similar to: Running R under Sun Grid Engine with OpenMPI tight integration

We have spent some time setting up Sun Grid Engine and OpenMPI on a group of linux boxes. I have created a parallel environment and everything seems to be working. I have Rmpi 0.5.5-5 installed on all machines. I would like to start an interactive R session using, say, 8 processors and then start the Rmpi cluster. I haven't been able to find what needs to be done in order to accomplish

Dear all In previous R versions I ran R jobs on our cluster managed by SUN Grid Engine using the Rsge package. With the R-3.0 release, the package Rsge has been discontinued. What would be the equivalent way of running jobs on the cluster using current packages? I understand that the parallel package has been updated. What would be the equivalent to the lines below: require(Rsge)

Hi I use the following code and it stores the results of density() in the list dr: dens <- function(run) { density( positions$X[positions$run==run], bw=3, cut=-2 ) } dr <- lapply(1:5, dens) but the results are stored in dr[[i]] and not dr[i], i.e. plot(dr[[1]]) works, but plot([1]) doesn't. Is there any way that I can store them in dr[i]? Thanks a lot, Rainer -- Rainer M. Krug,

Hi I am trying to utilize my dual core processor (and later a High-performance clusters (HPC) ) by using the Rmpi, snow, snowfall, ... packages, but I am struggling at the beginning, i.e. to initialise the "cluster" on my dual core computer. Whenever I try to initialize it (via sfInit(parallel=TRUE, cpus=2) or mpi.spawn.Rslaves(nslaves=2) ), I get an error message: >

Hi if I try to import a raster layer which consists only of NULL values from grass by using the readRAST6, I get an error message: > readRAST6("HSericea_seedsDisperse_2007") ERROR: Invalid value for null (integers only) Error in readBinGrid(rtmpfl11, colname = vname[i], proj4string = p4, integer = to_int) : no such file:

Hi I have a table called npl containing results of simulations. It contains about 19000 entries and the structure looks like this: NoPlants sim run year DensPlants 1 6 lng_cs99_renosterbos 1 4 0.00192 . . . it has 43 different entries for sim and year goes from 1 to 100, and run from 1 to 5. I would like to calculate the mean of DensPlants for each

Hello R experts, I've been searching for weeks a way to use my quad core xeon to increase speed of a very-very computer-intensive simulation I must do for my works. It seems that most purpose-made packages for R : Snow, Rmpi, snowfall,... are designed for Linux based OS. I do not have access to Linux due to professionnal reasons ... so I must work with windows XP. Do somebody know a way to

Hi I have the following code which I would like to simplify. Id does linear regressions and returns the r-squares, and the coefficients. It runs slow, as it is doing the regressions for each - is it possible to get the values in a dataframe which looks as follow: expert | xx | seeds | r.squared | slope | intercept Thanks in advance, Rainer library(reshape) rsqs <- as.data.frame(

I am trying to install the R package "Rmpi" which needs libmpi. I've installed openmpi and lam in Centos 5.2: [root at rab45-1 /]# rpm -qv openmpi openmpi-1.2.5-5.el5 openmpi-1.2.5-5.el5 [root at rab45-1 /]# rpm -qv lam lam-7.1.2-14.el5 lam-7.1.2-14.el5 But I get the following error message when trying to install Rmpi: /usr/bin/ld: skipping incompatible /usr/lib/lam/lib/libmpi.so

In principle, I'd like to be able to do something like this: sge.parLapply(seq(10), function(x) parLapply(seq(x), function(x) x^2)) In practice, however, I have to resort to acrobatics like this: sge.options(sge.remove.files=FALSE) sge.options(sge.qsub.options='-cwd -V') sge.parLapply(seq(10), function(x) { sge.options(sge.save.global=TRUE)

Hi I looked, but I didn't find it: I need an array [0 to 101] where each element is a list (the result of Kest in spatstat). I.e. I want to do: A[2] <- Kest(pp1) A[3] <- Kest(pp2) ... A[101] <- Kest(pp100) How can I create A ? Rainer -- Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation Biology (UCT) Department of Conservation Ecology University of Stellenbosch Matieland

Hi I installed R 2.2.0 from source and want to use install.packages but it doesn't work. http_proxy is set to http://proxy.sun.ac.za:3128 but it still can't connect to the repository. The mirror is available, I can connect to it via the internet. Any help welcome, Rainer -- NEW TELEPHONE NUMBER Tel: +27 - (0)72 808 2975 (w) Rainer M. Krug, Dipl. Phys. (Germany), MSc

Hi I have problems installing R 2.1.1. from rpm (R-base-2.2.0-1.i586.rpm) on SuSE 10. It installs fine, all dependances are OK (at least Yast does not complain) but when I try to run R, it gives the following error message: symbol lookup error: /usr/lib/libblas.so.3: undefined symbol: _gfortran_filename and R quits. blas version: 3.0-926 Any help appreciated, Rainer -- -- Rainer M.

Hi I have (8 measures * 96 groups) = 768 datasets for which I did linear regressions using lm(). Now I want to compare the slopes for each of the 8 measures in each of the 96 groups. As I understand , I can not use > anova(lm1, ..., lm8) as the lm1 ... lm8 are based on different datasets. I also read in previous discussions in this list, that I can see if the slope +- stddev(slope)

Hi is it possible to specify the shape of the point to be used in ggplot (as with pch in plot)? I couldn't find anything in the help. Thanks Rainer -- Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation Biology (UCT) Department of Conservation Ecology and Entomology University of Stellenbosch Matieland 7602 South Africa Tel: +27 - (0)72 808 2975 (w) Fax: +27 - (0)86 516 2782 Fax:

Hi I am using mathematical anotation to make the labels in a barplot in italics. as an example (adapted from http://finzi.psych.upenn.edu/R/Rhelp02a/archive/129808.html): tt <- c("italic(First~~set)", "italic(Second~~set)", "italic(third~~set") barplot(1:3, names.arg=parse(text=tt)) But I would like to have it with "set" in a second column, like tt

Hi I am using R scripts which are running remotely. To make debugging easier, I would like to have the possibility to execute traceback() automatically when an error occurs. Is this possible? OS: Linux Thanks Rainer -- Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany) Centre of Excellence for Invasion Biology Faculty of Science Natural

Has anybody tried to use Rmpi with the OpenMPI library instead of LAM/MPI? LAM appears to be somewhat hardcoded in the Rmpi setup. Before I start to experiment with changing this, has anybody else tried Rmpi with non-LAM MPI implementations? Dirk -- Hell, there are no rules here - we're trying to accomplish something. -- Thomas A. Edison

Hi I would like to implement the "Earth Movers Distance" into R and found the code in C on the following page: http://www.cs.duke.edu/~tomasi/software/emd.htm Unfortunately, I don't know much (nearly nothing) about C and how to call it from R. As far as I have seen, the calling of the code from R should be rather straight forward, but there are still several things I don't

specifically, imagine we have: fooStack <- list() for ( i in 1:5 ) fooStack[[i]] <- list() and we have a function: fooModifier <- function( foo ) { foo$bar <- "bar" } then, if we invoke fooModifier, i.e.: fooModifier( fooStack[[ 1 ]] ) the $bar elt is only set in the scope of the function, and if we use the