONFIG_MPI}

                                               ${PLUMED_CONFIG_OMP}

                                               CXX=${PLUMED_CONFIG_CXX}

                                               CC=${PLUMED_CONFIG_CC}

    )

    ExternalProject_get_property(plumed_build INSTALL_DIR)

    set(PLUMED_INSTALL_DIR ${INSTALL_DIR})
@@ -607,7 +623,10 @@ if(PKG_USER-MOLFILE) 
  set(MOLFILE_INCLUDE_DIRS "${LAMMPS_LIB_SOURCE_DIR}/molfile" CACHE STRING "Path to VMD molfile plugin headers")

  add_library(molfile INTERFACE)

  target_include_directories(molfile INTERFACE ${MOLFILE_INCLUDE_DIRS})

  # no need to link with -ldl on windows

  if(NOT ${CMAKE_SYSTEM_NAME} STREQUAL "Windows")

    target_link_libraries(molfile INTERFACE ${CMAKE_DL_LIBS})

  endif()

  list(APPEND LAMMPS_LINK_LIBS molfile)

endif()
@@ -944,7 +963,7 @@ if(PKG_USER-OMP) 


    # detects styles which have USER-OMP version

    RegisterStylesExt(${USER-OMP_SOURCES_DIR} omp OMP_SOURCES)

    RegisterFixStyle("${USER-OMP_SOURCES_DIR}/fix_omp.h")

    RegisterFixStyle(${USER-OMP_SOURCES_DIR}/fix_omp.h)



    get_property(USER-OMP_SOURCES GLOBAL PROPERTY OMP_SOURCES)
@@ -1057,37 +1076,79 @@ if(PKG_OPT) 
endif()



if(PKG_USER-INTEL)

    find_package(TBB REQUIRED)

    find_package(MKL REQUIRED)

  if(LAMMPS_SIZES STREQUAL BIGBIG)

    message(FATAL_ERROR "The USER-INTEL Package is not compatible with -DLAMMPS_BIGBIG")

  endif()

  add_definitions(-DLMP_USER_INTEL)



    if(NOT CMAKE_CXX_COMPILER_ID STREQUAL "Intel")

      message(FATAL_ERROR "USER-INTEL is only useful together with intel compiler")

  set(INTEL_ARCH "cpu" CACHE STRING "Architectures used by USER-INTEL (cpu or knl)")

  set(INTEL_ARCH_VALUES cpu knl)

  set_property(CACHE INTEL_ARCH PROPERTY STRINGS ${INTEL_ARCH_VALUES})

  validate_option(INTEL_ARCH INTEL_ARCH_VALUES)

  string(TOUPPER ${INTEL_ARCH} INTEL_ARCH)



  find_package(Threads QUIET)

  if(Threads_FOUND)

    set(INTEL_LRT_MODE "threads" CACHE STRING "Long-range threads mode (none, threads, or c++11)")

  else()

    set(INTEL_LRT_MODE "none" CACHE STRING "Long-range threads mode (none, threads, or c++11)")

  endif()

  set(INTEL_LRT_VALUES none threads c++11)

  set_property(CACHE INTEL_LRT_MODE PROPERTY STRINGS ${INTEL_LRT_VALUES})

  validate_option(INTEL_LRT_MODE INTEL_LRT_VALUES)

  string(TOUPPER ${INTEL_LRT_MODE} INTEL_LRT_MODE)

  if(INTEL_LRT_MODE STREQUAL "THREADS")

    if(Threads_FOUND)

      add_definitions(-DLMP_INTEL_USELRT)

      list(APPEND LAMMPS_LINK_LIBS ${CMAKE_THREAD_LIBS_INIT})

    else()

      message(FATAL_ERROR "Must have working threads library for Long-range thread support")

    endif()

  endif()

  if(INTEL_LRT_MODE STREQUAL "C++11")

    add_definitions(-DLMP_INTEL_USERLRT -DLMP_INTEL_LRT11)

  endif()



  if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")

    if(CMAKE_CXX_COMPILER_VERSION VERSION_LESS 16)

        message(FATAL_ERROR "USER-INTEL needs at least a 2016 intel compiler, found ${CMAKE_CXX_COMPILER_VERSION}")

      message(FATAL_ERROR "USER-INTEL needs at least a 2016 Intel compiler, found ${CMAKE_CXX_COMPILER_VERSION}")

    endif()

  else()

    message(WARNING "USER-INTEL gives best performance with Intel compilers")

  endif()



    if(NOT BUILD_OMP)

        message(FATAL_ERROR "USER-INTEL requires OpenMP")

  find_package(TBB QUIET)

  if(TBB_FOUND)

    list(APPEND LAMMPS_LINK_LIBS ${TBB_MALLOC_LIBRARIES})

  else()

    add_definitions(-DLMP_INTEL_NO_TBB)

    if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")

      message(WARNING "USER-INTEL with Intel compilers should use TBB malloc libraries")

    endif()

  endif()



    if(NOT ${LAMMPS_MEMALIGN} STREQUAL "64")

        message(FATAL_ERROR "USER-INTEL is only useful with LAMMPS_MEMALIGN=64")

  find_package(MKL QUIET)

  if(MKL_FOUND)

    add_definitions(-DLMP_USE_MKL_RNG)

    list(APPEND LAMMPS_LINK_LIBS ${MKL_LIBRARIES})

  else()

    message(STATUS "Pair style dpd/intel will be faster with MKL libraries")

  endif()



    set(INTEL_ARCH "cpu" CACHE STRING "Architectures used by USER-INTEL (cpu or knl)")

    set(INTEL_ARCH_VALUES cpu knl)

    set_property(CACHE INTEL_ARCH PROPERTY STRINGS ${INTEL_ARCH_VALUES})

    validate_option(INTEL_ARCH INTEL_ARCH_VALUES)

    string(TOUPPER ${INTEL_ARCH} INTEL_ARCH)

  if((NOT ${CMAKE_SYSTEM_NAME} STREQUAL "Windows") AND (NOT ${LAMMPS_MEMALIGN} STREQUAL "64") AND (NOT ${LAMMPS_MEMALIGN} STREQUAL "128") AND (NOT ${LAMMPS_MEMALIGN} STREQUAL "256"))

    message(FATAL_ERROR "USER-INTEL only supports memory alignment of 64, 128 or 256 on this platform")

  endif()



  if(INTEL_ARCH STREQUAL "KNL")

    if(NOT CMAKE_CXX_COMPILER_ID STREQUAL "Intel")

      message(FATAL_ERROR "Must use Intel compiler with USER-INTEL for KNL architecture")

    endif()

    set(CMAKE_EXE_LINKER_FLAGS  "${CMAKE_EXE_LINKER_FLAGS} -xHost -qopenmp -qoffload")

    set(MIC_OPTIONS "-qoffload-option,mic,compiler,\"-fp-model fast=2 -mGLOB_default_function_attrs=\\\"gather_scatter_loop_unroll=4\\\"\"")

    add_compile_options(-xMIC-AVX512 -qoffload -fno-alias -ansi-alias -restrict -qoverride-limits ${MIC_OPTIONS})

    add_definitions(-DLMP_INTEL_OFFLOAD)

  else()

    if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")

      if(CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.3 OR CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.4)

        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -xCOMMON-AVX512")

      else()
@@ -1100,28 +1161,28 @@ if(PKG_USER-INTEL) 
          add_compile_options(${_FLAG})

        endif()

      endforeach()

    else()

      add_compile_options(-O3 -ffast-math)

    endif()

  endif()



    add_definitions(-DLMP_INTEL_USELRT -DLMP_USE_MKL_RNG)



    list(APPEND LAMMPS_LINK_LIBS ${TBB_MALLOC_LIBRARIES} ${MKL_LIBRARIES})



  # collect sources

  set(USER-INTEL_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/USER-INTEL)

    set(USER-INTEL_SOURCES ${USER-INTEL_SOURCES_DIR}/intel_preprocess.h

                           ${USER-INTEL_SOURCES_DIR}/intel_buffers.h

  set(USER-INTEL_SOURCES ${USER-INTEL_SOURCES_DIR}/fix_intel.cpp

                         ${USER-INTEL_SOURCES_DIR}/fix_nh_intel.cpp

                         ${USER-INTEL_SOURCES_DIR}/intel_buffers.cpp

                           ${USER-INTEL_SOURCES_DIR}/math_extra_intel.h

                           ${USER-INTEL_SOURCES_DIR}/nbin_intel.h

                         ${USER-INTEL_SOURCES_DIR}/nbin_intel.cpp

                           ${USER-INTEL_SOURCES_DIR}/npair_intel.h

                         ${USER-INTEL_SOURCES_DIR}/npair_intel.cpp

                           ${USER-INTEL_SOURCES_DIR}/intel_simd.h

                           ${USER-INTEL_SOURCES_DIR}/intel_intrinsics.h)

                         ${USER-INTEL_SOURCES_DIR}/verlet_lrt_intel.cpp)



  set_property(GLOBAL PROPERTY "USER-INTEL_SOURCES" "${USER-INTEL_SOURCES}")



    # detects styles which have USER-INTEL version

    RegisterStylesExt(${USER-INTEL_SOURCES_DIR} opt USER-INTEL_SOURCES)

  # detect styles which have a USER-INTEL version

  RegisterStylesExt(${USER-INTEL_SOURCES_DIR} intel USER-INTEL_SOURCES)

  RegisterNBinStyle(${USER-INTEL_SOURCES_DIR}/nbin_intel.h)

  RegisterNPairStyle(${USER-INTEL_SOURCES_DIR}/npair_intel.h)

  RegisterFixStyle(${USER-INTEL_SOURCES_DIR}/fix_intel.h)

  RegisterIntegrateStyle(${USER-INTEL_SOURCES_DIR}/verlet_lrt_intel.h)



  get_property(USER-INTEL_SOURCES GLOBAL PROPERTY USER-INTEL_SOURCES)

cmake/Modules/StyleHeaderUtils.cmake

+4 −0
Original line number Diff line number Diff line
@@ -91,6 +91,10 @@ function(RegisterFixStyle path) 
    AddStyleHeader(${path} FIX)

endfunction(RegisterFixStyle)



function(RegisterIntegrateStyle path)

    AddStyleHeader(${path} INTEGRATE)

endfunction(RegisterIntegrateStyle)



function(RegisterStyles search_path)

    FindStyleHeaders(${search_path} ANGLE_CLASS     angle_     ANGLE     ) # angle     ) # force

    FindStyleHeaders(${search_path} ATOM_CLASS      atom_vec_  ATOM_VEC  ) # atom      ) # atom      atom_vec_hybrid

cmake/README.md

+17 −4
Original line number Diff line number Diff line
@@ -155,11 +155,13 @@ make 


The CMake build exposes a lot of different options. In the old build system

some of the package selections were possible by using special make target like

`make yes-std` or `make no-lib`. Achieving the same result with cmake requires

`make yes-std` or `make no-lib`. Achieving a similar result with cmake requires

specifying all options manually. This can quickly become a very long command

line that is hard to handle.  While these could be stored in a simple script

file, there is another way of defining "presets" to compile LAMMPS in a certain

way.

way. Since the cmake build process - contrary to the conventional build system -

includes the compilation of the bundled libraries into the standard build process,

the grouping of those presets is somewhat different.



A preset is a regular CMake script file that can use constructs such as

variables, lists and for-loops to manipulate configuration options and create
@@ -171,10 +173,10 @@ Such a file can then be passed to cmake via the `-C` flag. Several examples of 
presets can be found in the `cmake/presets` folder.



```bash

# build LAMMPS with all "standard" packages which don't use libraries and enable GPU package

# build LAMMPS with all packages enabled which don't use external libraries and enable GPU package

mkdir build

cd build

cmake -C ../cmake/presets/std_nolib.cmake -D PKG_GPU=on ../cmake

cmake -C ../cmake/presets/all_on.cmake -C ../cmake/presets/nolib.cmake -D PKG_GPU=on ../cmake

```



# Reference
@@ -1429,6 +1431,17 @@ TODO 
  </dl>

  </td>

</tr>

<tr>

  <td><code>INTEL_LRT_MODE</code></td>

  <td>How to support Long-range thread mode in Verlet integration</td>

  <td>

  <dl>

    <dt><code>threads</code> (default, if pthreads available)</dt>

    <dt><code>none</code> (default, if pthreads not available)</dt>

    <dt><code>c++11</code></dt>

  </dl>

  </td>

</tr>

</tbody>

</table>

cmake/presets/all_off.cmake

+13 −17
Original line number Diff line number Diff line 
set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU

                      GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MEAM MISC

                      MOLECULE MPIIO MSCG OPT PERI POEMS

                      PYTHON QEQ REAX REPLICA RIGID SHOCK SNAP SRD VORONOI)

# preset that turns on all existing packages off. can be used to reset

# an existing package selection without losing any other settings



set(USER_PACKAGES USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS

                  USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD

                  USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO

                  USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE

                  USER-NETCDF USER-OMP USER-PHONON USER-QMMM USER-QTB

                  USER-QUIP USER-REAXC USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY

                  USER-UEF USER-VTK)



set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MEAM MPIIO MSCG POEMS PYTHON REAX VORONOI

                      USER-ATC USER-AWPMD USER-COLVARS USER-H5MD USER-LB USER-MOLFILE

                      USER-NETCDF USER-PLUMED USER-QMMM USER-QUIP USER-SMD USER-VTK)



set(ALL_PACKAGES ${STANDARD_PACKAGES} ${USER_PACKAGES})

set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU

        GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MISC MOLECULE MPIIO

        MSCG OPT PERI POEMS PYTHON QEQ REPLICA RIGID SHOCK SNAP SPIN SRD

        VORONOI

        USER-ADIOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK

        USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP

        USER-H5MD USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO

        USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP

        USER-PHONON USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP

        USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH

        USER-TALLY USER-UEF USER-VTK USER-YAFF)



foreach(PKG ${ALL_PACKAGES})

  set(PKG_${PKG} OFF CACHE BOOL "" FORCE)

cmake/presets/all_on.cmake

+15 −17
Original line number Diff line number Diff line 
set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU

                      GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MEAM MISC

                      MOLECULE MPIIO MSCG OPT PERI POEMS

                      PYTHON QEQ REAX REPLICA RIGID SHOCK SNAP SRD VORONOI)

# preset that turns on all existing packages. using the combination

# this preset followed by the nolib.cmake preset should configure a

# LAMMPS binary, with as many packages included, that can be compiled

# with just a working C++ compiler and an MPI library.



set(USER_PACKAGES USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS

                  USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD

                  USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO

                  USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE

                  USER-NETCDF USER-OMP USER-PHONON USER-QMMM USER-QTB

                  USER-QUIP USER-REAXC USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY

                  USER-UEF USER-VTK)



set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MEAM MPIIO MSCG POEMS PYTHON REAX VORONOI

                      USER-ATC USER-AWPMD USER-COLVARS USER-H5MD USER-LB USER-MOLFILE

                      USER-NETCDF USER-PLUMED USER-QMMM USER-QUIP USER-SMD USER-VTK)



set(ALL_PACKAGES ${STANDARD_PACKAGES} ${USER_PACKAGES})

set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU

        GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MISC MOLECULE MPIIO

        MSCG OPT PERI POEMS PYTHON QEQ REPLICA RIGID SHOCK SNAP SPIN SRD

        VORONOI

        USER-ADIOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK

        USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP

        USER-H5MD USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO

        USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP

        USER-PHONON USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP

        USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH

        USER-TALLY USER-UEF USER-VTK USER-YAFF)



foreach(PKG ${ALL_PACKAGES})

  set(PKG_${PKG} ON CACHE BOOL "" FORCE)

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