mirror of
https://github.com/MillironX/nf-configs.git
synced 2024-11-15 06:03:10 +00:00
102 lines
3.1 KiB
Text
102 lines
3.1 KiB
Text
// UPPMAX Config Profile
|
|
params {
|
|
// Description is overwritten for other clusters below
|
|
config_profile_description = 'UPPMAX (Bianca) cluster profile provided by nf-core/configs.'
|
|
config_profile_contact = 'Phil Ewels (@ewels)'
|
|
config_profile_url = 'https://www.uppmax.uu.se/'
|
|
project = null
|
|
clusterOptions = null
|
|
schema_ignore_params = "genomes,input_paths,cluster-options,clusterOptions,project"
|
|
save_reference = true
|
|
// Defaults set for Bianca - other clusters set below
|
|
max_memory = 500.GB
|
|
max_cpus = 16
|
|
max_time = 240.h
|
|
// illumina iGenomes reference file paths on UPPMAX
|
|
igenomes_base = '/sw/data/igenomes/'
|
|
}
|
|
|
|
singularity {
|
|
enabled = true
|
|
envWhitelist = 'SNIC_TMP'
|
|
}
|
|
|
|
def hostname = "r1"
|
|
try {
|
|
hostname = "sinfo --local -N -h | grep -m 1 -F -v CLUSTER: | 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 ${params.clusterOptions ?: ''}"
|
|
// Do not use -p node on irma or if a thin node/core is enough
|
|
if (m <= 125.GB || hostname.startsWith("i")) {
|
|
return base
|
|
}
|
|
|
|
if (m <= 250.GB) {
|
|
return base + " -p node -C mem256GB "
|
|
}
|
|
|
|
|
|
// Use mem1TB for remaining cases on rackham (no 512 Gbyte nodes)
|
|
if (hostname.startsWith("r")) {
|
|
return base + " -p node -C mem1TB "
|
|
}
|
|
|
|
if (m > 500.GB) {
|
|
// Special case for snowy very fat node (only remaining case that's above 500 GB)
|
|
return base + " -p veryfat "
|
|
}
|
|
|
|
// Should only be cases for mem512GB left (snowy and bianca)
|
|
return base + " -p node -C mem512GB "
|
|
}
|
|
|
|
process {
|
|
executor = 'slurm'
|
|
clusterOptions = { clusterOptionsCreator(task.memory) }
|
|
// Use node local storage for execution.
|
|
scratch = '$SNIC_TMP'
|
|
}
|
|
|
|
// Cluster: Snowy
|
|
// Caution: Bianca nodes will be project name-nodenumber, e.g. sens2021500-001
|
|
// so cannot rely on just starting with 's'
|
|
if (hostname.matches("^s[0-9][0-9]*")) {
|
|
params.max_time = 700.h
|
|
params.max_memory = 3880.GB
|
|
params.config_profile_description = 'UPPMAX (Snowy) cluster profile provided by nf-core/configs.'
|
|
}
|
|
|
|
// Cluster: Irma
|
|
if (hostname.startsWith("i")) {
|
|
params.max_memory = 250.GB
|
|
params.config_profile_description = 'UPPMAX (Irma) cluster profile provided by nf-core/configs.'
|
|
}
|
|
|
|
// Cluster: Rackham
|
|
if (hostname.startsWith("r")) {
|
|
params.max_cpus = 20
|
|
params.max_memory = 970.GB
|
|
params.config_profile_description = 'UPPMAX (Rackham) cluster profile provided by nf-core/configs.'
|
|
}
|
|
|
|
// Cluster: Bianca - set in initial params block above
|
|
|
|
// Additional devel profile for running in devel queue
|
|
// Run with `-profile upppmax,devel`
|
|
profiles {
|
|
devel {
|
|
params {
|
|
config_profile_description = 'Testing & development profile for UPPMAX, provided by nf-core/configs.'
|
|
// Max resources to be requested by a devel job
|
|
max_memory = 120.GB
|
|
max_time = 1.h
|
|
}
|
|
executor.queueSize = 1
|
|
process.queue = 'devel'
|
|
}
|
|
}
|