[R] snow parLapply standard output
I am slightly confused by the way the standard output is redirected in a R snow cluster environment. I am using parLapply from the snow package to execute a function on my MPI/LAM cluster. How can I redirect standard output (produced using cat) from this function back to the terminal where I invoked it? I intend to transmit some status information in advance to the final result of the function. I investigated the chain of functions called by parLapply and it seems that snow is designed to just retrieve the final result of the computation. Thanks in advance for any hints, Frank Preiswerk [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] snow parLapply standard output
On Tue, 27 Mar 2007, Frank Preiswerk wrote: I am slightly confused by the way the standard output is redirected in a R snow cluster environment. I am using parLapply from the snow package to execute a function on my MPI/LAM cluster. How can I redirect standard output (produced using cat) from this function back to the terminal where I invoked it? I intend to transmit some status information in advance to the final result of the function. I investigated the chain of functions called by parLapply and it seems that snow is designed to just retrieve the final result of the computation. The R level only deals with final values. There is currently no means within snow to communicate status information back to the master. By default output is redirected to /dev/null. You can provide an alternate destination with the outfile option and monitor those files from another process. Best, luke Thanks in advance for any hints, Frank Preiswerk [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Luke Tierney Chair, Statistics and Actuarial Science Ralph E. Wareham Professor of Mathematical Sciences University of Iowa Phone: 319-335-3386 Department of Statistics andFax: 319-335-3017 Actuarial Science 241 Schaeffer Hall email: [EMAIL PROTECTED] Iowa City, IA 52242 WWW: http://www.stat.uiowa.edu __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] snow parLapply standard output
Frank -- Perhaps what you want to do is
summarize - function(lst) {
lapply(lst, function(elt) {
if (elt$status==ok) elt$value
else NA
})
}
summarize(parLapply(tasks, function(elt) {
# fancy calculation, then
list(status=ok, value=...)
}))
i.e., return status along with value from the nodes, and
'post-process' the result. Perhaps status is set by capture.output on
the node. Maybe you're hoping to change how later tasks are evaluated
based on results of earlier tasks; but this makes the lapply
sequential rather than parallel.
Martin
Frank Preiswerk [EMAIL PROTECTED] writes:
I am slightly confused by the way the standard output is redirected in a R
snow cluster environment.
I am using parLapply from the snow package to execute a function on my
MPI/LAM cluster. How can I redirect standard output (produced using cat)
from this function back to the terminal where I invoked it? I intend to
transmit some status information in advance to the final result of the
function. I investigated the chain of functions called by parLapply and it
seems that snow is designed to just retrieve the final result of the
computation.
Thanks in advance for any hints,
Frank Preiswerk
[[alternative HTML version deleted]]
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Martin Morgan
Bioconductor / Computational Biology
http://bioconductor.org
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
