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Executing mpirun commands

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Old 02-11-2004
Executing mpirun commands
Basically, I would like to run an mpirun query on my web server to query your databases via yours when using the BLAST program, however the server seems not able to execute even basic mpirun programs such as cpi (to calculate pi). Are there any settings I should take note of?

I am running Perl CGI scripts via the Apache v1.3.28 server in a Unix environment, is there settings that should be taken care of when running command line in this particular case for mpirun (the script alias has already been set up - ScriptAliasMatch .../cgi-bin/... /usr/users/$1/public_html/cgi-bin/$2) :

The line in Perl script is :
`/usr/local/apps/mpich/bin/mpirun -machinefile /usr/users/utess/machines.ALPHA -np 2 /usr/local/apps/mpich/examples/cpi -o /usr/local/d.txt 2> /usr/local/err.txt`;

The relevant error is :
/usr/local/apps/mpich/bin/mpirun: pwd: read error in ..
/usr/local/apps/mpich/bin/mpirun: test: argument expected

Is there anything that should be taken care of when running scripts of this nature? Even when "nobody" user account has been set to a writable directory such that I could execute the command in "nobody"'s account I still could not execute the command via Perl script.

Is it a problem with the server configuration since "nobody"'s account can execute the command?

I really would appreciate any help.
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LEARN ABOUT DEBIAN

orte-clean

orte-clean(1)							     Open MPI							     orte-clean(1)

NAME

       orte-clean - Cleans up any stale processes and files leftover from Open MPI jobs.

SYNOPSIS

       orte-clean [--verbose]
       mpirun --pernode [--host | --hostfile file] orte-clean [--verbose]

OPTIONS

       [-v | --verbose] This argument will run the command in verbose mode and print out the universes that are getting cleaned up as well as pro-
       cesses that are being killed.

DESCRIPTION

       orte-clean attempts to clean up any processes and files left over from Open MPI jobs that were run in the past as  well	as  any  currently
       running jobs.  This includes OMPI infrastructure and helper commands, any processes that were spawned as part of the job, and any temporary
       files.  orte-clean will only act upon processes and files that belong to the user running the orte-clean command.  If run as root, it  will
       kill off processes belonging to any users.

       When run from the command line, orte-clean will attempt to clean up the local node it is run from.  When launched via mpirun, it will clean
       up the nodes selected by mpirun.

EXAMPLES

       Example 1: Clean up local node only.

       example% orte-clean

       Example 2: To clean up on a specific set of nodes specified on command line, it is recommended to use the pernode option.   This  will  run
       one orte-clean for each node.

       example% mpirun --pernode --host node1,node2,node3 orte-clean

       To clean up on a specific set of nodes from a file.

       example% mpirun --pernode --hostfile nodes_file orte-clean

       Example 3: Within a resource managed environment like N1GE, SLURM, or Torque.  The following example is from N1GE.

       First, we see that we have two nodes with two CPUs each.

       example% qsh -pe orte 4
       example% mpirun -np 4 hostname
       node1
       node1
       node2
       node2

       Clean up all the nodes in the cluster.

       example% mpirun --pernode orte-clean

       Clean up a subset of the nodes in the cluster.

       example% mpirun --pernode --host node1 orte-clean

SEE ALSO

       orterun(1), orte-ps(1)

1.4.5								   Feb 10, 2012 						     orte-clean(1)