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Cellular blood flow.


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


Performance and HPC profile

Systems on which the software is deployed

Cartesius @ SURFsara.


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


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


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