From 12ec22838c5a23f74940b2912aa98bd3e3a78419 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Tue, 26 Nov 2019 15:29:03 +0100 Subject: [PATCH] Specified max sources currently at SDAG limits (exceeds cdag) --- docs/shh.md | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/docs/shh.md b/docs/shh.md index 78abed0..ec268b5 100644 --- a/docs/shh.md +++ b/docs/shh.md @@ -11,7 +11,11 @@ To use, run the pipeline with `-profile shh`. This will download and launch the however this will likely change to a read-only directory in the future that will be managed by IT. This configuration will automatically choose the correct SLURM queue (`short`,`medium`,`long`,`supercruncher`) depending on the time and memory required by each process. + Please note that there is no `supercruncher` queue on CDAG. >NB: You will need an account and VPN access to use the cluster at MPI-SHH in order to run the pipeline. If in doubt contact IT. + >NB: Nextflow will need to submit the jobs via SLURM to the clusters and as such the commands above will have to be executed on one of the head nodes. If in doubt contact IT. + +>NB: The maximum CPUs/Mem are currently adapted for SDAG resource maximums - i.e. will exceed CDAG. Be careful when running larges jobs that error-retries may exceed limits and get 'stuck' in SLURM.