Use With a Scheduler

Sun/Open Grid Engine

The --scheduler SGE argument allows one to use pyani with an an SGE-type scheduler.

In order for this work, one must be able to submit jobs using the qsub command. By default, this will batch the pairwise comparisons in array jobs of 10,000, in order to avoid clogging the scheduler queue. Each comparison will be run as a single-core task in an array job.

Arguments assigned by Pyani

The following arguments will be automatically set:

-N job_name  # this is the value passed to `--name`
 -o ./stdout  # cwd/ + "stdout"
 -e ./stderr  # cwd/ + "stderr"

Modifiable arguments

The number of pairwise comparisons submitted per chunk can be modified using:

--SGEgroupsize *number*

The job prefix to use can be modified using:

--jobprefix *prefix*

Specifying additional arguments

Additional SGE arguments may be specified with:

--SGEargs "<your arguments here>"

Additional arguments must be specified as a string which includes all flags and their values. For instance, to specify a value for the memory resource:

"-l h_mem=64G"

Or for both memory and run time:

"-l h_mem=64G -l h_rt=02:00:00"

An alternative to listing all desired options on the command line is to pass an optionfile:

"-@ optionfile"

This file only contains comments and the flags to be passed (do not include the #$ in front of the arguments):

# Memory to assign to the job
 -l h_mem=64G

 # Time to allow for job HH:MM:SS
 -l h_rt=10:20:00

 # Notification email address

 # Send notifications when job 'b'egins, 'a'borts (or is rescheduled), 'e'nds, or is 's'uspended
 -m baes

For more information on using an SGE/OGE scheduler, see:


Support for the SLURM scheduler is forthcoming.