Contacts

Find a list of contact persons here.

Summary

Domain

Cellular blood flow.

Description

An extensible HPC framework to simulate the flows of dense cellular suspensions. Extension modules include different cell material models, advection-diffusion of additional biochemical agents, platelet binding formation mechanisms.

Scientific articles and documentation

 

Hemocell user’s guide

 

Computational requirements

Programming language: C++, Python
Dependencies: CMake, metis, MPI, OpenMP, HDF5, Palabos (Eigen)
Memory requirements: 10-90 GB.
Disk requirements: A simulation checkpoint is ~2-3 GB. A typical full output is ~20-500 GB.
Complimentary tools:

Type of software license

Limited.

Performance and HPC profile

Systems on which the software is deployed

Cartesius @ SURFsara.

Parallelism

Type of parallelism: MPI for the simulation run, OpenMP for initialization.
Scalability: Typical runs 72 cores / 3 nodes. Large runs 768 cores cores / 32 nodes.

Mode of operation

Generation of initial conditions happen on single nodes using OpenMP parallelism. The actual simulation runs on up to 32 nodes. A typical investigation consists of about a dozen simulations.

I/O, as relevant to CompBioMed Application Pipeline

Input

Format: XML, STL, Simple TXT.
Coming from: Initial condition generator, which is part of the framework.
Disk use: Small. Several Megabytes.

Output

Format: HDF5, xdmf.
Used by: ParaView, custom python scripts.
Disk use: 20-500 GB for a simulation.

Benchmarks and examples

Instructions for running on dedicated platforms