[MMTK] problem with mpi velocityVerletIntegrator

wkbrowne at berkeley.edu wkbrowne at berkeley.edu
Sat Aug 5 01:20:48 CEST 2006


Hello,
I'm running a dual processor machine and am trying to get MMTK to perform
molecular dynamics with an otherwise functional version of mpirun from
MPICH and mpipython.  Execution goes perfectly with mpirun -np 1 mpipython
md.py. When I run code with mpirun -np 2 mpiython md.py, I get a traceback
from both processors (I've written this below). The crash happens at
integrator(steps=1000,
                    # Heat from 50 K to 300 K applying a temperature
                    # change of 0.5 K/fs; scale velocities at every step.
	   actions=[Heater(50.*Units.K, 300.*Units.K, 0.5*Units.K/Units.fs,
                           0, None, 1),
                    # Remove global translation every 50 steps.
		    TranslationRemover(0, None, 50),
                    # Remove global rotation every 50 steps.
		    RotationRemover(0, None, 50)] + output_actions)
Any ideas?
Thanks in advance,
Will

-- Processor 0 ----------------------------------------
Traceback (most recent call last):
  File "<console>", line 1, in ?
  File "/usr/lib64/python2.4/site-packages/MMTK/Dynamics.py", line 140, in
__call__
    mpi_communicator=comm)
  File "/usr/lib64/python2.4/site-packages/MMTK/Universe.py", line 618, in
energyEvaluator
    threads, mpi_communicator)
  File
"/usr/lib64/python2.4/site-packages/MMTK/ForceFields/ForceField.py",
line 181, in __init__
    self.global_data)
  File
"/usr/lib64/python2.4/site-packages/MMTK/ForceFields/MMForceField.py",
line 322, in evaluatorTerms
    global_data)
  File
"/usr/lib64/python2.4/site-packages/MMTK/ForceFields/ForceField.py",
line 88, in evaluatorTerms
    global_data)
  File
"/usr/lib64/python2.4/site-packages/MMTK/ForceFields/MMForceField.py",
line 85, in evaluatorTerms
    global_data)
  File
"/usr/lib64/python2.4/site-packages/MMTK/ForceFields/BondedInteractions.py",
line 53, in evaluatorTerms
    for angle in bu.bonds.bondAngles():
  File "/usr/lib64/python2.4/site-packages/MMTK/Bonds.py", line 242, in
bondAngles
    angles.append(BondAngle(p[0], p[1], atom))
  File "/usr/lib64/python2.4/site-packages/MMTK/Bonds.py", line 102, in
__init__
    if Utility.uniqueID(self.b2) < Utility.uniqueID(self.b1):
  File "/usr/lib64/python2.4/site-packages/MMTK/Utility.py", line 47, in
__call__
    return self.id[object]
KeyError: Bond(Atom bALA1.chain0.ACE1.CH3, Atom bALA1.chain0.ACE1.HH32)
-- Processor 1 ----------------------------------------
Traceback (most recent call last):
  File "<input>", line 1, in ?
  File "/usr/lib64/python2.4/site-packages/MMTK/Dynamics.py", line 140, in
__call__
    mpi_communicator=comm)
  File "/usr/lib64/python2.4/site-packages/MMTK/Universe.py", line 618, in
energyEvaluator
    threads, mpi_communicator)
  File
"/usr/lib64/python2.4/site-packages/MMTK/ForceFields/ForceField.py",
line 181, in __init__
    self.global_data)
  File
"/usr/lib64/python2.4/site-packages/MMTK/ForceFields/MMForceField.py",
line 322, in evaluatorTerms
    global_data)
  File
"/usr/lib64/python2.4/site-packages/MMTK/ForceFields/ForceField.py",
line 88, in evaluatorTerms
    global_data)
  File
"/usr/lib64/python2.4/site-packages/MMTK/ForceFields/MMForceField.py",
line 85, in evaluatorTerms
    global_data)
  File
"/usr/lib64/python2.4/site-packages/MMTK/ForceFields/BondedInteractions.py",
line 53, in evaluatorTerms
    for angle in bu.bonds.bondAngles():
  File "/usr/lib64/python2.4/site-packages/MMTK/Bonds.py", line 242, in
bondAngles
    angles.append(BondAngle(p[0], p[1], atom))
  File "/usr/lib64/python2.4/site-packages/MMTK/Bonds.py", line 102, in
__init__
    if Utility.uniqueID(self.b2) < Utility.uniqueID(self.b1):
  File "/usr/lib64/python2.4/site-packages/MMTK/Utility.py", line 47, in
__call__
    return self.id[object]
KeyError: Bond(Atom bALA1.chain0.ACE1.CH3, Atom bALA1.chain0.ACE1.HH32)





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