[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 15:20:08 CEST 2016
ok thanks
> Hi,
>
> Yes, that's one way to work around the problem. In some places, a module
> subsystem can be used to take care of the selection automatically, but you
> don't want to set one up for just you to use.
>
> Mark
>
> On Sun, May 15, 2016 at 11:48 AM <jkrieger at mrc-lmb.cam.ac.uk> wrote:
>
>> 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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