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125 lines
3.7 KiB
Plaintext
125 lines
3.7 KiB
Plaintext
// UPPMAX Config Profile
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params {
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// Description is overwritten for other clusters below
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config_profile_description = 'UPPMAX (Bianca) cluster profile provided by nf-core/configs.'
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config_profile_contact = 'Phil Ewels (@ewels)'
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config_profile_url = 'https://www.uppmax.uu.se/'
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project = null
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clusterOptions = null
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schema_ignore_params = "genomes,input_paths,cluster-options,clusterOptions,project"
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save_reference = true
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// Defaults set for Bianca - other clusters set below
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max_memory = 500.GB
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max_cpus = 16
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max_time = 240.h
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// illumina iGenomes reference file paths on UPPMAX
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igenomes_base = '/sw/data/igenomes/'
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}
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singularity {
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enabled = true
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envWhitelist = 'SNIC_TMP'
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}
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def hostname = "r1"
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try {
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hostname = ['/bin/bash', '-c', 'sinfo --local -N -h | grep -m 1 -F -v CLUSTER: | cut -f1 -d" "'].execute().text.trim()
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} catch (java.io.IOException e) {
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System.err.println("WARNING: Could not run sinfo to determine current cluster, defaulting to rackham")
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}
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// closure to create a suitable clusterOptions
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def clusterOptionsCreator = { m ->
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String base = "-A $params.project ${params.clusterOptions ?: ''}"
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// Do not use -p node on irma or if a thin node/core is enough
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if (m <= 125.GB || hostname.startsWith("i")) {
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return base
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}
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// cluster is miarka
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if (hostname.startsWith("m")) {
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// job will fit on a regular node
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if (m <= 357.GB) {
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return base
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}
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// job requires at least a 2TB node
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if (m <= 2000.GB) {
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return base + " --mem 2TB "
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}
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// job requires the largest node
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return base + " -C mem4TB "
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}
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if (m <= 250.GB) {
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return base + " -p node -C mem256GB "
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}
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// Use mem1TB for remaining cases on rackham (no 512 Gbyte nodes)
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if (hostname.startsWith("r")) {
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return base + " -p node -C mem1TB "
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}
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if (m > 500.GB) {
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// Special case for snowy very fat node (only remaining case that's above 500 GB)
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return base + " -p veryfat "
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}
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// Should only be cases for mem512GB left (snowy and bianca)
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return base + " -p node -C mem512GB "
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}
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process {
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executor = 'slurm'
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clusterOptions = { clusterOptionsCreator(task.memory) }
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// Use node local storage for execution.
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scratch = '$SNIC_TMP'
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}
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// Cluster: Snowy
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// Caution: Bianca nodes will be project name-nodenumber, e.g. sens2021500-001
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// so cannot rely on just starting with 's'
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if (hostname.matches("^s[0-9][0-9]*")) {
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params.max_time = 700.h
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params.max_memory = 3880.GB
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params.config_profile_description = 'UPPMAX (Snowy) cluster profile provided by nf-core/configs.'
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}
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// Cluster: Irma
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if (hostname.startsWith("i")) {
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params.max_memory = 250.GB
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params.config_profile_description = 'UPPMAX (Irma) cluster profile provided by nf-core/configs.'
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}
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// Cluster: Miarka
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if (hostname.startsWith("m")) {
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params.max_memory = 357.GB
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params.max_cpus = 48
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params.max_time = 480.h
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params.config_profile_description = 'UPPMAX (Miarka) cluster profile provided by nf-core/configs.'
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}
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// Cluster: Rackham
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if (hostname.startsWith("r")) {
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params.max_cpus = 20
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params.max_memory = 970.GB
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params.config_profile_description = 'UPPMAX (Rackham) cluster profile provided by nf-core/configs.'
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}
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// Cluster: Bianca - set in initial params block above
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// Additional devel profile for running in devel queue
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// Run with `-profile upppmax,devel`
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profiles {
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devel {
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params {
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config_profile_description = 'Testing & development profile for UPPMAX, provided by nf-core/configs.'
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// Max resources to be requested by a devel job
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max_memory = 120.GB
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max_time = 1.h
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}
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executor.queueSize = 1
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process.queue = 'devel'
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}
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}
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