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 )
Paolo On Thu, Nov 5, 2020 at 7:29 PM Baer, Bradly via users < users@lists.quantum-espresso.org> wrote: > Paolo, > > 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? > > Thanks, > Brad > > -------------------------------------------------------- > Bradly Baer > Graduate Research Assistant, Walker Lab > Interdisciplinary Materials Science > Vanderbilt University > > > ------------------------------ > *From:* users <users-boun...@lists.quantum-espresso.org> on behalf of > Paolo Giannozzi <p.gianno...@gmail.com> > *Sent:* Thursday, November 5, 2020 10:01 AM > *To:* Quantum ESPRESSO users Forum <users@lists.quantum-espresso.org> > *Subject:* Re: [QE-users] Running efficiently on multiple nodes > > On Thu, Nov 5, 2020 at 3:05 PM Baer, Bradly <bradly.b.b...@vanderbilt.edu> > wrote: > > > *Pseudo file Ga.pbe-dn-kjpaw_psl.1.0.0.UPF has been fixed on the fly.* > *To avoid this message in the future, permanently fix * > * your pseudo files following these instructions: * > *https://gitlab.com/QEF/q-e/blob/master/upftools/how_to_fix_upf.md > <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%7C73a5a5e938ac4ee11cb808d881a440f4%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C637401889751409012%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=511bORLQwH1OKUCoHg%2BbMb5I%2FiOEuHIFEbDlNl28678%3D&reserved=0>* > > > This is a possible source of trouble if the output directory is not > visible to all processors. Please try one of the following: > - do what it is suggested (or simply: edit Ga.pbe-dn-kjpaw_psl.1.0.0.UPF, > replace all occurrences of "&" with "&") > - get version 6.6, that reads the pseudopotential file on one processor > and broadcast its contents to all other processes > - get the development version, that in addition is not sensitive to the > presence of nonstandard "&" in the files, > > Paolo > > > > -Brad > > -------------------------------------------------------- > Bradly Baer > Graduate Research Assistant, Walker Lab > Interdisciplinary Materials Science > Vanderbilt University > > > ------------------------------ > *From:* users <users-boun...@lists.quantum-espresso.org> on behalf of > Paolo Giannozzi <p.gianno...@gmail.com> > *Sent:* Thursday, November 5, 2020 2:33 AM > *To:* Quantum ESPRESSO users Forum <users@lists.quantum-espresso.org> > *Subject:* Re: [QE-users] Running efficiently on multiple nodes > > On Wed, Nov 4, 2020 at 11:28 PM Baer, Bradly <bradly.b.b...@vanderbilt.edu> > wrote: > > > Now that I have two nodes, the script for a single node results in a crash > shortly after reading in the pseudopotentials. > > > which version of QE are you using, and which crash do you obtain, with > which executable? > > Paolo > -- > Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > _________________ > Quantum ESPRESSO is supported by MaX (www.max-centre.eu > <https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.max-centre.eu%2F&data=04%7C01%7Cbradly.b.baer%40vanderbilt.edu%7C73a5a5e938ac4ee11cb808d881a440f4%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C637401889751419008%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=hFpaUoIPz4sX3DRUpP09MjX5XOrIVQEtwjR25n%2BUwlk%3D&reserved=0> > ) > users mailing list users@lists.quantum-espresso.org > https://lists.quantum-espresso.org/mailman/listinfo/users > <https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.quantum-espresso.org%2Fmailman%2Flistinfo%2Fusers&data=04%7C01%7Cbradly.b.baer%40vanderbilt.edu%7C73a5a5e938ac4ee11cb808d881a440f4%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C637401889751419008%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=5BEAnLDjV8tgpwX7LRerSaKSiUsTwM8nRSoDNBcDJU4%3D&reserved=0> > > > > -- > Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > _______________________________________________ > Quantum ESPRESSO is supported by MaX (www.max-centre.eu) > users mailing list users@lists.quantum-espresso.org > https://lists.quantum-espresso.org/mailman/listinfo/users -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222
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