millironx/nf-configs
1
0
Fork 0
mirror of https://github.com/MillironX/nf-configs.git synced 2024-11-22 00:26:03 +00:00
Code Issues Releases Packages Activity

Merge pull request #226 from pontus/master

Browse source 
UPPMAX: Allow jobs needing more memory than thin nodes, pick up cluster info through slurm
This commit is contained in:
Pontus Freyhult 2021-10-10 12:05:07 +02:00 committed by GitHub
commit 33ae41bc91
No known key found for this signature in database
GPG key ID: 4AEE18F83AFDEB23
1 changed files with 41 additions and 7 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

48
conf/uppmax.config
View file

@ -12,25 +12,58 @@ singularity {
enabled = true
}
def hostname = "r1"
try {
hostname = "sinfo --local -N -h | grep -F -v CLUSTER: | head -1 | cut -f1 -d' ' ".execute().text.trim()
} catch (java.io.IOException e) {
System.err.println("WARNING: Could not run sinfo to determine current cluster, defaulting to rackham")
}
// closure to create a suitable clusterOptions
def clusterOptionsCreator = { m ->
String base = "-A $params.project ${params.clusterOptions ?: ''}"
// Do not use -p node on irma or if a thin node/core is enough
if (m < 125.GB || hostname ==~ "i.*") {
return base
}
if (m < 250.GB) {
return base + " -p node -C mem256GB "
}
// Use mem1TB for remaining cases on rackham (no 512 Gbyte nodes)
if (hostname ==~ "r.*") {
return base + " -p node -C mem1TB "
}
if (m > 500.GB) {
// Special case for snowy very fat node (only remaining case that's above 500 GB)
return base + " -p veryfat "
}
// Should only be cases for mem512GB left (snowy and bianca)
return base + " -p node -C mem512GB "
}
process {
executor = 'slurm'
clusterOptions = { "-A $params.project ${params.clusterOptions ?: ''}" }
clusterOptions = { clusterOptionsCreator(task.memory) }
}
params {
save_reference = true
max_memory = 125.GB
max_memory = 500.GB
max_cpus = 16
max_time = 240.h
// illumina iGenomes reference file paths on UPPMAX
igenomes_base = '/sw/data/uppnex/igenomes/'
igenomes_base = '/sw/data/igenomes/'
}
def hostname = "hostname".execute().text.trim()
if (hostname ==~ "b.*" || hostname ==~ "s.*") {
params.max_memory = 109.GB
if (hostname ==~ "s[0-9][0-9]*") {
params.max_time = 700.h
params.max_memory = 3880.GB
}
if (hostname ==~ "i.*") {
@ -39,6 +72,7 @@ if (hostname ==~ "i.*") {
if (hostname ==~ "r.*") {
params.max_cpus = 20
params.max_memory = 970.GB
}
profiles {