[gmx-users] Error while trying REMD on cluster

[Justin A. Lemkul]

vivek sharma wrote:
> HI GMX-users,
>  I am trying to run a REMD simulation on my system. I have created 10 
> .tpr files and fired the simulation using the following command
> ---------------------
> bsub -n 40 -o out_1 -e err_1 mpirun mdrun_d -s MD.tpr -multi 10 -replex 
> 2 -o MD.trr -e MD.edr -g MD.log -c MD.gro &
> -----------------------
> \
>  I am firing this run on a cluster. after firing the command teh 
> simulation is crashing with following error reported in err_1 file.
> ---------------------
> Program mdrun_d, VERSION 4.5.4
> Source code file: main.c, line: 420
> 
> Fatal error:
> The number of nodes (1) is not a multiple of the number of simulations (10)
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> ----------------------
> 
> Can anybody comment or suggest the reason for such error.
> 

You're only running on one processor.  You probably need "mpirun -np 40" rather 
than just "mpirun" in the command.

-Justin

-- 
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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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