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-- Paul Rigor http://www.ics.uci.edu/~prigor On Wed, May 25, 2011 at 10:54 AM, Scott Le Grand <varelse2005.gmail.com>wrote: > There is no I/O in the CUDA code whatsoever. All control of overall > program flow and execution is done through the existing FORTRAN > infrastructure. The CUDA code merely hotwires the calculation and > tricks the FORTRAN into thinking it's doing it itself through a > variety of jiggery pokery. That's my story and I'm sticking to it. > > Scott > > On Wed, May 25, 2011 at 10:27 AM, Jason Swails <jason.swails.gmail.com> > wrote: > > Just to chime in here -- NetCDF is hooked into pmemd and pmemd.cuda > through > > the netcdf fortran module, NOT through statically/dynamically linked > > libraries. The netcdf.mod file is taken from the AmberTools NetCDF > > installation, so libnetcdf.a and libnetcdff.a shouldn't be necessary in > the > > config.h > > > > Furthermore, I don't think any file writing is done through the CUDA code > > (just through the Fortran code), so you shouldn't need to add any NetCDF > > libraries to any CUDA variables. Also, libraries only ever need to be > > included on the link line, so I'm not sure what changes you claim to have > > had to make and how they could have possibly been necessary to build > > pmemd.cuda... > > > > I've tested it on AmberTools 1.5 + Amber11, and it works fine for me > without > > having to massage the config.h file any more than AT15_Amber11.py does > > already. > > > > All the best, > > Jason > > > > On Wed, May 25, 2011 at 12:38 PM, Ross Walker <ross.rosswalker.co.uk> > wrote: > > > >> Hi Paul, > >> > >> > Attached are the test logs running the test suite on a CentOS 5.6 > >> > machine > >> > with a Tesla C2070. > >> > >> The gb_ala3 case is, I believe, just an issue with the random number > stream > >> being different. This can happen a lot with ntt=3 since the use of > random > >> numbers changes depending on the hardware configuration. Working around > >> this, for test purposes, hurts performance a lot. This failure (and > >> dhfr_ntb2_ntt3). The rest look to just be rounding differences so I > think > >> you are good. I am not sure why there are so many differences though > since > >> the test case saved outputs should be based on C2070's. Thus given the > >> modifications you made below I would be a little wary. > >> > >> > There was a bit of massaging to compile the cuda config. In fact, I > had > >> > to > >> > modify PMEMD_CU_FLAGS to include the arlibs of libnetcdf.a and > >> > libnetcdff.a > >> > along with the full path to the installation path of the shared > >> > libraries. > >> > >> I am little confused why you needed to make these changes. Unless > something > >> in AMBER Tools 1.5 has messed up the GPU compilation. AMBER should > compile > >> it's own netcdf so you should not need to make any changes here. Did you > >> also apply all the bugfixes? - I guess I should find (invent) time to > try > >> building AMBER 11 + patches + AmberTools 1.5 myself. - What NVIDIA cuda > >> compiler version are you using? > >> > >> The development tree off of what AMBERTools 1.5 was based works fine for > me > >> and there will be a big GPU update shortly so I never bothered to test > with > >> AMBERTools 1.5 so it is possible someone messed something up with the > netcdf > >> libraries etc but I am still surprised you had to modify things to get > it to > >> build. > >> > >> Does the rest of AMBER (AmberTools and AMBER CPU etc build fine in > serial > >> or parallel?) - You should really make sure all the CPU compilation and > >> tests run fine before trying to build the GPU version. > >> > >> All the best > >> Ross > >> > >> /\ > >> \/ > >> |\oss Walker > >> > >> --------------------------------------------------------- > >> | Assistant Research Professor | > >> | San Diego Supercomputer Center | > >> | Adjunct Assistant Professor | > >> | Dept. of Chemistry and Biochemistry | > >> | University of California San Diego | > >> | NVIDIA Fellow | > >> | http://www.rosswalker.co.uk | http://www.wmd-lab.org/ | > >> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk | > >> --------------------------------------------------------- > >> > >> Note: Electronic Mail is not secure, has no guarantee of delivery, may > not > >> be read every day, and should not be used for urgent or sensitive > issues. > >> > >> > >> > >> > >> > >> _______________________________________________ > >> 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/amber > _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Wed May 25 2011 - 14:00:02 PDT