Linux

This plugin requires a configuration file to be prepared in advance. This is a plain text file that is located in your home directory as ~/.CPRynner.

It contains a few parameters that are used for remote job submission:

• cluster_address= - the domain name of the cluster;
• username= - you cluster username;
• tasks_per_node= - the maximum number of tasks a single node should accept, do not be greedy;
• setup_script= - a setup script that runs before the job, pre-loads Python libraries/CellProfiler module;
• work_dir= - the directory storing all data files;
• max_runtime= - the maximum possible runtime for a given job on the cluster, any other value provided via GUI has to be smaller than this one.

A typical script of a Supercomputing Wales user looks like this:

cluster_address=sunbird.swansea.ac.uk
username=s.user.name
tasks_per_node=40
setup_script="module load cellprofiler"
work_dir=/scratch/s.user.name/
max_runtime=72