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
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> 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 - 19:30:02 PDT
