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

Nash, Anthony a.nash at ucl.ac.uk
Fri Jan 9 13:46:22 CET 2015

Hi Justin,

I thought I would just give it a try at the risk of then being dropped back down on the queue. Turns out I end up with warnings rather than system-halting errors:

  #nodes mismatch,
    current program: 32
    checkpoint file: 64

  #PME-nodes mismatch,
    current program: -1
    checkpoint file: 16

Gromacs binary or parallel settings not identical to previous run.
Continuation is exact, but is not guaranteed to be binary identical.


I am now weighing up the pros and cons of this simulation. 


Dr Anthony Nash
Department of Chemistry
University College London
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [gromacs.org_gmx-users-bounces at maillist.sys.kth.se] on behalf of Justin Lemkul [jalemkul at vt.edu]
Sent: 09 January 2015 12:40
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Changing number of processors after a job restart

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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