lsf_logs_inspector: Inspects the logs of an LSF array job.

In caravagn/easypar: Easy parallaleization of R functions.

Inspects the logs of an LSF array job.

Description

If your an array job generated through ‘easypar'’s function run_lsf, you can use this function to inspect the logs. The functions takes a process identifier (PID), and then scans logs in a folder selecting those belonging to the array jobs run with that PID. For every output file, the standard LSF closing text "Successfully completed." is searched for. If it is not found the relative error file is scanned to find the error message (grepping an "Error" term in the file), and displayed to screen. Log files for jobs run succesfully are compressed into a zip file stored in the log folders, and error logs are retained. The list of input(s) that are associated with error logs is also print to screen, and a summary table is retuned.

Usage

lsf_logs_inspector(PID, errors_folder, input_file, delete_files = TRUE)

Arguments

PID	Process identier, it should appear in the names of the logfiles.
errors_folder	A folder with logs to inspect.
input_file	The input file associated to the job, if not NULL the inputs for the runs with error are shown to screen.

Value

A tibble with the name of the jobs analysed, file references and output status.

See Also

run_lsf

Examples

# very dummy example function
FUN = function(x, y){ print(x, y) }

# input for 25 array jobs
PARAMS = data.frame(x = runif(25), y = runif(25))

## Not run: 
# not run 
run_lsf(FUN, PARAMS)

# Once logs are produced... we can inspect them
 
# inspect using default params (as in job submission)
lsf_logs_inspector(PID = 1234, errors_folder = 'log', input_file = 'EASYPAR_LSF_input_jobarray.csv')

## End(Not run)

caravagn/easypar documentation built on June 4, 2022, 4:25 a.m.