[gmx-users] parallel run error

[Sanjay Nilapwar]

if you have made grompp with -np 2 command,
then possibly you have to write c0-1 instead of -np 2.

mpirun c0-1 mdrun_mpi -v -s md.tpr -o md.trr -c md.gro -e md.edr -g
> md.log >& md.out &


instead of 

mpirun -np 2 mdrun_mpi -v -s md.tpr -o md.trr -c md.gro -e md.edr -g
> md.log >& md.out &

cheers..
-- 
Sanjay Nilapwar
department Of Biochemistry and Molecular Biology
University College Lonodon,
Gower street, London
WC1E 6BT
Tel:- 0207 679 2170


Quoting sunita at chem.iitb.ac.in:

> Dear gmx-users,
> 
> We are trying to run a parallel job in a dual xeon machine (2.8 GHz)
> loaded with Enterprise Linux. It has its own lam-mpi version 6.5.9. We
> compliled fftw-2.1.3 and gromacs-3.2.1 from the source in this machine.
> Then we tried to run a 2 nodes mpi-parallel job with the command
> 
> mpirun -np 2 mdrun_mpi -v -s md.tpr -o md.trr -c md.gro -e md.edr -g
> md.log >& md.out &
> 
> 
> and got following error message in a output file and the log file.
> 
> Error message in md.out file
> -----------------------------------------------------------------------------
> It seems that [at least] one of processes that was started with mpirun
> did not invoke MPI_INIT before quitting (it is possible that more than
> one process did not invoke MPI_INIT -- mpirun was only notified of the
> first one, which was on node n0).
> 
> mpirun can *only* be used with MPI programs (i.e., programs that
> invoke MPI_INIT and MPI_FINALIZE).  You can use the "lamexec" program
> to run non-MPI programs over the lambooted nodes.
> -----------------------------------------------------------------------------
> 
> This error is found in the md.log file.
> 
> Fatal error: run input file md.tpr was made for 2 nodes,
>              while mdrun_mpi expected it to be for 1 nodes.
> 
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