Hi Ross,
Thanks for the response -- Following your instructions reduced my total
time down to ~8 seconds.
Best,
Parker
On Sun, Jul 7, 2013 at 2:17 AM, Ross Walker <rosscwalker.gmail.com> wrote:
> Hi Parker,
>
> The run is taking 10seconds of compute time which is about what i'd expect
> but for sone reason it takes 210 seconds of wallclock time. Are you sure
> nobody else is running on the same machine / same GPU? Are you using a
> remote (and slow?) filesystem?
>
> The run should take about 10 seconds but for some reason it is only
> running at about 5% efficiency on your machine.
>
> A few things to try:
>
> 1. Make sure you have the latest Nvidia driver.
> 2. Install the latest version of amber, should report v12.3 for GPU.
> 3. Reboot and kick everyone else off the machine.
> 4. Run on a local filesystem.
> 5. Download the benchmark suite from http://ambermd.org/gpus/ and see how
> your machine fairs with that.
>
> All the best
> Ross
>
>
>
> On Jul 6, 2013, at 22:04, Parker de Waal <Parker.deWaal09.kzoo.edu> wrote:
>
> > Hi AMBER Users!
> >
> > I'm currently running a step 1000 energy minimization, using steepest
> > descent on a system comprised of 54782 atoms on a single Tesla K20 card,
> > and the entire process seems very slow compared to the same setup in
> > GROMACS. .rst provided here which contains settings and timings etc:
> > https://gist.github.com/ParkerdeWaal/7c6c01c2b00327033e76
> >
> > If anyone can provide insight I would be extremely grateful.
> >
> > Best,
> > Parker
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> > AMBER.ambermd.org
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>
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Received on Sun Jul 07 2013 - 08:30:02 PDT
