Canu's Grid support

[danejo3]

https://canu.readthedocs.io/en/latest/parameter-reference.html

Grid Engine Support

Canu directly supports most common grid scheduling systems. Under normal use, Canu will query the system for grid support, configure itself for the machines available in the grid, then submit itself to the grid for execution. The Canu pipeline is a series of about a dozen steps that alternate between embarrassingly parallel computations (e.g., overlap computation) and sequential bookkeeping steps (e.g., checking if all overlap jobs finished). This is entirely managed by Canu.

Canu has first class support for the various schedulers derived from Sun Grid Engine (Univa, Son of Grid Engine) and the Simple Linux Utility for Resource Management (SLURM), meaning that the developers have direct access to these systems. Platform Computing’s Load Sharing Facility (LSF) and the various schedulers derived from the Portable Batch System (PBS, Torque and PBSPro) are supported as well, but without developer access bugs do creep in. As of Canu v1.5, support seems stable and working.

useGrid <boolean=true>
Master control. If ‘false’, no algorithms will run under grid control. Does not change the value of the other useGrid options.

If ‘remote’, jobs are configured for grid execution, but not submitted. A message, with commands to launch the job, is reported and canu halts execution.

Note that the host used to run canu for ‘remote’ execution must know about the grid, that is, it must be able to submit jobs to the grid.