Updating older BEAST .XML file for Beagle

[JP_Sullivan]

I would like to rerun a BEAST .XML file I assembled a while back in BEAUti 1.5.2. with a few parameters tweaked.  It runs fine in 1.6.1 in single processor mode, but I would like to take advantage of the multiprocessor acceleration available with Beagle on the XSEDE platform on CIPRES.  Is there any code I can add, or something, to make this existing file Beagle-compatible, or do I have to assemble a new .XML file from scratch in BEAUti 1.6.1?

I see that BEAUti 1.7.2 now has an "open" function, presumably so you can open and tweak an existing .XML file, however I get an error when I try to open .XML files created by earlier versions.  Is this to be expected?

[Andrew Rambaut]

On 25 May 2012, at 13:33, JP_Sullivan wrote:

I would like to rerun a BEAST .XML file I assembled a while back in BEAUti 1.5.2. with a few parameters tweaked.  It runs fine in 1.6.1 in single processor mode, but I would like to take advantage of the multiprocessor acceleration available with Beagle on the XSEDE platform on CIPRES.  Is there any code I can add, or something, to make this existing file Beagle-compatible, or do I have to assemble a new .XML file from scratch in BEAUti 1.6.1?

A BEAST 1.5 XML should run in BEAST 1.6 with BEAGLE. To break up the partitions into more threads use the -beagle_instances option.

I see that BEAUti 1.7.2 now has an "open" function, presumably so you can open and tweak an existing .XML file, however I get an error when I try to open .XML files created by earlier versions.  Is this to be expected?

The 'Open' function in BEAUti 1.7.2 will only open files saved by BEAUti 1.7 (they are a Java serialization). You can 'Import' XML files but it will only recover the data from the files not the model specification.

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  

[JP_Sullivan]

Some more details about my problem: My .XML file created in BEAUti 1.5.2 runs fine on CIPRES XSEDE in single processor mode, but creates this error when I try to use Beagle:

Failed to load parser: dr.app.beagle.evomodel.parsers.SVSGeneralSubstitutionModelParser

line = dr.app.beagle.evomodel.parsers.SVSGeneralSubstitutionModelParser

diff = 1.0E-10 freq = 1.0E-10

diff = 1.0E-10 freq = 1.0E-10

Parsing error - poorly formed BEAST file, infile.xml:

Error parsing '<treeLikelihood>' element with id, 'CP1+2.lacnewparpimdoids4BEAST.treeLikelihood':

BEAGLE_INSTANCES option cannot be used with BEAUti-selected codon partitioning.

I am using the SRD06 model and (I guess) BEAUti-selected codon partitioning.  Are there some easy changes I can make to the .XML file get it to run with Beagle?

Let me just say that I am hugely appreciative of the support available here from the software's authors!

[Andrew Rambaut]

Ah yes. Codon partitioning is not compatible with -beagle_instances. On the other hand, in BEAST 1.6 or later, the different codon partitions will be run in different threads (although if they have substantially different numbers of site patterns they may not balance very well).

Andrew

--
You received this message because you are subscribed to the Google Groups "beast-users" group.
To view this discussion on the web visit https://groups.google.com/d/msg/beast-users/-/m_af8pDwu0YJ.
To post to this group, send email to beast...@googlegroups.com.
To unsubscribe from this group, send email to beast-users...@googlegroups.com.
For more options, visit this group at http://groups.google.com/group/beast-users?hl=en.

[Derek]

Andrew,

Thank you for all your hard work on BEAST and BEAUti and for providing
support to this listserv.

If there were a place to submit feature request, I would love if
tBEAUti XML files were fully openable including loading the model.
This would allow users to efficiently tweak parameters and retry BEAST
runs with various parameters.

Sincerely,

Derek

>  EMAIL - a.ramb...@ed.ac.uk                TEL - +44 131 6508624
>
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.

[Andrew Rambaut]

Feature requests (and bug reports) can be directly entered into our issue database:

http://code.google.com/p/beast-mcmc/issues/list

Andrew

> --
> You received this message because you are subscribed to the Google Groups "beast-users" group.