[gmx-users] Restart simulation from checkpoint file with fewer nodes

[Husen R]

Hi,

Currently I'm running this tutorial (
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/08_MD.html)
to simulate restart with fewer nodes.
at restart, I changed the amount of nodes from 3 to 2 nodes.
I also changed the amount of processes from 24 to 16 processes.

While the application is running, I tried to see the output file.
This is the content of the output file :

#########################output file########################


Reading checkpoint file md_0_1.cpt generated: Sat May 14 13:10:25 2016

  #ranks mismatch,
    current program: 16
    checkpoint file: 24

  #PME-ranks mismatch,
    current program: -1
    checkpoint file: 6

GROMACS patchlevel, binary or parallel settings differ from previous run.
Continuation is exact, but not guaranteed to be binary identical.

Using 16 MPI processes
Using 1 OpenMP thread per MPI process

starting mdrun 'LYSOZYME in water'
500000 steps,   1000.0 ps (continuing from step 54500,    109.0 ps).

############################################################################

I got a mismatch note as described in the output file above. it is not a
problem, isn't it ?
I just want to make sure.

is it not allowed to use a different user when we restart simulation from
checkpoint file ?
Previously, I failed to restart simulation based on checkpoint file. I
guess, it is failed because I used a different user (Only a guess).
Thank you in advance.

regards,

Husen




On Sat, May 14, 2016 at 7:58 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 5/13/16 8:53 PM, Husen R wrote:
>
>> Dear all
>>
>> Does simulation able to be restarted from checkpoint file with fewer
>> nodes ?
>> let's say, at the first time, I run simulation with 3 nodes. At running
>> time, one of those nodes is crashed and the simulation is terminated.
>>
>> I want to restart that simulation immadiately based on checkpoint file
>> with
>> the remaining 2 nodes. does gromacs support such case ?
>> I need help.
>>
>
> Have you tried it?  It should work.  You will probably get a note about
> the continuation not being exact due to a change in the number of cores,
> but the run should proceed fine.
>
> -Justin
>
> --
> ==================================================
>
> 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
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>