From 42589853418c940829f3c763f3a63f8af7817578 Mon Sep 17 00:00:00 2001 From: verku Date: Wed, 6 Nov 2024 14:04:06 +0100 Subject: [PATCH] Update with simpler solution that does not require any manual configuration --- config/slurm/README.md | 26 +++++-------------- .../slurm/profile/config_plugin_dardel.yaml | 2 +- 2 files changed, 8 insertions(+), 20 deletions(-) diff --git a/config/slurm/README.md b/config/slurm/README.md index f470df8..e707a44 100644 --- a/config/slurm/README.md +++ b/config/slurm/README.md @@ -35,25 +35,13 @@ conda env create -f environment.yml -p /cfs/klemming/projects/supr/sllstore.../g ``` 4) Copy the configuration file `config/slurm/profile/config_plugin_dardel.yaml` -to `slurm/config.yaml`. This file specifies Snakemake parameters -that are used to run the pipeline, as well as compute resources -for each rule or group jobs to be run on Dardel. When you start -the pipeline on the command line with `--profile slurm` (as -described below), it expects a folder `slurm` with the file -`config.yaml` therein. - -The following changes to `slurm/config.yaml` are mandatory for -the pipeline to work for you on Dardel: - -- Please update the paths in line 8 (`apptainer-args`) with - the path to the project where all input data for GenErode - is located. Enter the same path before and after the `:`. - This is required for Apptainer (singularity) to correctly - bind (mount) the project directory so that the containers - run by the pipeline can find the input data. - -- Please add your slurm compute project ID in line 13 - (`slurm_account`). +to `slurm/config.yaml`. This file specifies Snakemake and apptainer +parameters that are used to run the pipeline, as well as compute +resources for each rule or group jobs to be run on Dardel. When +you start the pipeline on the command line with `--profile slurm` +(as described below), it expects a folder `slurm` with the file +`config.yaml` therein. Please make sure to add your slurm compute +project ID in line 13 of `slurm/config.yaml` (`slurm_account`). > If any rule or group job fails due to too little memory or run time, their compute resources can be updated in `slurm/config.yaml`. diff --git a/config/slurm/profile/config_plugin_dardel.yaml b/config/slurm/profile/config_plugin_dardel.yaml index a820e43..77fd813 100644 --- a/config/slurm/profile/config_plugin_dardel.yaml +++ b/config/slurm/profile/config_plugin_dardel.yaml @@ -5,7 +5,7 @@ jobs: 100 printshellcmds: true software-deployment-method: apptainer use-apptainer: True -apptainer-args: "-B /cfs/klemming/projects/supr/sllstoreXXXXXXXX:/cfs/klemming/projects/supr/sllstoreXXXXXXXX" # Update this path to the path to your project on Dardel where all input data is located (twice the same path) +apptainer-args: "-B /cfs/klemming" # slurm resources ## default-resources: applied to all jobs, overruled by resources defined below for jobs