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http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl Methodology Questions >> How to >> GA branch analysis with hyphy batch files http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?num=1207640736 Message started by line on Apr 8^th, 2008 at 12:45am

Title: GA branch analysis with hyphy batch files
Post by line on Apr 8^th, 2008 at 12:45am

Dear all,
I am trying to do a Gabranch analysis with about 80 sequences. Therefore I tryed to analyse my samples downloading the Ga branch batch file using a computer with 4 hard discs and Hyphy gave me this message: Invalid Matrix (O) (0) in a -2 by 2matrix current BL command: sorted scores (0) (0)=-crapAIC.
I tryed also to make the analysis with example provided with Hyphy and the message was the same. I suppose that comes from a problem of computers and I would like to know how many processirs ae necessary to make this kind of analysis.
Thank tou in advance for your reply,
Best regards
Céline

Title: Re: GA branch analysis with hyphy batch files
Post by artpoon on Apr 8^th, 2008 at 11:12am

Hi Céline,

You need to have multiple processors in your machine in order to carry out an MPI analysis --- I'm not sure whether that's what you meant to say when you said that your computer had 4 hard discs (?). As specified on the website, you'll also need an MPI-enabled build of HyPhy. The error message that you note in your post implies that the populationSize variable is set to -2 in the batch file ModelSelectorBranchLocal.bf, which in turn implies that MPI_NODE_COUNT = 0, i.e., you're not running an MPI-enabled build.

Cheers,
- Art.

Title: Re: GA branch analysis with hyphy batch files
Post by line on Apr 9^th, 2008 at 10:29am

Hi Art,
Thank you for your reply. I have 4 processors on my computer...is it enough?
And about the "MPI enabled build of hyphy" how can I get it? excuse me for my ignorance... and thank you for trying to understand me for that!!!
Cheers,
Céline

Title: Re: GA branch analysis with hyphy batch files
Post by artpoon on Apr 9^th, 2008 at 10:39am

Hi Céline,

You'll need to download the HyPhy source code from here:
Multimedia File Viewing and Clickable Links are available for Registered Members only!! You need to

Login

and compile an MPI-enabled build using the command:
bash build.sh MPI

What sort of machine are you using, PC, Mac, *nix? It would be easier if you were using one of the last two.

Cheers,
- Art.

Title: Re: GA branch analysis with hyphy batch files
Post by artpoon on Apr 9^th, 2008 at 10:40am

By the way, I posted a direct link for your convenience, but please fill out our user questionnaire on the way to the downloads page if you haven't already ;D

Title: Re: GA branch analysis with hyphy batch files
Post by prm42 on Jul 29^th, 2010 at 10:34am

Hi, I have the same problem. I downloaded the source you posted. I have a Mac OSX but do not know how to compile an MPI-enable build...any help?
Thanks,
prm42

Title: Re: GA branch analysis with hyphy batch files
Post by Sergei on Jul 29^th, 2010 at 10:52am

Hi prm42,

If you edit the build.sh script to replace

Code (]
COMPILER="g++";
COMPILERC="gcc";
[/code):

with

[code]
COMPILER="mpicc++";
COMPILERC="mpicc";

this should compile on OS X (10.5 or 10.6) with Developer Tools installed.

Sergei