From p_connolly at slingshot.co.nz  Wed Mar  3 20:15:29 2010
From: p_connolly at slingshot.co.nz (Patrick Connolly)
Date: Thu, 4 Mar 2010 08:15:29 +1300
Subject: [Rd] Rmpi on CentOS (64bit)
In-Reply-To: <alpine.LFD.2.00.1003030732430.11176@gannet.stats.ox.ac.uk>
References: <20100303065320.GA633@slingshot.co.nz>
	<alpine.LFD.2.00.1003030732430.11176@gannet.stats.ox.ac.uk>
Message-ID: <20100303191529.GB633@slingshot.co.nz>

On Wed, 03-Mar-2010 at 08:42AM +0000, Prof Brian Ripley wrote:

> 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'.

He knows less about it (MPI, at least) than I do.  Perhaps this is
'specialized hardware' in that it's a dual quad-core processor machine
-- but I'd have thought that's not particularly special nowadays.

I notice that my Fedora installation has no dat.conf file.  Perhaps
it pertains to something special on the CentOS machine.  I can't
check the CentOS machine right now, but at one time, I did find the
rpm that is associated with the dat.conf file.  Fedora seems not to
need that one.

>
> Incidentally, you should not have to set LD_LIBRARY_PATH, but I  

It might not be elegant, but at least it got over that problem.  Is
there any possibility that doing it so inelegantly has a bearing on
the issues I have now?

> 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  

Fedora 11 would appear to be like F12.  I'll check later if CentOS is
more like the way F10 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

Is that to say I could make a similar file to avoid setting
LD_LIBRARY_PATH?

Thanks for the help.



>
> 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

-- 
~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.   
   ___    Patrick Connolly   
 {~._.~}                   Great minds discuss ideas    
 _( Y )_  	         Average minds discuss events 
(:_~*~_:)                  Small minds discuss people  
 (_)-(_)  	                      ..... Eleanor Roosevelt
	  
~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.



[Rd] Rmpi on CentOS (64bit)
Patrick Connolly