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, rip...@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
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