Dear Luobin,
Quote:1) Is this BASEPATH an environment variable that HYPHY reads when it starts?
2) Is there anyway I can find out what kind of parameters that HYPHY takes when it starts? for example, can I type HYPHY --help or something else to get all the possible arguments?
3) Can I use the standard input redirect to make HYPHY run in real "batch"? for example, HYPHY batchfile < input_redirect, so all the options that HYPHY reads are from input_redirect?
1). By default HyPhy will assume that it's directory is the same one as returned by 'pwd'. BASEPATH command line argument overrides this behavior, but it is not an environment variable (just a command line argument)
2). No (but there should be). Here's a brief list:
Code:BASEPATH=absolute path (set base HyPhy directory where it looks to template files and such)
USEPATH=absolute path (tell HyPhy to write log files to this path, and also set it as a relative base for for subsequent batch file command line argument).
CPU=number (number of threads to spawn for an MP build)
-c (run in calulator mode)
-p (invoke a result post processing module)
-u (run web update, if curl has been linked in)
MPIOPTIMIZER (for MPI builds, tries to spread some of the optimization over multiple MPI nodes; works well if the function being optimized has N rate categories and there are N+1 available processors)
MPIPARTITIONS (for MPI builds, tries to spread optimization of likelihood functions on multiple partitions among MPI nodes. Needs at least N partitions if there are N nodes)
3). Input redirect should work fine, provided all the options are valid (otherwise HyPhy may go into an infinite prompt loop).
Cheers,
Sergei