Hi Alessandro, With gromacs versions <4 you have to generate the .tpr file with grompp using the flag -np 16 to be able to run on 16 processors. But why not upgrade to gromacs 4.02 and get much better scaling?
Cheers, Tsjerk On Fri, Nov 21, 2008 at 12:06 PM, <[EMAIL PROTECTED]> wrote: > Hi All, > > I'd need an help to run GROMACS 3.3.3 in parallel. I'm running mdrun in > parallel using the command: > > mpirun -machinefile /storage1/home/rgr/machines_16 -np 16 > /storage2/rgr/software/gromacs/bin/mdrun_d -s min0.tpr -g min0.log -e > min0.edr -o min0.trr -x min0.xtc -c min0.gro > > but the following error appear: > > Program mdrun_d, VERSION 3.3.3 > Source code file: init.c, line: 69 > > Fatal error: > run input file min0.tpr was made for 1 nodes, > while mdrun_d expected it to be for 16 nodes. > > Many thanks and regard > Alessandro > _______________________________________________ > 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 > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 _______________________________________________ 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
