Dear Brad, 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. Best wishes, Michal Krompiec Merck KGaA
On Thu, Nov 5, 2020 at 11:40 PM Baer, Bradly via users < users@lists.quantum-espresso.org> wrote: > Paolo, > > 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? > > 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. > > Thanks, > Brad > > -------------------------------------------------------- > Bradly Baer > Graduate Research Assistant, Walker Lab > Interdisciplinary Materials Science > Vanderbilt University > > > ------------------------------ > *From:* Paolo Giannozzi <p.gianno...@gmail.com> > *Sent:* Thursday, November 5, 2020 3:54 PM > *To:* Baer, Bradly <bradly.b.b...@vanderbilt.edu>; Quantum ESPRESSO users > Forum <users@lists.quantum-espresso.org> > > *Subject:* Re: [QE-users] Running efficiently on multiple nodes > > 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%7Ca843f95dcbc04eb71ed508d881d5735b%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C637402101063299076%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=e33bhAwBlBmEyzlOywulA5VrN6JkxWmXUv6JhSuKtNY%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 > <https://www.google.com/maps/search/Udine,+via+delle+Scienze+208,+33100+Udine,+Italy?entry=gmail&source=g> > 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%7Ca843f95dcbc04eb71ed508d881d5735b%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C637402101063309070%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=3WAEQsQAKgsnqkk%2FRpxTFQrgj0C1Fmm6ekNNZ2HkGyY%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%7Ca843f95dcbc04eb71ed508d881d5735b%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C637402101063309070%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=%2BIu52jsZQs6b%2FY%2Fk11ZBc%2FxC0xr2c8aOlNDvbJLo5rE%3D&reserved=0> > > > > -- > Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > <https://www.google.com/maps/search/Udine,+via+delle+Scienze+208,+33100+Udine,+Italy?entry=gmail&source=g> > 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%7Ca843f95dcbc04eb71ed508d881d5735b%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C637402101063319066%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=YLzRslbTYz%2B8EObze6WnE6SKsrCIzJUeXvyHYvr7ZOU%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%7Ca843f95dcbc04eb71ed508d881d5735b%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C637402101063319066%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=G2BtHxmpAJL4WDxv06ANzYYj4YGSJgOYqaEhE3GLNPg%3D&reserved=0> > > > > -- > Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > <https://www.google.com/maps/search/Udine,+via+delle+Scienze+208,+33100+Udine,+Italy?entry=gmail&source=g> > 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
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