cluster.slurm.cheaha.json

{
"#documenation": {
    "#A": "----------------------------------------------------------------------------------",
    "#raw_cmdline": "Use with snakemake --cluster-config cluster.slurm.cheaha.json --cluster 'sbatch --job-name {cluster.job-name} --ntasks {cluster.ntasks} --cpus-per-task {threads} --mem-per-cpu {cluster.mem-per-cpu} --partition {cluster.partition} --time {cluster.time} --mail-user {cluster.mail-user} --mail-type {cluster.mail-type} --error {cluster.error} --output {cluster.output} --gres {cluster.gres}'",
    "#cmdline": "Or use with module ngs-ccts/snakemakeslurm which builds the raw commandline for you.",
    "#slurm partitions": "See https://docs.uabgrid.uab.edu/wiki/Slurm#Slurm_Partitions",
    "#Z": "----------------------------------------------------------------------------------"
},
"__default__": {
    "# documentation": "# This is the default SLURM job config, except threads which are annotated directly on the rule",
    "job-name": "SM.{rule}.{wildcards}",
    "# partition": "# run sinfo to list available partitions and their run-time limitations",
    "partition": "express",
    "# time": "# Runtime in D-HH:MM:SS",
    "time": "02:00:00",
    "# ntasks": "# number of SLURM tasks. We assume that programs are SMP, so all cores must be on the same node, and thus ask for only 1 task",
    "ntasks": 1,
    "# cpus": "# number of threads/cpus comes from the 'threads' attribute on the individual rules in the Snakefile",
    "mem-per-cpu-mb": 2000,
    "# gres (GPUs)": "# number of GPU (1-4 in pascalnodes[-medium] partitions)",
    "gres": "gpu:0",
    "# output/error": "# output filenames for stdout and stderr",
    "# filename_pattern": "%j=jobid, %N=short_hostname, %x=job_name; see https://slurm.schedmd.com/sbatch.html#lbAH",
    "output": "logs/%j.%N.%x.out.txt",
    "error": "logs/%j.%N.%x.err.txt",
    "# mail-user": "USER@uab.edu  # this is set in snakemakeslurm, as there is no SLURM filename pattern for USER name",
    "mail-type": "ALL"
},
"#Template Rules": {
    "#A": "----------------------------------------------------------------------------------",
    "# Additional Rules": "If the name of the section matches the name of the rule, then the values in the section override the __default__ settings. For items not listed",
    "#Z": "----------------------------------------------------------------------------------"
},
"mapBWA_withMoreMem": {
    "mem-per-cpu-mb": 2200
},
"mapBWA_withMoreTime": {
    "time": "12:00:00",
    "partition": "short"
},
"mapBWA_withMuchMoreTime": {
    "time": "2-02:00:00",
    "partition": "medium"
},
"mapBWA_withOodlesOfTime": {
    "time": "6-06:00:00",
    "partition": "long"
}
}