[gmx-users] Restart simulation from checkpoint file with fewer nodes
jkrieger at mrc-lmb.cam.ac.uk
jkrieger at mrc-lmb.cam.ac.uk
Sun May 15 11:48:07 CEST 2016
Thanks Mark,
My sysadmins have let me install my own GROMACS versions and have not
informed me of any such mechanism. Would you suggest I qrsh into a node of
each type and build an mdrun-only version on each? I'd then select a
particular node type for a submit script with the relevant mdrun.
Many thanks
James
> Hi,
>
> On Sat, May 14, 2016 at 1:09 PM <jkrieger at mrc-lmb.cam.ac.uk> wrote:
>
>> In case it's relevant/interesting to anyone, here are the details on our
>> cluster nodes:
>>
>> nodes # model # cores cpu
>> model
>> RAM node_type
>> fmb01 - fmb33 33 IBM HS21XM 8 3 GHz
>> Xeon
>> E5450
>> 16GB hs21
>> fmb34 - fmb42 9 IBM HS22 8 2.4 GHz
>> Xeon E5530
>> 16GB hs22
>> fmb43 - fmb88 45 Dell PE M610 8 2.4 GHz
>> Xeon E5530
>> 16GB m610
>> fmb88 - fmb90 3 Dell PE M610+ 12 3.4 GHz
>> Xeon X5690
>> 48GB m610+
>> fmb91 - fmb202 112 Dell PE M620 24 (HT) 2.9 GHz
>> Xeon E5-2667
>> 64GB m620
>> fmb203 - fmb279 77 Dell PE M620 24 (HT) 3.5 GHz
>> Xeon E5-2643 v2 64GB
>> m620+
>> fmb280 - fmb359 80 Dell PE M630 24 (HT) 3.4 GHz
>> Xeon E5-2643 v3 64GB
>> m630
>>
>> I could only run GROMACS 4.6.2 on the last three node types and I
>> believe
>> the same is true for 5.0.4
>>
>
> Sure. GROMACS is designed to target whichever hardware was selected at
> configure time, which your sysadmins for such a heterogeneous cluster
> should have documented somewhere. They should also be making available to
> you a mechanism to target your jobs to nodes where they can run programs
> that use the hardware efficiently, or providing GROMACS installations that
> work regardless of which node you are actually on. You might like to
> respectfully remind them of the things we say at
> http://manual.gromacs.org/documentation/5.1.2/install-guide/index.html#portability-aspects
> (These thoughts are common to earlier versions also.)
>
> Mark
>
>
> Best wishes
>> James
>>
>> > I have found that only some kinds of nodes on our cluster work for
>> gromacs
>> > 4.6 (the ones we call m620, m620+ and m630 but not others - I can
>> check
>> > the details tomorrow). I haven't tested it again now I'm using 5.0 so
>> > don't know if that's still an issue but if it is it could explain why
>> your
>> > restart failed even and the initial run didn't.
>> >
>> >> thanks a lot for your fast response.
>> >>
>> >> I have tried it, and it failed. I ask in this forum just to make
>> sure.
>> >> However, there was something in my cluster that probably make it
>> failed.
>> >> I'll handle it first and then retry to restart again.
>> >>
>> >> 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
>> >>>
>> >>> ==================================================
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