snakemake snakemake-executor-plugin-slurm issues

snakemake / snakemake-executor-plugin-slurm

A Snakemake executor plugin for submitting jobs to a SLURM cluster

MIT License

18 stars 19 forks source link

issues

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fix: #121 by more robustly parsing the output returned by sbatch

#122 nigiord closed 3 months ago
1
Jobid is not properly parsed when cluster name is present

#121 nigiord closed 3 months ago
6
Can't unquote in slurm_extra

#120 willboulton opened 3 months ago
1
How to set `$TMPDIR` environment variable with a job to something like `<scratch>/$SLURM_JOB_ID/tmp`

#119 hermidalc closed 3 months ago
2
Make sure sbatch receives --comments correctly

#118 Zhongzheng99 closed 3 months ago
2
The account or account/partition combination is not recognized!

#117 Zhongzheng99 closed 3 months ago
2
problem with `--slurm-init-seconds-before-status-checks` option

#116 jbloom closed 4 months ago
1
Best practice: a short-running rule called many times

#115 bdelepine opened 4 months ago
0
Snakemake fails with executor SLURM with slurm_persist_conn_open_without_init

#114 mincej closed 4 months ago
5
Running snakemake in a SLURM job context

#113 visze closed 3 months ago
24
chore(main): release 0.8.0

#112 github-actions[bot] closed 4 months ago
1
feat: cli

#111 cmeesters closed 4 months ago
0
Why do all snakemake-jobs sent to the same group fail if one of them fail?

#110 bdelepine closed 4 months ago
2
Preempted jobs are spawned multiple times

#109 gtsitsiridis closed 2 months ago
15
chore(main): release 0.7.0

#108 github-actions[bot] closed 4 months ago
1
chore(main): release 0.7.0

#107 github-actions[bot] closed 4 months ago
0
Select partition automatically

#106 SilasK opened 5 months ago
15
Log file and comment string are not escaped

#105 denisalevi opened 5 months ago
0
sbatch: error: Batch job submission failed: Invalid feature specification

#104 Luke-ebbis closed 5 months ago
2
Invalid --distribution specification?

#103 brantfaircloth closed 5 months ago
12
chore(main): release 0.6.1

#102 github-actions[bot] closed 5 months ago
0
chore(main): release 0.6.1

#101 github-actions[bot] closed 5 months ago
0
chore(main): release 0.6.0

#100 github-actions[bot] closed 5 months ago
1
chore(main): release 0.5.2

#99 github-actions[bot] closed 5 months ago
1
fix: #97 preventing node confinment

#98 cmeesters closed 5 months ago
1
Batch job submission failed: Node count specification invalid

#97 KB1RD closed 5 months ago
5
Installing with mamba tries to downgrades to snakemake 7

#96 conchoecia closed 4 months ago
3
Separately logging stdout and stderr

#95 bentyeh opened 6 months ago
6
option to set the log directory?

#94 jbloom opened 6 months ago
5
feat: will reject jobs, which attempt setting job names by 'slurm_extra'

#93 cmeesters closed 5 months ago
2
chore(main): release 0.5.1

#92 github-actions[bot] closed 6 months ago
1
Unsuccessful attempt to use "srun" after job submission leads to abort of jobs

#91 Robin1em closed 6 months ago
5
Prevent job name overwrite by users

#90 cmeesters closed 4 months ago
1
chore(main): release 0.5.0

#89 github-actions[bot] closed 6 months ago
1
feat: wildcards in comment string #85

#88 mrvollger closed 6 months ago
0
fix: proper line ending status message

#87 cmeesters closed 6 months ago
0
fix: allowing for accounts containing whitespace

#86 cmeesters closed 6 months ago
2
Wildcards missing from comments

#85 mrvollger closed 6 months ago
4
SLURM logs path are unreasonably long and contains all wildcards

#84 xapple closed 6 months ago
1
All SLURM jobs created by snakemake have the same name

#83 xapple closed 6 months ago
3
Missing period or newline in status message when a SLURM job returns a failed status

#82 xapple closed 6 months ago
1
fix: null byte account guess

#81 cmeesters closed 4 months ago
2
docs: storage update

#80 cmeesters closed 5 months ago
0
docs: added paragraphs about dynamic resource allocation

#79 cmeesters closed 5 months ago
0
feat: warning if run in job

#78 cmeesters closed 4 months ago
3
Slurm executor plugin is not found after installation

#77 vsbuffalo closed 6 months ago
3
Make the `slurm_account` parameter optional, because it is in fact optional.

#76 xapple closed 6 months ago
7
Setting memory twice when submitting with slurm executor

#75 kwells4 opened 7 months ago
14
chore(main): release 0.4.5

#74 github-actions[bot] closed 7 months ago
1
How to set CommonSettings from command line?

#73 choosehappy closed 4 months ago
4

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