[gmx-users] About Error in mdrun

Justin Lemkul jalemkul at vt.edu
Fri Aug 16 20:00:26 CEST 2013

On 8/16/13 11:51 AM, vidhya sankar wrote:
> Dear justin Thank you for your previous reply
>   When i run the md in gromacs 4.6.2 with plumed1.3   Plugin i have got the error as follows
> 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).
> Back Off! I just backed up CNTPEPRSOLIONSfull.trr to
>        ./#CNTPEPRSOLIONSfull.trr.3#
> Back Off! I just backed up CNTPEPRSOLIONSfull.edr to
>        ./#CNTPEPRSOLIONSfull.edr.3#
> WARNING: This run will generate roughly 273370 Mb of data
> starting mdrun 'C225N99O45 in water'
> 100000000 steps, 200000.0 ps.
> !!!!! PLUMED ERROR: PluMed dead with errors: check log file
> Segmentation fault (core dumped)
> To avoid this May i use  -pin on ?

It's easier to try it and see (and have an answer in seconds) rather than wait 
several hours to get a reply...

The specific answer depends on your hardware and whether or not you are going to 
see any benefit.  I don't really know the mechanics of this process, though 
there have been numerous discussions in recent weeks and months.  First, upgrade 
to 4.6.3, then try again.



Justin A. Lemkul, Ph.D.
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


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