Thanks Justin for your advice, it was one of the mpi flags only which caused the error.<br><br>regards,<br>Vivek<br><br><div class="gmail_quote">On 27 May 2011 17:39, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div><div></div><div class="h5"><br>
<br>
vivek sharma wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
HI GMX-users,<br>
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<br>
---------------------<br>
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 &<br>
-----------------------<br>
\<br>
I am firing this run on a cluster. after firing the command teh simulation is crashing with following error reported in err_1 file.<br>
---------------------<br>
Program mdrun_d, VERSION 4.5.4<br>
Source code file: main.c, line: 420<br>
<br>
Fatal error:<br>
The number of nodes (1) is not a multiple of the number of simulations (10)<br>
For more information and tips for troubleshooting, please check the GROMACS<br>
website at <a href="http://www.gromacs.org/Documentation/Errors" target="_blank">http://www.gromacs.org/Documentation/Errors</a><br>
----------------------<br>
<br>
Can anybody comment or suggest the reason for such error.<br>
<br>
</blockquote>
<br></div></div>
You're only running on one processor. You probably need "mpirun -np 40" rather than just "mpirun" in the command.<br>
<br>
-Justin<br>
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
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