Please refer to CB-Geo MPM Documentation 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.
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Docker image for CB-Geo mpm code https://hub.docker.com/r/cbgeo/mpm
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Instructions for running mpm docker container: https://github.com/cb-geo/docker-mpm/blob/master/README.md.
The following prerequisite packages can be found in the docker image:
Please run the following command:
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 wgetPlease 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
mkdir -p ~/workspace && cd ~/workspace/ && git clone https://github.com/wdas/partio.git && \
cd partio && cmake . && makeHoudini supported (*.bgeo) files will be generated. These can be rendered using the non-commercial Houdini Apprentice.
cd ~/workspace/ && git clone https://github.com/schulzchristian/KaHIP && \
cd KaHIP && sh ./compile_withcmake.shSee CB-Geo MPM Documentation for more detailed instructions.
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Run
mkdir build && cd build && cmake -DCMAKE_CXX_COMPILER=g++ ... -
Run
make clean && make -jN(where N is the number of cores).
To compile without KaHIP partitioning use
cmake -DNO_KAHIP=True ..
- To compile either
mpmormpmtestalone, runmake mpm -jNormake mpmtest -jN(where N is the number of cores).
To compile without tests run: mkdir build && cd build && cmake -DMPM_BUILD_TESTING=Off -DCMAKE_CXX_COMPILER=g++ ...
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).
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Run
mkdir build && cd build && cmake -GNinja -DCMAKE_CXX_COMPILER=g++ ... -
Run
ninja
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
./mpmtest -s(for a verbose output) orctest -VV.
See CB-Geo MPM Documentation 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.
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
Please refer to the list of contributors to the CB-Geo MPM code.
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
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