[Bio-linux-dev] MrBayes and OpenMPI

[Tim Booth]

Hi Tony,

> I've created an OpenMPI version of bio-linux-mrbayes-multi:

Thanks - I'd been a bit naive regarding how OpenMPI and MPICH
interacted, or failed to interact.  It looks like my ApliconNoise
package is suffering from similar problems and I'll need to fix that
too.
I've rebuilt mb-multi as per your instructions, so I can now type:

mpirun.openmpi -np 4 mb-multi

I don't think we need the -dev dependency for OpenMPI so I've opted for.

"Depends: openmpi-bin"

I realise this may confuse anyone who is already happily using mpich and
mpd so I've held off releasing the package until I put a note on the
Bio-Linux list.

Cheers,

TIM

> Bye,
> 
>    Tony.
> 
> > aptitude download bio-linux-mrbayes-multi
> > dpkg-unpack bio-linux-mrbayes-multi_3.1.2-1_amd64.deb
> > cd bio-linux-mrbayes-multi_3.1.2-1_amd64/usr/local/bioinf/mrbayes/mrbayes-multi-3.1.2
> > make
> > cd ../../../DEBIAN
> > vim control # see patch below
> > cd ../..
> > mv -i bio-linux-mrbayes-multi_3.1.2-1_amd64 bio-linux-mrbayes-multi_3.1.2-2_amd64
> > dpkg-repack bio-linux-mrbayes-multi_3.1.2-2_amd64
> 
> You can download the deb at:
> 
> > http://bioinformatics.rri.sari.ac.uk/download/bio-linux-mrbayes-multi_3.1.2-2_amd64.deb
> 
> Patch to remove mpich2 dependency:
> 
> --- bio-linux-mrbayes-multi_3.1.2-1_amd64/DEBIAN/control	2010-03-23 
> 16:00:24.000000000 +0000
> +++ bio-linux-mrbayes-multi_3.1.2-2_amd64/DEBIAN/control	2011-06-09 
> 15:24:59.403563781 +0100
> @@ -1,11 +1,11 @@
>   Package: bio-linux-mrbayes-multi
> -Version: 3.1.2-1
> +Version: 3.1.2-2
>   Section: science
>   Priority: optional
> -Depends: bio-linux-base-directories (>= 1.0-1), mpich2, libopenmpi-dev
> +Depends: bio-linux-base-directories (>= 1.0-1), libopenmpi-dev
>   Architecture: amd64
>   Installed-Size: 7436
> -Maintainer: Oliver Buckley <helpdesk at nebc.nox.ac.uk>
> +Maintainer: Tony Travis <a.travis at abdn.ac.uk>
>   Provides: bio-linux-mrbayes-multi
> -Description: Multiprocessor version of MrBayes.
> +Description: OpenMPI version of MrBayes.
>    Bayesian inference of phylogeny is based upon a quantity called the 
> posterior probability distribution of trees, which is the probability of 
> a tree conditioned on the observations. This version has been compiled 
> to run on multiple processors.
> 
> Here are my easy-to-remember dpkg-unpack/dpkg-repack scripts:
> 
> #!/bin/sh
> # @(#)dpkg-unpack  2007-07-12  A.J.Travis
> 
> #
> # Unpack Debian package ready to rebuild
> #
> package=$1
> extract=`basename $package .deb`
> dpkg-deb -x ${package} ${extract}
> dpkg-deb -e ${package} ${extract}/DEBIAN
> 
> #!/bin/sh
> # @(#)dpkg-repack  2007-03-29  A.J.Travis
> 
> #
> # Re-pack unpacked Debian package
> #
> package=$1
> dpkg-deb -b ${package}
> 

-- 
Tim Booth <tbooth at ceh.ac.uk>
NERC Environmental Bioinformatics Centre 

Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford, England
OX10 8BB 

http://nebc.nerc.ac.uk
+44 1491 69 2705

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