Hi! I see that you still can scale a lot more than me. Can you, or someone, give me one of those testes? I would like to compare with a similar machine, where gromacs is scaling more than one node well.
Best regards, Tiago Marques On Thu, Sep 25, 2008 at 2:52 PM, vivek sharma <[EMAIL PROTECTED]>wrote: > Hi friends, > I am also facing the similar problem when tried to scale gromacs for more > number of processors , > I have tried one job using gromacs on EKA, in an attempt to scale it for > more number of processor I am able to get the reduction in simulation time > upto 20 processors, it is taking more time for 40 processor for same > simulation, and when tried with 60 processor, it crashed with segmentation > fault. > i HAVE TRIED OTHER OPTION LIKE CONSTRAINT_ALGO, COULOMBTYPE AND SHUFFLE > OPTION > > 2008/9/25 Tiago Marques <[EMAIL PROTECTED]> > >> We currently have no funds available to migrate to infiniband but we will >> in the future. >> >> I thought on doing interface bonding but I really think that isn't really >> the problem here, there must be something I'm missing, since most >> applications scale well to 32 cores on GbE. I can't scale any application to >> more than 8 though. >> >> Best regards, >> >> Tiago Marques >> >> On Tue, Sep 23, 2008 at 6:30 PM, Diego Enry <[EMAIL PROTECTED]> wrote: >> >>> Tiago you can try merging two network interfaces with "channel >>> bonding" it's native on all new (2.6.x) linux kernels. You only need >>> two network adapters (most dual socket boards come with then), two >>> network switches ( or two VPN on the same switch). >>> >>> To tell you the truth, you will not much improvement even with the >>> latest gromacs version (4beta). However other software that may be >>> used by your group like NAMD, GAMESS, will benefit a lot from this >>> approach. (it almost doubles network bandwidth) >>> >>> The best solution for gromacs is to migrate to infiniband. Go for it, >>> it is not super expensive anymore. >>> >>> >>> On Tue, Sep 23, 2008 at 1:48 PM, Jochen Hub <[EMAIL PROTECTED]> wrote: >>> > Tiago Marques wrote: >>> >> I don't know how large the system is. I'm the cluster's system >>> administrator >>> >> and don't understand much of what's going on. The test was given to me >>> by a >>> >> person who works with it. I can ask him or look at it, if you can >>> point me >>> >> how to do it. >>> > >>> > Hi, >>> > >>> > you can count the nr of atoms in the structure: >>> > >>> > grep -c ATOM protein.pdb >>> > >>> > Jochen >>> > >>> >> >>> >> Thanks, I will look at some of his posts. >>> >> >>> >> Best regards, >>> >> >>> >> Tiago Marques >>> >> >>> >> >>> >> On Tue, Sep 23, 2008 at 4:03 PM, Jochen Hub <[EMAIL PROTECTED]> wrote: >>> >> Tiago Marques wrote: >>> >>> Hi! >>> >>> >>> >>> I've been using Gromacs on dual-socket quad-core Xeons with 8GiB of >>> RAM, >>> >>> connected with Gigabit Ethernet and I always seem to have problems >>> scaling >>> >>> to more than a node. >>> >>> >>> >>> When I run a test on 16 cores, it does run but the result is often >>> slower >>> >>> than when running on only 8 cores on the same machine. The best >>> result >>> >> I've >>> >>> managed is not being slower than 8 cores on 16. >>> >>> >>> >>> What am I missing here, or are the tests inappropriate to run over >>> more >>> >> than >>> >>> one machine? >>> >> >>> >> How large is your system? Which gromacs version are you using? >>> >> >>> >> And have a look at the messages by Carsten Kutzner in this list, he >>> >> wrote a lot on gromacs scaling. >>> >> >>> >> Jochen >>> >> >>> >>> Best regards, >>> >>> >>> >>> Tiago Marques >>> >>> >>> >>> >>> >>> >>> >>> >>> ------------------------------------------------------------------------ >>> >>> >>> >>> _______________________________________________ >>> >>> gmx-users mailing list gmx-users@gromacs.org >>> >>> http://www.gromacs.org/mailman/listinfo/gmx-users >>> >>> Please search the archive at http://www.gromacs.org/search before >>> posting! >>> >>> Please don't post (un)subscribe requests to the list. Use the >>> >>> www interface or send it to [EMAIL PROTECTED] >>> >>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >>> >> >>> >> >>> >> -- >>> >> ************************************************ >>> >> Dr. Jochen Hub >>> >> Max Planck Institute for Biophysical Chemistry >>> >> Computational biomolecular dynamics group >>> >> Am Fassberg 11 >>> >> D-37077 Goettingen, Germany >>> >> Email: jhub[at]gwdg.de >>> >> Tel.: +49 (0)551 201-2312 >>> >> ************************************************ >>> >> _______________________________________________ >>> >> gmx-users mailing list gmx-users@gromacs.org >>> >> http://www.gromacs.org/mailman/listinfo/gmx-users >>> >> Please search the archive at http://www.gromacs.org/search before >>> posting! >>> >> Please don't post (un)subscribe requests to the list. Use the >>> >> www interface or send it to [EMAIL PROTECTED] >>> >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >>> >> >>> >> >>> >> >>> >> >>> ------------------------------------------------------------------------ >>> >> >>> >> _______________________________________________ >>> >> gmx-users mailing list gmx-users@gromacs.org >>> >> http://www.gromacs.org/mailman/listinfo/gmx-users >>> >> Please search the archive at http://www.gromacs.org/search before >>> posting! >>> >> Please don't post (un)subscribe requests to the list. Use the >>> >> www interface or send it to [EMAIL PROTECTED] >>> >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >>> > >>> > >>> > -- >>> > ************************************************ >>> > Dr. Jochen Hub >>> > Max Planck Institute for Biophysical Chemistry >>> > Computational biomolecular dynamics group >>> > Am Fassberg 11 >>> > D-37077 Goettingen, Germany >>> > Email: jhub[at]gwdg.de >>> > Tel.: +49 (0)551 201-2312 >>> > ************************************************ >>> > _______________________________________________ >>> > gmx-users mailing list gmx-users@gromacs.org >>> > http://www.gromacs.org/mailman/listinfo/gmx-users >>> > Please search the archive at http://www.gromacs.org/search before >>> posting! >>> > Please don't post (un)subscribe requests to the list. Use the >>> > www interface or send it to [EMAIL PROTECTED] >>> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >>> > >>> >>> >>> >>> -- >>> Diego Enry B. Gomes >>> Laboratório de Modelagem e Dinamica Molecular >>> Universidade Federal do Rio de Janeiro - Brasil. >>> _______________________________________________ >>> gmx-users mailing list gmx-users@gromacs.org >>> http://www.gromacs.org/mailman/listinfo/gmx-users >>> Please search the archive at http://www.gromacs.org/search before >>> posting! >>> Please don't post (un)subscribe requests to the list. Use the >>> www interface or send it to [EMAIL PROTECTED] >>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >>> >> >> >> >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> http://www.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before >> posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to [EMAIL PROTECTED] >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
_______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php