[MMTK] MMTK -2.5.16 Examples test

Konrad Hinsen hinsen at cnrs-orleans.fr
Wed Feb 14 10:37:55 UTC 2007

On Feb 13, 2007, at 21:39, Mark Heslep wrote:

> I ran through all of the examples provided, had many problems and
> thought I would provide the results  here:

Please note that the examples are not test cases. Many rely on  
additional modules or data files that are not shipped with MMTK.

> python-numeric-24.2-1 FC6 binary package

Please try Numeric 23.8. I have had numerous reports of problems with  
Numeric 24, even though I could never reproduc any of them.

> numpy-1.0.1-2  binary package

Did you compile ScientificPython for Numeric (default) or for NumPy?

> Forcefield
>     ElectricField
>                 C/test.py       yes
>                 pyrex           no - no module named  
> Pyrex.Distutils on
> build

All the Pyrex examples need Pyrex installed.

>                 python          no - NameError Scientific_vector.pyx,
> line 117 in Scientific_vector.vector.__mul__

That's a bug in the example, which I just fixed.

>     HarmonicOscillator
>         C/test.py               yes
>         pyrex/                  no - see above
>         python/test.py          yes
>         python/mdtest.py        no - segfault

This seems to happen on several platforms. I didn't yet find the time  
to investigate the cause.

> LangevinDynamics
>     setup.py build              no - ../MMTK/trajectory.h error  
> netcdf.h
> No such file

This has to be treated like the main MMTK setup.py if netCDF is not  
in the default compiler search path on your system (which I consider  
a system configuration bug).

> Miscellaneous
>     ccpn_data_model.py          no - ImportError: No module named
> ccp.api.molecule.MolSystem

You need the CCPN data model Python API for this example.

>     charge_fit.py               yes
>     construct_from_pdb.py       no, pdb not found

Normal. If you want to run the example, please download the PDB files.

>     lattice.py                  yes. vdb viewer auto starts and  
> looks good
>     molecule_factory.py         yes
>     vector_field.py             no - hangs in loop

This example requires a VRML browser. However, it should not hang in  
a loop, even if there is no VRML browser installed/configured. Could  
you please press Ctrl-C when it hangs and tell me in which loop it  
gets stuck?

> MolecularDynamics
>     argon.py                    ? never finishes but generates nc file

"Never finishes" meaning what? Does it get stuck in a loop? This  
resembles the problems caused by Numeric 24.

> MonteCarlo
>     backbone.py                 no, hangs in loop

Same comment.

> NormalModes
>     brownian_modes.py           no, hangs

Same again.

>     calpha_modes.py             no, "Calculating 24 low freq modes"  
> and
> hangs in loop


>     constrained_modes.py        no, steps to 550 and hangs

And again.

>     harmonic_force_field.py     no, BondFF.py, line23 IndexError tuple
> index out of range

A recently introduced bug that I just fixed.

>     mode_analysis.py            no, ../MMTK/Utilility.py line255,
> IOError no file :'myhome/proteins/lysozyme/lysomeme.umodes' - i.e. its
> looking in the wrong place

The file is not shipped with MMTK at all; it would be bigger than the  
rest of the distribution. I added instructions on how to generate  
such a file to the script.

>     modes.py                    no, steps to 550 and hangs

This looks again like a Numeric 24 problem.

> Proteins/
>     analysis_calpha.py          no, Database entry PDB/4q21.pdb.gz  
> not found

Normal, it is not provided.

>     analysis.py                 no, same
>     construction.py             ?   quits w/ no output

It should have produced an output file "insulin_with_h.pdb".

>     rotamers.py                 no, Database entry
> 'PDB//<myhome/hao/proteins/PDB/1931.pdb not found', ie looking in the
> wrong path.

Again the file is not provided. The error message indicates the last  
of several places where MMTK looks for the file. Normally it would be  
placed in the same directory as the script.

> Trajectories/
>     calpha_trajectory.py        no, ../Scientific/IO/NetCDF.py, line
> 177; IOError netcdf: no such file

As the comment in the script says, you need to provide a trajectory  
file as input.

>     dcd_export.py               no, same

As the comment in the script says, you must run the example  
"snapshot.py" first. It creates the trajectory file being read.

>     dcd_import.py               no, Database entry PDB/rotation.pdb  
> not
> found

This input file is created by running dcd_export.py after  
snapshot.py. This is explained in a comment.

>     fluctuations.py             no, same as top

Again, the trajectory file is not provided.

>     traj average.py             no
>     trag extraction.py          no
>     view_trajectory.py          ? what format file does it want? Tried
> rotation.nc as an argument but have no animation viewer defined.

It wants a netCDF file. You do need an animation viewer; at the  
moment only VMD is supported. Having VMD installed and setting  
PDBVIEWER to "vmd" should be sufficient.

> Visualization
>     additional_objects.py       no VRML viewer installed (only vdb)
>     graphics_data.py            no, hangs
> ---------------------------------------------------------------------- 
> -----------------------------------------------
> No doubt some of these had some interdependence ( run A, then B)  
> but its
> not in the docs and I lack the time to dig through.

The interdependences are mostly in the docs. As I said, these are not  
meant to be test cases, but examples for understanding how MMTK can  
be used. There is no point in trying to run them without first  
reading them.

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

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