# Qsub mdrun -pin and -pinoffset configurations

**URL:** <https://gromacs.bioexcel.eu/t/qsub-mdrun-pin-and-pinoffset-configurations/4538>\
**Category:** User discussions\
**Tags:** mdrun\
**Created:** [August 1, 2022, 12:24pm UTC](https://gromacs.bioexcel.eu/t/qsub-mdrun-pin-and-pinoffset-configurations/4538 "2022-08-01T12:24:34Z")\
**Posts on this page:** 1\
**Page:** 1

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**Author:** ![Roy\_Lizarovich](https://avatars.discourse-cdn.com/v4/letter/r/b19c9b/32.png) [@Roy\_Lizarovich](https://gromacs.bioexcel.eu/u/Roy_Lizarovich)\
**Post date:** [August 1, 2022, 12:24pm UTC](https://gromacs.bioexcel.eu/t/qsub-mdrun-pin-and-pinoffset-configurations/4538/1 "2022-08-01T12:24:34Z")

</div>

GROMACS version: gromacs-2020.1  
GROMACS modification: Yes/No

Greetings one and all,  
We are using a server to run our mdrun commends, we use interactive job via qsub and a bash script with the following parameters:

#PBS -l nodes=compute-0-332:ppn=4,mem=6gb  
#PBS -l ngpus=1

the mdrun command is:  
gmx mdrun -v -deffnm prot\_md -x prot\_md.xtc -nice 19 -dlb

when the simulation starts we get the following 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 threads to cores.  
This can lead to significant performance degradation.  
Consider using -pin on (and -pinoffset in case you run multiple jobs).”

we like to improve our un time so any suggestions on -pin and -pinoffset configurations will be welcomed.