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OpenMM: Difference between revisions
→Job submission
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module purge | module purge | ||
module load StdEnv/2020 | module load StdEnv/2020 gcc/9.3.0 cuda/11.4 openmpi/4.0.3 | ||
module load python/3.8.10 openmm/7.7.0 netcdf/4.7.4 hdf5/1.10.6 mpi4py/3.0.3 | module load python/3.8.10 openmm/7.7.0 netcdf/4.7.4 hdf5/1.10.6 mpi4py/3.0.3 | ||
source $HOME/env-parmed/bin/activate | source $HOME/env-parmed/bin/activate | ||
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Here openmm_input.py is a python script loading amber files, creating the OpenMM simulation system, setting up the integration, and running dynamics. Example openmm_input.py is available [https://mdbench.ace-net.ca/mdbench/idbenchmark/?q=129 here]. | Here openmm_input.py is a python script loading amber files, creating the OpenMM simulation system, setting up the integration, and running dynamics. Example openmm_input.py is available [https://mdbench.ace-net.ca/mdbench/idbenchmark/?q=129 here]. | ||
OpenMM on the CUDA platform requires only one CPU per GPU because it does not use CPUs for calculations. While OpenMM can use several GPUs in one node, the most efficient way to run simulations is to use a single GPU. As you can see from [https://mdbench.ace-net.ca/mdbench/bform/?software_contains=OPENMM.cuda&software_id=&module_contains=&module_version=&site_contains=Narval&gpu_model=&cpu_model=&arch=&dataset=6n4o Narval benchmarks] and [https://mdbench.ace-net.ca/mdbench/bform/?software_contains=OPENMM.cuda&software_id=&module_contains=&module_version=&site_contains=Cedar&gpu_model=V100-SXM2&cpu_model=&arch=&dataset=6n4o Cedar benchmarks], on nodes with NvLink (where GPUs are connected directly) OpenMM runs slightly faster on multiple GPUs. Without NvLink there is | OpenMM on the CUDA platform requires only one CPU per GPU because it does not use CPUs for calculations. While OpenMM can use several GPUs in one node, the most efficient way to run simulations is to use a single GPU. As you can see from [https://mdbench.ace-net.ca/mdbench/bform/?software_contains=OPENMM.cuda&software_id=&module_contains=&module_version=&site_contains=Narval&gpu_model=&cpu_model=&arch=&dataset=6n4o Narval benchmarks] and [https://mdbench.ace-net.ca/mdbench/bform/?software_contains=OPENMM.cuda&software_id=&module_contains=&module_version=&site_contains=Cedar&gpu_model=V100-SXM2&cpu_model=&arch=&dataset=6n4o Cedar benchmarks], on nodes with NvLink (where GPUs are connected directly) OpenMM runs slightly faster on multiple GPUs. Without NvLink there is a very little speedup of simulations on P100 GPUs ([https://mdbench.ace-net.ca/mdbench/bform/?software_contains=OPENMM.cuda&software_id=&module_contains=&module_version=&site_contains=Cedar&gpu_model=P100-PCIE&cpu_model=&arch=&dataset=6n4o Cedar benchmarks]). | ||