[gmx-users] Can we set the number of pure PME nodes when using GPU&CPU?

Xingcheng Lin linxingcheng50311 at gmail.com
Mon Aug 25 19:35:12 CEST 2014

Theodore Si <sjyzhxw at ...> writes:

> Hi,
> https://onedrive.live.com/redir?
> https://onedrive.live.com/redir?
> 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?

Thank you,

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