Soraj, Haven't had any experience with R in a distributed computing environment, but have used Condor (http://www.cs.wisc.edu/condor/) with several applications. It's free, has a public license for use, is easy to use, but is not open source. Since you can "batch up" R code, this might be a reasonable option. HTH steve -----Original Message----- From: r-help-bounces at stat.math.ethz.ch [mailto:r-help-bounces at stat.math.ethz.ch] On Behalf Of Saroj Mohapatra Sent: Wednesday, June 02, 2004 7:12 PM To: r-help at stat.math.ethz.ch Subject: [R] Distributed computing with R Dear all, We have started using R for data analysis since a few months and find it useful. We are planning to acquire a high-end dedicated system for microarray data analysis and thinking of a distributed environment. I would appreciate if some one could send some pointers regarding how to choose a proper hardware configuration, software (R or other software, esp. MATLAB), issues on setting up the cluster, etc. Has anyone here some experience of R on a cluster? Does it provide significant benefits as regards processing time? Is setting up the cluster more difficult than using R on it? Thanks. Saroj K Mohapatra, MD Research Associate Tainsky Lab Karmanos Cancer Institute Wayne State University School of Medicine 110 E. Warren, Room 311 Detroit MI 48201 313-833-0715 x2424 saroj at wayne.edu ______________________________________________ R-help at stat.math.ethz.ch mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Dear all, We have started using R for data analysis since a few months and find it useful. We are planning to acquire a high-end dedicated system for microarray data analysis and thinking of a distributed environment. I would appreciate if some one could send some pointers regarding how to choose a proper hardware configuration, software (R or other software, esp. MATLAB), issues on setting up the cluster, etc. Has anyone here some experience of R on a cluster? Does it provide significant benefits as regards processing time? Is setting up the cluster more difficult than using R on it? Thanks. Saroj K Mohapatra, MD Research Associate Tainsky Lab Karmanos Cancer Institute Wayne State University School of Medicine 110 E. Warren, Room 311 Detroit MI 48201 313-833-0715 x2424 saroj at wayne.edu
I would suggest installing PVM or LAM-MPI and using the R packages `snow' and `rpvm' (or `Rmpi'). I've found the `snow' package very simple to use and useful for quick and dirty solutions. I've used `snow' with an openMosix setup and on a simple cluster of workstations without any scheduler. openMosix is nice because you don't have to worry about which process goes where but that's not to say it doesn't have its own difficulties. Overall, my experience with parallel computing in R has been a little clunky but that's mostly because the problems I work on don't benefit much from such a setup. -roger Saroj Mohapatra wrote:> Dear all, > > We have started using R for data analysis since a few months and find it > useful. We are planning to acquire a high-end dedicated system for > microarray data analysis and thinking of a distributed environment. I > would appreciate if some one could send some pointers regarding how to > choose a proper hardware configuration, software (R or other software, > esp. MATLAB), issues on setting up the cluster, etc. Has anyone here > some experience of R on a cluster? Does it provide significant benefits > as regards processing time? Is setting up the cluster more difficult > than using R on it? > > Thanks. > > Saroj K Mohapatra, MD > Research Associate > Tainsky Lab > Karmanos Cancer Institute > Wayne State University School of Medicine > 110 E. Warren, Room 311 > Detroit MI 48201 > 313-833-0715 x2424 > saroj at wayne.edu > > ______________________________________________ > R-help at stat.math.ethz.ch mailing list > https://www.stat.math.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html >