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Single node 2.14 ``charmrun++ ++np 1`` with ``++ppn ##`` moved to left side should run equivalently to the same ``namd`` and same ``++ppn ##``. | Single node 2.14 ``charmrun++ ++np 1`` with ``++ppn ##`` moved to left side should run equivalently to the same ``namd`` and same ``++ppn ##``. | ||
- | With two nodes, in a few cases ``charmrun++`` scales fairly well, but because of better alternatives, | + | With two nodes, in a few cases ``charmrun++`` scales fairly well, but because of better alternatives, |
On Pinnacle I, 2.14 ``charmrun++ ++np 2`` scaled well but was still hardly faster than single-node 2.15a1 ``namd2``. | On Pinnacle I, 2.14 ``charmrun++ ++np 2`` scaled well but was still hardly faster than single-node 2.15a1 ``namd2``. | ||
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==GPU== | ==GPU== | ||
- | Here using the number of cores available on the node (24/32/64) and one GPU (two or more GPUs ``devices 0,1,2,3`` scale poorly, not recommended or approved for AHPCC public use partitions). | + | Here we are using the number of CPU cores available on the node (24/32/64) and one GPU (two or more GPUs ``devices 0,1,2,3`` scale poorly, not recommended or approved for AHPCC public use partitions). This benchmark simulation scaled significantly with the CPU cores used up to the number of cores present. |
- | On the ``gpu72`` | + | On the ``gpu72`` |
< | < | ||
+ | # | ||
module load namd/3.0a7 | module load namd/3.0a7 | ||
namd3 +p32 +setcpuaffinity +isomalloc_sync +devices 0 step7.2_production_colvar.inp | namd3 +p32 +setcpuaffinity +isomalloc_sync +devices 0 step7.2_production_colvar.inp | ||
Info: Benchmark time: 32 CPUs 0.0393942 s/step 0.227976 days/ns 0 MB memory | Info: Benchmark time: 32 CPUs 0.0393942 s/step 0.227976 days/ns 0 MB memory | ||
- | + | # | |
- | namd3 +p64 +setcpuaffinity +isomalloc_sync step7.24_production.inp | + | namd3 +p64 +setcpuaffinity +isomalloc_sync |
Info: Benchmark time: 64 CPUs 0.0344332 s/step 0.199266 days/ns 0 MB memory | Info: Benchmark time: 64 CPUs 0.0344332 s/step 0.199266 days/ns 0 MB memory | ||
</ | </ | ||