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Merge pull request #432 from nf-core/update/vsc_ugent

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Update vsc_ugent.config
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Matthias De Smet 2022-10-26 11:20:30 +02:00 committed by GitHub
commit 32f31fe98a
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1 changed files with 13 additions and 12 deletions
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conf/vsc_ugent.config
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@ -7,13 +7,19 @@ workDir = "$scratch_dir/work"
// Perform work directory cleanup when the run has succesfully completed // Perform work directory cleanup when the run has succesfully completed
// cleanup = true // cleanup = true
// Reduce the job submit rate to about 3 per second, this way the server won't be bombarded with jobs // Reduce the job submit rate to about 30 per minute, this way the server won't be bombarded with jobs
// Limit queueSize to keep job rate under control and avoid timeouts // Limit queueSize to keep job rate under control and avoid timeouts
executor { executor {
submitRateLimit = '3 sec' submitRateLimit = '30/1min'
queueSize = 50 queueSize = 50
} }
// Add backoff strategy to catch cluster timeouts
process {
errorStrategy = { sleep(Math.pow(2, task.attempt) * 200 as long); return 'retry' }
maxRetries = 5
}
// Specify that singularity should be used and where the cache dir will be for the images // Specify that singularity should be used and where the cache dir will be for the images
singularity { singularity {
enabled = true enabled = true
@ -30,7 +36,7 @@ profiles {
skitty { skitty {
params { params {
config_profile_description = 'HPC_SKITTY profile for use on the Skitty cluster of the VSC HPC.' config_profile_description = 'HPC_SKITTY profile for use on the Skitty cluster of the VSC HPC.'
config_profile_contact = 'Nicolas Vannieuwkerke (@nvnieuwk)' config_profile_contact = 'ict@cmgg.be'
config_profile_url = 'https://www.ugent.be/hpc/en' config_profile_url = 'https://www.ugent.be/hpc/en'
max_memory = 177.GB max_memory = 177.GB
max_cpus = 36 max_cpus = 36
@ -40,7 +46,6 @@ profiles {
process { process {
executor = 'slurm' executor = 'slurm'
queue = 'skitty' queue = 'skitty'
maxRetries = 2
scratch = "$scratch_dir" scratch = "$scratch_dir"
} }
} }
@ -48,7 +53,7 @@ profiles {
swalot { swalot {
params { params {
config_profile_description = 'HPC_SWALOT profile for use on the Swalot cluster of the VSC HPC.' config_profile_description = 'HPC_SWALOT profile for use on the Swalot cluster of the VSC HPC.'
config_profile_contact = 'Nicolas Vannieuwkerke (@nvnieuwk)' config_profile_contact = 'ict@cmgg.be'
config_profile_url = 'https://www.ugent.be/hpc/en' config_profile_url = 'https://www.ugent.be/hpc/en'
max_memory = 116.GB max_memory = 116.GB
max_cpus = 20 max_cpus = 20
@ -58,7 +63,6 @@ profiles {
process { process {
executor = 'slurm' executor = 'slurm'
queue = 'swalot' queue = 'swalot'
maxRetries = 2
scratch = "$scratch_dir" scratch = "$scratch_dir"
} }
} }
@ -66,7 +70,7 @@ profiles {
victini { victini {
params { params {
config_profile_description = 'HPC_VICTINI profile for use on the Victini cluster of the VSC HPC.' config_profile_description = 'HPC_VICTINI profile for use on the Victini cluster of the VSC HPC.'
config_profile_contact = 'Nicolas Vannieuwkerke (@nvnieuwk)' config_profile_contact = 'ict@cmgg.be'
config_profile_url = 'https://www.ugent.be/hpc/en' config_profile_url = 'https://www.ugent.be/hpc/en'
max_memory = 88.GB max_memory = 88.GB
max_cpus = 36 max_cpus = 36
@ -76,7 +80,6 @@ profiles {
process { process {
executor = 'slurm' executor = 'slurm'
queue = 'victini' queue = 'victini'
maxRetries = 2
scratch = "$scratch_dir" scratch = "$scratch_dir"
} }
} }
@ -84,7 +87,7 @@ profiles {
kirlia { kirlia {
params { params {
config_profile_description = 'HPC_KIRLIA profile for use on the Kirlia cluster of the VSC HPC.' config_profile_description = 'HPC_KIRLIA profile for use on the Kirlia cluster of the VSC HPC.'
config_profile_contact = 'Nicolas Vannieuwkerke (@nvnieuwk)' config_profile_contact = 'ict@cmgg.be'
config_profile_url = 'https://www.ugent.be/hpc/en' config_profile_url = 'https://www.ugent.be/hpc/en'
max_memory = 738.GB max_memory = 738.GB
max_cpus = 36 max_cpus = 36
@ -94,7 +97,6 @@ profiles {
process { process {
executor = 'slurm' executor = 'slurm'
queue = 'kirlia' queue = 'kirlia'
maxRetries = 2
scratch = "$scratch_dir" scratch = "$scratch_dir"
} }
} }
@ -102,7 +104,7 @@ profiles {
doduo { doduo {
params { params {
config_profile_description = 'HPC_DODUO profile for use on the Doduo cluster of the VSC HPC.' config_profile_description = 'HPC_DODUO profile for use on the Doduo cluster of the VSC HPC.'
config_profile_contact = 'Nicolas Vannieuwkerke (@nvnieuwk)' config_profile_contact = 'ict@cmgg.be'
config_profile_url = 'https://www.ugent.be/hpc/en' config_profile_url = 'https://www.ugent.be/hpc/en'
max_memory = 250.GB max_memory = 250.GB
max_cpus = 96 max_cpus = 96
@ -112,7 +114,6 @@ profiles {
process { process {
executor = 'slurm' executor = 'slurm'
queue = 'doduo' queue = 'doduo'
maxRetries = 2
scratch = "$scratch_dir" scratch = "$scratch_dir"
} }
} }