millironx/nf-configs
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update for vsc_ugent

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This commit is contained in:
Nicolas Vannieuwkerke 2022-06-07 11:33:22 +02:00
parent 4587fc4215
commit 44e25830e4
1 changed files with 16 additions and 13 deletions
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29
conf/vsc_ugent.config
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@ -1,8 +1,11 @@
// Define the Scratch directory
def scratch_dir = System.getenv("VSC_SCRATCH_VO_USER") ?: "scratch/"
// Specify the work directory
workDir = "$VSC_SCRATCH_VO_USER/work"
workDir = "$scratch_dir/work"
// Perform work directory cleanup when the run has succesfully completed
cleanup = true
// cleanup = true
// Reduce the job submit rate to about 10 per second, this way the server won't be bombarded with jobs
executor {
@ -13,7 +16,7 @@ executor {
singularity {
enabled = true
autoMounts = true
cacheDir = "$VSC_SCRATCH_VO_USER/singularity"
cacheDir = "$scratch_dir/singularity"
}
// Define profiles for each cluster
@ -32,8 +35,8 @@ profiles {
executor = 'slurm'
queue = 'skitty'
maxRetries = 2
beforeScript = "export SINGULARITY_CACHEDIR=$VSC_SCRATCH_VO_USER/.singularity"
scratch = "$VSC_SCRATCH_VO_USER"
beforeScript = "export SINGULARITY_CACHEDIR=$scratch_dir/.singularity"
scratch = "$scratch_dir"
}
}
@ -51,8 +54,8 @@ profiles {
executor = 'slurm'
queue = 'swalot'
maxRetries = 2
beforeScript = "export SINGULARITY_CACHEDIR=$VSC_SCRATCH_VO_USER/.singularity"
scratch = "$VSC_SCRATCH_VO_USER"
beforeScript = "export SINGULARITY_CACHEDIR=$scratch_dir/.singularity"
scratch = "$scratch_dir"
}
}
@ -70,8 +73,8 @@ profiles {
executor = 'slurm'
queue = 'victini'
maxRetries = 2
beforeScript = "export SINGULARITY_CACHEDIR=$VSC_SCRATCH_VO_USER/.singularity"
scratch = "$VSC_SCRATCH_VO_USER"
beforeScript = "export SINGULARITY_CACHEDIR=$scratch_dir/.singularity"
scratch = "$scratch_dir"
}
}
@ -89,8 +92,8 @@ profiles {
executor = 'slurm'
queue = 'kirlia'
maxRetries = 2
beforeScript = "export SINGULARITY_CACHEDIR=$VSC_SCRATCH_VO_USER/.singularity"
scratch = "$VSC_SCRATCH_VO_USER"
beforeScript = "export SINGULARITY_CACHEDIR=$scratch_dir/.singularity"
scratch = "$scratch_dir"
}
}
@ -108,8 +111,8 @@ profiles {
executor = 'slurm'
queue = 'doduo'
maxRetries = 2
beforeScript = "export SINGULARITY_CACHEDIR=$VSC_SCRATCH_VO_USER/.singularity"
scratch = "$VSC_SCRATCH_VO_USER"
beforeScript = "export SINGULARITY_CACHEDIR=$scratch_dir/.singularity"
scratch = "$scratch_dir"
}
}
}