[R-sig-hpc] Problems Installing Rmpi on openSUSE 11.1 x86_64
Rowe, Brian Lee Yung (Portfolio Analytics)
B_Rowe at ml.com
Fri Jun 26 16:28:00 CEST 2009
A couple additional points:
1. mpicc is available in LAM/MPI as well, so you ought to try using that to compile Rmpi
2. Are you talking about spawning R slaves across multiple machines from within an interactive R session? This is quite possible in OpenMPI, as I do this regularly. When calling R directly, you are limited to spawning slaves on the same host as the master. If you use mpirun to start R (still interactive session), you can launch slaves on remote hosts as well. The main issue with OpenMPI is that the R processes utilize 100% of the processor that it was initialized on. For certain environments, this may not be acceptable.
From: r-sig-hpc-bounces at r-project.org [mailto:r-sig-hpc-bounces at r-project.org] On Behalf Of Melwin
Sent: Friday, June 26, 2009 3:13 AM
To: r-sig-hpc at r-project.org
Subject: Re: [R-sig-hpc] Problems Installing Rmpi on openSUSE 11.1 x86_64
Thanks for the reply.
2009/6/24 Rowe, Brian Lee Yung (Portfolio Analytics) <B_Rowe at ml.com>:
> Did you confirm that your MPI installation is working? That is the
> probably the first step.
LAM seems to work ok:
johnson at linuxmodel:~> lamboot -v
LAM 7.1.4/MPI 2 C++/ROMIO - Indiana University
n-1<4165> ssi:boot:base:linear: booting n0 (localhost)
n-1<4165> ssi:boot:base:linear: finished
johnson at linuxmodel:~> lamexec C hostname
> Regarding LD_LIBRARY_PATH, since I don't know what your configuration
> is, make sure you export it to your environment and also don't overwrite
> any existing values.
> i.e. This is better:
> $ export LD_LIBRARY_PATH=/usr/lib64:$LD_LIBRARY_PATH
> since it looks like you're on a 64 bit platform.
Tried that. Same results as before:
johnson at linuxmodel:~> R CMD INSTALL Rmpi_0.5-7.tar.gz
* Installing to 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
I am here /usr
Try to find mpi.h ...
Found in /usr/include
Try to find libmpi.so or libmpich.a
checking for main in -lmpi... no
libmpi not found. exiting...
ERROR: configuration failed for package 'Rmpi'
** Removing '/home/johnson/R/x86_64-unknown-linux-gnu-library/2.8/Rmpi'
> I use OpenMPI and it include an mpi-based compiler which I found to work
> better than gcc directly. You might try that. Just make sure you export
> your MPI_ROOT.
I would love to use OpenMPI, but I gather the slave spawning from within R
is not yet possible - which is what I need in interactive mode
love to hear that this has changed.
> It would also probably help to include a bit more output
> from the compilation process.
The dump above contains the entire output, I hope that helps.
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