snakemake/snakemake-executor-plugin-slurm

Issues

• slurm job name could be more informative

  #154 opened 2 months ago by dgordon562
  1

• `threads` directive of a rule not taken into account when running through slurm

  #141 opened 3 months ago by blaiseli
  3

• Differences in SLURM command between what Snakemake says it runs and what is actually run

  #57 opened 8 months ago by stefmldk
  8

• --software-deployment-method argument has a different behaviour using CLI and profiles

  #151 opened 2 months ago by ArthurDondi
  1

• Determine dynamic resources depending on retry reason?

  #65 opened 8 months ago by nikostr
  4

• Preempted jobs are spawned multiple times

  #109 opened 3 months ago by gtsitsiridis
  14

• Select partition automatically

  #106 opened 5 months ago by SilasK
  15

• Getting an AttributeError: module 'pulp' has no attribute 'list_solvers'. Did you mean: 'listSolvers'?

  #150 opened 2 months ago by Pooshman
  1

• Snakemake fails to parse sbatch output to get slurm_jobid

  #146 opened 3 months ago by kennethabarr
  3

• threads directive of a rule not taken into account

  #145 opened 3 months ago by ArthurDondi
  2

• Missing support for --clusters option

  #53 opened 3 months ago by meliamne
  4

• Add seff support to evaluate resource allocation after executation

  #147 opened 3 months ago by sreichl
  2

• job submitted in login node not being cancelled if all rules fail?

  #127 opened 4 months ago by ifariasg
  15

• Running snakemake in a SLURM job context

  #113 opened 3 months ago by visze
  24

• Job submission with --prioritize runs all at once, then stalls

  #134 opened 3 months ago by KB1RD
  4

• snakemake exit with MissingOutputException when using --immediate-submit

  #133 opened 3 months ago by sirintra
  3

• Constraints that include logical "or" cause Snakemake to hang

  #58 opened 4 months ago by w8jcik
  4

• Way to make logging go to same logs as when running locally?

  #123 opened 4 months ago by hermidalc
  3

• Can't unquote in slurm_extra

  #120 opened 4 months ago by willboulton
  1

• Jobid is not properly parsed when cluster name is present

  #121 opened 4 months ago by nigiord
  6

• How to set `$TMPDIR` environment variable with a job to something like `<scratch>/$SLURM_JOB_ID/tmp`

  #119 opened 4 months ago by hermidalc
  2

• The account or account/partition combination is not recognized!

  #117 opened 4 months ago by Zhongzheng99
  2

• Snakemake fails with executor SLURM with slurm_persist_conn_open_without_init

  #114 opened 4 months ago by mincej
  5

• problem with `--slurm-init-seconds-before-status-checks` option

  #116 opened 4 months ago by jbloom
  1

• Best practice: a short-running rule called many times

  #115 opened 4 months ago by bdelepine
  0

• How to set CommonSettings from command line?

  #73 opened 4 months ago by choosehappy
  4

• Dynamic determination of queue

  #61 opened 8 months ago by johanneskoester
  3

• Installing with mamba tries to downgrades to snakemake 7

  #96 opened 4 months ago by conchoecia
  3

• Prevent job name overwrite by users

  #90 opened 4 months ago by cmeesters
  1

• Why do all snakemake-jobs sent to the same group fail if one of them fail?

  #110 opened 4 months ago by bdelepine
  2

• Separately logging stdout and stderr

  #95 opened 6 months ago by bentyeh
  6

• Log file and comment string are not escaped

  #105 opened 5 months ago by denisalevi
  0

• sbatch: error: Batch job submission failed: Invalid feature specification

  #104 opened 5 months ago by Luke-ebbis
  2

• Batch job submission failed: Node count specification invalid

  #97 opened 5 months ago by KB1RD
  5

• Invalid --distribution specification?

  #103 opened 5 months ago by brantfaircloth
  12

• option to set the log directory?

  #94 opened 6 months ago by jbloom
  3

• Missing period or newline in status message when a SLURM job returns a failed status

  #82 opened 6 months ago by xapple
  1

• Unsuccessful attempt to use "srun" after job submission leads to abort of jobs

  #91 opened 6 months ago by Robin1em
  5

• Wildcards missing from comments

  #85 opened 7 months ago by mrvollger
  4

• All SLURM jobs created by snakemake have the same name

  #83 opened 7 months ago by xapple
  3

• SLURM logs path are unreasonably long and contains all wildcards

  #84 opened 7 months ago by xapple
  1

• Make the `slurm_account` parameter optional, because it is in fact optional.

  #76 opened 7 months ago by xapple
  7

• Setting memory twice when submitting with slurm executor

  #75 opened 7 months ago by kwells4
  14

• "module command not found" using Snakemake with Slurm

  #63 opened 7 months ago by kevinrue
  15

• Slurm executor plugin is not found after installation

  #77 opened 7 months ago by vsbuffalo
  3

• Dynamic runtime resource fails with SLURM

  #62 opened 8 months ago by nikostr
  3

• Incorrect DAG evaluation in jobstep with ruleorder and checkpoint

  #60 opened 8 months ago by cademirch
  8

• Snakemake 8 not usable with Slurm clusters offering GPUs

  #52 opened 8 months ago by w8jcik
  3

• The benchmark directive does not work when slurm is used as the executor

  #55 opened 8 months ago by stefmldk
  3

• TypeError: SpawnedJobArgsFactory.general_args() got an unexpected keyword argument 'executor_common_settings'

  #54 opened 8 months ago by Parkerdow
  4