A parallel implementation on modern hardware for geo electrical tomographical software

HÀ NỘI – 2010

ĐẠI HỌC QUỐC GIA HÀ NỘI TRƯỜNG ĐẠI HỌC CÔNG NGHỆ

Nguyễn Hoàng Vũ‌

A PARALLEL IMPLEMENTATION ON MODERN HARDWARE FOR GEO‌

ELECTRICAL TOMOGRAPHICAL SOFTWARE

KHOÁ LUẬN TỐT NGHIỆP ĐẠI HỌC HỆ CHÍNH QUY

Ngành: Công nghệ thông tin

Cán bộ hướng dẫn: PGS. TSKH. Phạm Huy Điển Cán bộ đồng hướng dẫn: TS. Đoàn Văn Tuyến

HÀ NỘI – 2010

ABSTRACT‌

Geoelectrical tomographical software plays a crucial role in geophysical research. However, imported software is expensive and does not provide much customizability, which is essential for more advanced geophysical study. Besides, these programs are unable to exploit the full potential of modern hardware, so the running time is inadequate for largescale geophysical surveys. It is therefore an essential task to develop domestic software for overcoming all these problems. The development of this software is based on our research in using parallel programming on modern multicore processors and stream processors for high performance computing. While this project with its interdisciplinary aspect poses many challenges, it has also enabled us to gain valuable insights in making scientific software and especially the new field of personal supercomputing.

A PARALLEL IMPLEMENTATION ON 1

MODERN HARDWARE FOR GEOELECTRICAL TOMOGRAPHICAL SOFTWARE 1

NGUYỄN HOÀNG VŨ 2 A PARALLEL IMPLEMENTATION ON 2

MODERN HARDWARE FOR GEOELECTRICAL TOMOGRAPHICAL SOFTWARE 2

ABSTRACT 4

CHAPTER 2. THE FORWARD PROBLEM IN RESISTIVITY TOMOGRAPHY 33

CHAPTER 3 SOFTWARE IMPLEMENTATION 43 CONCLUSION 52

REFERENCES 53

List of Acronyms

CPU

Central Processing Unit
CUDA	Compute Unified Device Architecture
GPU	Graphical Processing Unit
OpenMP	Open Multi Processing
OpenCL	Open Computing Language
TBB	Intel Threading Building Blocks

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INTRODUCTION

Geophysical methods are based on studying the propagation of the different physical fields within the earth’s interior. One of the most widely used fields in geophysics is the electromagnetic field generated by natural or artificial (controlled) sources. Electromagnetic methods comprise one of the three principle technologies in applied geophysics (the other two being seismic methods and potential field methods). There are many geoelectromagnetic methods currently used in the world. Of these electromagnetic methods, resistivity tomography is the most widely used and it is of major interest in our work.

Resistivity tomography [17] or resistivity imaging is a method used in exploration geophysics [18] to measure underground physical properties in mineral, hydrocarbon, ground water or even archaeological exploration. It is closely related to the medical imaging technique called electrical impedance tomography (EIT), and mathematically is the same inverse problem. In contrast to medical EIT however, resistivity tomography is essentially a direct current method. This method is relatively new compared to other geophysical methods. Since the 1970s, extensive research has been done on the inversion theory for this method and it is still an active research field today. A detailed historical description can be seen in [27].

Resistivity tomography surveys searching for oil and gas (left) or

water (right)

Resistivity tomography has the advantage of being relatively easy to carry out with inexpensive equipment and therefore has seen widespread use all over the world for many decades.

With the increasing computing power of personal computers, inversion software for resistivity tomography has been made, most notably being Res2Dinv by Loke [5].

According to geophysicists at Institute of Geology (Vietnam Academy of Science and Technology), the use of imported resistivity software encountered the following serious problems:

The user interface is not userfriendly;

Some computation steps cannot be modified to adapt to measurement methods used in Vietnam;

With large datasets, the computational power of modern hardware is not fully exploit;

High cost for purchasing and upgrading software.

Resistivity software is a popular tool for both short term and long term projects in research, education and exploration by Vietnamese geophysicists. Replacing imported software is therefore essential not only to reduce cost but also to enable more advance research on the theoretical side, which requires custom software implementations. The development of this software is based on research in using modern multicore processors and stream processors for scientific software. This can also be the basis for solving larger geophysical problems on distributed systems if necessary.

Our resistivity tomographical software is an example of applying high performance computing on modern hardware to computational geoscience. For 2D surveys with small datasets, sequential programs still provide results in acceptable time. Parallelizing for these situations provides faster response time and therefore increases research productivity but is not a critical feature. However, for 3D surveys, datasets are much larger with high computational expenses. A solution for this situation is using clusters. Clusters, however, are not a feasible option for many

scientific institutions in Vietnam. Clusters are expensive with high power consumption. With limited availability only in large institutions, getting access to clusters is also inconvenient. Clusters are not suitable for field trip as well because of difficulties in transportation and power supply. Exploiting the parallel capabilities of modern hardware is therefore a must to enable costeffective scientific computing on desktop systems for such problems. This can help reduce hardware cost, power consumption and increase user convenience and software development productivity. These benefits are especially valuable to scientific software customers in Vietnam where cluster deployment is costly in both money and human resources.

Chapter 1 High Performance Computing on Modern Hardware

1.1 An overview of modern parallel architectures

Computer speed is crucial in most software, especially scientific applications. As a result, computer designers have always looked for mechanisms to improve hardware performance. Processor speed and packaging densities have been enhanced greatly over the past decades. However, due to the physical limitations of electronic components, other mechanisms have been introduced to improve hardware performance.

According to [1], the objectives of architectural acceleration mechanisms are to decrease latency, the time from start to completion of an operation; increase bandwidth, the width and rate of operations.

Direct hardware implementations of expensive operations help reduce execution latency. Memory latency has been improved with larger register files, multiple register sets and caches, which exploit the spatial and temporal locality of reference in the program.

With the bandwidth problem, the solutions can be classified into two forms of parallelism: pipelining and replication.

Pipelining [22] divides an operation into different stages to enable the concurrent execution of these stages for a stream of operations. If all of the stages of the pipeline are filled, a new result is available every unit of time it takes to complete the slowest stage. Pipelines are used in many kinds of processors. In the picture below, a generic pipeline with four stages is shown. Without pipelining, four instructions take 16 clock cycles to complete. With pipelining, this is reduced to just 8 clock cycles.

On the other hands, replication duplicates hardware components to enable concurrent execution of different operations.

Pipelining and replication appear at different architectural levels and in various forms complementing each other. While numerous, these architectures can be divided into three groups [1]: