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Update imperial.config

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Reworked to use internal profiles for the Imperial HPC and the MedBio cluster.
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Combiz Khozoie 2022-02-10 23:46:14 +00:00 committed by GitHub
parent e1d0bf0cd2
commit 38a05a6531
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1 changed files with 70 additions and 44 deletions
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conf/imperial.config
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@ -1,14 +1,76 @@
//Profile config names for nf-core/configs
params {
profiles {
imperial {
params {
// Config Params
config_profile_description = 'Imperial College London - HPC Profile -- provided by nf-core/configs.'
config_profile_contact = 'Combiz Khozoie (c.khozoie@imperial.ac.uk)'
config_profile_url = 'https://www.imperial.ac.uk/admin-services/ict/self-service/research-support/rcs/'
// Resources
max_memory = 480.GB
max_cpus = 40
max_time = 1000.h
}
process {
executor = 'pbspro'
// Process-specific resource requirements
withLabel:process_low {
// TARGET QUEUE: throughput
cpus = { 2 * task.attempt }
memory = { 12.GB * task.attempt }
time = { 4.h * task.attempt }
}
withLabel:process_medium {
// TARGET QUEUE: throughput
cpus = 8
memory = { 32.GB * task.attempt }
time = { 8.h * task.attempt }
}
withLabel:process_high {
// TARGET QUEUE: general
cpus = 32
memory = { 62.GB * task.attempt }
time = { 16.h * task.attempt }
}
withLabel:process_long {
// TARGET QUEUE: long
cpus = 8
memory = 96.GB
time = { 72.h * task.attempt }
}
withLabel:process_high_memory {
// TARGET QUEUE: large memory
cpus = { 10 * task.attempt }
memory = { 120.GB * task.attempt }
time = { 12.h * task.attempt }
}
}
}
medbio {
params {
// Config Params
config_profile_description = 'Imperial College London - MEDBIO QUEUE - HPC Profile -- provided by nf-core/configs.'
config_profile_contact = 'Combiz Khozoie (c.khozoie@imperial.ac.uk)'
config_profile_url = 'https://www.imperial.ac.uk/bioinformatics-data-science-group/resources/uk-med-bio/'
// Resources
max_memory = 480.GB
max_cpus = 40
max_time = 1000.h
}
process {
executor = 'pbspro'
queue = 'pqmedbio-tput'
//queue = 'med-bio' //!! this is an alias and shouldn't be used
}
}
}
executor {
@ -28,39 +90,3 @@ singularity {
autoMounts = true
runOptions = "-B /rds/,/rds/general/user/$USER/ephemeral/tmp/:/tmp,/rds/general/user/$USER/ephemeral/tmp/:/var/tmp"
}
process {
executor = 'pbspro'
// Process-specific resource requirements
withLabel:process_low {
// TARGET QUEUE: throughput
cpus = { check_max( 2 * task.attempt, 'cpus' ) }
memory = { check_max( 12.GB * task.attempt, 'memory' ) }
time = { check_max( 4.h * task.attempt, 'time' ) }
}
withLabel:process_medium {
// TARGET QUEUE: throughput
cpus = { check_max( 8, 'cpus' ) }
memory = { check_max( 32.GB * task.attempt, 'memory' ) }
time = { check_max( 8.h * task.attempt, 'time' ) }
}
withLabel:process_high {
// TARGET QUEUE: general
cpus = { check_max( 32, 'cpus' ) }
memory = { check_max( 62.GB * task.attempt, 'memory' ) }
time = { check_max( 16.h * task.attempt, 'time' ) }
}
withLabel:process_long {
// TARGET QUEUE: long
cpus = { check_max( 8, 'cpus' ) }
memory = { check_max( 96.GB, 'memory' ) }
time = { check_max( 72.h * task.attempt, 'time' ) }
}
withLabel:process_high_memory {
// TARGET QUEUE: large memory
cpus = { check_max( 10 * task.attempt, 'cpus' ) }
memory = { check_max( 120.GB * task.attempt, 'memory' ) }
time = { check_max( 12.h * task.attempt, 'time' ) }
}
}