[gmx-users] parallel run error

sunita at chem.iitb.ac.in sunita at chem.iitb.ac.in
Thu May 26 07:13:04 CEST 2005

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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