From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Tue Apr 05 2016 - 08:21:37 CDT
Something else that might have negative performance impact may be your enabled HyperThreading. I'm sure that your jobs will run faster using only the physical cores. Depending on the logical core layout, you jobs may be faster like:
taskset 0-11 namd2 +p12 A.conf
taskset 24-35 namd2 +p12 B.conf
or less likely
taskset 0,2,4,6,8,10,12,14,16,18,20,22 namd2 +p12 A.conf
taskset 24,26,28,30,32,34,36,38,40,42,44,46 namd2 +p12 B.conf
> -----Ursprüngliche Nachricht-----
> Von: nikolaev_at_spbau.ru [mailto:nikolaev_at_spbau.ru]
> Gesendet: Dienstag, 5. April 2016 14:41
> An: namd-l_at_ks.uiuc.edu; Norman Geist <norman.geist_at_uni-greifswald.de>
> Betreff: Re: AW: namd-l: problem with +devices using
> Well, I tried the taskset and everything works fine now, thank you.
> I also attach the cpuinfo here, just in case.
> > Ignoring the fact that the shared PCIE bus will cause a smaller
> > performance drop anyway, your significant slowdown may be caused by
> > the same cpus for your both jobs. Show us the output of
> > cat /proc/cpuinfo
> > You need to make sure each job will only use its subset of cpus. You can
> > accomplish that using taskset, depending on how many cores you have. An
> > example for a machine which would have 16 cores:
> > taskset -c 0-7 namd2 +p8 A.conf
> > taskset -c 8-15 namd2 +p8 B.conf
> > Norman Geist
> >> -----Ursprüngliche Nachricht-----
> >> Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im
> >> Auftrag von nikolaev_at_spbau.ru
> >> Gesendet: Dienstag, 5. April 2016 13:35
> >> An: namd-l_at_ks.uiuc.edu
> >> Betreff: namd-l: problem with +devices using
> >> Hello,
> >> I use a CUDA build of NAMD, and want to run 2 jobs simultaneously.
> >> We have 4 devices, so I assign +devices 0,1 for the first job and
> >> +devices 2,3 for the second.
> >> When I run the first job, everything is ok, and it runs well on 2
> >> devices
> >> and uses 65-70% of the devices' resources.
> >> But when I add the second job, the performance drops immediately to
> >> 11%
> >> on all 4 devices!
> >> How to solve this problem?
> >> Here is the command I run namd:
> >> /home/nikolaev_d/NAMD_2.11_Linux-x86_64-multicore-CUDA/namd2
> >> +setcpuaffinity +p18 +devices 0,1 +idlepoll A.conf > A.log
> >> Thank you in advance,
> >> Dmitrii.
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