mpm:CB-Geo高性能材料点方法

# High-Performance Material Point Method (CB-Geo mpm) > [CB-Geo Computational Geomechanics Research Group](https://www.cb-geo.com) [](https://raw.githubusercontent.com/cb-geo/mpm/develop/license.md) [](http://cb-geo.github.io/mpm) [](https://mpm.cb-geo.com/) [](https://circleci.com/gh/cb-geo/mpm) [](https://codecov.io/gh/cb-geo/mpm) [](https://github.com/cb-geo/mpm/issues) [](https://scan.coverity.com/projects/14389/badge.svg) [](https://lgtm.com/projects/g/cb-geo/mpm/context:cpp) [](https://github.com/orgs/cb-geo/projects/1) [](https://cb-geo.discourse.group/c/mpm/) ## Documentation Please refer to [CB-Geo MPM Documentation](https://mpm.cb-geo.com/) for information on compiling, and running the code. The documentation also include the MPM theory. If you have any issues running or compiling the MPM code please open a issue on the [CB-Geo Discourse forum](https://cb-geo.discourse.group/c/mpm/). ## Running code on Docker * Docker image for CB-Geo mpm code [https://hub.docker.com/r/cbgeo/mpm](https://hub.docker.com/r/cbgeo/mpm) * Instructions for running mpm docker container: [https://github.com/cb-geo/docker-mpm/blob/master/README.md](https://github.com/cb-geo/mpm-container/blob/master/README.md). ## Running code locally ### Prerequisite packages > The following prerequisite packages can be found in the docker image: * [Boost](http://www.boost.org/) * [Eigen](http://eigen.tuxfamily.org/) * [HDF5](https://support.hdfgroup.org/HDF5/) #### Optional * [MKL](https://software.intel.com/en-us/mkl) * [MPI](https://www.open-mpi.org/) * [OpenMP 5.0](https://www.openmp.org/specifications/) * [KaHIP](https://github.com/schulzchristian/KaHIP) * [Partio](https://github.com/wdas/partio) * [VTK](https://www.vtk.org/) ### Fedora installation (recommended) Please run the following command: ```shell dnf install -y boost boost-devel clang clang-analyzer clang-tools-extra cmake cppcheck dnf-plugins-core \ eigen3-devel findutils freeglut freeglut-devel gcc gcc-c++ git hdf5 hdf5-devel \ kernel-devel lcov libnsl make ninja-build openmpi openmpi-devel tar \ valgrind vim vtk vtk-devel wget ``` ### Ubuntu installation Please run the following commands to install dependencies: ``` sudo apt update sudo apt upgrade sudo apt install -y gcc git libboost-all-dev libeigen3-dev libhdf5-serial-dev libopenmpi-dev libomp-dev ``` If you are running Ubuntu 18.04 or below, you may want to update the GCC version to 9 to have OpenMP 5 specifications support. ``` sudo apt install software-properties-common sudo add-apt-repository -y ppa:ubuntu-toolchain-r/test sudo apt install gcc-9 g++-9 sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-9 90 --slave /usr/bin/g++ g++ /usr/bin/g++-9 --slave /usr/bin/gcov gcov /usr/bin/gcov-9 ``` To install other dependencies: > CMake 3.15 ``` sudo apt-add-repository 'deb https://apt.kitware.com/ubuntu/ bionic main' sudo apt update sudo apt upgrade ``` > OpenGL and X11:Xt ``` sudo apt-get install freeglut3-dev libxt-dev ``` > VTK ``` git clone https://gitlab.kitware.com/vtk/vtk.git VTK cd VTK && mkdir build && cd build/ cmake -DCMAKE_BUILD_TYPE:STRING=Release .. make -j sudo make install ``` ### Partio for Houdini SFX Visualization ```shell mkdir -p ~/workspace && cd ~/workspace/ && git clone https://github.com/wdas/partio.git && \ cd partio && cmake . && make ``` Houdini supported (*.bgeo) files will be generated. These can be rendered using the non-commercial [Houdini Apprentice](https://www.sidefx.com/download/). ### KaHIP installation for domain decomposition ```shell cd ~/workspace/ && git clone https://github.com/schulzchristian/KaHIP && \ cd KaHIP && sh ./compile_withcmake.sh ``` ## Compile > See [CB-Geo MPM Documentation](https://mpm.cb-geo.com/) for more detailed instructions. 0. Run `mkdir build && cd build && cmake -DCMAKE_CXX_COMPILER=g++ ..`. 1. Run `make clean && make -jN` (where N is the number of cores). > To compile without KaHIP partitioning use `cmake -DNO_KAHIP=True ..` ### Compile mpm or mpmtest * To compile either `mpm` or `mpmtest` alone, run `make mpm -jN` or `make mpmtest -jN` (where N is the number of cores). ### Compile without tests [Editing CMake options] To compile without tests run: `mkdir build && cd build && cmake -DMPM_BUILD_TESTING=Off -DCMAKE_CXX_COMPILER=g++ ..`. ## Compile with MPI (Running on a cluster) The CB-Geo mpm code can be compiled with `MPI` to distribute the workload across compute nodes in a cluster. Additional steps to load `OpenMPI` on Fedora: ``` source /etc/profile.d/modules.sh export MODULEPATH=$MODULEPATH:/usr/share/modulefiles module load mpi/openmpi-x86_64 ``` Compile with OpenMPI (with halo exchange): ``` mkdir build && cd build export CXX_COMPILER=mpicxx cmake -DCMAKE_BUILD_TYPE=Release -DKAHIP_ROOT=~/workspace/KaHIP/ -DHALO_EXCHANGE=On .. make -jN ``` To enable halo exchange set `-DHALO_EXCHANGE=On` in `CMake`. Halo exchange is a better MPI communication protocol, however, use this only for larger number of MPI tasks (> 4). ### Compile with Ninja build system [Alternative to Make] 0. Run `mkdir build && cd build && cmake -GNinja -DCMAKE_CXX_COMPILER=g++ ..`. 1. Run `ninja` ### Compile with Partio viz support Please include `-DPARTIO_ROOT=/path/to/partio/` in the cmake command. A typical cmake command would look like `cmake -DCMAKE_BUILD_TYPE=Release -DPARTIO_ROOT=~/workspace/partio/ ..` ## Run tests 0. Run `./mpmtest -s` (for a verbose output) or `ctest -VV`. ## Run MPM > See [CB-Geo MPM Documentation](https://mpm.cb-geo.com/) for more detailed instructions. The CB-Geo MPM code uses a `JSON` file for input configuration. To run the mpm code: ``` ./mpm [-p <parallel>] [-i <input_file>] -f <working_dir> [--] [--version] [-h] ``` For example: ``` export OMP_SCHEDULE="static,4" ./mpm -f /path/to/input-dir/ -i mpm-usf-3d.json ``` Where: ``` -p <parallel>, --parallel <parallel> Number of parallel threads -i <input_file>, --input_file <input_file> Input JSON file [mpm.json] -f <working_dir>, --working_dir <working_dir> (required) Current working folder --, --ignore_rest Ignores the rest of the labeled arguments following this flag. --version Displays version information and exits. -h, --help Displays usage information and exits. ``` ### Running the code with MPI To run the CB-Geo mpm code on a cluster with MPI: ``` mpirun -N <#-MPI-tasks> ./mpm -f /path/to/input-dir/ -i mpm.json ``` For example to run the code on 4 compute nodes (MPI tasks): ``` mpirun -N 4 ./mpm -f ~/benchmarks/3d/uniaxial-stress -i mpm.json ``` ## Authors Please refer to the [list of contributors to the CB-Geo MPM code](AUTHORS.md). ## Citation If you publish results using our code, please acknowledge our work by quoting the following paper: Kumar, K., Salmond, J., Kularathna, S., Wilkes, C., Tjung, E., Biscontin, G., & Soga, K. (2019). Scalable and modular material point method for large scale simulations. 2nd International Conference on the Material Point Method. Cambridge, UK. [https://arxiv.org/abs/1909.13380](https://arxiv.org/abs/1909.13380)