Just for the records. The problem was that the R version Rscript
starts is determined at compile time, and I had to move my R
installation to another place for some technical reasons. At the
compile-time place there was another R version and Rscript started
that one.
The solution was to create a dummy rscript file that sets up the RHOME
environment variable for the real Rscript:
-
#! /bin/sh
export RHOME=/home/gabor/software/lib64/R
/home/gabor/software/lib64/R/bin/Rscript $@
-
and then use this file with snow, via the setDefaultClusterOptions
function or some other way.
Gabor
On Tue, Jan 13, 2009 at 1:40 AM, l...@stat.uiowa.edu wrote:
As far as I can tell looking at the code and running on my stytem this
should use the one in rscript if you are starting via makeCluster or
makeMPIcluster. You might double check by doing debug(makeMPIcluster)
and stepping through and looking at what is uses in the call to
mpi.comm.spawn for mpitask and args.
luke
On Fri, 9 Jan 2009, Gábor Csárdi wrote:
Dear Luke and others,
I have many R versions on my machine and want to start a particular
one when snow builds its cluster. (The same version I start snow
from.) It seems that everything is set up correctly in
defaultClusterOptions:
mget(ls(defaultClusterOptions), defaultClusterOptions)
$homogeneous
[1] TRUE
$manual
[1] FALSE
$master
nodename
maya.unil.ch
$outfile
[1] /dev/null
$port
[1] 10187
$rhome
R_HOME sessionInfo()
R version 2.8.0 (2008-10-20)
x86_64-redhat-linux-gnu
locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] snow_0.3-3
/home/gabor/software/lib64/R
$rlibs
R_LIBS
/usr/lib64/R/library:/usr/share/R/library
$rprog
[1] /home/gabor/software/lib64/R/bin/R
$rscript
[1] /home/gabor/software/lib64/R/bin/Rscript
$rshcmd
[1] ssh
$scriptdir
[1] /home/gabor/.R/library/snow
$snowlib
[1] /home/gabor/.R/library
$timeout
[1] 31536000
$type
[1] MPI
$user
user
gabor
$useRscript
[1] TRUE
but snow still starts a different version, the one in /usr/bin/R. Is
this a bug? If not, how can I tell snow to start the same version, the
one that is listed in defaultClusterOptions?
Thanks,
Gabor
sessionInfo()
R version 2.8.0 (2008-10-20)
x86_64-redhat-linux-gnu
locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] snow_0.3-3
--
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: l...@stat.uiowa.edu
Iowa City, IA 52242 WWW: http://www.stat.uiowa.edu
--
Gabor Csardi gabor.csa...@unil.ch UNIL DGM
__
R-help@r-project.org 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.
