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Date:
2016-06-02 21:07
Priority:
3
State:
Open
Submitted by:
D Greene (tonberry)
Assigned to:
Nobody (None)
Resolution:
None
Summary:
OpenMM import error: undefined symbol

Detailed description
Hi everyone,

I am trying to install OpenMM and am running into an issue when I try to test the installation afterwards. I did not conda install openMM; instead, I followed the instructions given here for Linux: http://docs.openmm.org/7.0.0/userguide/application.html

I followed the linux instructions where I downloaded the distro, unzipped, entered the folder, and then did: sudo install.sh from the command line (I followed the steps exactly as given, using the default locations for python, etc. as the installation instructions recommended, and I skipped all of the optional steps for the Cuda and whatnot). There were no errors given during the installation itself, but when I ran the test script afterwards I got this error:

$ python -m simtk.testInstallation
Failed to import OpenMM packages; OpenMM will not work.
Make sure OpenMM is installed and the library path is set correctly.

Error message: /usr/local/lib/python2.7/dist-packages/simtk/openmm/_openmm.so: undefined symbol: _ZN6OpenMM23CustomCentroidBondForce20addTabulatedFunctionERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEPNS_17TabulatedFunctionE

If you need any other info from me please just let me know.

Thanks in advance for your time.

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Comments:

Message  ↓
Date: 2016-08-17 20:21
Sender: sbgrid admin

I've seen the same - install.sh completes with status 0 and then the test fails (not using Anaconda python).

As an aside - it looks like pip by default will install (the different) "openmm" that is rev 0.2, but "OpenMM" is apparently not known to pip by default. And pip apparently cannot distinguish between "openmm" and "OpenMM" once *either* one of them is installed in a given python distribution. Or apparently pip cannot work with/list/install both "openmm" and "OpenMM". It seems there is a kind of "package name space pollution" going on that is incompatible with the standard install tools.

Date: 2016-06-02 22:46
Sender: D Greene

I don't think I have multiple copies of OpenMM installed as I had never attempted to install it before last night. I have installed other things like numpy and openeye to run on python 2.7 and those run fine (to verify I just did a check a few moments ago, and I was able to import and run openeye and numpy on an ipython notebook without any issues).

I should mention that I did try to install mdtraj, nglview, parmed, and openmoltools last night before trying to install the main OpenMM package (I actually only attempted to install the main OpenMM after I got an error while running the test script for openmoltools).

Here are the contents of my /usr/local/lib/python2.7/dist-packages folder if it helps:

Cython
Cython-0.24.dist-info
cython.py
cython.pyc
easy-install.pth
ipywidgets
ipywidgets-4.1.1.dist-info
jupyter-1.0.0.dist-info
jupyter_console
jupyter_console-4.1.1.dist-info
jupyter.py
jupyter.pyc
mdtraj
mdtraj-1.7.2-py2.7.egg-info
nglview
nglview-0.4+202.ge7ee8e5-py2.7.egg-info
numpy
numpy-1.11.0-py2.7.egg-info
openeye
OpenEye_toolkits_python2.7_ubuntu_14.04_x64-2016.2.1-py2.7.egg-info
OpenMM-7.0.1.egg-info
openmoltools-0.7.1.dev0-py2.7.egg
ParmEd-2.5.1-py2.7-linux-x86_64.egg
pyximport
qtconsole
qtconsole-4.2.1.dist-info
simtk
solvationtoolkit-0.2.4.dev0-py2.7.egg

Thanks for the help!

Date: 2016-06-02 21:12
Sender: Peter Eastman

Just a guess, but do you have multiple copies of OpenMM installed on your computer? That looks to me like the Python module is from one release, but it's trying to link to the C++ libraries from a different release. That could happen, for example, if your LD_LIBRARY_PATH points to an older version.

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