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

References:

• Julio M. Multi-Scale Modeling of Tissues Using CompuCell3D. Computational Methods in Cell Biology, Methods in Cell Biology 110: 325-366 (2012)

• CompuCell3D Github Site
• CompuCell3D Main Site

This application requires a graphical connection using NX

• Module Name: CompuCell3D (see the modules page for more information)
• Multithreaded/singlethreaded/MPI...
• This application produces HTML reports. You can use hpcdrive to view these reports on your local workstation.
• Environment variables set
  • TEMPLATE_HOME
• Example files in ???
• Reference data in /fdb/TEMPLATE/

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load CompuCell3D

#run CC3D without GUI
[user@cn3144 ~]$ python -m cc3d.run_script
usage: run_script.py [-h] -i INPUT [-c OUTPUT_FILE_CORE_NAME] [--current-dir CURRENT_DIR] [-o OUTPUT_DIR] [-f OUTPUT_FREQUENCY]
                     [-fs SCREENSHOT_OUTPUT_FREQUENCY] [-fr RESTART_SNAPSHOT_FREQUENCY] [--restart-multiple-snapshots]
                     [--parameter-scan-iteration PARAMETER_SCAN_ITERATION]
                     [--log-level {,FATAL,CRITICAL,ERROR,WARNING,NOTICE,INFORMATION,DEBUG,TRACE,CURRENT}] [--log-to-file]
run_script.py: error: the following arguments are required: -i/--input 


#run CC3D with GUI in NX
[user@cn3144 ~]$  cc3d-player5 

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. TEMPLATE.sh). For example:

#!/bin/bash
set -e
module load CompuCell3D
TEMPLATE < TEMPLATE.in > TEMPLATE.out

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#] TEMPLATE.sh

Create a swarmfile (e.g. TEMPLATE.swarm). For example:

TEMPLATE < TEMPLATE.in > TEMPLATE.out
TEMPLATE < TEMPLATE.in > TEMPLATE.out
TEMPLATE < TEMPLATE.in > TEMPLATE.out
TEMPLATE < TEMPLATE.in > TEMPLATE.out

Submit this job using the swarm command.

swarm -f TEMPLATE.swarm [-g #] [-t #] --module TEMPLATE