Packmol error

[jchodera]

@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]

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 [email protected]
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

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David Mobley
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[davidlmobley]

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]

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]

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