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added requirements for uppmax cluster miarka
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4 changed files with 39 additions and 4 deletions
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@ -26,3 +26,15 @@ if (hostname ==~ "r.*") {
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if (hostname ==~ "i.*") {
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params.single_cpu_mem = 15.GB
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}
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// Miarka-specific config
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if (hostname ==~ "m.*") {
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params.single_cpu_mem = 7.GB
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process {
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withName:MapReads {
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cpus = {params.max_cpus}
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memory = {params.max_memory}
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}
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}
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}
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@ -36,6 +36,20 @@ def clusterOptionsCreator = { m ->
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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 + " --mem 4TB "
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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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@ -77,6 +91,15 @@ if (hostname.startsWith("i")) {
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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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// but what about the 96-core node?
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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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@ -15,4 +15,4 @@ Example: `nextflow run nf-core/sarek -profile uppmax`
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Specific configurations for uppmax clusters has been made for sarek.
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- Set paths to reference genomes
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- Set path to singularity containers for `irma`
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- Override resource requirements for MapReads on `miarka`
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@ -64,9 +64,9 @@ The UPPMAX nf-core configuration profile uses the `hostname` of the active envir
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- `bianca`
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- cpus available: 16 cpus
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- memory available: 109 GB
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- `irma`
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- cpus available: 16 cpus
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- memory available: 250 GB
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- `miarka`
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- cpus available: 48 cpus
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- memory available: 357 GB
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## Development config
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