Hi, You must have an odd sysconf version! Could you please check what is the sysconf system variable's name in the sysconf man page (man sysconf) where it says something like:
_SC_NPROCESSORS_ONLN The number of processors currently online. The first line should be one of the following: _SC_NPROCESSORS_ONLN, _SC_NPROC_ONLN, _SC_NPROCESSORS_CONF, _SC_NPROC_CONF, but I guess yours is something different. Can you also check what your glibc version is? Thanks, -- Szilárd On Fri, Nov 9, 2012 at 5:51 PM, Thomas Evangelidis <teva...@gmail.com>wrote: > > > > > 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 >> > >> >> That is bizzarre. Could you run with "-debug 1" and have a look at the >> mdrun.debug output which should contain a message like: >> "Detected N processors, will use this as the number of supported hardware >> threads." >> >> I'm wondering, is N=0 in your case!? >> >> It says "Detected 0 processors, will use this as the number of supported > hardware threads." > > >> >> > (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 guess there is not much point in not using all cores, is it? Note that >> the performance drops after 4 threads because Hyper-Threading with OpenMP >> doesn't always help. >> >> >> > >> > I have also attached my log file (from "mdrun_intel_cuda5 -v -s >> topol.tpr >> > -testverlet") in case you find it helpful. >> > >> >> I don't see it attached. >> >> >> > I have attached both mdrun_intel_cuda5.debug and md.log files. They will > possibly be filtered by the mailing list but will be delivered to your > email. > > thanksm > Thomas > -- 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