Thanks to Luke Tiernay and some experimenting I found out some issues. I
don't claim this infomation is complete, but it may be helpful for anyone
experimenting with SNOW on Linux:
- environment variables PATH and R_SNOW_LIB need to be set on master and
slaves.
(manually or permanent in ~/.bashrc (adjust your pathnames accordingly).
Don't use ~ for home directory, instead specify the full path. Example:
PATH=$PATH:/home/johnson/R/x86_64-unknown-linux-gnu-library/2.8/snow
export PATH
R_SNOW_LIB="/home/johnson/R/x86_64-unknown-linux-gnu-library/2.8"
export R_SNOW_LIB
- when creating a cluster, as in the example below, the "snowlib" argument
seems ignored, so use the environment variable as stated above:
lnxOptions <- list(host = "geoecology\\\\john...@geco01",snowlib =
"/home/GEOECOLOGY/johnson/R/i686-suse-linux-gnu-library/2.8")
cl <- makeCluster(rep(list(lnxOptions), 2), type = "SOCK")
- when specifying the hostname, most likely you'll need to include your
username (see example above). If this user is part of a domaine (e.g.
GEOECOLOGY), this prepends the username separated by quadruple backslashes
(see above)
- Finally, various postings and personal experience suggest that the
"SOCK"-based connection tends to break down easily, making it only
feasible to be used on a single multi-core computer. MPI and PVM seem more
tested, but are virtually impossible to install for Linux-newbies,
especially under Suse-Linux.
I begin to wonder what "parallelizing the work" really means.
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