Hi all, After spending time for troubleshooting, I found that gromacs checkpoint/restart feature is working well.
The failure occurred because I use root user to submit restart job (using slurm resource manager). After switching to non root user, the restart process is running. The reason why I use root user is because I run this job in bash scripting and execute it at designated time using Cron. I know this is not the right place to talk about slurm. Thank you for your reply ! Regards, Husen On Sun, May 15, 2016 at 8:20 PM, <jkrie...@mrc-lmb.cam.ac.uk> wrote: > 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 <jkrie...@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 <jkrie...@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 <jalem...@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 > >> >> >>> > >> >> >>> jalem...@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? 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