millironx/nf-configs
1
0
Fork 0
mirror of https://github.com/MillironX/nf-configs.git synced 2024-09-21 14:02:05 +00:00
Code Issues Releases Packages Activity

Use node queue when more memory than thin nodes have

Browse source
This commit is contained in:
Pontus Freyhult 2021-04-07 17:07:49 +02:00
parent 71a97ba316
commit c5070f3eba
1 changed files with 28 additions and 5 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

33
conf/uppmax.config
View file

@ -9,25 +9,48 @@ singularity {
enabled = true enabled = true
} }
def hostname = "hostname".execute().text.trim()
process { process {
// 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 "
}
// Remaining cases use the largest available node (1 Tbyte for rackham, 512 Gbyte for others)
if (hostname ==~ "r.*") {
return base + " -p node -C mem1TB "
}
return base + " -p node -C mem512GB "
}
executor = 'slurm' executor = 'slurm'
clusterOptions = { "-A $params.project ${params.clusterOptions ?: ''}" } clusterOptions = { clusterOptionsCreator(task.memory) }
} }
params { params {
save_reference = true save_reference = true
max_memory = 125.GB max_memory = 970.GB
max_cpus = 16 max_cpus = 16
max_time = 240.h max_time = 240.h
// illumina iGenomes reference file paths on UPPMAX // illumina iGenomes reference file paths on UPPMAX
igenomes_base = '/sw/data/uppnex/igenomes/' igenomes_base = '/sw/data/uppnex/igenomes/'
} }
def hostname = "hostname".execute().text.trim() if (hostname ==~ "b.*") {
params.max_memory = 500.GB
}
if (hostname ==~ "b.*" || hostname ==~ "s.*") { if (hostname ==~ "s.*") {
params.max_memory = 109.GB params.max_memory = 500.GB
params.max_time = 700.h
} }
if (hostname ==~ "i.*") { if (hostname ==~ "i.*") {