Displaying 20 results from an estimated 1000 matches similar to: "R on a computer cluster"
2012 Apr 04
1
npRmpi trouble - mpi.comm.spawn causes segfault
Dear all,
I have a large dataset of randomly generated weighed sample for which I
wish to compute a kernel density estimate.
I have used the "np" package successfully for smaller datasets, however
for the larger ones, they take too long when
using the cross validation options for bandwidth selection ("cv.ls" or
"cv.ml"). Of course, they are much quicker with
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
2008 Feb 25
1
Parallel R for dummies (on hpc)
Hi,
I had access to an hpc cluster, and wanted to parallelize some of my R code. I looked at the snow,nws, rscalapack documentation but was unable to make out how I should submit my job to the hpc, and how I should code a simple program. For example, if I had 10 matrices, and 10 processor how should I write the R (and the hpc submit code) so that I run the calculations (e.g. rowsums) for each
2008 Jun 28
2
Parallel R
Hello,
The problem I'm working now requires to operate on big matrices.
I've noticed that there are some packages that allows to run some
commands in parallel. I've tried snow and NetWorkSpaces, without much
success (they are far more slower that the normal functions)
My problem is very simple, it doesn't require any communication
between parallel tasks; only that it divides
2008 Jul 10
1
embarrassingly parallel problem - simple loop solution
I have an "embarrassingly parallel" routine that I need to run 24000^2/2
times (based on some microarray data). All I really need to do is
parallelize a nested for-loop. But I haven't found a clear list of what
packages/commands I'd need to do this. I've got a dual quad core xeon
system running RHEL5, so if I could use hyperthreading to increase the
number of (virtual)
2008 Jul 16
1
Problem with mpi.close.Rslaves()
I am running R 2.7.0 on a Suse 9.1 linux cluster with a job scheduler
dispatching jobs and openmpi-1.0.1. I have tried running one of the
examples at http://ace.acadiau.ca/math/ACMMaC/Rmpi/examples.html in Rmpi
and they seem to be working, except mpi.close.Rslaves() hangs. The
slaves are closed, but the master doesn't finish its script. Below is
the example script and the call to R. The job is
2006 Feb 13
1
Turning control back over to the terminal
I'm invoking R from withing a shell script like this
R --no-save --no-restore --gui=none > `hostname` 2>&1 <<BYE
# various commands here
BYE
I would like to regain control from the invoking terminal at some point.
I tried source(stdin()) but got a syntax error, presumably stdin is the
little shell here snippet (the part between <<BYE
and BYE).
Is there some way to
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
2005 Apr 27
1
dyn.load(), DLL, Fortran, TLNise software
Dear all,
I would like to call TLNise ("Two-Level Normal indipendent sampling estimation")
software within R.
This software estimates a hierarchical model and it can be download from
Philip Everson's website at
"http://www.swarthmore.edu/NatSci/peverso1/TLNise/tlnise.htm".
The TLNise software consists of:
1) a Fortran source code (tlnisemv1.f) and
2) a Splus code
2012 Aug 27
2
randomLCA
Can anybody, please, explain me how many parameter are estimated using
randomLCA?
For examples, model "dentistry.lca2random" estimate 1 scale (or
variance, b_j) parameter and 2 position parameters (a_cj)? Doesn't
it?
Do I need at least 4 diagnostic tests for such a model?
What happens if I specify options blocksize and byclass? How many
diagnostic tests (or rater) I need?
2007 Aug 27
2
Rmpi and x86
Dear R Gurus:
Is there a problem with Rmpi on x86 with SUSE 10.1, please?
I've tried everything and it still won't load.
Has anyone else dealt with this please?
Thanks,
Edna Bell
2009 Mar 04
1
info
Dear Sir or Madam,
I've been using R for one year and I really appreciate it.
I would like to know if a version performing parallel computations on multicore computers and computer clusters exists.
Thank you very much.
Yours sincerely.
Enrico Giorgi
_________________________________________________________________
[[alternative HTML version deleted]]
2009 Jul 31
2
Preparing for multi-core CPUs and parallel processing applications
Hello
I am fortunate (or in really big trouble) in that the research group I work
with will soon be receiving several high end dual quad core machines. We
will use the Ubuntu OS on these. We intend to use this cluster for some
extensive modeling applications. Our programming guru has demonstrated the
ability to link much simpler machines to share CPUs and we purchased the
new ones to take
2013 Apr 26
1
Lubuntu 13.04 raring ringtail: Problems installing pnmath_0.0-4
Hola!
This is 64bit Lubuntu 13.04, with R-3.0.0 installed from
deb http://ppa.launchpad.net/marutter/rrutter/ubuntu raring main
via synaptic. gcc --version
gcc (Ubuntu/Linaro 4.7.3-1ubuntu1) 4.7.3
> sessionInfo()
R version 3.0.0 (2013-04-03)
Platform: x86_64-pc-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
2008 Jul 10
1
compiling pnmath on an intel processor running mac OS 10.5
Has anyone successfully compiled pnmath (http://www.stat.uiowa.edu/~luke/R/experimental
) for an intel processor running mac OS 10.5? When I attempt to do so
via the R package installer (choosing "Local Source Package" and
pointing to the pnmath_0.0-2.tar.gz file), I get the following errors:
* Installing *source* package 'pnmath' ...
** libs
** arch - i386
gcc -arch i386
2008 Aug 21
1
pnmath compilation failure; dylib issue?
(1) ...need to speed up a monte-carlo sampling...any suggestions about
how I can get R to use all 8 cores of a mac pro would be most useful
and very appreciated...
(2) spent the last few hours trying to get pnmath to compile under os-
x 10.5.4...
using gcc version 4.2.1 (Apple Inc. build 5553) as downloaded from
CRAN, xcode 3.0...
...xcode 3.1 installed over top of above after
2011 Feb 01
1
Rmpi; sample code not running, the slaves won't execute commands
Hi All,
I'm trying to parallelize some code using Rmpi and I've started with a
sample 'hello world' program that's available at
http://math.acadiau.ca/ACMMaC/Rmpi/sample.html. The code is as
follows;
# Load the R MPI package if it is not already loaded.
if (!is.loaded("mpi_initialize")) {
library("Rmpi")
}
# Spawn as many slaves as possible
2003 Mar 07
1
start_transaction: Readonly filesystem error
On a 2.4.17 (MontaVista 2.1) kernel using ext3, I recently starting seeing the
error
EXT3-fs error (device ide1(22,1)) in start_transaction: Readonly filesystem
EXT3-fs error (device ide1(22,1)) in ext3_delete_inode: Readonly filesystem
on a file system within 10-20 seconds after remounting it r/o.
Apparemtly a write is being deferred past the remount point and then
runs into problems when it is
2002 Oct 03
3
Converting root ext3 to ext2?
Can anyone comment on whether or not it is possible to successfully
disable the journal of an ext3 root file system
prior to reboot? My application is to try and make sure there is no
journal prior to installing and rebooting into a system which does not
support ext3. I know that as long as the root is cleanly remounted r/o
with no journal updates pending, this
will be compatible. I'm
2007 Feb 19
1
Installing Rmpi on FC5 with lam
After several trial and error attempts, I managed to install the Rmpi
package without error on my Linux machine, running Fedora 5.
I installed lam-7.1.2, lam-devel-7.1.2 and R-2.4.1, R-devel-2.4.1
The Package Rmpi_5.0-3.tar.gz, I installed once from within R and once
from the command line to make sure, I link the right libraries:
R CMD INSTALL Rmpi_5.0-3.tar.gz