Snakemake-Profiles / slurm

Cookiecutter for snakemake slurm profile

Snakemake-Profiles/slurm Issues

Compatibility with snakemake version 8.0 and higher
Updated 4 months ago11
Jobs submitted to cluster fail without explanation
Updated 4 months ago9
Specify only one output file
Updated 8 months ago
Error spam (list index out of range, could not query sidecar)
Closed a year ago4
Snakemake and Slurm
Updated a year ago1
sidecar crashes when parsing malformed response
Closed 2 years ago7
How do I make mem_mb_per_cpu work?
Updated a year ago8
Sidecar shuts down too early when pressing Ctrl-C
Updated a year ago1
slurm-status.py: could not query side car
Updated a year ago
using conda with config without global snakemake install
Closed 3 years ago4
Fails with many input files
Closed 2 years ago7
SLURM --tasks-per-node, --cpus-per-task, etc.
Updated 2 years ago2
`mem` setting in resource is not working due to default `mem_mb` argument is generated in latest version of snakemake
Updated 2 years ago3
Problems with Snakemake 5.6.0 standard resources
Updated 2 years ago4
slurm fails when log path contains a Wildcards string that is a directory
Closed 2 years ago8
How to use with MPI jobs?
Updated 2 years ago1
add more option on config.yaml
Closed 2 years ago2
Specifying GRES (gpu, local storage) and constraints
Closed 2 years ago1
sacct running continuously
Closed 2 years ago3
Profile not working well on AWS ParallelCluster with Slurm
Updated 2 years ago
cluster-status should use squeue --iterate
Closed 2 years ago3
Provided cores differ to what's passed in the CLI
Updated 2 years ago1
Deprecate advanced argument conversion
Closed 2 years ago
slurm_utils.py submit_job function is very slow
Updated 2 years ago13
How to specify --output= Slurm parameter?
Closed 2 years ago2
Is config.yaml considered the new cluster_config?
Closed 2 years ago2
A simple alternative profile with a single config file
Closed 3 years ago6
Why the resources are not taken from the slurm configuration?
Closed 3 years ago5
Getting "/bin/sh: slurm-status.py: command not found" error
Closed 3 years ago3
TypeError: '>' not supported between instances of 'NoneType' and 'NoneType' when claiming nodes=1 with walltime
Closed 3 years ago2
multiple profiles for different projects?
Closed 3 years ago7
slurm profile is dead
Closed 3 years ago9
Grouped jobs: KeyError: 'params'
Closed 4 years ago8
Not quite understanding how to use this
Closed 4 years ago5
Suspend should be considered running.
Closed 3 years ago
Submission fails if memory UNIT is used (e.g. mem: 1000M)
Closed 3 years ago4
Reduce dependence upon cookiecutter
Closed 3 years ago1
Remove dependency on pandas
Closed 3 years ago1
Error submitting jobscript (exit code 1)
Closed 4 years ago4
Slurm Profile fails to detect or remove incomplete output from cancelled jobs
Closed 4 years ago2
Couple of questions
Closed 4 years ago4
Behaviour with the `--cores` snakemake parameter
Closed 4 years ago4
why mixed python/python3
Closed 4 years ago1
Jobs failing to submit for longer than 3 hours
Closed 4 years ago2
Priority / override order of parsing arguments to SLURM (sbatch)
Closed 4 years ago2
localrules in profile?
Closed 4 years ago3
Threads should map to "-c" instead of "-n"
Closed 4 years ago6
put cluster_config in config.yaml
Closed 4 years ago2
How to set output and error files?
Closed 4 years ago9
Simplify and clean up test code
Closed 4 years ago