queuechunk(1) queuechunk(1) NAME queuechunk - Place a csh script file on a queue or kill a job SYNOPSIS queuechunk [options] <root name of script file> DESCRIPTION Queuechunk will take a csh script file and submit it to a cluster queue, and also allows such jobs to be removed from the queue. It is designed to perform these actions when it is called by Processchunks with csh files produced from IMOD command files with Vmstocsh. The script file will be deleted when the operation finishes. The filesystem on which Queuechunk is run must be accessible from the cluster. The script file must be named with the extension .csh. The last argu- ment of the command to Queuechunk must be the root name of the script file, excluding the extension .csh but including everything before the extension (-001, etc). If the action is L to report a load average, this argument may be omitted. Options -t <type> Type of queue. This option must be entered with the value of either pbs or pbs-maui (for a PBS queue) or sge (for a Grid Engine queue). The type pbs-maui can be used if the queue soft- ware has been configured so that showq -p queuename gives output for the processors assigned to that queue of the form 0 Active Jobs 0 of 40 Processors Active (0.00%) -q <name> Name of queue to submit to. This option must entered if the queue type is pbs-maui. -h <name> Name of the head node. When this option is entered, the qsub, qstat, and qdel operations are run via ssh to the head node. It is necessary to have passwordless access between machines for this to work. -w <dir> Name of the current working directory, as it must be used by the machine running the job. If this name contains spaces, they should be escaped with backslashes. The default is the current directory name. -a <action> The action to be performed: R - Run the job by placing it on the queue S - Run the job on the queue but synchronously, waiting until it is done K - Kill the job unconditionally P - Delete the job if it has not started yet (pause) L - Report a load average Specifications Here are the essential features of this script, which would have to replicated by any program to be run from Processchunks. In order to work from eTomo as well, the script mush be in bash. The program must accept the -w option with a working directory name. The program must accept the -a option with at least the four actions, R, S, K, and P. For running from eTomo, the program must also respond to the L action with either NA for no information, or one or more val- ues separated by commas. A secondary script file should be created to submit to the queue, with the name rootname.job. It should run rootname.csh with "csh -ef" and end by deleting the rootname.csh file. The .job file will be cleaned up by Processchunks. Output from the queue when the job is submitted should be placed into a file named rootname.qid. This file will also be cleaned up by Process- chunks. When a job is run with the S action, the program must not return until the job is finished, and should exit with an error status if the job failed. Queuechunk does this by submitting to the queue, but as an alternative, the .csh file could be run on the local host with "csh -ef". FILES The program creates a script file named rootname.job and places queue submission output into a file named rootname.qid. The job script deletes the rootname.csh file upon completion. AUTHOR David Mastronarde <mast at colorado dot edu> SEE ALSO processchunks, vmstocsh BL3DEMC 4.3.7 queuechunk(1)