Problem about config Rmpi with LAM on 64 bits
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$dynlib.ext, :
la biblioteca din?mica/compartida
'/home/aplicaciones/R/lib64/R/library/Rmpi/libs/Rmpi.so' no fu?
cargada
.
If you do an ldd of Rmpi.so:
[marce at cluster ~]$ 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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