Python 2.6 compatibility

[cbenzer]

We are running all our scientific Linux boxes under CentOS 6 which means the default Python installation is 2.6. I ran into the following compatibility issues:

Issue 1 : ordereddict not available in Python 2.6. This could be resolved by installing the backport of ordereddict into Python 2.6 using "pip install ordereddict". Pip (python-pip) is available in EPEL repository. After that I had to change the line "from collections import OrderedDict" to "from ordereddict import OrderedDict" in the file openmm.

Issue 2: argparse not available in Python 2.6. This could be resolved by installing argparse into Python 2.6 using "pip install argparse".

After resolving issues 1 and 2 I was able to run "open-mm -h". Subsequently I tried running a simple test using the input.pdb file from the OpenMM 5.2 example folder.

Issue 3: Several warnings on TypeErrror:

Traceback (most recent call last):
  File "/usr/lib64/python2.6/logging/__init__.py", line 776, in emit
    msg = self.format(record)
  File "/usr/lib64/python2.6/logging/__init__.py", line 654, in format
    return fmt.format(record)
  File "/usr/lib/python2.6/site-packages/openmm-0.1-py2.6.egg/ipcfg/openmmapplication.py", line 88, in format
    return super(LevelFormatter, self).format(record)
TypeError: super() argument 1 must be type, not classobj

This is probably related to this issue http://stackoverflow.com/questions/1713038/super-fails-with-error-typeerror-argument-1-must-be-type-not-classobj and is somehow masked by being default in Python 3.X but the need to be declared explicitly in version below 3.0

Issue 4: Not researched so far ... :-)

Traceback (most recent call last):
  File "/usr/bin/openmm", line 5, in <module>
    pkg_resources.run_script('openmm==0.1', 'openmm')
  File "/usr/lib/python2.6/site-packages/pkg_resources.py", line 461, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/usr/lib/python2.6/site-packages/pkg_resources.py", line 1194, in run_script
    execfile(script_filename, namespace, namespace)
  File "/usr/lib/python2.6/site-packages/openmm-0.1-py2.6.egg/EGG-INFO/scripts/openmm", line 1077, in <module>
    openmm.start()
  File "/usr/lib/python2.6/site-packages/openmm-0.1-py2.6.egg/EGG-INFO/scripts/openmm", line 926, in start
    force_reporters(simulation)
  File "/usr/lib/python2.6/site-packages/openmm-0.1-py2.6.egg/EGG-INFO/scripts/openmm", line 1071, in force_reporters
    reporter.report(simulation, state)
  File "/usr/lib/python2.6/site-packages/openmm-0.1-py2.6.egg/ipcfg/restartreporter.py", line 190, in report
    with bz2.BZ2File(tmp_fn, 'w') as f:
AttributeError: 'bz2.BZ2File' object has no attribute '__exit__'

I would be grateful if you could work on the Python 2.6 compatibility and make life a little bit easier for all the RHEL and CentOS users.

Thanks a lot!

[rmcgibbo]

The argparse backport will probably be required, but I can fix the other problems. Thanks for the heads up!

[cbenzer]

Great. Looking forward to give the tool a test run, especially the restarting options as I need to break my simulations into smaller chunks.

[rmcgibbo]

I merged fixes for the issues you identified. With my python2.6.8 installation, everything is humming smoothly. Let me know if you have any issues.

[cbenzer]

Installed the updated code and first test run succeeded out of the box.