How can I restart a simulation from the last time step ?


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16 days ago by
Is there a way to write a restart file so that the next simulation starts from the last time step. As for example the total MCS that I have to run is 24000. However, with the resource allocation, I can only run approximately 5000 steps continuously. How can I write a restart file so I can start from where I last ended the simulation. What needs to be changed in the number of steps ?

EDIT: How would I do it without the GUI just through the terminal? I was able to write restart file but am not sure how to specify to read from that particular directory when restarting the next stage of simulation. More specifically ,

./runScript.sh  -i  < input.cc3d> -o  < Output directory >   ...... < restart directory > ?
Community: CompuCell3D

1 Answer


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1 day ago by
Have you tried following the manual?

http://pythonscriptingmanual.readthedocs.io/en/latest/restarting_simulations.html?highlight=restart

If you want to restart it make sure that you remove serialization line from the .cc3d file - you can do it as shown in the manual or simply edit .ccd file so that

<Simulation version="3.6.1">
   <XMLScript Type="XMLScript">Simulation/cellsort_2D.xml</XMLScript>
   <SerializeSimulation AllowMultipleRestartDirectories="False" FileFormat="text" OutputFrequency="100"/>
   <RestartSimulation RestartDirectory="restart"/>
</Simulation>​

goes to
<Simulation version="3.6.1">
   <XMLScript Type="XMLScript">Simulation/cellsort_2D.xml</XMLScript>
   <RestartSimulation RestartDirectory="restart"/>
</Simulation>​
when you remove the serialization line.

And if you want to run from command line you type

./runScript.command -i /Users/m/CC3DProjects/restart_01600/cellsort_2D.cc3d --noOutput

See attached file. Unpack it and change /Users/m/CC3DProjects/restart_01600/cellsort_2D.cc3d to the path where you unpacked the attached file. It has complete restart snapshot and it runs both from GUI and command line


File attached: restart_01600.zip (14.76 KB)


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