Mahendran E wrote:
hi all
while running gromacs in parallel environment
i am getting the following command,
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
You are specifying 5 nodes with "mpirun -np 5 ..." so just change the number
passed to the -np flag.
-Justin
thanks in advance
Regards
Mahendran.E
--
========================================
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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