Melwin
2009-Jun-16 10:18 UTC
[R] Connecting to "heterogenous" cluster using makeSOCKcluster of SNOW-package
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\\\\johnson at 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.