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update PSMN configuration to keep up with cluster changes #788

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update PSMN configuration to keep up with cluster changes #788

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4114403
psmn.config : delete Lake-Flix
helenepolveche Oct 31, 2024
9dc115c
Merge pull request #2 from helenepolveche/patch-1
l-modolo Nov 5, 2024
cdcfc1d
psmn.config: update slurm partition information
l-modolo Nov 5, 2024
5509eca
Merge branch 'master' of github.com:nf-core/configs
l-modolo Nov 5, 2024
fddf257
psmn.config: update number of space for linter
l-modolo Nov 5, 2024
bdfc3e0
psmn.config: add back resourceLimits
l-modolo Nov 6, 2024
df37bd9
psmn.config: change clusterOption --parition to queue
l-modolo Nov 6, 2024
52d57ab
Merge branch 'master' into master
l-modolo Nov 12, 2024
13278be
Merge branch 'master' into master
jfy133 Nov 13, 2024
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59 changes: 27 additions & 32 deletions conf/psmn.config
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Original file line number Diff line number Diff line change
Expand Up @@ -13,49 +13,44 @@ charliecloud {
}

process {
resourceLimits = [
memory: 370.GB,
cpus: 32,
time: 96.h
]
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Was this removal intended? Seems like you'd want to keep resourceLimits around.

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Using clusterOptions to select partition is not wrong, but one could consider queue instead to manage those needing to override clusterOptions.

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Oops, I missed that - yes the resource limits definitely should be included!

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Thank you for the comment, so I can replace :

clusterOptions = "--partition=E5,Lake"

by :

queue = "E5,Lake"

with slurm ?

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Yes.

executor = 'slurm'
clusterOptions = "--partition=E5,Lake,Lake-flix"
executor = 'slurm'
clusterOptions = "--partition=E5,Lake"

cpus = 1
memory = 32.GB
time = 24.h
cpus = 1
memory = 32.GB
time = 24.h

withLabel: 'process_single|process_single_thread|sc_tiny|sc_small|sc_medium' {
clusterOptions = "--partition=E5,Lake,Lake-flix"
cpus = 1
memory = 114.GB
time = 24.h
clusterOptions = "--partition=Lake"
cpus = 1
memory = 96.GB
time = 24.h
}
withLabel: 'process_low|mc_small|process_very_low' {
clusterOptions = "--partition=E5,Lake,Lake-flix"
cpus = 16
memory = 90.GB
time = 24.h
withLabel:'process_low|mc_small|process_very_low' {
clusterOptions = "--partition=Lake"
cpus = 16
memory = 80.GB
time = 24.h
}
withLabel: 'process_medium|mc_medium' {
clusterOptions = "--partition=Lake,Lake-flix"
cpus = 32
memory = 180.GB
time = 48.h
withLabel:'process_medium|mc_medium' {
clusterOptions = "--partition=Lake"
cpus = 32
memory = 180.GB
time = 48.h
}
withLabel: 'process_high|mc_large|mc_huge|process_high_cpus|cpus_max' {
clusterOptions = "--partition=Lake,Lake-flix"
cpus = 32
memory = 370.GB
time = 48.h
withLabel:'process_high|mc_large|mc_huge|process_high_cpus|cpus_max' {
clusterOptions = "--partition=Lake"
cpus = 32
memory = 370.GB
time = 48.h
}
withLabel: 'process_long|process_maximum_time|process_long_parallelized' {
clusterOptions = "--partition=Lake"
time = 96.h
time = 96.h
}
withLabel: 'process_high_memory|memory_max' {
clusterOptions = "--partition=Lake,Lake-flix"
memory = 370.GB
clusterOptions = "--partition=Epyc"
memory = 500.GB
}
withLabel: gpu {
clusterOptions = "--partition=E5-GPU"
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