[gmx-users] performance

[Szilárd Páll]

My guess is that the two jobs are using the same cores -- either all
cores/threads or only half of them, but the same set.

You should use -pinoffset; see:

- Docs and example:
http://manual.gromacs.org/documentation/2016/user-guide/mdrun-performance.html

- More explanation on the thread pinning behavior on the old website:
http://www.gromacs.org/Documentation/Acceleration_and_parallelization#Pinning_threads_to_physical_cores

Cheers,
--
Szilárd


On Wed, Sep 13, 2017 at 6:35 PM, gromacs query <gromacsquery at gmail.com> wrote:
> Sorry forgot to add; we thought the two jobs are using same GPU ids but
> cuda visible devices show both jobs are using different ids (0,1 and 2,3)
>
> -
> J
>
> On Wed, Sep 13, 2017 at 5:33 PM, gromacs query <gromacsquery at gmail.com>
> wrote:
>
>> Hi All,
>>
>> I have some issues with gromacs performance. There are many nodes and each
>> node has number of gpus and the batch process is controlled by slurm.
>> Although I get good performance with some settings of number of gpus and
>> nprocs but when I submit same job twice on the same node then the
>> performance is reduced drastically. e.g
>>
>> For 2 GPUs I get 300 ns per day when there is no other job running on the
>> node. When I submit same job twice on the same node & at the same time, I
>> get only 17 ns/day for both the jobs. I am using this:
>>
>> mpirun -np 4 gmx_mpi mdrun -deffnm test -ntomp 2 -maxh 0.12
>>
>> Any suggestions highly appreciated.
>>
>> Thanks
>>
>> Jiom
>>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.