Given a bash script that specifies the SGE option -t (that is, an array job),
this function submits that job using qsub for a given list of task
IDs. This function is useful in case some tasks for a given job failed which
you can find using qstat | grep Eqw or other options.
array_submit(
job_bash,
task_ids,
submit =
file.exists("/cm/shared/apps/sge/sge-8.1.9/default/common/accounting_20191007_0300.txt"),
restore = TRUE
)A character(1) vector with the name of a bash script
in the current working directory.
A set of task ids that will get parsed by parse_task_ids.
A logical(1) vector determining whether to actually submit
the tasks or not using qsub.
A logical(1) vector determining whether to restore the
script to the original state.
The path to job_bash.
## Choose a script name
job_name <- paste0("array_submit_example_", Sys.Date())
## Create an array job on the temporary directory
with_wd(tempdir(), {
## Create an array job script to use for this example
job_single(
name = job_name,
create_shell = TRUE,
task_num = 100
)
## Now we can submit the SGE job for a set of task IDs
array_submit(
job_bash = paste0(job_name, ".sh"),
task_ids = "225019-225038:1,225040,225043",
submit = FALSE
)
})
#> 2023-05-07 07:12:13.527015 creating the logs directory at: logs
#> 2023-05-07 07:12:13.528366 creating the shell file array_submit_example_2023-05-07.sh
#> To submit the job use: qsub array_submit_example_2023-05-07.sh
#> 2023-05-07 07:12:13.529713 resubmitting the SGE job for task 225019-225038:1
#> qsub array_submit_example_2023-05-07.sh
#> 2023-05-07 07:12:13.530386 resubmitting the SGE job for task 225040-225040
#> qsub array_submit_example_2023-05-07.sh
#> 2023-05-07 07:12:13.531011 resubmitting the SGE job for task 225043-225043
#> qsub array_submit_example_2023-05-07.sh
#> [1] "array_submit_example_2023-05-07.sh"