SimTK: OpenMM: [#2544] Error with First Example

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Date:
2017-06-06 12:30

Priority:
3

State:
Open

Submitted by:
Simon Stockes (simonstockes)

Assigned to:
Nobody (None)

Resolution:
none

Summary:
Error with First Example

Detailed description
Hi All, I got the following error on my imac(oxs 10.11.6) Eros:examples stockes$ python simulatePdb.py Traceback (most recent call last): File "simulatePdb.py", line 12, in <module> simulation.minimizeEnergy() File "/Applications/anaconda/lib/python3.6/site-packages/simtk/openmm/app/simulation.py", line 128, in minimizeEnergy mm.LocalEnergyMinimizer.minimize(self.context, tolerance, maxIterations) File "/Applications/anaconda/lib/python3.6/site-packages/simtk/openmm/openmm.py", line 14850, in minimize return _openmm.LocalEnergyMinimizer_minimize(context, tolerance, maxIterations) Exception: Particle coordinate is nan ------------------------------------------- Eros:examples stockes$ conda info Current conda install: platform : osx-64 conda version : 4.3.21 conda is private : False conda-env version : 4.3.21 conda-build version : not installed python version : 3.6.0.final.0 requests version : 2.14.2 root environment : /Applications/anaconda (writable) default environment : /Applications/anaconda envs directories : /Applications/anaconda/envs /Users/frchalaoux/.conda/envs package cache : /Applications/anaconda/pkgs /Users/stockes/.conda/pkgs channel URLs : https://conda.anaconda.org/acellera/osx-64 https://conda.anaconda.org/acellera/noarch https://conda.anaconda.org/julia/osx-64 https://conda.anaconda.org/julia/noarch https://conda.anaconda.org/rdkit/osx-64 https://conda.anaconda.org/rdkit/noarch https://conda.anaconda.org/anaconda-fusion/osx-64 https://conda.anaconda.org/anaconda-fusion/noarch https://pypi.python.org/pypi/jsonschema/osx-64 https://pypi.python.org/pypi/jsonschema/noarch https://repo.continuum.io/pkgs/free/osx-64 https://repo.continuum.io/pkgs/free/noarch https://repo.continuum.io/pkgs/r/osx-64 https://repo.continuum.io/pkgs/r/noarch https://repo.continuum.io/pkgs/pro/osx-64 https://repo.continuum.io/pkgs/pro/noarch config file : /Users/stockes/.condarc netrc file : None offline mode : False user-agent : conda/4.3.21 requests/2.14.2 CPython/3.6.0 Darwin/15.6.0 OSX/10.11.6 UID:GID : 501:20 ------------------------------------------- Eros:examples stockes$ python -m simtk.testInstallation There are 3 Platforms available: 1 Reference - Successfully computed forces 2 CPU - Successfully computed forces 3 OpenCL - Successfully computed forces Median difference in forces between platforms: Reference vs. CPU: 1.98056e-05 Reference vs. OpenCL: nan CPU vs. OpenCL: nan -------------------------------------- Can you help me ? Cheers, Simon.
Hi All, I got the following error on my imac(oxs 10.11.6) Eros:examples stockes$ python simulatePdb.py Traceback (most recent call last): File "simulatePdb.py", line 12, in <module> simulation.minimizeEnergy() File "/Applications/anaconda/lib/python3.6/site-packages/simtk/openmm/app/simulation.py", line 128, in minimizeEnergy mm.LocalEnergyMinimizer.minimize(self.context, tolerance, maxIterations) File "/Applications/anaconda/lib/python3.6/site-packages/simtk/openmm/openmm.py", line 14850, in minimize return _openmm.LocalEnergyMinimizer_minimize(context, tolerance, maxIterations) Exception: Particle coordinate is nan ------------------------------------------- Eros:examples stockes$ conda info Current conda install: platform : osx-64 conda version : 4.3.21 conda is private : False conda-env version : 4.3.21 conda-build version : not installed python version : 3.6.0.final.0 requests version : 2.14.2 root environment : /Applications/anaconda (writable) default environment : /Applications/anaconda envs directories : /Applications/anaconda/envs /Users/frchalaoux/.conda/envs package cache : /Applications/anaconda/pkgs /Users/stockes/.conda/pkgs channel URLs : https://conda.anaconda.org/acellera/osx-64 https://conda.anaconda.org/acellera/noarch https://conda.anaconda.org/julia/osx-64 https://conda.anaconda.org/julia/noarch https://conda.anaconda.org/rdkit/osx-64 https://conda.anaconda.org/rdkit/noarch https://conda.anaconda.org/anaconda-fusion/osx-64 https://conda.anaconda.org/anaconda-fusion/noarch https://pypi.python.org/pypi/jsonschema/osx-64 https://pypi.python.org/pypi/jsonschema/noarch https://repo.continuum.io/pkgs/free/osx-64 https://repo.continuum.io/pkgs/free/noarch https://repo.continuum.io/pkgs/r/osx-64 https://repo.continuum.io/pkgs/r/noarch https://repo.continuum.io/pkgs/pro/osx-64 https://repo.continuum.io/pkgs/pro/noarch config file : /Users/stockes/.condarc netrc file : None offline mode : False user-agent : conda/4.3.21 requests/2.14.2 CPython/3.6.0 Darwin/15.6.0 OSX/10.11.6 UID:GID : 501:20 ------------------------------------------- Eros:examples stockes$ python -m simtk.testInstallation There are 3 Platforms available: 1 Reference - Successfully computed forces 2 CPU - Successfully computed forces 3 OpenCL - Successfully computed forces Median difference in forces between platforms: Reference vs. CPU: 1.98056e-05 Reference vs. OpenCL: nan CPU vs. OpenCL: nan -------------------------------------- Can you help me ? Cheers, Simon.

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Date: 2017-06-06 23:46 Sender: Peter Eastman It looks like the OpenCL platform isn't working correctly on your computer. What kind of GPU do you have? (Select "About This Mac" in the Apple menu.)

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