The command I used this time :-<br><br>mdrun_mpi mdrun -s prefix_.tpr -multi 5 -replex 100<br><br><br>Here's the error that I got :-<br><br>Fatal error:<br>The number of nodes (1) is not a multiple of the number of simulations (5)<br>
For more information and tips for troubleshooting, please check the GROMACS<br>website at <a href="http://www.gromacs.org/Documentation/Errors">http://www.gromacs.org/Documentation/Errors</a><br>-------------------------------------------------------<br>
<br>"Look at these, my work-strong arms" (P.J. Harvey)<br><br>Halting program mdrun_mpi<br><br>gcq#345: "Look at these, my work-strong arms" (P.J. Harvey)<br><br>application called MPI_Abort(MPI_COMM_WORLD, -1) - process 0<br>
<br><br><div class="gmail_quote">On Thu, Jan 12, 2012 at 3:53 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 5:45 PM, bharat gupta wrote:
<blockquote type="cite">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" target="_blank">.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>
</blockquote>
<br></div>
You can't be getting an identical error, the numbers are different
now.<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>
If you have only four processors, you will not be able to run
efficient REMD on five replicas, even if you can work out how to get
MPI to over-allocate MPI processes to your physical processors.<br>
<br>
Please copy and paste command line and error together, so that
people who might help don't feel like they might be wasting their
time guessing. They have other things to do. Your example input
below did not produce your error below, because 20 != 3.<div><div class="h5"><br>
<br>
Mark<br>
<br>
<blockquote type="cite"><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" target="_blank">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> 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><font color="#888888"><br>
<br>
Mark</font></span>
<div>
<div><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>
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Ph.D. Candidate<br>
Room No. : 7202A, 2nd Floor<br>
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-- <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>
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<br>--<br>
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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>
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