Issue with python OpenMM import

[Christoph Klein]

Hello all,

I just installed the 4.0 and I am having an issue importing the package in python. I get the following error message:

import simtk.openmm
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/usr/local/lib/python2.7/site-packages/simtk/openmm/__init__.py", line 36, in <module>
from simtk.openmm.openmm import *
File "/usr/local/lib/python2.7/site-packages/simtk/openmm/openmm.py", line 37, in <module>
_openmm = swig_import_helper()
File "/usr/local/lib/python2.7/site-packages/simtk/openmm/openmm.py", line 33, in swig_import_helper
_mod = imp.load_module('_openmm', fp, pathname, description)
ImportError: /usr/local/lib/python2.7/site-packages/simtk/openmm/_openmm.so: undefined symbol: _ZN6OpenMM30AmoebaGeneralizedKirkwoodForce19setDielectricOffsetEd

Any idea on how to fix this? I installed all non-OpenCL and non-CUDA packages.

Thanks,

[Peter Eastman]

By any chance have you installed an OpenMM 4.1 beta on that machine? That error message looks like one that was present in the first beta (fixed in the second one). It definitely shouldn't be happening with 4.0.

Peter

[Christoph Klein]

Sorry for the delayed response. This was using 4.0. I have also tried installing the 4.1 beta but I get the same error.

[Peter Eastman]

What do you get if you type

nm -g /usr/local/lib/python2.7/site-packages/simtk/openmm/_openmm.so

That will list all the symbols defined in the library. Also check the creation date of that library. Is it really the version you think it is?

Peter

[Christoph Klein]

Ah ok that revealed the problem. The library apparently wasn't linked properly to my python 2.7 installation. All is well.

Thank you for the help!

[Peter Eastman]

Ok. Glad it turned out to be something simple!

Peter