High Performance Computing

An underlying drive for all research in the lab is to leverage large-scale supercomputers to enable studies of an unprecedented scale.  We are developing HARVEY, a massively parallel computational fluid dynamics code, to study both the mechanisms driving disease development as well as to inform treatment planning and improve clinical care.  The potential impact of blood flow simulations on the diagnosis and treatment of patients suffering from vascular disease is tremendous. Empowering models of the full arterial tree can provide insight into diseases such as arterial hypertension and enables the study of the influence of local factors on global hemodynamics. We are developing a new, highly scalable implementation of the lattice Boltzmann method to addresses key challenges such as multiscale coupling, limited memory capacity and bandwidth, and robust load balancing in complex geometries.

In pursuit of this goal, we initially worked to scale HARVEY efficiently to 1.6 million cores of the IBM Blue Gene/Q supercomputer at Lawrence Livermore National Laboratory (LLNL).  In collaboration with Erik Draeger, William Krauss, and Tomas Oppelstrup at LLNL and John Gunnels at IBM Watson, we were able to complete the first 3D simulation of flow in the arterial network of all vessels greater than 1mm in diameter.  This work was selected as an ACM Gordon Bell Finalist in 2015 for achievement in high performance computing. Results are shown below.

Full Body

To enable simulation of this scale, we developed techniques to improve load balance, enable distributed pre-processing, and optimize memory access. At this stage, we have demonstrated near-optimal scaling on the full Sequoia supercomputer at LLNL, as shown below.

 

scaling

We are continuing to focus on the parallel computing aspect of this research.  Two main areas of emphasis are on scaling the immersed boundary model introducing both deformable cells and walls to HARVEY's capabilities and scaling the code on heterogeneous architectures such as Oak Ridge National Laboratory's GPU-based Titan supercomputer.