Mapped missing Slurm job state codes

[stuvet]

Expected Behaviour

• Use of the default makeClusterFunctionsSlurm function would map all job state codes returned by squeue to reasonable defaults for general purpose.

Problem

• Unmapped Slurm job state codes in makeClusterFunctionsSlurm were resulting in an NA status returned by getStatusTable, triggering errors downstream or leaving running jobs orphaned by batchtools.

Mapping Strategy

• Full list of Slurm job state codes available here

Queued

• Job is awaiting reources, the infrastructure is being configured/booted, or the job has been requeued.
  • PD,CF,RF,RH,RQ,SE

Running

• Job is running, suspended, completing or otherwise retaining CPU resources, including resizing, being signalled, staging outfiles or in the 'stopped' state.
  • R,S,CG,RS,SI,SO,ST

Expired

• RD (RESV_DEL_HOLD) was initially mapped to queued, but querying squeue by status=RD throws an error on slurm v20.11.4, so left unhandled to result in an expired status.
• Job is not anticipated to require resources in the future, including failure of infrastructure, exit code, cancellation, completion, out of memory, preemption, & timeout.
  • BF,CA,CD,DL,F,NF,OOM,PR,RV,TO,RD

Custom Mapping

• This commit will solve the majority of errors caused by running squeue at the wrong moment, when an unmapped job state code for a running job would trigger batchtools to report an incorrect expired status.
• This commit will not solve all infrastructure-specific issues, for instance where Slurm requeues jobs after preemption. Users that need finer control over mapping could try the default makeClusterFunctions