Python Run Script

The Python Run Script

We focus on the first lines first:

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#!/usr/bin/env python # -*- coding: utf-8 -*- import sys, os, glob, rc from optparse import OptionParser sys.dont_write_bytecode = True parser = OptionParser(usage='%prog [options] rc_file') parser.add_option('-s', '--start', dest='startTime') parser.add_option('-e', '--end', dest='endTime') # Should we generate emission? parser.add_option('--emis', dest='emission', action="store_true", default=False) # Should we compile the model? parser.add_option('--compile', dest='compile', action="store_true", default=False) # Are there rc keys in need of modification? parser.add_option('-m', '--modify', action="append", dest='rc_args') (options, args) = parser.parse_args() os.environ['pyshell.rc'] = os.path.realpath(args[0]) # Add the proper python paths rcf = rc.RcFile(os.environ['pyshell.rc']) base_py_dir = os.path.join(rcf.get('my.home'), rcf.get('my.tm5.base'), 'py') f2py_py_dir = os.path.join(rcf.get('my.home'), rcf.get('my.tm5.base'), 'f2py', 'lib') proj_py_dir = os.path.join(rcf.get('my.home'), rcf.get('my.proj.root'), 'tracer', rcf.get('my.tracer'), 'py') sys.path.append(base_py_dir) sys.path.append(f2py_py_dir) sys.path.append(proj_py_dir)

Handling the actions is done by python, a general purpose programming language. First, the import statements add functionality to python, like OptionParser. This functionality os then used to process the call. Notice that python is object-oriented, so the object parser is created, and operations can be performed upon it.
Important functionality comes from the module rc. In fact, I found out that the module rc has to be present in your PYTHONPATH. On my system, I can use ipython and type:

import rc
rc?

And I see:

Type:       module
String Form:<module 'rc' from '/home/sbasu/pythonpackages/lib/python2.7/site-packages/rc.pyc'>
File:       /home/sbasu/pythonpackages/lib/python2.7/site-packages/rc.py
Docstring:
Deal with model settings in `rc` format.

RCFILES

A rcfile is a text file with key/value pairs seperated by a ':', e.g.

  my.flag    :  T
  my.answer  :  42

After parsing the header, the python-script assigns our .rc file to the environment variable pyshell.rc. Thus, all options are set (and can be read) in the file rc/rc/nam1x1-dummy_tr.rc.

The next thing that is done, is that the search path is extended, such that extra functionality can be added. I guess that the order in which this is done is important. I expect that these values are thus set in the .rc file, so lets have a look:

! common folders for this tree
#include include/folders.rc

! common job characteristics
#include include/jobs.rc

! variables unique to this run
my.project  : test_project
my.runmode  : 1 ! 1 for RUN_FORWARD, 2 for RUN_BACKWARD
par.openmp  : True
......etc.....

No keys like my.home, my.tm5.base, my.proj.root. I appears that (for readability) these settings are in #include statements, as you see. Indeed, the needed keys are found in include/folders.rc.

Lets browse further down in the run_fwd.py:

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#!/usr/bin/env python # -*- coding: utf-8 -*- ... d1 = options.startTime.split(',') d2 = options.endTime.split(',') d1 = tuple([int(x) for x in d1]) d2 = tuple([int(x) for x in d2]) from RunTM5 import RunTM5 r = RunTM5(d1, d2)

This means that the supplied dates are turned into python variables and a RunTM5 object r is created with the start and end times as arguments. Further down in the script we see that such a RunTM5 object has so-called methods that can operate on it. That makes it very convenient, also to run it interactively using ipython.

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#!/usr/bin/env python # -*- coding: utf-8 -*- ... r = RunTM5(d1, d2) ... r.SetupEmissions(Emission) ... r.Compile() ... r.RunForward()

Time for Sourish to explain the following:

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#!/usr/bin/env python # -*- coding: utf-8 -*- if options.emission: emis_module = r.rcf.get('my.emission.class') _temp = __import__('Emissions', fromlist=[emis_module]) try: Emission = _temp.__dict__[emis_module] except KeyError: sys.stderr.write("Class %s not defined in %s\n"%(emis_module,'Emission')) sys.exit() except: sys.stderr.write("Unknown error importing %s\n"%emis_module) sys.exit() r.SetupEmissions(Emission)

[How the general use of Emission class is organized]

Now lest move on and look a the output generated by r.SetupEmissions(Emission)

[SetupEmissions]