qsub_utils: SGE Job Submission
In ShadeWilson/ihme: Functions for Improving Life at IHME

Description Usage Arguments Value Examples

Submit jobs to IHME's SGE computing cluster for scheduling. Builds a qsub string and submits either a normal or array job, inserting the code file, jobs to hold on, arguments to pass, number of slots and memory, logging locations, intel instructions, project to run under, and shell to use.

qsub(jobname, code, hold = NULL, pass = NULL, slots = 1, mem = 0,
  submit = F, log = T, intel = F, proj = "proj_mortenvelope",
  shell = NULL)

array_qsub(jobname, code, hold = NULL, pass = NULL, slots = 1, mem = 0,
  submit = F, log = T, intel = F, proj = "proj_mortenvelope",
  num_tasks = 1, hold_jid_ad = NULL, shell = NULL)

`jobname`	character, Name for job, must start with a letter
`hold`	character, Optional comma-separated string of jobnames to hold the job on i.e. "hold_name_1, hold_name_2, ..."
`pass`	list (NOT character or numeric vector), arguments to pass on to the recieving script. e.g. list(arg1, arg2, arg3)
`slots`	integer, number of computing slots to request.
`mem`	integer, number of gb to request to be associated with this job. Defaults to 2 * slots (default is calculated in construct_qsub_string function). Specify a non-0 number if you want a specific memory allocation other than 2 * slots.
`submit`	logical, whether to submit the job to the system. If F, will print out the command to be submitted
`log`	logical, if T save in "/share/temp/sgeoutput/user/errors" and "/share/temp/sgeoutput/user/output"
`intel`	logical, if T, add flag to request a node with Intel CPUs
`proj`	character, project name to submit the job under
`shell`	character, filepath to a user-defined shell. Default: search for "r_shell.sh", "python_shell.sh", or "stata_shell.sh" within working directory (shell name based on script ending).
`num_tasks`	integer, for array_qsub only – number of array tasks to submit
`hold_jid_ad`	character, for array_qsub only – optional comma-separated string of jobnames to use array holds on i.e. "hold_name_1, hold_name_2, ..."
`filepath`	character, Filepath to code file

None

## Not run: 
hold_jobs <- c("job1", "job2")
args <- list(arg1, arg2)
qsub(jobname = "my_job", filepath = "code_dir/01_run_model.R", hold = paste(hold_jobs, collapse = ","), pass = args, slots = 10, submit = F, intel = T, log = T, shell = "code_dir/r_shell.sh")

## End(Not run)