Hi Mahendran, your minimum domain decomposition cell size seems to be 1.095 nm, as indicated in the error message. Probably your cutoffs are near 1 nm and your system is small. If you need to run on more processors, try 6 and 8, since then 3x2x1, 2x3x1, ... and 2x2x2, ... decompositions can be used. Right now the only possibilities are 5x1x1, 1x5x1, and 1x1x5, yielding a too small DD size in any direction. (What is your max. box length divided by 5?)
Carsten On Dec 10, 2009, at 2:38 PM, Mahendran E wrote: > > > hi all > > > while running gromacs in parallel environment > > mpirun -np 3 -machinefile machinefile /usr/local/gromacs/bin/mdrun_mpi -s > fws_md.tpr -o fws_md.trr -c fws_pmd.pdb -g md.log -e md.edr > for mpirun 3 nodes i got the output, > > while trying to increase the nodes to 5 or 8 i am getting the following error > > the command i used is > > mpirun -np 5 -machinefile machinefile /usr/local/gromacs/bin/mdrun_mpi -s > fws_md.tpr -o fws_md.trr -c fws_pmd.pdb -g md.log -e md.edr > > > error: > > > > Program mdrun_mpi, VERSION 4.0.5 > Source code file: domdec.c, line: 5873 > > Fatal error: > There is no domain decomposition for 5 nodes that is compatible with the > given box and a minimum cell size of 1.095 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 > ------------------------------------------------------- > > "Everybody Wants to Be Naked and Famous" (Tricky) > > Error on node 0, will try to stop all the nodes > Halting parallel program mdrun_mpi on CPU 0 out of 5 > > gcq#130: "Everybody Wants to Be Naked and Famous" (Tricky) > > [0] MPI Abort by user Aborting program ! > [0] Aborting program! > p0_16810: p4_error: : -1 > p4_error: latest msg from perror: No such file or directory > > > how to increase the nodes in mdrun option > > thanks in advance > > > Regards > > Mahendran.E > > -- > gmx-users mailing list gmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne
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