All of these values are retained, even after closing and restarting R.
pbat.set sets the name of the pbat executable.
pbat.get gets the current stored name of the pbat executable.
pbat.setmode sets the mode (single, multiple, or cluster), with
pbat.setmode.defaults returning it to default values.
pbat.getmode returns the current mode specifications.
pbat.setVersionCheck sets whether to check the version on startup.
pbat.setwine sets pbat up for use with wine. Intended for mac OS (darwine), or linux 32-bit version (temporarily with wine). Download the windows version of pbat, and use pbat.set to point it to pbat*.exe. See details below.
pbat.getwine returns the value, leave empty for windows
pbat.set(executableStr="", CLEAR=FALSE)
pbat.get()pbat.setmode.defaults(save=TRUE)
pbat.setmode(mode=NULL, jobs=NULL, clusterCommand=NULL,
clusterRefresh=NULL )
pbat.getmode()
pbat.setVersionCheck(check=TRUE)
pbat.setwine(wineStr="", CLEAR=FALSE)
pbat.getwine()
pbat.get returns a string of the currently stored name of the
pbat executable.
String of the pbat executable name, e.g. “c:/pbat/pbat25.exe”. If the string is omitted, then a file-choose dialogue will appear to selet the file (suggested).
If set to TRUE, the executable name is cleared, regardless of the string passed in the other option.
Used internally.
'single', 'multiple', or 'cluster'. See details.
The number of jobs to partition into for 'multiple' or 'cluster'.
The command used to submit a job to your cluster. The default is 'bsub'.
How often (in seconds) to check if jobs have finished.
Whether to perform the version check on startup (recommended).
Executable binary for wine. For linux 32-bit (64-bit is natively compiled), "wine" should suffice, assuming it is installed. For Mac, assuming you have installed Darwine (as detailed in the package), you should set it to be "/Applications/Darwine/Wine.bundle/Contents/bin/wine", NOT the wineHelper.
The default (upon installation) assumes that the executable is 'pbat'
and is in the path; pbat.set allows you to set the version you
wish to use, and easily toggle between other versions of the software
(in case you are testing the software it is easy to toggle to an older
version).
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The 'single' mode is meant for only one processor on a users personal computer (see also cluster for some special features of that mode). However, with putting several cores on one chip, it may be more advantageous to use 'multiple' or 'cluster'.
WARNING: if the number of jobs is 1, it will always be in this 'single' mode.
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The 'multiple' mode is meant for a single multiprocessor system, or a cluster that acts like one. You can then set 'jobs' to be however many processors that you have, or more depending on some of the newer technologies. If you have a cluster that acts like a multi-processor system, then this can be more efficient than the 'cluster' mode if and only if you are waiting for the output. The 'multiple' mode will work in all operating systems.
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In 'cluster' mode, you must specify the command and any additional flags (to keep it generic for all platforms) to submit a job that is represented in a file (i.e 'bsub -q normal sh' on some clusters, 'batch -f' or 'at now -f' in a very basic unix environment - see 'man batch' from the command line or search for it online).
When the 'refresh' option is set to '0' (zero), then the
output is batched, and R will not wait for the output to be
finished. If you do this, be sure to save your workspace when
exiting; then you can reload your output back in. See
is.finished,
pbat.load, and
pbat.concatenate for more information on this.
When 'refresh' is set to an integer greater than zero, it indicates the seconds that should elapse before the current R session checks to see if the other processes are done. The goal was to keep this as generic as possible.
Cluster mode may work in windows, but I am unfamiliar with any batching command system available in windows. Would there actually be any interest in this? Please e-mail me if this might be useful.
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System administrators could copy the '.pbat.Rmeta' file to the users
home directory after using pbat.set to set it themselves.
pbat.m
is.finished,
pbat.load,
pbat.concatenate