Rmpi installation trouble

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Rmpi installation trouble

Erin Hodgess-2
Dear R People:

I'm trying to install Rmpi (latest version) on Ubuntu.

However, I'm getting the following error:

erin@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

--
Erin Hodgess
Associate Professor
Department of Computer and Mathematical Sciences
University of Houston - Downtown
mailto: [hidden email]

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Re: 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@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,                  [hidden email]
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

______________________________________________
[hidden email] mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.