# CoMD-CUDA **Repository Path**: mirrors_NVIDIA/CoMD-CUDA ## Basic Information - **Project Name**: CoMD-CUDA - **Description**: GPU implementation of classical molecular dynamics proxy application. - **Primary Language**: Unknown - **License**: BSD-3-Clause-Clear - **Default Branch**: master - **Homepage**: None - **GVP Project**: No ## Statistics - **Stars**: 0 - **Forks**: 0 - **Created**: 2020-08-18 - **Last Updated**: 2026-03-29 ## Categories & Tags **Categories**: Uncategorized **Tags**: None ## README CoMD-CUDA ==== This is GPU implementation of CoMD 1.1 proxy application. The GPU code supports both cell-based and neighbor-lists methods for molecular dynamics and includes various parallelization strategies for both. Distributed multi-GPU implementation is supported as well by using one GPU per MPI rank. Build instructions ------------------------ Use src-mpi/Makefile.EAM for EAM forces and src-mpi/Makefile.NAMD for LJ forces. Modify Makefiles according to your environment, then make. Requirements: * CUDA toolkit (6.5, 7.0 and later versions are preferred) * MPI library (if building with DO_MPI = ON) Notes: * When building with MPI you need to update MPI_INCLUDE variable in Makefile. * You might need to do make clean/make after you modify header files. Sample run commands ------------------------ Single-GPU run with EAM forces and 49x49x49 grid size using default method (cell-based, thread per atom): ~~~ sh $ ./bin/CoMD-cuda-mpi -e -x 49 -y 49 -z 49 ~~~ Multi-GPU run with 2 GPUs, EAM forces and 98x49x49 overall grid size divided between GPUs along X dimension: ~~~ sh $ mpirun -np 2 ./bin/CoMD-cuda-mpi -e -x 98 -y 49 -z 49 -i 2 ~~~ Multi-GPU run with 2 GPUs, EAM forces, 98x49x49 overall grid size and neighbor lists method: ~~~ sh $ mpirun -np 2 ./bin/CoMD-cuda-mpi -e -x 98 -y 49 -z 49 -i 2 -m thread_atom_nl ~~~ Best single-GPU configuration using warp per atom approach with neighbor lists: ~~~ sh $ ./bin/CoMD-cuda-mpi -e -x 49 -y 49 -z 49 -m warp_atom_nl ~~~ To view all available options please check: * original CoMD Doxygen documentation at exmatex.github.io/CoMD/doxygen-mpi/index.html * for any GPU-only options in mycommand.c Output explanation ------------------------ Below is a sample output which you can use for the validation of the results. When modifying the code please check that all energies and # of atoms remain the same as in the original code. ~~~ sh # Performance # Loop Time(fs) Total Energy Potential Energy Kinetic Energy Temperature (us/atom) # Atoms 0 0.00 -3.460523233086 -3.538079224686 0.077555991600 600.0000 0.0000 470596 10 10.00 -3.460522622766 -3.529929454580 0.069406831814 536.9553 0.0707 470596 20 20.00 -3.460524220490 -3.509740515517 0.049216295027 380.7543 0.0711 470596 30 30.00 -3.460527806915 -3.488529040692 0.028001233777 216.6272 0.0660 470596 40 40.00 -3.460532196608 -3.477523402265 0.016991205657 131.4498 0.0662 470596 50 50.00 -3.460536497383 -3.479780609997 0.019244112614 148.8791 0.0709 470596 60 60.00 -3.460538213894 -3.488976046432 0.028437832538 220.0049 0.0665 470596 70 70.00 -3.460536800219 -3.496688002423 0.036151202204 279.6782 0.0663 470596 80 80.00 -3.460533977439 -3.498984084647 0.038450107208 297.4633 0.0713 470596 90 90.00 -3.460531463100 -3.497356126200 0.036824663100 284.8883 0.0664 470596 100 100.00 -3.460530040624 -3.495833910540 0.035303869916 273.1230 0.0666 470596 ~~~ Performance metric for CoMD is atoms/us (processed atoms per time), which is printed at the end of the execution. ~~~ sh --------------------------------------------------- Average atom rate: 14.66 atoms/us --------------------------------------------------- ~~~ Results and publications ------------------------ EAM code can achieve 34 atoms/us on NVIDIA Tesla K40m with the boost clocks. GTC 2014: Optimizing CoMD: A Molecular Dynamics Proxy Application Study CoMD version 1.1 ------------------------ CoMD is a reference implementation of typical classical molecular dynamics algorithms and workloads. It is created and maintained by ExMatEx: Exascale Co-Design Center for Materials in Extreme Environments (exmatex.org). The code is intended to serve as a vehicle for co-design by allowing others to extend and/or reimplement it as needed to test performance of new architectures, programming models, etc. Original CoMD code is available at github.com/exmatex/CoMD. To view the generated Doxygen documentation for CoMD, please visit exmatex.github.io/CoMD/doxygen-mpi/index.html. To contact the developers of CoMD send email to exmatex-comd@llnl.gov.