Displaying 20 results from an estimated 10000 matches similar to: "snow parLapply standard output"
2005 Nov 11
1
Snow parLapply
Dear R-user,
I am trying to use the function 'parLapply' from the 'snow' package
which is supposed to work the same wys as 'lapply' but for a
parallelized cluster of computers. The function I am trying to call in
parallel is 'dudi.pca' (from the 'ade4' package) which performs
principal component analyses. When I call this function on a list of
2011 Feb 03
1
problem with parLapply from snow
Hi,
The following function use to work, but now it doesn't giving the error
"> CallSnow(, 100)
Using snow package, asking for 2 nodes
2 slaves are spawned successfully. 0 failed.
Error in checkForRemoteErrors(val) :
2 nodes produced errors; first error: no applicable method for 'lapply' applied to an object of class "list"
".
Where this is the
2010 Dec 02
1
parLapply - Error in do.call("fun", lapply(args, enquote)) : could not find function "fun"
Hello everybody,
I've got a bit of a problem with parLapply that's left me scratching my head
today. I've tried this in R 2.11 and the 23 bit Revolution R Enterprise and
gotten the same result, OS in question is Windows XP, the package involved
is the snow package.
I've got a list of 20 rain/no rain (1/0) situations for these two stations i
and j, all the items in this list look
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
2008 Nov 30
2
Snow and multi-processing
Dear R gurus,
I have a very embarrassingly parallelizable job that I am trying to speed up with snow on our local cluster. Basically, I am doing ~50,000 t.test for a series of micro-array experiments, one gene at a time. Thus, I can easily spread the load across multiple processors and nodes.
So, I have a master list object that tells me what rows to pick up for each genes to do the t.test from
2012 Aug 03
1
Parallel runs of an external executable with snow in local
Hi everyone,
I'm aiming to run an external executable (say filetorun.EXE) in parallel. The external executable collect needed data from a file, say "input.txt" and, in turn,generates several output files, say "output.txt". I need to generate "input.txt", run the executable and keep "input.txt" and "output.txt". I'm using Windows 7, R
2012 Dec 21
1
Parallel code using parLapply
Dear R-users
I was running into problems with my R code trying to run clh sampling (clhs package) in parallel mode (=on various data sets simultaneously).
Here is the code (which I developed with some help:)):
******************************************
library("clhs")
library("snow")
a <- as.data.frame(replicate(1000, rnorm(20)))
b <- as.data.frame(replicate(1000,
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
2012 Jan 12
1
parLapply within a function
Dear R users,
I have some problems with the parLapply function from the "parallel"
package:
I use parLapply on a pretty big R object without changing the object
within the called function. If I execute parLapply alone, everything
works fine. It seems that the object resides only once in the memory.
But if I use the same call within another function, the object seems to
be multiplied to
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
2007 Feb 02
1
Snow Package and R: Exported Variable Problem
Hello and thanks in advance for your time.
I've created a simulation on my cluster which uses a custom package
developed by me for different functions and also the snow package.
Right now I'm using LAM to communicate between nodes and am currently
only testing my code on 3 nodes for simplicity, though I plan on
expanding to 16 later. My problem is this error:
"Error in
2008 Jul 16
3
Snow or alternative MPI packages on Windows
Guys,
I'm running R on both Windows & Linux. I'm looking at a number of packages
for parallel execution. It seems that the most used packages are "snow" and
"Rmpi".
snow seems more user friendly, but it doesn't run on windows. I see from
searching the mailing list that I'm not the first one to try it on Windows.
There was a message that kind of shed some
2008 May 08
1
rmpi/snow grabs all available CPU
Hi,
I'm testing affyPara on Debian lenny with
R 2.7 from unstable, and the corresponding bioconductor packages from
bioconductor.org downloaded using biocLite as per usual.
The command
cl = makeMPIcluster(k)
succeeds, but spawns k R slaves which promptly soak up all available CPU, which
is odd since they are not doing anything yet. This looks like a bug to me.
Similar behaviour is shown
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.
2004 Apr 08
2
socket clusters on snow dies easily
hello,
I'm using R 1.8.1 with the lastest snow package on FreeBSD 4.9.
However, when I try to using socket clusters, it's very unstable.
Sometimes it dies half way when I run parSapply(), sometimes
it dies when cluster connection is idle.
I create a socket cluster by following cmd
cl = makeCluster("foo", type = "SOCK", outfile="/tmp/rafanlog");
2013 Dec 24
2
Parallel computing: how to transmit multiple parameters to a function in parLapply?
Hi R-developers
In the package Parallel, the function parLapply(cl, x, f) seems to allow
transmission of only one parameter (x) to the function f. Hence in order to
compute f(x, y) parallelly, I had to define f(x, y) as f(x) and tried to
access y within the function, whereas y was defined outside of f(x).
Script:
library(parallel)
f <- function(x) {
z <- 2 * x + .GlobalEnv$y # Try to
2012 Aug 21
1
parLapply fails to detect default cluster?
invoking parLapply without a cluster fails to find a previously
registered cluster
> library(parallel)
> setDefaultCluster(makePSOCKcluster(2))
> parLapply(X=1:2, fun=function(...) {})
Error in cut.default(i, breaks) : invalid number of intervals
This is because in parLapply length(cl) is determined before
defaultCluster(cl) is called. By inspection, this appears to be true of
2009 Nov 17
2
SVM Param Tuning with using SNOW package
Hello,
Is the first time I am using SNOW package and I am trying to tune the cost
parameter for a linear SVM, where the cost (variable cost1) takes 10 values
between 0.5 and 30.
I have a large dataset and a pc which is not very powerful, so I need to
tune the parameters using both CPUs of the pc.
Somehow I cannot manage to do it. It seems that both CPUs are fitting the
model for the same values
2004 Mar 23
2
Status of Rmpi
Rmpi is not currently available on CRAN, and I don't think it has been
for a few months. It is available at
http://www.stats.uwo.ca/faculty/yu/Rmpi/
Does anyone know its current status?
A few months ago I corresponded with the author, who noted some build
problems (specifically on Debian) were the hang up, and seemed to be
working on it. I wasn't able to get it to work then (on a
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:
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