run_lsf | R Documentation |
This function submits array jobs to LSF clusters.
The input has to be a function that can carry out a full computation itself, plus a data.frame where each row represents the inputs that this function is expecting. The input data.frame is dumped to a file, the input function is wrapped inside an automatically generated R script that gathers inputs from the command line. A LSF submission script is generated for a bash shell. The function can also run the LSF command 'bsub' to submit the job, or just generate the required files and prompt the user to submit the job via the shell. LSF parameters can be provided as a list of parameters, similarly modules and custom filenames for the generated scripts.
run_lsf( FUN, PARAMS, BSUB_config = default_BSUB_config(), modules = c("R/3.5.0"), extra_commands = NULL, input_file = "EASYPAR_LSF_input_jobarray.csv", R_script = "EASYPAR_LSF_Run.R", Submission_script = "EASYPAR_LSF_submission.sh", output_folder = ".", run = FALSE )
FUN |
A function that takes any arguments in input, and performs a computation. This function should be runnable as a standalone R script. |
PARAMS |
A data.frame where each row represents inputs for |
BSUB_config |
A list of BSUB commands for the LSF cluster should
be provided. The default input is obtained from a call to |
modules |
A list of modules that will be added as dependencies of the
LSF submission script. For instance |
extra_commands |
Extra set of commands that will be executed in the submission script right after modules declaration. |
input_file |
The name of the data.frame input file that is generated
from |
R_script |
The name of the R script file that contains the definition
of |
Submission_script |
The name of the LSF script file that contains the submission routines. |
output_folder |
The output of thsi function will be sent to this folder. |
run |
If 'TRUE', the function all attempt invoking 'bsub' and submit the array jobs. Otherwise it will print to screen the instructions to run the job manually through the console. |
Nothing, this funciton just generates the required inputs to submit an array job via the LSF clusters. If required, it also attempts submitting the jobs.
The queue and the project ID in 'BSUB_config' should always be provided as they are cluster-specific. Default values will prompt errors submitting the job. Besides, we have found that automatic job submission can sometimes generate some 'command not found' types of errors. Manual submission seems generally the safest option to submit LSF jobs.
See default_BSUB_config
that is used to generate
default parameters for LSF jobs.
# 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: # call - not run since it's cluster-specific run_lsf(FUN, PARAMS) ## End(Not run)
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