runCommand: Issue the System Call That Invokes NONMEM
In metrumrg: Pharmacometric Tools for Data Preparation, Modeling, Simulation, and Reporting

Description Usage Arguments Details Value Author(s) References See Also

If udef is FALSE, command is passed to nm.pl with supporting arguments. If grid is TRUE, the result is passed to qsub with supporting arguments. If background is TRUE, ‘&’ is appended to the result. Each element of the result is executed in succession using a system call customized by platform.

runCommand(
	command,
	...,
	run,
	rdir,
	wait,
	checksum,
	grid,
	udef = FALSE,
	ctlfile,
	outfile,
	perl = if (nix()) 'perl -S' else if (!invisible) 'cmd /K perl -S' 
	else 'cmd /C perl -S',
	intern = invisible,
	minimized = invisible,
	invisible = FALSE,
	split = FALSE,
	N = glue('Run', run, if (split) c('c', 'e') else NULL),
	o = rdir,
	e = rdir,
	L=if(split & is.character(interface) & interface=='nm.pl')
	c(compileflag(compiler(config(dirname(command)))),NA)else NA,
	hold_jid = if (split) c(NA, glue('Run', run, 'c')) else NA,
	V = '',
	j = 'y',
	q=if(split) c('compile.q','all.q') else if(!execute)'compile.q' else 'all.q',
	sync = if (wait) 'y' else 'n',
	shell = 'n',
	b = 'y',
	cwd = '',
	compile = TRUE,
	execute = TRUE,
	background=FALSE,
	interface = 'nm.pl'
)

`command`	a command to pass to `system`
`run`	run name
`rdir`	run directory
`wait`	see `NONR`

`checksum`	see `NONR`
`grid`	see `NONR`
`udef`	see `NONR`
`ctlfile`	see `runNonmem`
`outfile`	see `runNonmem`
`perl`	a character string to invoke perl
`intern`	see `NONR`, passed to `system`
`minimized`	see `NONR`, passed to `system`
`invisible`	see `runNonmem`
`split`	whether compile and execute should be run separately; defaults to FALSE as of v. 5.22
`N`	passed to `qsub`
`o`	passed to `qsub`
`e`	passed to `qsub`
`L`	passed to `qsub` as an instance of ‘l’
`hold\_jid`	passed to `qsub`
`V`	passed to `qsub`
`j`	passed to `qsub`
`q`	passed to `qsub`
`sync`	passed to `qsub`. Bootstrap and simulation runs may occur in large quantities, whereas SGE has an internal limitation on number of synchronized processes. If `wait` is `FALSE`, no attempt is made to synchronize the runs.
`shell`	passed to `qsub`
`b`	passed to `qsub`
`cwd`	passed to `qsub`
`compile`	passed to `nm.pl`
`execute`	passed to `nm.pl`, influences default for `q`
`background`	`TRUE` appends ‘l’ to command lines to put the process in the background. Defunct?
`interface`	the name of a function to prepare NONMEM command lines
`...`	passed to `nm.pl` and `qsub`

The argument ‘L’ represents a possibly-constituative instance of qsub's ‘l’, but is not called ‘l’ so that other instances of ‘l’ (multiple are allowed) will not accidentally override it. Users can override intentionally, of course.

N, L, and hold_jid are coordinated so that if a run is split, compile status is flagged on the compile run, and the execute run waits for compile to finish.

‘q’ is handled specially. When overriding, be sure to pass a character vector of length one for a normal run, and of length two if split is TRUE (the default when grid is TRUE). By default, all standalone compile-only runs are diverted to ‘compile.q’, as well as all compile halves of split runs. By default, all execute-only runs as well as the execute halves of split runs are diverted to ‘all.q’.

character vector showing the result(s) of the system call(s)

Tim Bergsma

http://metrumrg.googlecode.com