similar to: problem with mpiexec and Rmpi

Hello, I try to install pbdMPI. Compilation successful, but load fails with segfault. Is anyone can help me? R version 3.0.0 pbdMPI version 0.1-6 Intel compiler version 13.1.1 OpenMPI version 1.6.4-1 CPU Intel x86_64 # R CMD INSTALL pbdMPI_0.1-6.tar.gz .. .... checking for gcc... icc -std=gnu99 checking whether the C compiler works... yes checking for C compiler default output file name...

I'd like someone familiar with the R options initialization to comment on a difference of behavior within/without mpiexec I have a (.NET) application with embedded R that is proven to run in a single process: ./Sample1.exe on a Debian Linux with R 3.0.2 Running the same code with mpiexec, it fails at the R engine initialization: mpiexec -n 1 ./Sample1.exe Fatal error: you must

Can someone please provide me with a little more information about this. It could be the source of some issues I am seeing with mpirun/mpiexec.hydra/ssh (post earlier today), and information about what it leads to (and any signatures) would be helpful. Thanks. -- Professor Laurence Marks Department of Materials Science and Engineering Northwestern University www.numis.northwestern.edu

R-users, My question is related to earlier posts about benefits of quadcore over dualcore computers; I am trying to setup a cluster of windows xp computers so that eventually I could make use of 10-20 cpu:s, but for learning how to do this, I am playing around with two laptops. I thought that the package snow would come handy in this situation, but to use snow, I would probably need to install

Hi all, Not sure if this is the best place to put this question since I'm not sure if it's a Libvirt issue but... I currently have two VMs up with networking and I can successfully ssh to and from each VM and I have confirmed that I can successfully download things from the internet. However, when trying to run mpiexec (which uses ssh), the connection fails and gives me the following

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: -------------------------------------------------------------------------------------------------------

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

Hello, We have R working with Rmpi/openmpi, but I'm a little worried. Specifically, (a) the -np flag doesn't seem to override the hostfile (it works fine with fortran hello world) and (b) I appear to have twice as many processes running as I think I should. Rmpi version 0.5.5 Openmpi version 1.1 Viglen HPC with (effectively) 9 blades and 8 nodes on each blade. myhosts file contains

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

Dear knowledgeable experts :-), I am trying to get openmpi, Rmpi and SNOW running on a Myrinet/GM cluster. I'm not an IT expert, but I surely could use a working installation of Rmpi and SNOW. I try to load the Rmpi library and get the following: > library(Rmpi) [master:07230] mca: base: component_find: unable to open osc pt2pt: file not found (ignored)

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

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

Dear R People: I am having some trouble with the snow package. It requires MPICH2 and Rmpi. Rmpi is fine. However, I downloaded the MPICH2 package, and installed. There is no mpicc, mpirun, etc. Does anyone have any suggestions, please? Thanks in advance! Sincerely, Erin Hodgess Associate Professor Department of Computer and Mathematical Sciences University of Houston - Downtown mailto:

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

1.I have a library fpmpi . I made the shared library fpmpi.so from this library.I am using ubuntu . 2.Now, I want to use in my R package .My R package has src folder the there is makevars.in file ### Setup R source code and objects. PKG_CPPFLAGS = @PKG_CPPFLAGS@ PKG_LIBS = -L/home/g/Desktop/Project -fpmpip ### For user configuration. USER_CONF = Makeconf ### Start making here. all:

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

Hello: Anybody knows how to run Rmpi through PBS (Portable Batch System) on a cluster computer. I'm using a supercomputer which require to submit jobs to PBS queue for dispatching. I tried use mpirun in my PBS script. But all my Rslaves are spawned to the same node. This is not desired. Any suggestions are welcome! Thanks in advance. ======================================== Shengqiao Li

Hi I am trying to utilize my dual core processor (and later a High-performance clusters (HPC) ) by using the Rmpi, snow, snowfall, ... packages, but I am struggling at the beginning, i.e. to initialise the "cluster" on my dual core computer. Whenever I try to initialize it (via sfInit(parallel=TRUE, cpus=2) or mpi.spawn.Rslaves(nslaves=2) ), I get an error message: >

??I installed Microsoft MPI. Then installed the foreach and Rmpi packages. Then built doMPI from source. mpi.remote.exec works. foreach hangs with the main process and all worker processes idle. I launch my script with mpiexec: "C:\Program Files\Microsoft MPI\Bin\mpiexec" -n 3 "C:\Program Files\R\R-3.2.0\bin\x64\Rterm.exe" --no-save -q -f "MPI Test.r" The

I have a network of four machines set up. I'm having trouble spawning my slaves on these machines. All the examples I have found so far use makeCluster with type="MPI", and I guess I'm missing some kind of cluster configuration in my environment variables because all my clusters are formed on the machine where my initial session is running. Can anyone refer me to a link that