Submitter and Monitor of the LSF Cluster

It sends R code/R scripts/shell commands to LSF cluster without leaving R.

Install

Directly from CRAN:

install.packages("bsub")

Or from GitHub:

if (!requireNamespace("devtools", quietly = TRUE))
    install.packages("devtools")
devtools::install_github("jokergoo/bsub")

Documentation

The online documentation is available at https://jokergoo.github.io/bsub/.

Submit jobs

Directly submit R chunk:

library(bsub)

# R code
bsub_chunk(name = "example", memory = 10, hours = 10, cores = 4, 
{
    fit = NMF::nmf(...)
    # you better save `fit` into a permanent file
    saveRDS(fit, file = "/path/of/fit.rds")
})

Submit an R script:

# R script
bsub_script(name = "example",
    script = "/path/of/foo.R", ...)

Submit shell commands:

# shell commands
bsub_cmd(name = "example",
    cmd = "samtools view ...", ...)

Kill jobs:

bkill(job_id)

Job dependencies

job1 = bsub_chunk(...)
job2 = bsub_chunk(...)
bsub_chunk(..., dependency = c(job1, job2))

View job info

View job summaries:

bjobs
brecent
bjobs_running
bjobs_pending
bjobs_done
bjobs_exit

An example of the job queries is as follows:

View job log:

job_log(job_id)

Interactive job monitor

monitor()

The job summary table:

<p><img width="907" alt="monitor" src="https://github.com/jokergoo/bsub/assets/449218/9970a50d-dbf6-4477-9a8b-5344f641b8ba"></p>

Job log:

<p><img width="905" alt="job_log" src="https://github.com/jokergoo/bsub/assets/449218/b2faa77c-6dc1-4578-b52c-73bc7a739ba9"></p>

Job dependency diagram:

<p><img width="895" alt="dependency_graph" src="https://github.com/jokergoo/bsub/assets/449218/eaf85ef6-32bb-4c09-a3d4-1069cf11a404"></p>

License

MIT @ Zuguang Gu