[MMTK] Runtime errors

Julien Michel J.MICHEL at soton.ac.uk
Tue Oct 7 19:55:05 CEST 2003


Hi ,

I recently downloaded MMTK and compiled the source for a linux PC, 
redhat9 by following the install instructions.

I have been running a number of examples to test the installation. A 
number of these examples fails, apparently for the same reasons (memory 
error) . It seems that for the script protein.py, I get an error similar 
to the one reported in an old message,  MMTK Windows problems (Achilleas 
Pitsillides, Jun 12), altough I am not working on windows.
 I list below the error message associated with each failing script.
Does somebody know if this is can be linked to an installation problem ?

Regards,

    Julien MICHEL

-->python2 protein.py
<...>
Step 1000
Time: 1.000000
Potential energy: -39.469451, Kinetic energy: 80.580309
Traceback (most recent call last):
  File "protein.py", line 51, in ?
    0, None, 2),
  File "/usr/lib/python2.2/site-packages/MMTK/Dynamics.py", line 189, in 
__call__
    apply(MMTK_dynamics.integrateVV, args)
MemoryError


---> python2 solvation.py
30 water molecules will be added
Solvent molecules have been added, now shrinking universe...
Traceback (most recent call last):
  File "solvation.py", line 60, in ?
    MMTK.Solvation.shrinkUniverse(universe, temperature, 'solvation.nc')
  File "/usr/lib/python2.2/site-packages/MMTK/Solvation.py", line 112, 
in shrinkUniverse
    snapshot()
  File "/usr/lib/python2.2/site-packages/MMTK/Trajectory.py", line 1261, 
in __call__
    snapshot(self.universe, data, actions, energy_terms)
MemoryError

--->python2 backbone.py
Traceback (most recent call last):
  File "backbone.py", line 48, in ?
    snapshot()
  File "/usr/lib/python2.2/site-packages/MMTK/Trajectory.py", line 1261, 
in __call__
    snapshot(self.universe, data, actions, energy_terms)
MemoryError

The simple water example from the manual
--->python2 testwater.py
Step 0
Time: 0.000000
Potential energy: 0.000209, Kinetic energy: 7.771315
Step 0
Time: 0.000000
Potential energy: 0.000209, Kinetic energy: 7.771315
Traceback (most recent call last):
  File "testwater.py", line 26, in ?
    0, None, 1)])
  File "/usr/lib/python2.2/site-packages/MMTK/Dynamics.py", line 189, in 
__call__
    apply(MMTK_dynamics.integrateVV, args)
MemoryError

The example solvent.py
--->python2 solvent.py
Current size:  4.00252042104
<...>
Current size:  0.842635878115
Traceback (most recent call last):
  File "solvent.py", line 85, in ?
    0, None, 10)])
  File "/usr/lib/python2.2/site-packages/MMTK/Dynamics.py", line 189, in 
__call__
    apply(MMTK_dynamics.integrateVV, args)
MemoryError









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