ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

Merge pull request #2023 from akohlmey/collected-small-changes

Browse Source 
Collected small changes and bugfixes
This commit is contained in:
Axel Kohlmeyer
2020-04-28 11:52:54 -04:00
committed by GitHub
parent 7863dfa1d2 ad47b64cb9
commit 2e07345cea
20 changed files with 179 additions and 56 deletions
Download Patch File Download Diff File Expand all files Collapse all files

19
cmake/CMakeLists.txt
View File

@ -135,23 +135,20 @@ if(PKG_USER-ADIOS)
target_link_libraries(lammps PRIVATE adios2::adios2)
endif()
if (CMAKE_SYSTEM_NAME STREQUAL Windows)
option(BUILD_MPI "Build MPI version" OFF)
else()
# do MPI detection after language activation,
# in case MPI for these languages is required
if(NOT CMAKE_CROSSCOMPILING)
set(MPI_CXX_SKIP_MPICXX TRUE)
find_package(MPI QUIET)
option(BUILD_MPI "Build MPI version" ${MPI_FOUND})
else()
option(BUILD_MPI "Build MPI version" OFF)
endif()
if(BUILD_MPI)
# We use a non-standard procedure to compile with MPI on windows
if (CMAKE_SYSTEM_NAME STREQUAL Windows)
# We use a non-standard procedure to cross-compile with MPI on Windows
if((CMAKE_SYSTEM_NAME STREQUAL Windows) AND CMAKE_CROSSCOMPILING)
include(MPI4WIN)
target_link_libraries(lammps PUBLIC MPI::MPI_CXX)
else()
set(MPI_CXX_SKIP_MPICXX ON)
find_package(MPI REQUIRED)
target_link_libraries(lammps PUBLIC MPI::MPI_CXX)
option(LAMMPS_LONGLONG_TO_LONG "Workaround if your system or MPI version does not recognize 'long long' data types" OFF)
@ -332,8 +329,9 @@ set(CMAKE_TUNE_FLAGS "${CMAKE_TUNE_DEFAULT}" CACHE STRING "Compiler specific opt
separate_arguments(CMAKE_TUNE_FLAGS)
include(CheckCXXCompilerFlag)
foreach(_FLAG ${CMAKE_TUNE_FLAGS})
check_cxx_compiler_flag("${_FLAG}" COMPILER_SUPPORTS${_FLAG})
if(COMPILER_SUPPORTS${_FLAG})
string(REGEX REPLACE "[=\"]" "" _FLAGX ${_FLAG})
check_cxx_compiler_flag("${_FLAG}" COMPILER_SUPPORTS${_FLAGX})
if(COMPILER_SUPPORTS${_FLAGX})
target_compile_options(lammps PRIVATE ${_FLAG})
else()
message(WARNING "${_FLAG} found in CMAKE_TUNE_FLAGS, but not supported by the compiler, skipping")
@ -705,6 +703,7 @@ else()
endif()
if(BUILD_MPI)
message(STATUS "<<< MPI flags >>>
-- MPI_defines: ${MPI_CXX_COMPILE_DEFINITIONS}
-- MPI includes: ${MPI_CXX_INCLUDE_PATH}
-- MPI libraries: ${MPI_CXX_LIBRARIES};${MPI_Fortran_LIBRARIES}")
endif()

5
cmake/Modules/MPI4WIN.cmake
View File

@ -23,3 +23,8 @@ set_target_properties(MPI::MPI_CXX PROPERTIES
INTERFACE_INCLUDE_DIRECTORIES "${SOURCE_DIR}/include"
INTERFACE_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX")
add_dependencies(MPI::MPI_CXX mpi4win_build)
# set variables for status reporting at the end of CMake run
set(MPI_CXX_INCLUDE_PATH "${SOURCE_DIR}/include")
set(MPI_CXX_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX")
set(MPI_CXX_LIBRARIES "${SOURCE_DIR}/lib/libmpi.a")

15
cmake/Modules/Packages/GPU.cmake
View File

@ -330,7 +330,7 @@ elseif(GPU_API STREQUAL "HIP")
if(HIP_PLATFORM STREQUAL "nvcc")
target_compile_definitions(gpu PRIVATE -D__HIP_PLATFORM_NVCC__)
target_include_directories(gpu PRIVATE ${HIP_ROOT_DIR}/include)
target_include_directories(gpu PRIVATE ${HIP_ROOT_DIR}/../include)
target_include_directories(gpu PRIVATE ${CUDA_INCLUDE_DIRS})
target_link_libraries(gpu PRIVATE ${CUDA_LIBRARIES} ${CUDA_CUDA_LIBRARY})
@ -338,6 +338,12 @@ elseif(GPU_API STREQUAL "HIP")
target_include_directories(hip_get_devices PRIVATE ${HIP_ROOT_DIR}/include)
target_include_directories(hip_get_devices PRIVATE ${CUDA_INCLUDE_DIRS})
target_link_libraries(hip_get_devices PRIVATE ${CUDA_LIBRARIES} ${CUDA_CUDA_LIBRARY})
elseif(HIP_PLATFORM STREQUAL "hcc")
target_compile_definitions(gpu PRIVATE -D__HIP_PLATFORM_HCC__)
target_include_directories(gpu PRIVATE ${HIP_ROOT_DIR}/../include)
target_compile_definitions(hip_get_devices PRIVATE -D__HIP_PLATFORM_HCC__)
target_include_directories(hip_get_devices PRIVATE ${HIP_ROOT_DIR}/../include)
endif()
target_link_libraries(lammps PRIVATE gpu)
@ -353,7 +359,12 @@ RegisterStylesExt(${GPU_SOURCES_DIR} gpu GPU_SOURCES)
get_property(GPU_SOURCES GLOBAL PROPERTY GPU_SOURCES)
target_link_libraries(gpu PRIVATE MPI::MPI_CXX)
if(NOT BUILD_MPI)
# mpistubs is aliased to MPI::MPI_CXX, but older versions of cmake won't work forward the include path
target_link_libraries(gpu PRIVATE mpi_stubs)
else()
target_link_libraries(gpu PRIVATE MPI::MPI_CXX)
endif()
if(NOT BUILD_SHARED_LIBS)
install(TARGETS gpu EXPORT LAMMPS_Targets LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
endif()

10
cmake/Modules/Packages/LATTE.cmake
View File

@ -1,4 +1,11 @@
enable_language(Fortran)
# using lammps in a super-build setting
if(TARGET LATTE::latte)
target_link_libraries(lammps PRIVATE LATTE::latte)
return()
endif()
find_package(LATTE)
if(LATTE_FOUND)
set(DOWNLOAD_LATTE_DEFAULT OFF)
@ -35,5 +42,6 @@ else()
if(NOT LATTE_FOUND)
message(FATAL_ERROR "LATTE library not found, help CMake to find it by setting LATTE_LIBRARY, or set DOWNLOAD_LATTE=ON to download it")
endif()
target_link_libraries(lammps PRIVATE LATTE::latte)
# latte needs lapack
target_link_libraries(lammps PRIVATE LATTE::latte ${LAPACK_LIBRARIES})
endif()

2
cmake/presets/clang.cmake
View File

@ -2,7 +2,7 @@
set(CMAKE_CXX_COMPILER "clang++" CACHE STRING "" FORCE)
set(CMAKE_C_COMPILER "clang" CACHE STRING "" FORCE)
set(CMAKE_CXX_FLAGS "-Wall -Wextra -g -O2 -DNDEBG" CACHE STRING "" FORCE)
set(CMAKE_CXX_FLAGS "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
set(MPI_CXX "clang++" CACHE STRING "" FORCE)
set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE)
unset(HAVE_OMP_H_INCLUDE CACHE)

12
cmake/presets/hip.cmake Normal file
View File

@ -0,0 +1,12 @@
# preset that will enable hipcc plus gcc with support for MPI and OpenMP (on Linux boxes)
set(CMAKE_CXX_COMPILER "hipcc" CACHE STRING "" FORCE)
set(CMAKE_C_COMPILER "gcc" CACHE STRING "" FORCE)
set(CMAKE_CXX_FLAGS "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
unset(HAVE_OMP_H_INCLUDE CACHE)
set(OpenMP_CXX "hipcc" CACHE STRING "" FORCE)
set(OpenMP_CXX_FLAGS "-fopenmp" CACHE STRING "" FORCE)
set(OpenMP_CXX_LIB_NAMES "omp" CACHE STRING "" FORCE)
set(OpenMP_omp_LIBRARY "libomp.so" CACHE PATH "" FORCE)

2
lib/message/cslib/src/STUBS_ZMQ/zmq.h
View File

@ -17,6 +17,8 @@
#ifndef ZMQ_DUMMY_H
#define ZMQ_DUMMY_H
#include <cstddef>
namespace CSLIB_NS {
#define ZMQ_REQ 0

8
src/KOKKOS/compute_orientorder_atom_kokkos.cpp
View File

@ -161,7 +161,7 @@ void ComputeOrientOrderAtomKokkos<DeviceType>::compute_peratom()
d_distsq = t_sna_2d_lr("orientorder/atom:distsq",chunk_size,maxneigh);
d_nearest = t_sna_2i_lr("orientorder/atom:nearest",chunk_size,maxneigh);
d_rlist = t_sna_3d_lr("orientorder/atom:rlist",chunk_size,maxneigh,3);
d_distsq_um = d_distsq;
d_rlist_um = d_rlist;
d_nearest_um = d_nearest;
@ -194,11 +194,11 @@ void ComputeOrientOrderAtomKokkos<DeviceType>::compute_peratom()
typename Kokkos::TeamPolicy<DeviceType, TagComputeOrientOrderAtomNeigh> policy_neigh(chunk_size,team_size,vector_length);
Kokkos::parallel_for("ComputeOrientOrderAtomNeigh",policy_neigh,*this);
}
//Select3
typename Kokkos::RangePolicy<DeviceType, TagComputeOrientOrderAtomSelect3> policy_select3(0,chunk_size);
Kokkos::parallel_for("ComputeOrientOrderAtomSelect3",policy_select3,*this);
//BOOP1
{
int vector_length = vector_length_default;
@ -207,7 +207,7 @@ void ComputeOrientOrderAtomKokkos<DeviceType>::compute_peratom()
typename Kokkos::TeamPolicy<DeviceType, TagComputeOrientOrderAtomBOOP1> policy_boop1(((chunk_size+team_size-1)/team_size)*maxneigh,team_size,vector_length);
Kokkos::parallel_for("ComputeOrientOrderAtomBOOP1",policy_boop1,*this);
}
//BOOP2
typename Kokkos::RangePolicy<DeviceType, TagComputeOrientOrderAtomBOOP2> policy_boop2(0,chunk_size);
Kokkos::parallel_for("ComputeOrientOrderAtomBOOP2",policy_boop2,*this);

0
src/MAKE/MINE/...
View File

1
src/MAKE/MINE/.gitignore vendored Normal file
View File

@ -0,0 +1 @@
/Makefile.*

28
src/MAKE/OPTIONS/Makefile.hip
View File

@ -27,12 +27,12 @@ SHLIBFLAGS = -shared
# if you change any -D setting, do full re-compile after "make clean"
# LAMMPS ifdef settings
# see possible settings in Section 2.2 (step 4) of manual
# see possible settings in Section 3.5 of the manual
LMP_INC = -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64
# MPI library
# see discussion in Section 2.2 (step 5) of manual
# see discussion in Section 3.4 of the manual
# MPI wrapper compiler/linker can provide this info
# can point to dummy MPI library in src/STUBS as in Makefile.serial
# use -D MPICH and OMPI settings in INC to avoid C++ lib conflicts
@ -45,7 +45,7 @@ MPI_PATH =
MPI_LIB =
# FFT library
# see discussion in Section 2.2 (step 6) of manual
# see discussion in Section 3.5.2 of manual
# can be left blank to use provided KISS FFT library
# INC = -DFFT setting, e.g. -DFFT_FFTW, FFT compiler settings
# PATH = path for FFT library
@ -56,7 +56,7 @@ FFT_PATH =
FFT_LIB =
# JPEG and/or PNG library
# see discussion in Section 2.2 (step 7) of manual
# see discussion in Section 3.5.4 of manual
# only needed if -DLAMMPS_JPEG or -DLAMMPS_PNG listed with LMP_INC
# INC = path(s) for jpeglib.h and/or png.h
# PATH = path(s) for JPEG library and/or PNG library
@ -91,18 +91,22 @@ vpath %.h ..
# Link target
$(EXE): $(OBJ) $(EXTRA_LINK_DEPENDS)
$(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE)
$(SIZE) $(EXE)
$(EXE): main.o $(LMPLIB) $(EXTRA_LINK_DEPENDS)
$(LINK) $(LINKFLAGS) main.o $(EXTRA_PATH) $(LMPLINK) $(EXTRA_LIB) $(LIB) -o $@
$(SIZE) $@
# Library targets
lib: $(OBJ) $(EXTRA_LINK_DEPENDS)
$(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ)
$(ARLIB): $(OBJ) $(EXTRA_LINK_DEPENDS)
$(ARCHIVE) $(ARFLAGS) ../$(ARLIB) $(OBJ)
@rm -f $(ARLIB)
@ln -s ../$(ARLIB) $(ARLIB)
shlib: $(OBJ) $(EXTRA_LINK_DEPENDS)
$(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o $(EXE) \
$(OBJ) $(EXTRA_LIB) $(LIB)
$(SHLIB): $(OBJ) $(EXTRA_LINK_DEPENDS)
$(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o ../$(SHLIB) \
$(OBJ) $(EXTRA_LIB) $(LIB)
@rm -f $(SHLIB)
@ln -s ../$(SHLIB) $(SHLIB)
# Compilation rules

5
src/USER-MISC/pair_drip.cpp
View File

@ -33,6 +33,7 @@
#include "neigh_request.h"
#include "memory.h"
#include "error.h"
#include "utils.h"
using namespace LAMMPS_NS;
@ -116,8 +117,8 @@ void PairDRIP::allocate()
void PairDRIP::settings(int narg, char ** /* arg */)
{
if (narg != 0) error->all(FLERR,"Illegal pair_style command");
if (strcmp(force->pair_style,"hybrid/overlay")!=0)
error->all(FLERR,"ERROR: requires hybrid/overlay pair_style");
if (!utils::strmatch(force->pair_style,"^hybrid/overlay"))
error->all(FLERR,"Pair style drip must be used as sub-style with hybrid/overlay");
}
/* ----------------------------------------------------------------------

2
src/pair_hybrid.cpp
View File

@ -1007,7 +1007,7 @@ void *PairHybrid::extract(const char *str, int &dim)
for (int m = 0; m < nstyles; m++) {
ptr = styles[m]->extract(str,dim);
if (ptr && strcmp(str,"cut_coul") == 0) {
if (cutptr && dim != couldim)
if (couldim != -1 && dim != couldim)
error->all(FLERR,
"Coulomb styles of pair hybrid sub-styles do not match");
double *p_newvalue = (double *) ptr;

2
tools/singularity/README.md
View File

@ -53,7 +53,7 @@ make
| ubuntu16.04.def | Ubuntu 16.04LTS with MPI == OpenMPI, no LaTeX |
| ubuntu18.04.def | Ubuntu 18.04LTS with MPI == OpenMPI |
| ubuntu18.04_amd_rocm.def | Ubuntu 18.04LTS with AMD ROCm toolkit |
| ubuntu18.04_amd_rocm_cuda.def | Ubuntu 18.04LTS with -"- plus Nvidia CUDA 10.2 |
| ubuntu18.04_gpu.def | Ubuntu 18.04LTS with -"- plus Nvidia CUDA 10.2 |
| ubuntu18.04_nvidia.def | Ubuntu 18.04LTS with Nvidia CUDA 10.2 toolkit |
| ubuntu18.04_intel_opencl.def | Ubuntu 18.04LTS with Intel OpenCL runtime |
| ubuntu20.04.def | Ubuntu 20.04LTS with MPI == OpenMPI |

10
tools/singularity/fedora30_mingw.def
View File

@ -3,9 +3,11 @@ From: fedora:30
%post
dnf -y update
dnf -y install vim-enhanced git file make cmake patch which file \
dos2unix findutils rsync \
ccache gcc-c++ gdb valgrind eigen3-devel \
dnf -y install vim-enhanced git file make cmake patch which file Lmod \
ninja-build clang libomp-devel libubsan libasan libtsan \
dos2unix findutils rsync python-devel libjpeg-devel libpng-devel \
ccache gcc-c++ gcc-gfortran gdb valgrind eigen3-devel openblas-devel \
openmpi-devel mpich-devel fftw-devel voro++-devel gsl-devel \
mingw-filesystem-base mingw32-nsis mingw-binutils-generic \
mingw32-filesystem mingw32-pkg-config \
mingw64-filesystem mingw64-pkg-config \
@ -39,7 +41,7 @@ From: fedora:30
# we need to reset any module variables
# inherited from the host.
unset LOADEDMODULES
source /etc/profile.d/modules.sh
. /etc/profile.d/modules.sh
module purge
module load mpi

2
tools/singularity/fedora32_mingw.def
View File

@ -38,6 +38,8 @@ From: fedora:32
%environment
LC_ALL=C
export LC_ALL
# we need to reset any module variables
# inherited from the host.
unset LOADEDMODULES
. /etc/profile.d/modules.sh
module purge

6
tools/singularity/ubuntu18.04_amd_rocm.def
View File

@ -57,12 +57,6 @@ From: rocm/dev-ubuntu-18.04
rocm-libs \
rsync \
ssh \
texlive \
texlive-latex-recommended \
texlive-pictures \
texlive-publishers \
texlive-science \
dvipng \
vim-nox \
virtualenv \
voro++-dev \

94
tools/singularity/ubuntu18.04_gpu.def Normal file
View File

@ -0,0 +1,94 @@
BootStrap: docker
From: rocm/dev-ubuntu-18.04
%environment
export PATH=/usr/local/nvidia/bin:/usr/local/cuda/bin:${PATH}:/opt/rocm/bin:/opt/rocm/profiler/bin:/opt/rocm/opencl/bin/x86_64
export CUDADIR=/usr/local/cuda
export CUDA_PATH=/usr/local/cuda
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/nvidia/lib:/usr/local/nvidia/lib64
export LIBRARY_PATH=/usr/local/cuda/lib64/stubs
%post
export DEBIAN_FRONTEND=noninteractive
apt-get update
apt-get upgrade --no-install-recommends -y
apt-get install --no-install-recommends -y software-properties-common
apt-get install --no-install-recommends -y \
bc \
build-essential \
ccache \
clang \
cmake \
cmake-curses-gui \
curl \
doxygen \
enchant \
g++ \
gcc \
gfortran \
git \
hdf5-tools \
kmod \
less \
libblas-dev \
libeigen3-dev \
libenchant-dev \
libfftw3-dev \
libgsl-dev \
libhdf5-serial-dev \
libhwloc-dev \
libjpeg-dev \
liblapack-dev \
libomp-dev \
libopenblas-dev \
libnuma-dev \
libpng-dev \
libproj-dev \
libvtk6-dev \
make \
mpi-default-bin \
mpi-default-dev \
ninja-build \
python-dev \
python-pip \
python-pygments \
python-virtualenv \
python3-dev \
python3-pip \
python3-pkg-resources \
python3-setuptools \
python3-virtualenv \
rocm-libs \
rsync \
ssh \
vim-nox \
virtualenv \
voro++-dev \
wget \
xxd
wget https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/cuda-ubuntu1804.pin
mv cuda-ubuntu1804.pin /etc/apt/preferences.d/cuda-repository-pin-600
apt-key adv --fetch-keys https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/7fa2af80.pub
add-apt-repository "deb http://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/ /"
apt-get update
apt-get install --no-install-recommends -y \
cuda \
cuda-compiler-10-2 \
export PATH=$PATH:/opt/rocm/bin:/opt/rocm/profiler/bin:/opt/rocm/opencl/bin/x86_64
git clone -b master-rocm-3.3 https://github.com/ROCmSoftwarePlatform/hipCUB.git
mkdir hipCUB/build
cd hipCUB/build
CXX=hcc cmake -D BUILD_TEST=off ..
make -j4
make package
make install
echo "/usr/local/nvidia/lib" >> /etc/ld.so.conf.d/nvidia.conf
echo "/usr/local/nvidia/lib64" >> /etc/ld.so.conf.d/nvidia.conf
%environment
LC_ALL=C
export LC_ALL
%labels
Author rbberger

6
tools/singularity/ubuntu18.04_intel_opencl.def
View File

@ -55,12 +55,6 @@ From: ubuntu:18.04
python3-virtualenv \
rsync \
ssh \
texlive \
texlive-latex-recommended \
texlive-pictures \
texlive-publishers \
texlive-science \
dvipng \
vim-nox \
virtualenv \
voro++-dev \

6
tools/singularity/ubuntu18.04_nvidia.def
View File

@ -55,12 +55,6 @@ From: nvidia/cuda:10.2-devel-ubuntu18.04
python3-virtualenv \
rsync \
ssh \
texlive \
texlive-latex-recommended \
texlive-pictures \
texlive-publishers \
texlive-science \
dvipng \
vim-nox \
virtualenv \
voro++-dev \