Ecosyste.ms: Issues

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GitHub / snakemake/snakemake-executor-plugin-slurm issues and pull requests

#171 - Define job groups in cluster config.yaml

Issue - State: open - Opened by freekvh 23 days ago

#170 - chore(main): release 0.12.0

Pull Request - State: closed - Opened by github-actions[bot] 23 days ago - 1 comment
Labels: autorelease: pending

#169 - chore(main): release 0.12.0

Pull Request - State: closed - Opened by github-actions[bot] 23 days ago - 1 comment
Labels: autorelease: pending

#168 - docs: fix headings in further.md

Pull Request - State: closed - Opened by johanneskoester 24 days ago - 2 comments

#167 - chore(main): release 0.11.2

Pull Request - State: closed - Opened by github-actions[bot] 24 days ago - 2 comments
Labels: autorelease: tagged

#166 - feat: experimenting with automated release post to Mastodon

Pull Request - State: closed - Opened by cmeesters 26 days ago - 2 comments

#165 - fix: sbatch stderr parsing #2

Pull Request - State: closed - Opened by cmeesters 26 days ago - 8 comments

#164 - sacctmgr error when running in job context

Issue - State: open - Opened by jprnz 27 days ago - 1 comment

#163 - chore(main): release 0.11.2

Pull Request - State: closed - Opened by github-actions[bot] 27 days ago - 2 comments
Labels: autorelease: pending

#162 - Localrules are ignored for grouped jobs

Issue - State: open - Opened by NoahHenrikKleinschmidt 30 days ago - 1 comment

#161 - fix: sbatch stderr parsing

Pull Request - State: closed - Opened by cmeesters about 1 month ago - 4 comments

#160 - chore(main): release 0.11.1

Pull Request - State: closed - Opened by github-actions[bot] about 1 month ago - 1 comment
Labels: autorelease: tagged

#159 - feat: custom log file behaviour

Pull Request - State: open - Opened by cmeesters about 1 month ago - 1 comment

#158 - support for slurm job arrays?

Issue - State: closed - Opened by andrewkern about 2 months ago - 2 comments

#157 - Slurm workslow submits intial jobs but then hangs until ctrl-c

Issue - State: closed - Opened by freekvh about 2 months ago - 26 comments

#156 - Allow simultaneous use of envmodules and conda environment

Issue - State: open - Opened by gatoniel about 2 months ago - 3 comments

#155 - Change jobnames to be meaningful

Issue - State: closed - Opened by iamh2o about 2 months ago - 1 comment

#154 - slurm job name could be more informative

Issue - State: closed - Opened by dgordon562 about 2 months ago - 10 comments

#153 - docs: requeue

Pull Request - State: closed - Opened by cmeesters 2 months ago - 3 comments

#152 - chore(main): release 0.11.0

Pull Request - State: closed - Opened by github-actions[bot] 2 months ago - 2 comments
Labels: autorelease: tagged

#152 - chore(main): release 0.11.0

Pull Request - State: closed - Opened by github-actions[bot] 2 months ago - 2 comments
Labels: autorelease: tagged

#149 - chore(main): release 0.10.2

Pull Request - State: closed - Opened by github-actions[bot] 3 months ago - 2 comments
Labels: autorelease: tagged

#149 - chore(main): release 0.10.2

Pull Request - State: closed - Opened by github-actions[bot] 3 months ago - 2 comments
Labels: autorelease: tagged

#148 - fix: added forgotten yield in case of job preemption

Pull Request - State: closed - Opened by cmeesters 3 months ago - 1 comment

#148 - fix: added forgotten yield in case of job preemption

Pull Request - State: closed - Opened by cmeesters 3 months ago - 1 comment

#147 - Add seff support to evaluate resource allocation after executation

Issue - State: open - Opened by sreichl 3 months ago - 2 comments

#146 - Snakemake fails to parse sbatch output to get slurm_jobid

Issue - State: open - Opened by kennethabarr 3 months ago - 3 comments

#146 - Snakemake fails to parse sbatch output to get slurm_jobid

Issue - State: open - Opened by kennethabarr 3 months ago - 3 comments

#145 - threads directive of a rule not taken into account

Issue - State: open - Opened by ArthurDondi 3 months ago - 5 comments

#144 - chore(main): release 0.10.1

Pull Request - State: closed - Opened by github-actions[bot] 3 months ago - 2 comments
Labels: autorelease: tagged

#144 - chore(main): release 0.10.1

Pull Request - State: closed - Opened by github-actions[bot] 3 months ago - 2 comments
Labels: autorelease: tagged

#143 - chore: test changes in testing framework in main branch of snakemake

Pull Request - State: closed - Opened by johanneskoester 3 months ago - 2 comments
Labels: WIP

#143 - chore: test changes in testing framework in main branch of snakemake

Pull Request - State: closed - Opened by johanneskoester 3 months ago - 2 comments
Labels: WIP

#142 - chore: update to stable snakemake

Pull Request - State: closed - Opened by johanneskoester 3 months ago - 7 comments

#142 - chore: update to stable snakemake

Pull Request - State: closed - Opened by johanneskoester 3 months ago - 7 comments

#140 - fix: logfile quoting and scancel error handling

Pull Request - State: closed - Opened by johanneskoester 3 months ago - 7 comments

#140 - fix: logfile quoting and scancel error handling

Pull Request - State: closed - Opened by johanneskoester 3 months ago - 7 comments

#139 - feat: cancel workflow#127

Pull Request - State: closed - Opened by cmeesters 3 months ago - 4 comments

#139 - feat: cancel workflow#127

Pull Request - State: closed - Opened by cmeesters 3 months ago - 4 comments

#138 - chore(main): release 0.10.0

Pull Request - State: closed - Opened by github-actions[bot] 3 months ago - 2 comments
Labels: autorelease: tagged

#138 - chore(main): release 0.10.0

Pull Request - State: closed - Opened by github-actions[bot] 3 months ago - 2 comments
Labels: autorelease: tagged

#137 - feat: in job stability

Pull Request - State: closed - Opened by cmeesters 4 months ago - 6 comments

#136 - feat: added requeue option to client

Pull Request - State: closed - Opened by slaube-jgu 4 months ago - 5 comments

#136 - feat: added requeue option to client

Pull Request - State: closed - Opened by slaube-jgu 4 months ago - 5 comments

#135 - chore(main): release 0.9.1

Pull Request - State: closed - Opened by github-actions[bot] 4 months ago - 1 comment
Labels: autorelease: pending

#135 - chore(main): release 0.9.1

Pull Request - State: closed - Opened by github-actions[bot] 4 months ago - 1 comment
Labels: autorelease: pending

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

Issue - State: open - Opened by KB1RD 4 months ago - 4 comments

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

Issue - State: open - Opened by KB1RD 4 months ago - 4 comments

#132 - fix: issue #109 - preemption is no longer considered a failed status

Pull Request - State: closed - Opened by cmeesters 4 months ago - 1 comment

#132 - fix: issue #109 - preemption is no longer considered a failed status

Pull Request - State: closed - Opened by cmeesters 4 months ago - 1 comment

#131 - chore(main): release 0.9.1

Pull Request - State: closed - Opened by github-actions[bot] 4 months ago
Labels: autorelease: pending

#130 - Update issue templates

Pull Request - State: closed - Opened by cmeesters 4 months ago

#130 - Update issue templates

Pull Request - State: closed - Opened by cmeesters 4 months ago

#129 - chore(main): release 0.9.1

Pull Request - State: closed - Opened by github-actions[bot] 4 months ago
Labels: autorelease: pending

#128 - Update issue templates

Pull Request - State: closed - Opened by cmeesters 4 months ago

#127 - job submitted in login node not being cancelled if all rules fail?

Issue - State: open - Opened by ifariasg 4 months ago - 15 comments

#126 - chore(main): release 0.9.1

Pull Request - State: closed - Opened by github-actions[bot] 4 months ago
Labels: autorelease: pending

#126 - chore(main): release 0.9.1

Pull Request - State: closed - Opened by github-actions[bot] 4 months ago
Labels: autorelease: pending

#125 - fix: add --parsable to sbatch call for a more robust output parsing

Pull Request - State: closed - Opened by nigiord 4 months ago - 3 comments

#124 - chore(main): release 0.9.0

Pull Request - State: closed - Opened by github-actions[bot] 4 months ago - 1 comment
Labels: autorelease: tagged

#124 - chore(main): release 0.9.0

Pull Request - State: closed - Opened by github-actions[bot] 4 months ago - 1 comment
Labels: autorelease: tagged

#123 - Way to make logging go to same logs as when running locally?

Issue - State: open - Opened by hermidalc 4 months ago - 3 comments

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

Pull Request - State: closed - Opened by nigiord 4 months ago - 1 comment

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

Pull Request - State: closed - Opened by nigiord 4 months ago - 1 comment

#121 - Jobid is not properly parsed when cluster name is present

Issue - State: closed - Opened by nigiord 4 months ago - 6 comments

#121 - Jobid is not properly parsed when cluster name is present

Issue - State: closed - Opened by nigiord 4 months ago - 6 comments

#120 - Can't unquote in slurm_extra

Issue - State: open - Opened by willboulton 4 months ago - 1 comment

#120 - Can't unquote in slurm_extra

Issue - State: open - Opened by willboulton 4 months ago - 1 comment

#118 - Make sure sbatch receives --comments correctly

Pull Request - State: closed - Opened by Zhongzheng99 4 months ago - 2 comments

#118 - Make sure sbatch receives --comments correctly

Pull Request - State: closed - Opened by Zhongzheng99 4 months ago - 2 comments

#117 - The account or account/partition combination is not recognized!

Issue - State: closed - Opened by Zhongzheng99 4 months ago - 2 comments

#116 - problem with `--slurm-init-seconds-before-status-checks` option

Issue - State: closed - Opened by jbloom 4 months ago - 1 comment

#113 - Running snakemake in a SLURM job context

Issue - State: closed - Opened by visze 5 months ago - 24 comments

#113 - Running snakemake in a SLURM job context

Issue - State: closed - Opened by visze 5 months ago - 24 comments

#112 - chore(main): release 0.8.0

Pull Request - State: closed - Opened by github-actions[bot] 5 months ago - 1 comment
Labels: autorelease: tagged

#111 - feat: cli

Pull Request - State: closed - Opened by cmeesters 5 months ago

#111 - feat: cli

Pull Request - State: closed - Opened by cmeesters 5 months ago

#109 - Preempted jobs are spawned multiple times

Issue - State: closed - Opened by gtsitsiridis 5 months ago - 15 comments
Labels: bug/fix, enhancement

#108 - chore(main): release 0.7.0

Pull Request - State: closed - Opened by github-actions[bot] 5 months ago - 1 comment
Labels: autorelease: tagged

#108 - chore(main): release 0.7.0

Pull Request - State: closed - Opened by github-actions[bot] 5 months ago - 1 comment
Labels: autorelease: tagged

#107 - chore(main): release 0.7.0

Pull Request - State: closed - Opened by github-actions[bot] 5 months ago
Labels: autorelease: pending

#106 - Select partition automatically

Issue - State: open - Opened by SilasK 5 months ago - 15 comments

#105 - Log file and comment string are not escaped

Issue - State: open - Opened by denisalevi 5 months ago

#103 - Invalid --distribution specification?

Issue - State: closed - Opened by brantfaircloth 6 months ago - 12 comments

#102 - chore(main): release 0.6.1

Pull Request - State: closed - Opened by github-actions[bot] 6 months ago
Labels: autorelease: pending

#101 - chore(main): release 0.6.1

Pull Request - State: closed - Opened by github-actions[bot] 6 months ago
Labels: autorelease: pending