[R] ADaCGH package crashes at mpiInit()

[Ramon Diaz-Uriarte]

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.
>
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>



-- 
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