[gmx-developers] Hardware threads vs. OpenMP threads

[Berk Hess]

On 2015-06-04 13:46, David van der Spoel wrote:
> 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.
So the queue system allocates parts of nodes, not whole nodes? How is a 
job supposed to know how many cores to use? If the job uses OpenMP this 
trick with omp_get_num_procs might do it, but I would think that in 
general the job should get the number of cores to use from some 
environment variable set by the queue system.

Berk
>
>>
>> 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,
>>>
>>
>
>