ok here the pbs file for the job #!/bin/bash #PBS -l nodes=1:ppn=1 #PBS -l walltime=00:01:59 #PBS -o output.out #PBS -j oe #PBS -N mdrun WORK_HOME=/auto/hpc-08/knomura/choubey/GROMACS/test cd $WORK_HOME source /usr/usc/mpich/default/setup.sh mdrun_mpi -v -s em -o em -c after_em -g emlog
Is my command line wrong? On Tue, Sep 15, 2009 at 6:25 PM, Justin A. Lemkul <[email protected]> wrote: > > > Amit Choubey wrote: > >> Hi everyone, >> >> I have the gromacs mpi version on my system and everything in the >> simulation works fine until i get to mdrun_mpi and when i use this >> executable the following pops error comes up >> >> MX:hpc-login2:mx_init:querying driver:error 5(errno=2):No MX device entry >> in /dev. >> >> Then i tried the to do mdrun_mpi -h on the terminal and the same thing >> comes out. >> >> MX:hpc-login2:mx_init:querying driver:error 5(errno=2):No MX device entry >> in /dev. >> >> Is this an installation problem? I am also not able to find the online >> manual for mpi version of gromacs, could someone send me the link? >> >> > Because MPI only applies to mdrun, so there's no need for a separate > manual. All the information for mdrun applies to mdrun_mpi, except that it > can be executed in parallel. > > It looks like there is either a problem with the MPI implementation of the > machine, or you're calling the command wrong. If you can post your command > line or the contents of whatever submission script you might be using, we > might be able to implicate (or rule out) the latter. > > -Justin > > Thank you, >> Amit >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> gmx-users mailing list [email protected] >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before >> posting! >> Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to [email protected]. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > _______________________________________________ > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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