How to make parameter scans using Chaste

+1 vote
37 views
asked Oct 23, 2017 by J-H Plank (440 points)
retagged Oct 23, 2017 by J-H Plank

Dear all,

I'm using the Heart component of Chaste. For my Master Thesis I want to do parameter scans for some simulations. What is the best way to do so in Chaste?

Thanks in advance for any answers!

Jan-Hendrik

Remark: This question was also asked to the mailing list (20.10.2017 "Some questions concerning using Chaste Heart")

1 Answer

+1 vote
answered Oct 23, 2017 by fcooper (390 points)

The typical way to do this would be to create a standalone executable that accepts command line arguments and can be scripted from a language such as Python.

This wiki page has information on how to build an executable "app" using the Chaste build system:
https://chaste.cs.ox.ac.uk/trac/wiki/ChasteGuides/BuildingExecutableApps

I am not sure if there are any cardiac pitfalls to my next suggestion (which I use for cell_based applications), but there is an incomplete wiki page here:
https://chaste.cs.ox.ac.uk/trac/wiki/ChasteGuides/DistributingCellBasedExecutables

which contains a barebones example of a C++ executable using boost::program_options, being driven by a python script using the multiprocessing module to distribute executable runs in parallel. I usually send a sequentially increasing integer as a command line argument, which is used in the directory name to ensure uniqueness, and also as a random seed, if needed.

commented Oct 23, 2017 by GaryM (940 points)

Yep - compiled tests can also access command line arguments using the CommandLineArguments class.

commented Nov 8, 2017 by J-H Plank (440 points)

Thanks a lot for your answers! Unfortunately I haven't found the time to try it yet.

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