Runner

There are two runners supported: LocalRunner and SGERunner.

The first one submits the job locally and uses local CPUs/GPUs, and the second one uses grid CPUs/GPUs.

Local runner

It is easy to initialize a local runner: runner = LocalRunner()

SGE runner

But to initialize an sge runner, you need pass in a couple of arguments, which will be translated as command line arguments for qsub.

For example:

from plkit import SGERunner

sge = SGERunner(o='/path/to/stdout')
# will be calling qsub like this:
# $ qsub -o /path/to/stdout

You can also specify the path to the qsub executable and the path to a workdir for the runner to save the outputs, errors and scripts for each jobs:

Note

The job is submitted in background, and the main process will be then streaming the stdandard output from the job. You may have to end the program yourself after it's done.

sge = SGERunner(qsub='/path/to/qsub', workdir='/path/to/workdir')