[gmx-users] nodes error

Albert mailmd2011 at gmail.com
Fri Jan 6 05:49:38 CET 2012

   I found that each time I would like to increase my nodes for MD run, 
my job always failed. it said:

Will use 192 particle-particle and 64 PME only nodes
This is a guess, check the performance at the end of the log file

Program mdrun_mpi_bg, VERSION 4.5.5
Source code file: ../../../src/mdlib/domdec.c, line: 6436

Fatal error:
There is no domain decomposition for 192 nodes that is compatible with 
the given box and a minimum cell size of
  1.02425 nm
Change the number of nodes or mdrun option -rcon or -dds or your LINCS 
Look in the log file for details on the domain decomposition
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

"Ohne Arbeit wird das Leben Oede" (Wir Sind Helden)

Does anybody have any idea for this? here is my scrips for submitting jobs;
# @ job_name = I213A
# @ class = kdm-large
# @ account_no = G07-13
# @ error = gromacs.err
# @ output = gromacs.out
# @ environment = COPY_ALL
# @ wall_clock_limit = 12:00:00
# @ notification = error
# @ notify_user = albert at icm.edu.pl
# @ job_type = bluegene
# @ bg_size = 64
# @ queue
mpirun -exe /opt/gromacs/4.5.5/bin/mdrun_mpi_bg -args "-nosum -dlb yes 
-v -s npt.tpr" -mode VN -np 256

if I change the bg_size=32 and -np=128, everything goes well....


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