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

Dirk Eddelbuettel edd at debian.org
Tue Apr 27 14:31:55 CEST 2010

On 27 April 2010 at 13:16, Paul Geeleher wrote:
| 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?

I think you should go back a step and see if you can run a standard 'hello,
world' MPI example.  If and when you can, then try installing Rmpi.  

Some of us work reasonably hard to provide all this via a simple apt-get
without further ado, hassles or worries. You don't have to tear your hair out
over this, depending on the platform you choose.  

  Regards, Dirk

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