<html><head></head><body>possibly. Make sure PATH includes /usr/local/bin and LD_LIBRARY_PATH includes the path where libmd_<a href="http://mpi.so">mpi.so</a> and libgmx_<a href="http://mpi.so">mpi.so</a> are located.<br>
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try using mdrun -v and > somelogfile after the mpirun line (like mpirun blah -np 8 mdrun -v -deffnm etcetc > mpilog). the contents of mpilog will tell you what mpi is trying to do...<br>
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Sent from my Android phone with K-9 Mail. Please excuse my brevity.<br><br><div class="gmail_quote">Andrew DeYoung <adeyoung@andrew.cmu.edu> wrote:<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<pre style="white-space: pre-wrap; word-wrap:break-word; font-family: monospace">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 />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 />executab
le, 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 col
leagues
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 /><br />Andrew DeYoung<br />Carnegie Mellon University<br /><br />-- <br />gmx-users mailing list gmx-users@gromacs.org<br /><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br />Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br />Please don't post (un)subscribe requests to the list. Use the <br />www interface or send it to
gmx-users-request@gromacs.org.<br />Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists">http://www.gromacs.org/Support/Mailing_Lists</a><br /></pre></blockquote></div></body></html>