sbatch_master_abc: Create sbatch Bash Shell Script ABC-SMC Workflow

In EpiModel/EasyABCMPI: Approximate Bayesian Computation for EpiModel on High-Performance Computing Clusters

Description

Creates a master-level SLURM::sbatch script given a ABC-SMC model prepared and output from abc_smc_prep.

Usage

sbatch_master_abc(
  input,
  nwaves,
  master.file = "master.sh",
  runsim.file = "runsim.sh",
  ckpt = FALSE,
  append = FALSE,
  mem = "55G",
  walltime = "1:00:00",
  user,
  partition.main = "csde",
  partition.ckpt = "ckpt",
  account.main = "csde",
  account.ckpt = "csde-ckpt"
)

Arguments

input	Output object from abc_smc_prep.
nwaves	Number of waves of SMC to run, not including wave = 0 that is the starting wave based on ABC rejection.
master.file	Name of the output bash shell script file to write. If "", then will print to console.
runsim.file	Name of the bash shell script file that runs the R simulation job.
ckpt	If TRUE, use the checkpoint queue to submit jobs. If numeric, will specify the first X jobs on the grid as non-backfill.
append	If TRUE, will append lines to a previously created shell script. New simno will either start with value of simno.start or the previous value if missing.
mem	Amount of memory needed per node within each Slurm job.
walltime	Amount of clock time needed per Slurm job.
user	Hyak user name.
partition.main	Name of primary HPC partition (passed to -p).
partition.ckpt	Name of checkpoint HPC partition (passed to -p).
account.main	Name of primary account (passed to -A).
account.ckpt	Name of checkpoint account (passed to -A).

EpiModel/EasyABCMPI documentation built on Dec. 5, 2020, 8:43 p.m.