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

#100 - chore(main): release 0.6.0

Pull Request - State: closed - Opened by github-actions[bot] 6 months ago - 1 comment
Labels: autorelease: tagged

#99 - chore(main): release 0.5.2

Pull Request - State: closed - Opened by github-actions[bot] 6 months ago - 1 comment
Labels: autorelease: tagged

#98 - fix: #97 preventing node confinment

Pull Request - State: closed - Opened by cmeesters 6 months ago - 1 comment

#97 - Batch job submission failed: Node count specification invalid

Issue - State: closed - Opened by KB1RD 6 months ago - 5 comments

#96 - Installing with mamba tries to downgrades to snakemake 7

Issue - State: closed - Opened by conchoecia 6 months ago - 3 comments

#95 - Separately logging stdout and stderr

Issue - State: open - Opened by bentyeh 6 months ago - 6 comments

#94 - option to set the log directory?

Issue - State: open - Opened by jbloom 6 months ago - 5 comments

#93 - feat: will reject jobs, which attempt setting job names by 'slurm_extra'

Pull Request - State: closed - Opened by cmeesters 7 months ago - 2 comments
Labels: enhancement

#92 - chore(main): release 0.5.1

Pull Request - State: closed - Opened by github-actions[bot] 7 months ago - 1 comment
Labels: autorelease: tagged

#91 - Unsuccessful attempt to use "srun" after job submission leads to abort of jobs

Issue - State: closed - Opened by Robin1em 7 months ago - 5 comments

#90 - Prevent job name overwrite by users

Issue - State: closed - Opened by cmeesters 7 months ago - 1 comment
Labels: bug/fix, enhancement

#89 - chore(main): release 0.5.0

Pull Request - State: closed - Opened by github-actions[bot] 7 months ago - 1 comment
Labels: autorelease: tagged

#88 - feat: wildcards in comment string #85

Pull Request - State: closed - Opened by mrvollger 7 months ago

#87 - fix: proper line ending status message

Pull Request - State: closed - Opened by cmeesters 7 months ago
Labels: bug/fix

#86 - fix: allowing for accounts containing whitespace

Pull Request - State: closed - Opened by cmeesters 7 months ago - 2 comments
Labels: bug/fix

#85 - Wildcards missing from comments

Issue - State: closed - Opened by mrvollger 7 months ago - 4 comments
Labels: enhancement

#84 - SLURM logs path are unreasonably long and contains all wildcards

Issue - State: closed - Opened by xapple 7 months ago - 1 comment

#83 - All SLURM jobs created by snakemake have the same name

Issue - State: closed - Opened by xapple 7 months ago - 3 comments

#82 - Missing period or newline in status message when a SLURM job returns a failed status

Issue - State: closed - Opened by xapple 7 months ago - 1 comment
Labels: bug/fix

#81 - fix: null byte account guess

Pull Request - State: closed - Opened by cmeesters 7 months ago - 2 comments
Labels: bug/fix

#80 - docs: storage update

Pull Request - State: closed - Opened by cmeesters 7 months ago
Labels: documentation

#79 - docs: added paragraphs about dynamic resource allocation

Pull Request - State: closed - Opened by cmeesters 7 months ago
Labels: documentation

#78 - feat: warning if run in job

Pull Request - State: closed - Opened by cmeesters 7 months ago - 3 comments
Labels: enhancement

#77 - Slurm executor plugin is not found after installation

Issue - State: closed - Opened by vsbuffalo 7 months ago - 3 comments

#76 - Make the `slurm_account` parameter optional, because it is in fact optional.

Issue - State: closed - Opened by xapple 7 months ago - 7 comments

#75 - Setting memory twice when submitting with slurm executor

Issue - State: open - Opened by kwells4 7 months ago - 14 comments

#74 - chore(main): release 0.4.5

Pull Request - State: closed - Opened by github-actions[bot] 8 months ago - 1 comment
Labels: autorelease: tagged

#73 - How to set CommonSettings from command line?

Issue - State: closed - Opened by choosehappy 8 months ago - 4 comments

#72 - fix: fix path typo

Pull Request - State: closed - Opened by fgvieira 8 months ago

#71 - chore(main): release 0.4.4

Pull Request - State: closed - Opened by github-actions[bot] 8 months ago - 1 comment
Labels: autorelease: tagged

#70 - Revert "chore: updated testcase with directory path in wildcards"

Pull Request - State: closed - Opened by johanneskoester 8 months ago

#69 - chore: updated testcase with directory path in wildcards

Pull Request - State: closed - Opened by johanneskoester 8 months ago

#68 - chore(main): release 0.4.3

Pull Request - State: closed - Opened by github-actions[bot] 8 months ago - 1 comment
Labels: autorelease: tagged

#67 - fix: always create logdir before sbatch

Pull Request - State: closed - Opened by johanneskoester 8 months ago - 1 comment

#66 - refactor: get cpus_per_task from jobstep executor

Pull Request - State: closed - Opened by johanneskoester 8 months ago - 3 comments

#65 - Determine dynamic resources depending on retry reason?

Issue - State: open - Opened by nikostr 8 months ago - 4 comments
Labels: discussion

#64 - fix: fixed string for constraints - see issue #58

Pull Request - State: closed - Opened by cmeesters 8 months ago - 3 comments
Labels: bug/fix

#63 - "module command not found" using Snakemake with Slurm

Issue - State: closed - Opened by kevinrue 8 months ago - 15 comments

#62 - Dynamic runtime resource fails with SLURM

Issue - State: open - Opened by nikostr 8 months ago - 3 comments

#61 - Dynamic determination of queue

Issue - State: open - Opened by johanneskoester 8 months ago - 3 comments
Labels: enhancement

#60 - Incorrect DAG evaluation in jobstep with ruleorder and checkpoint

Issue - State: closed - Opened by cademirch 8 months ago - 8 comments

#59 - fix: ensuring setting of job.resources.cpus_per_task

Pull Request - State: closed - Opened by cmeesters 8 months ago
Labels: enhancement

#58 - Constraints that include logical "or" cause Snakemake to hang

Issue - State: closed - Opened by w8jcik 8 months ago - 4 comments
Labels: bug/fix

#57 - Differences in SLURM command between what Snakemake says it runs and what is actually run

Issue - State: open - Opened by stefmldk 8 months ago - 8 comments

#56 - feat: multicluster

Pull Request - State: closed - Opened by cmeesters 8 months ago - 9 comments

#55 - The benchmark directive does not work when slurm is used as the executor

Issue - State: closed - Opened by stefmldk 8 months ago - 3 comments

#54 - TypeError: SpawnedJobArgsFactory.general_args() got an unexpected keyword argument 'executor_common_settings'

Issue - State: closed - Opened by Parkerdow 8 months ago - 4 comments

#53 - Missing support for --clusters option

Issue - State: closed - Opened by meliamne 8 months ago - 4 comments

#52 - Snakemake 8 not usable with Slurm clusters offering GPUs

Issue - State: closed - Opened by w8jcik 8 months ago - 3 comments

#51 - chore(main): release 0.4.2

Pull Request - State: closed - Opened by github-actions[bot] 9 months ago - 1 comment
Labels: autorelease: tagged

#50 - main.py: error: argument --executor/-e: invalid choice: 'slurm-jobstep' (choose from 'local', 'dryrun', 'touch')

Issue - State: closed - Opened by Carsten-Ke 9 months ago - 1 comment

#49 - fix: adapt to latest snakemake-interface-executor-plugins

Pull Request - State: closed - Opened by johanneskoester 9 months ago

#48 - fix: replace os.path.sep in wildcard strings with "" in logfile name

Pull Request - State: closed - Opened by jaicher 9 months ago

#47 - Directory separator in wildcards not handled in updated logfile names

Issue - State: closed - Opened by jaicher 9 months ago - 3 comments

#46 - `--cache` is ignored when using the executor

Issue - State: closed - Opened by jlanga 9 months ago - 6 comments

#45 - chore(main): release 0.4.1

Pull Request - State: closed - Opened by github-actions[bot] 9 months ago - 1 comment
Labels: autorelease: tagged

#44 - fix: fixes issue #40 - ntasks set explicitly

Pull Request - State: closed - Opened by cmeesters 9 months ago

#43 - chore(main): release 0.4.0

Pull Request - State: closed - Opened by github-actions[bot] 9 months ago - 1 comment
Labels: autorelease: tagged

#42 - docs: added mini paragraph about Conda and Env Modules

Pull Request - State: closed - Opened by cmeesters 9 months ago - 2 comments
Labels: documentation

#41 - Inheriting cpus-per-task in srun (Slurm 22.05+)

Issue - State: closed - Opened by paudano 9 months ago - 7 comments
Labels: bug/fix

#40 - setting ntasks for non-MPI jobs

Issue - State: closed - Opened by tatumdmortimer 9 months ago - 6 comments

#39 - chore(main): release 0.3.2

Pull Request - State: closed - Opened by github-actions[bot] 9 months ago - 1 comment
Labels: autorelease: tagged

#38 - Job status query fails if slurm accounting storage is disabled

Issue - State: open - Opened by prs513rosewood 9 months ago - 4 comments

#37 - docs: extended docs

Pull Request - State: closed - Opened by cmeesters 10 months ago - 1 comment
Labels: documentation

#36 - chore(main): release 0.3.1

Pull Request - State: closed - Opened by github-actions[bot] 10 months ago - 1 comment
Labels: autorelease: tagged

#35 - feat: add wildcards to output and comment

Pull Request - State: closed - Opened by Ulthran 10 months ago - 4 comments

#34 - add human job name with wildcards

Issue - State: closed - Opened by sravel 10 months ago - 3 comments

#33 - Slurm doesn't exit on completion

Issue - State: closed - Opened by Ulthran 10 months ago - 13 comments

#32 - chore(main): release 0.3.0

Pull Request - State: closed - Opened by github-actions[bot] 10 months ago - 1 comment
Labels: autorelease: tagged

#31 - chore(main): release 0.2.2

Pull Request - State: closed - Opened by github-actions[bot] 10 months ago - 1 comment
Labels: autorelease: tagged

#30 - Usefulness of this plugin

Issue - State: closed - Opened by mlarjim 10 months ago - 5 comments

#29 - `sbatch` call does not escape quotes in `exec_job`

Issue - State: open - Opened by ebete 10 months ago - 15 comments

#28 - fix: Typos in documentation

Pull Request - State: closed - Opened by MrSquidward 10 months ago

#27 - feat: support --qos as a resource

Pull Request - State: closed - Opened by kdm9 10 months ago - 4 comments

#26 - fix: Use sacct syntax that is compatible with slurm < 20.11.0

Pull Request - State: closed - Opened by dnerini 10 months ago - 4 comments

#25 - Plugin is not compatible with older SLURM versions

Issue - State: closed - Opened by dnerini 10 months ago

#24 - srun: error: slurm_init_msg_engine_port error Address already in use

Issue - State: closed - Opened by y9c 10 months ago - 3 comments

#23 - Conflicting use of arguments for global and workflow specific profiles

Issue - State: closed - Opened by TBradley27 10 months ago - 3 comments

#22 - `SLURM_*` environment variables can interfere with execution of MPI workloads

Issue - State: closed - Opened by ocaisa 10 months ago - 3 comments

#21 - Traceback when trying to execute workflow with 0.2.1 release

Issue - State: closed - Opened by ocaisa 11 months ago - 2 comments

#20 - chore(main): release 0.2.1

Pull Request - State: closed - Opened by github-actions[bot] 11 months ago - 1 comment
Labels: autorelease: tagged

#19 - chore(main): release 0.2.0

Pull Request - State: closed - Opened by github-actions[bot] 11 months ago - 1 comment
Labels: autorelease: tagged

#18 - Unterminated string literal syntax error parsing slurm_extra

Issue - State: closed - Opened by paudano 11 months ago - 29 comments

#17 - prefix jobname with rule name

Issue - State: closed - Opened by cmeesters 11 months ago - 7 comments
Labels: enhancement

#16 - feat: include rule name as comment

Pull Request - State: closed - Opened by fgvieira 11 months ago - 3 comments

#15 - Memorize job nodes and exclude broken nodes

Issue - State: open - Opened by cmeesters 11 months ago
Labels: enhancement

#14 - snakemake-executor-plugin-slurm-jobstep is a dependency

Issue - State: closed - Opened by cmeesters 11 months ago - 1 comment

#13 - chore(main): release 0.1.5

Pull Request - State: closed - Opened by github-actions[bot] 11 months ago - 2 comments
Labels: autorelease: tagged

#12 - Feature Request: Bring back --cluster-status equivalent?

Issue - State: closed - Opened by juzb 11 months ago - 6 comments

#11 - Interpolation of wildcards in profile slurm configuration

Issue - State: closed - Opened by TBradley27 11 months ago - 6 comments

#10 - feat: print run id to log

Pull Request - State: closed - Opened by fgvieira 11 months ago - 2 comments

#9 - fix: Force sacct to look at the last 2 days

Pull Request - State: closed - Opened by fgvieira 12 months ago - 2 comments

#8 - chore(main): release 0.1.4

Pull Request - State: closed - Opened by github-actions[bot] 12 months ago - 1 comment
Labels: autorelease: tagged

#7 - chore(main): release 0.1.3

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

#6 - chore(main): release 0.1.2

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

#5 - fix: Handle unresponsive sacct

Pull Request - State: closed - Opened by fgvieira about 1 year ago - 2 comments

#4 - chore(main): release 0.1.1

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

#3 - build(deps): update snakemake-interface-executor-plugins requirement from ^4.0.1 to ^5.0.2

Pull Request - State: closed - Opened by dependabot[bot] about 1 year ago - 1 comment
Labels: dependencies

#2 - fix: update to fixed version of snakemake-interface-executor-plugins

Pull Request - State: closed - Opened by johanneskoester about 1 year ago

#1 - chore(main): release 0.1.0

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

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