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<p>Hi Matt,</p>
<p><br>
</p>
<p>so for the sudden crash of the run, do you think the problem is in the code or it may be something with graham (compute Canada)?</p>
<p><br>
</p>
<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 4:28:30 PM<br>
<b>To:</b> mitgcm-support@mitgcm.org<br>
<b>Subject:</b> Re: [MITgcm-support] jobs died suddenly</font>
<div> </div>
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<div>That is a separate issue. The model crashed but the HPC didn’t stop the job. I don’t know how to remedy that and the HPC support should be able to help with that.
<div class="">The model was not running. The executable had stopped and that is your primary issue. I am not sure why the model crashed, but my first guess is it happened while trying to read an OBW or OBE file.
<div class=""><br class="">
</div>
<div class="">Matt</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
<div>
<blockquote type="cite" class="">
<div class="">On Mar 25, 2020, at 1:22 PM, Yangxin He <<a href="mailto:y67he@uwaterloo.ca" class="">y67he@uwaterloo.ca</a>> wrote:</div>
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<div class="">
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<div style="margin-top: 0px; margin-bottom: 0px;" class="">Hi Matt,</div>
<div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class="">
</div>
<div style="margin-top: 0px; margin-bottom: 0px;" class="">Yep. This is part of my data file:</div>
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<span style="font-variant-ligatures: no-common-ligatures;" class="">#obcs forcing</span></div>
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<span style="font-variant-ligatures: no-common-ligatures;" class=""> periodicExternalForcing=.TRUE.,</span></div>
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<span style="font-variant-ligatures: no-common-ligatures;" class=""> externForcingPeriod=36.,</span></div>
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<span style="font-variant-ligatures: no-common-ligatures;" class=""> externForcingCycle=86148.,</span></div>
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<span style="font-variant-ligatures: no-common-ligatures;" class=""> &</span></div>
<div class=""><span style="font-variant-ligatures: no-common-ligatures;" class=""><br class="">
</span></div>
<div style="margin-top: 0px; margin-bottom: 0px;" class="">Apart from this, Enrico has the same problem as to run not producing files but still running.</div>
<div style="margin-top: 0px; margin-bottom: 0px;" class="">I submitted a ticket to graham compute Canada, they did not know why and suggested me to try here.</div>
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</div>
<div style="margin-top: 0px; margin-bottom: 0px;" class="">Yangxin</div>
</div>
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<font face="Calibri, sans-serif" style="font-size: 11pt;" class=""><b class="">From:</b><span class="Apple-converted-space"> </span>MITgcm-support <<a href="mailto:mitgcm-support-bounces@mitgcm.org" class="">mitgcm-support-bounces@mitgcm.org</a>> on behalf
of Matthew Mazloff <<a href="mailto:mmazloff@ucsd.edu" class="">mmazloff@ucsd.edu</a>><br class="">
<b class="">Sent:</b><span class="Apple-converted-space"> </span>Wednesday, March 25, 2020 4:17:53 PM<br class="">
<b class="">To:</b><span class="Apple-converted-space"> </span><a href="mailto:mitgcm-support@mitgcm.org" class="">mitgcm-support@mitgcm.org</a><br class="">
<b class="">Subject:</b><span class="Apple-converted-space"> </span>Re: [MITgcm-support] jobs died suddenly</font>
<div class=""> </div>
</div>
<div style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
Well it definitely died while trying to read something for the obcs:
<div class="">
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<span class="" style="font-variant-ligatures: no-common-ligatures;">ABNORMAL END: S/R MDS_READ_SEC_YZ</span></div>
<div class=""><span class="" style="font-variant-ligatures: no-common-ligatures;"><br class="">
</span></div>
<div class=""><span class="" style="font-variant-ligatures: no-common-ligatures;">Do you also give boundary files that have a start time and period given in data.exf?</span></div>
<div class=""><span class="" style="font-variant-ligatures: no-common-ligatures;">E.g.:</span></div>
<div class=""><span class="" style="font-variant-ligatures: no-common-ligatures;"> obcsWstartdate1 = 20081216,<br class="">
obcsWstartdate2 = 00000,<br class="">
obcsWperiod = 2629800,<br class="">
<br class="">
</span></div>
<div class=""><span class="" style="font-variant-ligatures: no-common-ligatures;">Matt</span></div>
<div class=""><span class="" style="font-variant-ligatures: no-common-ligatures;"><br class="">
</span></div>
<div class=""><br class="">
<blockquote type="cite" class="">
<div class="">On Mar 25, 2020, at 1:11 PM, Yangxin He <<a href="mailto:y67he@uwaterloo.ca" class="">y67he@uwaterloo.ca</a>> wrote:</div>
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<div class="" style="margin-top: 0px; margin-bottom: 0px;">Hi Matt,</div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;"><br class="">
</div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;">This would be really confusing.</div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;">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?</div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;">Another thing is, I have been using this set up for about a year now, and it was running fine only until recently.</div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;"><br class="">
</div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;">Yangxin</div>
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<font face="Calibri, sans-serif" class="" style="font-size: 11pt;"><b class="">From:</b><span class="Apple-converted-space"> </span>MITgcm-support <<a href="mailto:mitgcm-support-bounces@mitgcm.org" class="">mitgcm-support-bounces@mitgcm.org</a>> on behalf
of Matthew Mazloff <<a href="mailto:mmazloff@ucsd.edu" class="">mmazloff@ucsd.edu</a>><br class="">
<b class="">Sent:</b><span class="Apple-converted-space"> </span>Wednesday, March 25, 2020 4:06:38 PM<br class="">
<b class="">To:</b><span class="Apple-converted-space"> </span><a href="mailto:mitgcm-support@mitgcm.org" class="">mitgcm-support@mitgcm.org</a><br class="">
<b class="">Subject:</b><span class="Apple-converted-space"> </span>Re: [MITgcm-support] jobs died suddenly</font>
<div class=""> </div>
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Hello
<div class=""><br class="">
</div>
<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>
<div class=""><br class="">
</div>
<div class="">-Matt</div>
<div class=""><br class="">
<div class=""><br class="">
<blockquote type="cite" class="">
<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 class="" style="margin-top: 0px; margin-bottom: 0px;">Hello there,</div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;"><br class="">
</div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;">Recently several jobs of mine died of no reason. The error message is</div>
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<span class="" style="font-variant-ligatures: no-common-ligatures;">[y67he@gra-login1 b6]$ more sim-29315632.err </span></div>
<div class="" style="margin: 0px; font-stretch: normal; font-size: 12px; line-height: normal; font-family: Courier; color: rgb(255, 238, 149); background-color: rgb(21, 102, 47);">
<span class="" style="font-variant-ligatures: no-common-ligatures;">ABNORMAL END: S/R MDS_READ_SEC_YZ</span></div>
<div class="" style="margin: 0px; font-stretch: normal; font-size: 12px; line-height: normal; font-family: Courier; color: rgb(255, 238, 149); background-color: rgb(21, 102, 47);">
<span class="" style="font-variant-ligatures: no-common-ligatures;">srun: Job step aborted: Waiting up to 62 seconds for job step to finish.</span></div>
<div class="" style="margin: 0px; font-stretch: normal; font-size: 12px; line-height: normal; font-family: Courier; color: rgb(255, 238, 149); background-color: rgb(21, 102, 47);">
<span class="" style="font-variant-ligatures: no-common-ligatures;">slurmstepd: error: *** JOB 29315632 ON gra228 CANCELLED AT 2020-03-25T08:30:08 DUE TO TIME LIMIT ***</span></div>
<p class="" style="margin-top: 0px; margin-bottom: 0px;"></p>
<div class="" style="margin: 0px; font-stretch: normal; font-size: 12px; line-height: normal; font-family: Courier; color: rgb(255, 238, 149); background-color: rgb(21, 102, 47);">
<span class="" style="font-variant-ligatures: no-common-ligatures;">slurmstepd: error: *** STEP 29315632.0 ON gra228 CANCELLED AT 2020-03-25T08:30:08 DUE TO TIME LIMIT ***</span></div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;">The time limit was not the problem. The code simply stopped producing any new results, however, it was still running.</div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;">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>
<div class="" style="margin-top: 0px; margin-bottom: 0px;"><br class="">
</div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;">I ran my code on graham in compute Canada, and the people there suggested it may be the problem in the code.</div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;">Can anyone shed any lights on this?</div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;"><br class="">
</div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;">Thanks</div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;"><br class="">
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<div class="" style="margin-top: 0px; margin-bottom: 0px;">Yangxin</div>
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