Hi Ross,
Input is read from local hard disk and binary is on SSD. This is all on
my workstation and I don't have any issues with these. Serial run looks
fine but I do see that hostname is always 'Unknown' (also for serial
and MPI CPU). I see in the code (master_setup.F90) that the HOSTNAME
environment variable is queried but this doesn't work (inerr==0).
Many thanks,
Hannes.
On Wed, 21 Sep 2016 12:16:40 -0700
Ross Walker <ross.rosswalker.co.uk> wrote:
> Hi Hannes,
>
> That behavior sounds really weird. My initial guess would be file I/O
> issues meaning the reading of the input files is ridiculously slow.
> The second might be some kind of crazy long DNS timeout. PMEMD calls
> hostname so it record the hostname of the machine running the
> calculation in mdout. If this is timing out for some reason that
> might be why the setup time is always 240s.
>
> Both of those should be independent of GPU though. Can you try the
> serial CPU code with the exact same input setting and see if you get
> the same behavior?
>
> All the best
> Ross
>
> > On Sep 21, 2016, at 11:06 AM, Hannes Loeffler
> > <Hannes.Loeffler.stfc.ac.uk> wrote:
> >
> > Hi,
> >
> > I have a strange issue with the GPU variant of pmemd and seemingly
> > overlong runtimes. I have benchmarked a 30000 atoms sytems which is
> > reported to make about 32 ns/day. But the wall clock time just
> > doesn't match with that. After running with different nstlim I
> > realized that the setup time is constant at 240 s and top shows me
> > that the CPU only gets busy after that time (not sure what the GPU
> > does if it does anything).
> >
> > What could be the cause of this behaviour? The card is a Quadro
> > M4000, pmemd16 compiled with gcc4.9.2/cuda 7.5.17, driver is
> > currently 370.28 but I have also tried the current long term
> > version.
> >
> > Many thanks,
> > Hannes.
> >
> >
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Received on Wed Sep 21 2016 - 13:30:02 PDT
