Error in library(Rmpi)

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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Dear Hao,

I recognized that Rmoi.so points to MPICH libraries by mistake, as you may
see followed the result of "R CMD ldd path_to_Rmpi.so". It must be the
cause
of its wrong behavior at run time. May you please advise me how I can
dictate the right pathe to LAM libraries at the installation time.

Thank you,
Arash
Odum School of Ecology
The University of Georgia

[root at furcatus ~]# R CMD ldd /usr/local/lib64/R/library/Rmpi/libs/Rmpi.so
        PIC => not found
        libmpich-gnu.so.1 => /usr/lib64/MPICH/p4/gnu/libmpich-gnu.so.1
(0x0000002a95697000)
        libutil.so.1 => /lib64/libutil.so.1 (0x0000002a9586b000)
        libpthread.so.0 => /lib64/tls/libpthread.so.0 (0x0000002a9596e000)
        libc.so.6 => /lib64/tls/libc.so.6 (0x0000002a95a84000)
        libX11.so.6 => /usr/X11R6/lib64/libX11.so.6 (0x0000002a95cbd000)
        libbproc.so.2 => /usr/lib64/libbproc.so.2 (0x0000002a95eb6000)
        libbeomap.so.0.1 => /usr/lib64/libbeomap.so.0.1
(0x0000002a95fbd000)
        libbeostat.so.0 => /usr/lib64/libbeostat.so.0 (0x0000002a960c0000)
        libdl.so.2 => /lib64/libdl.so.2 (0x0000002a961c4000)
        /lib64/ld-linux-x86-64.so.2 (0x000000552aaaa000)


On Thu, Jul 16, 2009 at 9:53 AM, Hao Yu <hyu at stats.uwo.ca> wrote:

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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