[MMTK] Loading minimizer crashes python

Michiel Jan Laurens de Hoon mdehoon at ims.u-tokyo.ac.jp
Tue Aug 12 01:42:21 EDT 2003

On Mac OS X, netlib installed by fink is not found by ScientificPython's 
setup.py file. This causes Python to crash due to a bus error when 
importing some MMTK modules. I ran into the same problem earlier today; 
the solution was to edit the setup.py file and add the location where to 
find netlib. I wouldn't be surprised if it has problems finding netlib 
on Windows machines also. So I would suggest to check ScientificPython's 
setup.py and make sure it can find the right location for netlib. If it 
does, you will notice that some C files get compiled when building 
ScientificPython, in addition to the Python files.

--Michiel, U Tokyo.

Konrad Hinsen wrote:
> On Monday 11 August 2003 15:58, Robin Maytum wrote:
>>So far, so good. However :
>>>>>from MMTK.Minimization import CojugateGradientMinimizer
>>Then crashes python.
>>Program Error
>>Pythonw.exe has generated errors and will be closed by Windows.
>>You need to restart the program.
>>Any ideas as to why loading the minimizer should crash python ?
> One thing to check is the netCDF interface and trajectory operations. Since 
> minimization can produce trajectories, all the netCDF stuff is loaded, which 
> might cause the crash. Just a guess of course, but otherwise there is nothing 
> special about the minimization module.
> Konrad.

Michiel de Hoon
Assistant Professor
University of Tokyo, Institute of Medical Science
Human Genome Center
4-6-1 Shirokane-dai, Minato-ku
Tokyo 108-8639

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