From 8d5ae4c3ab53c8892bce378c58fb0e881c2e6cd0 Mon Sep 17 00:00:00 2001 From: Austyn Trull Date: Tue, 23 Aug 2022 15:30:13 -0500 Subject: [PATCH 1/2] Committing changes made by Brandon Wilk so that singularity containers will use scratch space --- conf/cheaha.config | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/conf/cheaha.config b/conf/cheaha.config index 323a625..578259c 100644 --- a/conf/cheaha.config +++ b/conf/cheaha.config @@ -5,9 +5,15 @@ params { config_profile_url = 'https://www.uab.edu/cores/ircp/bds' } +env { + TMPDIR="$USER_SCRATCH" + SINGULARITY_TMPDIR="$USER_SCRATCH" +} + singularity { enabled = true autoMounts = true + runOptions = "--contain --workdir $USER_SCRATCH" } process { From 90f638d3761a6b8fa6560e1a3d09a6a62a6ee44a Mon Sep 17 00:00:00 2001 From: Austyn Trull Date: Mon, 29 Aug 2022 10:47:46 -0500 Subject: [PATCH 2/2] Updating the cheaha documentation to clarify that /data/temporary-scratch/atrull will be used as storage for files that would normally go into one of the temporary locations when using Singularity --- docs/cheaha.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/docs/cheaha.md b/docs/cheaha.md index 9d871c3..fb04c88 100644 --- a/docs/cheaha.md +++ b/docs/cheaha.md @@ -13,6 +13,8 @@ module load Singularity module load Nextflow ``` +Various tasks will be run inside of Singularity containers and all temp files typically written to `/tmp` and `/var/tmp` are instead written to the path pointed to by the `USER_SCRATCH` environment variable. This means that these temp files are stored in a user specific location, making them inaccessible to other users for pipeline reruns. Some of these temp files can be large and cleanup is also the responsibility of the user. + All of the intermediate files required to run the pipeline will be stored in the `work/` directory. It is recommended to delete this directory after the pipeline has finished successfully because it can get quite large, and all of the main output files will be saved in the `results/` directory anyway. > NB: You will need an account to use the HPC cluster on Cheaha in order to run the pipeline. If in doubt contact UAB IT Research Computing.