On Mon, Aug 25, 2014 at 7:12 PM, Xingcheng Lin <linxingcheng50...@gmail.com> wrote: > Theodore Si <sjyzhxw@...> writes: > >> >> Hi, >> >> https://onedrive.live.com/redir? > resid=990FCE59E48164A4!2572&authkey=!AP82sTNxS6MHgUk&ithint=file%2clog >> https://onedrive.live.com/redir? > resid=990FCE59E48164A4!2482&authkey=!APLkizOBzXtPHxs&ithint=file%2clog >> >> 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. >> > Hi, > > 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That's an outdated message which is only correct if a single rank/GPU is used.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 Cheers, -- Szilárd > 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-requ...@gromacs.org. -- 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-requ...@gromacs.org.