Re: [AMBER] Test results for amber-cuda, single node, single GPU, Tesla C2070

From: Paul Rigor <paul.rigor.uci.edu>
Date: Wed, 25 May 2011 19:25:56 -0700

Hi Jason,

Yes, that patch wasn't applied. My sys admin still hasn't responded.
However, I've included the test results for the cuda_DPDP and cuda_SPDP
binaries. The DPDP binary passes all the tests while the hybrid had benign
issues.

But it does look like I've got at least a working system that's been patched
upto having the "cuda_parallel" target, ie, properly set the netCDF path.
 I've gone ahead and downloaded the latest patches myself. I'll ping the
group and hopefully this will server as a test for SDK 4.0!

Cheers,
Paul


--
Paul Rigor
http://www.ics.uci.edu/~prigor
On Wed, May 25, 2011 at 7:17 PM, Jason Swails <jason.swails.gmail.com>wrote:
> See http://ambermd.org/bugfixes11.html
>
> bugfix.9 <http://ambermd.org/bugfixes/11.0/bugfix.9>: This is a large
> scale
> bug and feature patch for the AMBER 11 NVIDIA GPU (CUDA) code developed in
> close collaboration with NVIDIA. Specifically pmemd.cuda. The patch
> addresses a number of outstanding bugs, includes some minor single GPU
> performance improvements, and most importantly, through funding provided by
> NSF Grant 1047875 and UC Lab award 09-LR-06-117792-WALR, provides support
> for MPI runs over multiple GPUs. For updated installation instructions and
> performance numbers please see http://ambermd.org/gpus/
>
> If you look at that patch, it clearly adds a cuda_parallel target to each
> Makefile.  This patch must not be getting applied.
>
> HTH,
> Jason
>
> On Wed, May 25, 2011 at 9:51 PM, Paul Rigor <paul.rigor.uci.edu> wrote:
>
> > Here's the log after recompiling, applying the patches, etc (but still no
> > cuda_parallel target) and without having to mess with the netCDF library.
> >
> > 42 file comparisons passed
> > 12 file comparisons failed
> > 0 tests experienced errors
> > Test log file saved as logs/test_amber_cuda/2011-05-25_18-22-30.log
> > Test diffs file saved as logs/test_amber_cuda/2011-05-25_18-22-30.diff
> >
> > Thanks,
> > Paul
> >
> >
> > --
> > Paul Rigor
> > http://www.ics.uci.edu/~prigor
> >
> >
> >
> > On Wed, May 25, 2011 at 5:53 PM, Paul Rigor <paul.rigor.uci.edu> wrote:
> >
> > > Hi gang,
> > >
> > > So I'm still checking with our system admin, I still do not see the
> > > cuda_parallel target, just serial, parallel and cuda. So we probably
> > don't
> > > have the latest sources? In any case, here are the logs for the serial
> > and
> > > mpi versions of amber.  I've made sure to patch and also clean up
> before
> > > running their respective make target.
> > >
> > > I'll keep you posted on the cuda and cuda_parallel builds for SDK 4.0
> > (and
> > > 3.2).
> > >
> > > Thanks,
> > > Paul
> > >
> > >
> > >
> > > --
> > > Paul Rigor
> > > http://www.ics.uci.edu/~prigor
> > >
> > >
> > >
> > > On Wed, May 25, 2011 at 4:18 PM, Ross Walker <ross.rosswalker.co.uk
> > >wrote:
> > >
> > >> > > Yes it does. Line 45 of $AMBERHOME/src/Makefile
> > >> > >
> > >> > > cuda_parallel: configured_cuda configured_parallel clean
> > $(NETCDFLIB)
> > >> > >        .echo "Starting installation of ${AMBER} (cuda parallel) at
> > >> > `date`".
> > >> > >        cd pmemd && $(MAKE) cuda_parallel
> > >> > >
> > >> > > Something smells fishy with your copy of AMBER 11 to me if it is
> > >> > missing
> > >> > > this.
> > >> > >
> > >> >
> > >> > Could be unpatched.  I don't think we had cuda_parallel at Amber11
> > >> > release, right?
> > >>
> > >> But how would he get any parallel version compiled??? - Or maybe it is
> > >> just
> > >> the serial version linked with MPI. Ugh...
> > >>
> > >>
> > >> _______________________________________________
> > >> AMBER mailing list
> > >> AMBER.ambermd.org
> > >> http://lists.ambermd.org/mailman/listinfo/amber
> > >>
> > >
> > >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
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Received on Wed May 25 2011 - 19:30:05 PDT
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