I successfully compiled an mpi version of hyphy and it appears to run but now I'm having some trouble getting the GABranch batch files to run properly. hyphy seems to prompt twice for some questions, or perhaps is printing the text strings and waiting for user response out of order.
I ran hyphy with this command:
openmpirun -np 8 /Users/mike/apps/hyphyjan2008/HYPHY_Source/HYPHYMPI BASEPATH=/Users/mike/apps/hyphyjan2008/HYPHY_Source /Users/mike/GABranchFiles/ModelSelectorBranchLocal.bf
and then hyphy printed the list of Genetic Codes, and waited for user input, but did not ask to enter a code:
Code:1
Please choose an option (or press q to cancel selection):
1
/Users/mike/GABranchFiles/Codon file to analyze::
/Users/mike/laeatest/laea.fasta
/Users/mike/GABranchFiles/Codon file to analyze::
/Users/mike/laeatest/laea.fasta
/Users/mike/apps/hyphyjan2008/HYPHY_Source/TemplateBatchFiles/Please select a tree file for the data::
This doesn't seem to be a valid Newick string file. Can't find the opening parenthesis.
Had:Error:MPI Node:0
Node names should begin with a letter, a number, or an underscore. Had:>?Bofuc20320 Bofuc20320
----------
Current BL Command:Build Tree givenTree from string treeString
The third prompt seems to want a tree file, even though it asks for the codon file a second time. Then it prints "Please select a tree file for the data" but does not wait for user input. It prints the error shown above and then quits.
The HYPHYMP version seems to work ok for me on the command line. At least I have used it for phylogeny reconstruction using the standard analyses.