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<p>Hi Prof. Blaha,</p>
<p><br>
</p>
<p>Sorry about the confusion with subject of the email. It is not a spin-orbit calculation,</p>
<p>just a normal scf calculation. I was using one my previous emails and forgot to change </p>
<p>the subject line before I sent it to the user group.</p>
<p><br>
</p>
<p>This job is a surface supercell calculation with 360 atoms. With 20 cores <span style="font-size: 12pt;">it takes about </span></p>
<p><span style="font-size: 12pt;">3 hours for each scf cycle, so I was trying to test if 40 cores speedup calculations.</span><span style="font-size: 12pt;"> </span></p>
<p><span style="font-size: 12pt;">Eventually, I will have to run spin-orbit calculations for some jobs of similar size, which</span></p>
<p><span style="font-size: 12pt;">will take even more time. So I need to speedup the calculations. </span></p>
<p><span style="font-size: 12pt;"><br>
</span></p>
<p><span style="font-size: 12pt;">During compilation of MPI version (see below) I have used shared memory architecture, </span></p>
<p><span style="font-size: 12pt;">which is true </span><span style="font-size: 12pt;">for 1 node </span><span style="font-size: 12pt;">with 20 cores. But each nodes are physically separated from one </span></p>
<p><span style="font-size: 12pt;">another and </span><span style="font-size: 12pt;">don't share </span><span style="font-size: 12pt;">common memory. So I am wondering if the error is related to my </span></p>
<p><span style="font-size: 12pt;">choice of </span><span style="font-size: 12pt;">shared memory architecture. If it it the case, should I recompile Wien2k with</span></p>
<p><span style="font-size: 12pt;"></span><span style="font-size: 12pt;">no shared memory option?</span><span style="font-size: 12pt;"> </span></p>
<p><span style="font-size: 12pt;"> </span></p>
<p><span style="font-size: 12pt;"><br>
</span></p>
<p><span style="font-size: 12pt;"><span style="font-family: monospace; font-size: 16px;"> * Configure parallel execution *</span><br style="font-family: monospace; font-size: 16px;">
<span style="font-family: monospace; font-size: 16px;"> ********************************** </span><br style="font-family: monospace; font-size: 16px;">
<span style="font-family: monospace; font-size: 16px;"> </span><br style="font-family: monospace; font-size: 16px;">
<span style="font-family: monospace; font-size: 16px;"> These options are stored in parallel_options of WIENROOT</span><br style="font-family: monospace; font-size: 16px;">
<span style="font-family: monospace; font-size: 16px;"> You can change them later also manually.</span><br style="font-family: monospace; font-size: 16px;">
<br style="font-family: monospace; font-size: 16px;">
<span style="font-family: monospace; font-size: 16px;"> Do you use ONLY a shared memory parallel architecture (ONE single multi-core </span><br style="font-family: monospace; font-size: 16px;">
<span style="font-family: monospace; font-size: 16px;"> node) ?</span><br style="font-family: monospace; font-size: 16px;">
<br style="font-family: monospace; font-size: 16px;">
<span style="font-family: monospace; font-size: 16px;"> On shared memory system it is normally better to start jobs in the </span><br style="font-family: monospace; font-size: 16px;">
<span style="font-family: monospace; font-size: 16px;"> background rather than using remote commands. If you select a shared memory </span><br style="font-family: monospace; font-size: 16px;">
<span style="font-family: monospace; font-size: 16px;"> system WIEN will by default not use remote shell commands </span><br style="font-family: monospace; font-size: 16px;">
<span style="font-family: monospace; font-size: 16px;"> (USE_REMOTE and MPI_REMOTE = 0 in parallel_options)</span><br style="font-family: monospace; font-size: 16px;">
<span style="font-family: monospace; font-size: 16px;"> and set the default granularity to 1. </span><br style="font-family: monospace; font-size: 16px;">
<span style="font-family: monospace; font-size: 16px;"> </span><br style="font-family: monospace; font-size: 16px;">
<span style="font-family: monospace; font-size: 16px;"> You still can override this default granularity in your .machines file.</span><br style="font-family: monospace; font-size: 16px;">
<br style="font-family: monospace; font-size: 16px;">
<span style="font-family: monospace; font-size: 16px;"> You may also set a specific TASKSET command to bind your executables</span><br style="font-family: monospace; font-size: 16px;">
<span style="font-family: monospace; font-size: 16px;"> to a specific core on multicore machines. </span><br style="font-family: monospace; font-size: 16px;">
<span style="font-family: monospace; font-size: 16px;"> Shared Memory Architecture? (y/N):y</span><br style="font-family: monospace; font-size: 16px;">
<span style="font-family: monospace; font-size: 16px;"> Do you know/need a command to bind your jobs to specific nodes ?</span><br style="font-family: monospace; font-size: 16px;">
<span style="font-family: monospace; font-size: 16px;"> (like taskset -c). Enter N / your_specific_command: </span><br>
</span></p>
<div><br>
</div>
Thanks,
<div>Fhokrul<br>
<br>
<div style="color: rgb(0, 0, 0);">
<div>
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<div id="x_divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> Wien <wien-bounces@zeus.theochem.tuwien.ac.at> on behalf of Peter Blaha <pblaha@theochem.tuwien.ac.at><br>
<b>Sent:</b> Thursday, December 8, 2016 6:47 PM<br>
<b>To:</b> A Mailing list for WIEN2k users<br>
<b>Subject:</b> Re: [Wien] lapwso_mpi error</font>
<div> </div>
</div>
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<font size="2"><span style="font-size:10pt;">
<div class="PlainText">What kind of job is it, that lapw0_mpi runs for 9800 seconds ???<br>
<br>
Is there any speedup when using 40 instead of 20 cores ?<br>
<br>
Your error is in lapw1_mpi, not in lapwso_mpi ???<br>
<br>
No idea about your software, but I doubt that it is wien2k.<br>
<br>
Am 08.12.2016 um 16:56 schrieb Md. Fhokrul Islam:<br>
> Hi Prof Blaha,<br>
><br>
> I am trying to run an MPI job in 2 nodes each with 20 cores. But the job<br>
> crashes<br>
> with the following error messages. I have tried with both USE_REMOTE 0 and<br>
> USE_REMOTE 1 in parallel_options file but didn't make much of a deference.<br>
> Our system administrator told me it is not probably not a hardware issue<br>
> and<br>
> suggested me to contact Wien2k. So could you please let me know if I<br>
> need to<br>
> make any change in MPI setting and recompileWien2k.<br>
><br>
> By the way, the same job runs fine if I use only 1 node with 20 cores.<br>
><br>
> Error message:<br>
><br>
> case.dayfile<br>
><br>
> cycle 1 (Thu Dec 8 15:44:06 CET 2016) (100/99 to go)<br>
><br>
>> lapw0 -p (15:44:06) starting parallel lapw0 at Thu Dec 8<br>
> 15:44:07 CET 2016<br>
> -------- .machine0 : 40 processors<br>
> 9872.562u 20.276s 8:20.46 1976.7% 0+0k 220752+386840io 332pf+0w<br>
>> lapw1 -up -p -c (15:52:27) starting parallel lapw1 at<br>
> Thu Dec 8 15:52:27 CET 2016<br>
> -> starting parallel LAPW1 jobs at Thu Dec 8 15:52:27 CET 2016<br>
> running LAPW1 in parallel mode (using .machines)<br>
> 1 number_of_parallel_jobs<br>
> au039 au039 au039 au039 au039 au039 au039 au039 au039 au039 au039<br>
> au039 au039 au039 au039 au039 au039 au039 au039 au039 au042 au042 au042<br>
> au042 au042 au042 au042 au042 au042 au042 au042 au042 au042 au042 au042<br>
> au042 au042 au042 au042 au042(1)<br>
> --------------------------------------------------------------------------<br>
> MPI_ABORT was invoked on rank 8 in communicator MPI_COMM_WORLD<br>
> with errorcode -726817712.<br>
><br>
><br>
> Output error file:<br>
><br>
> LAPW0 END<br>
> w2k_dispatch_signal(): received: Terminated<br>
> w2k_dispatch_signal(): received: Terminated<br>
> forrtl: Interrupted system call<br>
> w2k_dispatch_signal(): received: Terminated<br>
> w2k_dispatch_signal(): received: Terminated<br>
><br>
><br>
> Thanks,<br>
> Fhokrul<br>
><br>
><br>
><br>
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