[R] Help with Rmpi install

[Prof Brian Ripley]

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> If I knew more about R, I might know how to keep that Rmpi.so file
> around so that I could see if it is linked to a library that is
> missing from my LD_LIBRARY_PATH or something. How do you stop R from
> deleting the files that didn't load properly?

Try R CMD INSTALL --help (surely the standard way to find out about 
options!): you seem to be looking for --no-test-load or 
--no-clean-on-error .  But if you unpack the tarball before 
installation, the things built in the src directory are not deleted 
(unless you ask for them to be).

On Fri, 27 May 2011, Brian Mendenhall wrote:

> Hello R-help!
>
> I am a systems administrator for the University of Southern California. I take care of it's general-purpose research cluster, and have recently been asked to provide access to a parallelized R platform. I do not have any previous experience using R, and have only ever had to do anything more then 'yum -y install R'.
>
> We have a myrinet MPI network, and use mpich1 as our standard compiling environment which will link programs with libmyriexpress.so as well as libmpich.so
>
> Our myrinet driver package is Myrinet Express (MX) 1.2.12big. (I believe it was custom-built for us by myricom)
>
> The R package that my predecessor built was version 2.6.1. I have since installed 2.13.0 in an NFS exported shared software directory, and intend for the Rmpi package to be installed there as well.
>
> The compiler is gcc 4.3.3, the mpich version is 1.2.7..7
>
> The install command and its output are:
> [brianm at hpc-string R]$ /usr/usc/R/2.13.0/bin/R CMD INSTALL Rmpi_0.5-9.tar.gz --configure-args="--prefix=/usr/usc/R/2.13.0 --with-Rmpi-type=MPICH --with-Rmpi-include=/usr/usc/mpich/default/default/include --with-Rmpi-libpath=/usr/usc/mpich/default/default/lib64 --with-mpi=/usr/usc/mpich/default/default"
> * installing to library ‘/auto/usc/R/2.13.0/lib64/R/library’
> * installing *source* package ‘Rmpi’ ...
> checking for openpty in -lutil... no
> checking for main in -lpthread... no
> configure: creating ./config.status
> config.status: creating src/Makevars
> ** libs
> gcc -std=gnu99 -I/usr/usc/R/2.13.0/lib64/R/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -I/usr/usc/mpich/default/default/include   -DMPICH -I/usr/local/include    -fpic  -g -O2 -c RegQuery.c -o RegQuery.o
> gcc -std=gnu99 -I/usr/usc/R/2.13.0/lib64/R/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -I/usr/usc/mpich/default/default/include   -DMPICH -I/usr/local/include    -fpic  -g -O2 -c Rmpi.c -o Rmpi.o
> gcc -std=gnu99 -I/usr/usc/R/2.13.0/lib64/R/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -I/usr/usc/mpich/default/default/include   -DMPICH -I/usr/local/include    -fpic  -g -O2 -c conversion.c -o conversion.o
> gcc -std=gnu99 -I/usr/usc/R/2.13.0/lib64/R/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -I/usr/usc/mpich/default/default/include   -DMPICH -I/usr/local/include    -fpic  -g -O2 -c internal.c -o internal.o
> gcc -std=gnu99 -shared -L/usr/local/lib64 -o Rmpi.so RegQuery.o Rmpi.o conversion.o internal.o -L/usr/usc/mpich/default/default/lib64 -lmpich
> installing to /auto/usc/R/2.13.0/lib64/R/library/Rmpi/libs
> ** R
> ** demo
> ** inst
> ** preparing package for lazy loading
> ** help
> *** installing help indices
> ** building package indices ...
> ** testing if installed package can be loaded
> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>  unable to load shared object '/auto/usc/R/2.13.0/lib64/R/library/Rmpi/libs/Rmpi.so':
>  /auto/usc/R/2.13.0/lib64/R/library/Rmpi/libs/Rmpi.so: undefined symbol: MX_ERRORS_ARE_FATAL
> Error: loading failed
> In addition: Warning message:
> .Last.lib failed in detach() for 'Rmpi', details:
>  call: dyn.unload(file.path(libpath, "libs", paste("Rmpi", .Platform$dynlib.ext,
>  error: shared object '/auto/usc/R/2.13.0/lib64/R/library/Rmpi/libs/Rmpi.so' was not loaded
> Execution halted
> ERROR: loading failed
> * removing ‘/auto/usc/R/2.13.0/lib64/R/library/Rmpi’
>
> I've tried google, but didn't get very far. The only information I found was relative to mpich2... Is it that I need to move towards mpich2? All of the testing done by my predecessor indicated that mpich2 was much slower then mpich1, so we never put much time into installing it.
>
> If I knew more about R, I might know how to keep that Rmpi.so file 
> around so that I could see if it is linked to a library that is 
> missing from my LD_LIBRARY_PATH or something. How do you stop R from 
> deleting the files that didn't load properly?
>
> Any help would be greatly appreciated.
>
> Regards,
> -----
> Brian Mendenhall
> Linux/HPCC Administrator
> University of Southern California
>
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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