updates and bugfixes for liblammpsplugin plugin loader for LAMMPS shared lib
This commit is contained in:
Axel Kohlmeyer
1
examples/COUPLE/plugin/.gitignore
vendored
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1
examples/COUPLE/plugin/.gitignore
vendored
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@ -0,0 +1 @@
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/build
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47
examples/COUPLE/plugin/CMakeLists.txt
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47
examples/COUPLE/plugin/CMakeLists.txt
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@ -0,0 +1,47 @@
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##########################################
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# CMake build system for coupling to the LAMMPS library
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# where the library is loaded dynamically at runtime.
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##########################################
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cmake_minimum_required(VERSION 3.10)
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# enforce out-of-source build
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if(${CMAKE_SOURCE_DIR} STREQUAL ${CMAKE_BINARY_DIR})
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message(FATAL_ERROR "In-source builds are not allowed. You must create and use a build directory. "
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"Please remove CMakeCache.txt and CMakeFiles first.")
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endif()
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project(liblammpsplugin VERSION 1.0 LANGUAGES C)
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# by default, install into $HOME/.local (not /usr/local),
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# so that no root access (and sudo) is needed
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if(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)
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set(CMAKE_INSTALL_PREFIX "$ENV{HOME}/.local" CACHE PATH "Default install path" FORCE)
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endif()
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# ugly hacks for MSVC which by default always reports an old C++ standard in the __cplusplus macro
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# and prints lots of pointless warnings about "unsafe" functions
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if(MSVC)
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if(CMAKE_C_COMPILER_ID STREQUAL "MSVC")
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if(LAMMPS_EXCEPTIONS)
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add_compile_options(/EHsc)
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endif()
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endif()
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add_compile_definitions(_CRT_SECURE_NO_WARNINGS)
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endif()
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find_package(MPI REQUIRED)
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# do not include the (obsolete) MPI C++ bindings which makes
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# for leaner object files and avoids namespace conflicts
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set(MPI_CXX_SKIP_MPICXX TRUE)
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##########################
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add_executable(simple-plugin simple.c liblammpsplugin.c)
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target_link_libraries(simple-plugin PRIVATE MPI::MPI_C)
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target_compile_definitions(simple-plugin PRIVATE LAMMPS_LIB_MPI)
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# link with -ldl or equivalent for plugin loading; except on Windows
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if(NOT ${CMAKE_SYSTEM_NAME} STREQUAL "Windows")
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target_link_libraries(simple-plugin PRIVATE ${CMAKE_DL_LIBS})
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endif()
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@ -11,9 +11,16 @@ liblammpsplugin.c is the LAMMPS library plugin loader
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You can then build the driver executable codes with a compile line
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like below.
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mpicc -c -O -Wall -g -I$HOME/lammps/src liblammpsplugin.c
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mpicc -c -O -Wall -g simple.c
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mpicc simple.o liblammpsplugin.o -ldl -o simpleC
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mpicc -c -O -DLAMMPS_LIB_MPI -Wall -g liblammpsplugin.c
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mpicc -c -O -DLAMMPS_LIB_MPI -Wall -g simple.c
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mpicc simple.o liblammpsplugin.o -ldl -o simple-plugin
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or using the provided CMake file with:
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mkdir build
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cd build
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cmake ../
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cmake --build .
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You also need to build LAMMPS as a shared library
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(see examples/COUPLE/README), e.g.
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@ -26,17 +33,17 @@ or
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cd $HOME/lammps
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mkdir build-shared
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cd build-shared
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cmake -D BUILD_LIB=on -D BUILD_SHARED_LIBS=on ../cmake
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cmake -D BUILD_MPI=on -D BUILD_SHARED_LIBS=on ../cmake
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make
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You then run simpleC on a parallel machine
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You then run simple-plugin on a parallel machine
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on some number of processors Q with 3 arguments:
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% mpirun -np Q simpleC P in.lj $HOME/lammps/src/liblammps.so
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% mpirun -np Q simple-plugin P in.lj $HOME/lammps/src/liblammps.so
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or
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% mpirun -np Q simpleC P in.lj $HOME/lammps/build-shared/liblammps.so
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% mpirun -np Q simple-plugin P in.lj $HOME/lammps/build-shared/liblammps.so
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P is the number of procs you want LAMMPS to run on (must be <= Q) and
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in.lj is a LAMMPS input script and the last argument is the path to
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@ -1,7 +1,7 @@
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/* -*- c++ -*- ----------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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https://www.lammps.org/ Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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https://www.lammps.org/, Sandia National Laboratories
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LAMMPS development team: developers@lammps.org
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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@ -18,10 +18,29 @@
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a LAMMPS plugin to some other software.
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*/
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#include "library.h"
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#include "liblammpsplugin.h"
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#include <stdlib.h>
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#if defined(_WIN32)
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#ifndef WIN32_LEAN_AND_MEAN
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#define WIN32_LEAN_AND_MEAN
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#endif
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#if defined(_WIN32_WINNT)
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#undef _WIN32_WINNT
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#endif
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// target Windows version is windows 7 and later
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#define _WIN32_WINNT _WIN32_WINNT_WIN7
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#define PSAPI_VERSION 2
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#include <windows.h>
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#else
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#include <dlfcn.h>
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#endif
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#include <stdlib.h>
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liblammpsplugin_t *liblammpsplugin_load(const char *lib)
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{
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@ -29,14 +48,29 @@ liblammpsplugin_t *liblammpsplugin_load(const char *lib)
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void *handle;
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if (lib == NULL) return NULL;
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#ifdef _WIN32
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handle = (void *) LoadLibrary(lib);
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#else
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handle = dlopen(lib,RTLD_NOW|RTLD_GLOBAL);
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#endif
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if (handle == NULL) return NULL;
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lmp = (liblammpsplugin_t *) malloc(sizeof(liblammpsplugin_t));
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lmp->handle = handle;
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#define ADDSYM(symbol) lmp->symbol = dlsym(handle,"lammps_" #symbol)
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#ifdef _WIN32
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#define ADDSYM(symbol) *(void **) (&lmp->symbol) = (void *) GetProcAddress((HINSTANCE) handle, "lammps_" #symbol)
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#else
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#define ADDSYM(symbol) *(void **) (&lmp->symbol) = dlsym(handle,"lammps_" #symbol)
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#endif
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#if defined(LAMMPS_LIB_MPI)
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ADDSYM(open);
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#else
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lmp->open = NULL;
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#endif
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ADDSYM(open_no_mpi);
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ADDSYM(open_fortran);
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ADDSYM(close);
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@ -46,6 +80,8 @@ liblammpsplugin_t *liblammpsplugin_load(const char *lib)
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ADDSYM(kokkos_finalize);
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ADDSYM(python_finalize);
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ADDSYM(error);
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ADDSYM(file);
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ADDSYM(command);
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ADDSYM(commands_list);
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@ -70,6 +106,7 @@ liblammpsplugin_t *liblammpsplugin_load(const char *lib)
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ADDSYM(extract_compute);
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ADDSYM(extract_fix);
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ADDSYM(extract_variable);
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ADDSYM(extract_variable_datatype);
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ADDSYM(set_variable);
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ADDSYM(gather_atoms);
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@ -77,8 +114,15 @@ liblammpsplugin_t *liblammpsplugin_load(const char *lib)
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ADDSYM(gather_atoms_subset);
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ADDSYM(scatter_atoms);
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ADDSYM(scatter_atoms_subset);
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ADDSYM(gather_bonds);
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ADDSYM(gather);
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ADDSYM(gather_concat);
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ADDSYM(gather_subset);
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ADDSYM(scatter);
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ADDSYM(scatter_subset);
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ADDSYM(create_atoms);
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ADDSYM(find_pair_neighlist);
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@ -116,6 +160,9 @@ liblammpsplugin_t *liblammpsplugin_load(const char *lib)
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ADDSYM(plugin_count);
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ADDSYM(plugin_name);
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ADDSYM(encode_image_flags);
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ADDSYM(decode_image_flags);
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ADDSYM(set_fix_external_callback);
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ADDSYM(fix_external_get_force);
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ADDSYM(fix_external_set_energy_global);
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@ -125,6 +172,8 @@ liblammpsplugin_t *liblammpsplugin_load(const char *lib)
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ADDSYM(fix_external_set_vector_length);
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ADDSYM(fix_external_set_vector);
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ADDSYM(flush_buffers);
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ADDSYM(free);
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ADDSYM(is_running);
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@ -139,6 +188,8 @@ liblammpsplugin_t *liblammpsplugin_load(const char *lib)
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lmp->has_error = NULL;
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lmp->get_last_error_message = NULL;
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#endif
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ADDSYM(python_api_version);
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return lmp;
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}
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@ -147,7 +198,11 @@ int liblammpsplugin_release(liblammpsplugin_t *lmp)
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if (lmp == NULL) return 1;
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if (lmp->handle == NULL) return 2;
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#ifdef _WIN32
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FreeLibrary((HINSTANCE) lmp->handle);
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#else
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dlclose(lmp->handle);
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#endif
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free((void *)lmp);
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return 0;
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}
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@ -1,7 +1,7 @@
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/* -*- c++ -*- ----------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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https://www.lammps.org/ Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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https://www.lammps.org/, Sandia National Laboratories
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LAMMPS development team: developers@lammps.org
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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@ -28,11 +28,71 @@
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#define LAMMPS_SMALLBIG
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#endif
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#if defined(LAMMPS_LIB_MPI)
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#include <mpi.h>
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#if defined(LAMMPS_BIGBIG) || defined(LAMMPS_SMALLBIG)
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#include <inttypes.h> /* for int64_t */
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#endif
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#if defined(LAMMPS_BIGBIG) || defined(LAMMPS_SMALLBIG)
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#include <stdint.h> /* for int64_t */
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#endif
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/* The following enums must be kept in sync with the equivalent enums
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* or constants in python/lammps/constants.py, fortran/lammps.f90,
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* tools/swig/lammps.i, and examples/COUPLE/plugin/liblammpsplugin.h */
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/* Data type constants for extracting data from atoms, computes and fixes */
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enum _LMP_DATATYPE_CONST {
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LAMMPS_INT = 0, /*!< 32-bit integer (array) */
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LAMMPS_INT_2D = 1, /*!< two-dimensional 32-bit integer array */
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LAMMPS_DOUBLE = 2, /*!< 64-bit double (array) */
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LAMMPS_DOUBLE_2D = 3, /*!< two-dimensional 64-bit double array */
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LAMMPS_INT64 = 4, /*!< 64-bit integer (array) */
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LAMMPS_INT64_2D = 5, /*!< two-dimensional 64-bit integer array */
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LAMMPS_STRING = 6 /*!< C-String */
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};
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/* Style constants for extracting data from computes and fixes. */
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enum _LMP_STYLE_CONST {
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LMP_STYLE_GLOBAL = 0, /*!< return global data */
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LMP_STYLE_ATOM = 1, /*!< return per-atom data */
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LMP_STYLE_LOCAL = 2 /*!< return local data */
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};
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/* Type and size constants for extracting data from computes and fixes. */
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enum _LMP_TYPE_CONST {
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LMP_TYPE_SCALAR = 0, /*!< return scalar */
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LMP_TYPE_VECTOR = 1, /*!< return vector */
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LMP_TYPE_ARRAY = 2, /*!< return array */
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LMP_SIZE_VECTOR = 3, /*!< return length of vector */
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LMP_SIZE_ROWS = 4, /*!< return number of rows */
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LMP_SIZE_COLS = 5 /*!< return number of columns */
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};
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/* Error codes to select the suitable function in the Error class */
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enum _LMP_ERROR_CONST {
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LMP_ERROR_WARNING = 0, /*!< call Error::warning() */
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LMP_ERROR_ONE = 1, /*!< called from one MPI rank */
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LMP_ERROR_ALL = 2, /*!< called from all MPI ranks */
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LMP_ERROR_WORLD = 4, /*!< error on Comm::world */
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LMP_ERROR_UNIVERSE = 8 /*!< error on Comm::universe */
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};
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/** Variable style constants for extracting data from variables.
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*
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* Must be kept in sync with the equivalent constants in python/lammps/constants.py,
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* fortran/lammps.f90, and tools/swig/lammps.i */
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enum _LMP_VAR_CONST {
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LMP_VAR_EQUAL = 0, /*!< compatible with equal-style variables */
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LMP_VAR_ATOM = 1, /*!< compatible with atom-style variables */
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LMP_VAR_VECTOR = 2, /*!< compatible with vector-style variables */
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LMP_VAR_STRING = 3 /*!< return value will be a string (catch-all) */
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};
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#ifdef __cplusplus
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extern "C" {
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#endif
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@ -49,7 +109,11 @@ struct _liblammpsplugin {
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int abiversion;
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int has_exceptions;
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void *handle;
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#if defined(LAMMPS_LIB_MPI)
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void *(*open)(int, char **, MPI_Comm, void **);
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#else
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void *open;
|
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#endif
|
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void *(*open_no_mpi)(int, char **, void **);
|
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void *(*open_fortran)(int, char **, void **, int);
|
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void (*close)(void *);
|
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@ -59,13 +123,15 @@ struct _liblammpsplugin {
|
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void (*kokkos_finalize)();
|
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void (*python_finalize)();
|
||||
|
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void (*error)(void *, int, const char *);
|
||||
|
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void (*file)(void *, char *);
|
||||
char *(*command)(void *, const char *);
|
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void (*commands_list)(void *, int, const char **);
|
||||
void (*commands_string)(void *, const char *);
|
||||
|
||||
double (*get_natoms)(void *);
|
||||
double (*get_thermo)(void *, char *);
|
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double (*get_thermo)(void *, const char *);
|
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|
||||
void (*extract_box)(void *, double *, double *,
|
||||
double *, double *, double *, int *, int *);
|
||||
@ -78,12 +144,13 @@ struct _liblammpsplugin {
|
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int *(*extract_global_datatype)(void *, const char *);
|
||||
void *(*extract_global)(void *, const char *);
|
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|
||||
void *(*extract_atom_datatype)(void *, const char *);
|
||||
int *(*extract_atom_datatype)(void *, const char *);
|
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void *(*extract_atom)(void *, const char *);
|
||||
|
||||
void *(*extract_compute)(void *, const char *, int, int);
|
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void *(*extract_fix)(void *, const char *, int, int, int, int);
|
||||
void *(*extract_variable)(void *, const char *, char *);
|
||||
int (*extract_variable_datatype)(void *, const char *);
|
||||
int (*set_variable)(void *, char *, char *);
|
||||
|
||||
void (*gather_atoms)(void *, char *, int, int, void *);
|
||||
@ -94,21 +161,25 @@ struct _liblammpsplugin {
|
||||
|
||||
void (*gather_bonds)(void *, void *);
|
||||
|
||||
// lammps_create_atoms() takes tagint and imageint as args
|
||||
// ifdef insures they are compatible with rest of LAMMPS
|
||||
// caller must match to how LAMMPS library is built
|
||||
void (*gather)(void *, char *, int, int, void *);
|
||||
void (*gather_concat)(void *, char *, int, int, void *);
|
||||
void (*gather_subset)(void *, char *, int, int, int, int *,void *);
|
||||
void (*scatter)(void *, char *, int, int, void *);
|
||||
void (*scatter_subset)(void *, char *, int, int, int, int *, void *);
|
||||
|
||||
/* lammps_create_atoms() takes tagint and imageint as args
|
||||
* the ifdef insures they are compatible with rest of LAMMPS
|
||||
* caller must match to how LAMMPS library is built */
|
||||
|
||||
#ifndef LAMMPS_BIGBIG
|
||||
void (*create_atoms)(void *, int, int *, int *, double *,
|
||||
double *, int *, int);
|
||||
void (*create_atoms)(void *, int, int *, int *, double *, double *, int *, int);
|
||||
#else
|
||||
void (*create_atoms)(void *, int, int64_t *, int *, double *,
|
||||
double *, int64_t *, int);
|
||||
void (*create_atoms)(void *, int, int64_t *, int *, double *, double *, int64_t *, int);
|
||||
#endif
|
||||
|
||||
int (*find_pair_neighlist)(void *, const char *, int, int, int);
|
||||
int (*find_fix_neighlist)(void *, const char *, int);
|
||||
int (*find_compute_neighlist)(void *, char *, int);
|
||||
int (*find_compute_neighlist)(void *, const char *, int);
|
||||
int (*neighlist_num_elements)(void *, int);
|
||||
void (*neighlist_element_neighbors)(void *, int, int, int *, int *, int **);
|
||||
|
||||
@ -141,8 +212,16 @@ struct _liblammpsplugin {
|
||||
int (*plugin_count)();
|
||||
int (*plugin_name)(int, char *, char *, int);
|
||||
|
||||
void (*set_fix_external_callback)(void *, const char *, FixExternalFnPtr, void*);
|
||||
void (*fix_external_get_force)(void *, const char *);
|
||||
#if !defined(LAMMPS_BIGBIG)
|
||||
int (*encode_image_flags)(int, int, int);
|
||||
void (*decode_image_flags)(int, int *);
|
||||
#else
|
||||
int64_t (*encode_image_flags)(int, int, int);
|
||||
void (*decode_image_flags)(int64_t, int *);
|
||||
#endif
|
||||
|
||||
void (*set_fix_external_callback)(void *, const char *, FixExternalFnPtr, void *);
|
||||
double **(*fix_external_get_force)(void *, const char *);
|
||||
void (*fix_external_set_energy_global)(void *, const char *, double);
|
||||
void (*fix_external_set_energy_peratom)(void *, const char *, double *);
|
||||
void (*fix_external_set_virial_global)(void *, const char *, double *);
|
||||
@ -150,6 +229,8 @@ struct _liblammpsplugin {
|
||||
void (*fix_external_set_vector_length)(void *, const char *, int);
|
||||
void (*fix_external_set_vector)(void *, const char *, int, double);
|
||||
|
||||
void (*flush_buffers)(void *);
|
||||
|
||||
void (*free)(void *);
|
||||
|
||||
void (*is_running)(void *);
|
||||
@ -157,6 +238,8 @@ struct _liblammpsplugin {
|
||||
|
||||
int (*has_error)(void *);
|
||||
int (*get_last_error_message)(void *, char *, int);
|
||||
|
||||
int (*python_api_version)();
|
||||
};
|
||||
|
||||
typedef struct _liblammpsplugin liblammpsplugin_t;
|
||||
|
||||
@ -1,7 +1,7 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
www.cs.sandia.gov/~sjplimp/lammps.html
|
||||
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
|
||||
https://www.lammps.org, Sandia National Laboratories
|
||||
LAMMPS development team: developers@lammps.org
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
@ -19,10 +19,16 @@
|
||||
in.lammps = LAMMPS input script
|
||||
See README for compilation instructions */
|
||||
|
||||
#include <mpi.h>
|
||||
|
||||
#include <stdio.h>
|
||||
#include <stdlib.h>
|
||||
#include <string.h>
|
||||
#include <mpi.h>
|
||||
|
||||
/* define so interface to lammps_open() is available,
|
||||
since we will run on split communicator */
|
||||
#define LAMMPS_LIB_MPI 1
|
||||
|
||||
#include "liblammpsplugin.h" /* this is the include for the plugin loader */
|
||||
|
||||
int main(int narg, char **arg)
|
||||
@ -87,7 +93,13 @@ int main(int narg, char **arg)
|
||||
MPI_Abort(MPI_COMM_WORLD,1);
|
||||
}
|
||||
}
|
||||
if (lammps == 1) lmp = plugin->open(0,NULL,comm_lammps,NULL);
|
||||
if (lammps == 1) {
|
||||
if (plugin->open == NULL) {
|
||||
printf("ERROR: liblammpsmpi.c must be compiled with -DLAMMPS_LIB_MPI=1 for this program\n");
|
||||
MPI_Abort(MPI_COMM_WORLD,2);
|
||||
}
|
||||
lmp = plugin->open(0,NULL,comm_lammps,NULL);
|
||||
}
|
||||
|
||||
while (1) {
|
||||
if (me == 0) {
|
||||
@ -112,23 +124,23 @@ int main(int narg, char **arg)
|
||||
|
||||
int natoms = plugin->get_natoms(lmp);
|
||||
x = (double *) malloc(3*natoms*sizeof(double));
|
||||
plugin->gather_atoms(lmp,"x",1,3,x);
|
||||
plugin->gather_atoms(lmp,(char *)"x",1,3,x);
|
||||
v = (double *) malloc(3*natoms*sizeof(double));
|
||||
plugin->gather_atoms(lmp,"v",1,3,v);
|
||||
plugin->gather_atoms(lmp,(char *)"v",1,3,v);
|
||||
double epsilon = 0.1;
|
||||
x[0] += epsilon;
|
||||
plugin->scatter_atoms(lmp,"x",1,3,x);
|
||||
plugin->scatter_atoms(lmp,(char *)"x",1,3,x);
|
||||
|
||||
plugin->command(lmp,"run 1");
|
||||
}
|
||||
|
||||
// extract force on single atom two different ways
|
||||
/* extract force on single atom two different ways */
|
||||
|
||||
if (lammps == 1) {
|
||||
double **f = (double **) plugin->extract_atom(lmp,"f");
|
||||
printf("Force on 1 atom via extract_atom: %g\n",f[0][0]);
|
||||
|
||||
double *fx = (double *) plugin->extract_variable(lmp,"fx","all");
|
||||
double *fx = (double *) plugin->extract_variable(lmp,"fx",(char *)"all");
|
||||
printf("Force on 1 atom via extract_variable: %g\n",fx[0]);
|
||||
}
|
||||
|
||||
@ -160,7 +172,7 @@ int main(int narg, char **arg)
|
||||
if (v) free(v);
|
||||
if (type) free(type);
|
||||
|
||||
// close down LAMMPS
|
||||
/* close down LAMMPS */
|
||||
|
||||
if (lammps == 1) {
|
||||
plugin->close(lmp);
|
||||
|
||||
Reference in New Issue
Block a user