bsub v1.0.0
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Submitter and Monitor of the 'LSF Cluster'
It submits R code/R scripts/shell commands to 'LSF cluster'
(<https://en.wikipedia.org/wiki/Platform_LSF>, the 'bsub' system) without
leaving R. There is also an interactive 'shiny' app for monitoring the job status.
Functions in bsub
| Name | Description | |
| bsub_opt | Parameters for bsub | |
| monitor | A browser-based interactive job monitor | |
| run_cmd | Run command on submission node | |
| job_status_by_name | Job status by name | |
| retrieve_var | Retrieve saved variable | |
| wait_jobs | Wait until all jobs are finished | |
| bsub_cmd | Submit shell commands | |
| check_dump_files | Check whether there are dump files | |
| print.bjobs | Summary of jobs | |
| random_job | Submit a random job | |
| clear_temp_dir | Clear temporary dir | |
| get_dependency | Get the dependency of current jobs | |
| job_log | Log for the running/finished/failed job | |
| bsub_script | Submit R script | |
| plot_dependency | Plot the job dependency tree | |
| job_status_by_id | Job status by id | |
| print.bconf | Print the configurations | |
| is_job_finished | Test whether the jobs are finished | |
| ssh_disconnect | Disconnect ssh connection | |
| ssh_connect | Connect to submisstion via ssh | |
| brecent | Recent jobs from all status | |
| bkill | Kill jobs | |
| bjobs_exit | Failed jobs | |
| bjobs_done | Finished jobs | |
| bconf | Print current configuation | |
| bjobs | Summary of jobs | |
| bsub_chunk | Submit R code | |
| bjobs_running | Running jobs | |
| bjobs_pending | Pending jobs | |
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Details
| Type | Package |
| Date | 2020-07-25 |
| biocViews | Software, Infrastructure |
| URL | https://github.com/jokergoo/bsub |
| License | MIT + file LICENSE |
| NeedsCompilation | no |
| SystemRequirements | Platform LSF, bsub |
| Packaged | 2020-07-25 11:43:10 UTC; jokergoo |
| Repository | CRAN |
| Date/Publication | 2020-07-30 11:00:06 UTC |
| imports | clisymbols , crayon , digest , GetoptLong (>= 0.1.8) , GlobalOptions (>= 0.1.1) , graphics , grDevices , methods , stats , utils |
| suggests | DT (>= 0.13) , graph , igraph , knitr , Rgraphviz , shiny (>= 1.0.0) , shinyjqui , ssh |
| depends | R (>= 3.0.0) |
| Contributors | Zuguang Gu |
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