[gmx-developers] Hardware threads vs. OpenMP threads

[David van der Spoel]

On 04/06/15 12:51, Berk Hess wrote:
> PS There is something strange on that machine. If Gromacs detects 16
> threads, omp_get_num_procs should return 16, not 8.
Nope.
The queue system allocates 8 cores out of 16 physical cores to my job.
GROMACS see both values, reports a conflict, and follows the hardware 
rather than OpenMP settings. I would think it should do the reverse.

>
> Berk
>
> On 2015-06-04 12:49, Berk Hess wrote:
>> Hi,
>>
>> I don't think anything changed in the master branch.
>>
>> But we do adhere to the OpenMP environment. The value reported in the
>> message comes from omp_get_num_procs, which should be a report about
>> the hardware available. OMP_NUM_THREADS sets the number of OpenMP
>> threads to use, that is respected.
>>
>> Cheers,
>>
>> Berk
>>
>> On 2015-06-04 11:21, David van der Spoel wrote:
>>> Hi,
>>>
>>> why does GROMACS in the master branch not adhere to the OpenMP
>>> environment?
>>>
>>> Number of hardware threads detected (16) does not match the number
>>> reported by OpenMP (8).
>>> Consider setting the launch configuration manually!
>>> Reading file md.tpr, VERSION 5.1-beta1-dev-20150603-99a1e1f-dirty
>>> (single precision)
>>> Changing nstlist from 10 to 40, rlist from 1.1 to 1.1
>>>
>>> Using 1 MPI process
>>> Using 16 OpenMP threads
>>>
>>> Cheers,
>>
>


-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se