Evaluate Function Calls on HPC Schedulers (LSF, SGE, SLURM, PBS/Torque)


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Documentation for package ‘clustermq’ version 0.8.5

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clustermq-package Evaluate Function Calls on HPC Schedulers (LSF, SGE, SLURM)
.onAttach Report queueing system on package attach if not set
.onLoad Select the queueing system on package loading
bind_avail Binds an rzmq to an available port in given range
check_args Function to check arguments with which Q() is called
chunk Subset index chunk for processing
clustermq Evaluate Function Calls on HPC Schedulers (LSF, SGE, SLURM)
cmq_foreach clustermq foreach handler
DO_CHUNK Chunk of iterated arguments for the worker
DO_SETUP Message contains common data
host Construct the ZeroMQ host
LOCAL Placeholder for local processing
LSF LSF scheduler functions
master Master controlling the workers
MULTICORE Process on multiple cores on one machine
PROXY_CMD Message is an SSH command
PROXY_READY Message ID indicating SSH proxy is ready to distribute data
PROXY_STOP Message telling the SSH proxy to clean up
PROXY_UP Message ID indicating SSH proxy is up
purrr_lookup Lookup table for return types to purrr functions
Q Queue function calls on the cluster
QSys Class for basic queuing system functions
Q_rows Queue function calls defined by rows in a data.frame
register_dopar_cmq Register clustermq as 'foreach' parallel handler
SGE SGE scheduler functions
SLURM SLURM scheduler functions
SSH SSH scheduler functions
ssh_proxy SSH proxy for different schedulers
summarize_result Print a summary of errors and warnings that occurred during processing
vec_lookup Lookup table for return types to vector NAs
worker R worker submitted as cluster job
workers Creates a pool of workers
WORKER_DONE Message ID indicating worker is shutting down
WORKER_READY Message ID indicating worker is accepting jobs
WORKER_STOP Message ID telling worker to stop
WORKER_UP Message ID indicating worker is accepting jobs
work_chunk Function to process a chunk of calls