[MMTK] Matrices not aligned

Konrad Hinsen hinsen at cnrs-orleans.fr
Mon Nov 3 09:30:53 UTC 2008

On Oct 31, 2008, at 19:04, Lars Skjærven wrote:

> - The python compilation complained one time: "Can't locate Tcl/Tk
> libs and/or headers". However, it continued, and finished
> successfully.

That just means you won't be able to run GUI programs using Tk,  
everything else should not suffer.

> - numpy compilation went fine, and I performed the numpy test (with
> nose). ended up with "OK (KNOWNFAIL=1, SKIP=1)".
> - scientific python: last line after "python setup.py install":
> "error: Invalid argument". However, all test finished successfully.
> - MMTK: only "basic_tests.py" succeeded. All other test fails with the
> fatal error mentioned above.

I guess the only way to figure out what goes wrong is to single-step  
through the initialization routine of MMTK_universe. Or modify the  
source code of MMTK_universe.c, inserting

	if (PyErr_Occurred()) printf("Error after line...");

after every statement in the initialization routine, recompile and  
run the tests.

> The benefits from using numpy instead of numeric is the increase of
> the allowed size of the force constant matrix, right? at the moment,

With Numeric, arrays are limited to what 32 bits can index, i.e. 4  
GB. That means about 7500 atoms for a normal mode calculation. With  
NumPy (and Python 2.5) you can use larger arrays, assuming of course  
that your machine has enough memory. Mine don't, so I didn't actually  
check that you can work with larger arrays.

Konrad Hinsen
Centre de Biophysique Moléculaire, CNRS Orléans
Synchrotron Soleil - Division Expériences
Saint Aubin - BP 48
91192 Gif sur Yvette Cedex, France
Tel. +33-1 69 35 97 15
E-Mail: hinsen at cnrs-orleans.fr
Web: http://dirac.cnrs-orleans.fr/~hinsen/

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