A reviewer ran into error due to slurm related issues when slurmpy attempts to submit the parent quac job to slurm.
We believe we fixed a variation of this issue in #73 where snakemake would be submitting jobs to slurm. Ideally we should have fixed above issues as part of that PR, but we didn't catch it back then.
Planned solution:
When CLI script gathers slurm args to use with parent quac job submission to slurm:
add a step to read cluster config file and include any args that are not already in slurm_resources
Remove default for --cluster_config and force user to provide it manually. Its help message will instruct the user to use configs/cluster_config.json as template and edit to match their slurm environment. We think this will let user take a second and set up the configs as needed.
Update docs to include example on how to edit cluster config to match user's slurm env.
A reviewer ran into error due to slurm related issues when slurmpy attempts to submit the parent quac job to slurm.
We believe we fixed a variation of this issue in #73 where snakemake would be submitting jobs to slurm. Ideally we should have fixed above issues as part of that PR, but we didn't catch it back then.
Planned solution:
add a step to read cluster config file and include any args that are not already in
slurm_resources
--cluster_config
and force user to provide it manually. Its help message will instruct the user to useconfigs/cluster_config.json
as template and edit to match their slurm environment. We think this will let user take a second and set up the configs as needed.