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<p class="MsoNormal"><span style="mso-fareast-language:EN-US">Thanks for your quick response Laurence.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US">“cat $WIENROOT/parallel_options” gave the following output:<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-family:"Courier New";mso-fareast-language:EN-US">setenv TASKSET "no"<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-family:"Courier New";mso-fareast-language:EN-US">if ( ! $?USE_REMOTE ) setenv USE_REMOTE 1<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-family:"Courier New";mso-fareast-language:EN-US">if ( ! $?MPI_REMOTE ) setenv MPI_REMOTE 0<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-family:"Courier New";mso-fareast-language:EN-US">setenv WIEN_GRANULARITY 1<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-family:"Courier New";mso-fareast-language:EN-US">setenv DELAY 0.1<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-family:"Courier New";mso-fareast-language:EN-US">setenv SLEEPY 1</span><span style="mso-fareast-language:EN-US"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US">I believe Intel MPI is the default on the cluster we are using. I double checked by loading in the Intel_mpi module and re-running, but I still encounter the same errors as before.
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US">Also, I have now modified the .machines file as you suggested (see below), but the same errors still arise. (Note: I am aware that choosing 16 cores for each omp_XXX may not be optimal for speed,
but for now I am just testing if it works)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-family:"Courier New";mso-fareast-language:EN-US"># .machines file for Wien2k<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-family:"Courier New";mso-fareast-language:EN-US">#<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-family:"Courier New";mso-fareast-language:EN-US">omp_global:16<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-family:"Courier New";mso-fareast-language:EN-US">omp_lapw1:16<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-family:"Courier New";mso-fareast-language:EN-US">omp_lapw2:16<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-family:"Courier New";mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-family:"Courier New";mso-fareast-language:EN-US">1:sqg1cintr20.bullx:16<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-family:"Courier New";mso-fareast-language:EN-US">granularity:1<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-family:"Courier New";mso-fareast-language:EN-US">extrafine:1<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-family:"Courier New";mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-family:"Courier New";mso-fareast-language:EN-US">lapw0: sqg1cintr20.bullx:16
<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-family:"Courier New";mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-family:"Courier New";mso-fareast-language:EN-US">dstart: sqg1cintr20.bullx:16
<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-family:"Courier New";mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-family:"Courier New";mso-fareast-language:EN-US">nlvdw: sqg1cintr20.bullx:16<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span lang="EN-US">From:</span></b><span lang="EN-US"> Wien <wien-bounces@zeus.theochem.tuwien.ac.at>
<b>On Behalf Of </b>Laurence Marks<br>
<b>Sent:</b> 31 January 2023 17:11<br>
<b>To:</b> A Mailing list for WIEN2k users <wien@zeus.theochem.tuwien.ac.at><br>
<b>Subject:</b> Re: [Wien] Parallel execution of SCF cycle<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<div>
<p class="MsoNormal"><span style="font-family:"Verdana",sans-serif;color:black">Please do "cat $WIENROOT/parallel_options", as I suspect you have an issue there. <o:p></o:p></span></p>
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<div>
<p class="MsoNormal"><span style="font-family:"Verdana",sans-serif;color:black">Do you have a "normal" mpirun or does your cluster require something different? <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Verdana",sans-serif;color:black">Which mpirun are you using?<o:p></o:p></span></p>
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<div>
<p class="MsoNormal"><span style="font-family:"Verdana",sans-serif;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal">Also, I doubt you need "lapw2_vector_split:2", and you do not appear to have set the "omp_XXX" variables which are needed for
<span class="gmaildefault"><span style="font-family:"Verdana",sans-serif;color:black">recent versions</span></span>.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<div>
<p class="MsoNormal">On Tue, Jan 31, 2023 at 10:59 AM Calum Cunningham <<a href="mailto:Calum.Cunningham@uknnl.com">Calum.Cunningham@uknnl.com</a>> wrote:<o:p></o:p></p>
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<div>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Dear WIEN2k users,<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">My colleagues and I are having some trouble running SCF calculations in parallel mode. I have had no issues when working in serial mode. We are using version 21.1 on a computer
cluster that operates the LSF queuing system. <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">As an example, I will explain my attempt to run a parallel execution for the TiO2 (rutile) test case. I am using the default values of RKmax, k-points, VXC, etc.
<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">The .machines file was created using a bespoke script that updates the names of the processors being used for the current job. In this case, I am using 16 cores on a single node.
The .machines file is below:<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt">
<span style="font-family:"Courier New""># .machines file for Wien2k</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt">
<span style="font-family:"Courier New"">#</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt">
<span style="font-family:"Courier New"">1:sqg1cintr16.bullx:16</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt">
<span style="font-family:"Courier New"">granularity:1</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt">
<span style="font-family:"Courier New"">extrafine:1</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt">
<span style="font-family:"Courier New""> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt">
<span style="font-family:"Courier New"">lapw0: sqg1cintr16.bullx:16 </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt">
<span style="font-family:"Courier New""> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt">
<span style="font-family:"Courier New"">dstart: sqg1cintr16.bullx:16 </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt">
<span style="font-family:"Courier New""> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt">
<span style="font-family:"Courier New"">nlvdw: sqg1cintr16.bullx:16 </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt">
<span style="font-family:"Courier New""> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt">
<span style="font-family:"Courier New"">lapw2_vector_split:2</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">After I initialise the calculation interactively via the w2web GUI (i.e. not in parallel), I attempted to execute the SCF cycle in w2web with the parallel option selected. I received
the following error in STDOUT:<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt">
<span style="font-family:"Courier New"">LAPW0 END</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt">
<span style="font-family:"Courier New"">[1] Done mpirun -np 16 /lustre/scafellpike/local/apps/intel/wien2k/21.1/lapw0_mpi lapw0.def >> .time00</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt">
<span style="font-family:"Courier New"">LAPW1 END</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt">
<span style="font-family:"Courier New"">[1] + Done ( cd $PWD; $t $ttt; rm -f .lock_$lockfile[$p] ) >> .time1_$loop</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt">
<span style="font-family:"Courier New"">tmpmach: Subscript out of range.</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt">
<span style="font-family:"Courier New"">grep: lapw2*.error: No such file or directory</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt">
<span style="font-family:"Courier New""> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt">
<span style="font-family:"Courier New"">> stop error</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Note that I consistently receive this “grep: lapw2*.error” error when attempting to run SCF calculations in parallel! After this, I tested each of lapw0, lapw1 and lapw2 as single
programmes (in parallel) to try to fix the problem. I think that lapw1 ran correctly, but I have given the output below just in case there is a problem here. There is, however, an obvious error when lapw2 is executed (see below).<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt">
<span style="font-family:"Courier New"">starting parallel lapw1 at Tue Jan 31 15:00:07 GMT 2023</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt">
<span style="font-family:"Courier New"">-> starting parallel LAPW1 jobs at Tue Jan 31 15:00:07 GMT 2023</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt">
<span style="font-family:"Courier New"">running LAPW1 in parallel mode (using .machines)</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt">
<span style="font-family:"Courier New"">granularity set to 1 because of nonlocal SCRATCH variable</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt">
<span style="font-family:"Courier New"">1 number_of_parallel_jobs</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt">
<span style="font-family:"Courier New"">[1] 46212</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt">
<span style="font-family:"Courier New"">LAPW1 END</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt">
<span style="font-family:"Courier New"">[1] + Done ( cd $PWD; $t $ttt; rm -f .lock_$lockfile[$p] ) >> .time1_$loop</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt">
<span style="font-family:"Courier New""> (70) 0.011u 0.027s 0:14.52 0.2% 0+0k 0+8io 0pf+0w</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt">
<span style="font-family:"Courier New""> Summary of lapw1para:</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt">
<span style="font-family:"Courier New""> sqg1cintr16.bullx k= user= wallclock=</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt">
<span style="font-family:"Courier New"">0.100u 0.299s 0:16.85 2.3% 0+0k 616+248io 0pf+0w</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt">
<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt">
#lapw2 as a single programme (parallel):<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt">
<span style="font-family:"Courier New"">running LAPW2 in parallel mode</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt">
<span style="font-family:"Courier New"">tmpmach: Subscript out of range.</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt">
<span style="font-family:"Courier New"">0.016u 0.043s 0:00.06 83.3% 0+0k 32+24io 0pf+0w</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt">
<span style="font-family:"Courier New"">error: command /lustre/scafellpike/local/apps/intel/wien2k/21.1/lapw2para lapw2.def failed</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Please let me know if you need any more information. I would particularly like to know why the errors are occurring at lapw2 (e.g. what is the “tmpmach” error?)<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Many thanks,<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Calum Cunningham<o:p></o:p></p>
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<p class="MsoNormal">-- <o:p></o:p></p>
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<p class="MsoNormal">Professor Laurence Marks<br>
Department of Materials Science and Engineering<br>
Northwestern University<br>
<a href="https://gbr01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.numis.northwestern.edu%2F&data=05%7C01%7Ccalum.cunningham%40uknnl.com%7C57f497e7e9cc49eee6a808db03ae2e58%7C6ae79c91466c4c6fae9b5c2a99158a4e%7C0%7C0%7C638107818857583875%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=Xvjz1y98sh5YY2MyN9I4904RHPiRHMoC3IEwLBInD7c%3D&reserved=0" target="_blank">www.numis.northwestern.edu</a>
<br>
"Research is to see what everybody else has seen, and to think what nobody else has thought", Albert Szent-Györgyi<o:p></o:p></p>
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