compucell3d / compucell3d

CompuCell3D public source code repository

CompuCell3D

CompuCell3D is a multiscale multicellular virtual tissue modeling and simulation environment. CompuCell3D is written in C++ and provides Python bindings for model and simulation development in Python. CompuCell3D is supported on Windows, Mac and Linux.

Installation

Binaries

Binary distributions of CompuCell3D are available for download at the CompuCell3D project page. Binaries of CompuCell3D are also available via conda,

conda install -c compucell3d -c conda-forge cc3d

Source

Instructions for building CompuCell3D from source are available at the CompuCell3D project page.

Getting Started

• Model development for CompuCell3D is best performed using the Twedit++ IDE.
• CompuCell3D simulations can be interactively executed with real-time rendering using CompuCell3D Player.
• Core CompuCell3D modeling and simulation features are documented in the CompuCell3D Reference Manual.
• CompuCell3D Python model and simulation development and walkthroughs are documented in the Python Scripting Manual for CompuCell3D.
• CompuCell3D is distributed with an extensive repository of demos.
• CompuCell3D Extensions offer integrated third-party modeling and simulation capabilities.

compucell3d's Issues

Twedit++: We should be able to edit and view '.cc3d' file from the project

We should be able to look at and edit the .cc3d files in twedit++ to check if resources are properly loaded.

Source: James email with subject- 'Some more minor twedit++ issues'

Problem in runing a model

Dear Mr. Maciekswat,
I want to run a model published in https://www.ncbi.nlm.nih.gov/pubmed/22461894
I got the following image after I run it:

Is there any configuration to change before running it?

Thanks,
Nada

How to compile CompuCell3D from CLI?

I am trying to compile cc3d on a virtual machine with no access to GUI, therefore I cannot run cmake-gui.

Could you shortly explain how to compile the project from CLI using plain old cmake?

Thank you,
Lukasz

error in cc3d

Hi,
I installed some python libraries, then cc3d didn't work properly!
This is the errors I receive

Note that( I have miniconda installed, when I change the default python to miniconda, cc3d doesn't work. How I can fix this?) I want to run my program and compucell3 simulation together?

How to resolve this?

Thanks

Add periodic BC button in CC3D Project Wizard

Unable to access Menu on Startup on Mac

Opening CompuCell3D on Mac disables the menu at top. It is visible but inaccessible.

WORKAROUND:
You can access menu once you switch between between windows and come back to CompuCell3D.

Twedit++: Incorrect annotation on simulation file

urrent version of twedit__ is annotating these files as Simulation version="3.6.2" rather than 3.7.6

<Simulation version="3.6.2">
   <XMLScript Type="XMLScript">Simulation/DemonstrationOfParameters.xml</XMLScript>
   <PythonScript Type="PythonScript">Simulation/DemonstrationOfParameters.py</PythonScript>
   <Resource Type="Python">Simulation/Demonstration3.py</Resource>
   <Resource Type="Python">Simulation/DemonstrationOfParametersSteppables.py</Resource>
   <Resource Type="Python">Simulation/Parameters1.py</Resource>
   <Resource Type="Python">Simulation/Parameters3.py</Resource>
</Simulation>

Source: James email with subject- 'Some more minor twedit++ issues'

CC3D hangs while running

Hi,
I have noticed that sometimes cc3d simulation hangs after running, there is no error . It may work if I rerun it again!. What is the cause of this?

Thanks

Build without VTK?

Hi,

I am trying to build CompuCell3D on a CentOS cluster at my university. I am running ccmake to emulate cmake-gui so that I can build the configuration files to be able to make and make install.

I do not need the visualizations to run, I just need to use my own modules (built in python) to be able to save all the data I need for post processing). Is there a way for me to build CompuCell3D without VTK as the cluster doesn't include VTK.

Zaf

(Note: I did look at #8 but it doesn't seem to be what I am looking for)

VTK files not being saved

Hi

I'm running CompuCell3D 3.75 Rev: 20170130 on Windows 7. Standard install to C:\CompuCell3D-64bit
Followed tutorial https://www.youtube.com/watch?v=cEE6IeaQRwU I am using the Angiogenesis.cc3d file and am trying to output 3D VTK to be rendered in Blender 3D.

However no output folder is being created or VTK files outputted.

Please let me know what steps to take to diagnose and remedy. I can't see anything abnormal in the command window. There appears to be no evidence in the command window of lattice files being written out.

Thanks

D

Develop tutorial for parameter optimization

Develop tutorial demonstrating how to use optimization of simulation parameters

Waves in model

Hi there,

I had a quick question, when running models with the Mitosis and Growth plugin enabled, we observe "wave"-like phenomenon which resembles a bubble bursting somewhere and then propagating through the whole lattice. This especially happens if two cell types have slightly differing growth rates.

This even occurs in clusterMitsosis.cc3d

• sudden increase in # of cells at ≈6500MCS due to contraction
  

I was curious as to why this happens and if here is a tweak to fix it?

Add actions that restore default settings

DLL load failed error

Hi,
I installed compucell3d -3.7.5 on windows 64 bit. When I run the player via cmd, I get this error:
"c://compucell3d/player/compucell3d.pyw line 9
import sip
DLL failed: The specified module couldn't be found"

It seems something is missing?

Thanks

PIFDumper steppable ignores Frequency that is inserted by Twedit

Twedit generates:

<Steppable Frequency="100" Type="PIFDumper">
    <!-- Periodically stores cell layout configuration in a piff format -->
    <PIFName>NewSimulation</PIFName>
    <PIFFileExtension>piff</PIFFileExtension>
</Steppable>

but in PIFDumper.cpp the Frequency is ignored.

Twedit++ does not launch from the player and vice versa on OSX

Issues when launching process from either twedit or player

Parameter estimation in CC3D

Hi,
I have a CC3D model with more than 10 parameters, and I want to write some code to estimate few sensitive parameters values based on experimental data. However, I still don't have much experience in CC3D development. Thus I need some advice. I have the following questions in mind:

-How is it easy to interrupt and reestablish the simulation with adapted parameters values?
-How to integrate additional code into CC3D?.
-I've read that parameters in CC3D are dependent!. Is that mean I shall change all parameters at once?

I don't know if this is the right place to ask these questions!. If not I do apologize.

Regards,
Nada

error in cc3d (sip module missing)

Hi,

I had cc3d on linux virtual machine, it was working properly.
Recently, I installed Miniconda with some packages such as numpy,scikit-image,matplotlib,opencv..
whenI run cc3d, I got an error"File "/home/nada/cc3d_install/player/compucell3d.pyw", line 9, in
import sip
ImportError: No module named sip"

Any suggestions to resolve this?

Thanks
Nada

numpy failed-(linux)

I installed cc3d v3.7.5 on linux by following the steps in http://www.compucell3d.org/SrcBin/LinuxCompile
When I ran CC3D, a message shows that I should install numpy.
I tested the default python in the terminal, and imported numpy, it was there!

What can I do to resolve this issue?
Thanks

[BUG] self.stopSimulation() doesn't call steppable.finish()

Hi,

I noticed that calling self.stopSimulation() in a steppable does not call the finish() for the registered steppables. Is this a deliberate design decision? I would assume that finish() runs regardless of how the simulation has been ended.

Add new chemotaxis formulas

Re-starting simulation that results depend on MCS

Hi,
I'm doing tissue modelling and I'd like to be able to re-start the simulation from a previous configuration to try different treatments but because my steppables depend on the MCS I'm not succeeding. Any suggestions on how to setup the MCS to the one at which the configuration was saved? Thanks a lot, Angela

Twedit++ Create Cell does not initialize values of x, y, size and output does not match that in tutorial.

In following PythonScriptingManual_v.3.7.2.pdf, the code snippet generated in CC3D Python -> Cell Manipulation -> Create Cell does not include
x=10
y=10
size=5

While these values obviously need to be edited, having them show up in the code snippet would make this more clear. Perhaps x=SIZEOFX or something similar to remind that this needs to be present. As generated, the console output simply reports "Error: NameError: global name 'x' is not defined".

The values are specified on page 13 of the manual, but not mentioned when going through the next page of the manual which makes them easy to miss.

In addition, the options in CC3D Python -> Cell Manipulation are slightly different than shown in the manual. Options include:
Create Cell
Create Cell (old style)
Create Cell (one liner)
Delete Cell
Fetch Cell by Id
Get Cell At a Pixel
Move Cell

The snippet generated with Create Cell does not match that shown in the manual. Rather than:
cell=self.potts.createCell()
cell.type=self.CONDENSING

the output is:
cell=self.newCell(self.TYPENAME)

Trying both, the one included in the tutorial,
cell=self.potts.createCell()
cell.type=self.CONDENSING
does not seem to work correctly. When I try this, it creates a cell in the correct location with the correct size, but it is empty and rapidly disappears. Using cell=self.newCell(self.CONDENSING)
works and behaves as expected.

Simulation-Function?

Hi,
it's me again...
I'm trying to optimize some simulations for getting better and better fitness results. I tried to use the Parameter Scan function but it's just a parameter-listing I cannot use efficiently for my optimization tool. Is there a better solution, for example some kind of fitness- or objective function/mathematical model the simulations uses? Is it possible to extract it from code? Maybe after initializing a simulation?

Sincerely,
Karinski

running cc3d simulation in silent mode

Hi,

I tried to use the the following command ,but it doesn't work!
./compucell3d.sh --silent -i
-s

Thanks

change name simulation output directory

Hi,

I want to change the name of output directory (simulation name_cc3d_month_day_year_###) of each simulation. Instead ,it can be as (simulation name_ Simulation num), from where I can do that?

Thanks

Player crashes when changing invisible types in 3D view

Twedit++ new project wizard version

From package CC3D_3.7.2_MacOSX_10.9_20140429.zip, creating a new CC3D Project using the wizard in Twedit++ sets the first line of the project.xml to:

This should be 3.7.2

new release not opening player

I've tried loading a couple of simulations including demos but I can't open player
I'm using Mac OS El Capitan 10.11.6

closing the player after the simulation ends

Hi,

Is there a function to call allow us to close player once the simulation ends?

Thanks

Save all in Twedit should not change active document

mapping timesteps to real time

Hi,

How can I convert real time to cc3d time steps?

Thanks

Save simulation running as a video

Hi,
Is there any option incc3d to record model progress and save it as a video format?

Thanks

Twedit++ : 'Save All' does not save newly added resources

"SaveAll" button/menu item does NOT save these added resources. If I create a resource, hit save all and then close Twedit++ and reopen the simulation, these files are lost. This means that if Twedit++ dies for some reason, you lose everything. Only if I select "close project" then Twedit++ opens a dialogue box which asks me if I want to save changes to the project. If I answer "Yes" then Twedit++ does save the added resources, so it isn't impossible to save them, but "SaveAll should really save all of the project.

Source: James email with subject- 'Some issues with Twedit++'

Access SimFileName, if Thread is of Type CMLFieldHandler ? (executed by runScript.bat)

If you execute cc3d python scripts by opening the cc3d files in the GUI version of Compucell, the variable "simthread" will be an instance of Simulation.Simulationthread.

This way you are able to access the methods of SimulationThread.py, for example getSimFileName(), to identify the path of the executed cc3d file.

If you run the same file using the runSim.bat, the instance of simthread will be of CMLFieldHandler.CMLFieldHandler and this class has other methods available. If you call the method simFileName=self.simthread.getSimFileName() this will cause python to crash without further logging.

I added this code to my python setup:

 def __init__(self, sim, simthread):
        print "Simthread:",simthread

Output if you run the script from compucell GUI:
Simthread: <Simulation.SimlationThread.SimulationThread object at 0x04BD1030>
Output if you run the script from runScript.bat:

Simthread: <CMLFieldHandler.CMLFieldHandler instance at 0x0369B5A8>

This is how I start the runscript.bat file:

.\runScript.bat -i "C:\Users\Myuser\Documents\compucellmodels\SpaSdbCdiInDa\1485109855769\runJson.cc3d" -f 10000

EDIT:
This is how I initialize the Compucell3d Setup.

import sys
from os import environ

import CompuCellSetup
sys.path.append(environ["PYTHON_MODULE_PATH"])

sim, simthread = CompuCellSetup.getCoreSimulationObjects()

# Now load the model to simulate!
from ModuroModel.Sd.JsonBasedModelDa import JsonBasedModelDa
model = JsonBasedModelDa(sim, simthread)
print "Model initialized. Running simulation...."
model._run()

I have to identify the path of the current cc3d file to load a matching configuration file, which is always located in the same directory as the cc3d file. Each cc3d file refers to the same python script, so I cannot use static paths.

Is there a way to receive the path of the current cc3d file, if you execute the cc3d-file by the runScript.bat?

Is there something like a parameter map you can access for each simulation, which also includes this info?

Sincerly

Karin

[BUG] I/O related random segfaults

Hi,

I experience segmentation faults at the end of simulation when writing some data to a file. The bug is not very reproducible. It might happen e.g. after I ran the simulation three times.

Here is an example of a steppable producing the segfault:

class RegisterSteppable(SteppableBasePy):
    ''' Class governing cell growth steps.

    '''

    def __init__(self, _simulator, _frequency=1):

        SteppableBasePy.__init__(self, _simulator, _frequency)

    def start(self):
        self.cell_data = []

        self.cell_columns = ['mcs', 'id',
                             'type', 'age', 'P_sr',
                             'n_type1', 'n_type2', # Number of neighbors by types
                             'a_type1', 'a_type2'] # Total contact area by types

    def step(self, mcs):

        for cell in self.cellList:
            n_type1 = 0
            n_type2 = 0
            a_type1 = 0
            a_type2 = 0

            for neighbor, contact_area in self.getCellNeighborDataList(cell):
                if neighbor is None: # Medium
                    continue
                if neighbor.type == 1:
                    n_type1 += 1
                    a_type1 += contact_area
                elif neighbor.type == 2:
                    n_type2 += 1
                    a_type2 += contact_area

            cellDict = self.getDictionaryAttribute(cell)

            step_data = [mcs, cell.id,
                         cell.type,
                         cellDict['age'],
                         cellDict['P_sr'],
                         n_type1, n_type2,
                         a_type1, a_type2]
            self.cell_data.append(step_data)

    def finish(self):

        # sim_dir = CompuCellSetup.getSimulationOutputDir()

        timestamp = datetime.datetime.now().__str__()
        timestamp = timestamp.replace(' ','-')
        timestamp = timestamp.replace('.','-')
        timestamp = timestamp.replace(':','-')

        full_fname = '/home/guillaume/Bureau/sim_cell_data_%s.csv' %timestamp
        metadata = full_fname
        col_names = ','.join(self.cell_columns)
        header = '\n'.join([metadata, col_names])
         np.savetxt(full_fname, np.asarray(self.cell_data),
                    header=col_names, delimiter=',')

         print('saved sim cell data to {}'.format(full_fname))

Commenting out the np.savetxt line removes the segfault, that also happens with the file opening mechanism provided in the docs, or during parameter scans.

Best,

Guillaume

CompuCell3D licence?

Hi, thank you for your great work!

I can't find a license statement or file on the code. Which is it?

Best,

Guillaume

Doesn't start in Mac OS El Capitan

CompuCell doesn't start in Mac OS El Capitan. Here is the error I get:

Now starting CompuCell3D 3.7.4 in GUI mode:

Traceback (most recent call last):
File "/Applications/CC3D_3.7.4/player/compucell3d.pyw", line 47, in
from PyQt4.QtCore import *
ImportError: dlopen(/Applications/CC3D_3.7.4/player/PyQt4/QtCore.so, 2): Library not loaded: @rpath/Deps/QtCore
Referenced from: /Applications/CC3D_3.7.4/player/PyQt4/QtCore.so
Reason: image not found
logout
Saving session...
...copying shared history...
...saving history...truncating history files...
...completed.
Deleting expired sessions...6 completed.

[Process completed]

Fix update notification popup

Crash when running DynamicNumberOfProcessors.cc3d

After a fresh unzip of CC3D, this simulation will run to completion. However, if I try to run it again, it errors out. I have attached some output from the terminal farther down. The first was one where I stopped it after 274 MCS, then clicked 'play' and it crashed. The second file was after closing CC3D, opening a new terminal, opening CC3D again, and trying to run the simulation. You can see that in this case, there was an error after MCS 10 when changing the lattice size.

I just opened at new terminal window and was able to run SBMLSolverOscilatorDemo.cc3d without error.

I then get the same error as before when trying to run DynamicNumberOfProcessors.cc3d, with the error between MCS 10 and 11.

I just now unzipped into my downloads folder, and ran DynamicNumberOfProcessors.cc3d from there. It ran and finished without error. I clicked play to run it again, it got further than MCS 10, but still resulted in an error:

Number of Attempted Energy Calculations=5717
Step 1010 Flips 166/160000 Energy -286 Cells 793 Inventory=793
2608.86 ms spent in solving diffusion problem
CompuCell3D(63054,0x11d42f000) malloc: *** error for object 0x7feb3ba36208: incorrect checksum for freed object - object was probably modified after being freed.
*** set a breakpoint in malloc_error_break to debug
./compucell3d.command: line 125: 63054 Abort trap: 6 ${PYTHON_EXEC} ${PREFIX_CC3D}/player/compucell3d.pyw $* --currentDir=${PREFIX_CC3D}

In addition, it doesn't seem to actually use multiple CPUs. CPU load only reaches 16%, which on a 6 core system is 1 core. It is spread out over multiple cores, however.

System information:
Mac Pro 2013 edition, 6 core, D700 video cards.
OSX 10.9.5

I had previously run 3.7.1 on this computer, so it is possible that some setting has been changed in a figure file somewhere other than the main CC3D folder.

Sorry for the copy and paste from terminal, but apparently I can not attach text files here. I can email text files if that would be easier.

First:
ericwatt@R2D2 19> cc3d

---

CompuCell3D version 3.7.3
(OS X 10.8 x86_64 build)

---

====> CompuCell3D working directory: /Applications/CC3D_3.7.3
/Applications/CC3D_3.7.3

---

setting shell variables used by CompuCell3D:
====> PYTHON_MODULE_PATH: /Applications/CC3D_3.7.3/pythonSetupScripts
====> COMPUCELL3D_PLUGIN_PATH: /Applications/CC3D_3.7.3/lib/CompuCell3DPlugins
====> COMPUCELL3D_STEPPABLE_PATH: /Applications/CC3D_3.7.3/lib/CompuCell3DSteppables
====> SWIG_LIB_INSTALL_DIR: /Applications/CC3D_3.7.3/lib/python
====> SOSLIB_PATH: /Applications/CC3D_3.7.3

---

setting the DYLD_LIBRARY_PATH shell variable as used by CompuCell3D:
====> DYLD_LIBRARY_PATH: /Applications/CC3D_3.7.3/player/VTKLibs:/Applications/CC3D_3.7.3/player/vtk:/Applications/CC3D_3.7.3/Deps/QtDeps:/Applications/CC3D_3.7.3/Deps:/Applications/CC3D_3.7.3/lib/CompuCell3DSteppables:/Applications/CC3D_3.7.3/lib/CompuCell3DPlugins:/Applications/CC3D_3.7.3/lib/python:/Applications/CC3D_3.7.3/lib

---

setting the PYTHONLIB_SYSTEM shell variable as used by CompuCell3D:
ln: /Applications/CC3D_3.7.3/CompuCell3D: File exists
====> PYTHONLIB_SYSTEM: /System/Library/Frameworks/Python.framework/Versions/2.7

---

setting the PATH shell variable as used by CompuCell3D:
====> PATH: /System/Library/Frameworks/Python.framework/Versions/2.7/bin:/usr/bin:/usr/local/bin:/usr/local/mysql/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin:/usr/local/git/bin:/usr/texbin

---

Hello World. Python --version says:

---

Python 2.7.5

---

Now starting CompuCell3D 3.7.3 in GUI mode:

compucell3d.pyw: type(argv)= <type 'list'>
compucell3d.pyw: argv= ['--currentDir=/Applications/CC3D_3.7.3']
argv[0:] = ['--currentDir=/Applications/CC3D_3.7.3']
type(opts), opts= <type 'list'> [('--currentDir', '/Applications/CC3D_3.7.3')]
type(args), args= <type 'list'> []
o= --currentDir
a= /Applications/CC3D_3.7.3
------ PlotManagerSetup.py: plotSupportFlag= -1
------ PlotManagerSetup.py: importing PyQwt PlotManager
CONSOLE PARENT= <PyQt4.QtGui.QDockWidget object at 0x111064640>
self.baseFont.fixedPitch()= True
TWEDIT socket.socketDescriptor()= -1
TRY TO FIGURE OUT PORT

CHECKING PORT= 47406
established empty port= 47406
o= --currentDir
a= /Applications/CC3D_3.7.3
currentDirectory= /Applications/CC3D_3.7.3
projectVersion= 3.6.2
currentVersion= 3.7.3
<CC3DSimulationDataHandler.CC3DSimulationData instance at 0x111c88d40>
runSim self.screenshotDirectoryName=
__runSim self.screenshotDirectoryName=
__builtins {'bytearray': <type 'bytearray'>, 'IndexError': <type 'exceptions.IndexError'>, 'all': , 'help': Type help() for interactive help, or help(object) for help about object., 'vars': , 'SyntaxError': <type 'exceptions.SyntaxError'>, 'unicode': <type 'unicode'>, 'UnicodeDecodeError': <type 'exceptions.UnicodeDecodeError'>, 'memoryview': <type 'memoryview'>, 'isinstance': , 'copyright': Copyright (c) 2001-2013 Python Software Foundation.
All Rights Reserved.

Copyright (c) 2000 BeOpen.com.
All Rights Reserved.

Copyright (c) 1995-2001 Corporation for National Research Initiatives.
All Rights Reserved.

Copyright (c) 1991-1995 Stichting Mathematisch Centrum, Amsterdam.
All Rights Reserved., 'NameError': <type 'exceptions.NameError'>, 'BytesWarning': <type 'exceptions.BytesWarning'>, 'dict': <type 'dict'>, 'input': , 'oct': , 'bin': , 'SystemExit': <type 'exceptions.SystemExit'>, 'StandardError': <type 'exceptions.StandardError'>, 'format': , 'repr': , 'sorted': , 'False': False, 'RuntimeWarning': <type 'exceptions.RuntimeWarning'>, 'list': <type 'list'>, 'iter': , 'reload': , 'Warning': <type 'exceptions.Warning'>, 'package': None, 'round': , 'dir': , 'cmp': , 'set': <type 'set'>, 'bytes': <type 'str'>, 'reduce': , 'intern': , 'issubclass': , 'Ellipsis': Ellipsis, 'EOFError': <type 'exceptions.EOFError'>, 'locals': , 'BufferError': <type 'exceptions.BufferError'>, 'slice': <type 'slice'>, 'FloatingPointError': <type 'exceptions.FloatingPointError'>, 'sum': , 'getattr': , 'abs': , 'exit': Use exit() or Ctrl-D (i.e. EOF) to exit, 'print': , 'True': True, 'FutureWarning': <type 'exceptions.FutureWarning'>, 'ImportWarning': <type 'exceptions.ImportWarning'>, 'None': None, 'hash': , 'ReferenceError': <type 'exceptions.ReferenceError'>, 'len': , 'credits': Thanks to CWI, CNRI, BeOpen.com, Zope Corporation and a cast of thousands
for supporting Python development. See www.python.org for more information., 'frozenset': <type 'frozenset'>, 'name': 'builtin', 'ord': , 'super': <type 'super'>, 'TypeError': <type 'exceptions.TypeError'>, 'license': Type license() to see the full license text, 'KeyboardInterrupt': <type 'exceptions.KeyboardInterrupt'>, 'UserWarning': <type 'exceptions.UserWarning'>, 'filter': , 'range': , 'staticmethod': <type 'staticmethod'>, 'SystemError': <type 'exceptions.SystemError'>, 'BaseException': <type 'exceptions.BaseException'>, 'pow': , 'RuntimeError': <type 'exceptions.RuntimeError'>, 'float': <type 'float'>, 'MemoryError': <type 'exceptions.MemoryError'>, 'StopIteration': <type 'exceptions.StopIteration'>, 'globals': , 'divmod': , 'enumerate': <type 'enumerate'>, 'apply': , 'LookupError': <type 'exceptions.LookupError'>, 'open': , 'quit': Use quit() or Ctrl-D (i.e. EOF) to exit, 'basestring': <type 'basestring'>, 'UnicodeError': <type 'exceptions.UnicodeError'>, 'zip': , 'hex': , 'long': <type 'long'>, 'next': , 'ImportError': <type 'exceptions.ImportError'>, 'chr': , 'xrange': <type 'xrange'>, 'type': <type 'type'>, 'doc': "Built-in functions, exceptions, and other objects.\n\nNoteworthy: None is the nil' object; Ellipsis represents...' in slices.", 'Exception': <type 'exceptions.Exception'>, 'tuple': <type 'tuple'>, 'UnicodeTranslateError': <type 'exceptions.UnicodeTranslateError'>, 'reversed': <type 'reversed'>, 'UnicodeEncodeError': <type 'exceptions.UnicodeEncodeError'>, 'IOError': <type 'exceptions.IOError'>, 'hasattr': , 'delattr': , 'setattr': , 'raw_input': , 'SyntaxWarning': <type 'exceptions.SyntaxWarning'>, 'compile': , 'ArithmeticError': <type 'exceptions.ArithmeticError'>, 'str': <type 'str'>, 'property': <type 'property'>, 'GeneratorExit': <type 'exceptions.GeneratorExit'>, 'int': <type 'int'>, 'import': , 'KeyError': <type 'exceptions.KeyError'>, 'coerce': , 'PendingDeprecationWarning': <type 'exceptions.PendingDeprecationWarning'>, 'file': <type 'file'>, 'EnvironmentError': <type 'exceptions.EnvironmentError'>, 'unichr': , 'id': , 'OSError': <type 'exceptions.OSError'>, 'DeprecationWarning': <type 'exceptions.DeprecationWarning'>, 'min': , 'UnicodeWarning': <type 'exceptions.UnicodeWarning'>, 'execfile': , 'any': , 'complex': <type 'complex'>, 'bool': <type 'bool'>, 'ValueError': <type 'exceptions.ValueError'>, 'NotImplemented': NotImplemented, 'map': , 'buffer': <type 'buffer'>, 'max': , 'object': <type 'object'>, 'TabError': <type 'exceptions.TabError'>, 'callable': , 'ZeroDivisionError': <type 'exceptions.ZeroDivisionError'>, 'eval': , 'debug': True, 'IndentationError': <type 'exceptions.IndentationError'>, 'AssertionError': <type 'exceptions.AssertionError'>, 'classmethod': <type 'classmethod'>, 'UnboundLocalError': <type 'exceptions.UnboundLocalError'>, 'NotImplementedError': <type 'exceptions.NotImplementedError'>, 'AttributeError': <type 'exceptions.AttributeError'>, 'OverflowError': <type 'exceptions.OverflowError'>}
steppablePath=/Applications/CC3D_3.7.3/lib/CompuCell3DSteppables
pluginPath=/Applications/CC3D_3.7.3/lib/CompuCell3DPlugins
THIS IS JUST BEFORE LOADING LIBRARIES
AFTER LOAD LIBRARIES
Platform: darwin
Did not find dl module, will try manual dl initialization...
steppablePath=/Applications/CC3D_3.7.3/lib/CompuCell3DSteppables
pluginPath=/Applications/CC3D_3.7.3/lib/CompuCell3DPlugins
THIS IS JUST BEFORE LOADING LIBRARIES
AFTER LOAD LIBRARIES
INSIDE IF CompuCellPythonSimulationNewPlayer

Platform: darwin
Did not find dl module, will try manual dl initialization...
steppablePath=/Applications/CC3D_3.7.3/lib/CompuCell3DSteppables
pluginPath=/Applications/CC3D_3.7.3/lib/CompuCell3DPlugins
THIS IS JUST BEFORE LOADING LIBRARIES
AFTER LOAD LIBRARIES

self.basePath= /Applications/CC3D_3.7.3/Demos/SimulationSettings/ParallelCC3DExamples/DynamicNumberOfProcessors
self.playerSimulationXMLFileName= /Applications/CC3D_3.7.3/Demos/SimulationSettings/ParallelCC3DExamples/DynamicNumberOfProcessors/Simulation/DynamicNumberOfProcessors.xml
simulationPythonScriptName= /Applications/CC3D_3.7.3/Demos/SimulationSettings/ParallelCC3DExamples/DynamicNumberOfProcessors/Simulation/DynamicNumberOfProcessors.py simulationFileName= /Applications/CC3D_3.7.3/Demos/SimulationSettings/ParallelCC3DExamples/DynamicNumberOfProcessors/Simulation/DynamicNumberOfProcessors.xml
Element Plugin
Element Plugin
Element Plugin
Element Steppable
Element Steppable
Element Potts
Element Metadata
BEFORE initializePotts
INSIDE initializePottsCC3D=

ppdCC3DPtr=0x7fd8361ee340ppdCC3DPtr->dim=(0,0,0)
_xmlData->getFirstElement(Dimensions)->getAttributeAsUInt(x)=200
_xmlData->getFirstElement(Dimensions)->getAttributeAsUInt(y)=200
_xmlData->getFirstElement(Dimensions)->getAttributeAsUInt(z)=1
_ppdCC3DPtr->algorithmName =
ppdCC3DPtr->seed = 0
ppdCC3DPtr->boundary_x =
_ppdCC3DPtr->boundary_y =
ppdCC3DPtr->boundary_z =
ppdCC3DPtr->latticeType = square
BoundaryStrategy singleton is ALIVE!
initialized square lattice
potts.getLatticeType()=1
setNeighborOrder maxNeighborIndex=7
ppdCC3DPtr->depthFlag = 0
ppdCC3DPtr->debugOutputFrequency = 1
setNeighborOrder maxNeighborIndex=7
_numberOfProcessors =1 numArrayElements=33
SINGLE PROCESSOR RUN minDim=(0,0,0) maxDim=(200,200,1)
_numberOfProcessors =1 numArrayElements=33
SINGLE PROCESSOR RUN minDim=(0,0,0) maxDim=(200,200,1)
_numberOfProcessors =4 numArrayElements=33
gridId=0 minDim=(0,0,0) maxDim=(100,100,1)
gridId=1 minDim=(100,0,0) maxDim=(200,100,1)
gridId=2 minDim=(0,100,0) maxDim=(100,200,1)
gridId=3 minDim=(100,100,0) maxDim=(200,200,1)
GID=0 subgridId=0 minSubDim=(0,0,0) maxSubDim=(50,50,1)
GID=0 subgridId=1 minSubDim=(50,0,0) maxSubDim=(100,50,1)
GID=0 subgridId=2 minSubDim=(0,50,0) maxSubDim=(50,100,1)
GID=0 subgridId=3 minSubDim=(50,50,0) maxSubDim=(100,100,1)
GID=1 subgridId=0 minSubDim=(100,0,0) maxSubDim=(150,50,1)
GID=1 subgridId=1 minSubDim=(150,0,0) maxSubDim=(200,50,1)
GID=1 subgridId=2 minSubDim=(100,50,0) maxSubDim=(150,100,1)
GID=1 subgridId=3 minSubDim=(150,50,0) maxSubDim=(200,100,1)
GID=2 subgridId=0 minSubDim=(0,100,0) maxSubDim=(50,150,1)
GID=2 subgridId=1 minSubDim=(50,100,0) maxSubDim=(100,150,1)
GID=2 subgridId=2 minSubDim=(0,150,0) maxSubDim=(50,200,1)
GID=2 subgridId=3 minSubDim=(50,150,0) maxSubDim=(100,200,1)
GID=3 subgridId=0 minSubDim=(100,100,0) maxSubDim=(150,150,1)
GID=3 subgridId=1 minSubDim=(150,100,0) maxSubDim=(200,150,1)
GID=3 subgridId=2 minSubDim=(100,150,0) maxSubDim=(150,200,1)
GID=3 subgridId=3 minSubDim=(150,150,0) maxSubDim=(200,200,1)
_numberOfProcessors =4 numArrayElements=33
gridId=0 minDim=(0,0,0) maxDim=(100,100,1)
gridId=1 minDim=(100,0,0) maxDim=(200,100,1)
gridId=2 minDim=(0,100,0) maxDim=(100,200,1)
gridId=3 minDim=(100,100,0) maxDim=(200,200,1)
GID=0 subgridId=0 minSubDim=(0,0,0) maxSubDim=(50,50,1)
GID=0 subgridId=1 minSubDim=(50,0,0) maxSubDim=(100,50,1)
GID=0 subgridId=2 minSubDim=(0,50,0) maxSubDim=(50,100,1)
GID=0 subgridId=3 minSubDim=(50,50,0) maxSubDim=(100,100,1)
GID=1 subgridId=0 minSubDim=(100,0,0) maxSubDim=(150,50,1)
GID=1 subgridId=1 minSubDim=(150,0,0) maxSubDim=(200,50,1)
GID=1 subgridId=2 minSubDim=(100,50,0) maxSubDim=(150,100,1)
GID=1 subgridId=3 minSubDim=(150,50,0) maxSubDim=(200,100,1)
GID=2 subgridId=0 minSubDim=(0,100,0) maxSubDim=(50,150,1)
GID=2 subgridId=1 minSubDim=(50,100,0) maxSubDim=(100,150,1)
GID=2 subgridId=2 minSubDim=(0,150,0) maxSubDim=(50,200,1)
GID=2 subgridId=3 minSubDim=(50,150,0) maxSubDim=(100,200,1)
GID=3 subgridId=0 minSubDim=(100,100,0) maxSubDim=(150,150,1)
GID=3 subgridId=1 minSubDim=(150,100,0) maxSubDim=(200,150,1)
GID=3 subgridId=2 minSubDim=(100,150,0) maxSubDim=(150,200,1)
GID=3 subgridId=3 minSubDim=(150,150,0) maxSubDim=(200,200,1)
AFTER initializePotts
INITIALIZING Volume
GOT HERE BEFORE CALLING INIT
INITIALIZING CellType
INITIALIZING Contact
Default constructor DiffusableVectorCommon
INITIALIZING DiffusionSolverFE

INSIDE UPDATE XML
DiffusionConstant: 0.1
DecayConstant: 1e-05
DeltaX: 1
DeltaT: 1
fieldName: FGF

diffSecrFieldTuppleVec.size()=1
concentrationFieldNameVector[i]=FGF
FIELDS THAT I HAVE
Field 0 name: FGF
DiffusionSolverFE: extra Init in read XML
registring field: FGF field address=0x7fd8361f1180
INITIALIZING BlobInitializer
radius=80 gap=0 types=Condensing,NonCondensing
GOT HERE BEFORE EXIT
SIMTHREAD= <Simulation.SimulationThread.SimulationThread object at 0x111c8ad60>
SIMULATION FILE NAME= /Applications/CC3D_3.7.3/Demos/SimulationSettings/ParallelCC3DExamples/DynamicNumberOfProcessors/DynamicNumberOfProcessors.cc3d
EXTRACTING restartEnabled
WILL RUN SIMULATION FROM BEGINNING
, extraInit for: VolumeTracker
, extraInit for: CellTypeMonitor
, extraInit for: CellType
size=3
contact[0][0]=0
contact[0][1]=16
contact[0][2]=16
contact[1][0]=16
contact[1][1]=2
contact[1][2]=11
contact[2][0]=16
contact[2][1]=11
contact[2][2]=16
Contact maxNeighborIndex=7
typeNameMap.size()=3
, extraInit for: Contact
automaton=0x7fd8361efed8
, extraInit for: Volume
Simulator::start(): Plugins:, VolumeTracker, CellTypeMonitor, CellType, Contact, Volume
_BLOB INIT_***
GOT HERE
itDim=(40,40,1)
Step 0 Energy 0 Cells 793
windowNames= []
self.graphicsWindowDict= {}
GOT HERE REMOVE ALL VTK
self.graphicsWindowDict= {}
len(self.subWindowList())= 0
2014-10-16 15:26:38.485 CompuCell3D[62761:507] invalid drawable
2014-10-16 15:26:38.486 CompuCell3D[62761:507] invalid drawable
pluginName = Volume
pluginName = CellType
pluginName = Contact

self.basicSimulationData= ['doc', 'init', 'module', 'fieldDim', 'numberOfSteps', 'sim']
self.basicSimulationData.fieldDim= (200,200,1)
self.basicSimulationData.numberOfSteps= 1000
self.basicSimulationData.sim= <CompuCell.Simulator; proxy of <Swig Object of type 'CompuCell3D::Simulator *' at 0x111ca2930> >
windowName= 1
after windowName= 1
AFTER setInitialCrossSection
CREATING SCREENSHOT WINDOW
2014-10-16 15:26:38.614 CompuCell3D[62761:507] invalid drawable
2014-10-16 15:26:38.615 CompuCell3D[62761:507] invalid drawable
xSize= 600 ySize= 600
ADDITIONAL SCREENSHOT WINDOW SIZE= (600, 600)
THIS IS ROOT ITEM= CompuCell3D
ROOT ITEM DOMNode= CompuCell3D
---- SimpleTabView.py: initializeSimulationViewWidget(): before TRY ACQUIRE
---- SimpleTabView.py: initializeSimulationViewWidget(): AFTER RELEASE
FAST numberOfAttempts=40000
Number of Attempted Energy Calculations=6015
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PYSTEPPABLES INSIDE resizeAndShiftLattice
okFlag= True
_numberOfProcessors =4 numArrayElements=33
gridId=0 minDim=(0,0,0) maxDim=(200,200,1)
gridId=1 minDim=(200,0,0) maxDim=(400,200,1)
gridId=2 minDim=(0,200,0) maxDim=(200,400,1)
gridId=3 minDim=(200,200,0) maxDim=(400,400,1)
GID=0 subgridId=0 minSubDim=(0,0,0) maxSubDim=(100,100,1)
GID=0 subgridId=1 minSubDim=(100,0,0) maxSubDim=(200,100,1)
GID=0 subgridId=2 minSubDim=(0,100,0) maxSubDim=(100,200,1)
GID=0 subgridId=3 minSubDim=(100,100,0) maxSubDim=(200,200,1)
GID=1 subgridId=0 minSubDim=(200,0,0) maxSubDim=(300,100,1)
GID=1 subgridId=1 minSubDim=(300,0,0) maxSubDim=(400,100,1)
GID=1 subgridId=2 minSubDim=(200,100,0) maxSubDim=(300,200,1)
GID=1 subgridId=3 minSubDim=(300,100,0) maxSubDim=(400,200,1)
GID=2 subgridId=0 minSubDim=(0,200,0) maxSubDim=(100,300,1)
GID=2 subgridId=1 minSubDim=(100,200,0) maxSubDim=(200,300,1)
GID=2 subgridId=2 minSubDim=(0,300,0) maxSubDim=(100,400,1)
GID=2 subgridId=3 minSubDim=(100,300,0) maxSubDim=(200,400,1)
GID=3 subgridId=0 minSubDim=(200,200,0) maxSubDim=(300,300,1)
GID=3 subgridId=1 minSubDim=(300,200,0) maxSubDim=(400,300,1)
GID=3 subgridId=2 minSubDim=(200,300,0) maxSubDim=(300,400,1)
GID=3 subgridId=3 minSubDim=(300,300,0) maxSubDim=(400,400,1)
resetAllCameras in GraphicsFrame = <Graphics.GraphicsFrameWidget.GraphicsFrameWidget object at 0x114380348>
FAST numberOfAttempts=160000
Number of Attempted Energy Calculations=6676
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_numberOfProcessors =8 numArrayElements=33
gridId=0 minDim=(0,0,0) maxDim=(100,200,1)
gridId=1 minDim=(100,0,0) maxDim=(200,200,1)
gridId=2 minDim=(200,0,0) maxDim=(300,200,1)
gridId=3 minDim=(300,0,0) maxDim=(400,200,1)
gridId=4 minDim=(0,200,0) maxDim=(100,400,1)
gridId=5 minDim=(100,200,0) maxDim=(200,400,1)
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Number of Attempted Energy Calculations=6801
Step 262 Flips 2746/160000 Energy 693 Cells 793 Inventory=793
FAST numberOfAttempts=160000
Number of Attempted Energy Calculations=6920
Step 263 Flips 2808/160000 Energy -160 Cells 793 Inventory=793
FAST numberOfAttempts=160000
Number of Attempted Energy Calculations=6747
Step 264 Flips 2753/160000 Energy -560 Cells 793 Inventory=793
FAST numberOfAttempts=160000
Number of Attempted Energy Calculations=6906
Step 265 Flips 2832/160000 Energy 228 Cells 793 Inventory=793
FAST numberOfAttempts=160000
Number of Attempted Energy Calculations=6660
Step 266 Flips 2646/160000 Energy -456 Cells 793 Inventory=793
FAST numberOfAttempts=160000
Number of Attempted Energy Calculations=6641
Step 267 Flips 2671/160000 Energy 673 Cells 793 Inventory=793
FAST numberOfAttempts=160000
Number of Attempted Energy Calculations=6815
Step 268 Flips 2715/160000 Energy -239 Cells 793 Inventory=793
FAST numberOfAttempts=160000
Number of Attempted Energy Calculations=6787
Step 269 Flips 2745/160000 Energy -399 Cells 793 Inventory=793
FAST numberOfAttempts=160000
Number of Attempted Energy Calculations=6784
Step 270 Flips 2739/160000 Energy -783 Cells 793 Inventory=793
FAST numberOfAttempts=160000
Number of Attempted Energy Calculations=6777
Step 271 Flips 2711/160000 Energy 400 Cells 793 Inventory=793
FAST numberOfAttempts=160000
Number of Attempted Energy Calculations=6675
Step 272 Flips 2705/160000 Energy 101 Cells 793 Inventory=793
FAST numberOfAttempts=160000
Number of Attempted Energy Calculations=6783
Step 273 Flips 2732/160000 Energy 37 Cells 793 Inventory=793
FAST numberOfAttempts=160000
Number of Attempted Energy Calculations=6693
Step 274 Flips 2649/160000 Energy 330 Cells 793 Inventory=793
END OF SIMULATION
CALLING UNLOAD MODULES NEW PLAYER
SIMULATION RUNTIME 5 s : 816 ms
EQUIVALENT OF 5.817 seconds
COMPLETED execfile in CompuCellPythonSimulationNewPlayer

INSIDE handleSimulationFinishedRegular
JUST BEFORE CLOSING self.screenshotGraphicsWidget
numberOfActors= 0
actorsList= []
QVTK INTERACTOR CLOSE EVENT
CompuCell3D(62761,0x7fff79367310) malloc: *** error for object 0x101010101010101: pointer being freed was not allocated
*** set a breakpoint in malloc_error_break to debug
/Applications/CC3D_3.7.3/compucell3d.command: line 125: 62761 Abort trap: 6 ${PYTHON_EXEC} ${PREFIX_CC3D}/player/compucell3d.pyw $* --currentDir=${PREFIX_CC3D}
ericwatt@R2D2 20>

Second:

Last login: Thu Oct 16 15:27:56 on ttys005
ericwatt@R2D2 1> cc3d

---

CompuCell3D version 3.7.3
(OS X 10.8 x86_64 build)

---

====> CompuCell3D working directory: /Applications/CC3D_3.7.3
/Applications/CC3D_3.7.3

---

setting shell variables used by CompuCell3D:
====> PYTHON_MODULE_PATH: /Applications/CC3D_3.7.3/pythonSetupScripts
====> COMPUCELL3D_PLUGIN_PATH: /Applications/CC3D_3.7.3/lib/CompuCell3DPlugins
====> COMPUCELL3D_STEPPABLE_PATH: /Applications/CC3D_3.7.3/lib/CompuCell3DSteppables
====> SWIG_LIB_INSTALL_DIR: /Applications/CC3D_3.7.3/lib/python
====> SOSLIB_PATH: /Applications/CC3D_3.7.3

---

setting the DYLD_LIBRARY_PATH shell variable as used by CompuCell3D:
====> DYLD_LIBRARY_PATH: /Applications/CC3D_3.7.3/player/VTKLibs:/Applications/CC3D_3.7.3/player/vtk:/Applications/CC3D_3.7.3/Deps/QtDeps:/Applications/CC3D_3.7.3/Deps:/Applications/CC3D_3.7.3/lib/CompuCell3DSteppables:/Applications/CC3D_3.7.3/lib/CompuCell3DPlugins:/Applications/CC3D_3.7.3/lib/python:/Applications/CC3D_3.7.3/lib

---

setting the PYTHONLIB_SYSTEM shell variable as used by CompuCell3D:
ln: /Applications/CC3D_3.7.3/CompuCell3D: File exists
====> PYTHONLIB_SYSTEM: /System/Library/Frameworks/Python.framework/Versions/2.7

---

setting the PATH shell variable as used by CompuCell3D:
====> PATH: /System/Library/Frameworks/Python.framework/Versions/2.7/bin:/usr/bin:/usr/local/bin:/usr/local/mysql/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin:/usr/local/git/bin:/usr/texbin

---

Hello World. Python --version says:

---

Python 2.7.5

---

Now starting CompuCell3D 3.7.3 in GUI mode:

compucell3d.pyw: type(argv)= <type 'list'>
compucell3d.pyw: argv= ['--currentDir=/Applications/CC3D_3.7.3']
argv[0:] = ['--currentDir=/Applications/CC3D_3.7.3']
type(opts), opts= <type 'list'> [('--currentDir', '/Applications/CC3D_3.7.3')]
type(args), args= <type 'list'> []
o= --currentDir
a= /Applications/CC3D_3.7.3
------ PlotManagerSetup.py: plotSupportFlag= -1
------ PlotManagerSetup.py: importing PyQwt PlotManager
CONSOLE PARENT= <PyQt4.QtGui.QDockWidget object at 0x11ebc9640>
self.baseFont.fixedPitch()= True
TWEDIT socket.socketDescriptor()= -1
TRY TO FIGURE OUT PORT

CHECKING PORT= 47406
established empty port= 47406
o= --currentDir
a= /Applications/CC3D_3.7.3
currentDirectory= /Applications/CC3D_3.7.3
openSim: self.__fileName= /Applications/CC3D_3.7.3/Demos/SimulationSettings/ParallelCC3DExamples/DynamicNumberOfProcessors/DynamicNumberOfProcessors.cc3d
projectVersion= 3.6.2
currentVersion= 3.7.3
<CC3DSimulationDataHandler.CC3DSimulationData instance at 0x11f7f4368>
__runSim self.screenshotDirectoryName=
__runSim self.screenshotDirectoryName=
__builtins {'bytearray': <type 'bytearray'>, 'IndexError': <type 'exceptions.IndexError'>, 'all': , 'help': Type help() for interactive help, or help(object) for help about object., 'vars': , 'SyntaxError': <type 'exceptions.SyntaxError'>, 'unicode': <type 'unicode'>, 'UnicodeDecodeError': <type 'exceptions.UnicodeDecodeError'>, 'memoryview': <type 'memoryview'>, 'isinstance': , 'copyright': Copyright (c) 2001-2013 Python Software Foundation.
All Rights Reserved.

Copyright (c) 2000 BeOpen.com.
All Rights Reserved.

Copyright (c) 1995-2001 Corporation for National Research Initiatives.
All Rights Reserved.

Copyright (c) 1991-1995 Stichting Mathematisch Centrum, Amsterdam.
All Rights Reserved., 'NameError': <type 'exceptions.NameError'>, 'BytesWarning': <type 'exceptions.BytesWarning'>, 'dict': <type 'dict'>, 'input': , 'oct': , 'bin': , 'SystemExit': <type 'exceptions.SystemExit'>, 'StandardError': <type 'exceptions.StandardError'>, 'format': , 'repr': , 'sorted': , 'False': False, 'RuntimeWarning': <type 'exceptions.RuntimeWarning'>, 'list': <type 'list'>, 'iter': , 'reload': , 'Warning': <type 'exceptions.Warning'>, 'package': None, 'round': , 'dir': , 'cmp': , 'set': <type 'set'>, 'bytes': <type 'str'>, 'reduce': , 'intern': , 'issubclass': , 'Ellipsis': Ellipsis, 'EOFError': <type 'exceptions.EOFError'>, 'locals': , 'BufferError': <type 'exceptions.BufferError'>, 'slice': <type 'slice'>, 'FloatingPointError': <type 'exceptions.FloatingPointError'>, 'sum': , 'getattr': , 'abs': , 'exit': Use exit() or Ctrl-D (i.e. EOF) to exit, 'print': , 'True': True, 'FutureWarning': <type 'exceptions.FutureWarning'>, 'ImportWarning': <type 'exceptions.ImportWarning'>, 'None': None, 'hash': , 'ReferenceError': <type 'exceptions.ReferenceError'>, 'len': , 'credits': Thanks to CWI, CNRI, BeOpen.com, Zope Corporation and a cast of thousands
for supporting Python development. See www.python.org for more information., 'frozenset': <type 'frozenset'>, 'name': 'builtin', 'ord': , 'super': <type 'super'>, 'TypeError': <type 'exceptions.TypeError'>, 'license': Type license() to see the full license text, 'KeyboardInterrupt': <type 'exceptions.KeyboardInterrupt'>, 'UserWarning': <type 'exceptions.UserWarning'>, 'filter': , 'range': , 'staticmethod': <type 'staticmethod'>, 'SystemError': <type 'exceptions.SystemError'>, 'BaseException': <type 'exceptions.BaseException'>, 'pow': , 'RuntimeError': <type 'exceptions.RuntimeError'>, 'float': <type 'float'>, 'MemoryError': <type 'exceptions.MemoryError'>, 'StopIteration': <type 'exceptions.StopIteration'>, 'globals': , 'divmod': , 'enumerate': <type 'enumerate'>, 'apply': , 'LookupError': <type 'exceptions.LookupError'>, 'open': , 'quit': Use quit() or Ctrl-D (i.e. EOF) to exit, 'basestring': <type 'basestring'>, 'UnicodeError': <type 'exceptions.UnicodeError'>, 'zip': , 'hex': , 'long': <type 'long'>, 'next': , 'ImportError': <type 'exceptions.ImportError'>, 'chr': , 'xrange': <type 'xrange'>, 'type': <type 'type'>, 'doc': "Built-in functions, exceptions, and other objects.\n\nNoteworthy: None is the nil' object; Ellipsis represents...' in slices.", 'Exception': <type 'exceptions.Exception'>, 'tuple': <type 'tuple'>, 'UnicodeTranslateError': <type 'exceptions.UnicodeTranslateError'>, 'reversed': <type 'reversed'>, 'UnicodeEncodeError': <type 'exceptions.UnicodeEncodeError'>, 'IOError': <type 'exceptions.IOError'>, 'hasattr': , 'delattr': , 'setattr': , 'raw_input': , 'SyntaxWarning': <type 'exceptions.SyntaxWarning'>, 'compile': , 'ArithmeticError': <type 'exceptions.ArithmeticError'>, 'str': <type 'str'>, 'property': <type 'property'>, 'GeneratorExit': <type 'exceptions.GeneratorExit'>, 'int': <type 'int'>, 'import': , 'KeyError': <type 'exceptions.KeyError'>, 'coerce': , 'PendingDeprecationWarning': <type 'exceptions.PendingDeprecationWarning'>, 'file': <type 'file'>, 'EnvironmentError': <type 'exceptions.EnvironmentError'>, 'unichr': , 'id': , 'OSError': <type 'exceptions.OSError'>, 'DeprecationWarning': <type 'exceptions.DeprecationWarning'>, 'min': , 'UnicodeWarning': <type 'exceptions.UnicodeWarning'>, 'execfile': , 'any': , 'complex': <type 'complex'>, 'bool': <type 'bool'>, 'ValueError': <type 'exceptions.ValueError'>, 'NotImplemented': NotImplemented, 'map': , 'buffer': <type 'buffer'>, 'max': , 'object': <type 'object'>, 'TabError': <type 'exceptions.TabError'>, 'callable': , 'ZeroDivisionError': <type 'exceptions.ZeroDivisionError'>, 'eval': , 'debug': True, 'IndentationError': <type 'exceptions.IndentationError'>, 'AssertionError': <type 'exceptions.AssertionError'>, 'classmethod': <type 'classmethod'>, 'UnboundLocalError': <type 'exceptions.UnboundLocalError'>, 'NotImplementedError': <type 'exceptions.NotImplementedError'>, 'AttributeError': <type 'exceptions.AttributeError'>, 'OverflowError': <type 'exceptions.OverflowError'>}
steppablePath=/Applications/CC3D_3.7.3/lib/CompuCell3DSteppables
pluginPath=/Applications/CC3D_3.7.3/lib/CompuCell3DPlugins
THIS IS JUST BEFORE LOADING LIBRARIES
AFTER LOAD LIBRARIES
Platform: darwin
Did not find dl module, will try manual dl initialization...
steppablePath=/Applications/CC3D_3.7.3/lib/CompuCell3DSteppables
pluginPath=/Applications/CC3D_3.7.3/lib/CompuCell3DPlugins
THIS IS JUST BEFORE LOADING LIBRARIES
AFTER LOAD LIBRARIES
INSIDE IF CompuCellPythonSimulationNewPlayer

Platform: darwin
Did not find dl module, will try manual dl initialization...
steppablePath=/Applications/CC3D_3.7.3/lib/CompuCell3DSteppables
pluginPath=/Applications/CC3D_3.7.3/lib/CompuCell3DPlugins
THIS IS JUST BEFORE LOADING LIBRARIES
AFTER LOAD LIBRARIES

self.basePath= /Applications/CC3D_3.7.3/Demos/SimulationSettings/ParallelCC3DExamples/DynamicNumberOfProcessors
self.playerSimulationXMLFileName= /Applications/CC3D_3.7.3/Demos/SimulationSettings/ParallelCC3DExamples/DynamicNumberOfProcessors/Simulation/DynamicNumberOfProcessors.xml
simulationPythonScriptName= /Applications/CC3D_3.7.3/Demos/SimulationSettings/ParallelCC3DExamples/DynamicNumberOfProcessors/Simulation/DynamicNumberOfProcessors.py simulationFileName= /Applications/CC3D_3.7.3/Demos/SimulationSettings/ParallelCC3DExamples/DynamicNumberOfProcessors/Simulation/DynamicNumberOfProcessors.xml
Element Plugin
Element Plugin
Element Plugin
Element Steppable
Element Steppable
Element Potts
Element Metadata
BEFORE initializePotts
INSIDE initializePottsCC3D=

ppdCC3DPtr=0x7ff543cb9bc0ppdCC3DPtr->dim=(0,0,0)
_xmlData->getFirstElement(Dimensions)->getAttributeAsUInt(x)=200
_xmlData->getFirstElement(Dimensions)->getAttributeAsUInt(y)=200
_xmlData->getFirstElement(Dimensions)->getAttributeAsUInt(z)=1
_ppdCC3DPtr->algorithmName =
ppdCC3DPtr->seed = 0
ppdCC3DPtr->boundary_x =
_ppdCC3DPtr->boundary_y =
ppdCC3DPtr->boundary_z =
ppdCC3DPtr->latticeType = square
BoundaryStrategy singleton is ALIVE!
initialized square lattice
potts.getLatticeType()=1
setNeighborOrder maxNeighborIndex=7
ppdCC3DPtr->depthFlag = 0
ppdCC3DPtr->debugOutputFrequency = 1
setNeighborOrder maxNeighborIndex=7
_numberOfProcessors =1 numArrayElements=33
SINGLE PROCESSOR RUN minDim=(0,0,0) maxDim=(200,200,1)
_numberOfProcessors =1 numArrayElements=33
SINGLE PROCESSOR RUN minDim=(0,0,0) maxDim=(200,200,1)
_numberOfProcessors =4 numArrayElements=33
gridId=0 minDim=(0,0,0) maxDim=(100,100,1)
gridId=1 minDim=(100,0,0) maxDim=(200,100,1)
gridId=2 minDim=(0,100,0) maxDim=(100,200,1)
gridId=3 minDim=(100,100,0) maxDim=(200,200,1)
GID=0 subgridId=0 minSubDim=(0,0,0) maxSubDim=(50,50,1)
GID=0 subgridId=1 minSubDim=(50,0,0) maxSubDim=(100,50,1)
GID=0 subgridId=2 minSubDim=(0,50,0) maxSubDim=(50,100,1)
GID=0 subgridId=3 minSubDim=(50,50,0) maxSubDim=(100,100,1)
GID=1 subgridId=0 minSubDim=(100,0,0) maxSubDim=(150,50,1)
GID=1 subgridId=1 minSubDim=(150,0,0) maxSubDim=(200,50,1)
GID=1 subgridId=2 minSubDim=(100,50,0) maxSubDim=(150,100,1)
GID=1 subgridId=3 minSubDim=(150,50,0) maxSubDim=(200,100,1)
GID=2 subgridId=0 minSubDim=(0,100,0) maxSubDim=(50,150,1)
GID=2 subgridId=1 minSubDim=(50,100,0) maxSubDim=(100,150,1)
GID=2 subgridId=2 minSubDim=(0,150,0) maxSubDim=(50,200,1)
GID=2 subgridId=3 minSubDim=(50,150,0) maxSubDim=(100,200,1)
GID=3 subgridId=0 minSubDim=(100,100,0) maxSubDim=(150,150,1)
GID=3 subgridId=1 minSubDim=(150,100,0) maxSubDim=(200,150,1)
GID=3 subgridId=2 minSubDim=(100,150,0) maxSubDim=(150,200,1)
GID=3 subgridId=3 minSubDim=(150,150,0) maxSubDim=(200,200,1)
_numberOfProcessors =4 numArrayElements=33
gridId=0 minDim=(0,0,0) maxDim=(100,100,1)
gridId=1 minDim=(100,0,0) maxDim=(200,100,1)
gridId=2 minDim=(0,100,0) maxDim=(100,200,1)
gridId=3 minDim=(100,100,0) maxDim=(200,200,1)
GID=0 subgridId=0 minSubDim=(0,0,0) maxSubDim=(50,50,1)
GID=0 subgridId=1 minSubDim=(50,0,0) maxSubDim=(100,50,1)
GID=0 subgridId=2 minSubDim=(0,50,0) maxSubDim=(50,100,1)
GID=0 subgridId=3 minSubDim=(50,50,0) maxSubDim=(100,100,1)
GID=1 subgridId=0 minSubDim=(100,0,0) maxSubDim=(150,50,1)
GID=1 subgridId=1 minSubDim=(150,0,0) maxSubDim=(200,50,1)
GID=1 subgridId=2 minSubDim=(100,50,0) maxSubDim=(150,100,1)
GID=1 subgridId=3 minSubDim=(150,50,0) maxSubDim=(200,100,1)
GID=2 subgridId=0 minSubDim=(0,100,0) maxSubDim=(50,150,1)
GID=2 subgridId=1 minSubDim=(50,100,0) maxSubDim=(100,150,1)
GID=2 subgridId=2 minSubDim=(0,150,0) maxSubDim=(50,200,1)
GID=2 subgridId=3 minSubDim=(50,150,0) maxSubDim=(100,200,1)
GID=3 subgridId=0 minSubDim=(100,100,0) maxSubDim=(150,150,1)
GID=3 subgridId=1 minSubDim=(150,100,0) maxSubDim=(200,150,1)
GID=3 subgridId=2 minSubDim=(100,150,0) maxSubDim=(150,200,1)
GID=3 subgridId=3 minSubDim=(150,150,0) maxSubDim=(200,200,1)
AFTER initializePotts
INITIALIZING Volume
GOT HERE BEFORE CALLING INIT
INITIALIZING CellType
INITIALIZING Contact
Default constructor DiffusableVectorCommon
INITIALIZING DiffusionSolverFE

INSIDE UPDATE XML
DiffusionConstant: 0.1
DecayConstant: 1e-05
DeltaX: 1
DeltaT: 1
fieldName: FGF

diffSecrFieldTuppleVec.size()=1
concentrationFieldNameVector[i]=FGF
FIELDS THAT I HAVE
Field 0 name: FGF
DiffusionSolverFE: extra Init in read XML
registring field: FGF field address=0x7ff543c636a0
INITIALIZING BlobInitializer
radius=80 gap=0 types=Condensing,NonCondensing
GOT HERE BEFORE EXIT
SIMTHREAD= <Simulation.SimulationThread.SimulationThread object at 0x11f7efdf8>
SIMULATION FILE NAME= /Applications/CC3D_3.7.3/Demos/SimulationSettings/ParallelCC3DExamples/DynamicNumberOfProcessors/DynamicNumberOfProcessors.cc3d
EXTRACTING restartEnabled
WILL RUN SIMULATION FROM BEGINNING
, extraInit for: VolumeTracker
, extraInit for: CellTypeMonitor
, extraInit for: CellType
size=3
contact[0][0]=0
contact[0][1]=16
contact[0][2]=16
contact[1][0]=16
contact[1][1]=2
contact[1][2]=11
contact[2][0]=16
contact[2][1]=11
contact[2][2]=16
Contact maxNeighborIndex=7
typeNameMap.size()=3
, extraInit for: Contact
automaton=0x7ff543cab9d8
, extraInit for: Volume
Simulator::start(): Plugins:, VolumeTracker, CellTypeMonitor, CellType, Contact, Volume
_BLOB INIT_***
GOT HERE
itDim=(40,40,1)
Step 0 Energy 0 Cells 793
windowNames= []
self.graphicsWindowDict= {}
GOT HERE REMOVE ALL VTK
self.graphicsWindowDict= {}
len(self.subWindowList())= 0
2014-10-16 15:35:19.925 CompuCell3D[62851:507] invalid drawable
2014-10-16 15:35:19.926 CompuCell3D[62851:507] invalid drawable
pluginName = Volume
pluginName = CellType
pluginName = Contact

self.basicSimulationData= ['doc', 'init', 'module', 'fieldDim', 'numberOfSteps', 'sim']
self.basicSimulationData.fieldDim= (200,200,1)
self.basicSimulationData.numberOfSteps= 1000
self.basicSimulationData.sim= <CompuCell.Simulator; proxy of <Swig Object of type 'CompuCell3D::Simulator *' at 0x11f803d50> >
windowName= 1
after windowName= 1
AFTER setInitialCrossSection
CREATING SCREENSHOT WINDOW
2014-10-16 15:35:20.058 CompuCell3D[62851:507] invalid drawable
2014-10-16 15:35:20.060 CompuCell3D[62851:507] invalid drawable
xSize= 600 ySize= 600
ADDITIONAL SCREENSHOT WINDOW SIZE= (600, 600)
THIS IS ROOT ITEM= CompuCell3D
ROOT ITEM DOMNode= CompuCell3D
---- SimpleTabView.py: initializeSimulationViewWidget(): before TRY ACQUIRE
---- SimpleTabView.py: initializeSimulationViewWidget(): AFTER RELEASE
FAST numberOfAttempts=40000
Number of Attempted Energy Calculations=5995
Step 0 Flips 1650/40000 Energy 5845 Cells 793 Inventory=793
FAST numberOfAttempts=40000
Number of Attempted Energy Calculations=6262
Step 1 Flips 2095/40000 Energy 2260 Cells 793 Inventory=793
FAST numberOfAttempts=40000
Number of Attempted Energy Calculations=6431
Step 2 Flips 2240/40000 Energy 1569 Cells 793 Inventory=793
FAST numberOfAttempts=40000
Number of Attempted Energy Calculations=6517
Step 3 Flips 2413/40000 Energy 2123 Cells 793 Inventory=793
FAST numberOfAttempts=40000
Number of Attempted Energy Calculations=6520
Step 4 Flips 2331/40000 Energy -55 Cells 793 Inventory=793
FAST numberOfAttempts=40000
Number of Attempted Energy Calculations=6570
Step 5 Flips 2567/40000 Energy 906 Cells 793 Inventory=793
FAST numberOfAttempts=40000
Number of Attempted Energy Calculations=6664
Step 6 Flips 2508/40000 Energy 88 Cells 793 Inventory=793
FAST numberOfAttempts=40000
Number of Attempted Energy Calculations=6692
Step 7 Flips 2490/40000 Energy -307 Cells 793 Inventory=793
FAST numberOfAttempts=40000
Number of Attempted Energy Calculations=6681
Step 8 Flips 2497/40000 Energy 15 Cells 793 Inventory=793
FAST numberOfAttempts=40000
Number of Attempted Energy Calculations=6803
Step 9 Flips 2690/40000 Energy 390 Cells 793 Inventory=793
FAST numberOfAttempts=40000
Number of Attempted Energy Calculations=6724
Step 10 Flips 2588/40000 Energy -155 Cells 793 Inventory=793
PYSTEPPABLES INSIDE resizeAndShiftLattice
okFlag= True
_numberOfProcessors =4 numArrayElements=33
gridId=0 minDim=(0,0,0) maxDim=(200,200,1)
gridId=1 minDim=(200,0,0) maxDim=(400,200,1)
gridId=2 minDim=(0,200,0) maxDim=(200,400,1)
gridId=3 minDim=(200,200,0) maxDim=(400,400,1)
GID=0 subgridId=0 minSubDim=(0,0,0) maxSubDim=(100,100,1)
GID=0 subgridId=1 minSubDim=(100,0,0) maxSubDim=(200,100,1)
GID=0 subgridId=2 minSubDim=(0,100,0) maxSubDim=(100,200,1)
GID=0 subgridId=3 minSubDim=(100,100,0) maxSubDim=(200,200,1)
GID=1 subgridId=0 minSubDim=(200,0,0) maxSubDim=(300,100,1)
GID=1 subgridId=1 minSubDim=(300,0,0) maxSubDim=(400,100,1)
GID=1 subgridId=2 minSubDim=(200,100,0) maxSubDim=(300,200,1)
GID=1 subgridId=3 minSubDim=(300,100,0) maxSubDim=(400,200,1)
GID=2 subgridId=0 minSubDim=(0,200,0) maxSubDim=(100,300,1)
GID=2 subgridId=1 minSubDim=(100,200,0) maxSubDim=(200,300,1)
GID=2 subgridId=2 minSubDim=(0,300,0) maxSubDim=(100,400,1)
GID=2 subgridId=3 minSubDim=(100,300,0) maxSubDim=(200,400,1)
GID=3 subgridId=0 minSubDim=(200,200,0) maxSubDim=(300,300,1)
GID=3 subgridId=1 minSubDim=(300,200,0) maxSubDim=(400,300,1)
GID=3 subgridId=2 minSubDim=(200,300,0) maxSubDim=(300,400,1)
GID=3 subgridId=3 minSubDim=(300,300,0) maxSubDim=(400,400,1)
resetAllCameras in GraphicsFrame = <Graphics.GraphicsFrameWidget.GraphicsFrameWidget object at 0x1229b93e0>
FAST numberOfAttempts=160000
Number of Attempted Energy Calculations=6665
Step 11 Flips 2563/160000 Energy -152 Cells 793 Inventory=793
/Applications/CC3D_3.7.3/compucell3d.command: line 125: 62851 Segmentation fault: 11 ${PYTHON_EXEC} ${PREFIX_CC3D}/player/compucell3d.pyw $* --currentDir=${PREFIX_CC3D}

move "add parameter scan" away from the open simulation in player - twedit++

Event Logs

Hi!

I was wondering if CompuCell3D has a built in way of storing events (mitosis, division, growth) etc.
Are there any plugins which allow us to do this?

Also was wondering which genome expression network you recommend to use with CC3D?

Thanks

Twedit++ : Reopening displays previously opened random files

When you close twedit++ and reopen it, it has a somewhat random bunch of previously opened files in it, but these are not visible or accessible from the leftmost CC3D Project tree subwindow. They should either not open at all, or should come with their hierarchy.

Zoom button not working on windows - Fix QVTKWindowInteractor.py

Twedit++: Clicking 'Save All' jumps to main python script

When you hit "Save All" it should leave you where you were in the editor, not jump you to the main python script.

Add more config options to plots

Thing such as plots​ background, legend on off, location etc have to be easily configurable

Sent from my Motorola Moto G (4) using FastHub

Mac version build reporting

After unzipping CC3D_3.7.2_MacOSX_10.9_20140429.zip and running compucell3d.command the terminal reports:

CompuCell3D version 3.7.2
(OS X 10.8 x86_64 build)

Should be OS X 10.9 not 10.8. Either the build is being reported incorrectly, or the wrong version was packaged.

Twedit++: Creating new resources python file unable to edit names

Unable change the name of the file in a convenient way (have to hand edit everything). We need a rename function for resources.

Source: James Email with subject- 'Some issues with Twedit++'

Random Seed to Investigate Faults, Errors and Crashes

Hi,

Is there any way to obtain and fix the seed being used by the random number generator in CC3D?
I am experiencing segmentation faults , bus errors and random crashes and would like to investigate if it is due to certain seeds or a problem with the code.

Some errors I have received:
1.

END OF SIMULATION  
emiting finish request
11217.7 ms spent in solving diffusion problem
./compucell3d.command: line 125:   583 Segmentation fault: 11  ${PYTHON_EXEC} ${PREFIX_CC3D}/player/compucell3d.pyw $* --currentDir=${PREFIX_CC3D}

terminate called after throwing an instance of 'BasicException'
./compucell3d.command: line 125:  3309 Abort trap: 6           ${PYTHON_EXEC} ${PREFIX_CC3D}/player/compucell3d.pyw $* --currentDir=${PREFIX_CC3D}

./compucell3d.command: line 125:  1514 Bus error: 10           ${PYTHON_EXEC} ${PREFIX_CC3D}/player/compucell3d.pyw $* --currentDir=${PREFIX_CC3D}

./compucell3d.command: line 125:   685 Segmentation fault: 11  ${PYTHON_EXEC} ${PREFIX_CC3D}/player/compucell3d.pyw $* --currentDir=${PREFIX_CC3D}

documenting this progress at:
zafarali/metastasis#5