From 99f4d9b9bd1bdd7465e9453c0ff209654a0ed8a0 Mon Sep 17 00:00:00 2001 From: arontommi Date: Wed, 6 Nov 2019 13:10:09 +0100 Subject: [PATCH 1/2] documentation on how to fix bianca cluster configuration problem --- docs/uppmax.md | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/docs/uppmax.md b/docs/uppmax.md index 07a7f14..d5bba37 100644 --- a/docs/uppmax.md +++ b/docs/uppmax.md @@ -26,6 +26,12 @@ If running on Bianca, you will have no internet connection and these configs wil Please use the nf-core helper tool on a different system to download the required pipeline files, and transfer them to bianca. This helper tool bundles the config files in this repo together with the pipeline files, so the profile will still be available. +Please note that Bianca only allocates 7 GB memory per core so max memory needs to be configured: + +```bash +--max_memory "112GB" +``` + ## Getting more memory If your nf-core pipeline run is running out of memory, you can run on a fat node with more memory using the following nextflow flags: From 5e7d13df89b45932cdc054fd1123d57c49f12dc1 Mon Sep 17 00:00:00 2001 From: Phil Ewels Date: Fri, 8 Nov 2019 10:59:34 +0100 Subject: [PATCH 2/2] Update uppmax.md --- docs/uppmax.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/uppmax.md b/docs/uppmax.md index d5bba37..61a1832 100644 --- a/docs/uppmax.md +++ b/docs/uppmax.md @@ -26,7 +26,7 @@ If running on Bianca, you will have no internet connection and these configs wil Please use the nf-core helper tool on a different system to download the required pipeline files, and transfer them to bianca. This helper tool bundles the config files in this repo together with the pipeline files, so the profile will still be available. -Please note that Bianca only allocates 7 GB memory per core so max memory needs to be configured: +Note that Bianca only allocates 7 GB memory per core so the max memory needs to be limited: ```bash --max_memory "112GB"