Mahendran E wrote:
Please construct a coherent email, *then* ask for help.
Mark
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
-------------------------------------------------------
"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
thanks in advance
Regards
Mahendran.E
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