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
