Running Beast on Linux (Ubuntu)

[Gavin Thomas]

Hi,

I'm running Beast on Ubuntu 7.10 but it seems way too slow. On the
benchmarks page (http://beast.bio.ed.ac.uk/Benchmarks) the time listed
for Beast to complete the benchmark example is 17.42mins for Beast
1.4.6, Java 1.6.0_03-b05, Ubuntu 7.10, Intel Xeon "Clovertown" X5355
and 2.66GHz processor.

I am getting times of ~36min for the benchmark with an almost
identical set up (I am running Beast 1.4.8). I suspect the problem is
that I don't have java installed and set up appropriately because it
runs from the java core rather than native but I don't know how to
rectify it.

Any help would be gratefully received.

Thanks
Gavin

-----------------------------------------------------------
Gavin Thomas
NERC Centre for Population Biology
Imperial College London, Silwood Park Campus
Ascot, Berkshire, SL5 7PY, UK
http://www3.imperial.ac.uk/people/g.thomas

g.th...@imperial.ac.uk
020 75942357
-----------------------------------------------------------

[Andrew Rambaut]

Hi Gavin,

As you suggest it sounds like BEAST is not finding the native library
(the compiled C library that speeds up the calculations). You can
check this by looking at the output from BEAST and seeing if it says
"Using Java Nucleotide Likelihood Core" rather than "Native Nucleotide
Likelihood Core".

Java will look for the library in a path given by a command line when
it is run:

java -Djava.library.path=/usr/local/BEAST/lib /usr/local/BEAST/lib/
beast.jar

This would work if you had installed beast in /usr/local

If you look in the bin/ directory of the BEAST package, you will see
an executable shell script (called 'beast') that should set this up
for you automatically. Thus if you run:

/usr/local/BEAST/bin/beast

it should work fine. Or you could put a link to this in your /usr/
local/bin directory.

Hope this helps,
Andrew

___________________________________________________________________
Andrew Rambaut
Institute of Evolutionary Biology University of Edinburgh
Ashworth Laboratories Edinburgh EH9 3JT
EMAIL - a.ra...@ed.ac.uk TEL - +44 131 6508624





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