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<p>Hi Matt,</p>
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<p>This would be really confusing.</p>
<p>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?</p>
<p>Another thing is, I have been using this set up for about a year now, and it was running fine only until recently.</p>
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<p>Yangxin</p>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> MITgcm-support <mitgcm-support-bounces@mitgcm.org> on behalf of Matthew Mazloff <mmazloff@ucsd.edu><br>
<b>Sent:</b> Wednesday, March 25, 2020 4:06:38 PM<br>
<b>To:</b> mitgcm-support@mitgcm.org<br>
<b>Subject:</b> Re: [MITgcm-support] jobs died suddenly</font>
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<div>Hello
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<div class="">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.</div>
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<div class="">-Matt</div>
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<div class="">On Mar 25, 2020, at 12:24 PM, Yangxin He <<a href="mailto:y67he@uwaterloo.ca" class="">y67he@uwaterloo.ca</a>> wrote:</div>
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<div style="margin-top: 0px; margin-bottom: 0px;" class="">Hello there,</div>
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<div style="margin-top: 0px; margin-bottom: 0px;" class="">Recently several jobs of mine died of no reason. The error message is</div>
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<span style="font-variant-ligatures: no-common-ligatures;" class="">[y67he@gra-login1 b6]$ more sim-29315632.err </span></div>
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<span style="font-variant-ligatures: no-common-ligatures;" class="">ABNORMAL END: S/R MDS_READ_SEC_YZ</span></div>
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<span style="font-variant-ligatures: no-common-ligatures;" class="">srun: Job step aborted: Waiting up to 62 seconds for job step to finish.</span></div>
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<span style="font-variant-ligatures: no-common-ligatures;" class="">slurmstepd: error: *** JOB 29315632 ON gra228 CANCELLED AT 2020-03-25T08:30:08 DUE TO TIME LIMIT ***</span></div>
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<span style="font-variant-ligatures: no-common-ligatures;" class="">slurmstepd: error: *** STEP 29315632.0 ON gra228 CANCELLED AT 2020-03-25T08:30:08 DUE TO TIME LIMIT ***</span></div>
<div style="margin-top: 0px; margin-bottom: 0px;" class="">The time limit was not the problem. The code simply stopped producing any new results, however, it was still running.</div>
<div style="margin-top: 0px; margin-bottom: 0px;" class="">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.</div>
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<div style="margin-top: 0px; margin-bottom: 0px;" class="">I ran my code on graham in compute Canada, and the people there suggested it may be the problem in the code.</div>
<div style="margin-top: 0px; margin-bottom: 0px;" class="">Can anyone shed any lights on this?</div>
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<div style="margin-top: 0px; margin-bottom: 0px;" class="">Thanks</div>
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<div style="margin-top: 0px; margin-bottom: 0px;" class="">Yangxin</div>
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