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

[Blanchette, Marco]

Thanks Dirk for the suggestions. I am just starting to experiment with our large Linux computation cluster and I am not completely familiar with alternative strategies for installing libraries. (I have been running on a Mac workstation for the past 10 years...).

In addition I don't have sudo privileges and I wanted to test whether this would be a valuable solution before bugging our sys admin.

Hoa solution fixed all my problems. Here is the final strategy that gave me satisfactory results

./configure prefix=$HOME/lam-mpi --enable-shared
make -j 8
make -j 8 install
R CMD INSTALL Rmpi --configure-args=--with-mpi=$HOME/lam-mpi

Thanks all,

Marco

On 12/8/08 12:43 PM, "Dirk Eddelbuettel" <edd at debian.org> wrote:



Hi Marco,

On 8 December 2008 at 12:15, Blanchette, Marco wrote:
| 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.

Just checking -- are you aware that 'sudo apt-get install r-cran-rmpi' gives
a pre-built and working Rmpi (albeit based off Open MPI) ?

By the same token, do you know that 'sudo apt-get install lam4-dev' gets you
a working LAM implementation ... for which Rmpi should automatically find
headers and libraries.

| 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.

As Hoa indicated in the earlier reply, this error seems to stem from the fact
that your local libmpia.a is statically built wheresas R needs it as a
dynamic library.

But as suggested above, maybe you can use the prebuilt packages?

Cheers, Dirk

--
Three out of two people have difficulties with fractions.


--
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