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 and Fax: 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.
