Contacts

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Summary

Domain

Cancer, Heart And Soft Tissue Environment.

Description

Electrophysiology solver using FEM. Highly scalable parallel code.

Scientific articles and documentation

 

Chaste user’s guide

 

Computational requirements

Programming language: C++
Dependencies: ParMETIS, Scons, PETSC
Memory requirements:
Disk requirements: Parallel writing, reading files (10-30 GB of data) and writing files (50GB-200GB) per simulation.
Complimentary tools:

Type of software license

Open source.

Performance and HPC profile

Systems on which the software is deployed

Archer

Parallelism

Type of parallelism: MPI.
Scalability: Typical runs 720 cores / 30 nodes. Large runs 1080 cores / 45 nodes.

Mode of operation

Multiple independent runs, one per scenario.

I/O, as relevant to CompBioMed Application Pipeline

Input

Format: Binary meshes.
Coming from: CG-scan segmentation.
Disk use: Several files, total of 10-30 GB.

Output

Format: HDF5, VTK.
Used by: ParaView, Matlab.
Disk use: Optional output format. Between 50 and 200 GB.

Benchmarks and examples

Instructions for running on dedicated platforms