I got Rmpi to compile with little difficulty, but had a tricky time setting the LD_LIBRARY_PATH to use the OpenMPI libs. I now get a different error when I try to load Rmpi> require(Rmpi)Loading required package: Rmpi 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 don't have this problem with Fedora 11 and I'd have thought there would be little difference with CentOS (apart from the latter being 64 bit). Is there something else that needs to be specified? TIA -- ~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~. ___ Patrick Connolly {~._.~} Great minds discuss ideas _( Y )_ Average minds discuss events (:_~*~_:) Small minds discuss people (_)-(_) ..... Eleanor Roosevelt ~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.
There are many different versions of OpenMPI about. It looks like you have one that is set up for specialized hardware. Either this is the wrong version or a configuration error, and you will need to talk to your 'local System Administrator'. Incidentally, you should not have to set LD_LIBRARY_PATH, but I frequently have had to add configuration files in /etc/ld.so.conf.d, including for openmpi on Fedora 12. On Fedora 10 (but not 12) MPI was under the /etc/alternatives mechanism, and had other problems. I currently have gannet% cat /etc/ld.so.conf.d/openmpi-x86_64.conf /usr/lib64/openmpi/lib on F12. On Wed, 3 Mar 2010, Patrick Connolly wrote:> I got Rmpi to compile with little difficulty, but had a tricky time > setting the LD_LIBRARY_PATH to use the OpenMPI libs. I now get a > different error when I try to load Rmpi > > >> require(Rmpi) > Loading required package: Rmpi > 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 don't have this problem with Fedora 11 and I'd have thought there > would be little difference with CentOS (apart from the latter being 64 > bit). > > Is there something else that needs to be specified? > > > TIA > > -- > ~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~. > ___ Patrick Connolly > {~._.~} Great minds discuss ideas > _( Y )_ Average minds discuss events > (:_~*~_:) Small minds discuss people > (_)-(_) ..... Eleanor Roosevelt > > ~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~. > > ______________________________________________ > R-devel at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel >-- 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
On Wed, 03-Mar-2010 at 07:53PM +1300, Patrick Connolly wrote:
|> I got Rmpi to compile with little difficulty, but had a tricky time
|> setting the LD_LIBRARY_PATH to use the OpenMPI libs. I now get a
|> different error when I try to load Rmpi
|>
|>
|> > require(Rmpi)
|> Loading required package: Rmpi
|> 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 looked further into this uDAPL thing and found an FAQ:
http://www.open-mpi.org/faq/?category=udapl
This one was particularly interesting:
3. Where is the static uDAPL Registry found?
Solaris: /etc/dat/dat.conf
Linux: /etc/dat.conf
On my CentOS installation, I have two, neither of which is where it's
supposed to be for "Linux" in the opinion of open-mpi.org.
$ locate dat.conf
/etc/ofed/dat.conf
/etc/ofed/compat-dapl/dat.conf
/usr/share/man/man5/dat.conf.5.gz
Would there be a way at the time of compiling Rmpi to specify a
configure arg to use one or other of the ones I have? Or would it be
simpler to make a link in /etc/ to one or other of them? Is there any
danger that such a link could bother anything else?
best
--
~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.
___ Patrick Connolly
{~._.~} Great minds discuss ideas
_( Y )_ Average minds discuss events
(:_~*~_:) Small minds discuss people
(_)-(_) ..... Eleanor Roosevelt
~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.