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Hi, I was having this same problem. I tried running like this: /opt/mpich/intel/bin/mpirun -v -np $NPROC -machinefile \$TMPDIR/machines ~/gromacs-mpi/bin/mdrun -np $NPROC -s $CONF -o $CONF -c After$CONF -e $CONF -g $CONF >& $CONF.job mpirun with the -v option (I'm not exactly sure what that does, but it seemed to circumvent the problem). But then I got another problem. GMX seems to start up ok, but then stalls. I just posted to the group about this, you should have it in your inbox soon. If this helps, and you do get GMX running in parallel, please let me know. thanks, Arneh Sridhar Acharya wrote: But lamd is very well running, because I could get the status of lam nodes with the "lamnodes" command. ######################################################################################## [EMAIL PROTECTED] WT_SINGLE_PARALLEL]$ lamnodes n0 cdfd-grid-node2:1: n1 cdfd-grid-node4:1: n2 cdfd-grid-node12:1: n3 cdfd-grid-node13:1: n4 cdfd-grid-node14:1: n5 cdfd-grid-node16:1: n6 cdfd-grid-node17:1:origin,this_node ########################################################################################### Do I have to define any paths so that it could recognise this? Waiting for your suggessions. sridharHi All, I am facing a problem for parallel mdrun. I tried to run in 2 nodes with the following command. The program reports that lamd is not running as follows. #################################################################################################### mpirun -np 2 /users/soft/GromacsSingle/bin/mdrun_mpi -s b4em_1CYP_WT.tpr -o em_1CYP_WT.trr -np 2 ----------------------------------------------------------------------------- It seems that there is no lamd running on this host, which indicates that the LAM/MPI runtime environment is not operating. The LAM/MPI runtime environment is necessary for MPI programs to run (the MPI program tired to invoke the "MPI_Init" function).Please run the "lamboot" command the start the LAM/MPI runtime environment. See the LAM/MPI documentation for how to invoke "lamboot" across multiple machines. ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- It seems that [at least] one of the 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. ----------------------------------------------------------------------------- ################################################################################################## _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php |
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