Re: [R] ADaCGH package crashes at mpiInit()

From: Ramon Diaz-Uriarte <rdiaz02_at_gmail.com>
Date: Thu, 12 Jun 2008 12:03:06 +0200

Dear Daren,

First, please note that since this problem concerns a particular package, you are supposed to contact the package maintainer (me) directly. (See the R-FAQ, 9.2).

Anyway, I've never seen that error message before. But I think it indicates a problem with your MPI setup, nothing related to R (and, thus, neither ADaCGH nor Rmpi). A few things to try:

  1. When ADaCGH fails, could you do a "traceback()" to see where exactly is failing?
  2. (in a newly started R session) please try something like the following:

library(Rmpi)

mpi.universe.size()
mpi.spawn.Rslaves()
mpi.remote.exec(rnorm(2))

And lets see how far the example gets.

3. How is MPI started? Is it LAM-MPI or OpenMPI?

Best,

R.

On Thu, Jun 12, 2008 at 9:31 AM, Daren Tan <daren76_at_hotmail.com> wrote:
>
> I have successfully installed ADaCGH package, and trying the example in SegmentPlotWrite did produce alot of pngs and html. I tried again the same example this morning (after a long night of installation), ADaCGH crashes at mpiInit() showing the error:
>
> Loading required package: Rmpi
> ELAN_EXCEPTION @ --: 6 (Initialisation error)
> elan_init: Can't get capability from environment
> Aborted
>
> I suspect the cluster adminstrator may have modified the mpi program or environment variables, but being new to mpi and am unsure what questions to pose to the adminstrator.
>
> ______________________________________________
> R-help_at_r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

-- 
Ramon Diaz-Uriarte
Statistical Computing Team
Structural Biology and Biocomputing Programme
Spanish National Cancer Centre (CNIO)
http://ligarto.org/rdiaz
Phone: +34-91-224-6900 ext. 3019

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Received on Thu 12 Jun 2008 - 11:47:44 GMT

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