Displaying 20 results from an estimated 1300 matches similar to: "Parallel R for dummies (on hpc)"
2008 Jul 04
2
experinental revision of the 'snow' package
A new version of the 'snow' package for parallel computing in R is
available at
http://www.stat.uiowa.edu/~luke/R/cluster/snow_0.3-3.tar.gz
This substantially revises the way in which worker processes are
started to allow snow to be used on Windows and Mac/Windows/Linux
combinations. I have successfully used the SOCK version on a
standalone Windows machine and combinations of
2008 Mar 20
1
Rmpi and C Code, where to get the communicator
Hello,
I try to write parts of my code in C to accelerate the for-loops. But
basic operations I want to do in R (e.g. start cluster). My R code looks
something like this:
library(Rmpi)
mpi.spawn.Rslaves()
mpi.remote.exec(....)
dyn.load("test.so")
erg <- .Call("test", ....)
....
mpi.close.Rslaves()
mpi.quit()
And my C function looks something like this:
#include
2007 Sep 07
2
ploting missing data
Hello,
I have this kind of dataframe and have to plot it.
data <- data.frame(sw= c(1,2,3,4,5,6,7,8,9,10,11,12,15),
zehn =
c(33.44,20.67,18.20,18.19,17.89,19.65,20.05,19.87,20.55,22.53,NA,NA,NA),
zwanzig =
c(61.42,NA,26.60,23.28,NA,24.90,24.47,24.53,26.41,28.26,NA,29.80,35.49),
fuenfzig =
2007 Jun 11
3
simultaneous computing
Hello,
which possibilities are available in R for simultaneous or parallel
computing?
I only could find biopara
(http://cran.r-project.org/src/contrib/Descriptions/biopara.html)
Are there other possibilities?
Are there special groups working on simultaneous computing with R?
Thanks
Markus
--
Dipl.-Tech. Math. Markus Schmidberger
Ludwig-Maximilians-Universit?t M?nchen
IBE - Institut f?r
2009 Aug 10
1
multicore mclapply hangs
When I execute mclapply it creates the needed processes, but these
processes never begin computing anything, they just wait indefinitely.
I recently upgraded to version 2.9.1, which might have caused the problem.
--
Med venlig hilsen
Rune Schjellerup Philosof
Ph.d.-studerende, Statistik, IST, SDU
Telefon: 6550 3607
E-mail: rphilosof at health.sdu.dk
Adresse: J.B. Winsl?wsvej 9, 5000 Odense
2008 Jun 02
4
exit function in R?
Hi,
This is likely an stupid question, but I cannot find the solution.
I am searching for an "exit" function, to end the execution of an R
script if some condition is not filled.
Any clue?
Thank you in advance!
Federico
2008 Oct 22
1
torque/psb & snow library
Hello all;
I'm trying to execute parallel jobs trough library snow on a cluster built
through torque/PSB. I'm succesfully obtaining the cluster with:
>system("cat $PBS_NODEFILE > cluster.txt")
>mycluster <- scan(file="cluster.txt",what="character")
>cl <- makeSOCKcluster(mycluster)
The only problem, at the moment, is that if I use
2008 Oct 22
1
Problem about spawn nodes with Rmpi
Hi all,
now I'm testing R in a "virtual cluster", made it with VirtualBox. This one
has 3 nodes, running CentOS 5 and OpenMPI 1.2.8, and the principal node
(called "server") exports the /home to other nodes.
I have installed R and OpenMPI in /home, in fact, it seems work OK. Editing
the openmpi-default-hostfile and run "mpirun -np 3 hostname" I can see the
2008 Sep 08
1
cluster/snow question
Dear R Users,
I am attempting to use the snow package for clustering. Is there a way to
identfy, in the environment of each node, a rank for that node and also,
the total size of the cluster ?
By way of analogy, I am looking for the functions in snow equivalent to
mpi.comm.rank() and mpi.comm.size() from RMPI, in case that makes things
clearer.
Thanks in advance,
Tolga
Generally, this
2008 Oct 08
5
ParallelR
Anyone using or has access to ParallelR? I was looking at the page and
found nothing really useful!
http://www.revolution-computing.com/sitegenius/topic.php?id=195
I want to see if I can run R on a cluster of workstation, and use
batch systems like Grid Engine or Xgrid:
http://gridengine.sunsource.net/
http://ww.apple.com/acg/xgrid/
--Chi
2007 Mar 28
4
Rmpi and OpenMPI ?
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
2008 Nov 07
1
Rmpi task-pull
Hi, I'm testing the efficiency of the Rmpi package regarding parallelization
using a cluster.
I've found and tried the task pull programming method, but even if it is
described as the best method, it seems to cause deadlock, anyone could help
me in using this method?
here is the code I've found and tried:
# Initialize MPI
library("Rmpi")
# Notice we just say "give us
2008 Jul 18
3
How to cut data elements included in a text line
Hello,
assume I have an "unstructured" text line from a connection. Unfortunately,
it is in string format:
R> x
[1] "\talpha0\t-0.638\t0.4043\t0.4043\t-2.215\t-0.5765\t-0.137\t501\t2000"
How can I extract the data included in this string object "x" in order to
get the elements for the parameter vector called "alpha0", i.e.
-0.638 0.4043 0.0467
2007 Aug 06
1
Problems with expresso
Hello,
I want to use expresso for preprocessing the hgu133a-spikein data from
affycompII. But there is an error:
> library(affy)
> path <- "z:/Microarray/hgu133a-spikein/rawdata"
> celFile <- list.celfiles(path=path,full.names=TRUE);
> affyBatch <- ReadAffy(filenames=celFile[1:6]);
> eset1 <-
2007 Jan 19
5
Problem with C extension
Hello,
I try to write an extension in C, to get a faster functions.
Therefore I have to add an element (vector) to a vector. The command in
R is very simple: x = c(x,a)
But in C I have the problem to reallocate my vector for getting more
space. Everything I tried, I get a "Segmentation fault".
So, how can I combine two vectors in C and give the result back to R
(return(x))?
Thanks
2009 May 20
1
Extracting correlation in a nlme model
Hi R users:
Is there a function to obtain the correlation within groups
from this very simple lme model?
> modeloMx1
Linear mixed-effects model fit by REML
Data: barrag
Log-restricted-likelihood: -70.92739
Fixed: fza_tension ~ 1
(Intercept)
90.86667
Random effects:
Formula: ~1 | molde
(Intercept) Residual
StdDev: 2.610052 2.412176
Number of Observations: 30
Number
2008 Apr 08
1
Rmpi 0.5-6 : error spawning process
Hi,
I am using a cluster with LAM 7.1.3/MPI 2 and R 2.6.0.
Rmpi version 0.5-5 is working very well.
Now I have tested "Rmpi 0.5-6". During spawning the Rslaves I get an
error: MPI_Error_string: error spawning process
> sessionInfo()
R version 2.6.0 (2007-10-03)
x86_64-unknown-linux-gnu
locale:
2008 Mar 27
1
snow, stopping cluster
Hello,
is there any function in the package snow to check for a really running
cluster?
The function checkCluster only checks the variable cl. And the variable
is still available after stopping the cluster!
( a simple solution would be deleting the cluster variable cl in the
function stopCluster)
> library(snow)
> cl <- makeCluster(5)
5 slaves are spawned successfully. 0
2007 Sep 03
1
Snow on Windows Cluster
Hello,
the package snow is not working on a windows cluster with MPICH2 and
Rmpi. There is an error in makeCluster:
launch failed: CreateProcess(/usr/bin/env
"RPROG="C:\Programme\R\R-2.5.1\bin\R" "OUT=/dev/null" "R_LIBS="
C:/Programme/R/R-2.5.1/library/snow/RMPInode.sh) on 'cl1' failed, error
3 - Das System kann den angegbenen Pfad nicht finden.
I
2005 Dec 14
3
package for factor analysis
I have Windows XP Professional Version 2002 and the R-Version 2.1.1.
I want to do factor analysis with R.
In Google Search I find the reference to the RScaLAPACK-Package, but my
R-Version 2.1.1. told me that "RScaLAPACK is invalid package, bevor
2.0.0. installed" .
Which package can I take for factor analysis?
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