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

Collected small changes and bugfixes

cmake/CMakeLists.txt

@@ -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()

cmake/Modules/MPI4WIN.cmake

@@ -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")

cmake/Modules/Packages/GPU.cmake

@@ -330,14 +330,20 @@ 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})
 
     target_compile_definitions(hip_get_devices PRIVATE -D__HIP_PLATFORM_NVCC__)
     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()

cmake/Modules/Packages/LATTE.cmake

@@ -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()

cmake/presets/clang.cmake

@@ -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)

cmake/presets/hip.cmake

@@ -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)
+

lib/message/cslib/src/STUBS_ZMQ/zmq.h

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

src/KOKKOS/compute_orientorder_atom_kokkos.cpp

@@ -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);

src/MAKE/MINE/.gitignore

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

src/MAKE/OPTIONS/Makefile.hip

@@ -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
 

src/USER-MISC/pair_drip.cpp

@@ -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");
 }
 
 /* ----------------------------------------------------------------------

src/pair_hybrid.cpp

@@ -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;

tools/singularity/README.md

@@ -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            |

tools/singularity/fedora30_mingw.def

@@ -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
 

tools/singularity/fedora32_mingw.def

@@ -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

tools/singularity/ubuntu18.04_amd_rocm.def

@@ -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 \