[R] Problem installing Rmpi with Open MPI

[Linh Tran]

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