[R-sig-hpc] Error in library(Rmpi)

[Hao Yu]

Did you turn on dynamic lib when you were installing lam? The default was
static lib. Rmpi needs libmpi.so and liblam.so to work. Also use
             R CMD ldd path_to_Rmpi.so
to see if Rmpi finds all libs.

Hao

Arash Fard wrote:
> Hi,
> I successfully installed Rmpi_0.5-7 for R-2.9.1; the installation command
> was:
>
> ./R CMD INSTALL /root/src/Rmpi/Rmpi_0.5-7.tar.gz
> --configure-args=--with-mpi=/usr/lam
>
> However, when I call it inside R, I face this error:
>
>> library(Rmpi)
> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>   unable to load shared library
> '/usr/local/lib64/R/library/Rmpi/libs/Rmpi.so':
>   /usr/local/lib64/R/library/Rmpi/libs/Rmpi.so: undefined symbol:
> lam_mpi_double
> Error in library(Rmpi) : .First.lib failed for 'Rmpi'
> Error in dyn.unload(file.path(libpath, "libs", paste("Rmpi",
> .Platform$dynlib.ext,  :
>   dynamic/shared library '/usr/local/lib64/R/library/Rmpi/libs/Rmpi.so'
> was
> not loaded
>
> Please be informed that the environmental variables that I have set for
> LAM
> are:
> LD_LIBRARY_PATH=/usr/lib64/LAM/gnu:$LD_LIBRARY_PATH
> PATH=/usr/lam/bin/gnu:/usr/lam/bin:$PATH
> MANPATH=/usr/lam/share/man:$MANPATH
>
> The result for "lamboot -v" is:
> LAM 7.1.2/MPI 2 C++/ROMIO/bproc - Indiana University
>
> n-1<26696> ssi:boot:bproc: beomap now in use, ignoring boot schema file
> n-1<26696> ssi:boot:bproc: found master node (scyld.localdomain).
> Skipping
> checks.
> n-1<26696> ssi:boot:bproc:vector: launching on nodes -1
> n-1<26696> ssi:boot:base:linear_windowed: booting n0 (scyld.localdomain)
> n-1<26696> ssi:boot:bproc: starting lamd on (scyld.localdomain)
>
> The result for "lamnodes" is:
> n0      master:1:origin,this_node
>
> The result for "lamexec C hostname" is:
> furcatus.ecology.uga.edu
>
> I also added LD_LIBRARY_PATH to R script, but it was useless. I would
> appreciate it if you could help me.
>
> Thank you,
> Arash
>
> Odum School of Ecology
> The University of Georgia
>
> 	[[alternative HTML version deleted]]
>
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