[R-sig-hpc] Problem compiling Rmpi on Linux

[Blanchette, Marco]

Dear list,

I am trying without success to install the Rmpi package on our large computing cluster but it keeps failing at compilation time. The machine is:
bash-3.2$ uname -a
Linux cluster04 2.6.18-53.el5 x86_64 x86_64 x86_64 GNU/Linux

I have downloaded and successfully installed LAM-MPI under $HOME.

If I try to install the Rmpi package by
$  R CMD INSTALL Rmpi --configure-args=--with-mpi=$HOME

I am getting the following error at compilation time (I also put the full transcript of the instalation at the end of this message).
/usr/bin/ld: /home/mab/lib/libmpi.a(recv.o): relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC
/home/mab/lib/libmpi.a: could not read symbols: Bad value

Any help to resolve that issue would be greatly appreciated.

Thanks

Marco


---Instalation transcript ---
mab cluster04 ~/src$ R CMD INSTALL Rmpi --configure-args=--with-mpi=$HOME
* Installing to library '/home/mab/RLibrary'
* 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
Try to find mpi.h ...
Found in /home/mab/include
Try to find libmpi.so or libmpich.a
checking for main in -lmpi... yes
Try to find liblam.so ...
checking for main in -llam... yes
checking for openpty in -lutil... yes
checking for main in -lpthread... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -std=gnu99 -shared -L/usr/local/lib64 -o Rmpi.so RegQuery.o Rmpi.o conversion.o internal.o -L/home/mab/lib -lmpi -llam -lutil -lpthread -fPIC   -L/n/site/inst/Linux-x86_64/bioinfo/R/2.8.0/lib64/R/lib -lR
/usr/bin/ld: /home/mab/lib/libmpi.a(recv.o): relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC
/home/mab/lib/libmpi.a: could not read symbols: Bad value
collect2: ld returned 1 exit status
make: *** [Rmpi.so] Error 1
chmod: cannot access `/home/mab/RLibrary/Rmpi/libs/*': No such file or directory
ERROR: compilation failed for package 'Rmpi'
** Removing '/home/mab/RLibrary/Rmpi'
--
Marco Blanchette, Ph.D.
Assistant Investigator
Stowers Institute for Medical Research
1000 East 50th St.

Kansas City, MO 64110

Tel: 816-926-4071
Cell: 816-726-8419
Fax: 816-926-2018