We built HYPHY 0.99 on a cluster of amd opterons (running 64 bit RHEL 4)  We used openmpi-1.0.2  and it built just fine. 

The user wants to use the BranchSelector.bf batch file. 
The program never promptes for the "How many batch classes?" 
Unless i give a key stroke at which point HYPHY dies with a error:

[brockp@nyx BatchFiles]$ mpirun -np 2 ../HYPHYMPI BranchSelector.bf


How many branch classes?Error:MPI Node:0
Could not read batch file:/home/software/src/HYPHY_Source/BatchFiles/TemplateBatchFiles/TemplateModel
s/chooseGeneticCode.def.
Path stack: {/home/software/src/HYPHY_Source/BatchFiles/,/home/software/src/HYPHY_Source/Bat
chFiles/,/home/software/src/HYPHY_Source/BatchFiles/,/home/software/src/HYPHY_So
urce/BatchFiles/TemplateBatchFiles/TemplateModels/}
Current BL Command:ExecuteCommands in string "#include \""+incFileName+"\";"


Also (this might need to be another thread)  How do users run HYPHY in batch?  We use PBS (Torque)  Can all the needed inputs be placed in a file and indrected?  mpirun -np 6 HYPHYMPI batchfile.bf < commands

Brock