similar to: snowfall: sfExport apparently harmless 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

Hello, I don't know if the question pertains to Rmpi, snow or snowfall. I run my job by: mpirun -np N -hostfile $PBS_NODEFILE RMPISNOW -f my-script.r --slave In the snowfall sfInit call I have to specify one less CPU respect to the mpirun call sfInit(parallel=TRUE, cpus=N-1, type="MPI") otherwise I receive an error similar to: "cluster size N-1 already

Greetings, I am trying to use Reference Class methods in Snowfall, using R 2.12.1 on Ubuntu Natty. Using then directly seems to work (stanza 2 below), but using them indirectly does not (stanza 3 below). I get an "attempt to apply non-function" error. In addition to exporting the instance of the object I created to the Snowfall slaves, I also made several attempts to export the

Hello, I'm trying to run a code that uses the snowfall package. Here is the structure of my code. sfInit(parallel=T, cpus = 5, slaveOutfile="ErrorMessage.txt") sfExportAll() sfLibrary(rgdal) sfLibrary(raster) sfLibrary(sp) sfLibrary(rgeos) sfLibrary(snowfall) system.time( sfClusterApplyLB(1:10, function(k) { sfCat(paste("Iteration ", k),

Dear R-listers, I have been using Snowfall (version 1.84) for parallel computing on a quad-PC running Windows 7 for a month or so without much problem. I started having problems runnnig R with Snowfall over our network when a new Novell client was installed for Windows 7. I experinenced network mapping problem with this new client. Our network colleague provided a fix which worked but a little

Dear expeRts, I'm currently trying to get data from a PostgreSQL database _in parallel_. I tried two methods: * passing the DBI Connection object to the cluster nodes * connecting the the DB on each node (1) The execution of the first method looks like this: > result = sfClusterApplyLB(input, fun, dbiCon) and produces an "expired PostgreSQLConnection" error. (Of course the

Dear All, I have a question of how to export S4 class specification to clusters/workers in parallel computing. The package I used is snowfall. The problem is reproducible as follows. Any hint is greatly appreciated. Edwin Sun === begin =========== library(snowfall) sfInit(parallel = TRUE, cpus = 2) setClass("catt", representation(aa = "numeric")) setClass("dogg",

  Hi,   The code below does exactly what I want in sequential mode. But, it is slow and I want to run it in parallel mode. I examined some windows version packages (parallel, snow, snowfall,..) but could not solve my specific problem. As far as I understood, either I have to write a new function like sfRollapplyr or I have to change my code in a way that it utilizes lapply, or sapply instead of

Hi, I am trying to write the Realized GARCH model with order (1,1) The model can be describe bellow: r_t = sqrt( h_t) * z_t logh_t = w + b*logh_(t-1) + r*logx_(t-1) logx_t = c + q*logh_t + t1*z_t +t2*(z_t ^2 -1) + u_t and z follow N(0,1) , u follow N(0, sigma.u^2) But I'm troubled with the simulation check for my code. After I simulate data from the model and estimate the data, I

Hi team, I am beginning on R and I try to install Rmpi library and I have problems, I have installed LAM-MPI on Rocks; [rcnavarro at hpc-cip ~]$ laminfo LAM/MPI: 7.1.1 Prefix: /opt/lam/gnu Architecture: x86_64-unknown-linux-gnu Configured by: root Configured on: Wed Oct 19 18:12:25 EDT 2005 Configure host: rocks-156.sdsc.edu Memory

Hi there fellow R-users, Can anyone tell me how to build a prediction interval for a gaussian log-link model for the reponse variable?? I can find the standard error of the predictions but I cant seem to find the prediction interval. Is there a way I can calculate the prediction interval from the standard errors?? Here's the example: logX<-rnorm(100)

Dear all, I am trying to execute the simple example in snowfall http://cran.r-project.org/web/packages/snowfall/vignettes/snowfall.pdf ... require(snow) require(snowfall) sfInit( parallel=TRUE, cpus=2 ) sfLapply( 1:10, exp ) sfStop() I have installed the snow and snowfall packages in R on a machine with windows xp, however, after running the "sfInit( parallel=TRUE, cpus=2 )" line I

There seems to be a minor bug in barplot.default when used with log scale w= here one or more values is NA: dat <- matrix(1:25, 5) dat[2,3] <- NA barplot(dat, beside =3D T) #Plots and appropriate barplot with gaps for m= issing data barplot(dat, beside =3D T, log =3D "y") #Error in if (min(height + offset) <=3D 0) stop("log scale error: at least = one 'height +

Hello dear R community. I just started playing with the snowfall package (a wrapper for the snow package), and found it very convenient. (See also this great website: http://www.imbi.uni-freiburg.de/parallel/ ) I was wondering if it is possible to connect snowfall with the foreach package (since it has some connection to snow). My final goal is to do some simple parallel simulations on my two

Dear Ola, I cannot say anything about Windows 7, as we do not have any Win7 machines here in our institute and I even do not know someone who have Win7 on a private machine. I will try to find a machine with this OS and test it. Anybody having experiences with Win7 yet? Greetings Jo > -------- Original Message -------- > Subject: [R] snowfall on Win7 > Date: Tue, 15 Dec 2009 11:25:37

Dear users, I want to set up R to use one R-script directory and one R-library (directory for packages) for many end-users. I try to do this by using one network-share. This works fine as long as we don't use the snowfall package with parallel=TRUE (sfInit(parallel=TRUE, cpus=4, type="SOCK")). When running R with default settings (local library and local script directory)

Hello, I'm new to R and I'm building a system that uses a cluster of computers to parallelize computations. To handle cluster setup I'm using the R package Snowfall, but knowledge of Snowfall may not be necessary to answer my question. I'm using a socket-based approach to cluster setup, so all I need to do is give Snowfall a vector of hostnames and it handles the rest. The problem

Hello T I want to order some calculation "result", there will be lots of "result" that need to calculate and order PS: the "result" is just a intermediate varible and ordering them is the very aim # problem: # For fixed NT and CT, and some pair (c,n). order the pair by corresponding result # c and n are both random variable CT<-6000 #assignment to CT

I feel like I've tried the works on something that should be obvious but I'm stuck. Package snowfall used to run just great under debian etch (amd-64, 2x quad-core). After upgrading to lenny (debian 5, reinstalled from scratch), I haven't been able to get snowfall running again. Password-less ssh works fine to localhost, its IP, or zero- config name. But when calling sfInit I

Hi there, I have some question about how to use this package: My code structure is as follows: rm(list=ls()) set.seed(2014) library(snowfall) ############# #part 1: generate the initial value for simulation #part 2: some functions will be used in the simulation #simulation part, start from "while loop" sink('SnowFallExample.Rout', split=TRUE) .Platform .Machine R.version