[R] shared object for Rmpi

[Erin Hodgess]

Dear R yet again!

I finally got the Rmpi package to install!  Yay!.

However, when I go into R to use it, there is an error with the dyn.load
file.

This should be simple (allegedly).

Please help.
Thanks,
Sincerely,
Erin
mailto: hodgess at gator.uhd.edu




/home/faculty/hodgess/R-2.6.0/bin
[hodgess at gator bin]$ ./R CMD INSTALL Rmpi_0.5-4.tar.gz --configure-args=--with-mpi=/home/faculty/hodgess
* Installing to library '/home/faculty/hodgess/R-2.6.0/library'
* Installing *source* package 'Rmpi' ...
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
Try to find mpi.h ...
Found in /home/faculty/hodgess/include
Try to find libmpi or libmpich ...
Found libmpich in /home/faculty/hodgess/lib
Try to find liblam ...
Found liblam in /home/faculty/hodgess/lib
checking for main in -lpthread... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -std=gnu99 -I/home/faculty/hodgess/R-2.6.0/include -I/home/faculty/hodgess/R-2.6.0/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -I/home/faculty/hodgess/include -DMPI2 -fPIC -I/usr/local/include    -fpic  -g -O2 -c conversion.c -o conversion.o
gcc -std=gnu99 -I/home/faculty/hodgess/R-2.6.0/include -I/home/faculty/hodgess/R-2.6.0/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -I/home/faculty/hodgess/include -DMPI2 -fPIC -I/usr/local/include    -fpic  -g -O2 -c internal.c -o internal.o
gcc -std=gnu99 -I/home/faculty/hodgess/R-2.6.0/include -I/home/faculty/hodgess/R-2.6.0/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -I/home/faculty/hodgess/include -DMPI2 -fPIC -I/usr/local/include    -fpic  -g -O2 -c RegQuery.c -o RegQuery.o
gcc -std=gnu99 -I/home/faculty/hodgess/R-2.6.0/include -I/home/faculty/hodgess/R-2.6.0/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -I/home/faculty/hodgess/include -DMPI2 -fPIC -I/usr/local/include    -fpic  -g -O2 -c Rmpi.c -o Rmpi.o
gcc -std=gnu99 -shared -L/usr/local/lib -o Rmpi.so conversion.o internal.o RegQuery.o Rmpi.o -L/home/faculty/hodgess/lib -lmpich -llam -lpthread -fPIC   
** R
** demo
** inst
** preparing package for lazy loading
** help
 >>> Building/Updating help pages for package 'Rmpi'
     Formats: text html latex example 
  hosts                             text    html    latex
  internal                          text    html    latex
  mpi.abort                         text    html    latex
  mpi.apply                         text    html    latex   example
  mpi.barrier                       text    html    latex
  mpi.bcast                         text    html    latex
  mpi.bcast.Robj                    text    html    latex
  mpi.bcast.cmd                     text    html    latex
  mpi.cart.coords                   text    html    latex   example
  mpi.cart.create                   text    html    latex   example
  mpi.cart.get                      text    html    latex   example
  mpi.cart.rank                     text    html    latex   example
  mpi.cart.shift                    text    html    latex   example
  mpi.cartdim.get                   text    html    latex   example
  mpi.comm                          text    html    latex   example
  mpi.comm.disconnect               text    html    latex
  mpi.comm.free                     text    html    latex
  mpi.comm.inter                    text    html    latex
  mpi.comm.set.errhandler           text    html    latex
  mpi.comm.spawn                    text    html    latex
  mpi.const                         text    html    latex
  mpi.dims.create                   text    html    latex   example
  mpi.exit                          text    html    latex
  mpi.finalize                      text    html    latex
  mpi.gather                        text    html    latex   example
  mpi.gather.Robj                   text    html    latex   example
  mpi.get.count                     text    html    latex
  mpi.get.processor.name            text    html    latex
  mpi.get.sourcetag                 text    html    latex
  mpi.info                          text    html    latex
  mpi.init.sprng                    text    html    latex
  mpi.intercomm.merge               text    html    latex
  mpi.parSim                        text    html    latex
  mpi.parapply                      text    html    latex   example
  mpi.probe                         text    html    latex
  mpi.realloc                       text    html    latex
  mpi.reduce                        text    html    latex
  mpi.remote.exec                   text    html    latex   example
  mpi.scatter                       text    html    latex   example
  mpi.scatter.Robj                  text    html    latex   example
  mpi.send                          text    html    latex   example
  mpi.send.Robj                     text    html    latex
  mpi.sendrecv                      text    html    latex   example
  mpi.setup.rng                     text    html    latex
  mpi.spawn.Rslaves                 text    html    latex   example
  mpi.universe.size                 text    html    latex
  mpi.wait                          text    html    latex
** building package indices ...
* DONE (Rmpi)
[hodgess at gator bin]$ ./R

R version 2.6.0 (2007-10-03)
Copyright (C) 2007 The R Foundation for Statistical Computing
ISBN 3-900051-07-0

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

[Previously saved workspace restored]

> library(Rmpi)
Error in dyn.load(file, ...) : 
  unable to load shared library '/home/faculty/hodgess/R-2.6.0/library/Rmpi/libs/Rmpi.so':
  /home/faculty/hodgess/R-2.6.0/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$dynlib.ext,  : 
  dynamic/shared library '/home/faculty/hodgess/R-2.6.0/library/Rmpi/libs/Rmpi.so' was not loaded
> 
> 
> q()
Save workspace image? [y/n/c]: y
[hodgess at gator bin]$ pwd
/home/faculty/hodgess/R-2.6.0/bin