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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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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>
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Brad</div>
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Bradly Baer</div>
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<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>
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Vanderbilt University</div>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Paolo Giannozzi <p.giannozzi@gmail.com><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 <users@lists.quantum-espresso.org><br>
<b>Subject:</b> Re: [QE-users] Running efficiently on multiple nodes</font>
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<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>
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<div>Paolo<br>
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<div dir="ltr" class="x_gmail_attr">On Thu, Nov 5, 2020 at 7:29 PM Baer, Bradly via users <<a href="mailto:users@lists.quantum-espresso.org">users@lists.quantum-espresso.org</a>> wrote:<br>
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Paolo,</div>
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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>
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Thanks,</div>
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Brad </div>
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Bradly Baer</div>
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Vanderbilt University</div>
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<div id="x_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>
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<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>
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<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" originalsrc="https://gitlab.com/QEF/q-e/blob/master/upftools/how_to_fix_upf.md" shash="AsWuDt8ACq6lUmPuv6yJHbwf+ibJf9NmlGfpZIvGZuMPvHvCNKXJYY6iW1UBZJYrKGxmSbeFYIc/AxIKKC512gs0C2BvuOyu04mCt55aWWdUPoyOsk+jFCvEMwJEX9eWzQJ4IMvKgTgYsn+dMlJZ11sPyRwm/10NL3TzT898Epc=" target="_blank">https://gitlab.com/QEF/q-e/blob/master/upftools/how_to_fix_upf.md</a></i></div>
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<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>
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<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,
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<div>Paolo<br>
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-Brad</div>
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Bradly Baer</div>
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<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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Vanderbilt University</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>
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<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>
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<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.
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<div>which version of QE are you using, and which crash do you obtain, with which executable?<br>
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Paolo<br>
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<div>Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,<br>
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy<br>
Phone +39-0432-558216, fax +39-0432-558222<br>
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<div>Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,<br>
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy<br>
Phone +39-0432-558216, fax +39-0432-558222<br>
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