[gmx-users] Can we set the number of pure PME nodes when using GPU&CPU?
linxingcheng50311 at gmail.com
Mon Aug 25 19:35:12 CEST 2014
Theodore Si <sjyzhxw at ...> writes:
> These are 2 log files. The first one is using 64 cpu cores(64 / 16 = 4
> nodes) and 4nodes*2 = 8 GPUs, and the second is using 512 cpu cores, no GPU.
> When we look at the 64 cores log file, we find that in the R E A L C
> Y C L E A N D T I M E A C C O U N T I N G table, the total wall
> time is the sum of every line, that is 37.730=2.201+0.082+...+1.150. So
> we think that when the CPUs is doing PME, GPUs are doing nothing. That's
> why we say they are working sequentially.
> As for the 512 cores log file, the total wall time is approximately the
> sum of PME mesh and PME wait for PP. We think this is because
> PME-dedicated nodes finished early, and the total wall time is the time
> spent on PP nodes, therefore time spent on PME is covered.
I have a naive question:
In your log file there are only 2 GPUs being detected:
2 GPUs detected on host gpu42:
#0: NVIDIA Tesla K20m, compute cap.: 3.5, ECC: yes, stat: compatible
#1: NVIDIA Tesla K20m, compute cap.: 3.5, ECC: yes, stat: compatible
In the end you selected 8 GPUs
8 GPUs user-selected for this run: #0, #0, #0, #0, #1, #1, #1, #1
Did you choose 8 GPUs or 2 GPUs? What is your mdrun command?
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