Submit programs for execution in order defined by structure of input list. Programs inside sublists will be executed in parallel, and sublists themselves would be submitted sequentially.

Usage

abba_submit_batch(
  prog_list,
  sequential = FALSE,
  submit_func = abba_rslauncher_submit_job_local,
  wait_func = abba_rslauncher_watch_job_local,
  succeed_func = abba_rslauncher_get_job_succeeded_local,
  col_name = "run_group",
  halt_on_error = TRUE,
  rerun_unchanged_programs = TRUE,
  update_cache = FALSE,
  cache_folder = getOption("abba.default_cache_folder"),
  ...
)

Arguments

prog_list: A list of R program paths to execute
sequential: when sequential=TRUE, prog_list is flattened and everything is executed sequentially.
submit_func: function that will be used to submit jobs
wait_func: function that checks job status and returns when job finishes executing
succeed_func: function that returns TRUE if job finished running without errors and FALSE otherwise
col_name: Name of the column that contains run group numbers when prog_list is a data frame
halt_on_error: If TRUE: if prog_list contains program inputs/outputs - programs that depend on failed program will not be executed; if prog_list contains only program paths - when program fails, entire batch will stop executing. TRUE by default
rerun_unchanged_programs: If FALSE: will not re-run programs whose code and inputs have not been modified since last batch run with update_cache=TRUE.
update_cache: if TRUE, file hash for programs and their inputs will be calculated and saved in .abba_cache folder. It will be done after batch run(.abba_cache folder will be created if it does not exist). If FALSE, .abba_cache folder will not be created/updated. FALSE by default.
cache_folder: specify a path to the folder where hash-sums of programs and their inputs will be stored. By default, those hashes are saved in the subfolder .abba_cache of the same folder as target(program/programs input). The default value can be set by specifying abba.default_cache_folder option.
...: arguments that will be passed to submit_func and wait_func functions

Value

list job IDs associated with executed programs

Examples

if (FALSE) { # \dontrun{
job_ids <- abba_submit_batch(list(
  c("/mnt/work_drive/proj/comp/prot/task/development/prod/program/sdtm/dm.sas"),
  c("/mnt/work_drive/proj/comp/prot/task/development/prod/program/sdtm/ae.sas"),
  c("/mnt/work_drive/proj/comp/prot/task/development/prod/program/tfl/t1_dm.sas",
    "/mnt/work_drive/proj/comp/prot/task/development/prod/program/tfl/t1_ae.sas")))
 } # }