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choderalab / openmoltools

An open set of tools for automating tasks relating to small molecules
MIT License
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Packmol error #223

Open jchodera opened 8 years ago

jchodera commented 8 years ago

@davidlmobley, can you take a look at this failing test in packmol on master?

=====================================================================
ERROR: test_packmol.test_packmol_simulation_ternary_bydensity
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/travis/miniconda/envs/_test/lib/python2.7/site-packages/nose/case.py", line 197, in runTest
    self.test(*self.arg)
  File "/home/travis/miniconda/envs/_test/lib/python2.7/site-packages/openmoltools-0.7.1.dev0-py2.7.egg/openmoltools/tests/test_packmol.py", line 88, in test_packmol_simulation_ternary_bydensity
    simulation.step(25)
  File "/home/travis/miniconda/envs/_test/lib/python2.7/site-packages/simtk/openmm/app/simulation.py", line 132, in step
    self._simulate(endStep=self.currentStep+steps)
  File "/home/travis/miniconda/envs/_test/lib/python2.7/site-packages/simtk/openmm/app/simulation.py", line 198, in _simulate
    self.integrator.step(stepsToGo)
  File "/home/travis/miniconda/envs/_test/lib/python2.7/site-packages/simtk/openmm/openmm.py", line 4796, in step
    return _openmm.LangevinIntegrator_step(self, steps)
Exception: Particle coordinate is nan
davidlmobley commented 8 years ago

Yes, though it will take me til early this afternoon at least - I'm tied up this morning running job interviews.

On Fri, May 27, 2016 at 5:32 AM, John Chodera notifications@github.com wrote:

@davidlmobley https://github.com/davidlmobley, can you take a look at this failing test https://travis-ci.org/choderalab/openmoltools/jobs/133226140#L2781-L2795 in packmol on master?

ERROR: test_packmol.test_packmol_simulation_ternary_bydensity

Traceback (most recent call last): File "/home/travis/miniconda/envs/_test/lib/python2.7/site-packages/nose/case.py", line 197, in runTest self.test(*self.arg) File "/home/travis/miniconda/envs/_test/lib/python2.7/site-packages/openmoltools-0.7.1.dev0-py2.7.egg/openmoltools/tests/test_packmol.py", line 88, in test_packmol_simulation_ternary_bydensity simulation.step(25) File "/home/travis/miniconda/envs/_test/lib/python2.7/site-packages/simtk/openmm/app/simulation.py", line 132, in step self._simulate(endStep=self.currentStep+steps) File "/home/travis/miniconda/envs/_test/lib/python2.7/site-packages/simtk/openmm/app/simulation.py", line 198, in _simulate self.integrator.step(stepsToGo) File "/home/travis/miniconda/envs/_test/lib/python2.7/site-packages/simtk/openmm/openmm.py", line 4796, in step return _openmm.LangevinIntegrator_step(self, steps) Exception: Particle coordinate is nan

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/choderalab/openmoltools/issues/223, or mute the thread https://github.com/notifications/unsubscribe/AGzUYZRDG60u6WwRm0xKKV2vbf3Ym1cYks5qFuRFgaJpZM4IodMe .

David Mobley dmobley@gmail.com 949-385-2436

davidlmobley commented 8 years ago

So far, failing to replicate on my machine. Investigating whether it is an issue with openmm-dev, perhaps an API change there or something.

davidlmobley commented 8 years ago

I can't replicate so far, even using openmm-dev. However, it does not seem to be an issue with packmol in that nothing has changed on that front, and it is still working fine elsewhere, so I'm suspecting OpenMM issues.

@pgrinaway @andrrizzi @juliebehr , any ideas how to troubleshoot when I can't replicate a failure on my own machine? (And can you see if running these tests fails for you?)

davidlmobley commented 8 years ago

This is because of no minimization prior to simulation, it seems.