similar to: send and receiving objects with Rmpi

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 I've written a function that uses Rmpi to perform a calculation in parallel. It works fine, but I'm trying to improve efficiency in terms of memory usage and the amount of data being passed back and forth between mater and slaves. Calculations are performed on a symmetrical matrix in order to zero-out some of the cells. In the parallel

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

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

Hi everybody! I have the next code which makes a reduction of the *a *variable in two slaves, using the Rmpi package. library(Rmpi) mpi.spawn.Rslaves(nslaves=2) reduc<-function(){ a<-mpi.comm.rank()+2 mpi.reduce(a,type=2, op="prod") return(paste("a=",a)) } mpi.bcast.Robj2slave(reduc) mpi.remote.exec(reduc()) cat("Product: ")

Hi everybody! I have the next code which makes a reduction of the *a *variable in two slaves, using the Rmpi package. library(Rmpi) mpi.spawn.Rslaves(nslaves=2) reduc<-function(){ a<-mpi.comm.rank()+2 mpi.reduce(a,type=2, op="prod") return(paste("a=",a)) } mpi.bcast.Robj2slave(reduc) mpi.remote.exec(reduc()) cat("Product: ")

I've tweaked Rmpi and want to have some variables that hold data in the package. One of the R files starts mpi.isend.obj <- vector("list", 500) #mpi.request.maxsize()) mpi.isend.inuse <- rep(FALSE, 500) #mpi.request.maxsize()) and then functions update those variables with <<-. When run:

I'm aiming to compare the workings of Rmpi and multicore on a duel processor quad core machine with 64 bit R-2.11.1 Kubuntu 10.4. It's impossible for me to get a small reproducable code segment to show what I mean, but if I show what works for mclapply, I'd hope it's possible to be shown what would be the equivalent way with mpi.apply. The function lr.gbm has variables trees,

Dear R list, In the course of learning to work with Rmpi, we are confused about a few points. The following simple program is based on some examples we retrieved from the web. Each slave is writing the same output line multiple times (a multiple equal to the number of slaves). In other words, the write statements are being executed a number of times equal to the number of slaves. I am

Dear R yet again! I finally got the Rmpi package to install! Yay!. However, when I go into R to use it, there is an error with the dyn.load file. This should be simple (allegedly). Please help. Thanks, Sincerely, Erin mailto: hodgess at gator.uhd.edu /home/faculty/hodgess/R-2.6.0/bin [hodgess at gator bin]$ ./R CMD INSTALL Rmpi_0.5-4.tar.gz

Dear all, I have used the Rmpi package many times before however this time I've installed it as I always do with openMPI tar.gz file direct from the website. I'm installing on my ubuntu 8.10. Linux 2.6.27-11-generic #1 SMP Thu Jan 29 19:28:32 UTC 2009 x86_64 GNU/Linux All i get is: > library(Rmpi) Segmentation fault :~$ Which dumps me back into the shell, and doens't give me much

This is a rather obscure question, I realize. I have written to the package author but have not heard back as of yet. I have read the README in the package, as well, but it didn't give me enough detail to diagnose the problems that I am having. (I did edit out the LAM-MPI check in zzz.R.in.) I am working to install Rmpi on top of MPICH on a beowulf cluster. Below is the output of the

I have just installed Rmpi on a Suse 9.1 linux cluster with openmpi-1.0.1. I am trying the example included below from the tutorial website. However, I keep getting the following error: > # Load the R MPI package if it is not already loaded. > if (!is.loaded("mpi_initialize")) { + library("Rmpi") + } > > # Spawn as many slaves as possible >

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

Dear R-users, I got problem when using both RMPI and RMySQL together and I thought some body in this forum can help me. I have a huge data set (more than 300,000 rows) and I would like to modify only few observations. I wrote the modifications in a function form and able to send the function to slaves using Robj2slaves from RMPI package. However the function needs MySQL data base name to extract

R objects can disappear if they are garbage collected; can they move, i.e., change their location in memory? I don't see any indication this might happen in "Writing R Extensions" or "R Internals". But I'd like to be sure. Context: Rmpi serializes objects in raw vectors for transmission by mpi. Some send operations (isend) return before transmission is complete and

Dear R People: I'm running Rmpi on a single machine and I have the following statement from the command line: mpirun -np 3 ./R --no-save < eek1.in >stuff4.out The stuff4.out file only contains the third result. Is there a way to fix this such that it shows all 3 sets, please Thanks in advance, Erin -- Erin Hodgess Associate Professor Department of Computer and Mathematical

I have a package that can use rmpi, but works fine without it. None of the automatic test code invokes rmpi functionality. (One test file illustrates how to use it, but has quit() as its first command.) What's the best way to handle this? In particular, what is the appropriate form for upload to CRAN? When I omitted rmpi from the DESCRITPION file R CMD check gave <quote> * checking

Dear R People: I'm having some trouble with mpiexec and Rmpi. I would like to be able to pass in the number of "children" via the mpiexec command (from the command line). this is in SUSE10.1, with R-2.7.1 Here are my files: cat eb.R library(Rmpi) mpi.remote.exec(paste("i am",mpi.comm.rank(),"of",mpi.comm.size())) mpi.quit() hodgesse at

Signed-off-by: Maarten Lankhorst <maarten.lankhorst at canonical.com> --- drivers/gpu/drm/radeon/radeon_gem.c | 19 ++++++++++++++----- 1 file changed, 14 insertions(+), 5 deletions(-) diff --git a/drivers/gpu/drm/radeon/radeon_gem.c b/drivers/gpu/drm/radeon/radeon_gem.c index d09650c1d720..7ba883843668 100644 --- a/drivers/gpu/drm/radeon/radeon_gem.c +++

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