SystemError when handling KeyboardInterrupt

[jaimergp]

Hello.

I am using a custom script to run MD simulations with OpenMM. This script has the following code in it:

try:
    simulation.step(steps)
except (Exception, KeyboardInterrupt) as ex:
    if isinstance(ex, KeyboardInterrupt):
        report = input('\nCtr+C detected. Save current state? (y/N): ')
        if report not in ('Y', 'y', 'yes', 'YES'):
            sys.exit('Ok, bye!')
    else:
        print('An error occurred. Attempting emergency report...')
    try:
        backup_simulation(simulation)
    except Exception:
        print('FAILED!')
    else:
        print('SUCCESS!')
    finally:
        raise ex

This was working with OpenMM 6.3, but it fails with OpenMM 7.0:

^CKeyboardInterrupt

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/XXX/.local/anaconda/envs/openmm/bin/ommprotocol", line 9, in <module>
    load_entry_point('ommprotocol', 'console_scripts', 'ommprotocol')()
  File "/home/XXX/dev/ommprotocol/ommprotocol/ommprotocol.py", line 357, in run_protocol
    loaded_input, positions=pos, velocities=vel, box_vectors=box, **options)
  File "/home/XXX/dev/ommprotocol/ommprotocol/ommprotocol.py", line 237, in stage
    simulation = app.Simulation(input_top.topology, system, _integrator, **platform_kwargs)
  File "/home/XXX/.local/anaconda/envs/openmm/lib/python3.5/site-packages/simtk/openmm/app/simulation.py", line 101, in __init__
    self.context = mm.Context(self.system, self.integrator)
SystemError: <built-in function delete_Context> returned a result with an error set

How can I handle Ctrl+C inputs in OpenMM 7.0?

[peastman]

What is ommprotocol? Is that something you've developed?

[jchodera]

Looks like the source is here: https://github.com/insilichem/ommprotocol

[peastman]

It looks to me like this may be related: https://bugs.python.org/issue23571. Python 3.5 changed how exceptions are handled. But still, this shouldn't be happening. If an OpenMM function is throwing an exception, the SWIG wrapper should catch it and translate it to a Python exception. It shouldn't let the C++ except propagate up to the Python level.

Are you using a precompiled OpenMM library, or did you build it yourself? If the latter, here are a couple of things I would try. First, make sure you're using the latest version of SWIG. If this behavior just recently changed in Python, it's possible older versions would cause problems. Second, try deleting the "wrappers" and "python" folders inside your build directory. Then run CMake to regenerate them and rebuild. It's possible something in those folders has just gotten out of sync or something.

[jaimergp]

Hi guys, thanks for the prompt answer.

Yes, @jchodera is right. That's the source code, but I am rewriting most of it in OO style (dev branch). Anyways, the error is the same in both versions. I have observed that the error does not always happen - it is more likely to happen when the simulation has been running for very little time (10-100 fs).

My environment is Arch Linux, Python 3.5, latest OpenMM from conda binaries, so no, I am not compiling it myself. I'll have a look at that patch you are referencing, @peastman, and also different Python versions.

I'll keep you informed. Thanks again!