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software:namd:caviness [2024-03-19 09:43] – [Batch job] anita | software:namd:caviness [2024-05-12 15:25] (current) – [Scaling] bkang | ||
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[/ | [/ | ||
- | namd Scalable Molecular Dynamics | + | namd |
- | 2.12 Version 2.12 | + | 2.12 |
- | * 2.13 Version 2.13 | + | * 2.13 |
- | 2.13: | + | 2.13: |
+ | 2.14 | ||
+ | 3.0b3 compiled with Intel 2020, Open MPI 4.1.4 | ||
+ | 3.0b3: | ||
+ | 3.0b3: | ||
</ | </ | ||
- | The '' | + | The '' |
<code bash> | <code bash> | ||
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<note tip>It is always a good idea to periodically check if the templates in ''/ | <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 | ||
+ | </ | ||
+ | {{: | ||
+ | {{: |