From ripley at stats.ox.ac.uk  Wed Mar  3 20:24:22 2010
From: ripley at stats.ox.ac.uk (Prof Brian Ripley)
Date: Wed, 3 Mar 2010 19:24:22 +0000 (GMT)
Subject: [Rd] Rmpi on CentOS (64bit)
In-Reply-To: <20100303191529.GB633@slingshot.co.nz>
References: <20100303065320.GA633@slingshot.co.nz>
	<alpine.LFD.2.00.1003030732430.11176@gannet.stats.ox.ac.uk>
	<20100303191529.GB633@slingshot.co.nz>
Message-ID: <alpine.LFD.2.00.1003031921550.29730@gannet.stats.ox.ac.uk>

On Thu, 4 Mar 2010, Patrick Connolly wrote:

> 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.

No, it is high-speed interconnects, used in high-performance clusters.

> 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.

It does if you have that sort of hardware (and we do on one of the 
clusters we use).

>> 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?

Unlikely, unless you got the wrong libmpi.

>> 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?

Indeed, that is the recommended mechanism.

> 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
>
> ~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.
>

-- 
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



[Rd] Rmpi on CentOS (64bit)
Prof Brian Ripley