Hi Berk, Thanks for your suggestion, It is working well now, Can you explain Why it didn't worked for prime number?
Thanks & Regards, Vivek 2009/9/25 Berk Hess <[email protected]> > Hi, > > Why do you want to run on exactly 57 nodes? > That is a nasty prime number. > I guess 56 or 60 nodes would work fine. > > Berk > > ------------------------------ > Date: Fri, 25 Sep 2009 14:39:27 +0530 > From: [email protected] > To: [email protected] > Subject: [gmx-users] Error while scaling mdrun for more number of nodes. > > > Hi There, > I was trying to rum mdrun on large number of nodes. When I tried the run on > 57 nodes, I got an error which is pasted below. > ------------------------------------------------------- > Program mpi_mdrun_d, VERSION 4.0.3 > Source code file: domdec_setup.c, line: 147 > > Fatal error: > Could not find an appropriate number of separate PME nodes. i.e. >= > 0.409991*#nodes (44) and <= #nodes/2 (57) and reasonable performance wise > (grid_x=63, grid_y=63). > Use the -npme option of mdrun or change the number of processors or the PME > grid dimensions, see the manual for details. > ------------------------------------------------------- > then I tried with -npme option as "-npme 20", this time it failed with the > following error. > ------------------------------------------------------- > Program mpi_mdrun_d, VERSION 4.0.3 > Source code file: domdec.c, line: 5858 > > Fatal error: > There is no domain decomposition for 94 nodes that is compatible with the > given box and a minimum cell size of 1.025 nm > Change the number of nodes or mdrun option -rcon or -dds or your LINCS > settings > Look in the log file for details on the domain decomposition > ------------------------------------------------------- > Same system was running fine when I tried it on 4 nodes. > I havn't used gromacs4.0 very well, so i don't understand these errors. > Please suggest me a way to get out of these errors, It will be really > helpful if anybody can explain me these errors. > > With thanks in advance. > > Thanks & Regards, > Vivek > > ------------------------------ > What can you do with the new Windows Live? Find > out<http://www.microsoft.com/windows/windowslive/default.aspx> > > _______________________________________________ > gmx-users mailing list [email protected] > http://lists.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 >
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