[gmx-users] mpirun error

[Justin Lemkul]

On 4/18/14, 6:53 PM, maggin wrote:
> Hi,
>
> I use
>                grompp -f nvt.mdp -c em.gro -p box.6.top -o nvt.tpr
>                mpirun -np 8 mdrun_mpi -deffnm nvt
>
> and get
>
>   NOTE: The number of threads is not equal to the number of (logical) cores
>        and the -pin option is set to auto: will not pin thread to cores.
>        This can lead to significant performance degradation.
>        Consider using -pin on (and -pinoffset in case you run multiple jobs).
>
> So, I fix it as  mpirun -np 8 mdrun_mpi -deffnm nvt -pinoffset
>
> is it right?
>

No.  The -pinoffset option takes an integer argument to define the first logical 
core to be used.  It is only relevant in the case that multiple jobs are using 
the same set of nodes.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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