[gmx-users] GPU warnings

[Szilárd Páll]

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 <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
>> 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
>