Hello, I can confirm that Rmpi 0.5.5 works fine with openmpi 1.1 But if (a) the cluster you are running on is set up to allow spawning and (b) you have lam-mpi installed, there is a function within zzz.R which will spawn a lam-mpi process as well which you might need to prevent.
The package README tells you what to do to prevent lam-mpi starting up. You either hack at the zzz.R, or you set up a file called lamnodes (I think) as a shell script which contains echo lamnodes NULL (or similar) and put this somewhere on your path. That tells Rmpi not to fire up lammpi, you can run it under mpirun -np 1 -hostfile myhosts R --vanilla --slave CMD BATCH diddlededoo.R & Best Paul -=-=-==-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Paul Hewson Lecturer in Statistics University of Plymouth Drake Circus Plymouth PL4 8AA tel ++44(0)1752 232778 email [EMAIL PROTECTED] web http://www.plymouth.ac.uk/staff/phewson ________________________________________ From: [EMAIL PROTECTED] [EMAIL PROTECTED] On Behalf Of Sklyar, Oleg (MI London) [EMAIL PROTECTED] Sent: 11 June 2008 10:38 To: Mark Kimpel; [EMAIL PROTECTED]; Dirk Eddelbuettel Subject: Re: [Rd] Rmpi segfault after install on Ubuntu Hardy Heron Does Rmpi work with OpenMPI at all? It calls lamboot on load from LAM MPI. I would think that mpi_initialize calls a shared library function from LAM MPI which simply does not exist in OpenMPI or which does something different from what it expects. If you ever make Rmpi working with OpenMPI I would be thankful for the solution. It does compile against OpenMPI though because the header seems to be matching. Dr Oleg Sklyar Technology Group Man Investments Ltd +44 (0)20 7144 3803 [EMAIL PROTECTED] > -----Original Message----- > From: [EMAIL PROTECTED] > [mailto:[EMAIL PROTECTED] On Behalf Of Mark Kimpel > Sent: 11 June 2008 05:47 > To: [EMAIL PROTECTED]; Dirk Eddelbuettel > Subject: [Rd] Rmpi segfault after install on Ubuntu Hardy Heron > > I just installed Rmpi on my 64-bit Ubuntu Hardy Heron OS and > using the following without errors: > "R CMD INSTALL Rmpi_0.5-5.tar.gz > --configure-args=--with-mpi=/usr/lib64/openmpi" > > Immediately at library(Rmpi) I get the segfault displayed in > my complete output below. My first thought is that perhaps I > used the wrong library for openmpi, but with my 64 bit > install it seemed like a logical choice and the install went > without a hitch. > > Two other general comments: > 1. Am I addressing this to the correct list or should I use > R-help? As I read the posting guide, I'm not sure. > 2. Has anyone considered an R-SIG-HPC list? Anyone besides me > interested? > > Mark > > > R version 2.7.0 Patched (2008-05-18 r45728) Copyright (C) > 2008 The R Foundation for Statistical Computing ISBN 3-900051-07-0 > > R is free software and comes with ABSOLUTELY NO WARRANTY. > You are welcome to redistribute it under certain conditions. > Type 'license()' or 'licence()' for distribution details. > > Natural language support but running in an English locale > > R is a collaborative project with many contributors. > Type 'contributors()' for more information and 'citation()' > on how to cite R or R packages in publications. > > Type 'demo()' for some demos, 'help()' for on-line help, or > 'help.start()' for an HTML browser interface to help. > Type 'q()' to quit R. > > Loading required package: datasets > Loading required package: utils > Loading required package: grDevices > Loading required package: graphics > Loading required package: stats > Loading required package: graph > [1] "packages do not need updated" > > options(STERM='iESS', editor='emacsclient') > > library("Rmpi") > > *** caught segfault *** > address 0x2104008, cause 'memory not mapped' > > Traceback: > 1: .Call("mpi_initialize", PACKAGE = "Rmpi") > 2: f(libname, pkgname) > 3: firstlib(which.lib.loc, package) > 4: doTryCatch(return(expr), name, parentenv, handler) > 5: tryCatchOne(expr, names, parentenv, handlers[[1]]) > 6: tryCatchList(expr, classes, parentenv, handlers) > 7: tryCatch(expr, error = function(e) { call <- conditionCall(e) > if (!is.null(call)) { if (identical(call[[1]], > quote(doTryCatch))) call <- sys.call(-4) dcall <- > deparse(call)[1] prefix <- paste("Error in", dcall, ": ") > LONG <- 75 msg <- conditionMessage(e) sm <- > strsplit(msg, "\n")[[1]] if (14 + nchar(dcall, type = "w") + > nchar(sm[1], type = "w") > LONG) prefix <- > paste(prefix, "\n ", sep = "") } else prefix <- "Error : " > msg <- paste(prefix, conditionMessage(e), "\n", sep = "") > .Internal(seterrmessage(msg[1])) if (!silent && > identical(getOption("show.error.messages"), TRUE)) { > cat(msg, file = stderr()) .Internal(printDeferredWarnings()) > } invisible(structure(msg, class = "try-error"))}) > 8: try(firstlib(which.lib.loc, package)) > 9: library("Rmpi") > > Possible actions: > 1: abort (with core dump, if enabled) > 2: normal R exit > 3: exit R without saving workspace > 4: exit R saving workspace > Selection: > > -- > Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry > Indiana University School of Medicine > > 15032 Hunter Court, Westfield, IN 46074 > > (317) 490-5129 Work, & Mobile & VoiceMail > (317) 663-0513 Home (no voice mail please) > > ______________________________________________ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel > ********************************************************************** The contents of this email are for the named addressee(s...{{dropped:6}} ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel