Snakemake-Profiles/slurm

Issues

• Specify only one output file

  #116 opened 17 days ago by robinfallegger
  0

• Append top level job name to rule-based job name

  #118 opened 4 months ago by CJREID
  2

• Compatibility with snakemake version 8.0 and higher

  #117 opened 10 months ago by TBradley27
  11

• Jobs submitted to cluster fail without explanation

  #109 opened 2 years ago by jonahcullen
  9

• Error spam (list index out of range, could not query sidecar)

  #113 opened a year ago by nienkevanunen
  4

• Snakemake and Slurm

  #110 opened 2 years ago by mweberr
  1

• sidecar crashes when parsing malformed response

  #96 opened 2 years ago by messersc
  7

• How do I make mem_mb_per_cpu work?

  #112 opened a year ago by hepcat72
  8

• Sidecar shuts down too early when pressing Ctrl-C

  #99 opened 2 years ago by holtgrewe
  1

• slurm-status.py: could not query side car

  #111 opened a year ago by mhorlacher
  0

• using conda with config without global snakemake install

  #75 opened 3 years ago by LZeitler
  4

• Fails with many input files

  #87 opened 2 years ago by alanocallaghan
  7

• SLURM --tasks-per-node, --cpus-per-task, etc.

  #94 opened 2 years ago by whophil
  2

• `mem` setting in resource is not working due to default `mem_mb` argument is generated in latest version of snakemake

  #107 opened 2 years ago by y9c
  3

• Problems with Snakemake 5.6.0 standard resources

  #89 opened 3 years ago by holtgrewe
  4

• slurm fails when log path contains a Wildcards string that is a directory

  #104 opened 2 years ago by maarten-k
  8

• How to use with MPI jobs?

  #103 opened 2 years ago by bilke
  1

• add more option on config.yaml

  #80 opened 2 years ago by sravel
  2

• Specifying GRES (gpu, local storage) and constraints

  #86 opened 2 years ago by holtgrewe
  1

• sacct running continuously

  #74 opened 2 years ago by rmvpaeme
  3

• Profile not working well on AWS ParallelCluster with Slurm

  #102 opened 2 years ago by cbrueffer
  0

• cluster-status should use squeue --iterate

  #81 opened 2 years ago by holtgrewe
  3

• Provided cores differ to what's passed in the CLI

  #97 opened 2 years ago by vinisalazar
  1

• Deprecate advanced argument conversion

  #91 opened 2 years ago by percyfal
  0

• slurm_utils.py submit_job function is very slow

  #79 opened 3 years ago by atermanini
  13

• How to specify --output= Slurm parameter?

  #90 opened 3 years ago by holtgrewe
  2

• Is config.yaml considered the new cluster_config?

  #88 opened 3 years ago by ftabaro
  2

• A simple alternative profile with a single config file

  #73 opened 3 years ago by jdblischak
  6

• Why the resources are not taken from the slurm configuration?

  #77 opened 3 years ago by ekushele
  5

• Getting "/bin/sh: slurm-status.py: command not found" error

  #76 opened 3 years ago by anilthanki
  3

• TypeError: '>' not supported between instances of 'NoneType' and 'NoneType' when claiming nodes=1 with walltime

  #68 opened 3 years ago by zihhuafang
  2

• multiple profiles for different projects?

  #51 opened 3 years ago by giovp
  7

• Grouped jobs: KeyError: 'params'

  #55 opened 4 years ago by CharlesJB
  8

• Not quite understanding how to use this

  #46 opened 4 years ago by proteins247
  5

• Suspend should be considered running.

  #71 opened 4 years ago by cErikson
  0

• Submission fails if memory UNIT is used (e.g. mem: 1000M)

  #62 opened 4 years ago by sschmeier
  4

• Reduce dependence upon cookiecutter

  #63 opened 4 years ago by frankier
  1

• Remove dependency on pandas

  #64 opened 4 years ago by frankier
  1

• Error submitting jobscript (exit code 1)

  #48 opened 4 years ago by lczech
  4

• Slurm Profile fails to detect or remove incomplete output from cancelled jobs

  #49 opened 4 years ago by johnstonmj
  2

• Couple of questions

  #52 opened 4 years ago by chrarnold
  4

• Behaviour with the `--cores` snakemake parameter

  #61 opened 4 years ago by tdido
  4

• why mixed python/python3

  #60 opened 4 years ago by kkmann
  1

• Jobs failing to submit for longer than 3 hours

  #56 opened 4 years ago by moldach
  2

• Priority / override order of parsing arguments to SLURM (sbatch)

  #42 opened 4 years ago by johnstonmj
  2

• localrules in profile?

  #45 opened 4 years ago by rneher
  3

• Threads should map to "-c" instead of "-n"

  #35 opened 5 years ago by jdwheaton
  6

• put cluster_config in config.yaml

  #37 opened 4 years ago by jos4uke
  2

• How to set output and error files?

  #40 opened 5 years ago by mufernando
  9

• Simplify and clean up test code

  #39 opened 5 years ago by percyfal
  0