[R] Problem installing Rmpi with Open MPI

[Prof Brian Ripley]

As the posting guide asked, please discuss this with the maintainer.  He 
knows about this.

In short: Rmpi does not work if OpenMPI was compiled to dynamically load 
extensions, which is nowadays the default installation.  If your OpenMPI 
is >= 1.5 (and for some installs of 1.4.x) you will need to install it 
from the sources disabling dlopen.

On 29/08/2012 19:37, Linh Tran wrote:
> Hi guys,
>
> I've spent a few days trying to install Rmpi with no luck. I originally
> tried using mpich, moved on to mpich2, and then to openmpi. I've gotten
> the furthest with openmpi, though am still running into this problem and
> can't figure it out. Can someone help!? Thanks so much in advanced.
>
> I'm using an HP Envy laptop with Ubuntu 12.04. Output is below, with the
> error at the bottom.
>
>
> link at Ubuntu12-04:~/Downloads$ R CMD INSTALL Rmpi_0.6-1.tar.gz
> --configure-args="--with-mpi=/usr/local/ --with-Rmpi-type=OPENMPI"
>
> * installing to library ‘/home/link/R/x86_64-pc-linux-gnu-library/2.15’
> * installing *source* package ‘Rmpi’ ...
> ** package ‘Rmpi’ successfully unpacked and MD5 sums checked
> checking for gcc... gcc -std=gnu99
> checking whether the C compiler works... yes
> checking for C compiler default output file name... a.out
> checking for suffix of executables...
> checking whether we are cross compiling... no
> checking for suffix of object files... o
> checking whether we are using the GNU C compiler... yes
> checking whether gcc -std=gnu99 accepts -g... yes
> checking for gcc -std=gnu99 option to accept ISO C89... none needed
> Trying to find mpi.h ...
> Found in /usr/local//include
> Trying to find libmpi.so or libmpich.a ...
> Found libmpi in /usr/local//lib
> 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 -I/usr/share/R/include -DNDEBUG -DPACKAGE_NAME=\"\"
> -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
> -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -I/usr/local//include  -DMPI2
> -DOPENMPI     -fpic  -O3 -pipe  -g  -c RegQuery.c -o RegQuery.o
> gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPACKAGE_NAME=\"\"
> -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
> -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -I/usr/local//include  -DMPI2
> -DOPENMPI     -fpic  -O3 -pipe  -g  -c Rmpi.c -o Rmpi.o
> gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPACKAGE_NAME=\"\"
> -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
> -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -I/usr/local//include  -DMPI2
> -DOPENMPI     -fpic  -O3 -pipe  -g  -c conversion.c -o conversion.o
> gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPACKAGE_NAME=\"\"
> -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
> -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -I/usr/local//include  -DMPI2
> -DOPENMPI     -fpic  -O3 -pipe  -g  -c internal.c -o internal.o
> gcc -std=gnu99 -shared -o Rmpi.so RegQuery.o Rmpi.o conversion.o
> internal.o -L/usr/local//lib -lmpi -lutil -lpthread -L/usr/lib/R/lib -lR
> installing to /home/link/R/x86_64-pc-linux-gnu-library/2.15/Rmpi/libs
> ** R
> ** demo
> ** inst
> ** preparing package for lazy loading
> ** help
> *** installing help indices
> ** building package indices
> ** testing if installed package can be loaded
>
> [Ubuntu12-04:03523] mca: base: component_find: unable to open
> /usr/local/lib/openmpi/mca_paffinity_hwloc:
> /usr/local/lib/openmpi/mca_paffinity_hwloc.so: undefined symbol:
> opal_hwloc_topology (ignored)
> [Ubuntu12-04:03523] mca: base: component_find: unable to open
> /usr/local/lib/openmpi/mca_shmem_posix:
> /usr/local/lib/openmpi/mca_shmem_posix.so: undefined symbol:
> opal_shmem_base_output (ignored)
> [Ubuntu12-04:03523] mca: base: component_find: unable to open
> /usr/local/lib/openmpi/mca_ess_hnp: /usr/local/lib/openmpi/mca_ess_hnp.so:
> undefined symbol: orte_timing_output (ignored)
> [Ubuntu12-04:03523] mca: base: component_find: unable to open
> /usr/local/lib/openmpi/mca_ess_singleton:
> /usr/local/lib/openmpi/mca_ess_singleton.so: undefined symbol:
> orte_local_cpu_model (ignored)
> [Ubuntu12-04:03523] mca: base: component_find: unable to open
> /usr/local/lib/openmpi/mca_ess_slurm:
> /usr/local/lib/openmpi/mca_ess_slurm.so: undefined symbol:
> orte_orted_exit_with_barrier (ignored)
> [Ubuntu12-04:03523] mca: base: component_find: unable to open
> /usr/local/lib/openmpi/mca_ess_slurmd:
> /usr/local/lib/openmpi/mca_ess_slurmd.so: undefined symbol:
> orte_pmap_t_class (ignored)
> [Ubuntu12-04:03523] [[INVALID],INVALID] ORTE_ERROR_LOG: Unknown error: -1
> in file ../../../orte/runtime/orte_globals.c at line 176
> input in flex scanner failed
> ERROR: loading failed
> * removing ‘/home/link/R/x86_64-pc-linux-gnu-library/2.15/Rmpi’
>
>
> --
> Kind regards,
>
> Linh Tran, MPH
>
> ______________________________________________
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> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>


-- 
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