qrun is a simplified method for submitting a set of related commands to the grid, inspired by gnu parallel. Using a command template and a tab-delimited input you can submit a batch job to run the script for each line of the input file.
For Example:
echo >>_options
Alex sheep great
Dan cows yummy
Bill cockroaches gross
_options | qrun -P 1010 -c 'echo "{1} says {2} are {3}'
Will start three grid jobs, with the output:
Alex says sheep are great
Dan says cows are yummy
Bill says cockroaches are gross
Run qrun --man
for full documentation.
If you want to see what would be run, use qrun --dry_run
. If you want details on what is run (with output to STDERR) use qrun -v
qstatus is a wrapper around SGE qstat to give more detailed information about running and queued jobs. Beyond having nicer output, it differs from qstat -g by also showing queued jobs and by summing by slot(node) rather by job, and by showing entire job names, instead of truncating them.
See Modes Below
qstatus queues
qstatus users [-q <queue>]
qstatus jobs [-q <queue>] [-a|-u <user>]
Summary of jobs per queue
$ qstatus queues
Queue Load Total Available Disabled Running Error Queued
default.q 0.94 704 0 0 704 2 125865
fast.q 0.01 48 48 0 0 0 0
himem.q 0.11 196 165 0 31 0 0
interactive.q 0.03 40 23 0 17 0 0
medium.q 0.01 816 814 0 2 0 0
Summary of jobs by user by queue, optionally filtered by queue
$ qstatus users -q default.q
User Queue Running Pending Error
razrichter default.q 703 125858 0
inger default.q 0 3 0
bwayne default.q 0 4 0
estark default.q 0 0 2
sauron default.q 1 0 0
Summary of jobs by job-id, optionally filtered by user and queue
By default, filtered for only your jobs
$ qstatus jobs -u razrichter
Job-ID Owner Queue r Job-Name
5264368 razrichter himem.q 8 mira e_coli
5264370 razrichter normal.q 1 bwa
qwait simply waits for a job to complete, optionally printing "." every 60 seconds.
qwait [-q] <job_id>
- -q -- suppress progress dots
- <job_id> -- the number (or name) of the job you want to wait for.