batmanabcdefg / mpm-1

CB-Geo High-Performance Material Point Method

High-Performance Material Point Method (CB-Geo mpm)

CB-Geo Computational Geomechanics Research Group

Documentation

Please refer to CB-Geo MPM Documentation for information on compiling, and running the code. The documentation also include the MPM theory.

Install dependencies

• Docker image for CB-Geo mpm code https://hub.docker.com/r/cbgeo/mpm

• Instructions for running mpm docker container: https://github.com/cb-geo/docker-mpm/blob/master/README.md.

Prerequisite packages

The following prerequisite packages can be found in the docker image:

• Boost
• Eigen
• Intel TBB
• HDF5

Optional

• MPI
• VTK

Fedora installation

Please run the following command:

dnf install -y boost boost-devel clang cmake cppcheck eigen3-devel findutils gcc gcc-c++ \
                   git hdf5 hdf5-devel hdf5-openmpi hdf5-openmpi-devel kernel-devel lcov\
                   make openmpi openmpi-devel sqlite sqlite-devel tar tbb tbb-devel valgrind vim \
                   voro++ voro++-devel vtk vtk-devel wget

Ubuntu installation

Please run the following commands to install dependencies:

sudo apt-get install -y cmake gcc git libboost-all-dev libeigen3-dev libhdf5-serial-dev libopenmpi-dev \
                        libtbb-dev libvtk7-dev

Compile

See https://mpm-doc.cb-geo.com/ for more detailed instructions.

0. Run mkdir build && cd build && cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_CXX_COMPILER=g++ ...

1. Run make clean && make -jN (where N is the number of cores).

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 -DCMAKE_BUILD_TYPE=Release -DMPM_BUILD_TESTING=Off ...

Run tests

0. Run ./mpmtest -s (for a verbose output) or ctest -VV.

Run MPM

See https://mpm-doc.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 <tbb_parallel>] [-i <input_file>] -f <working_dir> [--]
          [--version] [-h]

For example:

./mpm -f /path/to/input-dir/ -i mpm-usf-3d.json -p 8

Where:

   -p <tbb_parallel>,  --tbb_parallel <tbb_parallel>
     Number of parallel TBB 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.

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:

mkdir build && cd build 
export CXX_COMPILER=mpicxx
cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_CXX_COMPILER=mpicxx -DCMAKE_EXPORT_COMPILE_COMMANDS=On ..
make -jN

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