Just to clarify something in my previous message - using grompp with and without -shuffle gave the same output, which is given in my first message.
Sorry for any confusion. -Justin Quoting "Justin A. Lemkul" <[EMAIL PROTECTED]>: > Hi all, > > I'm running a very simple system consisting of a globular protein with a > ligand > in a box of SPC water with counterions (ffG43a1 for all components). I ran > my > normal routine of minimization, equilibration, and production, but I've been > getting poor scaling and decided to try again with a different number of > processors. The system contains roughly 39,000 atoms, and I initially used > 24 > processors. Now I would like to try 36. When I run grompp, it allocates 0 > atoms to the first node: > > Division over nodes in atoms: > 0 3135 1059 1059 1059 1059 1059 1059 1059 > 1059 > 1059 1059 1059 1059 1059 1059 1059 1059 1059 > 1059 > 1059 1059 1059 1056 1059 1056 1059 1056 1059 > 1056 > 1059 1056 1059 1056 1059 1056 > > I tried the -shuffle option, just to see if it would change anything, > although I > didn't expect that it would do much since my system is so simple. > > The Gromacs version is 3.3, and I have not tried newer versions for > consistency's sake with some older simulations we have done. > > Has anyone ever experienced anything like this? Is there anything wrong? It > seems odd to allow zero atoms to be on one node. > > Thanks for any insights, > Justin > > > ======================================== > > Justin A. Lemkul > Graduate Research Assistant > Department of Biochemistry > Virginia Tech > Blacksburg, VA > [EMAIL PROTECTED] | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ > > ======================================== > _______________________________________________ > gmx-users mailing list [email protected] > 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 > ======================================== Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ======================================== _______________________________________________ gmx-users mailing list [email protected] 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
