Actually I am trying to do REMD(Replica Exchange Molecular Dynamics) on my system , which needs MPI for parallel calculation. But I want to know how can I enable MPI for all the 4 processors in my CPU for parallel calculation. Also, what does this error means :-<div>
<span style>Fatal error:</span><br style><span style>> The number of nodes (1) is not a multiple of the number of simulations (4)</span><br style><font color="#500050" face="arial, sans-serif"><br></font><div><br></div>
<div><br><div class="gmail_quote">On Sat, Feb 11, 2012 at 7:32 AM, Reuti <span dir="ltr"><<a href="mailto:reuti@staff.uni-marburg.de">reuti@staff.uni-marburg.de</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi,<br>
<br>
Am 10.02.2012 um 05:51 schrieb bharat gupta:<br>
<div class="im"><br>
> I have installed MPICH as per the instruction mentioned in README file for using it in gromacs. After executing the command :<br>
><br>
> mdrun_mpi mdrun -np 4 -s prefix_.tpr -multi 4 -replex 1000<br>
><br>
> I am getting the following error :-<br>
><br>
> Fatal error:<br>
> The number of nodes (1) is not a multiple of the number of simulations (4)<br>
><br>
><br>
> I asked the for help in gromacs user list and they replied that :<br>
><br>
> If mdrun is reporting the number of nodes is 1, then you have not configured your MPI environment correctly so that it knows how many processors you have available. You will need to solve this by reading your MPI documentation.<br>
><br>
> I have also checked my installation by running the following command on MPICH :-<br>
><br>
> [root@BHARATPC mpich2-1.4.1p1]# mpiexec -n 4 ./examples/cpi<br>
> Process 0 of 4 is on BHARATPC<br>
> Process 1 of 4 is on BHARATPC<br>
><br>
> Process 2 of 4 is on BHARATPC<br>
><br>
> Process 3 of 4 is on BHARATPC<br>
> pi is approximately 3.1415926544231239, Error is 0.0000000008333307<br>
> wall clock time = 0.000447<br>
><br>
> I am having 4 processors in my PC. I want to know how to configure MPI to recognize these 4 processors, so that I can use it in gromacs . Please help in this regard<br>
<br>
</div>Although it should work with MPI: if you use only one machine you don't need MPI any longer as they implemented to use threads in Gromacs. Please have a look at the option -nt to mdrun in their man page.<br>
<span class="HOEnZb"><font color="#888888"><br>
-- Reuti<br>
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</font></span></blockquote></div><br><br clear="all"><div><br></div>-- <br>Bharat<br>Ph.D. Candidate<br>Room No. : 7202A, 2nd Floor<br>Biomolecular Engineering Laboratory<br>Division of Chemical Engineering and Polymer Science<br>
Pusan National University<br>Busan -609735<br>South Korea<br>Lab phone no. - +82-51-510-3680, +82-51-583-8343<div>Mobile no. - 010-5818-3680<br>E-mail : <a href="mailto:monu46010@yahoo.com" target="_blank">monu46010@yahoo.com</a></div>
<br>
</div></div>