From ffd430250bdbacaeee0b313ba4510707d151846e Mon Sep 17 00:00:00 2001
From: Brice Letcher <bletcher@ebi.ac.uk>
Date: Mon, 20 Feb 2023 17:05:33 +0100
Subject: [PATCH] Updates to src/nextflow.config
* Restore `charliecloud` prefixes
* Remove `--bind`ing as nextflow takes care of it
* Use `queue` not `clusterOptions` for Lake partition
* Use `slurm` executor always under `process`
---
src/nextflow.config | 15 ++++-----------
1 file changed, 4 insertions(+), 11 deletions(-)
diff --git a/src/nextflow.config b/src/nextflow.config
index 20c5d307..97a98834 100644
--- a/src/nextflow.config
+++ b/src/nextflow.config
@@ -85,39 +85,32 @@ profiles {
}
psmn {
charliecloud.enabled = true
- cacheDir = "/Xnfs/abc/charliecloud"
- runOptions = "--bind /scratch:/scratch --bind /Xnfs:/Xnfs --bind /home:/home"
- readOnlyInputs = true
+ charliecloud.cacheDir = "/Xnfs/abc/charliecloud"
+ charliecloud.readOnlyInputs = true
process{
errorStrategy = { sleep(Math.pow(2, task.attempt) * 200 as long); return 'retry' }
maxRetries = 3
+ executor = "slurm"
+ queue = "Lake"
withLabel: big_mem_mono_cpus {
- executor = "slurm"
cpus = 1
memory = "128GB"
time = "24h"
- clusterOptions = "--partition=Lake"
}
withLabel: big_mem_multi_cpus {
- executor = "slurm"
cpus = 32
memory = "192GB"
time = "24h"
- clusterOptions = "--partition=Lake"
}
withLabel: small_mem_mono_cpus {
- executor = "slurm"
cpus = 1
memory = "16GB"
time = "24h"
- clusterOptions = "--partition=Lake"
}
withLabel: small_mem_multi_cpus {
- executor = "slurm"
cpus = 32
memory = "16GB"
time = "24h"
- clusterOptions = "--partition=Lake"
}
}
}
--
GitLab