similar to: Running R embedded in an mpiexec spawned process - Fatal error: you must specify '--save', '--no-save' or '--vanilla'

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

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

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

After a long processing, I was able to create a version of a small C# class that was able to emulate the rproxy by P/Invoke. This is mostly to find a workaround a performance problem of the StatConnector. It's almost work but ... I have strange memory exception when I call the print function. The variable seems to not survive from one call to the other. As there is no debug symbol for

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...

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 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

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:

??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

Hi - I wrapped R.dll up using somebody code online (see below). I am comparing R on .NET IPC with R(D)COM. I got it all working. Except, I realize that in my client code of the IPC remoting, if I call 'plot' function in R via EvaluateNoReturn, I don't seem to see any results on the R plot window (although the window pops up). Is there anything to do with the code of R.dll wrapper

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

Dear all, my aim is to integrate R in an interactive visualisation software called Bulk Analyzer developed by VrVis (http://www.vrvis.at). the code: SEXP e, tmp; ParseStatus status; PROTECT(tmp = mkString("x <- c(1.234,-3.45)")); PrintValue(tmp); PROTECT(e = R_ParseVector(tmp, -1, &status, R_NilValue)); PrintValue(e); UNPROTECT(2); produces the following output: [1] "x

Dear list, I am trying to implement a publish-subscribe mechanism in for an embedded R interpreter. But somehow my registered closures seem to get collected by the GC, even though I have protected them. I have reducted my code to the following sample. Sorry if it is a little verbose. The first couple of call of calls still work, but at some point one of the callbacks (callback1 in my

Hi, I would like to compile a shared C++ library but using MPI. Is there away to compile shared libraries using the functionality of mpiexec supplied with MPICH-2. Thanks for any help, Jarrod

I'm invoking R from withing a shell script like this R --no-save --no-restore --gui=none > `hostname` 2>&1 <<BYE # various commands here BYE I would like to regain control from the invoking terminal at some point. I tried source(stdin()) but got a syntax error, presumably stdin is the little shell here snippet (the part between <<BYE and BYE). Is there some way to

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

Dear r-helpers, I have been trying to invoke R from Java in a Windows 2000 computer (unfortunately). All my environment variables seem to be properly set, everything seems to be in order, but I obtaining a Fatal error: unable to open the base package error window. Also, the output of the invoker is Loading RInterpreter library R_HOME: R_HOME=C:/Programas/R RVersion: R_VERSION=1.6.1 whereas

Hi, I've installed recently OpenOffice.org 3.1 on Centos 5.3. I use OOo in headless mode. I have no problem when running as root, but I'd prefer run it as non-root user (oooserver user). When I run the script in debug mode this is the output: sh -x /tmp/ooo-headless-nonroot start + . /etc/rc.d/init.d/functions ++ TEXTDOMAIN=initscripts ++ umask 022 ++

The call to system() probably is an internal call used to delete the session's tempdir(). This sort of failure means that a potentially large amount of disk space is not being recovered when R is done. Perhaps R_CleanTempDir() could call R_unlink() instead of having a subprocess call 'rm -rf ...'. Then it could also issue a specific warning if it was impossible to delete all of