SimTK: OpenMM: [#2302] OpenMM import error: undefined symbol

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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.
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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Date: 2018-02-12 18:22 Sender: Kent Wenger I installed miniconda (version is 4.4.9) (it installed into ~/miniconda2). Then I think I just ran ~/miniconda2/bin/conda install -c omnia openmm
Date: 2018-02-10 00:29 Sender: Peter Eastman Sounds like it didn't get installed correctly. Can you describe exactly what steps you followed? What python distribution did you start with (e.g. Anaconda 5.0.1 Python 3.6 for Linux), where is it installed (in your home directory I assume?), and what command did you type to install OpenMM?
Date: 2018-02-09 19:49 Sender: Kent Wenger With the conda install I got: Failed to import OpenMM packages; OpenMM will not work. Make sure OpenMM is installed and the library path is set correctly. Error message: libOpenMM.so: cannot open shared object file: No such file or directory (Note that I didn't do 'sudo conda install...' I just did it as a normal user, so it installed everything in my home directory. I'm not sure if it would have put things in /usr/local or something if I had sudo'ed it.) I didn't try setting LD_LIBRARY_PATH to the appropriate directory, which might have fixed things...
Date: 2018-02-09 19:46 Sender: Peter Eastman What failure did you get running the test script with the conda install?
Date: 2018-02-09 19:33 Sender: Kent Wenger I was installing OpenMM 7.1.1 on Ubuntu 16.04, and I ran into exactly the same problem (when I installed with install.sh). So after looking at the various comments here, I tried installing with conda. That also gave me a (different) failure when running the test script -- I'm not sure I did the conda installation correctly. However, the really interesting thing is this: when I did the conda installation, I got a different _openmm.so than when I did the install.sh installation. The install.sh one has (undefined) references to the CustomCentroidBondForce method, and the one from conda does not. (Even though version.py is the same, including the git_revision string.) I got things to work by installing with install.sh, and then manually copying the _openmm.so from the conda installation over the one from the install.sh installation...
Date: 2017-10-10 16:48 Sender: Peter Eastman Try installing with conda. That tends to have fewer problems.
Date: 2017-10-10 16:31 Sender: weitong ren I got the similar error: --------------------------------------- Failed to import OpenMM packages; OpenMM will not work. Make sure OpenMM is installed and the library path is set correctly. Error message: /share/home/wangj/software/anaconda2/lib/python2.7/site-packages/simtk/openmm/_openmm.so: undefined symbol: _ZTVNSt7__cxx1115basic_stringbufIcSt11char_traitsIcESaIcEEE ----------------------------------------- I installed the OpenMM-7.1.1 on a cluster followed the linux instructions. Does anyone have a solution?
Date: 2017-06-21 10:51 Sender: Mateusz Bieniek I compiled the code on Ubuntu 16.04 and now I can import openmm and run the examples.
Date: 2017-06-21 09:25 Sender: Mateusz Bieniek The same issue happened to me on Ubuntu 16.04. After installation I cannot import openmm: python -c 'from simtk import openmm' Traceback (most recent call last): File "<string>", line 1, in <module> File "/usr/local/lib/python2.7/dist-packages/simtk/openmm/__init__.py", line 19, in <module> from simtk.openmm.openmm import * File "/usr/local/lib/python2.7/dist-packages/simtk/openmm/openmm.py", line 28, in <module> _openmm = swig_import_helper() File "/usr/local/lib/python2.7/dist-packages/simtk/openmm/openmm.py", line 24, in swig_import_helper _mod = imp.load_module('_openmm', fp, pathname, description) ImportError: /usr/local/lib/python2.7/dist-packages/simtk/openmm/_openmm.so: undefined symbol: _ZN6OpenMM23CustomCentroidBondForce20addTabulatedFunctionERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEPNS_17TabulatedFunctionE The following variables were present: OPENMM_INCLUDE_PATH to /usr/local/openmm/include OPENMM_LIB_PATH to /usr/local/openmm/lib LD_LIBRARY_PATH to /usr/local/openmm/lib:... Thanks
Date: 2017-06-19 14:35 Sender: Mateusz Bieniek I am running into a similar issue using the linux installation. python -m simtk.testInstallation dresio@archy Failed to import OpenMM packages; OpenMM will not work. Make sure OpenMM is installed and the library path is set correctly. Error message: /usr/lib/python3.6/site-packages/simtk/openmm/_openmm.cpython-36m-x86_64-linux-gnu.so: undefined symbol: _ZN6OpenMM23CustomCentroidBondForce20addTabulatedFunctionERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEPNS_17TabulatedFunctionE Similarly: python -c 'from simtk import openmm' dresio@archy Traceback (most recent call last): File "<string>", line 1, in <module> File "/usr/lib/python3.6/site-packages/simtk/openmm/__init__.py", line 19, in <module> from simtk.openmm.openmm import * File "/usr/lib/python3.6/site-packages/simtk/openmm/openmm.py", line 28, in <module> _openmm = swig_import_helper() File "/usr/lib/python3.6/site-packages/simtk/openmm/openmm.py", line 24, in swig_import_helper _mod = imp.load_module('_openmm', fp, pathname, description) File "/usr/lib/python3.6/imp.py", line 242, in load_module return load_dynamic(name, filename, file) File "/usr/lib/python3.6/imp.py", line 342, in load_dynamic return _load(spec) ImportError: /usr/lib/python3.6/site-packages/simtk/openmm/_openmm.cpython-36m-x86_64-linux-gnu.so: undefined symbol: _ZN6OpenMM23CustomCentroidBondForce20addTabulatedFunctionERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEPNS_17TabulatedFunctionE Which looks rather similar to: https://github.com/omnia-md/openmm-dev/issues/15 I am using arch linux.
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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