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<div>Try using the mpi submissions flags with just a test submission, you might have to look at the stats after 15 minutes though, as I do not know what would happen if it was not compiled with mpi (if they work or not), but they would make a noticable difference.</div>
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<div>just a suggestion, there might be an easier way.</div>
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<div>Stephan Watkins</div>
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<div style="margin:0 0 10px 0;"><b>Gesendet:</b> Sonntag, 24. November 2013 um 23:13 Uhr<br/>
<b>Von:</b> "Andrew DeYoung" <adeyoung@andrew.cmu.edu><br/>
<b>An:</b> gmx-users@gromacs.org<br/>
<b>Betreff:</b> [gmx-users] How can I tell whether or not Gromacs was compiled with MPI?</div>
<div name="quoted-content">Hi,<br/>
<br/>
I am running Gromacs version 4.5.5. However, I did not compile it myself;<br/>
the system administrator did many months ago. I have been running<br/>
"standard" MD simulations (i.e., no replica exchange) over the 24 cores that<br/>
are available on the node. To run "standard" MD, I just call mdrun directly<br/>
-- without referencing MPI or mpirun (at least not explicitly) -- using a<br/>
command like this:<br/>
<br/>
mdrun -v -s topol.tpr -nt 24<br/>
<br/>
>From looking at the old release notes, it looks like this "thread-based<br/>
parallelization" was introduced sometime in version 4.5 (maybe from the<br/>
beginning of version 4.5?). As the page<br/>
<a href="http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.5.x" target="_blank">http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.5.x</a> says,<br/>
<br/>
"Running on a multi-core node now uses thread-based parallelization to<br/>
automatically spawn the optimum number of threads in the default build. MPI<br/>
is now only required for parallelization over the network."<br/>
<br/>
Now, however, I want to run replica exchange simulations. I have no<br/>
experience with such simulations, but the page<br/>
<a href="http://www.gromacs.org/Documentation/How-tos/REMD" target="_blank">http://www.gromacs.org/Documentation/How-tos/REMD</a> says:<br/>
<br/>
"REMD with any version of GROMACS requires mdrun compiled with MPI (i.e. not<br/>
threading), and that the number of processors be a multiple of the number of<br/>
replicas."<br/>
<br/>
But, my question is, how can I tell whether Gromacs was compiled with MPI?<br/>
Probably it was not compiled with MPI, since I am using threading, but how<br/>
can I be sure?<br/>
<br/>
Thanks so much for your time!<br/>
<br/>
Andrew DeYoung<br/>
Carnegie Mellon University<br/>
<br/>
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