<br><br><div class="gmail_quote">On Sat, Apr 28, 2012 at 10:22 PM, Andrew DeYoung <span dir="ltr"><<a href="mailto:adeyoung@andrew.cmu.edu" target="_blank">adeyoung@andrew.cmu.edu</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>
Typically, I use Gromacs 4.5.5 compiled with automatic threading. As you<br>
know, automatic threading is awesome because it allows me to start parallel<br>
runs without calling mpirun. So on version 4.5.5, I can start a job on eight<br>
CPUs using simply the command:<br>
<br>
mdrun -s topol.tpr -nt 8<br>
<br>
However, now I am using a different node on my department's cluster, and<br>
this node instead has Gromacs 4.5.4 (compiled without automatic threading).<br>
So, I must use mpirun to start parallel runs. I have tried this command:<br>
<br>
mpirun -machinefile mymachines -np 8 mdrun -s topol.tpr<br>
<br></blockquote><div><br></div><div>I suppose this mdrun executable is not mpi-enabled. Have you compiled mdrun with "--enable-mpi" option?</div><div><br></div><div>-Anirban </div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
where mymachines is an (extensionless) file containing only the text "c60<br>
slots=8". (c60 is the name of the node that I am using.)<br>
<br>
I get this error message:<br>
<br>
"Missing: program name. Program mdrun either does not exist, is not<br>
executable, or is an erroneous argument to mpirun."<br>
<br>
This is strange, because mdrun is, I think, in my path. For example, if I<br>
type "mdrun -h", I get the manual page for mdrun (version 4.5.4).<br>
<br>
Then I tried the command "which mdrun", and it gave me this output:<br>
<br>
/usr/local/gromacs/bin/mdrun<br>
<br>
So, next I tried to call mdrun via mpirun using the specific path for mdrun:<br>
<br>
mpirun -machinefile mymachines -np 8 /usr/local/gromacs/bin/mdrun -s<br>
topol.tpr<br>
<br>
This starts running my simulation, but when I look in "top", the simulation<br>
is only running on a single CPU; there is only one entry for mdrun in "top",<br>
and it has only %CPU=100 (not eight different entries for mdrun, nor one<br>
entry with %CPU=800). Also, the simulation is going at the speed I would<br>
expect for running on a single CPU -- it is very slow, so I am convinced<br>
that, as "top" suggests, mdrun is running on only one CPU.<br>
<br>
Strangely, my colleagues are able to run jobs in parallel using the exact<br>
commands that I described above. So apparently something is wrong with my<br>
user ID, although there are no error messages (except the error message<br>
about "Missing: program name" that I described).<br>
<br>
If you have time, do you have any suggestions for other things that I can<br>
try? Do you think that something could be wrong with my bashrc file?<br>
<br>
Thanks for your time!<br>
<span class="HOEnZb"><font color="#888888"><br>
Andrew DeYoung<br>
Carnegie Mellon University<br>
<br>
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