configs/conf/cambridge.config at 93254771a8c79692d049f3898b5ea466af542da8 · RaqManzano/configs · GitHub

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// nf-core/configs: Cambridge CSD3 cluster profile
// Available partitions:
//   - icelake        : 76 CPUs, 256 GB RAM
//   - icelake-himem  : 76 CPUs, 512 GB RAM
//   - sapphire       : 112 CPUs, 512 GB RAM
//
// The profile defaults to the broadly available `icelake` partition but allows
// users to override it with `--partition`. Walltime is inferred from the SLURM
// account name when possible: projects containing `-SL3-` use a 12 h cap,
// otherwise the profile assumes the common SL1/SL2 36 h limit.

params {
    config_profile_description = 'Cambridge HPC CSD3 cluster profile.'
    config_profile_contact     = 'Raquel Manzano (rm889@cam.ac.uk) and Andries van Tonder (ajv37@cam.ac.uk)'
    config_profile_url         = 'https://docs.hpc.cam.ac.uk/hpc'

    partition = 'icelake'
    project   = null

    // Compatibility with nf-core schema validation across pipeline versions.
    schema_ignore_params         = 'partition,project,max_memory,max_cpus,max_time,csd_time,csd_parts,csd_selected,validationSchemaIgnoreParams'
    validationSchemaIgnoreParams = 'partition,project,max_memory,max_cpus,max_time,csd_time,csd_parts,csd_selected,schema_ignore_params,validationSchemaIgnoreParams'
}

validation {
    ignoreParams = ['partition', 'project', 'max_memory', 'max_cpus', 'max_time', 'csd_time', 'csd_parts', 'csd_selected', 'schema_ignore_params', 'validationSchemaIgnoreParams']
}

params.csd_time = {
    params.project?.toUpperCase()?.contains('-SL3-') ? 12.h : 36.h
}.call()

params.csd_parts = [
    icelake        : [memory: 256.GB, cpus: 76, time: params.csd_time],
    'icelake-himem': [memory: 512.GB, cpus: 76, time: params.csd_time],
    sapphire       : [memory: 512.GB, cpus: 112, time: params.csd_time]
]

params.csd_selected = {
    def selected = params.csd_parts[params.partition]

    if (!selected) {
        System.err.println("ERROR: cambridge params.partition must be one of 'icelake', 'icelake-himem', or 'sapphire' (got '${params.partition}').")
        System.exit(1)
    }

    selected
}.call()

params.max_memory = params.csd_selected.memory
params.max_cpus   = params.csd_selected.cpus
params.max_time   = params.csd_selected.time

singularity {
    enabled    = true
    autoMounts = true
}

process {
    resourceLimits = params.csd_selected

    beforeScript = """
    . /etc/profile.d/modules.sh
    module purge
    module load rhel8/default-${params.partition == 'sapphire' ? 'sar' : 'icl'}
    """

    executor       = 'slurm'
    queue          = params.partition
    clusterOptions = { params.project ? "--account=${params.project}" : '' }
    cache          = 'lenient'
    scratch        = true
}

executor {
    name              = 'slurm'
    queueSize         = 200
    pollInterval      = '5 min'
    queueStatInterval = '5 min'
    submitRateLimit   = '10 sec'
    exitReadTimeout   = '30 min'
}