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)
Sklyar, Oleg (MI London)
2008-Jun-11 09:38 UTC
[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 osklyar at maninvestments.com> -----Original Message----- > From: r-devel-bounces at r-project.org > [mailto:r-devel-bounces at r-project.org] On Behalf Of Mark Kimpel > Sent: 11 June 2008 05:47 > To: r-devel at stat.math.ethz.ch; 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 at 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:22}}
Dirk Eddelbuettel
2008-Jun-11 10:10 UTC
[Rd] Rmpi segfault after install on Ubuntu Hardy Heron
On 11 June 2008 at 10:38, Sklyar, Oleg \(MI London\) wrote: | Does Rmpi work with OpenMPI at all? It calls lamboot on load from LAM Yes. | 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. Debian switched in October 2007 and with Rmpi 0.5-4. Rmpi 0.5-5 definitely supports it, Hao Yu made some upstream changes. I have been using it on Ubuntu/x86 at work all that time (but then I was also testing the newer Open MPI code). You may want Open MPI 1.2.* though it may work with 1.1.* as well. Dirk -- Three out of two people have difficulties with fractions.
Dirk Eddelbuettel
2008-Jun-11 12:22 UTC
[Rd] Rmpi segfault after install on Ubuntu Hardy Heron
On 11 June 2008 at 00:46, Mark Kimpel wrote: | 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" And it concluded without warnings or errors? Configure found all the right files? As Paul suggested, make sure you're not getting it mixed with exisiting LAM headers or MPICH2 headers or, say, that you're getting your gcc and icc experiemenst mixed up or ... ? I control this by locally re-building the Debian packages for Open MPI. That way I only keep one -dev package for MPI and can ensure that I do not get mixups with other MPI installation. But then I do buy into the Package Management mantra, but not everybody does... | 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. Check ldd on Rmpi.so to ensure that you linked against what you thought you should link against. And if everything else fails, debug the compiled code and run R under the debuggger. See the 'R Extensions' manual. | 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? I'd join. Dirk -- Three out of two people have difficulties with fractions.