Software Projects: Hemocell

Contact Find a list of contact persons here.
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.
User’s guide
Scientific articles
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.
Complementary tools:
Type of software licence Limited.
Input requirements Format: XML, STL, Simple TXT.
Coming from: Initial condition generator, which is part of the framework.
Disk use: Small. Several Megabytes.
Output requirements Format: HDF5, xdmf.
Used by: ParaView, custom python scripts.
Disk use: 20-500 GB for a simulation.
Performance and HPC profile
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.
Deployed on Cartesius @ SURFsara.
Getting started
Benchmarks and examples
Instructions for running on dedicated platforms