[R] Rmpi installation trouble

[Prof Brian Ripley]

Note:

libmpi.dylib: cannot open shared object file: No such file or directory

Linux does not have .dylib's: Darwin (part of Mac OS X) does.

This is not an R question (it seems to be about your MPI installation) 
and you need to discuss it with the package maintainer (see the posting 
quide).

OpenMPI was found in /usr/local so it seems not to be a system 
installation.  So you'll need to give full details about that.

On 10/10/2012 05:46, Erin Hodgess wrote:
> Dear R People:
>
> I'm trying to install Rmpi (latest version) on Ubuntu.
>
> However, I'm getting the following error:
>
> erin at erin-Y480:~$ R
>
> R version 2.15.1 (2012-06-22) -- "Roasted Marshmallows"
> Copyright (C) 2012 The R Foundation for Statistical Computing
> ISBN 3-900051-07-0
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> 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.
>
>> install.packages("Rmpi",depen=TRUE)
> Installing package(s) into ‘/home/erin/R/x86_64-pc-linux-gnu-library/2.15’
> (as ‘lib’ is unspecified)
> --- Please select a CRAN mirror for use in this session ---
> Loading Tcl/Tk interface ... done
> trying URL 'http://cran.at.r-project.org/src/contrib/Rmpi_0.6-1.tar.gz'
> Content type 'application/x-gzip' length 92977 bytes (90 Kb)
> opened URL
> ==================================================
> downloaded 90 Kb
>
> * installing *source* package ‘Rmpi’ ...
> ** package ‘Rmpi’ successfully unpacked and MD5 sums checked
> checking for gcc... gcc -std=gnu99
> checking whether the C compiler works... yes
> checking for C compiler default output file name... a.out
> checking for suffix of executables...
> checking whether we are cross compiling... no
> checking for suffix of object files... o
> checking whether we are using the GNU C compiler... yes
> checking whether gcc -std=gnu99 accepts -g... yes
> checking for gcc -std=gnu99 option to accept ISO C89... none needed
> I am here /usr/local and it is OpenMPI
> Trying to find mpi.h ...
> Found in /usr/local/include
> Trying to find libmpi.so or libmpich.a ...
> Found libmpi in /usr/local/lib
> checking for openpty in -lutil... yes
> checking for main in -lpthread... yes
> configure: creating ./config.status
> config.status: creating src/Makevars
> ** libs
> gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPACKAGE_NAME=\"\"
> -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
> -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -I/usr/local/include
> -DMPI2 -DOPENMPI     -fpic  -O3 -pipe  -g  -c RegQuery.c -o RegQuery.o
> gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPACKAGE_NAME=\"\"
> -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
> -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -I/usr/local/include
> -DMPI2 -DOPENMPI     -fpic  -O3 -pipe  -g  -c Rmpi.c -o Rmpi.o
> gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPACKAGE_NAME=\"\"
> -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
> -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -I/usr/local/include
> -DMPI2 -DOPENMPI     -fpic  -O3 -pipe  -g  -c conversion.c -o
> conversion.o
> gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPACKAGE_NAME=\"\"
> -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
> -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -I/usr/local/include
> -DMPI2 -DOPENMPI     -fpic  -O3 -pipe  -g  -c internal.c -o internal.o
> gcc -std=gnu99 -shared -o Rmpi.so RegQuery.o Rmpi.o conversion.o
> internal.o -L/usr/local/lib -lmpi -lutil -lpthread -L/usr/lib/R/lib
> -lR
> installing to /home/erin/R/x86_64-pc-linux-gnu-library/2.15/Rmpi/libs
> ** R
> ** demo
> ** inst
> ** preparing package for lazy loading
> ** help
> ** help
> *** installing help indices
> ** building package indices
> ** testing if installed package can be loaded
> libmpi.dylib: cannot open shared object file: No such file or directory
> Error : .onLoad failed in loadNamespace() for 'Rmpi', details:
>    call: fun(libname, pkgname)
>    error: Cannot start MPI_Init(). Exit
> Error: loading failed
> Execution halted
> ERROR: loading failed
> * removing ‘/home/erin/R/x86_64-pc-linux-gnu-library/2.15/Rmpi’
>
> The downloaded source packages are in
> 	‘/tmp/RtmpWCdvrW/downloaded_packages’
> Warning message:
> In install.packages("Rmpi", depen = TRUE) :
>    installation of package ‘Rmpi’ had non-zero exit status
>>
>
> Any suggestions would be much appreciated.
>
> Sincerely,
> Erin
>


-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595