bsub_opt: Parameters for bsub

Description

Parameters for bsub

Usage

bsub_opt(..., RESET = FALSE, READ.ONLY = NULL, LOCAL = FALSE, ADD = FALSE)

Arguments

...

Arguments for the parameters, see "details" section

RESET

reset to default values

READ.ONLY

please ignore

LOCAL

please ignore

ADD

please ignore

Value

The corresponding option values.

Details

There are following parameters:

packages: A character vector with package names that will be loaded before running the script.
image: A character vector of RData/rda files that will be loaded before running the script.
temp_dir: Path of temporary folder where the temporary R/bash scripts will be put.
output_dir: Path of output folder where the output/flag files will be put.
enforce: If a flag file for the job is found, whether to enforce to rerun the job.
R_version: The version of R.
working_dir: The working directory.
ignore: Whether ignore bsub_chunk, bsub_script and bsub_cmd.
local: Run job locally (not submitting to the LSF cluster)?
call_Rscript: How to call Rscript by specifying an R version number.
submission_node: A list of node names for submitting jobs.
login_node: This value basically is the same as submission_node unless the login nodes are different from submission nodes.
sh_head: Commands that are written as head of the sh script.
user: Username on the submission node.
group: The user group
ssh_envir: The commands for setting bash environment for successfully running bjobs, bsub, ...
bsub_template: Template for constructing bsub command.
parse_time: A function that parses time string from the LSF bjobs command to a POSIXct object.
verbose: Whether to print more messages.

ssh_envir should be properly set so that LSF binaries such as bsub or bjobs can be properly found. There are some environment variables initialized when logging in the bash terminal while they are not initialized with the ssh connection. Thus, some environment variables should be manually set.

An example for ssh_envir is as follows. The LSF_ENVDIR and LSF_SERVERDIR should be defined and exported.

    c("source /etc/profile",
      "export LSF_ENVDIR=/opt/lsf/conf",
      "export LSF_SERVERDIR=/opt/lsf/10.1/linux3.10-glibc2.17-x86_64/etc")

The values of these two variables can be obtained by entering following commands in your bash terminal (on the submission node):

    echo $LSF_ENVDIR
    echo $LSF_SERVERDIR

The time strings by LSF bjobs command might be different for different configurations. The **bsub** package needs to convert the time strings to POSIXlt objects for calculating the time difference. Thus, if the default time string parsing fails, users need to provide a user-defined function and set with parse_time option in bsub_opt. The function accepts a vector of time strings and returns a POSIXlt object. For example, if the time string returned from bjobs command is in a form of Dec 1 18:00:00 2019, the parsing function can be defined as:

    bsub_opt$parse_time = function(x) {
        as.POSIXlt(x, format = "\
    }

Examples

Run this code

# NOT RUN {
# The default bsub_opt
bsub_opt
# }

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