[gmx-users] Job crash: checkpoint file
David van der Spoel
spoel at xray.bmc.uu.se
Mon Oct 25 18:21:48 CEST 2010
On 2010-10-25 17.58, Shi, Chuanyin wrote:
> I am having exactly the same problem recently.
> The replica exchange job stops around 11000 steps.
> Switch to another cluster and the job is running fine.
> I wonder how often you've seen this type of crashing and any solutions for this?
Have you checked your quota?
I had the same problem recently, and I was indeed out of quota.
> Chuanyin Shi
> Department of Chemistry& Biochemistry
> University of Oklahoma
> Email: cshi at ou.edu
> From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on behalf of Justin A. Lemkul [jalemkul at vt.edu]
> Sent: Friday, October 08, 2010 1:19 PM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] Job crash: checkpoint file
> Jianhui Tian wrote:
>> Dear GMX users,
>> I am running a replica simulation and the job crashed with the following
>> File input/output error:
>> Cannot rename checkpoint file; maybe you are out of quota?
>> From the mailling list, I see this might be a permission problem.
>> However, I checked the file permission and nothing wrong was noticed.
>> If I rerun the crashed simulation, it goes through the second time. This
>> seems strong. Any suggestion is welcomed.
> I've seen this happen when our filesystem blips. It seems like you're able to
> run your job, so I don't think there's anything to do about it, except perhaps
> inquire with your sysadmins about the stability of the filesystem, and whether
> or not you can expect to have this happen frequently.
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
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David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
spoel at xray.bmc.uu.se http://folding.bmc.uu.se
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