11th Symposium

学際大規模情報基盤共同利用・共同研究拠点公募型共同研究 平成31年度採択課題

jh190040-MDJ
Kengo Nakajima (The University of Tokyo, Japan)

Physiologically realistic study of subcellular calciuc dynacics withnanoceter resolution
X. Cai, G. T. Lines, C. Jarvis, J. van den Brink, J. Langguth (Simula Research Laboratory, Norway)
A. Bda, T. Hanawa, T. Hoshino, M. Matsumoto (The University of Tokyo, Japan), M. Kawai (RBKEN R-CCS, Japan)

Motivation
Cardiac diseases can degrade the micro-anatomical structures incardiac muscle cells responsible for the excitation-contraction (EC)
coupling, which is vital for the functioning of the heart. In silico
experiments (computer simulations) are important for studying
the structure-functional relationships of EC coupling and thefunctional impacts of disease-driven structural remodeling, e.g.,disintegration of calcium release units, as well as changes in thenumber and distribution of calcium release channels.

Results obtained in FY2018
1. OpenMP parallelization added to the old MPI-only simulator.
MPI communication
Diffusion comp.
Reaction comp.
Increment comp.
Whole simulation

OpenMP

Average per MPI
process

Max per MPI
process

Min per MPI
process

N/A
31.17
16.86
12.21
64.05

25.69
27.18
14.50
3.94
79.70

27.78
29.57
15.46
4.68
79.76

3.56
25.58
14.34
3.45
79.60

2. Reduction of memory footprint by adopting a lookup table forthe diffusion computation involved, instead of using 3D arrays ofcoefficients. The saving of memory usage is more than 50%.
int di = domain_ids[xi][yi][zi];int di_xm = domain_ids[xi-1][yi][zi], di_xp = domain_ids[xi+1][yi][zi];int di_ym = domain_ids[xi][yi-1][zi], di_yp = domain_ids[xi][yi+1][zi];int di_zm = domain_ids[xi][yi][zi-1], di_zp = domain_ids[x][yi][zi+1];
du[xi][yi][zi] = (lookup[di][di_xm]*(u[xi-1][yi][zi]-u[xi][yi][zi])+ lookup[di][di_xp]*(u[xi+1][yi][zi]-u[xi][yi][zi])+ lookup[di][di_ym]*(u[xi][yi-1][zi]-u[xi][yi][zi])+ lookup[di][di_yp]*(u[xi][yi+1][zi]-u[xi][yi][zi])+ lookup[di][di_zm]*(u[xi][yi][zi-1]-u[xi][yi][zi])+ lookup[di][di_zp]*(u[xi][yi][zi+1]-u[xi][yi][zi]))/h/h*dt;

The pipeline fop studying the stpuctupe-functional pelationships of EC coupling in the heapt
and the effects of disease-dpiven pemodeling

3. Explicit code vectorization using AVX-512 intrinsics, applied tothe diffusion and reaction computations. (Experiments show thatcompiler-enabled auto vectorization is not sufficiently effective.)

4. Quantitative study of the impact of SR load (model validation).
A schematic ovepview of a sapcomepe (1/50 of a capdiac cell) and a calcium pelease unit

Challenges & goals
In each heart cell, there are about 10,000 calcium release units,with structural details down to the nanometer scale. Extremely
high spatial and temporal resolutions are thus needed to solve theinvolved differential equations, leading to huge computations that
require efficient use of supercomputers.
In this project, we aim to enable subcellular calcium dynamics
simulations with physiological realism. This requires (1) using data
provided by 3D super-resolution microscopy and (2) simulating alarge number of calcium release units together. The challenges
include hardware-compatible optimizations of an old 3D simulatorof subcellular calcium dynamics, plus calibration and validation of
the mathematical model and the parameters.
This project will help to consolidate a multi-scale mathematicalmodel that gives a physiologically accurate description of healthy
and pathological calcium releases, thus advancing the current
scientific understanding of subcellular calcium dynamics. The workon optimizing the subcellular simulator for Oakforest-PACS will
also produce new knowledge about coding multiple inter-tangled
stencil computations for the Knights Landing architecture.

5. Medium-scale simulations involving many calcium release units.

Plan for FY2019
We will continue with the following activities in FY2019:• Verification of the single-processor-core SIMD performance• Profiling and optimization of the MPI communication• Performance tuning of the hybrid MPI+OpenMP code
• Further validation of the mathematical model• Large and extreme-scale simulations on Oakforest-PACS• Experiments with high-speed file cache systems
学際大規模情報基盤共同利用・共同研究拠点 第11回シンポジウム
2019年 7月 11日，12日

THE GRAND HALL （品川）