<div dir="auto">Dear Brad,</div><div dir="auto">Fast communications means here Infiniband or other RDMA. Make sure your MPI uses RDMA, I’ve seen systems where it isn’t enabled by default. That said, if you use k-point parallelization you can get away with gigabit ethernet as Paolo mentioned.</div><div dir="auto">Best wishes,</div><div dir="auto">Michal Krompiec</div><div dir="auto">Merck KGaA </div><div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Thu, Nov 5, 2020 at 11:40 PM Baer, Bradly via users <<a href="mailto:users@lists.quantum-espresso.org">users@lists.quantum-espresso.org</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
Paolo,</div>
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I believe the nodes I am using have gigabit connections. There are additional nodes that have 10 or 25 gigabit connections but I don't think I would land on one of them without specifically requesting them. What communication speed would be appropriate for
QE's needs?</div>
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<br>
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I also did consider trying to manually set the parallelization but I don't currently know enough about SLURM to identify each node and ensure that all 16 cores assigned from a pool are on the same node. I will keep it in mind though as a possible future solution.</div>
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Thanks,</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
Brad</div>
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<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
Bradly Baer</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
<span style="font-family:Calibri,Arial,Helvetica,sans-serif;background-color:rgb(255,255,255);display:inline!important">Graduate Research Assistant, Walker Lab</span><br>
</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
<span style="font-family:Calibri,Arial,Helvetica,sans-serif;background-color:rgb(255,255,255);display:inline!important">Interdisciplinary Materials Science</span><br>
</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
Vanderbilt University</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
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<div id="m_7302475323095056452divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Paolo Giannozzi <<a href="mailto:p.giannozzi@gmail.com" target="_blank">p.giannozzi@gmail.com</a>><br>
<b>Sent:</b> Thursday, November 5, 2020 3:54 PM<br>
<b>To:</b> Baer, Bradly <bradly.b.baer@Vanderbilt.Edu>; Quantum ESPRESSO users Forum <<a href="mailto:users@lists.quantum-espresso.org" target="_blank">users@lists.quantum-espresso.org</a>></font></div></div><div dir="ltr"><div id="m_7302475323095056452divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><br>
<b>Subject:</b> Re: [QE-users] Running efficiently on multiple nodes</font>
<div> </div>
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<div>
<div dir="ltr">
<div>Are there fast communications between the two nodes? if not, the parallel distributed 3D FFT will be very slow (note the time taken by fft_scatt_yz). You might find convenient to exploit k-point parallelization, that requires much less communication: for
instance, "mpirun -n 32 pw.x -nk 2" (2 pools of 16 processors, each pool performing parallel FFT), but you have to figure out a way to convince the first pool of 16 processors on node 1, the second on node 2 (or vice versa, as long as FFT parallelization happens
inside a node, k-point parallelization across nodes )</div>
<div><br>
</div>
<div>Paolo<br>
</div>
</div>
<br>
<div>
<div dir="ltr">On Thu, Nov 5, 2020 at 7:29 PM Baer, Bradly via users <<a href="mailto:users@lists.quantum-espresso.org" target="_blank">users@lists.quantum-espresso.org</a>> wrote:<br>
</div>
<blockquote style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
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<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
Paolo,</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
<br>
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<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
Thank you for your suggestion. I will add recompiling to move to 6.6 to my to do list. For now, I corrected the pseudopotential files as you indicated and the calculation ran successfully. It has become slightly faster, but still much slower than running
on a single node (3:30s vs 0:30s). Is there more that I should be doing to improve performance or is my test problem too small to see the benefits of parallelization?</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
<br>
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<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
Thanks,</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
Brad </div>
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--------------------------------------------------------</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
Bradly Baer</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
<span style="font-family:Calibri,Arial,Helvetica,sans-serif;background-color:rgb(255,255,255);display:inline">Graduate Research Assistant, Walker Lab</span><br>
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<span style="font-family:Calibri,Arial,Helvetica,sans-serif;background-color:rgb(255,255,255);display:inline">Interdisciplinary Materials Science</span><br>
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Vanderbilt University</div>
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<br>
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<div id="m_7302475323095056452x_gmail-m_-4475069457157334453divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> users <<a href="mailto:users-bounces@lists.quantum-espresso.org" target="_blank">users-bounces@lists.quantum-espresso.org</a>>
on behalf of Paolo Giannozzi <<a href="mailto:p.giannozzi@gmail.com" target="_blank">p.giannozzi@gmail.com</a>><br>
<b>Sent:</b> Thursday, November 5, 2020 10:01 AM<br>
<b>To:</b> Quantum ESPRESSO users Forum <<a href="mailto:users@lists.quantum-espresso.org" target="_blank">users@lists.quantum-espresso.org</a>><br>
<b>Subject:</b> Re: [QE-users] Running efficiently on multiple nodes</font>
<div> </div>
</div>
<div>
<div dir="ltr">
<div dir="ltr">On Thu, Nov 5, 2020 at 3:05 PM Baer, Bradly <<a href="mailto:bradly.b.baer@vanderbilt.edu" target="_blank">bradly.b.baer@vanderbilt.edu</a>> wrote:<br>
</div>
<div>
<div> </div>
<blockquote style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
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<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
<div><i>Pseudo file Ga.pbe-dn-kjpaw_psl.1.0.0.UPF has been fixed on the fly.</i></div>
<div><i>To avoid this message in the future, permanently fix </i></div>
<div><i> your pseudo files following these instructions: </i></div>
<div><i><a href="https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgitlab.com%2FQEF%2Fq-e%2Fblob%2Fmaster%2Fupftools%2Fhow_to_fix_upf.md&data=04%7C01%7Cbradly.b.baer%40vanderbilt.edu%7Ca843f95dcbc04eb71ed508d881d5735b%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C637402101063299076%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=e33bhAwBlBmEyzlOywulA5VrN6JkxWmXUv6JhSuKtNY%3D&reserved=0" target="_blank">https://gitlab.com/QEF/q-e/blob/master/upftools/how_to_fix_upf.md</a></i></div>
</div>
</div>
</blockquote>
<div><br>
</div>
<div>This is a possible source of trouble if the output directory is not visible to all processors. Please try one of the following:<br>
</div>
<div>- do what it is suggested (or simply: edit Ga.pbe-dn-kjpaw_psl.1.0.0.UPF, replace all occurrences of "&" with "&")</div>
<div>- get version 6.6, that reads the pseudopotential file on one processor and broadcast its contents to all other processes</div>
<div>- get the development version, that in addition is not sensitive to the presence of nonstandard "&" in the files,
</div>
<div><br>
</div>
<div>Paolo<br>
</div>
<blockquote style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
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-Brad</div>
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<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
Bradly Baer</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
<span style="font-family:Calibri,Arial,Helvetica,sans-serif;background-color:rgb(255,255,255);display:inline">Graduate Research Assistant, Walker Lab</span><br>
</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
<span style="font-family:Calibri,Arial,Helvetica,sans-serif;background-color:rgb(255,255,255);display:inline">Interdisciplinary Materials Science</span><br>
</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
Vanderbilt University</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
<br>
</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
<br>
</div>
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<font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> users <<a href="mailto:users-bounces@lists.quantum-espresso.org" target="_blank">users-bounces@lists.quantum-espresso.org</a>> on behalf of Paolo Giannozzi <<a href="mailto:p.giannozzi@gmail.com" target="_blank">p.giannozzi@gmail.com</a>><br>
<b>Sent:</b> Thursday, November 5, 2020 2:33 AM<br>
<b>To:</b> Quantum ESPRESSO users Forum <<a href="mailto:users@lists.quantum-espresso.org" target="_blank">users@lists.quantum-espresso.org</a>><br>
<b>Subject:</b> Re: [QE-users] Running efficiently on multiple nodes</font>
<div> </div>
</div>
<div>
<div dir="ltr">
<div dir="ltr">On Wed, Nov 4, 2020 at 11:28 PM Baer, Bradly <<a href="mailto:bradly.b.baer@vanderbilt.edu" target="_blank">bradly.b.baer@vanderbilt.edu</a>> wrote:<br>
</div>
<div>
<div> </div>
<blockquote style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div dir="ltr">Now that I have two nodes, the script for a single node results in a crash shortly after reading in the pseudopotentials.
</div>
</blockquote>
<div><br>
</div>
<div>which version of QE are you using, and which crash do you obtain, with which executable?<br>
</div>
<br clear="all">
</div>
Paolo<br>
<div>-- <br>
<div dir="ltr">
<div dir="ltr">
<div>
<div dir="ltr">
<div>Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,<br>
Univ. <a href="https://www.google.com/maps/search/Udine,+via+delle+Scienze+208,+33100+Udine,+Italy?entry=gmail&source=g">Udine, via delle Scienze 208, 33100 Udine, Italy</a><br>
Phone +39-0432-558216, fax +39-0432-558222<br>
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<div>Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,<br>
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