millironx/nf-configs
1
0
Fork 0
mirror of https://github.com/MillironX/nf-configs.git synced 2024-11-22 08:29:54 +00:00
Code Issues Releases Packages Activity

Merge pull request #385 from nvnieuwk/fix-for-failing-tests-vsc-ugent-profile

Browse source 
Fix for failing tests for vsc_ugent
This commit is contained in:
James A. Fellows Yates 2022-06-07 11:41:00 +02:00 committed by GitHub
commit 515cbf0a77
No known key found for this signature in database
GPG key ID: 4AEE18F83AFDEB23
1 changed files with 16 additions and 13 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

29
conf/vsc_ugent.config
View file

@ -1,8 +1,11 @@
// Define the Scratch directory
def scratch_dir = System.getenv("VSC_SCRATCH_VO_USER") ?: "scratch/"
// Specify the work directory // Specify the work directory
workDir = "$VSC_SCRATCH_VO_USER/work" workDir = "$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 10 per second, this way the server won't be bombarded with jobs // Reduce the job submit rate to about 10 per second, this way the server won't be bombarded with jobs
executor { executor {
@ -13,7 +16,7 @@ executor {
singularity { singularity {
enabled = true enabled = true
autoMounts = true autoMounts = true
cacheDir = "$VSC_SCRATCH_VO_USER/singularity" cacheDir = "$scratch_dir/singularity"
} }
// Define profiles for each cluster // Define profiles for each cluster
@ -32,8 +35,8 @@ profiles {
executor = 'slurm' executor = 'slurm'
queue = 'skitty' queue = 'skitty'
maxRetries = 2 maxRetries = 2
beforeScript = "export SINGULARITY_CACHEDIR=$VSC_SCRATCH_VO_USER/.singularity" beforeScript = "export SINGULARITY_CACHEDIR=$scratch_dir/.singularity"
scratch = "$VSC_SCRATCH_VO_USER" scratch = "$scratch_dir"
} }
} }
@ -51,8 +54,8 @@ profiles {
executor = 'slurm' executor = 'slurm'
queue = 'swalot' queue = 'swalot'
maxRetries = 2 maxRetries = 2
beforeScript = "export SINGULARITY_CACHEDIR=$VSC_SCRATCH_VO_USER/.singularity" beforeScript = "export SINGULARITY_CACHEDIR=$scratch_dir/.singularity"
scratch = "$VSC_SCRATCH_VO_USER" scratch = "$scratch_dir"
} }
} }
@ -70,8 +73,8 @@ profiles {
executor = 'slurm' executor = 'slurm'
queue = 'victini' queue = 'victini'
maxRetries = 2 maxRetries = 2
beforeScript = "export SINGULARITY_CACHEDIR=$VSC_SCRATCH_VO_USER/.singularity" beforeScript = "export SINGULARITY_CACHEDIR=$scratch_dir/.singularity"
scratch = "$VSC_SCRATCH_VO_USER" scratch = "$scratch_dir"
} }
} }
@ -89,8 +92,8 @@ profiles {
executor = 'slurm' executor = 'slurm'
queue = 'kirlia' queue = 'kirlia'
maxRetries = 2 maxRetries = 2
beforeScript = "export SINGULARITY_CACHEDIR=$VSC_SCRATCH_VO_USER/.singularity" beforeScript = "export SINGULARITY_CACHEDIR=$scratch_dir/.singularity"
scratch = "$VSC_SCRATCH_VO_USER" scratch = "$scratch_dir"
} }
} }
@ -108,8 +111,8 @@ profiles {
executor = 'slurm' executor = 'slurm'
queue = 'doduo' queue = 'doduo'
maxRetries = 2 maxRetries = 2
beforeScript = "export SINGULARITY_CACHEDIR=$VSC_SCRATCH_VO_USER/.singularity" beforeScript = "export SINGULARITY_CACHEDIR=$scratch_dir/.singularity"
scratch = "$VSC_SCRATCH_VO_USER" scratch = "$scratch_dir"
} }
} }
} }