snakemake/snakemake-executor-plugin-slurm
A Snakemake executor plugin for submitting jobs to a SLURM cluster
PythonMIT
Issues
- 5
- 4
Running snakemake in a SLURM job context
#113 opened by visze - 1
- 1
- 0
- 4
How to set CommonSettings from command line?
#73 opened by choosehappy - 3
Dynamic determination of queue
#61 opened by johanneskoester - 3
- 1
Prevent job name overwrite by users
#90 opened by cmeesters - 2
- 2
Preempted jobs are spawned multiple times
#109 opened by gtsitsiridis - 6
Separately logging stdout and stderr
#95 opened by bentyeh - 13
Select partition automatically
#106 opened by SilasK - 0
Log file and comment string are not escaped
#105 opened by denisalevi - 2
- 5
- 12
Invalid --distribution specification?
#103 opened by brantfaircloth - 3
option to set the log directory?
#94 opened by jbloom - 1
Missing period or newline in status message when a SLURM job returns a failed status
#82 opened by xapple - 5
Unsuccessful attempt to use "srun" after job submission leads to abort of jobs
#91 opened by Robin1em - 3
`--cache` is ignored when using the executor
#46 opened by jlanga - 4
Wildcards missing from comments
#85 opened by mrvollger - 3
- 1
- 7
- 14
- 15
- 3
- 7
Inheriting cpus-per-task in srun (Slurm 22.05+)
#41 opened by paudano - 4
- 3
- 3
- 3
Dynamic runtime resource fails with SLURM
#62 opened by nikostr - 8
- 7
Differences in SLURM command between what Snakemake says it runs and what is actually run
#57 opened by stefmldk - 3
- 3
- 3
Missing support for --clusters option
#53 opened by meliamne - 4
TypeError: SpawnedJobArgsFactory.general_args() got an unexpected keyword argument 'executor_common_settings'
#54 opened by Parkerdow - 1
main.py: error: argument --executor/-e: invalid choice: 'slurm-jobstep' (choose from 'local', 'dryrun', 'touch')
#50 opened by Carsten-Ke - 15
`sbatch` call does not escape quotes in `exec_job`
#29 opened by ebete - 6
setting ntasks for non-MPI jobs
#40 opened by tatumdmortimer - 5
Usefulness of this plugin
#30 opened by mlarjim - 13
Slurm doesn't exit on completion
#33 opened by Ulthran - 3
- 3
- 3
- 3
add human job name with wildcards
#34 opened by sravel - 0
- 3