[R] Installing Rmpi on FC5 with lam

[Prof Brian Ripley]

Is /usr/lib/lam in your ld search path?  This sort of message usually 
means a shared library cannot be found.  You do need lam-libs as well 
according to yum.

R CMD ldd /usr/lib/R/library/Rmpi/libs/Rmpi.so
/sbin/ldconfig -p | grep /usr/lib/lam

might be illuminating.

There are various problems with the configure scripts in Rmpi for Fedora 
layouts that the maintainer is looking into: it fails completely on x86_64 
systems.  I don't understand how your line worked: that looks for -lmpi in
/usr/lib/lam/lib/libmpi.a and that is not where FC5 puts the libraries.


On Mon, 19 Feb 2007, Thomas Mangold wrote:

> After several trial and error attempts, I managed to install the Rmpi
> package without error on my Linux machine, running Fedora 5.
> I installed lam-7.1.2, lam-devel-7.1.2 and R-2.4.1, R-devel-2.4.1
> The Package Rmpi_5.0-3.tar.gz, I installed once from within R and once
> from the command line to make sure, I link the right libraries:
> R CMD INSTALL Rmpi_5.0-3.tar.gz --configure-args="--with-mpi=/usr/lib/lam"
>
> Rmpi is correctly installed in $R_HOME/library/Rmpi.
> However on compiling, I get strange warnings:
>
> internal.c: In function ?mystrcpy?:
> internal.c:64: warning: operation on ?i? may be undefined
> internal.c: In function ?mpitype?:
> internal.c:43: warning: ?datatype? may be used uninitialized in this
> function
> Rmpi.c: In function ?mpi_testany?:
> Rmpi.c:1315: warning: unused variable ?index?
> Rmpi.c: In function ?mpi_get_count?:
> Rmpi.c:768: warning: ?datatype? may be used uninitialized in this function
> Rmpi.c: In function ?mpi_allreduce?:
> Rmpi.c:672: warning: ?op? may be used uninitialized in this function
> Rmpi.c:673: warning: ?sexp_recv? may be used uninitialized in this function
> Rmpi.c: In function ?mpi_reduce?:
> Rmpi.c:586: warning: ?op? may be used uninitialized in this function
> Rmpi.c:587: warning: ?sexp_recv? may be used uninitialized in this function
> Rmpi.c: In function ?mpi_scatterv?:
> Rmpi.c:320: warning: ?displs? may be used uninitialized in this function
> Rmpi.c: In function ?mpi_gatherv?:
> Rmpi.c:225: warning: ?displs? may be used uninitialized in this function
>
> On loading the library occurs the following error:
> > library(Rmpi)
> Error in dyn.load(x, as.logical(local), as.logical(now)) :
> unable to load shared library '/usr/lib/R/library/Rmpi/libs/Rmpi.so':
> /usr/lib/R/library/Rmpi/libs/Rmpi.so: undefined symbol: lam_mpi_double
> Error in library(Rmpi) : .First.lib failed for 'Rmpi'
> Error in dyn.unload(x) : dynamic/shared library
> '/usr/lib/R/library/Rmpi/libs/Rmpi.so' was not loaded
>
> I'm running kernel 2.6.18-1.2257.fc5smp on a i686 machine
>
> Thank you for any ideas.
>
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>

-- 
Brian D. Ripley,                  ripley at 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