Update imports for python 3 compatibility #3

jchodera · 2017-04-15T22:48:31Z

I've updated enough imports to get baoab_vs_vvvr.py to run!

Fixes #2

…rmal ints by swig

…to find them

jchodera · 2017-04-16T02:55:52Z

Wow, that was a lot more work than I bargained for. I fixed a large number of relative imports for things that had been rearranged, and the remaining errors suggest there is still code that isn't working yet:

======================================================================
ERROR: Failure: ImportError (cannot import name 'get_equilibrium_samples')
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/choderaj/miniconda3/lib/python3.5/site-packages/nose/failure.py", line 39, in runTest
    raise self.exc_val.with_traceback(self.tb)
  File "/Users/choderaj/miniconda3/lib/python3.5/site-packages/nose/loader.py", line 418, in loadTestsFromName
    addr.filename, addr.module)
  File "/Users/choderaj/miniconda3/lib/python3.5/site-packages/nose/importer.py", line 47, in importFromPath
    return self.importFromDir(dir_path, fqname)
  File "/Users/choderaj/miniconda3/lib/python3.5/site-packages/nose/importer.py", line 94, in importFromDir
    mod = load_module(part_fqname, fh, filename, desc)
  File "/Users/choderaj/miniconda3/lib/python3.5/imp.py", line 234, in load_module
    return load_source(name, filename, file)
  File "/Users/choderaj/miniconda3/lib/python3.5/imp.py", line 172, in load_source
    module = _load(spec)
  File "<frozen importlib._bootstrap>", line 693, in _load
  File "<frozen importlib._bootstrap>", line 673, in _load_unlocked
  File "<frozen importlib._bootstrap_external>", line 665, in exec_module
  File "<frozen importlib._bootstrap>", line 222, in _call_with_frames_removed
  File "/Users/choderaj/github/choderalab/integrator-benchmark/integrator-benchmark/benchmark/experiments/waterbox_test.py", line 16, in <module>
    from benchmark.experiments.tools import get_equilibrium_samples, \
ImportError: cannot import name 'get_equilibrium_samples'

======================================================================
ERROR: Failure: FileNotFoundError ([Errno 2] No such file or directory: 'serialized_testsystems/alanine_constrained.xml')
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/choderaj/miniconda3/lib/python3.5/site-packages/nose/failure.py", line 39, in runTest
    raise self.exc_val.with_traceback(self.tb)
  File "/Users/choderaj/miniconda3/lib/python3.5/site-packages/nose/loader.py", line 418, in loadTestsFromName
    addr.filename, addr.module)
  File "/Users/choderaj/miniconda3/lib/python3.5/site-packages/nose/importer.py", line 47, in importFromPath
    return self.importFromDir(dir_path, fqname)
  File "/Users/choderaj/miniconda3/lib/python3.5/site-packages/nose/importer.py", line 94, in importFromDir
    mod = load_module(part_fqname, fh, filename, desc)
  File "/Users/choderaj/miniconda3/lib/python3.5/imp.py", line 234, in load_module
    return load_source(name, filename, file)
  File "/Users/choderaj/miniconda3/lib/python3.5/imp.py", line 172, in load_source
    module = _load(spec)
  File "<frozen importlib._bootstrap>", line 693, in _load
  File "<frozen importlib._bootstrap>", line 673, in _load_unlocked
  File "<frozen importlib._bootstrap_external>", line 665, in exec_module
  File "<frozen importlib._bootstrap>", line 222, in _call_with_frames_removed
  File "/Users/choderaj/github/choderalab/integrator-benchmark/integrator-benchmark/benchmark/serialization/serialize_testsystems.py", line 11, in <module>
    with open("serialized_testsystems/{}_{}.xml".format(name, c), "w") as f:
FileNotFoundError: [Errno 2] No such file or directory: 'serialized_testsystems/alanine_constrained.xml'

======================================================================
ERROR: Failure: Exception (Unknown global variable: shadow_work)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/choderaj/miniconda3/lib/python3.5/site-packages/nose/failure.py", line 39, in runTest
    raise self.exc_val.with_traceback(self.tb)
  File "/Users/choderaj/miniconda3/lib/python3.5/site-packages/nose/loader.py", line 418, in loadTestsFromName
    addr.filename, addr.module)
  File "/Users/choderaj/miniconda3/lib/python3.5/site-packages/nose/importer.py", line 47, in importFromPath
    return self.importFromDir(dir_path, fqname)
  File "/Users/choderaj/miniconda3/lib/python3.5/site-packages/nose/importer.py", line 94, in importFromDir
    mod = load_module(part_fqname, fh, filename, desc)
  File "/Users/choderaj/miniconda3/lib/python3.5/imp.py", line 234, in load_module
    return load_source(name, filename, file)
  File "/Users/choderaj/miniconda3/lib/python3.5/imp.py", line 172, in load_source
    module = _load(spec)
  File "<frozen importlib._bootstrap>", line 693, in _load
  File "<frozen importlib._bootstrap>", line 673, in _load_unlocked
  File "<frozen importlib._bootstrap_external>", line 665, in exec_module
  File "<frozen importlib._bootstrap>", line 222, in _call_with_frames_removed
  File "/Users/choderaj/github/choderalab/integrator-benchmark/integrator-benchmark/benchmark/tests/substep_test.py", line 13, in <module>
    simulation = simulation_factory(scheme)
  File "/Users/choderaj/github/choderalab/integrator-benchmark/integrator-benchmark/benchmark/tests/tests.py", line 89, in simulation_factory
    simulation = app.Simulation(topology, system, lsi, platform)
  File "/Users/choderaj/miniconda3/lib/python3.5/site-packages/simtk/openmm/app/simulation.py", line 103, in __init__
    self.context = mm.Context(self.system, self.integrator, platform)
  File "/Users/choderaj/miniconda3/lib/python3.5/site-packages/simtk/openmm/openmm.py", line 6269, in __init__
    this = _openmm.new_Context(*args)
Exception: Unknown global variable: shadow_work

======================================================================
ERROR: benchmark.testsystems.testsystems.get_src_implicit_test_system
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/choderaj/miniconda3/lib/python3.5/site-packages/nose/case.py", line 198, in runTest
    self.test(*self.arg)
TypeError: get_src_implicit_test_system() missing 1 required positional argument: 'temperature'

======================================================================
ERROR: benchmark.testsystems.testsystems.get_src_explicit_test_system
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/choderaj/miniconda3/lib/python3.5/site-packages/nose/case.py", line 198, in runTest
    self.test(*self.arg)
TypeError: get_src_explicit_test_system() missing 1 required positional argument: 'temperature'

[success] 95.15% benchmark.testsystems.testsystems.load_mts_test: 0.0179s
[error] 2.54% benchmark.testsystems.testsystems.get_src_explicit_test_system: 0.0005s
[error] 1.36% nose.failure.Failure.runTest: 0.0003s
[error] 0.94% benchmark.testsystems.testsystems.get_src_implicit_test_system: 0.0002s
----------------------------------------------------------------------
Ran 6 tests in 0.032s

FAILED (errors=5)

I'm going to stop here and hand this back to @maxentile to carry forward, since it looks like I've fixed enough to look into the original benchmark/experiments/baoab_vs_vvvr.py issue.

…byte reading/writing

…ng shadow work to avoid initial energy loss for some integrators.

…and velocities at the beginning of each integrator step.

jchodera · 2017-04-16T17:32:43Z

The last two commits fix the problem noted in #12 where it looked like energy was leaking out of integrator splittings that begin with V or R steps (but not O steps) for constrained systems.

I went a bit overboard and constrained positions and velocities at the beginning of each integrator step just for safety, but this may be unnecessary if we simply ensure to apply position and velocity constraints at the beginning of integration (step = 0). Note that I think we'll need to fix this in the openmmtools version too.

I've also temporarily disabled the solvated alanine dipeptide and modified the parameters for the vacuum alanine dipeptide data collection to ensure the samples were less correlated.

This should be ready to merge after #4 is merged, and then we should get the refactor branch merged into master ASAP.

maxentile · 2017-04-17T16:09:27Z

Wow, that was a lot more work than I bargained for.

Ahh, sorry about this! Thank you for all of these fixes and improvements.

I fixed a large number of relative imports for things that had been rearranged

Thanks! Just reviewed all changes,

and the remaining errors suggest there is still code that isn't working yet:

Sorry about this -- I believe I removed this file in the refactor branch

The last two commits fix the problem noted in #12 where it looked like energy was leaking out of integrator splittings that begin with V or R steps (but not O steps) for constrained systems.

Ahh, that would do it! Thanks for tracking down this error. I thought I had checked at the beginning of the study that setVelocitiesToTemperature already applies constraints, but I must have been mistaken...

I went a bit overboard and constrained positions and velocities at the beginning of each integrator step just for safety, but this may be unnecessary if we simply ensure to apply position and velocity constraints at the beginning of integration (step = 0). Note that I think we'll need to fix this in the openmmtools version too.

Thanks! Will think about how to address this efficiently. If this is only an issue on the very first step, then the most direct thing might be to patch the sample_v_from equilibrium function.

I've also temporarily disabled the solvated alanine dipeptide and modified the parameters for the vacuum alanine dipeptide data collection to ensure the samples were less correlated.

Thanks!

This should be ready to merge after #4 is merged, and then we should get the refactor branch merged into master ASAP.

Will do

Update imports for python 3 compatibility

2a90519

jchodera mentioned this pull request Apr 15, 2017

Debugging issues with experiments/baoab_vs_vvvr.py #2

Open

Fix more path issues

440bdfc

jchodera mentioned this pull request Apr 16, 2017

Add support for continuous integration via travis #5

Merged

jchodera added 5 commits April 15, 2017 21:39

Fix more imports

b68a3ec

Fix #6 by falling back to CPU if OpenCL unavailable

360f19c

Fix python3 bug with addBond() where numpy ints aren't accepted as no…

ac0c60c

…rmal ints by swig

tests must be moved into benchmark/ directory in order for nosetests …

de5b4b3

…to find them

Fix a lot more imports

9f597f7

jchodera added 3 commits April 15, 2017 23:41

Fix python 3.x issue with pickle; files need to be opened/closed for …

b6195f6

…byte reading/writing

Apply constraints to initial positions and velocities when accumulati…

a06e6c5

…ng shadow work to avoid initial energy loss for some integrators.

Temporarily disable solvated alanine dipeptide; constraint positions …

a11431b

…and velocities at the beginning of each integrator step.

jchodera mentioned this pull request Apr 16, 2017

Issues in measuring work with constrained systems #12

Closed

maxentile merged commit b0a6f4c into refactor Apr 17, 2017

maxentile deleted the python3 branch April 17, 2017 16:10

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Update imports for python 3 compatibility #3

Update imports for python 3 compatibility #3

jchodera commented Apr 15, 2017 •

edited

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jchodera commented Apr 16, 2017

jchodera commented Apr 16, 2017

maxentile commented Apr 17, 2017

Update imports for python 3 compatibility #3

Update imports for python 3 compatibility #3

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jchodera commented Apr 15, 2017 • edited Loading

jchodera commented Apr 16, 2017

jchodera commented Apr 16, 2017

maxentile commented Apr 17, 2017

jchodera commented Apr 15, 2017 •

edited

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