pdf_array_job: Submit an array job to plot PDFs, then bind back together.
In ihmeuw/ihme.covid: Shared functions for IHME's covid-19 research

pdf_array_job

R Documentation

Submit an array job to plot PDFs, then bind back together.

Description

Submit an array job to plot PDFs, then bind back together.

Usage

pdf_array_job(
  jobs_file,
  r_script,
  final_out_dir,
  write_file_name = "all_jobs.pdf",
  rshell = "/ihme/singularity-images/rstudio/shells/execRscript.sh -s",
  fthread = 5,
  fmem = "10G",
  h_rt = "02:00:00",
  queue = "all.q",
  project = "proj_covid",
  job_name = "pdf_array",
  output = NULL,
  errors = NULL,
  remove_temp_files = TRUE,
  args = NULL
)

Arguments

`jobs_file`	.csv that has one row for each job you want to run, with arguments for plots as columns.
`r_script`	Full path to the R script that has your plotting code.
`final_out_dir`	Path to directory to save final file. Needs to be to a path on the cluster.
`write_file_name`	Final file name to write. Defaults to "all_jobs.pdf".
`rshell`	R-shell to use. Defaults to SciComp shell.
`fthread`	fthreads for cluster jobs. Defaults to 5.
`fmem`	fmem for cluster jobs. Defaults to 10G.
`h_rt`	h_rt for cluster jobs. Defaults to 2 hours.
`queue`	Queue for cluster jobs. Options are 'all.q', 'i.q', 'long.q', or 'd.q'. Defaults to 'all.q'.
`project`	Cluster project. Defaults to 'proj_covid'.
`job_name`	Cluster job name. Defaults to 'pdf_array'.
`output`	Path to write cluster output messages to. Defaults to "/ihme/temp/slurmoutput/USERNAME/output"
`errors`	Path to write cluster error messages to. Defaults to "/ihme/temp/slurmoutput/USERNAME/errors"
`remove_temp_files`	Remove temporary files after jobs have completed? Defaults to TRUE.
`args`	Additional arguments to pass to array job launch script.