[gmx-users] Changing number of processors after a job restart

Justin Lemkul jalemkul at vt.edu
Fri Jan 9 13:40:52 CET 2015

On 1/9/15 2:00 AM, Nash, Anthony wrote:
> Hi all,
> This is probably quite a fundamental bit of knowledge I am missing (and struggling to find). In an effort to just get a system running rather than waiting on a queue I am considering taking my job which has already ran for 48 hours and reducing the requested number of nodes. I would use the usual -cpi ----.cpt -noappend notation in the job script to resubmit.
> I have a feeling though, that all manor of parallel calculations were preserved in the check point file and are loaded upon restart. Would my job reload and recalculate all the relevant cell decomposition, etc., without throwing up an error.

IIRC, you will get errors when reading from the checkpoint file.  The 
alternative is to re-create the .tpr with grompp (using -t to pass the .cpt) 
rather than the usual tpbconv/mdrun -cpi approach.



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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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