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-- 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 > _______________________________________________ > 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/amberReceived on Wed May 25 2011 - 19:30:05 PDT