[MMTK] Matrices not aligned

Lars Skjærven larsss at gmail.com
Mon Nov 3 14:37:24 UTC 2008


Apparently I had a numpy compilation problem although no error
messages was written, and the numpy test succeeded. Problem solved by
specifying the F95 compiler:
python setup.py config --fcompiler=gnu95  install

Lars

On Mon, Nov 3, 2008 at 10:30 AM, Konrad Hinsen <hinsen at cnrs-orleans.fr> wrote:
> 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.
> --
> ---------------------------------------------------------------------
> 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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