[Rd] Rmpi segfault after install on Ubuntu Hardy Heron

[Paul Hewson]

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 paul.hewson at plymouth.ac.uk
web http://www.plymouth.ac.uk/staff/phewson

________________________________________
From: r-devel-bounces at r-project.org [r-devel-bounces at r-project.org] On Behalf Of Sklyar, Oleg (MI London) [osklyar at maninvestments.com]
Sent: 11 June 2008 10:38
To: Mark Kimpel; r-devel at stat.math.ethz.ch; 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
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
>
>
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> 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
>
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