That sounds strange. Does the error happen at step? Assuming the it does occur within the first 10 steps, here are a few things to try: - Run "cuda-memcheck mdrun -nsteps 10"; - Try running with GMX_EMULATE_GPU env. var. set? This will run the GPU acceleration code-path, but will use CPU kernels (equivalent to the CUDA but slow implementation). - Run with GMX_EMULATE_GPU using valgrind: "GMX_EMULATE_GPU=1 valgrind mdrun -nsteps 10"
Cheers, -- Szilárd On Thu, Jan 30, 2014 at 11:47 AM, AOWI (Anders Ossowicki) <a...@novozymes.com> wrote: > Thanks for your suggestions! > >> I would not make any assumptions though, but rather try a few things first: >> - Does the card pass a memtest (sourceforge.net/projects/cudagpumemtest/)? > The memtest ran for about an hour with no errors. > >> - Does the installation pass the regressiontests? > No. These four complex tests fail, all with the usual error: > > FAILED. Check mdrun.out, md.log files in nbnxn_pme > FAILED. Check mdrun.out, md.log files in nbnxn_rf > FAILED. Check mdrun.out, md.log files in nbnxn_rzero > FAILED. Check mdrun.out, md.log files in nbnxn_vsite > > Everything else passes. > >> - Is the error reproducible with other inputs? > Yes, so far anything that has caused Gromacs to engage the GPU has failed. > Our own runs, the samples from the Gromacs website, and the four tests above. > >> Also note that with the default invocation of mdrun you are attempting to >> use all cores/hardware threads in your machine (I assume a 2x12-core IVB-E >> node with HT on). > > Two Xeon E5-2697V2 processors yes. This is a test server for gauging the > potential performance gains of GPGPU with our own runs. We'll stick to a > proper CPU-GPU ratio for the performance measurements. This was just me > trying to pare it down to the simplest invocation. > > We have had no trouble using other CUDA-enabled tools on this particular test > server. NAMD, for example, works fine. > -- > Anders Ossowicki > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
