Each week on the InSilico World and CompBioMed Slack Scalability channel one of our research group outlines the work that they have done to scale their codes. We are happy that 60 experts have already joined this channel and we would like more interaction and discussions taking place on the channel around the codes being described and more general help and advice for our members. Here we give a short outline of each of these codes and we hope it encourages people to view the full posts on the channel and increase the discussions in this field.
The second post was on December 14th, in which Jonas Lätt from University of Geneva posted information on the Palabos software library, its use in computational biology, and their methodology used to approach exascale performance.
Palabos is a fluid simulation software with emphasis on multi-scale and multi-physics simulations . It is based on the Lattice-Boltzmann method, which is known to preserve massively parallel performance even when tackling complex physical couplings. The addressed cases of complex physics include fully resolved porous media, which may be used to understand mechanical properties of blood clots, and the coupling of fluid flow with rigid or deformable solid components, which offer for example a detailed view on blood constituents.
Parallelization of the Palabos algorithms is managed within a highly scalable framework which includes all stages of the simulation workflow, including pre-processing, simulation, and post-processing, and as such avoids bottlenecks frequently occurring when preparing or analyzing the large data sets manipulated by massively parallel simulation codes. Palabos has been traditionally developed for large parallel CPU systems and is parallelized with MPI, both within a computational node and across nodes…
For the full report and all references, please join and access the InSilico World and CompBioMed Slack Scalability channel by following the link.