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Summary

Domain

Within CompBioMed, Palabos is used for Cardio-vascular simulations.

Description

Palabos is a general library for fluid flow simulation with the lattice Boltzmann method.

Scientific articles and documentation

http://www.palabos.org/software/publications

Palabos user’s guide

http://www.palabos.org/documentation/userguide/

Computational requirements

Programming language: C++
Dependencies: MPI. Needs Python for compilation.
Memory requirements: Typical run, cardio-vascular: 200 GB of ram, distributed.
Disk requirements: Parallel I/O is not a strict requirement, but important for large runs.
Complimentary tools:

Type of software license

Open-source licence AGPLv3.0.

Performance and HPC profile

Systems on which the software is deployed

Cluster-type parallel computers of UniGe and CADMOS.

Parallelism

Type of parallelism: MPI
Scalability: Typical runs 1e2 cores. Large runs 1e5+ cores.

Mode of operation

Single parallel runs.

I/O, as relevant to CompBioMed Application Pipeline

Input

Format: STL geometry files.
Coming from:

Output

Format: Own format, vtk.
Used by: Paraview, VisIt.
Disk use: Typical cardio-vascular run: 2 TB (mostly for checkpointing).

Benchmarks and examples

Benchmarks: http://www.palabos.org/academia/usecases
Examples: http://www.palabos.org/documentation-quick

Instructions for running on dedicated platforms