Error in library(Rmpi)
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
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