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Revised base and sarek configs to provide memory on per core basis

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lquayle88 2022-10-04 00:25:16 +01:00
parent e7ac3ecd19
commit 3f2ffa314d
2 changed files with 11 additions and 11 deletions
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20
conf/pipeline/sarek/sbc_sharc.config
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@ -25,19 +25,19 @@ process {
withLabel:process_low { withLabel:process_low {
cpus = { check_max( 2 * task.attempt, 'cpus' ) } cpus = { check_max( 2 * task.attempt, 'cpus' ) }
memory = { check_max( 8.GB * task.attempt, 'memory' ) } memory = { check_max( 16.GB * task.attempt, 'memory' ) }
time = { check_max( 6.h * task.attempt, 'time' ) } time = { check_max( 4.h * task.attempt, 'time' ) }
} }
withLabel:process_medium { withLabel:process_medium {
cpus = { check_max( 6 * task.attempt, 'cpus' ) } cpus = { check_max( 6 * task.attempt, 'cpus' ) }
memory = { check_max( 12.GB * task.attempt, 'memory' ) } memory = { check_max( 72.GB * task.attempt, 'memory' ) }
time = { check_max( 8.h * task.attempt, 'time' ) } time = { check_max( 6.h * task.attempt, 'time' ) }
} }
withLabel:process_high { withLabel:process_high {
cpus = { check_max( 12 * task.attempt, 'cpus' ) } cpus = { check_max( 12 * task.attempt, 'cpus' ) }
memory = { check_max( 16.GB * task.attempt, 'memory' ) } memory = { check_max( 192.GB * task.attempt, 'memory' ) }
time = { check_max( 8.h * task.attempt, 'time' ) } time = { check_max( 8.h * task.attempt, 'time' ) }
} }
@ -46,7 +46,7 @@ process {
} }
withLabel:process_high_memory { withLabel:process_high_memory {
memory = { check_max( 16.GB * task.attempt, 'memory' ) } memory = { check_max( 240.GB * task.attempt, 'memory' ) }
} }
@ -54,7 +54,7 @@ process {
withName:'BWAMEM1_MEM|BWAMEM2_MEM' { withName:'BWAMEM1_MEM|BWAMEM2_MEM' {
cpus = { check_max( 12 * task.attempt, 'cpus' ) } cpus = { check_max( 12 * task.attempt, 'cpus' ) }
memory = { check_max( 16.GB * task.attempt, 'memory' ) } memory = { check_max( 192.GB * task.attempt, 'memory' ) }
time = { check_max( 8.h * task.attempt, 'time' ) } time = { check_max( 8.h * task.attempt, 'time' ) }
} }
@ -71,12 +71,12 @@ process {
} }
withName:'GATK4_APPLYBQSR|GATK4_APPLYBQSR_SPARK|GATK4_BASERECALIBRATOR|GATK4_GATHERBQSRREPORTS' { withName:'GATK4_APPLYBQSR|GATK4_APPLYBQSR_SPARK|GATK4_BASERECALIBRATOR|GATK4_GATHERBQSRREPORTS' {
memory = { check_max( 16.GB * task.attempt, 'memory' ) } memory = { check_max( 72.GB * task.attempt, 'memory' ) }
} }
withName:'GATK4_MARKDUPLICATES' { withName:'GATK4_MARKDUPLICATES' {
cpus = { check_max( 8 * task.attempt, 'cpus' ) } cpus = { check_max( 12 * task.attempt, 'cpus' ) }
memory = { check_max( 16.GB * task.attempt, 'memory' ) } memory = { check_max( 240.GB * task.attempt, 'memory' ) }
time = { check_max( 8.h * task.attempt, 'time' ) } time = { check_max( 8.h * task.attempt, 'time' ) }
} }

2
conf/sbc_sharc.config
View file

@ -42,7 +42,7 @@ process {
executor = 'sge' executor = 'sge'
penv = 'smp' penv = 'smp'
queue = { task.time <= 6.h ? 'shortint.q' : 'all.q' } queue = { task.time <= 6.h ? 'shortint.q' : 'all.q' }
clusterOptions = { "-l rmem=${task.memory.toGiga()}G" } clusterOptions = { "-l rmem=${task.memory.toGiga()/task.cpus}G" }
} }