[R] R with MPI

[Martin Morgan]

Hi Polemon --

polemon wrote:
> On Mon, Aug 24, 2009 at 2:20 PM, polemon <polemon at gmail.com> wrote:
> 
>> Hello, I plan to use R with my cluster with OpenMPI.
>> I need the packaged 'snow' and 'Rmpi' for that, however, I get an error
>> while downloading and installing them:
>> When I do a:
>>     install.packages("Rmpi", dependencies=T)
>>
>> I get this error:
>>     checking for mpi.h... no
>>     Try to find libmpi.so or libmpich.a
>>     checking for main in -lmpi... no
>>     libmpi not found. exiting...
>>
>> However, mpi.h is present via the openmpi-devel package on my RHEL 5.3.

This is a configuration error, try install.pacakges("Rmpi",
dependencies=TRUE, configure.args="--with-mpi=/folder/with/mpiheaders").
More below

>> Some of those packages need sprng 2.0 (rsprng, for instance, which is a
>> dependency for another MPI-related package). Sprng 2.0, however, isn't in
>> developement for years, I wonder how I am supposed to keep my software up to
>> date...

rsprng is listed as 'Suggests' for both Rmpi and snow, so don't need to
be installed for successful Rmpi or snow installation.

Your message in the next post is that

> library(Rmpi)
Error in dyn.load(file, DLLpath = DLLpath, ...) :
  unable to load shared library '/opt/R/lib64/R/library/Rmpi/libs/Rmpi.so':
  libmpi.so.0: cannot open shared object file: No such file or directory
Error in library(Rmpi) : .First.lib failed for 'Rmpi'
Error in dyn.unload(file.path(libpath, "libs", paste("Rmpi",
.Platform$dynlib.ext,  :
  dynamic/shared library '/opt/R/lib64/R/library/Rmpi/libs/Rmpi.so' was not
loaded


This is a run-time error, and is because your mpi installation has not
registered the location of the shared object libraries (or has not been
compiled as a shared object?) correctly. See the system command
'ldconfig', or as a workaround launch R with something like

  LD_LIBRARY_PATH=/path/to/libmpifolder R

I'm guessing that path is /usr/lib64/openmpi/1.2.7-gcc/lib, but I didn't
look carefully enough at your solution to installing Rmpi to know for sure.

For more help, try the R-sig-HPC mailing list, for instance Hao Yu's
response to this

  https://stat.ethz.ch/pipermail/r-sig-hpc/2009-August/000329.html

thread.

Martin

>>
>> Any ideas on how to workaround that mpi.h problem?
>>
>> Please help,
>>
>> --polemon
>>
> 
> I did as described here:
> http://www.cybaea.net/Blogs/Data/R-tips-Installing-Rmpi-on-Fedora-Linux.html
> 
> Since Fedora and RHEL are pretty equal, I gave that installation a shot, and
> from what I can tell, I got pretty far.
> The package installed well, but when I try to load it with library(Rmpi):
> 
>> library(Rmpi)
> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>   unable to load shared library '/opt/R/lib64/R/library/Rmpi/libs/Rmpi.so':
>   libmpi.so.0: cannot open shared object file: No such file or directory
> Error in library(Rmpi) : .First.lib failed for 'Rmpi'
> Error in dyn.unload(file.path(libpath, "libs", paste("Rmpi",
> .Platform$dynlib.ext,  :
>   dynamic/shared library '/opt/R/lib64/R/library/Rmpi/libs/Rmpi.so' was not
> loaded
> 
> As you can see, R is installed in /opt/R, libmpi.so.0 is available:
> 
> /usr/lib/lam/lib/libmpi.so.0
> /usr/lib/lam/lib/libmpi.so.0.0.0
> /usr/lib/openmpi/1.2.7-gcc/lib/libmpi.so
> /usr/lib/openmpi/1.2.7-gcc/lib/libmpi.so.0
> /usr/lib/openmpi/1.2.7-gcc/lib/libmpi.so.0.0.0
> /usr/lib64/lam/lib/libmpi.so.0
> /usr/lib64/lam/lib/libmpi.so.0.0.0
> /usr/lib64/openmpi/1.2.7-gcc/lib/libmpi.so
> /usr/lib64/openmpi/1.2.7-gcc/lib/libmpi.so.0
> /usr/lib64/openmpi/1.2.7-gcc/lib/libmpi.so.0.0.0
> 
> What should I do, to make Rmpi available in R?
> 
> Cheers,
> 
> --polemon
> 
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> 
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