From 40d094c7c42a64fecdb39dd1a1434279440d34cf Mon Sep 17 00:00:00 2001 From: Verena Kutschera Date: Wed, 6 Nov 2024 10:03:54 +0100 Subject: [PATCH] Update README.md with new instructions on apptainer parameter --- config/slurm/README.md | 39 +++++++++++++++++++++++++++------------ 1 file changed, 27 insertions(+), 12 deletions(-) diff --git a/config/slurm/README.md b/config/slurm/README.md index 439ac3c..f470df8 100644 --- a/config/slurm/README.md +++ b/config/slurm/README.md @@ -35,23 +35,38 @@ 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 compute resources -for each rule or group jobs to be run on Dardel. Any rule or -group job that is not listed under `set-threads` or `set-resources` -uses default resources specified under `default-resources`. If -any rule or group job fails due to too little memory or run -time, their compute resources can be updated in this file. Please -add your slurm compute project ID in line 13 of `slurm/config.yaml` -(`slurm_account`). - -> Note that memory requirements are specified three times in -the configuration file: 1) under `set-threads` (used by Snakemake +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`). + +> 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`. +Note that memory requirements are specified three times in the +configuration file: 1) under `set-threads` (used by Snakemake to specify threads in rules), 2) under `set-resources` and therein under `mem_mb`, specifying the memory in Megabytes (multiplying the number of threads with the available memory per thread), and 3) under `set-resources` and therein under `cpus-per-task` (the same number as specified under `set-threads`, required for -correct memory assignment on Dardel). +correct memory assignment on Dardel). Any rule or group job that +is not listed under `set-threads` or `set-resources` uses the +resources specified under`default-resources`. 5) Start GenErode the following: