[gmx-users] Can we set the number of pure PME nodes when using GPU&CPU?
pall.szilard at gmail.com
Mon Aug 25 19:40:42 CEST 2014
On Mon, Aug 25, 2014 at 7:12 PM, Xingcheng Lin
<linxingcheng50311 at gmail.com> wrote:
> 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?
That's an outdated message which is only correct if a single rank/GPU
is used. If you use a more up-to-date 4.6.x or 5.0.x version, you'd
get something like this instead:
2 GPUs user-selected for this run.
Mapping of GPUs to the 8 PP ranks in this node: #0, #0, #0, #0, #1, #1, #1, #1
> Thank you,
> Gromacs Users mailing list
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.
More information about the gromacs.org_gmx-users