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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Cambria","serif"">Because the application works when less intensive runs and fails for more intensive runs, it is likely that the application is requesting too many resources. When\where should
I run ulimit –a and dmesg, after I get the error? If that is true, is there any way to change the environment in MPI to increase the capacity so that the increased resources can be accommodated?<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Cambria","serif""><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Cambria","serif"">If I run it in new terminal – here is what I get
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Cambria","serif""><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Cambria","serif"">core file size (blocks, -c) 0<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Cambria","serif"">data seg size (kbytes, -d) unlimited<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Cambria","serif"">scheduling priority (-e) 0<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Cambria","serif"">file size (blocks, -f) unlimited<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Cambria","serif"">pending signals (-i) 250598<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Cambria","serif"">max locked memory (kbytes, -l) 64<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Cambria","serif"">max memory size (kbytes, -m) unlimited<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Cambria","serif"">open files (-n) 1024<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Cambria","serif"">pipe size (512 bytes, -p) 8<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Cambria","serif"">POSIX message queues (bytes, -q) 819200<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Cambria","serif"">real-time priority (-r) 0<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Cambria","serif"">stack size (kbytes, -s) 10240<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Cambria","serif"">cpu time (seconds, -t) unlimited<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Cambria","serif"">max user processes (-u) 1024<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Cambria","serif"">virtual memory (kbytes, -v) unlimited<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Cambria","serif"">file locks (-x) unlimited<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Cambria","serif""><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Cambria","serif"">in my job, I try to set the stack size to – unlimited but I guess it is not working.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Cambria","serif""><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Cambria","serif"">Let me know. Thank you for all the help.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Cambria","serif"">Abhishek<o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-left:.75pt;text-autospace:none"><span style="font-size:11.0pt;font-family:"Cambria","serif";color:#004080">………………………………………………………………………………………………….<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.75pt;text-autospace:none"><b><span style="font-size:11.0pt;font-family:"Cambria","serif";color:#004080">Abhishek Bhat, PhD, EPI,<br>
</span></b><span style="font-size:11.0pt;font-family:"Cambria","serif";color:#004080">Senior Consultant<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.75pt;text-autospace:none"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#004080"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Cambria","serif""><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">From:</span></b><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""> Seo, Sangmin [mailto:sseo@anl.gov]
<br>
<b>Sent:</b> Sunday, September 14, 2014 11:16 AM<br>
<b>To:</b> <discuss@mpich.org><br>
<b>Subject:</b> Re: [mpich-discuss] Error Running MPICH for Photochemical Modeling<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Abhishek,<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Signal 9 is caused by many reasons, e.g., CPU time, out of memory, etc., but it is mostly because the application requests too many resources. You can check the environment settings with ulimit -a. And, you may find some information about
your error from dmesg.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Thanks,<o:p></o:p></p>
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<p class="MsoNormal">Sangmin<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">On Sep 12, 2014, at 5:51 PM, Abhishek Bhat <<a href="mailto:abhat@trinityconsultants.com">abhat@trinityconsultants.com</a>> wrote:<o:p></o:p></p>
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<br>
<o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Cambria","serif"">Sangmin.</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Cambria","serif""> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Cambria","serif"">I updated to mpich3 and getting the following error</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Cambria","serif""> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Cambria","serif"">Fatal error in MPI_Recv: A process has failed, error stack:</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Cambria","serif"">MPI_Recv(187).............: MPI_Recv(buf=0x7fff93840c30, count=644490, MPI_REAL, src=1, tag=14131, MPI_COMM_WORLD, status=0x7fff94444f20) failed</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Cambria","serif"">dequeue_and_set_error(865): Communication error with rank 1</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Cambria","serif"">rank 1 in job 1 dfw-camx_55000 caused collective abort of all ranks</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Cambria","serif""> exit status of rank 1: killed by signal 9</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Cambria","serif""> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Cambria","serif"">Same situation, successful runs for smaller resource runs and for up to 7 processes. Error at more than 7. Here is the mpich command I am using to run from my job file…</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Cambria","serif""> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Cambria","serif"">cat << ieof > nodes</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Cambria","serif"">dfw-camx:1</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Cambria","serif"">dfw-camx-n1:1</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Cambria","serif"">dfw-camx-n2:1</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Cambria","serif"">dfw-camx-n3:1</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Cambria","serif"">dfw-camx-n4:1</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Cambria","serif"">dfw-camx-n5:1</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Cambria","serif"">dfw-camx-n6:1</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Cambria","serif"">dfw-camx-n7:1</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Cambria","serif"">ieof</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Cambria","serif"">set NUMPROCS =<span class="apple-converted-space"> </span><span style="color:red">8</span></span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Cambria","serif"">set RING = `wc -l nodes | awk '{print $1}'`</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Cambria","serif"">mpdboot -n $RING -f nodes –verbose</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Cambria","serif""> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Cambria","serif"">if( ! { mpiexec -machinefile nodes -np $NUMPROCS $EXEC } ) then</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Cambria","serif""> mpdallexit</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Cambria","serif""> exit</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Cambria","serif"">endif</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Cambria","serif""> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Cambria","serif""> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Cambria","serif"">For a successful run the NUMPROCS has to be < = 7.</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Cambria","serif""> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Cambria","serif"">Any help is much appreciated.</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Cambria","serif""> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Cambria","serif"">Thank You</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Cambria","serif"">Abhishek</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Cambria","serif";color:#004080">………………………………………………………………………………………………….</span><o:p></o:p></p>
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<p class="MsoNormal"><b><span style="font-size:11.0pt;font-family:"Cambria","serif";color:#004080">Abhishek Bhat, PhD, EPI,<br>
</span></b><span style="font-size:11.0pt;font-family:"Cambria","serif";color:#004080">Senior Consultant</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#004080"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Cambria","serif""> </span><o:p></o:p></p>
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<p class="MsoNormal"><b><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">From:</span></b><span class="apple-converted-space"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""> </span></span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">Seo,
Sangmin [<a href="mailto:sseo@anl.gov">mailto:sseo@anl.gov</a>]<span class="apple-converted-space"> </span><br>
<b>Sent:</b><span class="apple-converted-space"> </span>Friday, September 12, 2014 1:11 PM<br>
<b>To:</b><span class="apple-converted-space"> </span><<a href="mailto:discuss@mpich.org">discuss@mpich.org</a>><br>
<b>Subject:</b><span class="apple-converted-space"> </span>Re: [mpich-discuss] Error Running MPICH for Photochemical Modeling</span><o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">Hi Abhishek,<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">Can you try with the recent MPICH release to see if the same error happens? You can download the recent release, 3.1.2, from <a href="http://www.mpich.org/downloads/"><span style="color:purple">http://www.mpich.org/downloads/</span></a>.<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">Thanks,<o:p></o:p></p>
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<p class="MsoNormal">Sangmin<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">On Sep 12, 2014, at 12:59 PM, Abhishek Bhat <<a href="mailto:abhat@trinityconsultants.com"><span style="color:purple">abhat@trinityconsultants.com</span></a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal"><br>
<br>
<br>
<o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Cambria","serif"">I am running a photochemical modeling on Linux cluster (CentOS_64 bit) with 1 master and 8 slave nodes with quad core (intel i7) on each node. I have two scenarios, in first
scenario, I am running less data intensive run on all 8 nodes (NUMPROCS = 9) and the run will go fine. When running same configuration for a more intense run, I am getting following error.</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Cambria","serif""> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Cambria","serif"">Fatal error in MPI_Recv: Other MPI error, error stack:</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Cambria","serif"">MPI_Recv(187).....................: MPI_Recv(buf=0x7fff989d53b0, count=644490, MPI_REAL, src=1, tag=14131, MPI_COMM_WORLD, status=0x7fff995d96a0) failed</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Cambria","serif"">MPIDI_CH3I_Progress(150)..........:</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Cambria","serif"">MPID_nem_mpich2_blocking_recv(948):</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Cambria","serif"">MPID_nem_tcp_connpoll(1720).......:</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Cambria","serif"">state_commrdy_handler(1556).......:</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Cambria","serif"">MPID_nem_tcp_recv_handler(1446)...: socket closed</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Cambria","serif"">rank 1 in job 1 dfw-camx_55000 caused collective abort of all ranks</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Cambria","serif""> exit status of rank 1: killed by signal 9</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Cambria","serif""> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Cambria","serif"">If I run the program with smaller nodes (smaller than 7 NUMPROCS) the run goes fine.</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Cambria","serif""> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Cambria","serif"">It appears that the rank 1 (my first node) is collectively causing all the ranks, but I could identify why. I tried following solutions –</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Cambria","serif""> </span><o:p></o:p></p>
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<p class="MsoNormal" style="text-indent:-.25in"><span style="font-size:11.0pt;font-family:"Cambria","serif"">1.</span><span style="font-size:7.0pt"> <span class="apple-converted-space"> </span></span><span style="font-size:11.0pt;font-family:"Cambria","serif"">Increased
master memory to 32 gb</span><o:p></o:p></p>
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<p class="MsoNormal" style="text-indent:-.25in"><span style="font-size:11.0pt;font-family:"Cambria","serif"">2.</span><span style="font-size:7.0pt"> <span class="apple-converted-space"> </span></span><span style="font-size:11.0pt;font-family:"Cambria","serif"">Increased
all nodes memory to 32 gb</span><o:p></o:p></p>
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<p class="MsoNormal" style="text-indent:-.25in"><span style="font-size:11.0pt;font-family:"Cambria","serif"">3.</span><span style="font-size:7.0pt"> <span class="apple-converted-space"> </span></span><span style="font-size:11.0pt;font-family:"Cambria","serif"">Exchanged
the rank 1 to different node in the parallel.</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Cambria","serif""> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Cambria","serif"">In all situations, I am getting this error. Surprisingly, when I am running smaller (less data intensive runs), I am not getting this error even if I increase the NUMPROCS to
32 processes.</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Cambria","serif""> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Cambria","serif"">Any help will be highly appreciated.</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Cambria","serif""> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Cambria","serif"">I am running mpich 1.4</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Cambria","serif"">Thank You<br>
Abhishek</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Cambria","serif";color:#004080">………………………………………………………………………………………………….</span><o:p></o:p></p>
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<p class="MsoNormal"><b><span style="font-size:11.0pt;font-family:"Cambria","serif";color:#004080">Abhishek Bhat, PhD, EPI,<br>
</span></b><span style="font-size:11.0pt;font-family:"Cambria","serif";color:#004080">Senior Consultant</span><o:p></o:p></p>
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<p class="MsoNormal"><b><span style="font-size:11.0pt;font-family:"Cambria","serif";color:#004080">Trinity Consultants</span></b><o:p></o:p></p>
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