How do I use the submit to the single-user batch queue? (qsub)

qsub   --   submit an executable to run in single-user mode on a single-user machine

SYNOPSIS

qsub [ options ] executable & parameters

qsub will execute the given executable on a single-user machine using your account once the machine can be placed in single-user mode. The purpose is to allow a parallel program developer to test the performance of her/his code on a parallel machine without interference from other jobs. The intended use is to use this batch script for short running jobs to get immediate single-user access, even during the work day.

You can supply your executable with parameters, just as if you executed a command line.

-m machine	single-user machine to run your job on (currently runs on lagavulin)
-d run-directory	directory to run your executable in
-omp	number of OpenMP threads, sets OMP_NUM_THREADS
-np	number of processors, sets NTASK used by mpi
-t	maximum time to allow your code to execute, default is 5 minutes
-csh -sh -tcsh -ksh	You may specify a subshell to execute your executable in, such as '/bin/sh myshellscript'
-p	copy path; by default, all environment variables other than path and LD_LIBRARY_PATH, host, and pwd variables are copied. If you also want the two path variables to be copied then include the -p option.

executable & parameters
After the options you must include an executable, which can be any executable file. It can be a script that sets certain environment variables and executes an executable or a script that executes several executables, or just an executable file.
If parameters are necessary for the executable then just place them after the executable as you would on the command line. For example,

qsub run.seis.sh -ds test -ph 1 -timex

qsub will set up a script to execute your executable on the single-user machine. The script is given the a name:
${USER}_${MACHINE}_${EXECUTABLE}_#
The script is placed in the queue directory. The first part of the script sets up your environment to be the same as the one in which you executed qsub.
The second part of the script will execute your executable in a subshell (if you specified one.) If you do not specify a full path for the executable, qsub will either use the executable given relative to directory that qsub was executed in, or the executable in the run directory (if a run directory is given.) For example,
1. I execute qsub in my directory, ~/bench, to run the executable exec.sh in a run directory of /tmp/mytemp:

qsub -d /tmp/mytemp exec.sh
2. Since I did not give a full path name of exec.sh qsub will attempt to find an exec.sh in the specified run directory (/tmp/mytemp). If /tmp/mytemp/exec.sh does not exist then it will assume I meant exec.sh in the directory from which I ran qsub (~/bench/exec.sh).

qsub will create the specified run directory if it does not already exist.

Your job will be killed using at -s KILL after the MAXTIME specified (or 5 minutes by default) from the time your script begins to execute.

NOTE: you must have your account set up to allow sut to log in as you. sut will do the following to run the script that qsub creates:

ssh ${MACHINE} -l ${USER} ${QUEUE_SCRIPT}
If you have ssh set up in your account, copy: ~sut/.ssh/identity.pub to your ~/.ssh/authorized_keys . If you don't mind people logging into your account then just use .rhosts .

The qsub script will assign a job name to your submitted job and place it in the queue directory to be run by the single-user queue monitor. When completed, the stdout and stderr will be mailed to you. The job script will be placed in the completed-queue folder.

/home/peak/a/sut/suQueue the queue folder holding jobs not yet executed.

/home/peak/a/sut/suQueue_completed where all the completed jobs get placed.

/home/peak/a/sut/suQ_sh/qsub

/home/peak/a/sut/suQ_sh/suQ-monitor.sh