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gabrielelanaro / chemview

The new generation molecular viewer for IPython notebook
GNU Lesser General Public License v2.1
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Using chemview from Julia #35

Closed cortner closed 8 years ago

cortner commented 8 years ago

I work mostly from Julia and I'd love to use chemview for visualising within an IJulia notebook. I appreciate that you may not be interested in fixing anything related to this, but I am hoping you can give me some pointers.

I use Julia 0.5 and Anaconda. To import python packages I use PyCall. When I first tried, even numba import failed, but eventually I built llvmlite from source, pointing to the LLVM 3.7.1 library that comes included with Julia. I can now successfully @pyimport numba.

But when I try @pyimport chemview I get the following error message (in the Julia REPL; from the notebook I don't get anything useful at all): (sorry for the very long output)

signal (11): Segmentation fault: 11
while loading no file, in expression starting on line 426
_ZN4llvm17PMTopLevelManager16findAnalysisPassEPKv at /Users/ortner/anaconda/lib/python2.7/site-packages/llvmlite/binding/libllvmlite.dylib (unknown line)
_ZN4llvm17PMTopLevelManager12schedulePassEPNS_4PassE at /Users/ortner/anaconda/lib/python2.7/site-packages/llvmlite/binding/libllvmlite.dylib (unknown line)
_ZN4llvm18PassManagerBuilder25populateModulePassManagerERNS_6legacy15PassManagerBaseE at /Users/ortner/anaconda/lib/python2.7/site-packages/llvmlite/binding/libllvmlite.dylib (unknown line)
ffi_call_unix64 at /Users/ortner/anaconda/lib/python2.7/lib-dynload/_ctypes.so (unknown line)
ffi_call at /Users/ortner/anaconda/lib/python2.7/lib-dynload/_ctypes.so (unknown line)
_ctypes_callproc at /Users/ortner/anaconda/lib/python2.7/lib-dynload/_ctypes.so (unknown line)
PyCFuncPtr_call at /Users/ortner/anaconda/lib/python2.7/lib-dynload/_ctypes.so (unknown line)
PyObject_Call at /Users/ortner/anaconda/lib/libpython2.7.dylib (unknown line)
PyEval_EvalFrameEx at /Users/ortner/anaconda/lib/libpython2.7.dylib (unknown line)
PyEval_EvalCodeEx at /Users/ortner/anaconda/lib/libpython2.7.dylib (unknown line)
fast_function at /Users/ortner/anaconda/lib/libpython2.7.dylib (unknown line)
PyEval_EvalFrameEx at /Users/ortner/anaconda/lib/libpython2.7.dylib (unknown line)
PyEval_EvalCodeEx at /Users/ortner/anaconda/lib/libpython2.7.dylib (unknown line)
fast_function at /Users/ortner/anaconda/lib/libpython2.7.dylib (unknown line)
PyEval_EvalFrameEx at /Users/ortner/anaconda/lib/libpython2.7.dylib (unknown line)
PyEval_EvalCodeEx at /Users/ortner/anaconda/lib/libpython2.7.dylib (unknown line)
fast_function at /Users/ortner/anaconda/lib/libpython2.7.dylib (unknown line)
PyEval_EvalFrameEx at /Users/ortner/anaconda/lib/libpython2.7.dylib (unknown line)
PyEval_EvalCodeEx at /Users/ortner/anaconda/lib/libpython2.7.dylib (unknown line)
fast_function at /Users/ortner/anaconda/lib/libpython2.7.dylib (unknown line)
PyEval_EvalFrameEx at /Users/ortner/anaconda/lib/libpython2.7.dylib (unknown line)
PyEval_EvalCodeEx at /Users/ortner/anaconda/lib/libpython2.7.dylib (unknown line)
function_call at /Users/ortner/anaconda/lib/libpython2.7.dylib (unknown line)
PyObject_Call at /Users/ortner/anaconda/lib/libpython2.7.dylib (unknown line)
instancemethod_call at /Users/ortner/anaconda/lib/libpython2.7.dylib (unknown line)
PyObject_Call at /Users/ortner/anaconda/lib/libpython2.7.dylib (unknown line)
slot_tp_init at /Users/ortner/anaconda/lib/libpython2.7.dylib (unknown line)
type_call at /Users/ortner/anaconda/lib/libpython2.7.dylib (unknown line)
PyObject_Call at /Users/ortner/anaconda/lib/libpython2.7.dylib (unknown line)
PyEval_EvalFrameEx at /Users/ortner/anaconda/lib/libpython2.7.dylib (unknown line)
PyEval_EvalCodeEx at /Users/ortner/anaconda/lib/libpython2.7.dylib (unknown line)
fast_function at /Users/ortner/anaconda/lib/libpython2.7.dylib (unknown line)
PyEval_EvalFrameEx at /Users/ortner/anaconda/lib/libpython2.7.dylib (unknown line)
PyEval_EvalCodeEx at /Users/ortner/anaconda/lib/libpython2.7.dylib (unknown line)
function_call at /Users/ortner/anaconda/lib/libpython2.7.dylib (unknown line)
PyObject_Call at /Users/ortner/anaconda/lib/libpython2.7.dylib (unknown line)
instancemethod_call at /Users/ortner/anaconda/lib/libpython2.7.dylib (unknown line)
PyObject_Call at /Users/ortner/anaconda/lib/libpython2.7.dylib (unknown line)
slot_tp_init at /Users/ortner/anaconda/lib/libpython2.7.dylib (unknown line)
type_call at /Users/ortner/anaconda/lib/libpython2.7.dylib (unknown line)
PyObject_Call at /Users/ortner/anaconda/lib/libpython2.7.dylib (unknown line)
PyEval_EvalFrameEx at /Users/ortner/anaconda/lib/libpython2.7.dylib (unknown line)
PyEval_EvalCodeEx at /Users/ortner/anaconda/lib/libpython2.7.dylib (unknown line)
fast_function at /Users/ortner/anaconda/lib/libpython2.7.dylib (unknown line)
PyEval_EvalFrameEx at /Users/ortner/anaconda/lib/libpython2.7.dylib (unknown line)
PyEval_EvalCodeEx at /Users/ortner/anaconda/lib/libpython2.7.dylib (unknown line)
function_call at /Users/ortner/anaconda/lib/libpython2.7.dylib (unknown line)
PyObject_Call at /Users/ortner/anaconda/lib/libpython2.7.dylib (unknown line)
PyObject_CallFunctionObjArgs at /Users/ortner/anaconda/lib/libpython2.7.dylib (unknown line)
slot_tp_descr_get at /Users/ortner/anaconda/lib/libpython2.7.dylib (unknown line)
_PyObject_GenericGetAttrWithDict at /Users/ortner/anaconda/lib/libpython2.7.dylib (unknown line)
PyEval_EvalFrameEx at /Users/ortner/anaconda/lib/libpython2.7.dylib (unknown line)
PyEval_EvalCodeEx at /Users/ortner/anaconda/lib/libpython2.7.dylib (unknown line)
function_call at /Users/ortner/anaconda/lib/libpython2.7.dylib (unknown line)
PyObject_Call at /Users/ortner/anaconda/lib/libpython2.7.dylib (unknown line)
call_function_tail at /Users/ortner/anaconda/lib/libpython2.7.dylib (unknown line)
PyObject_CallFunction at /Users/ortner/anaconda/lib/libpython2.7.dylib (unknown line)
property_descr_get at /Users/ortner/anaconda/lib/libpython2.7.dylib (unknown line)
_PyObject_GenericGetAttrWithDict at /Users/ortner/anaconda/lib/libpython2.7.dylib (unknown line)
PyEval_EvalFrameEx at /Users/ortner/anaconda/lib/libpython2.7.dylib (unknown line)
PyEval_EvalCodeEx at /Users/ortner/anaconda/lib/libpython2.7.dylib (unknown line)
function_call at /Users/ortner/anaconda/lib/libpython2.7.dylib (unknown line)
PyObject_Call at /Users/ortner/anaconda/lib/libpython2.7.dylib (unknown line)
instancemethod_call at /Users/ortner/anaconda/lib/libpython2.7.dylib (unknown line)
PyObject_Call at /Users/ortner/anaconda/lib/libpython2.7.dylib (unknown line)
slot_tp_init at /Users/ortner/anaconda/lib/libpython2.7.dylib (unknown line)
type_call at /Users/ortner/anaconda/lib/libpython2.7.dylib (unknown line)
PyObject_Call at /Users/ortner/anaconda/lib/libpython2.7.dylib (unknown line)
PyEval_EvalFrameEx at /Users/ortner/anaconda/lib/libpython2.7.dylib (unknown line)
PyEval_EvalCodeEx at /Users/ortner/anaconda/lib/libpython2.7.dylib (unknown line)
fast_function at /Users/ortner/anaconda/lib/libpython2.7.dylib (unknown line)
PyEval_EvalFrameEx at /Users/ortner/anaconda/lib/libpython2.7.dylib (unknown line)
PyEval_EvalCodeEx at /Users/ortner/anaconda/lib/libpython2.7.dylib (unknown line)
PyEval_EvalCode at /Users/ortner/anaconda/lib/libpython2.7.dylib (unknown line)
PyImport_ExecCodeModuleEx at /Users/ortner/anaconda/lib/libpython2.7.dylib (unknown line)
load_source_module at /Users/ortner/anaconda/lib/libpython2.7.dylib (unknown line)
import_submodule at /Users/ortner/anaconda/lib/libpython2.7.dylib (unknown line)
load_next at /Users/ortner/anaconda/lib/libpython2.7.dylib (unknown line)
PyImport_ImportModuleLevel at /Users/ortner/anaconda/lib/libpython2.7.dylib (unknown line)
builtin___import__ at /Users/ortner/anaconda/lib/libpython2.7.dylib (unknown line)
PyObject_Call at /Users/ortner/anaconda/lib/libpython2.7.dylib (unknown line)
PyEval_CallObjectWithKeywords at /Users/ortner/anaconda/lib/libpython2.7.dylib (unknown line)
PyEval_EvalFrameEx at /Users/ortner/anaconda/lib/libpython2.7.dylib (unknown line)
PyEval_EvalCodeEx at /Users/ortner/anaconda/lib/libpython2.7.dylib (unknown line)
PyEval_EvalCode at /Users/ortner/anaconda/lib/libpython2.7.dylib (unknown line)
PyImport_ExecCodeModuleEx at /Users/ortner/anaconda/lib/libpython2.7.dylib (unknown line)
load_source_module at /Users/ortner/anaconda/lib/libpython2.7.dylib (unknown line)
import_submodule at /Users/ortner/anaconda/lib/libpython2.7.dylib (unknown line)
load_next at /Users/ortner/anaconda/lib/libpython2.7.dylib (unknown line)
PyImport_ImportModuleLevel at /Users/ortner/anaconda/lib/libpython2.7.dylib (unknown line)
builtin___import__ at /Users/ortner/anaconda/lib/libpython2.7.dylib (unknown line)
PyObject_Call at /Users/ortner/anaconda/lib/libpython2.7.dylib (unknown line)
PyEval_CallObjectWithKeywords at /Users/ortner/anaconda/lib/libpython2.7.dylib (unknown line)
PyEval_EvalFrameEx at /Users/ortner/anaconda/lib/libpython2.7.dylib (unknown line)
PyEval_EvalCodeEx at /Users/ortner/anaconda/lib/libpython2.7.dylib (unknown line)
PyEval_EvalCode at /Users/ortner/anaconda/lib/libpython2.7.dylib (unknown line)
PyImport_ExecCodeModuleEx at /Users/ortner/anaconda/lib/libpython2.7.dylib (unknown line)
load_source_module at /Users/ortner/anaconda/lib/libpython2.7.dylib (unknown line)
load_package at /Users/ortner/anaconda/lib/libpython2.7.dylib (unknown line)
import_submodule at /Users/ortner/anaconda/lib/libpython2.7.dylib (unknown line)
load_next at /Users/ortner/anaconda/lib/libpython2.7.dylib (unknown line)
PyImport_ImportModuleLevel at /Users/ortner/anaconda/lib/libpython2.7.dylib (unknown line)
builtin___import__ at /Users/ortner/anaconda/lib/libpython2.7.dylib (unknown line)
PyObject_Call at /Users/ortner/anaconda/lib/libpython2.7.dylib (unknown line)
call_function_tail at /Users/ortner/anaconda/lib/libpython2.7.dylib (unknown line)
PyObject_CallFunction at /Users/ortner/anaconda/lib/libpython2.7.dylib (unknown line)
PyImport_Import at /Users/ortner/anaconda/lib/libpython2.7.dylib (unknown line)
PyImport_ImportModule at /Users/ortner/anaconda/lib/libpython2.7.dylib (unknown line)
# lots more julia related lines
Allocations: 3500342 (Pool: 3497996; Big: 2346); GC: 5
Segmentation fault: 11
cortner commented 8 years ago

To follow up on this: my next step was to turn off numba. (should have thought of that earlier). Ok so far, I can now import chemview into Julia. The next problem I have is 

mv = chemview.MolecularViewer(coordinates, topology=Dict("atom_types" => atomic_types, "bonds" => bonds))

gives

LoadError: PyError (:PyObject_Call) <class 'traitlets.traitlets.TraitError'>
TraitError("The 'kernel' trait of a Comm instance must be a Kernel, but a value of type 'NoneType' (i.e. None) was specified.",)
  File "/Users/ortner/anaconda/lib/python2.7/site-packages/chemview-0.6-py2.7.egg/chemview/viewer.py", line 22, in __init__
    super(MolecularViewer, self).__init__(width, height)
  File "/Users/ortner/anaconda/lib/python2.7/site-packages/chemview-0.6-py2.7.egg/chemview/widget.py", line 71, in __init__
    super(RepresentationViewer, self).__init__()
  File "/Users/ortner/anaconda/lib/python2.7/site-packages/ipywidgets/widgets/widget.py", line 505, in __init__
    super(DOMWidget, self).__init__(*pargs, **kwargs)
  File "/Users/ortner/anaconda/lib/python2.7/site-packages/ipywidgets/widgets/widget.py", line 175, in __init__
    self.open()
  File "/Users/ortner/anaconda/lib/python2.7/site-packages/ipywidgets/widgets/widget.py", line 192, in open
    self.comm = Comm(**args)
  File "/Users/ortner/anaconda/lib/python2.7/site-packages/ipykernel/comm/comm.py", line 63, in __init__
    self.open(data=data, metadata=metadata, buffers=buffers)
  File "/Users/ortner/anaconda/lib/python2.7/site-packages/ipykernel/comm/comm.py", line 94, in open
    comm_manager = getattr(self.kernel, 'comm_manager', None)
  File "/Users/ortner/anaconda/lib/python2.7/site-packages/traitlets/traitlets.py", line 529, in __get__
    return self.get(obj, cls)
  File "/Users/ortner/anaconda/lib/python2.7/site-packages/traitlets/traitlets.py", line 508, in get
    value = self._validate(obj, dynamic_default())
  File "/Users/ortner/anaconda/lib/python2.7/site-packages/traitlets/traitlets.py", line 564, in _validate
    value = self.validate(obj, value)
  File "/Users/ortner/anaconda/lib/python2.7/site-packages/traitlets/traitlets.py", line 1589, in validate
    self.error(obj, value)
  File "/Users/ortner/anaconda/lib/python2.7/site-packages/traitlets/traitlets.py", line 1436, in error
    raise TraitError(e)

I'm afraid I am lost what this actually means?

gabrielelanaro commented 8 years ago

Hi! First of all, really nice job putting this together!

It looks like ipywidgets is having some problems communicating with the kernel. Does using ipywidgets works at all?

You could try an example of those... http://ipywidgets.readthedocs.io/en/latest/examples/Widget%20Basics.html

If you're using latest version of ipywidgets, you should try the branch new-widget of the chemview repository.

cortner commented 8 years ago

Yes - ipywidgets creates the same error message, or the following code to be precise:

using PyCall
@pyimport ipywidgets
ipywidgets.IntSlider()

I'll try to follow up on your suggestions. I really appreciate the help!

cortner commented 8 years ago

I found that Interact.jl uses ipywidgets, but looking through their code I don't see at all how. I'll keep trying but I fear this may be beyond my skill-set (and available time).

hainm commented 8 years ago

You need to figure out how to make ipywidgets work in Julia first.

cortner commented 8 years ago

I'm trying to talk to the Interact.jl people. It may turn out impossible.

cortner commented 8 years ago

The only example in Julia that I know uses ipywidgets is Interact.jl and according to its author "Interact.jl doesn't directly deal with ipywidgets, instead it only sends messages to jupyter according to its widgets protocol".

It looks like it would not be a straightforward modification for chemview to make it work in Julia, so I'll unfortunately have to drop this idea for now. Maybe I'll come back to this at a later time. Thank you for the help anyways.