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software:namd:caviness [2021-04-27 16:21] – external edit 127.0.0.1 | software:namd:caviness [2024-05-12 15:25] (current) – [Scaling] bkang | ||
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+ | ====== NAMD on Caviness ====== | ||
+ | ===== Batch job ===== | ||
+ | |||
+ | Open MPI Slurm job submission script should be used for NAMD jobs on Caviness and can be found in ''/ | ||
+ | <code bash> | ||
+ | $ vpkg_versions namd | ||
+ | |||
+ | Available versions in package (* = default version): | ||
+ | |||
+ | [/ | ||
+ | namd | ||
+ | 2.12 | ||
+ | * 2.13 | ||
+ | 2.13: | ||
+ | 2.14 | ||
+ | 3.0b3 compiled with Intel 2020, Open MPI 4.1.4 | ||
+ | 3.0b3: | ||
+ | 3.0b3: | ||
+ | </ | ||
+ | |||
+ | The '' | ||
+ | |||
+ | <code bash> | ||
+ | ${UD_MPIRUN} namd2 +idlepoll +p${SLURM_CPUS_ON_NODE} +devices ${CUDA_VISIBLE_DEVICES} ... | ||
+ | </ | ||
+ | |||
+ | Documentation for '' | ||
+ | |||
+ | |||
+ | <note tip>It is always a good idea to periodically check if the templates in ''/ | ||
+ | |||
+ | ===== Scaling ===== | ||
+ | |||
+ | Using ApoA1 as an example, the scaling results are presented. The performance improved with increasing CPU and GPU numbers. | ||
+ | |||
+ | <code bash> | ||
+ | vpkg_require namd/3.0b3 | ||
+ | charmrun namd3 +p$SLURM_NTASKS | ||
+ | </ | ||
+ | {{: | ||
+ | |||
+ | <code bash> | ||
+ | vpkg_require namd/ | ||
+ | charmrun namd3 +idlepoll +p$SLURM_CPUS_PER_TASK +devices $CUDA_VISIBLE_DEVICES apoa1.namd > apoa1.log | ||
+ | </ | ||
+ | {{: | ||
+ | {{: |