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Dear Klaus, <br>
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Thank you for the response.</div>
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<li>I included <font size="2"><span style="font-size:11pt">memory_stat_freq = 1 in the parfile. Please find attached the lasslab.log attached. To me, it seems that this is not a memory problem as I am using 8 GB memory for each processors.</span></font></li><li><font size="2"><span style="font-size:11pt">How could I know whether the segmentation fault is coming from the batch system? Please find the message error below<br>
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<font size="2"><span style="font-size:11pt"></span></font><font size="2"><span style="font-size:11pt"><span>*** Wrote plotfile to lasslab_hdf5_plt_cnt_0006 ****<br>
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<div> iteration, no. not moved = 0 39<br>
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<div> iteration, no. not moved = 1 0<br>
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<div> refined: total leaf blocks = 71<br>
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<div> refined: total blocks = 94<br>
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<div> 60 3.0348E-12 3.0448E-13 ( 3.281E-04, 5.953E-03, 0.00 ) | 1.622E-12 9.868E+84 1.014E+88 0.4000000<br>
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<div> *** Wrote checkpoint file to lasslab_hdf5_chk_0003 ****<br>
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<div>srun: error: sh02-01n31: task 1: Segmentation fault<br>
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<div>srun: Terminating job step 3490332.0<br>
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<div>slurmstepd: error: *** STEP 3490332.0 ON sh02-01n31 CANCELLED AT 2020-07-02T11:04:11 ***<br>
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<span>srun: error: sh02-01n31: task 0: Segmentation fault</span><br>
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<font size="2"><span style="font-size:11pt"><font size="2"><span style="font-size:11pt"><br>
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<li><font size="2"><span style="font-family: calibri, arial, helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgba(0, 0, 0, 0);">It seems to run fine with I/O. I set the maximum number of steps to 100 and it runs fine for all of
it.</span></font></li></ul>
<div><font size="2"><span style="font-family: calibri, arial, helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgba(0, 0, 0, 0);">Thank you for your help,</span></font></div>
<div><font size="2"><span style="font-family: calibri, arial, helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgba(0, 0, 0, 0);">Adrien</span></font><br>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> flash-users-bounces@flash.uchicago.edu <flash-users-bounces@flash.uchicago.edu> on behalf of Klaus Weide <klaus@flash.uchicago.edu><br>
<b>Sent:</b> Thursday, July 2, 2020 10:48 AM<br>
<b>To:</b> flash-users@flash.uchicago.edu <flash-users@flash.uchicago.edu><br>
<b>Subject:</b> Re: [FLASH-USERS] LaserSlab Segmentation Fault</font>
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<div class="PlainText">> I am running into segmentation fault when running the LaserSlab example in parallel. I already posted this problem a week ago and I conducted more tests to try to figure out where the issue might be coming from. My initial guess is
that the segmentation might be happening when writing part the hdf5 files.<br>
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1. Make sure you don't have a problem with memory.<br>
Set memory_stat_freq = 1 (or so) in the parfile,<br>
and check the numbers in the log file whether memory<br>
use grows significantly.<br>
<br>
2. You still haven't shared the actual abort message<br>
for standard output or error files.<br>
You seem to run under a batch system. Are you sure that that<br>
isn't killing your runs?<br>
<br>
3. I see no indications that the abort is directly caused by HDF5 IO.<br>
But you could try to setup with +noio (you may also have to add something <br>
like --without-unit=.../LaserIO for +noio to take effect), and see<br>
whether the code runs successfully.<br>
<br>
Klaus<br>
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