Other grid worker options

Some java options can be set specifically for grid workers. This is done by creating a file called:

clcgridworker.vmoptions

and placing it in the same folder as the deployed clcgridworker script, that is, within the folder specified in the Path to CLC Grid Worker field of the grid preset.

Options that may be of particular use for grid workers include:

For example, if a clcgridworker.vmoptions was created, containing the following two lines, it would, for the CLC Grid Worker specified in a given preset, set memory limits for the CLC Server java process and set a temporary directory for the grid nodes, overriding defaults that would otherwise apply:

-Xmx1000m
-Djava.io.tmpdir=/path/to/tmp

Each grid preset can have its own clcgridworker.vmoptions file. So, for example, a different memory limit for the CLC Server java process could be specified for different presets. This could be useful where separate queues are used for low overheads tasks, such as import jobs and trimming jobs, and high overhead tasks, such as de novo assemblies or read mappings.