It says that "The number of cores must be a multiple of the number of replicas (given with <code>-multi</code>, which must equal the number of <a title="Documentation/File_Formats/Topology_(.tpr)_File" rel="internal" href="http://www.gromacs.org/Documentation/File_Formats/Topology_%28.tpr%29_File">.tpr</a> files i.e., 10 for the above general example using <code>prefix_0.tpr</code> through <code>prefix_9.tpr</code>)"<br>
<br>I gave the options -multi 5 . But still I am getting the same error. Can you please explain, why is it so. Do I need to have the same no. of cores as the no. of .tpr files ??<br><br><div class="gmail_quote">On Thu, Jan 12, 2012 at 3:38 PM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000"><div class="im">
On 12/01/2012 5:29 PM, bharat gupta wrote:
<blockquote type="cite">Thanks for the advice I re-complied everything again
with static libraries and the installation went fine. But while
executing the following command I am again getting error :- <br>
<br>
<br>
mdrun_mpi mdrun -s prefix_.tpr -multi 20 -replex 500 -v <br>
<br>
<br>
Fatal error:<br>
The number of nodes (1) is not a multiple of the number of
simulations (3)<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>
"BioBeat is Not Available In Regular Shops" (P.J. Meulenhoff)<br>
<br>
Halting program mdrun_mpi<br>
<br>
gcq#155: "BioBeat is Not Available In Regular Shops" (P.J.
Meulenhoff)<br>
<br>
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 0<br>
<br>
<br>
I am trying to simulate 5 replicas and I have 4 cpu . <br>
</blockquote>
<br></div>
See <a href="http://www.gromacs.org/Documentation/How-tos/REMD" target="_blank">http://www.gromacs.org/Documentation/How-tos/REMD</a>
Execution Steps point 2. You cannot simulate an arbitrary number of
replicas on an arbitrary number of processors.<span class="HOEnZb"><font color="#888888"><br>
<br>
Mark</font></span><div><div class="h5"><br>
<br>
<blockquote type="cite"><br>
<br>
<br>
<div class="gmail_quote">On Thu, Jan 12, 2012 at 1:37 PM, lina <span dir="ltr"><<a href="mailto:lina.lastname@gmail.com" target="_blank">lina.lastname@gmail.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div>On Thursday 12,January,2012 08:54 AM, bharat
gupta wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi,<br>
<br>
I am trying to run a REMD of a peptide. But while
executing the<br>
following command after nvt and npt equilibration , I am
getting the<br>
following error:-<br>
<br>
mdrun_mpi mdrun -s prefix_.tpr -multi 20 -replex 1000<br>
mdrun_mpi: error while loading shared libraries:
libgmx_mpi.so.6: cannot<br>
enable executable stack as shared object requires:
Permission denied<br>
</blockquote>
<br>
</div>
Can you run a normal md smoothly?<br>
try:<br>
mdrun_mpi mdrun -deffnm prefix_0<br>
<br>
if it works, then some of your trajectories not sound. means
system does not equilibrium well.
<div><br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
<br>
Can anybody suggest me how could I rectify this error.<br>
<br>
--<br>
Bharat<br>
<br>
</blockquote>
<br>
</div>
<div>
<div>
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<br>
-- <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
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<br>
<br>
<fieldset></fieldset>
<br>
</blockquote>
<br>
</div></div></div>
<br>--<br>
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Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br></blockquote></div><br><br clear="all"><br>-- <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>