Displaying 20 results from an estimated 8000 matches similar to: "double boostrap with clusterApplyLB"
2006 Nov 23
2
loading libraries on MPI cluster
Dear R-users,
we are using library(snow) for computation on a linux cluster with RMPI.
We have a problem with clusterEvalQ: after launching clusterEvalQ it seems
loading the required library on each node but if we type a function
belonging to the loaded package R doesn't find it.
> library(snow)
# making cluster with 3 nodes
> cl <- makeCluster(3, type = "MPI")
Loading
2006 Oct 13
3
Rmpi performance
Dear R users,
we are trying to do some parallel computing using library(snow).
In particular we have a cluster with 3 nodes
>cl <- makeCluster(3, type = "MPI")
3 slaves are spawned successfully. 0 failed.
and we want to compute the function op_mat (see below) first with the
master and then with the cluster using system.time for checking the
computational performance.
2011 Feb 01
1
using SNOW and clusterApplyLB to run jobs parallel
I have this function and want to run it parallel with different sets of data.
Using SNOW and clusterApplyLB.
system.time(out <- mclapply(cData, plotGraph)) #each cData contains 100X6000
doubles
system.time(out <- mclapply(cData2, plotGraph))
system.time(out <- mclapply(cData3, plotGraph))
system.time(out <- mclapply(cData4, plotGraph))
system.time(out <- mclapply(cData5,
2006 Apr 04
2
EM algorithm
Dear R-Users,
I have a model with a latent variable for a spatio-temporal process.
I would like to use EM algorithm to estimate the parameters.
Does anybody know how to implement the algorithm in R?
Thank you very much in advance,
Michela
2006 Jan 02
0
boostrap astronomy problem
Hi,
I am an astronomer and somewhat new to boostrap statistics. I understand
the basic idea of bootstrap resampling, but am uncertain if it would be
useful in my case or not. My problem consists of maximizing a likelihood
function based on the velocities of a number of stars. My assumed
distribution of velocities of these stars is:
2011 Feb 03
1
boostrap an nls regression
Hello there
I have the following model based on the hollings disc equation for the type
II functional response for 2 data sets:
nls(eaten~(a*suppl)/(1+a*h*suppl)
where eaten is the number of prey eaten by a predator and suppl is the
number of prey initially supplied to the same predator.
I have parameter estimates of 'a' and 'h' for the two populations studied
and would like
2008 Oct 15
0
R-help Digest, Vol 67, Issue 31
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2013 Feb 07
1
R intermittently crashes across cluster
Greetings,
I am having an interesting problem and I wonder if anyone else has
seen this behavior.
I am running R 2.11.1 with SNOW 0.3-3 on a Dell cluster running CentOS 5.5.
I create my cluster using:
cluster<- makeCluster(nodes,type="SOCK",port=10191) # nodes is a
vector of compute nodes
I then wrap a loop around clusterApplyLB to evaluate my function
multiple times, with
2005 Oct 27
2
installing Rmpi
Hello,
I've installed R on my RHEL3 cluster and I am trying to get Rmpi to
work properly.
R is installed using the following
./configure --prefix=/home/apps/R-2.2.0
I installed snow using
R CMD INSTALL /home/apps/snow
And finaly Rmpi
R CMD INSTALL /home/apps/Rmpi --configure-args=--with-mpi=/path/to/lam
There were no errors or warnings upon installation. However when i
perform the test
2009 Sep 22
0
(correction) snowfall+Rmpi: sfExport error
Sorry for wasting your time with an incorrect diagnosis in my previous mail!
I'm running my script using mpirun -mp 4 and using snowfall+Rmpi on
Linux 64bits. I receive the following error, that terminates the run.
Any idea?
I'm able to reproduce the problem with a minimal script (below).
If n < 16371 it completes 9 iterations without problems. Already at
16371 it dies at iteration 7
2006 Apr 04
1
Mpirun with R CMD scripts
Hi,
I am working on a 64-bit rocks cluster and am relatively new to the
R package. I am trying to get Snow working with R and Rmpi and have
run into the following issue. R is able to load the Rmpi and snow
libraries and is able to run simple commands both interactively and
batch as follows:
-------------------------------------------------------------------------------------------------------
2008 Sep 04
1
Erlang-style message-passing in R: Rmpi, Snow, NetWorkSpaces, etc.
I see about 7 different R packages for multi-process parallel
programming. Which do you think is the best, most complete, and most
robust to pick for general purpose Erlang-style message-passing
programming in R, and why?
First here's my use case, and then my analysis so far. I often have
code whose basic organization looks something like this:
1. Fetch step: For each date, gather up or
2007 Oct 04
1
Rmpi_0.5-4 and OpenMPI questions
Many thanks to Dr Yu for updating Rmpi for R 2.6.0, and for starting to make
the changes to support Open MPI.
I have just built the updated Debian package of Rmpi (i.e. r-cran-rmpi) under
R 2.6.0 but I cannot convince myself yet whether it works or not. Simple
tests work. E.g. on my Debian testing box, with Rmpi installed directly
using Open Mpi 1.2.3-2 (from Debian) and using 'r' from
2011 Dec 12
1
(no subject)
Hi all,
I'm trying to get the snow package with mpi working on my linux ubuntu 10.04 machine. When I tried to install it (see below) it already had problems with the dependencies.
R version 2.14.0 (2011-10-31)
Copyright (C) 2011 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You
2007 Mar 19
1
data.frame handling
Dear R-users,
I have a little problem that I can't solve by myself.
I have a data frame with 2 factors and 8 observations (see the following
code):
y <- c(1,1,1,2,2,3,3,3)
y <- factor(y)
levels(y) <- c("a","b","c")
x <- c(1,2,3,1,2,1,2,3)
x <- factor(x)
levels(x) <- c("x","y","z")
X <-
2007 Feb 14
1
Snow vs Rmpi
Hi,
I have few high-level questions about the Snow and Rmpi packages . I understand that Snow uses Rmpi as one of possible transport layers, yet my questions about user experience, not technical details:
1. Does Snow install and work well in Windows?
2. Interruptibility. I understand that currently it is impossible to interrupt a running top-level command in Snow ( Ctl-c or the likes), the
2006 Jan 16
0
Snow Rmpi Heterogeneous Cluster
Dear R-users,
I am trying to make Snow and Rmpi working on an heterogenous cluster of
linux computers. The master computer is built on a 64 bit architecture
whereas all nodes are built on a 32 bit architecture. LAM/MPI was
installed successfully on all machine. LAM boots correctly on the master
computer and it recognizes all nodes defined in the lamhosts file.
However, when starting R,
2008 Mar 05
0
rsprng, snow, rmpi interactions
The proper use of SPRNG is a little unclear to me in each of these
packages, even more so when I put them all together.
My immediate question: in snow I did clusterSetupSRNG. If a later want
to (re) set the system to a known seed, how do I do it? That is, I want
each distributed process to recreate exactly the same random numbers
that it did before; I assume SPRNG assures the streams are
2012 Jan 04
1
rmpi vs snow - which one is better from communication overhead point of view
Hi,
I need to understand when is it best to use /rmpi/ and when is it best to
use /snow/ for parallel programming in R? I understand snow can be used for
a group of non-clustered work stations also. But I wish to understand from
the point of view of using both on clusters for a problem which has few
chunks of straightforward data-parallelism interleaved with some
communication. Since both are
2009 Sep 22
0
snowfall: sfExport apparently harmless error
I'm running my script using mpirun -mp 4 and using snowfall+Rmpi on
Linux 64bits. I receive the following error, but apparently without
consequences on the results.
Any idea?
I'm able to reproduce it with a minimal script (below). Seems the
critical issue is the for loop. Without it no error.
Thanks for your help!
TERM: Undefined variable.
TERM: Undefined variable.
TERM: Undefined