[gmx-users] Job crash: checkpoint file

[Shi, Chuanyin]

I wish the error would come from the quota.
But the disk quota is fine, we still have 2.0TB on the scratch space which is shared by everyone.
And I have other jobs running and no problem with writing outputs.
I've tried smaller REMD jobs on the cluster using only 1 node (8 cpus) and seems to be no problem.
But using 7 nodes and one (or two) node complains about that.
And several weird files are generated: mdrun_mpi.80s-12939,v002.local.btr, mdrun_mpi.80s-12940,v002.local.btr, ....
v002 is the name of the node.


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 David van der Spoel [spoel at xray.bmc.uu.se]
Sent: Monday, October 25, 2010 11:21 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Job crash: checkpoint file

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?
> Thanks.

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
>> message:
>>
>> 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
>
>> JH
>>
>
> --
> ========================================
>
> 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
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
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--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
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