[R-sig-hpc] Problem about config Rmpi with LAM on 64 bits

[Hao Yu]

Hi Marce,

R and Lam on nfs should work. Your errors seem indicating that R cannot
find the path to lam lib. Can you make sure LAM is working: try
lamboot -v
lamnodes
lamexec C hostname

Any errors will indicate Lam is not configured right and Rmpi will not work.

If Lam is working but R still has the same errors, can you modify the R
script within R's bin dir to add something like (in the third line)
LD_LIBRARY_PATH=/usr/local/lam/lib

This is how I configure R and Lam to work on my cluster. I have LAM and
OpenMPI coexist but I separate them on different paths (not in PATH). I
installed two R's and modify R script with different LD_LIBRARY_PATH and
both R's work under different MPI.

Hao

Marce wrote:
> Hi all, now I'm trying to configure Rmpi in a 64 bit-cluster with LAM.
> I have installed R 2.6.2 and LAM 7.1.4. When I compiled LAM, I
> configured it with --enable-shared option, and all went ok. After
> that, I defined LD_LIBRARY_PATH with the libs of LAM that I want to
> use.
> The problem is when I want to install Rmpi (0.5.5 and 0.5.6 give me
> the same error), this one:
>
>> library(Rmpi)
> Error in dyn.load(file, ...) :
>   imposible cargar la biblioteca compartida
> '/home/aplicaciones/R/lib64/R/library/Rmpi/libs/Rmpi.so':
>   /home/aplicaciones/R/lib64/R/library/Rmpi/libs/Rmpi.so: undefined
> symbol: lam_mpi_double
> Error en library(Rmpi) : .First.lib failed for 'Rmpi'
> Error in dyn.unload(file.path(libpath, "libs", paste("Rmpi",
> .Platform$dynlib.ext,  :
>   la biblioteca dinámica/compartida
> '/home/aplicaciones/R/lib64/R/library/Rmpi/libs/Rmpi.so' no fué
> cargada
> .
>
> If you do an ldd of Rmpi.so:
>
> [marce at cluster ~]$ ldd
> /home/aplicaciones/R/lib64/R/library/Rmpi/libs/Rmpi.so
>         libmpi.so.0 => /home/aplicaciones/LAM/lib/libmpi.so.0
> (0x0000002a95663000)
>         liblam.so.0 => /home/aplicaciones/LAM/lib/liblam.so.0
> (0x0000002a9580c000)
>         libutil.so.1 => /lib64/libutil.so.1 (0x0000002a95978000)
>         libpthread.so.0 => /lib64/tls/libpthread.so.0 (0x0000002a95a7c000)
>         libc.so.6 => /lib64/tls/libc.so.6 (0x0000002a95b91000)
>         libdl.so.2 => /lib64/libdl.so.2 (0x0000002a95dc6000)
>         /lib64/ld-linux-x86-64.so.2 (0x000000552aaaa000)
>
> I have installed R and LAM-MPI in a shared file-system (with Lustre)
> by all nodes. Install LAM localy in all nodes is a better option?
> Somebody has configured a cluster with R, LAM and Rmpi? Now I am in a
> "bypass mode", I don't know the course to follow :s.
>
> Thanks for all
>
> PD:  The output of laminfo is:
>
> [marce at cluster ~]$ /home/aplicaciones/LAM/bin/laminfo
>          LAM/MPI: 7.1.4
>          Prefix: /home/aplicaciones/LAM/
>          Architecture: x86_64-unknown-linux-gnu
>          Configured by: root
>          Configured on: Wed Dec 10 11:45:49 CET 2008
>          Configure host: cluster
>          Memory manager: ptmalloc2
>          C bindings: yes
>          C++ bindings: yes
>          Fortran bindings: yes
>          C compiler: gcc
>          C++ compiler: g++
>          Fortran compiler: g77
>          Fortran symbols: double_underscore
>          C profiling: yes
>          C++ profiling: yes
>          Fortran profiling: yes
>          C++ exceptions: no
>          Thread support: yes
>          ROMIO support: yes
>          IMPI support: no
>          Debug support: no
>          Purify clean: no
>             SSI boot: globus (API v1.1, Module v0.6)
>             SSI boot: rsh (API v1.1, Module v1.1)
>             SSI boot: slurm (API v1.1, Module v1.0)
>             SSI coll: lam_basic (API v1.1, Module v7.1)
>             SSI coll: shmem (API v1.1, Module v1.0)
>             SSI coll: smp (API v1.1, Module v1.2)
>             SSI rpi: crtcp (API v1.1, Module v1.1)
>             SSI rpi: lamd (API v1.0, Module v7.1)
>             SSI rpi: sysv (API v1.0, Module v7.1)
>             SSI rpi: tcp (API v1.0, Module v7.1)
>             SSI rpi: usysv (API v1.0, Module v7.1)
>             SSI cr: self (API v1.0, Module v1.0)
>
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