[MITgcm-support] jobs died suddenly

[Matthew Mazloff]

Well it definitely died while trying to read something for the obcs:
ABNORMAL END: S/R MDS_READ_SEC_YZ

Do you also give boundary files that have a start time and period given in data.exf?
E.g.:
 obcsWstartdate1     = 20081216,
 obcsWstartdate2     = 00000,
 obcsWperiod         = 2629800,

Matt


> On Mar 25, 2020, at 1:11 PM, Yangxin He <y67he at uwaterloo.ca> wrote:
> 
> Hi Matt,
> 
> This would be really confusing.
> My file seems to be the right size, and the run died after running fine for 34 tidal periods. If the size of boundary files is the problem, then the run would have died in the beginning?
> Another thing is, I have been using this set up for about a year now, and it was running fine only until recently.
> 
> Yangxin
> From: MITgcm-support <mitgcm-support-bounces at mitgcm.org> on behalf of Matthew Mazloff <mmazloff at ucsd.edu>
> Sent: Wednesday, March 25, 2020 4:06:38 PM
> To: mitgcm-support at mitgcm.org
> Subject: Re: [MITgcm-support] jobs died suddenly
>  
> Hello
> 
> The code crashed trying to read a file. The file is size NY*NZ*NT so I suspect it is an eastern or western boundary condition file. Make sure your files are long enough.
> 
> -Matt
> 
> 
>> On Mar 25, 2020, at 12:24 PM, Yangxin He <y67he at uwaterloo.ca <mailto:y67he at uwaterloo.ca>> wrote:
>> 
>> Hello there,
>> 
>> Recently several jobs of mine died of no reason. The error message is
>> [y67he at gra-login1 b6]$ more sim-29315632.err 
>> ABNORMAL END: S/R MDS_READ_SEC_YZ
>> srun: Job step aborted: Waiting up to 62 seconds for job step to finish.
>> slurmstepd: error: *** JOB 29315632 ON gra228 CANCELLED AT 2020-03-25T08:30:08 DUE TO TIME LIMIT ***
>> slurmstepd: error: *** STEP 29315632.0 ON gra228 CANCELLED AT 2020-03-25T08:30:08 DUE TO TIME LIMIT ***
>> The time limit was not the problem. The code simply stopped producing any new results, however, it was still running.
>> This is confusing, because I have been using the same set up for a while and this only started to happen in the past few weeks.
>> 
>> I ran my code on graham in compute Canada, and the people there suggested it may be the problem in the code.
>> Can anyone shed any lights on this?
>> 
>> Thanks
>> 
>> Yangxin
>> _______________________________________________
>> MITgcm-support mailing list
>> MITgcm-support at mitgcm.org <mailto:MITgcm-support at mitgcm.org>
>> http://mailman.mitgcm.org/mailman/listinfo/mitgcm-support <http://mailman.mitgcm.org/mailman/listinfo/mitgcm-support>
> _______________________________________________
> MITgcm-support mailing list
> MITgcm-support at mitgcm.org <mailto:MITgcm-support at mitgcm.org>
> http://mailman.mitgcm.org/mailman/listinfo/mitgcm-support <http://mailman.mitgcm.org/mailman/listinfo/mitgcm-support>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.mitgcm.org/pipermail/mitgcm-support/attachments/20200325/6079f804/attachment.html>