[R-sig-hpc] Trouble using Rmpi after successful installation

[Paul Geeleher]

Okay I've actually managed to sort this error by creating a simlink to
libmpi.so.0 in another directory:

ln -s /usr/lib64/openmpi/1.3.2-gcc/lib/libmpi.so.0 /usr/lib64/R/lib/

Unfortunately this has led to another error:
> library(Rmpi)
[syd:25489] mca: base: components_open: component timer / linux open
function failed
[syd:25583] mca: base: components_open: component timer / linux open
function failed
librdmacm: couldn't read ABI version.
librdmacm: assuming: 4
libibverbs: Fatal: couldn't read uverbs ABI version.
CMA: unable to open /dev/infiniband/rdma_cm
--------------------------------------------------------------------------
WARNING: Failed to open "OpenIB-cma" [DAT_INTERNAL_ERROR:].
This may be a real error or it may be an invalid entry in the uDAPL
Registry which is contained in the dat.conf file. Contact your local
System Administrator to confirm the availability of the interfaces in
the dat.conf file.
--------------------------------------------------------------------------


I think this has something to do with the fact that I'm trying to
install Rmpi on the slave image, i.e. I do a "chroot
/cm/images/default-image" before running the installation. I do need
to install this on the slave image also right? As I said it installed
fine on the master node?

Thanks,

Paul


On Tue, Apr 27, 2010 at 12:40 PM, Sean Davis <sdavis2 at mail.nih.gov> wrote:
> On Tue, Apr 27, 2010 at 7:23 AM, Paul Geeleher <paulgeeleher at gmail.com> wrote:
>> Hi guys,
>>
>> I'm trying to install Rmpi on the slave nodes of my cluster. The
>> installation seems to work with no errors or warnings using this
>> command:
>>
>> R CMD INSTALL --configure-args="--with-Rmpi-include=/usr/lib64/openmpi/1.3.2-gcc/include
>> --with-Rmpi-libpath=/usr/lib64/openmpi/1.3.2-gcc/lib
>> --with-Rmpi-type=OPENMPI" Rmpi_0.5-8.tar.gz
>
> This has worked for me in the past:
>
> CC=mpicc R CMD INSTALL --clean Rmpi_.....
>
> However, I haven't tried it very recently.
>
> Sean
>
>
>
>> But when I attempt to load Rmpi I get the following error:
>>
>>> library(Rmpi)
>> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>>  unable to load shared library '/usr/lib64/R/library/Rmpi/libs/Rmpi.so':
>>  libmpi.so.0: cannot open shared object file: No such file or directory
>> Error in library(Rmpi) : .First.lib failed for 'Rmpi'
>> Error in dyn.unload(file.path(libpath, "libs", paste("Rmpi",
>> .Platform$dynlib.ext,  :
>>  dynamic/shared library '/usr/lib64/R/library/Rmpi/libs/Rmpi.so' was not loaded
>>
>> I wonder does anybody have an ideas as to what might be wrong here?
>>
>> It seemed to install just fine on my master node by the way.
>>
>> Thanks,
>>
>> Paul.
>>
>>
>> --
>> Paul Geeleher
>> School of Mathematics, Statistics and Applied Mathematics
>> National University of Ireland
>> Galway
>> Ireland
>> --
>> www.bioinformaticstutorials.com
>>
>> --
>> Paul Geeleher
>> School of Mathematics, Statistics and Applied Mathematics
>> National University of Ireland
>> Galway
>> Ireland
>> --
>> www.bioinformaticstutorials.com
>>
>> _______________________________________________
>> R-sig-hpc mailing list
>> R-sig-hpc at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/r-sig-hpc
>>
>



-- 
Paul Geeleher
School of Mathematics, Statistics and Applied Mathematics
National University of Ireland
Galway
Ireland
--
www.bioinformaticstutorials.com