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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,5 +1,26 @@ | ||
| // Set up the Tier 1 parameter | ||
| params.validationSchemaIgnoreParams = params.validationSchemaIgnoreParams.toString() + ",tier1_project" | ||
| if (!params.tier1_project) { | ||
| params.tier1_project = null | ||
| } | ||
|
|
||
| // Get the hostname and check some values for tier1 | ||
| def hostname = "doduo" | ||
| try { | ||
| hostname = ['/bin/bash', '-c', 'sinfo --local -N -h | head -n 1 | cut -d " " -f1'].execute().text.trim() | ||
| } catch (java.io.IOException e) { | ||
| System.err.println("WARNING: Could not run sinfo to determine current cluster, defaulting to doduo") | ||
| } | ||
|
|
||
| if(!params.tier1_project && hostname.contains("dodrio")){ | ||
| System.err.println("Please specify your project with --tier1_project in your Nextflow command or with params.tier1_project in your config file.") | ||
| System.exit(1) | ||
| } | ||
|
|
||
| // Define the Scratch directory | ||
| def scratch_dir = System.getenv("VSC_SCRATCH_VO_USER") ?: System.getenv("VSC_SCRATCH") | ||
| def scratch_dir = System.getenv("VSC_SCRATCH_PROJECTS_BASE") ? "${System.getenv("VSC_SCRATCH_PROJECTS_BASE")}/${params.tier1_project}" : // Tier 1 scratch | ||
| System.getenv("VSC_SCRATCH_VO_USER") ?: // VO scratch | ||
| System.getenv("VSC_SCRATCH") // user scratch | ||
|
|
||
| // Specify the work directory | ||
| workDir = "$scratch_dir/work" | ||
|
|
@@ -35,7 +56,7 @@ env { | |
|
|
||
| // AWS maximum retries for errors (This way the pipeline doesn't fail if the download fails one time) | ||
| aws { | ||
| maxErrorRetry = 3 | ||
| maxErrorRetry = 3 | ||
| } | ||
|
|
||
| // Define profiles for each cluster | ||
|
|
@@ -120,6 +141,142 @@ profiles { | |
| } | ||
| } | ||
|
|
||
| cpu_rome { | ||
| params { | ||
| config_profile_description = 'HPC_DODRIO_cpu_rome profile for use on the Dodrio/cpu_rome cluster of the VSC HPC.' | ||
| config_profile_contact = '[email protected]' | ||
| config_profile_url = 'https://www.ugent.be/hpc/en' | ||
| max_memory = 256.GB | ||
| max_cpus = 128 | ||
| max_time = "3day" | ||
| } | ||
|
|
||
| process { | ||
| executor = 'slurm' | ||
| queue = 'dodrio/cpu_rome' | ||
| clusterOptions = "-A ${params.tier1_project}" | ||
| } | ||
| } | ||
|
|
||
| cpu_rome_512 { | ||
| params { | ||
| config_profile_description = 'HPC_DODRIO_cpu_rome_512 profile for use on the Dodrio/cpu_rome_512 cluster of the VSC HPC.' | ||
| config_profile_contact = '[email protected]' | ||
| config_profile_url = 'https://www.ugent.be/hpc/en' | ||
| max_memory = 512.GB | ||
| max_cpus = 128 | ||
| max_time = "3day" | ||
| } | ||
|
|
||
| process { | ||
| executor = 'slurm' | ||
| queue = 'dodrio/cpu_rome_512' | ||
| clusterOptions = "-A ${params.tier1_project}" | ||
| } | ||
| } | ||
|
|
||
| cpu_milan { | ||
| params { | ||
| config_profile_description = 'HPC_DODRIO_cpu_milan profile for use on the Dodrio/cpu_milan cluster of the VSC HPC.' | ||
| config_profile_contact = '[email protected]' | ||
| config_profile_url = 'https://www.ugent.be/hpc/en' | ||
| max_memory = 256.GB | ||
| max_cpus = 128 | ||
| max_time = "3day" | ||
| } | ||
|
|
||
| process { | ||
| executor = 'slurm' | ||
| queue = 'dodrio/cpu_milan' | ||
| clusterOptions = "-A ${params.tier1_project}" | ||
| } | ||
| } | ||
|
|
||
| gpu_rome_a100_40 { | ||
| params { | ||
| config_profile_description = 'HPC_DODRIO_gpu_rome_a100_40 profile for use on the Dodrio/gpu_rome_a100_40 cluster of the VSC HPC.' | ||
| config_profile_contact = '[email protected]' | ||
| config_profile_url = 'https://www.ugent.be/hpc/en' | ||
| max_memory = 256.GB | ||
| max_cpus = 48 | ||
| max_time = "3day" | ||
| } | ||
|
|
||
| process { | ||
| executor = 'slurm' | ||
| queue = 'dodrio/gpu_rome_a100_40' | ||
| clusterOptions = "-A ${params.tier1_project}" | ||
| } | ||
| } | ||
|
|
||
| gpu_rome_a100_80 { | ||
| params { | ||
| config_profile_description = 'HPC_DODRIO_gpu_rome_a100_80 profile for use on the Dodrio/gpu_rome_a100_80 cluster of the VSC HPC.' | ||
| config_profile_contact = '[email protected]' | ||
| config_profile_url = 'https://www.ugent.be/hpc/en' | ||
| max_memory = 512.GB | ||
| max_cpus = 48 | ||
| max_time = "3day" | ||
| } | ||
|
|
||
| process { | ||
| executor = 'slurm' | ||
| queue = 'dodrio/gpu_rome_a100_80' | ||
| clusterOptions = "-A ${params.tier1_project}" | ||
| } | ||
| } | ||
|
|
||
| debug_rome { | ||
| params { | ||
| config_profile_description = 'HPC_DODRIO_debug_rome profile for use on the Dodrio/debug_rome cluster of the VSC HPC.' | ||
| config_profile_contact = '[email protected]' | ||
| config_profile_url = 'https://www.ugent.be/hpc/en' | ||
| max_memory = 256.GB | ||
| max_cpus = 48 | ||
| max_time = "3day" | ||
| } | ||
|
|
||
| process { | ||
| executor = 'slurm' | ||
| queue = 'dodrio/debug_rome' | ||
| clusterOptions = "-A ${params.tier1_project}" | ||
| } | ||
| } | ||
|
|
||
| cpu_rome_all { | ||
| params { | ||
| config_profile_description = 'HPC_DODRIO_cpu_rome_all profile for use on the Dodrio/cpu_rome_all cluster of the VSC HPC.' | ||
| config_profile_contact = '[email protected]' | ||
| config_profile_url = 'https://www.ugent.be/hpc/en' | ||
| max_memory = 250.GB | ||
| max_cpus = 128 | ||
| max_time = "3day" | ||
| } | ||
|
|
||
| process { | ||
| executor = 'slurm' | ||
| queue = 'dodrio/cpu_rome_all' | ||
| clusterOptions = "-A ${params.tier1_project}" | ||
| } | ||
| } | ||
|
|
||
| gpu_rome_a100 { | ||
| params { | ||
| config_profile_description = 'HPC_DODRIO_gpu_rome_a100 profile for use on the Dodrio/gpu_rome_a100 cluster of the VSC HPC.' | ||
| config_profile_contact = '[email protected]' | ||
| config_profile_url = 'https://www.ugent.be/hpc/en' | ||
| max_memory = 384.GB | ||
| max_cpus = 48 | ||
| max_time = "3day" | ||
| } | ||
|
|
||
| process { | ||
| executor = 'slurm' | ||
| queue = 'dodrio/gpu_rome_a100' | ||
| clusterOptions = "-A ${params.tier1_project}" | ||
| } | ||
| } | ||
|
|
||
| stub { | ||
| params { | ||
| config_profile_description = 'Stub profile for the VSC HPC. Please also specify the `-stub` argument when using this profile.' | ||
|
|
||
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