similar to: MPI and R CMD SHLIB

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

??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

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

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

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:

Hi guys, I've spent a few days trying to install Rmpi with no luck. I originally tried using mpich, moved on to mpich2, and then to openmpi. I've gotten the furthest with openmpi, though am still running into this problem and can't figure it out. Can someone help!? Thanks so much in advanced. I'm using an HP Envy laptop with Ubuntu 12.04. Output is below, with the error at the

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

Hello everybody, I am trying to install Rmpi on 64-bit HP-Proliant server. I am facing the following error: * Installing *source* package 'Rmpi' ... Try to find mpi.h ... Found in /usr/local/mpich-1.2.7p1/include Try to find libmpi or libmpich ... Found libmpich in /usr/local/mpich-1.2.7p1/lib Try to find liblam ... checking for main in -llam... no liblam not found. Probably not LAM-MPI

Hello R-help! I am a systems administrator for the University of Southern California. I take care of it's general-purpose research cluster, and have recently been asked to provide access to a parallelized R platform. I do not have any previous experience using R, and have only ever had to do anything more then 'yum -y install R'. We have a myrinet MPI network, and use mpich1 as our

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Hi Everyone, I'm trying to load some C++ code using dyn.load but I'm getting unresolved symbols associated with some external libraries (CSparse). I gather this is something to do with linking as the the code compiles fine. However, I've passed -L/home/jarrod/My_Programs/SuiteSparse/CSparse/Lib -lcsparse to the complier (g++), either directly using R CMD SHLIB or as

Dear All, I have created a virtual high performance computing (HPC) cluster of 6 compute nodes with MPICH2 using Xen-based Fedora 11 Linux 64-bit paravirtualized (PV) domU guests. Dom0 is Fedora 11 Linux 64-bit. My Intel Desktop Board DQ45CB has a single onboard Gigabit LAN network adapter. I am able to bring up the ring of mpd on the set of 6 compute nodes. However, I am consistently

Dear All, I have created a virtual high performance computing (HPC) cluster of 6 compute nodes with MPICH2 using Xen-based Fedora 11 Linux 64-bit paravirtualized (PV) domU guests. Dom0 is Fedora 11 Linux 64-bit. My Intel Desktop Board DQ45CB has a single onboard Gigabit LAN network adapter. I am able to bring up the ring of mpd on the set of 6 compute nodes. However, I am consistently

Hi List, I've run into a library problem I believe might be related to the portland group compiler, and / or the libs on CentOS. Essentially what is happening is the primary executable I'm trying to run is failing under mpi. Here's the output from the command (which would be the same as the script calling it) $ /usr/local/mpich/bin/mpirun -machinefile machines.LINUX -np 2

I am working on a SLES 10 cluster with R available on it. To better use my resources, I want to use Rmpi, but I am having a difficult time installing it. I have set the $R_LIBS variable correctly. The MPI libraries are available through the PGI compiler, but this R instance was compiled with GCC. The Rmpi package can be compiled and installed with %R CMD INSTALL Rmpi_0.5-5.tar.gz

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, You should look at Pinheiro and Bates (2000) Mixed-effects models in S and S-Plus. It describes how to format the correlation matrix to pass to functions lme and gls. Basically, the correlation matrix has to be one of the corStruct classes, probably corSymm for your example. So in the call to lme (or gls if you really have no random effects), use something like:

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 have a slightly complicated question. I am using an mpi application (Intel impi) which uses ssh to launch applications. For about 0.1-0.2% of the ssh connections I end up with a zombie, i.e. ps will show [ssh] <defunct>. Something is going wrong with the ssh when it starts, perhaps a race condition, it is not disconnecting after some time, that I have been able to verify. The most obvious