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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.

Add A Comment: Notepad

Comments:

Message  ↓
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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