<br><div class="gmail_quote"><br>hi all<br><br><br>while running gromacs in parallel environment<br><br><b>mpirun -np 3</b> -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 <br>
<b>for mpirun 3 nodes i got the output,</b><br><br>while trying to increase the nodes to 5 or 8 i am getting the following error <br>
<br>the command i used is<br><br>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<br>
<br><br>error:<br><br><br><br>Program mdrun_mpi, VERSION 4.0.5<br>Source code file: domdec.c, line: 5873<br><br>Fatal error:<br>There is no domain decomposition for 5 nodes that is compatible with the given box and a minimum cell size of 1.095 nm<br>
Change the number of nodes or mdrun option -rcon or -dds or your LINCS settings<br>Look in the log file for details on the domain decomposition<br>-------------------------------------------------------<br><br>"Everybody Wants to Be Naked and Famous" (Tricky)<br>
<br>Error on node 0, will try to stop all the nodes<br>Halting parallel program mdrun_mpi on CPU 0 out of 5<br><br>gcq#130: "Everybody Wants to Be Naked and Famous" (Tricky)<br><br>[0] MPI Abort by user Aborting program !<br>
[0] Aborting program!<br>p0_16810: p4_error: : -1<br> p4_error: latest msg from perror: No such file or directory<br><br><br>how to increase the nodes in mdrun option<br><br>thanks in advance<br><br><br>Regards<br><font color="#888888"><br>
Mahendran.E<br>
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