Problem installing Rmpi with OpenMP
Solved tanks to Hao Yu, Rmpi maintainer. The steps are: Download the Rmpi_0.5-8.tar.gz kit
R CMD INSTALL \ --configure-args="--with-Rmpi-include=/path_to_mpi_include \ --with-Rmpi-libpath=/path_to_mpi_lib \ --with-Rmpi-type=OPENMPI" Rmpi_0.5-8.tar.gz Once done compiling, try to see if Rmpi can find all mpi libs R CMD ldd path_to_Rmpi.so
Hope can be useful to someone. mario
Mario Valle wrote:
I'm trying to install Rmpi on our new cluster under 2.11.0 (linux)
After loading OpenMPI, inside R I execute:
install.packages("Rmpi",
configure.args=c("--with-mpi=/usr/mpi/gcc/openmpi-1.4.1",
"--with-mpi-type=OPENMPI"))
trying URL 'http://stat.ethz.ch/CRAN/src/contrib/Rmpi_0.5-8.tar.gz'
Content type 'application/x-gzip' length 87528 bytes (85 Kb)
opened URL
==================================================
downloaded 85 Kb
* installing *source* package ?Rmpi? ...
checking for gcc... gcc -std=gnu99
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 -std=gnu99 accepts -g... yes
checking for gcc -std=gnu99 option to accept ISO C89... none needed
Trying to find mpi.h ...
Found in /usr/mpi/gcc/openmpi-1.4.1/include
Trying to find libmpi.so or libmpich.a ...
checking for main in -lmpi... no
libmpi not found. exiting...
ERROR: configuration failed for package ?Rmpi?
* removing ?/gpfs/home/xt-home/mvalle/apps/R-2.11.0/library/Rmpi?
The downloaded packages are in
?/tmp/RtmpaLhj2t/downloaded_packages?
Updating HTML index of packages in '.Library'
Warning message:
In install.packages("Rmpi", configure.args =
c("--with-mpi=/usr/mpi/gcc/openmpi-1.4.1", :
installation of package 'Rmpi' had non-zero exit status
>
Our IT says that I should specify the use of the shared libraries and not the static ones, because openmpi 1.4.1 does not provide these. Can you help me to find the correct configure.vars string? Thanks a lot! mario
Ing. Mario Valle Data Analysis and Visualization Group | http://www.cscs.ch/~mvalle Swiss National Supercomputing Centre (CSCS) | Tel: +41 (91) 610.82.60 v. Cantonale Galleria 2, 6928 Manno, Switzerland | Fax: +41 (91) 610.82.82