[gmx-users] Error while trying REMD on cluster

[vivek sharma]

Thanks Justin for your advice, it was one of the mpi flags only which caused
the error.

regards,
Vivek

On 27 May 2011 17:39, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
> --
> ========================================
>
> 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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