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/TemplateModels/chooseGeneticCode.def.
Path stack: {/home/software/src/HYPHY_Source/BatchFiles/,/home/software/src/HYPHY_Source/BatchFiles/,/home/software/src/HYPHY_Source/BatchFiles/,/home/software/src/HYPHY_Source/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

Dear Brock,

Try running


Code (]
mpirun -np 2 ../HYPHYMPI BASEPATH=absolute path to HyPhy install directory (no trailing slash) BranchSelector.bf
[/code):

HyPhy (by default) tries to find its distribution files in the working directory (i.e. the one you launch it from). You should be able to pipe input in and out using redirection just as you suggested: [code] $mpirun -np 16 ./HYPHYMPI ... < commandsin > output

To generate the stdin files just run the command interactively once, record the needed inputs and place one per line in the pipe-in file.

Cheers,
Sergei