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Thank you all for taking the time to share your experience. It looks like I have some work to do this weekend to learn more about how our cluster handles inter-node communication. I appreciate all the help.</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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<span style="font-family:Calibri,Arial,Helvetica,sans-serif; background-color:rgb(255,255,255); display:inline!important">Interdisciplinary Materials Science</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> users <users-bounces@lists.quantum-espresso.org> on behalf of Antoine Jay via users <users@lists.quantum-espresso.org><br>
<b>Sent:</b> Friday, November 6, 2020 1:14 AM<br>
<b>To:</b> 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>Dear Brad,<br>
I can only confirm what Paolo and Michal suggested.<br>
Even with infiniband the efficiency of the FFT parallelization drastically decreases at each new node, WHATEVER THE CODE (not only QE) or the librairy.<br>
For SLURM jobs, if you ask 2 nodes of 16 cores, the first 16 are indexed 1 to 16 and 16 last 17-32, that is exactlly the same repartition implemented in QE for k points, bands or images parallelization.<br>
Thanks to this, I never face trouble concerning the way the mpi processes are spread to the cores when the number of pools (or images) equals the number of nodes.<br>
For these reason, except for large supercells at gamma only, I always do npool=nodes<br>
<br>
Regards,<br>
Antoine Jay<br>
LAAS CNRS<br>
Toulouse France<br>
<br>
Le Vendredi, Novembre 06, 2020 01:04 CET, Michal Krompiec via users <users@lists.quantum-espresso.org> a écrit:<br>
<blockquote type="cite">
<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>
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<div dir="ltr" class="x_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:</div>
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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></div>
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<span style="font-family:Calibri,Arial,Helvetica,sans-serif; background-color:rgb(255,255,255); display:inline!important">Interdisciplinary Materials Science</span></div>
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Vanderbilt University</div>
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<div id="x_m_7302475323095056452divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> Paolo Giannozzi <<a target="_blank" href="mailto:p.giannozzi@gmail.com">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 target="_blank" href="mailto:users@lists.quantum-espresso.org">users@lists.quantum-espresso.org</a>></font></div>
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<font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><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>
<div> </div>
<div>Paolo</div>
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<div dir="ltr">On Thu, Nov 5, 2020 at 7:29 PM Baer, Bradly via users <<a target="_blank" href="mailto:users@lists.quantum-espresso.org">users@lists.quantum-espresso.org</a>> wrote:</div>
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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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<span style="font-family:Calibri,Arial,Helvetica,sans-serif; background-color:rgb(255,255,255); display:inline">Graduate Research Assistant, Walker Lab</span></div>
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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 target="_blank" href="mailto:users-bounces@lists.quantum-espresso.org">users-bounces@lists.quantum-espresso.org</a>> on behalf of Paolo Giannozzi <<a target="_blank" href="mailto:p.giannozzi@gmail.com">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 target="_blank" href="mailto:users@lists.quantum-espresso.org">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">
<div dir="ltr">On Thu, Nov 5, 2020 at 3:05 PM Baer, Bradly <<a target="_blank" href="mailto:bradly.b.baer@vanderbilt.edu">bradly.b.baer@vanderbilt.edu</a>> wrote:</div>
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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 target="_blank" 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%7Cbb9dbbbf6caf4f5c264708d88223b838%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C1%7C637402437232156388%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=Dow2rXyGSRZd%2FvKNOc5T1izM%2FiPxPoAJzVJjU28DHfo%3D&reserved=0" originalsrc="https://gitlab.com/QEF/q-e/blob/master/upftools/how_to_fix_upf.md" shash="ZyY/+GaUA70piWTJMXfDWyZVXodT3cyeVYMgmc6BqZG4H60CaBw7XebxePJFJZKTiVXTtcdeT0QAn5Nilke6ZqSkvxLEBhcYg7BQ1hlsx9NjMh3vTF8uu9ZoUwXfQ81vvp6mQfmcpA+EhxprnVvvtzRtimXt7ZldbT2M9XENXc0=">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:</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> </div>
<div>Paolo</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">Graduate Research Assistant, Walker Lab</span></div>
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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></div>
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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 target="_blank" href="mailto:users-bounces@lists.quantum-espresso.org">users-bounces@lists.quantum-espresso.org</a>> on behalf of Paolo Giannozzi <<a target="_blank" href="mailto:p.giannozzi@gmail.com">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 target="_blank" href="mailto:users@lists.quantum-espresso.org">users@lists.quantum-espresso.org</a>><br>
<b>Subject:</b> Re: [QE-users] Running efficiently on multiple nodes</font>
<div> </div>
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<div>
<div dir="ltr">
<div dir="ltr">On Wed, Nov 4, 2020 at 11:28 PM Baer, Bradly <<a target="_blank" href="mailto:bradly.b.baer@vanderbilt.edu">bradly.b.baer@vanderbilt.edu</a>> wrote:</div>
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<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>
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<div>which version of QE are you using, and which crash do you obtain, with which executable?</div>
</div>
Paolo
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<div>Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,<br>
Univ. <a href="https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.google.com%2Fmaps%2Fsearch%2FUdine%2C%2Bvia%2Bdelle%2BScienze%2B208%2C%2B33100%2BUdine%2C%2BItaly%3Fentry%3Dgmail%26source%3Dg&data=04%7C01%7Cbradly.b.baer%40vanderbilt.edu%7Cbb9dbbbf6caf4f5c264708d88223b838%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C1%7C637402437232166380%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=%2FL9RjqUBnCiGTjxZVVqXjTGLXNDgdKtBbKq%2BYmoz2zY%3D&reserved=0" originalsrc="https://www.google.com/maps/search/Udine,+via+delle+Scienze+208,+33100+Udine,+Italy?entry=gmail&source=g" shash="QbZGn0VHiPNN2pHgIJ7pli1mH/Wx+Kz4nY42xn+dOxP/CZMhFm1OFNIchrbuooihVMc1veuVhfR78jkuMG4hkMstm72CaDZhd4po91lqMkkFLE73FM41YtMhMhMw1TJ8mbnKo6F3ScMqATJd8Aol2n38ZXBkSA2kSbexETTaoCA=">
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>
Univ. <a href="https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.google.com%2Fmaps%2Fsearch%2FUdine%2C%2Bvia%2Bdelle%2BScienze%2B208%2C%2B33100%2BUdine%2C%2BItaly%3Fentry%3Dgmail%26source%3Dg&data=04%7C01%7Cbradly.b.baer%40vanderbilt.edu%7Cbb9dbbbf6caf4f5c264708d88223b838%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C1%7C637402437232176369%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=JvhttsG%2FN90fLTCY9U1smphqVslvjmX28T18DsReo98%3D&reserved=0" originalsrc="https://www.google.com/maps/search/Udine,+via+delle+Scienze+208,+33100+Udine,+Italy?entry=gmail&source=g" shash="xSnaKgU8Le0oG211xNyz8mhuE7unizrzN8rySdeRFfkd2+s9PbxfQ2uux4d23j7nbyZV4mVCa/Xp5JrPf/hSctUZUeL80/b8EEfSRnOObO83cEzmajgRk30XtAyk8RtBDABYEx/sM6aLipTlIw5mBEudUUJ9x0J3YABbbjiDRyU=">
Udine, via delle Scienze 208, 33100 Udine, Italy</a><br>
Phone +39-0432-558216, fax +39-0432-558222<br>
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_______________________________________________<br>
Quantum ESPRESSO is supported by MaX (<a rel="noreferrer" target="_blank" href="https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.max-centre.eu%2F&data=04%7C01%7Cbradly.b.baer%40vanderbilt.edu%7Cbb9dbbbf6caf4f5c264708d88223b838%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C1%7C637402437232186367%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=9uUZAM1sqTl76J4cOO0WLIgLI24HBlDiIAX0L0HBVDg%3D&reserved=0" originalsrc="http://www.max-centre.eu/" shash="DqH9AkWqlHSn+5vCBPEAM2jykjK0odIHWdW2y7W2SDICmhyUp98J8FBS4e2kBPaF1Uwp3PT3tX8ErIhE9ulPlDLlI39xYFhnACIq97rHaK7WmStFcWYRFVaPOGhgYWZ5fol4vKA53XiF2VNctyw6LrRhATxQ7J0jTBDU0Kk/Myg=">www.max-centre.eu</a>)<br>
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<div>Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,<br>
Univ. <a href="https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.google.com%2Fmaps%2Fsearch%2FUdine%2C%2Bvia%2Bdelle%2BScienze%2B208%2C%2B33100%2BUdine%2C%2BItaly%3Fentry%3Dgmail%26source%3Dg&data=04%7C01%7Cbradly.b.baer%40vanderbilt.edu%7Cbb9dbbbf6caf4f5c264708d88223b838%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C1%7C637402437232196360%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=2SohlU0wvyYOy%2FqnoLKlytqDkaIDtW9OD7CnGgXBRfM%3D&reserved=0" originalsrc="https://www.google.com/maps/search/Udine,+via+delle+Scienze+208,+33100+Udine,+Italy?entry=gmail&source=g" shash="sCNV6YzfrIZ1Zsb+zDg3NQTM4xNgsutHpAJ2YSsBm/05qsEga+NEBwoun1SR3jIjFO4UrdiKp6qfawhtWuqp2iOrG9McPszRhE459k2zC/962BT8GUGJdB7DAglVO3CeROS7sD3xuM9+Vnn0VGCIG/o1SuZGLA91M/eYdAO+xzc=">
Udine, via delle Scienze 208, 33100 Udine, Italy</a><br>
Phone +39-0432-558216, fax +39-0432-558222<br>
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_______________________________________________<br>
Quantum ESPRESSO is supported by MaX (<a rel="noreferrer" target="_blank" href="https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.max-centre.eu%2F&data=04%7C01%7Cbradly.b.baer%40vanderbilt.edu%7Cbb9dbbbf6caf4f5c264708d88223b838%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C1%7C637402437232206353%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=bA%2FcKlXHLFuQXVZY%2BQCVAmTjoDchhqt9iIqM2fmqfAI%3D&reserved=0" originalsrc="http://www.max-centre.eu/" shash="sWv8PliTtQIiNTZwvhbIF5mM14DplXFVs1x+QAeAk9r3gci9VfkAXKz5QBQOclVwBLAVnLN3CQ9MZssNu3R1M9KPi1nCUbKkxmzIl4fRhFIR7Ga+JYtYkL/VGtvOrF7j4SguDHhNkdYIdXmjoKoYs8EqYP+8+tfw3jrY1uJJN3w=">www.max-centre.eu</a>)<br>
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