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grid_scripts's Introduction

Grid Scripts

qrun

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

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.

Usage

See Modes Below

    qstatus queues

    qstatus users [-q <queue>]

    qstatus jobs [-q <queue>] [-a|-u <user>]

Modes

Queues

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

Users

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

Jobs

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

qwait simply waits for a job to complete, optionally printing "." every 60 seconds.

Usage

    qwait [-q] <job_id>

Options

  • -q -- suppress progress dots
  • <job_id> -- the number (or name) of the job you want to wait for.

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