Hi There,<br>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.<br>-------------------------------------------------------<br>Program mpi_mdrun_d, VERSION 4.0.3<br>
Source code file: domdec_setup.c, line: 147<br><br>Fatal error:<br>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). <br>
Use the -npme option of mdrun or change the number of processors or the PME grid dimensions, see the manual for details.<br>-------------------------------------------------------<br>then I tried with -npme option as "-npme 20", this time it failed with the following error.<br>
-------------------------------------------------------<br>Program mpi_mdrun_d, VERSION 4.0.3<br>Source code file: domdec.c, line: 5858<br><br>Fatal error:<br>There is no domain decomposition for 94 nodes that is compatible with the given box and a minimum cell size of 1.025 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>Same system was running fine when I tried it on 4 nodes.<br>
I havn't used gromacs4.0 very well, so i don't understand these errors.<br>Please suggest me a way to get out of these errors, It will be really helpful if anybody can explain me these errors.<br><br>With thanks in advance.<br>
<br>Thanks & Regards,<br>Vivek<br>