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
-------------------------------------------------------
Have you followed this advice? There is a minimum size requirement for DD cells
based on the cutoffs used, etc. You can alter these parameters by using the
mdrun options that have been spelled out for you. If this does not work, then
your system is simply too small to be split over more than a small amount of
processors.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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