Compucell3d
Overview
Compucell3d is a flexible scriptable modeling environment, which allows the rapid construction of sharable Virtual Tissue in silico simulations of a wide variety of multi-scale, multi-cellular problems including angiogenesis, bacterial colonies, cancer, developmental biology, evolution, the immune system, tissue engineering, toxicology and even non-cellular soft materials.
Version 4.2.4 is installed on the CSF, via a singularity image.
Restrictions on use
There are no restrictionson access Compucell3d on the CSF.
Set up procedure
We now recommend loading modulefiles within your jobscript so that you have a full record of how the job was run. See the example jobscript below for how to do this. Alternatively, you may load modulefiles on the login node and let the job inherit these settings.
Load one of the following modulefiles:
module load apps/singularity/compucell3d/4.2.4
Running the application
Please do not run compucell3d on the login node. The GUI should be used via an interactive session (see below). Non-GUI jobs should be submitted to the compute nodes via batch.
Interactive Gui session
Please DO NOT run the compucell3d GUI on the login node. The login node is a light-weight node for job-submission and file management.
Instead please start an interactive session. This will log you in to one of the back-end compute-nodes (where batch jobs usually run) and allow you to use it as though you were at the login node. The compute nodes are more powerful – they have more memory and more CPU cores.
So please run:
# To use a single CPU core run the following on the login node qrsh -l inter # # Wait until you logged in to a backend node. # Now on the backend node module load apps/singularity/compucell3d/4.2.4 # Start the app compucell3d # # Occasionally you might be asked if you like to install a new version. # Please click No (you don't have write-permission to the install area). # Instead email its-ri-team@manchester.ac.uk to tell use a new version # is available. # You can also run these apps paramScan.sh runScript.sh twedit++.sh # When you have finished with your interactive session, to go back to the login node: exit
Serial batch job submission
Create a batch submission script (which will load the modulefile in the jobscript), for example:
#!/bin/bash --login #$ -cwd # Job will run from the current directory # NO -V line - we load modulefiles in the jobscript module load apps/singularity/compucell3d/4.2.4 runScript.sh -i INPUT args...
Submit the jobscript using:
qsub scriptname
where scriptname is the name of your jobscript.
Parallel batch job submission
Create a batch submission script (which will load the modulefile in the jobscript), for example:
#!/bin/bash --login #$ -cwd # Job will run from the current directory #$ -pe smp.pe 8 # Number of cores (can be 2--32) # NO -V line - we load modulefiles in the jobscript module load apps/singularity/compucell3d/4.2.4 # Inform python how many cores it can use export OMP_NUM_THREADS=$NSLOTS runScript.sh -i INPUT args...
Submit the jobscript using:
qsub scriptname
where scriptname is the name of your jobscript.
Further info
Updates
None.