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Merge pull request #226 from pontus/master
UPPMAX: Allow jobs needing more memory than thin nodes, pick up cluster info through slurm
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commit
33ae41bc91
1 changed files with 41 additions and 7 deletions
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@ -12,25 +12,58 @@ singularity {
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enabled = true
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}
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def hostname = "r1"
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try {
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hostname = "sinfo --local -N -h | grep -F -v CLUSTER: | head -1 | 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 ==~ "i.*") {
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return base
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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 ==~ "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 = { "-A $params.project ${params.clusterOptions ?: ''}" }
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clusterOptions = { clusterOptionsCreator(task.memory) }
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}
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params {
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save_reference = true
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max_memory = 125.GB
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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/uppnex/igenomes/'
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igenomes_base = '/sw/data/igenomes/'
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}
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def hostname = "hostname".execute().text.trim()
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if (hostname ==~ "b.*" || hostname ==~ "s.*") {
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params.max_memory = 109.GB
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if (hostname ==~ "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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}
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if (hostname ==~ "i.*") {
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@ -39,6 +72,7 @@ if (hostname ==~ "i.*") {
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if (hostname ==~ "r.*") {
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params.max_cpus = 20
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params.max_memory = 970.GB
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}
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profiles {
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