Mark Abraham wrote: > Gurpreet Singh wrote: >> I get the following errors while using paralled version of mdrun compiled >> with openmpi. >> mpirun -np 4 mdrun_d_mpi -np 4 -v -deffnm EQUI1 >> ***** >> Program mdrun_d_mpi, VERSION 3.3.99_development_20070720 >> Source code file: gmx_parallel_3dfft.c, line: 90 >> >> Fatal error: >> nx (50) and ny (50) must be divisible by the number of nodes (4). >> ******* >> I am using a cubic box of 5nm and grid spacing is 0.1. The simulations >> runs fine if i use 5 nodes >> I am using a machines with 2 dual xeon processors so -np 4 is more >> appropriate for my sytems. >> Is there any way to use -np 4 without changing the gridspacing or >> box size? > > No. I'm guessing your .mdp file is trying to specify nx/ny/nz, rather > than the grid spacing. If you specify the latter, grompp will take care > of this issue so that you get the largest allowable spacing smaller than > (or equal to) the requested grid spacing. > Hi,
in the current CVS version of grompp you cannot use the -np switch anymore. You will have to comment out the 'fourierspacing = 0.1' line and set fourier_nx = 52 fourier_ny = 52 fourier_nz = 52 in order to get a tpr file that you can run on 4 processors. Alternatively, stick to the original mpd settings but use the 3.3.1 version of grompp with -np 4. These tpr files are read by CVS gromacs. Hope that helps, Carsten _______________________________________________ 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
