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? 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.
