configs/conf/cheaha.config at 9b2a2c603dea25a001f816a8b8ffba395ccd191d · U-BDS/configs · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
// Prevent schemas warnings for profile parameters
validation {
    ignoreParams = [
        'cheaha_scratch_dir'
    ]
}

// Define the Scratch directory
params.cheaha_scratch_dir = env('USER_SCRATCH') ?: '/tmp'

params {
    config_profile_name = 'cheaha'
    config_profile_description = 'University of Alabama at Birmingham Cheaha HPC'
    config_profile_contact = 'Lara Ianov (lianov@uab.edu) or Austyn Trull (atrull@uab.edu)'
    config_profile_url = 'https://www.uab.edu/cores/ircp/bds'
}

env {
    TMPDIR=params.cheaha_scratch_dir
    SINGULARITY_TMPDIR=params.cheaha_scratch_dir
}

singularity {
    enabled = true
    autoMounts = true
    runOptions = "--contain --workdir ${params.cheaha_scratch_dir} -B /scratch"
}

process {
    resourceLimits = [
        memory: 750.GB,
        cpus: 128,
        time: 150.h
    ]
    executor = 'slurm'
    maxRetries = 3
    beforeScript = 'module load Singularity/3.5.2-GCC-5.4.0-2.26'
    queue = {
        def queue_list = ["long"]

        if (task.time <= 2.h) {
            queue_list.add("express")
        }

        if (task.time <= 12.h) {
            queue_list.add("short")
        }

        if (task.time <= 50.h) {
            queue_list.add("medium")
        }

        if (task.memory >= 300.GB) {
            queue_list.add("largemem-long")

            if (task.time <= 50.h) {
                queue_list.add("largemem")
            }
        }

        return queue_list.join(",")
    }
}