From f5c3d4c6b9bdcba68a512388d36d72d2700920bf Mon Sep 17 00:00:00 2001 From: Johannes Koester Date: Tue, 16 Jan 2024 10:23:50 +0000 Subject: [PATCH] fix: ensure proper handling of group jobs in combination with the slurm-jobstep executor --- pyproject.toml | 4 ++-- snakemake_executor_plugin_slurm/__init__.py | 3 ++- 2 files changed, 4 insertions(+), 3 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index e06c17e..136125b 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -16,8 +16,8 @@ keywords = ["snakemake", "plugin", "executor", "cluster", "slurm"] [tool.poetry.dependencies] python = "^3.11" snakemake-interface-common = "^1.13.0" -snakemake-interface-executor-plugins = "^8.0.2" -snakemake-executor-plugin-slurm-jobstep = "^0.1.5" +snakemake-interface-executor-plugins = "^8.2.0" +snakemake-executor-plugin-slurm-jobstep = "^0.1.10" throttler = "^1.2.2" [tool.poetry.group.dev.dependencies] diff --git a/snakemake_executor_plugin_slurm/__init__.py b/snakemake_executor_plugin_slurm/__init__.py index 230706c..6432f8d 100644 --- a/snakemake_executor_plugin_slurm/__init__.py +++ b/snakemake_executor_plugin_slurm/__init__.py @@ -39,6 +39,7 @@ auto_deploy_default_storage_provider=False, # wait a bit until slurmdbd has job info available init_seconds_before_status_checks=40, + pass_group_args=True, ) @@ -51,7 +52,7 @@ def __post_init__(self): self._fallback_partition = None def additional_general_args(self): - return "--executor slurm-jobstep" + return "--executor slurm-jobstep --jobs 1" def run_job(self, job: JobExecutorInterface): # Implement here how to run a job.