# Xing Cai

External collaborator

## Publications

Simula-affiliated publications listed

### 2023

#### Journal Articles

Å. Telle, J. D. Trotter, X. Cai, H. Finsberg, M. Kuchta, J. Sundnes and S. Wall

A cell-based framework for modeling cardiac mechanics

Biomechanics and Modeling in Mechanobiology

Å. Telle, J. D. Trotter, X. Cai, H. Finsberg, M. Kuchta, J. Sundnes and S. Wall

A cell-based framework for modeling cardiac mechanics

Biomechanics and Modeling in Mechanobiology

A. Thune, S. Reinemo, T. Skeie and X. Cai

Detailed Modeling of Heterogeneous and Contention-Constrained Point-to-Point MPI Communication

IEEE Transactions on Parallel and Distributed Systems

L. Burchard, K. G. Hustad, J. Langguth and X. Cai

Enabling unstructured-mesh computation on massively tiled AI processors: An example of accelerating in silico cardiac simulation

Frontiers in Physics

J. D. Trotter, J. Langguth and X. Cai

Targeting performance and user-friendliness: GPU-accelerated finite element computation with automated code generation in FEniCS

Parallel Computing

### 2022

#### Journal Articles

J. D. Trotter, X. Cai and S. W. Funke

On memory traffic and optimisations for low-order finite element assembly algorithms on multi-core CPUs

ACM Transactions on Mathematical Software

K. G. Hustad and X. Cai

Resource-efficient use of modern processor architectures for numerically solving cardiac ionic cell models

Frontiers in Physiology

#### Talks, contributed

Å. Telle, J. D. Trotter, X. Cai, M. Kuchta, H. Finsberg, J. Sundnes and S. Wall

Modeling cardiac mechanics using a cell-based framework

15th World Congress on Computational Mechanics (WCCM-XV), Yokohama, Japan

### 2021

#### Journal Articles

K. H. Jæger, K. G. Hustad, X. Cai and A. Tveito

Efficient numerical solution of the EMI model representing the extracellular space (E), cell membrane (M) and intracellular space (I) of a collection of cardiac cells

Frontiers in Physics

A. Thune, X. Cai and A. B. Rustad

On the impact of heterogeneity-aware mesh partitioning and non-contributing computation removal on parallel reservoir simulations

Journal of Mathematics in Industry

#### Proceedings, refereed

L. Burchard, X. Cai and J. Langguth

iPUG for multiple Graphcore IPUs: Optimizing performance and scalability of parallel breadth-first search

28th IEEE International Conference on High Performance Computing, Data, & Analytics (HiPC)

#### Book Chapters

K. H. Jæger, K. G. Hustad, X. Cai and A. Tveito

Operator Splitting and Finite Difference Schemes for Solving the EMI Model

Modeling Excitable Tissue: The EMI Framework

#### Posters

J. D. Trotter, J. Langguth and X. Cai

Automated Code Generation for GPU-Based Finite Element Computations in FEniCS

### 2020

#### Journal Articles

J. D. Trotter, J. Langguth and X. Cai

Cache simulation for irregular memory traffic on multi-core CPUs: Case study on performance models for sparse matrix–vector multiplication

Journal of Parallel and Distributed Computing

#### Posters

K. G. Hustad, X. Cai, J. Langguth and H. Arevalo

Efficient simulations of patient-specific electrical heart activity on the DGX-2

J. Langguth, N. Gaur, H. Arevalo, C. Jarvis, N. Altanaite, Q. Lan and X. Cai

Towards detailed Organ-Scale Simulations in Cardiac Electrophysiology

#### Talks, invited

X. Cai

On parallel simulation of porous media flow

Schlumberger Eureka Applied Math Special Interest Group Meeting

### 2019

#### Journal Articles

J. Lagravière, J. Langguth, M. Prugger, L. Einkemmer, P. H. Ha and X. Cai

Performance optimization and modeling of fine-grained irregular communication in UPC

Scientific Programming

#### Proceedings, refereed

C. Jarvis, G. T. Lines, J. Langguth, K. Nakajima and X. Cai

Combining algorithmic rethinking and AVX-512 intrinsics for efficient simulation of subcellular calcium signaling

International Conference on Computational Science (ICCS 2019)

J. Langguth, H. Arevalo and X. Cai

Towards Detailed Real-Time Simulations of Cardiac Arrhythmia

Computing in Cardiology

#### Posters

J. Langguth, H. Arevalo, K. G. Hustad and X. Cai

Towards Detailed Real-Time Simulations of Cardiac Arrhythmia

#### Talks, invited

X. Cai

Heterogeneous computing for cardiac electrophysiology

PREAPP workshop on Efficient Frameworks for Compute- and Data-intensive Computing (EFFECT), University of Tromsø, Norway

X. Cai

Unstructured computational meshes and data locality

Fifth Workshop on Programming Abstractions for Data Locality (PADAL'19), Inria Bordeaux, France

X. Cai

Use of modern processor architectures for computing the electrical activity in the heart

Schlumberger Eureka Applied Math Special Interest Group Meeting

#### Talks, contributed

A. Thune and X. Cai

Balancing the numerical and parallel performance for reservoir simulations

SIAM Conference on Computational Science and Engineering (CSE19), Spokane, Washington, USA

J. D. Trotter, X. Cai, S. W. Funke and J. Langguth

Compiling finite element variational forms for GPU-based assembly

FEniCS‘19, Washington DC, USA

### 2018

#### Proceedings, refereed

J. Langguth, M. Sourouri and X. Cai

Memory Bandwidth Contention: Communication vs Computation Tradeoffs in Supercomputers with Multicore Architectures

International Conference on Parallel and Distributed Systems (ICPADS)

#### Posters

J. D. Trotter

Quantifying data traffic of sparse matrix-vector multiplication in a multi-level memory hierarchy

J. Langguth, H. Arevalo, C. Jarvis and X. Cai

Towards Detailed Organ-Scale Simulations in Cardiac Electrophysiology

#### Talks, invited

X. Cai

Heterogeneous Computing: Programming, Performance and Applications

CoSaS 2018 Symposium, Erlangen, Germany

#### Talks, contributed

X. Cai

Education in HPC and Data Science at Simula Research Lab and UiO

SUPERDATA Workshop on curriculum development, Yunan, China

A. Thune and X. Cai

Unstructured mesh partitioning in the presence of strong coefficient heterogeneity

PDESoft 2018 Conference, Bergen, Norway

### 2017

#### Proceedings, refereed

G. Y. Paulsen, S. Clark, B. Nordmoen, S. Nenakhov, A. Andersson, X. Cai and H. P. Dahle

Automated Translation of MATLAB Code to C++ with Performance and Traceability

The Eleventh International Conference on Advanced Engineering Computing and Applications in Sciences (ADVCOMP 2017)

J. Langguth, C. Jarvis and X. Cai

Porting Tissue-Scale Cardiac Simulations to the Knights Landing Platform

International Conference on High Performance Computing

#### Talks, keynote

X. Cai and J. Langguth

Accelerated high-performance computing for computational cardiac electrophysiology

The University of Tokyo, Tokyo, Japan

#### Talks, contributed

J. Langguth, X. Cai and J. Chai

Heterogeneous Manycore Simulations in Cardiac Electrophysiology

Tenth International Workshop on Programmability and Architectures for Heterogeneous Multicores (MULTIPROG-2017), Stockholm, Sweden

### 2016

#### Journal Articles

J. Langguth, Q. Lan, N. Gaur and X. Cai

Accelerating Detailed Tissue-Scale 3D Cardiac Simulations Using Heterogeneous CPU-Xeon Phi Computing

International Journal of Parallel Programming

M. Sourouri, S. Baden and X. Cai

Panda: A Compiler Framework for Concurrent CPU+GPU Execution of 3D Stencil Computations on GPU-accelerated Supercomputers

International Journal of Parallel Programming

W. Zhang and X. Cai

Solving 3D Time-Fractional Diffusion Equations by High-Performance Parallel Computing

Fractional Calculus and Applied Analysis

#### Proceedings, refereed

J. Langguth, Q. Lan, N. Gaur, X. Cai and M. Wen

Enabling Tissue-Scale Cardiac Simulations Using Heterogeneous Computing on Tianhe-2

IEEE 22nd International Conference on Parallel and Distributed Systems (ICPADS)

G. Y. Paulsen, J. Feinberg, X. Cai and B. Nordmoen

Matlab2cpp: A Matlab-to-C++ code translator

IEEE 2016 11th System of Systems Engineering Conference (SoSE)

J. Lagravière, J. Langguth, M. Sourouri and X. Cai

On the Performance and Energy Efficiency of the PGAS Programming Model on Multicore Architectures

High Performance Computing & Simulation (2016) - International Workshop on Optimization of Energy Efficient HPC & Distributed Systems

### 2015

#### Journal Articles

H. Su, X. Cai, M. Wen and C. Zhang

An Analytical GPU Performance Model for 3D Stencil Computations from the Angle of Data Traffic

The Journal of Supercomputing

X. Dong, M. Wen, J. Chai, X. Cai, M. Zhao and C. Zhang

Communication-Hiding Programming for Clusters with Multi-Coprocessor Nodes

Concurrency and Computation: Practice and Experience

D. Huang, C. Xun, N. Wu, M. Wen, C. Zhang, X. Cai and Q. Yang

Enabling a Uniform OpenCL Device View for Heterogeneous Platforms

IEICE Transactions on Information and Systems

J. Langguth, N. Wu, J. Chai and X. Cai

Parallel performance modeling of irregular applications in cell-centered finite volume methods over unstructured tetrahedral meshes

Journal of Parallel and Distributed Computing

J. Langguth, M. Sourouri, G. T. Lines, S. Baden and X. Cai

Scalable heterogeneous CPU-GPU computations for unstructured tetrahedral meshes

IEEE Micro

J. Chai, J. E. Hake, N. Wu, M. Wen, X. Cai, G. T. Lines, J. Yang, H. Su, C. Zhang and X. Liao

Towards Simulation of Subcellular Calcium Dynamics at Nanometre Resolution

International Journal of High Performance Computing Applications

#### Proceedings, refereed

M. Sourouri, J. Langguth, F. Spiga, S. Baden and X. Cai

CPU+GPU Programming of Stencil Computations for Resource-Efficient Use of GPU Clusters

IEEE 18th International Conference on Computational Science and Engineering

E. Krishnasamy, M. Sourouri and X. Cai

Multi-GPU Implementations of Parallel 3D Sweeping Algorithms with Application to Geological Folding

ICCS 2015

Q. Lan, N. Gaur, J. Langguth and X. Cai

Towards Detailed Tissue-Scale 3D Simulations of Electrical Activity and Calcium Handling in the Human Cardiac Ventricle

The 15th International Conference on Algorithms and Architectures for Parallel Processing (ICA3PP 2015)

#### Book Chapters

X. Cai

Parallel Computing

Encyclopedia of Applied and Computational Mathematics

#### Posters

N. Gaur, X. Cai and Y. Rudy

Dysfunctional Sarcoplasmic Reticulum Ca2+ Release Underlies Arrhythmogenic Triggers in Catecholaminergic Polymorphic Ventricular Tachycardia: A Simulation Study in a Human Ventricular Myocyte Model

Gordons Research Conference on Cardiac Arrhythmia

#### Technical reports

J. Lagravière, P. H. Ha and X. Cai

Is PGAS ready for the challenge of energy efficiency? A study with the NAS benchmark.

### 2014

#### Journal Articles

M. Wen, H. Su, W. Wei, N. Wu, X. Cai and C. Zhang

High Efficient Sedimentary Basin Simulations on Hybrid CPU-GPU Clusters

Cluster Computing

W. Zhang, W. Wei and X. Cai

Performance Modeling of Serial and Parallel Implementations of the Fractional Adams-Bashforth-Moulton Method

Fractional Calculus and Applied Analysis

W. Zhang, X. Cai and S. Holm

Time-Fractional Heat Equations and Negative Absolute Temperatures

Computers & Mathematics with Applications

#### Proceedings, refereed

D. Huang, M. Wen, C. Xun, D. Chen, X. Cai, Y. Qiao, N. Wu and C. Zhang

Automated Transformation of GPU-Specific OpenCL Kernels Targeting Performance Portability on Multi-Core/Many-Core CPUs

Proceedings of Euro-Par 2014

M. Sourouri, T. Gillberg, S. Baden and X. Cai

Effective Multi-GPU Communication Using Multiple CUDA Streams and Threads

20th International Conference on Parallel and Distributed Systems (ICPADS 2014)

J. Langguth and X. Cai

Heterogeneous CPU-GPU Computing for the Finite Volume Method on 3D Unstructured Meshes

20th International Conference on Parallel and Distributed Systems (ICPADS 2014)

X. Dong, J. Chai, J. Yang, M. Wen, N. Wu, X. Cai, C. Zhang and Z. Chen

Utilizing Multiple Xeon Phi Coprocessors on One Compute Node

International Conference on Algorithms and Architectures for Parallel Processing

#### Posters

N. Gaur, X. Cai and Y. Rudy

Cellular Arrhythmogenesis in CPVT in a Computational Model of Cardiac Ventricular Myocyte

N. Gaur, X. Cai and Y. Rudy

Cellular Arrhythmogenesis in CPVT in a computational model of cardiac ventricular myocyte

N. Gaur, X. Cai and Y. Rudy

Spontaneous Ca2+ Release and Ca2+ Waves Underlie Early and Delayed Afterdepolarizations, and Triggered Activity in Ryanodine Receptor Mutation associated with Catecholaminergic Polymorphic Ventricular Tachycardia

N. Gaur, X. Cai and Y. Rudy

Spontaneous Ca2+ Release and Ca2+ Waves Underlie Early and Delayed Afterdepolarizations, and Triggered Activity, in Ryanodine Receptor Mutations Associated With Catecholaminergic Polymorphic Ventricular Tachycardia

#### Talks, contributed

N. Gaur, X. Cai and Y. Rudy

Arrhythmogenic Mechanisms and Therapeutic Targets for Catecholaminergic Polymorphic Ventricular Tachycardia: A Simulation Study in a Human Ventricular Myocyte

Simula Research Laboratory

N. Gaur, X. Cai and Y. Rudy

Mathematical Modeling of Ca Handling and Computational Studies of Ca-related Arrhythmogenesis in Heart

National University of Defense Technology, China

#### Public outreach

X. Cai, J. E. Hake and G. T. Lines

Supercomputing-Enabled Study of Subcellular Calcium Dynamics

### 2013

#### Journal Articles

W. Wei, S. Clark, H. Su, M. Wen and X. Cai

Balancing Efficiency and Accuracy for Sediment Transport Simulations

Computational Science & Discovery

J. Chai, H. Su, M. Wen, X. Cai, N. Wu and C. Zhang

Resource-Efficient Utilization of CPU/GPU-Based Heterogeneous Supercomputers for Bayesian Phylogenetic Inference

The Journal of Supercomputing

J. Chai, M. Wen, N. Wu, D. Huang, J. Yang, X. Cai, C. Zhang and Q. Yang

Simulating Cardiac Electrophysiology in the Era of GPU-Cluster Computing

IEICE Transactions on Information and Systems

#### Proceedings, refereed

H. Su, N. Wu, M. Wen, C. Zhang and X. Cai

On the GPU Performance of 3D Stencil Computations Implemented in OpenCL

Proceedings of International Supercomputing Conference, ISC 2013

J. Langguth, N. Wu, J. Chai and X. Cai

On the GPU Performance of Cell-Centered Finite Volume Method Over Unstructured Tetrahedral Meshes

Proceedings of the 3rd Workshop on Irregular Applications: Architectures and Algorithms

H. Su, N. Wu, M. Wen, C. Zhang and X. Cai

On the GPU-CPU Performance Portability of OpenCL for 3D Stencil Computations

Proceedings of IEEE 19th International Conference on Parallel and Distributed Systems

H. Su, N. Wu, M. Wen, C. Zhang and X. Cai

Performance of Sediment Transport Simulations on NVIDIA's Kepler Architecture

The International Conference on Computational Science, ICCS 2013

#### Talks, invited

X. Cai

Adopting Heterogeneous Hardware Platforms for Scientific Computing

Guest lecture at Technical Unviersity of Denmark, December 5

X. Cai

Introduction to Scientific Writing

Intensive course given at National University of Defence Technology, China, October 17-19

X. Cai

Scientific Computing on Accelerator-Based Supercomputers

Guest lecture at FFI, September 20

#### Talks, contributed

X. Cai, D. Unat and S. Baden

Mint: a User-Friendly C-to-CUDA Code Translator

Talk given at SIAM CSE'13, February 25

### 2012

#### Journal Articles

D. Unat, J. Zhou, Y. Cui, S. Baden and X. Cai

Accelerating a 3D Finite-Difference Earthquake Simulation With a C-to-CUDA Translator

Computing in Science & Engineering

#### Proceedings, refereed

T. Gillberg, M. Sourouri and X. Cai

A New Parallel 3D Front Propagation Algorithm for Fast Simulation of Geological Folds

The International Conference on Computational Science, ICCS 2012

W. Zhang and X. Cai

Efficient Implementations of the Adams-Bashforth-Moulton Method for Solving Fractional Differential Equations

Proceedings of FDA'12

M. Wen, H. Su, W. Wei, N. Wu, X. Cai and C. Zhang

Using 1000+ GPUs and 10000+ CPUs for Sedimentary Basin Simulations

Proceedings of IEEE Cluster 2012

#### Talks, invited

G. T. Lines and X. Cai

Elements of Scientific Computing

3-day intensive course given at National University of Defence Technology, China, October 16-18

X. Cai

Scientific Computing Needs Supercomputers, But Also Something Else!

Invited lecture at National University of Defence Technology, China, March 29

#### Talks, contributed

X. Cai

Some Perspectives on High-Performance Computing in the Geosciences

Computational Geoscience Workshop, Geilo, January 19

X. Cai

Understanding the Performance of Stencil-Based Computations on Multicore CPU

CBC Seminar series

#### Public outreach

X. Cai and M. Wen

Simulating Basin Evolution on GPU-Enhanced Hybrid Supercomputers

### 2011

#### Journal Articles

M. Hanslien, R. Artebrant, A. Tveito, G. T. Lines and X. Cai

Stability of Two Time-Integrators for the Aliev-Panfilov System

International Journal of Numerical Analysis and Modeling

#### Proceedings, refereed

W. Wei, O. Al-Khayat and X. Cai

An OpenMP-Enabled Parallel Simulator for Particle Transport in Fluid Flows

Proceedings of the International Conference on Computational Science, ICCS 2011

D. Unat, X. Cai and S. Baden

Mint: Realizing CUDA Performance in 3D Stencil Methods With Annotated C

Proceedings of the 25th International Conference on Supercomputing (ICS'11)

#### Talks, invited

X. Cai

Parallel Simulation of Particle Transport Using OpenMP

Guest lecture at UCSD on January 31

X. Cai

Programming With OpenMP and Mixed MPI-OpenMP

Invited lecture at pre-conference workshop of NOTUR 2011

X. Cai

Programming With OpenMP and Mixed MPI-OpenMP

Invited lecture during USIT's Research Computing Services training week, November 14-17

#### Talks, contributed

X. Cai

A Function-Centric Generic Framework for Parallelization

Talk at CLS Workshop at UiO on April 13

X. Cai and W. Zhang

Efficient Computations of Initial-Value Problems Involving Fractional Derivatives

Talk at the seminar on wave propagation in complex media, November 23

X. Cai

Study of the Computational Efficiency for Different Usages of Pythoning

Talk at CLS Workshop at UiO on April 13

### 2010

#### Journal Articles

P. Li, W. Wei, X. Cai, C. Soeller, M. Cannell and A. V. Holden

Computational Modeling of the Initiation and Development of Spontaneous Intracellular Ca2+ Waves in Ventricular Myocytes

Philosophical Transactions of the Royal Society A

J. K. Nilsen, X. Cai, B. Høyland and H. P. Langtangen

Simplifying the Parallelization of Scientific Codes by a Function-Centric Approach in Python

Computational Science & Discovery

#### Books

A. Tveito, H. P. Langtangen, B. F. Nielsen and X. Cai

Elements of Scientific Computing

#### Proceedings, refereed

S. Clark, W. Wei and X. Cai

Numerical Analysis of a Dual-Sediment Transport Model Applied to Lake Okeechobee, Florida

Proceedings of the 2010 Ninth International Symposium on Parallel and Distributed Computing

#### Book Chapters

J. T. C. Yeh, X. Cai, H. P. Langtangen, J. Zhu and C. Ni

Parallel Computing Engines for Subsurface Imaging Technologies

Advanced Computational Infrastructures for Parallel and Distributed Adaptive Applications

#### Talks, invited

X. Cai

A Non-Invasive Approach to Parallelizing Sequential Simulators of Partial Differential Equations

Guest lecture at UCSD on October 28

#### Talks, contributed

X. Cai, D. Unat and S. Baden

Detailed Numerical Analyses of the Aliev-Panfilov Model on GPGPU

Talk at PARA2010 Conference

W. Wei and X. Cai

OpenMP: an Easy Parallel Approach for Scientific Computing on Multi-Core Architecture

A short course respectively given at Simula in March and University of Oslo in May

D. Unat, X. Cai and S. Baden

Optimizing the Aliev-Panfilov Model of Cardiac Excitation on Heterogeneous Systems

Talk at Para 2010: State of the Art in Scientific and Parallel Computing in Reykjavik on June 6-9, 2010

X. Cai

Parallel Programming Using Python

CBC Seminar on advanced use of Python programming language

### 2009

#### Journal Articles

N. Bouhmala and X. Cai

A Multilevel Approach for the Satisfiability Problem

ISAST Transactions on Computers and Intelligent Systems

W. Chen, X. Zhang and X. Cai

A Study on Modified Szabo's Wave Equation Modeling of Frequency-Dependent Dissipation in Ultrasonic Medical Imaging

Physica Scripta

J. Zhu, X. Cai and J. T. C. Yeh

Analysis of Tracer Tomography Using Temporal Moments of Tracer Breakthrough Curves

Advances in Water Resources

B. F. Nielsen, X. Cai, J. Sundnes and A. Tveito

Towards a Computational Method for Imaging the Extracellular Potassium Concentration During Regional Ischemia

Mathematical Biosciences

#### Proceedings, refereed

P. Li, W. Wei, X. Cai, C. Soeller, M. Cannell and A. V. Holden

Evolution of Intracellular Ca2+ Waves From About 10,000 RyR Clusters: Towards Solving a Computationally Daunting Task

The Fifth International Conference on Functional Imaging and Modeling of the Heart

#### Book Chapters

A. Logg, H. P. Langtangen and X. Cai

Past and Future Perspectives on Scientific Software

Simula Research Laboratory - by thinking constantly about it

#### Posters

W. Wei, S. Clark, X. Cai and A. M. Bruaset

Parallel Simulation of Dual Lithology Sedimentation

### 2008

#### Journal Articles

J. T. C. Yeh, C. Lee, K. Hsu, W. A. Illman, W. Barrash, X. Cai, J. Daniels, E. Sudicky, L. Wan, G. Li and C. L. Winter

A View Toward the Future of Subsurface Characterization: CAT Scanning Groundwater Basins

Water Resources Research

#### Proceedings, refereed

H. P. Langtangen and X. Cai

On the Efficiency of Python for High-Performance Computing: a Case Study Involving Stencil Updates for Partial Differential Equations

Modeling, Simulation and Optimization of Complex Processes

#### Book Chapters

N. Bouhmala and X. Cai

A Multilevel Greedy Algorithm for the Satisfiability Problem

Advances in Greedy Algorithms

#### Edited books

X. Cai and J. T. C. Yeh

Quantitative Information Fusion for Hydrological Sciences

#### Talks, contributed

X. Cai

High-Performance Computing on Distributed-Memory Architecture

Lecture at the 2008 Winter School on Parallel Computing, Jan. 20-25, Geilo, Norway

X. Cai

Parallel Computing; Why & How?

Lecture at the 2008 Winter School on Parallel Computing, Jan. 20-25, Geilo, Norway

X. Cai

Resource-Efficient Simulation Of Tsunami Wave Propagation on Parallel Computers

Invited talk at 2nd Internationsal Symposium for Integrated Predictive Simulation System for Earthequake and Tsunami Disaster, October 21-22, Tokyo, Japan

X. Cai

Simulation of Tsunami Propagation

Talk at the 2nd eScience Meeting, Jan. 21-22, Geilo, Norway

X. Cai

Use of Advanced Computing in Tomographic Surveys

Talk at PARA 2008, May 13-16, Trondheim, Norway

### 2007

#### Journal Articles

X. Cai, B. F. Nielsen and A. Tveito

A Note on the Efficiency of the Conjugate Gradient Method for a Class of Time-Dependent Problems

Numerical Linear Algebra with Applications

X. Cai and N. Bouhmala

A Unified Framework of Multi-Objective Cost Functions for Partitioning Unstructured Finite Element Meshes

Applied Mathematical Modelling

K. Mardal, B. F. Nielsen, X. Cai and A. Tveito

An Order Optimal Solver for the Discretized Bidomain Equations

Numerical Linear Algebra with Applications

B. F. Nielsen, X. Cai and O. M. Lysaker

On the Possibility for Computing the Transmembrane Potential in the Heart With a One Shot Method; an Inverse Problem

Mathematical Biosciences

#### Proceedings, refereed

X. Cai and H. P. Langtangen

Making Hybrid Tsunami Simulators in a Parallel Software Framework

International Workshop on Applied Parallel Computing (PARA'06)

J. B. Haga, A. M. Bruaset, X. Cai, H. P. Langtangen, H. Osnes and J. Skogseid

Parallelisation and Numerical Performance of a 3D Model for Coupled Deformation, Fluid Flow and Heat Transfer in Sedimentary Basins

MekIT'07. Fourth National Conference on Computational Mechanics

#### Talks, contributed

X. Cai

Bridging the Gap Between Computational Scientists and HPC

Article published in Meta, Number 3

X. Cai

Building Hybrid Parallel PDE Software by Domain Decomposition and Object-Oriented Programming

Talk at the ICCM 2007 Conference, April 4-6, Hiroshima, Japan

X. Cai

Making Parallel PDE Software by Object-Oriented Programming

Guest lecture given at Hohai University, China, May 17

X. Cai

On Building Parallel Algorithms and Software for Hydraulic Tomography

Talk at SIAM GS2007 Conference, March 19-22, Santa Fe, New Mexico, USA

X. Cai and H. P. Langtangen

On a Future Software Platform for Demanding Multi-Scale and Multi-Physics Problems

Talk at SIAM CSE07 Conference, Costa Mesa, CA, Feb. 19-23

J. B. Haga, A. M. Bruaset, X. Cai, H. P. Langtangen, H. Osnes and J. Skogseid

Parallelisation and Numerical Performance of a 3D Model for Coupled Deformation, Fluid Flow, and Heat Transport in Porous Geological Formations

Talk at the Fourth National Conference on Computational Mechanics (MekIT'07), Trondheim, Norway

X. Cai

Simulating Tsunami Propagation on Parallel Computers Using a Hybrid Software Framework

Guest lecture given at the University of Stuttgart, March 12

### 2006

#### Journal Articles

J. Sundnes, B. F. Nielsen, K. Mardal, X. Cai, G. T. Lines and A. Tveito

On the Computational Complexity of the Bidomain and the Monodomain Models of Electrophysiology

Annals of Biomedical Engineering

#### Books

J. Sundnes, G. T. Lines, X. Cai, B. F. Nielsen, K. Mardal and A. Tveito

Computing the Electrical Activity in the Heart

#### Proceedings, refereed

X. Cai

Improving the Performance of Large-Scale Unstructured PDE Applications

Proceedings of the PARA'04 Workshop, June 20-23, 2004, Lyngby, Denmark

B. F. Nielsen, O. M. Lysaker, C. Tarrou, J. Sundnes, X. Cai and K. Mardal

On the Use of the Bidomain Equations for Computing the Transmembrane Potential Throughout the Heart Wall: an Inverse Problem

Computers in Cardiology 2006

X. Cai, G. K. Pedersen, H. P. Langtangen and S. Glimsdal

Parallel Simulation of Tsunamis Using a Hybrid Software Approach

Proceedings of the International Conference ParCo 2005, September 13-16, Malaga, Spain

#### Book Chapters

X. Cai and G. T. Lines

Full-Scale Simulation of Cardiac Electrophysiology on Parallel Computers

Numerical Solution of Partial Differential Equations on Parallel Computers

X. Cai and H. P. Langtangen

Parallelizing PDE Solvers Using the Python Programming Language

Numerical Solution of Partial Differential Equations on Parallel Computers

#### Proceedings, non-refereed

C. Tarrou, O. M. Lysaker, X. Cai, K. Mardal, C. Tarrou, T. S. Ruud, M. C. MacLachlan and A. Tveito

Identifying Ischemic Heart Disease in Terms of ECG Recordings and an Inverse Problem for the Bidomain Equations; Modeling and Experiments

The Third International Conference "Inverse Problems: Modeling and Simulation"

#### Talks, contributed

X. Cai

A Hybrid Software Framework for Parallel Tsunami Simulations

Talk at SIAM PP06 Conference, February 22-24, 2006, San Francisco

B. F. Nielsen, O. M. Lysaker, X. Cai, K. Mardal, C. Tarrou, M. C. MacLachlan, J. Sundnes, G. T. Lines and A. Tveito

Computational Issues in Heart Modeling

Presented at the Johann Radon Institute for Computational and Applied Mathematics, Linz, Austria

J. Zhu, J. T. C. Yeh and X. Cai

Fusion of Hydraulic and Tracer Tomography for DNAPL Detection

Poster presented at AGU Fall Meeting 2006, Dec. 11-15, San Francisco

X. Cai, J. Zhu, Y. Zhang and J. T. C. Yeh

Hybrid Parallelization of a 3D Transient Hydraulic Tomography Code

Poster presented at Western Pacific Geophysics Meeting 2006, Beijng, July 24-27

B. F. Nielsen, O. M. Lysaker, C. Tarrou, J. Sundnes, X. Cai and K. Mardal

On the Use of the Bidomain Equations for Computing the Transmembrane Potential Throughout the Heart Wall: an Inverse Problem

Presented at the Computers in Cardiology conference in Valencia, Spain

X. Cai, J. Zhu, C. Ni and J. T. C. Yeh

Parallel Computational Methodology for Hydraulic Tomography

Poster presented at AGU Fall Meeting 2006, San Francisco, Dec. 11-15

X. Cai, J. Zhu and J. T. C. Yeh

Parallel Programming and Computing for Large-Scale Hydraulic Tomography

Poster presented at Workshop on Hydraulic Tomography, Boise, June 8-9

X. Cai

Parallelizing Serial PDE Software Using a Generic Approach

Seminar at the University of Arizona, February 27

M. S. Alnæs, A. M. Bruaset, X. Cai, H. P. Langtangen, K. Mardal, H. Moe, O. Skavhaug and Å. Ødegård

Python in High Performance Computing

Tutorial presented at the Para06 Workshop

X. Cai

Simulating Tsunamis on Parallel Computers

Invited talk at Notur 2006 Conference, May 11-12, Bergen, Norway

### 2005

#### Journal Articles

X. Cai, P. Jeberg and H. P. Langtangen

A Numerical Method for Computing the Profile of Weld Pool Surfaces

International Journal for Computational Methods in Engineering Science and Mechanics

X. Cai, G. K. Pedersen and H. P. Langtangen

A Parallel Multi-Subdomain Strategy for Solving Boussinesq Water Wave Equations

Advances in Water Resources

X. Cai, H. P. Langtangen and H. Moe

On the Performance of the Python Programming Language for Serial and Parallel Scientific Computations

Scientific Programming

#### Technical reports

K. Mardal, B. F. Nielsen, X. Cai and A. Tveito

An Order Optimal Solver for the Discretized Bidomain Equations

#### Talks, contributed

X. Cai, G. K. Pedersen, H. P. Langtangen and S. Glimsdal

Parallel Simulation of Tsunamis Using a Hybrid Software Approach

Talk at ParCo 2005 Conference, 13 - 16 September, Malaga, Spain

X. Cai and H. P. Langtangen

Parallelization of PDE Codes

Talk at the CMA Workshop on High-Performance Computing in Physics, November 4, Oslo, Norway

X. Cai, G. K. Pedersen and H. P. Langtangen

Solving Boussinesq Water Wave Equations on Parallel Computers

Talk at the International Workshop on Numerical Ocean Modeling, Oslo, Norway

### 2004

#### Journal Articles

M. Sosonkina, Y. Saad and X. Cai

Using the Parallel Algebraic Recursive Multilevel Solver in Modern Physical Applications

Future Generation Computer Systems

#### Book Chapters

X. Cai and M. Sosonkina

A Numerical Study of Some Parallel Algebraic Preconditioners

Parallel and Distributed Scientific and Engineering Computing: Practice and Experience

X. Cai, G. T. Lines and A. Tveito

Parallel Solution of the Bidomain Equations With High Resolutions

Parallel Computing: Software Technology, Algorithms, Architectures & Applications

#### Talks, contributed

X. Cai

Using Linux Clusters for Full-Scale Simulation of Cardiac Electrophysiology

Invited talk at the fifth annual workshop on Linux Clusters for Super Computing, October 18-21, 2004, Linköping, Sweden

### 2003

#### Proceedings, refereed

P. Jeberg, X. Cai, H. P. Langtangen and H. Holm

A Flexible Architecture for Welding Simulators Used in Weld Planning

Proceedings of International Conference on Productive Welding in Industrial Applications

#### Book Chapters

X. Cai

Overlapping Domain Decomposition Methods

Advanced Topics in Computational Partial Differential Equations - Numerical Methods and Diffpack Programming

X. Cai, E. Acklam, H. P. Langtangen and A. Tveito

Parallel Computing

Advanced Topics in Computational Partial Differential Equations - Numerical Methods and Diffpack Programming

X. Cai, A. M. Bruaset, H. P. Langtangen, G. T. Lines, K. Samuelsson, W. Shen, A. Tveito and G. Zumbusch

Performance Modeling of PDE Solvers

Advanced Topics in Computational Partial Differential Equations - Numerical Methods and Diffpack Programming

#### Talks, contributed

X. Cai and M. Sosonkina

A Numerical Study of Some Parallel Algebraic Preconditioners

Talk at the IPDPS 2003 Conference, April 22-26, 2003, Nice, France

G. T. Lines, B. F. Nielsen, A. Tveito, J. Sundnes, P. Grøttum, X. Cai and K. Mardal

Computing the Electrical Activity in the Human Heart

Presented at the Centre of Mathematics for Applications, Oslo

A. Tveito, G. T. Lines, J. Sundnes, B. F. Nielsen, P. Grøttum, X. Cai and K. Mardal

Computing the Electrical Activity in the Human Heart

Presented at the European Conference on Numerical Mathematics and Advanced Applications, Prague, Czech Republic

A. Tveito, G. T. Lines, B. F. Nielsen, J. Sundnes, P. Grøttum, X. Cai and K. Mardal

Computing the Heart

Presented at the 21st CAD-FEM users' meeting 2003 - International congress on FEM technology, Potsdam, Germany

W. Chen, A. Bounaim, X. Cai, S. Holm, A. Tveito and Å. Ødegård

Mathematical and Numerical Modeling of Medical Ultrasound Wave Propagation

Invited talk to MACSI-Workshop for Numerical Simulations for Ultrasound Imaging and Inversion, St. Georgen, Austria, pages 8-13

G. T. Lines, X. Cai and J. Sundnes

Parallel Algorithms for Simulating the Electrical Activity of the Heart

Presented at the Dagstuhl seminar Challenges in computational science and engineering

X. Cai, G. T. Lines and A. Tveito

Toward Extremely High-Resolution Simulation of Human Heart

Talk at the ParCo 2003 Conference, 2 - 5 September 2003, Dresden, Germany

### 2002

#### Proceedings, refereed

X. Cai and H. P. Langtangen

Developing Parallel Object-Oriented Simulation Codes in Diffpack

Proceedings of the Fifth World Congress on Computational Mechanics

X. Cai and G. T. Lines

Enabling Numerical and Software Technologies for Studying the Electrical Activity in Human Heart

Applied Parallel Computing - Advanced Scientific Computing, 6th International Conference, PARA 2002

X. Cai, M. Sosonkina and Y. Saad

Parallel Iterative Methods in Modern Physical Applications

Computational Science - ICCS 2002

#### Talks, contributed

X. Cai and H. P. Langtangen

Developing Parallel Object-Oriented Simulation Codes in Diffpack

Invited talk at the Fifth World Congress on Computational Mechanics, Vienna, Austria

G. T. Lines, J. Sundnes, A. Tveito, X. Cai, K. Mardal and A. M. Bruaset

Diffpack Simulation of the Electrical Activity in the Heart

Invited minisymposium talk at the 20th CAD-FEM User's Meeting, Friedrichshafen, Germany

### 2001

#### Proceedings, refereed

H. P. Langtangen and X. Cai

A Software Framework for Easy Parallelization of PDE Solvers

Proceedings of Parallel Computational Fluid Dynamics 2000

X. Cai and H. P. Langtangen

How Modern Programming Techniques Can Greatly Simplify the Development of Parallel Simulation Codes in Computational Mechanics

Proceedings of the MekIT'01 Conference

X. Cai and Å. Ødegård

On the Performance of PC Clusters in Solving Partial Differential Equations

Proceedings of the Tenth SIAM Conference on Parallel Processing for Scientific Computing

N. Bouhmala and X. Cai

Partition of Unstructured Finite Element Meshes by a Multilevel Approach

Applied Parallel Computing - New Paradigms for HPC in Industry and Academia, 5th International Conference, PARA 2000

#### Technical reports

G. T. Lines, X. Cai and A. Tveito

A Parallel Solution of the Bidomain Equations Modeling the Electrical Activity of the Heart

#### Talks, contributed

X. Cai and H. P. Langtangen

How Modern Programming Techniques Can Greatly Simplify the Development of Parallel Simulation Codes in Computational Mechanics

Talk at the National Conference on Computational Mechanics (MekIT'01), Trondheim, Norway

### 2000

#### Journal Articles

X. Cai and K. Samuelsson

Parallel Multilevel Methods With Adaptivity on Unstructured Grids

Computing and Visualization in Science

#### Proceedings, refereed

X. Cai, H. P. Langtangen and O. Munthe

An Object-Oriented Software Framework for Building Parallel Navier-Stokes Solvers

Parallel Computational Fluid Dynamics

X. Cai and Å. Ødegård

Parallel Simulation of 3D Nonlinear Acoustic Fields on a Linux-Cluster

Proceedings of 2nd IEEE International Conference on Cluster Computing, Germany

#### Talks, contributed

H. P. Langtangen and X. Cai

A Software Framework for Easy Parallelization of PDE Solvers

Keynote lecture at the Parallel CFD 2000 Conference, Trondheim, Norway

H. P. Langtangen and X. Cai

A Software Strategy for Easy Parallelization of Sequential PDE Solvers

Talk at the minisymposium on Modern Software Aspects for PDE Solvers (organized by H. P. Langtangen and Stefan Turek (University of Dortmund)) at the IMACS 2000 Conference, Lausanne, Switzerland

### 1999

#### Journal Articles

X. Cai, B. F. Nielsen and A. Tveito

An Analysis of a Preconditioner for the Discretized Pressure Equation Arising in Reservoir Simulation

IMA Journal of Numerical Analysis

#### Proceedings, refereed

X. Cai

Two Object-Orientated Approaches to the Parallelization of Diffpack

Proceedings of the HiPer'99 Conference

#### Talks, contributed

X. Cai, H. P. Langtangen and O. Munthe

An Object-Oriented Software Framework for Building Parallel Navier-Stokes Solvers

Talk at Parallel CFD'99, Williamsburg, Virgina, USA

### 1998

#### Journal Articles

X. Cai, H. P. Langtangen, B. F. Nielsen and A. Tveito

A Finite Element Method for Fully Nonlinear Water Waves

J. Comput. Phys.

X. Cai and E. Mehlum

Application of Cauchy Integrals and Singular Integral Equations in Scattered Data Problems

BIT

#### Proceedings, refereed

X. Cai

Domain Decomposition in High-Level Parallelization of PDE Codes

Proceedings of the 11th international conference on Domain Decomposition Methods

X. Cai

Numerical Simulation of 3D Fully Nonlinear Water Waves on Parallel Computers

Applied Parallel Computing - Large Scale Scientific and Industrial Problems, 4th International Conference, PARA'98

#### PhD Thesis

X. Cai

Numerical Methods for Partial Differential Equations and Their Object-Oriented Parallel Implementations

#### Technical reports

X. Cai, A. M. Bruaset, H. P. Langtangen, G. T. Lines, K. Samuelsson, W. Shen, A. Tveito and G. Zumbusch

Performance Modeling of PDE Solvers

### 1997

#### Proceedings, refereed

A. M. Bruaset, X. Cai, H. P. Langtangen and A. Tveito

Numerical Solution of PDEs on Parallel Computers Utilizing Sequential Simulators

Scientific Computing in Object-Oriented Parallel Environments

#### Talks, contributed

X. Cai and E. Mehlum

Animation of Wave Forces on Offshore Installations in IRIS Explorer

Render Issue 8 - The newsletter for IRIS Explorer users

A. M. Bruaset, X. Cai, H. P. Langtangen, A. Tveito and G. W. Zumbusch

Design Issues and Recent Developments in Diffpack

Invited minisymposium talk at the SIAM Annual meeting, Stanford University, California, USA

A. M. Bruaset, X. Cai, H. P. Langtangen and A. Tveito

Diffpack: an Object-Oriented Software Environment for Scientific Computing

Invited minisymposium talk at the Fourth US National Congress on Computational Mechanics, San Fransisco

A. M. Bruaset, X. Cai, H. P. Langtangen and A. Tveito

Numerical Solution of PDEs on Parallel Computers Utilizing Sequential Simulators

Talk at the ISCOPE Conference 1997, California

### 1996

#### Book Chapters

X. Cai and E. Mehlum

Two Fragments of a Method for Fully Nonlinear Simulations of Water Waves

Waves and Nonlinear Processesin Hydrodynamics

### 1995

#### Talks, contributed

B. F. Nielsen, X. Cai and A. Tveito

A Preconditioner for the Pressure Equation in Reservoir Simulation

Presented at Institut für Mathematik, Johannes Kepler Universität in Linz, Austria

B. F. Nielsen, X. Cai and A. Tveito

A Preconditioner for the Pressure Equation in Reservoir Simulation

Presented at Institut für Mathematik, Johannes Kepler Universität in Linz, Austria

### 1994

#### Technical reports

X. Cai and H. P. Langtangen

A B-Spline Package in C++