Submitter and Monitor of the LSF Cluster

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

Install

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

If you want the full functionality of the package, you need to install a few more packages:

devtools::install_github('jokergoo/bsub', dependencies = 'Suggests')

Documentation

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

There are four vignettes:

• Send R code/R scripts/shell commands to LSF cluster
• Configure bsub package for other LSF institutes
• What if you need to establish two ssh connections to reach the submission node

Submit jobs

Directly submit R chunk:

library(bsub)

# R code
bsub_chunk(name = "example", memory = 10, hour = 10, core = 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)

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:

Job log:

Job dependency tree:

Kill jobs:

License

MIT @ Zuguang Gu