[gmx-users] using dual CPU's

Szilárd Páll pall.szilard at gmail.com
Tue Dec 11 19:14:53 CET 2018

Without having read all details (partly due to the hard to read log
files), what I can certainly recommend is: unless you really need to,
avoid running single simulations with only a few 10s of thousands of
atoms across multiple GPUs. You'll be _much_ better off using your
limited resources by running a few independent runs concurrently. If
you really need to get maximum single-run throughput, please check
previous discussions on the list on my recommendations.

Briefly, what you can try for 2 GPUs is (do compare against the
single-GPU runs to see if it's worth it):
mdrun -ntmpi N -npme 1 -nb gpu -pme gpu -gpustasks TASKSTRING
where typically N = 4, 6, 8 are worth a try (but N <= #cores) and the
TASKSTRING should have N digits with either N-1 zeros and the last 1
or N-2 zeros and the last two 1, i.e..

I suggest to share files using a cloud storage service like google
drive, dropbox, etc. or a dedicated text sharing service like
paste.ee, pastebin.com, or termbin.com -- especially the latter is
very handy for those who don't want to leave the command line just to
upload a/several files for sharing (i.e. try "echo "foobar" | nc
termbin.com 9999)

On Tue, Dec 11, 2018 at 2:44 AM paul buscemi <pbuscemi at q.com> wrote:
> > On Dec 10, 2018, at 7:33 PM, paul buscemi <pbuscemi at q.com> wrote:
> >
> >
> > Mark, attached are the tail ends of three  log files for
> >  the same system but run on an AMD 8  Core/16 Thread 2700x, 16G ram
> > In summary:
> > for ntpmi:ntomp of 1:16 , 2:8, and auto selection (4:4) are 12.0, 8.8 , and 6.0 ns/day.
> > Clearly, I do not have a handle on using 2 GPU's
> >
> > Thank you again, and I'll keep probing the web for more understanding.
> > I’ve propbably sent too much of the log, let me know if this is the case
> Better way to share files - where is that friend ?
> >
> > Paul
> --
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