[gmx-users] GPU warnings
szilard.pall at cbr.su.se
Sat Nov 10 02:21:40 CET 2012
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:
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
Can you also check what your glibc version is?
On Fri, Nov 9, 2012 at 5:51 PM, Thomas Evangelidis <tevang3 at 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
>> 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
>> > -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
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