Hi, I get these two warnings when I run the dhfr/GPU/dhfr-solv-PME.bench benchmark with the following command line:
mdrun_intel_cuda5 -v -s topol.tpr -testverlet "WARNING: Oversubscribing the available 0 logical CPU cores with 1 thread-MPI threads." 0 logical CPU cores? Isn't this bizarre? My CPU is Intel Core i7-3610QM (2.3 GHz). Unlike Albert, I don't see any performance loss, I get 13.4 ns/day on a single core with 1 GPU and 13.2 ns/day with GROMACS v4.5.5 on 4 cores (8 threads) without the GPU. Yet, I don't see any performance gain with more that 4 -nt threads. mdrun_intel_cuda5 -v -nt 2 -s topol.tpr -testverlet : 15.4 ns/day mdrun_intel_cuda5 -v -nt 3 -s topol.tpr -testverlet : 16.0 ns/day mdrun_intel_cuda5 -v -nt 4 -s topol.tpr -testverlet : 16.3 ns/day mdrun_intel_cuda5 -v -nt 6 -s topol.tpr -testverlet : 16.2 ns/day mdrun_intel_cuda5 -v -nt 8 -s topol.tpr -testverlet : 15.4 ns/day I have also attached my log file (from "mdrun_intel_cuda5 -v -s topol.tpr -testverlet") in case you find it helpful. Thanks, Thomas On 5 November 2012 18:54, Szilárd Páll <szilard.p...@cbr.su.se> wrote: > The first warning indicates that you are starting more threads than the > hardware supports which would explain the poor performance. > > Could share a log file of the suspiciously slow run as well as the command > line you used to start mdrun? > > Cheers, > > -- > Szilárd > > > On Sun, Nov 4, 2012 at 5:32 PM, Albert <mailmd2...@gmail.com> wrote: > > > well, IC. > > the performance is rather poor than GTX590..... 32ns/day vs 4 ns/day > > probably that's also something related to the warnings? > > > > THX > > > > > > > > On 11/04/2012 01:59 PM, Justin Lemkul wrote: > > > >> > >> > >> On 11/4/12 4:55 AM, Albert wrote: > >> > >>> hello: > >>> > >>> I am running Gromacs 4.6 GPU on a workstation with two GTX 660 Ti (2 > x > >>> 1344 > >>> CUDA cores), and I got the following warnings: > >>> > >>> thank you very much. > >>> > >>> ---------------------------**messages----------------------** > >>> ------------- > >>> > >>> WARNING: On node 0: oversubscribing the available 0 logical CPU cores > >>> per node > >>> with 2 MPI processes. > >>> This will cause considerable performance loss! > >>> > >>> 2 GPUs detected on host boreas: > >>> #0: NVIDIA GeForce GTX 660 Ti, compute cap.: 3.0, ECC: no, stat: > >>> compatible > >>> #1: NVIDIA GeForce GTX 660 Ti, compute cap.: 3.0, ECC: no, stat: > >>> compatible > >>> > >>> 2 GPUs auto-selected to be used for this run: #0, #1 > >>> > >>> Using CUDA 8x8x8 non-bonded kernels > >>> Making 1D domain decomposition 1 x 2 x 1 > >>> > >>> * WARNING * WARNING * WARNING * WARNING * WARNING * WARNING * > >>> We have just committed the new CPU detection code in this branch, > >>> and will commit new SSE/AVX kernels in a few days. However, this > >>> means that currently only the NxN kernels are accelerated! > >>> In the mean time, you might want to avoid production runs in 4.6. > >>> > >>> > >> I can't address the first warning, but the second is fairly obvious. > >> You're not using an official release, you're using the development > version > >> - let the user beware. The code is not yet production-ready. > >> > >> -Justin > >> > >> > > -- > > gmx-users mailing list gmx-users@gromacs.org > > http://lists.gromacs.org/**mailman/listinfo/gmx-users< > http://lists.gromacs.org/mailman/listinfo/gmx-users> > > * Please search the archive at http://www.gromacs.org/** > > Support/Mailing_Lists/Search< > http://www.gromacs.org/Support/Mailing_Lists/Search>before posting! > > * Please don't post (un)subscribe requests to the list. Use the www > > interface or send it to gmx-users-requ...@gromacs.org. > > * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists< > http://www.gromacs.org/Support/Mailing_Lists> > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- ====================================================================== Thomas Evangelidis PhD student University of Athens Faculty of Pharmacy Department of Pharmaceutical Chemistry Panepistimioupoli-Zografou 157 71 Athens GREECE email: tev...@pharm.uoa.gr teva...@gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/
-- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
