What is Faster - CPU, GPU or FPGA? Our Investigation of Leading Alignment Algorithms

What is Faster - CPU, GPU or FPGA? Our Investigation of Leading Alignment Algorithms

This commentary provides you with a general introduction of the three hardware technologies without referring to any bioinformatics algorithm.

How does a Computing Chip Work?

In two earlier commentaries, we explained how a traffic signal light chip is designed.

Designing a Traffic Signal Light

Designing a Traffic Signal Light II

Every digital chip is designed following similar rules. Only differences are in the details and the level of complexity.

Software vs Hardware

In the design of a computer chip, the designer has the option to make the design flexible enough so that few variable parameters can be controlled externally. For example, let us say the designer of the traffic signal light chip builds it in such a way that users can later adjust how long yellow light stays on compared to red or green. That is ‘software control’. Hardware control, on the other hand, means everything is hard-coded within the chip.

A computer chip is a black box (see figure) and those externally controls take place by passing electric signal through one of those legs of the chip. ‘Software programming’ is essentially the way to modulate the signals on those legs. Software control gives immense flexibility to the users of the chips, but often at the cost of speed. The loss of speed comes from the design flexibility built into hardware design.

Also it is less understood that the entire thinking of the software world (known as ‘computer science’) has been been shaped by the underlying hardware technology. When you pick up a computer science book and read about various algorithms (suffix array, hashing, sorting, etc.) you may think that they are general mathematical methods to be applicable everywhere. In reality, they are reflections of von Neumann architecture being used in CPU architecture.

The above observation has several ramifications -

(i) Moving from one hardware technology to another is not only a matter of re- coding the algorithm for a different architecture. It requires new thinking.

(ii) Even within the CPU world, it is becoming difficult to go from one core to multi-core due to basic algorithm-level limitations. Von Neumann architecture is highly biased toward single processing unit.

(iii) The code and performance can change dramatically, when Intel modifies its core set of CPU codes. All those hardware level details are hidden in ‘hash function’, which computer science professors stops investigating over a decade back and left to the industrial users and bioinformaticians, for whom performance is more important than mathematical elegance of algorithm.

Why Computer Science Professors Dislike Hash Functions

NGS Assembly Programs What Hash Functions Do They Use?

Perfect Hash Algorithm of Meraculous Assembler

Hardware-based Hash Functions



About a decade years back, ‘CPU’ referred to a large spectrum of computing chips developed by various companies to execute the von Neumann architecture. Today the description only includes Intel’s processor with AMD remaining as a distant competitor. Intel’s victory has been purely due to economic reasons. It was the only company, which managed to scale up its fabrication technology and commoditize the processor market.

The other companies, who lost the processor market, has been using their technical excellence in power consumption to come up with embedded board alternatives such as Raspberry Pi, or are staying relevant in the mobile- computing market.

Someone interested in understanding the difference between CPU, GPU and FPGA needs to understand the von Neumann architecture in detail.

The term Von Neumann architecture, also known as the Von Neumann model or the Princeton architecture, derives from a 1945 computer architecture description by the mathematician and early computer scientist John von Neumann and others, First Draft of a Report on the EDVAC[1]. This describes a design architecture for an electronic digital computer with subdivisions of a processing unit consisting of an arithmetic logic unit and processor registers, a control unit containing an instruction register and program counter, a memory to store both data and instructions, external mass storage, and input and output mechanisms.[1][2] The meaning of the term has evolved to mean a stored-program computer in which an instruction fetch and a data operation cannot occur at the same time because they share a common bus. This is referred to as the Von Neumann bottleneck and often limits the performance of the system.[3]

The design of a Von Neumann architecture is simpler than the more modern Harvard architecture which is also a stored-program system but has one dedicated set of address and data buses for reading data from and writing data to memory, and another set of address and data buses for fetching instructions.

A stored-program digital computer is one that keeps its programmed instructions, as well as its data, in read-write, random-access memory (RAM). Stored-program computers were an advancement over the program-controlled computers of the 1940s, such as the Colossus and the ENIAC, which were programmed by setting switches and inserting patch leads to route data and to control signals between various functional units. In the vast majority of modern computers, the same memory is used for both data and program instructions, and the Von Neumann vs. Harvard distinction applies to the cache architecture, not main memory.


The weakness of CPU architecture in parallel processing was apparent from the early days in display units of computers, because human eye is highly sensitive to any apparent discrepancy in graphical rendering of information. An ecosystem of companies developed to address the needs of video games market, and Nvidia emerged as a competitor to Intel.

In the early- and mid-1990s, CPU-assisted real-time 3D graphics were becoming increasingly common in computer and console games, which led to an increasing public demand for hardware-accelerated 3D graphics. Early examples of mass-marketed 3D graphics hardware can be found in fifth generation video game consoles such as PlayStation and Nintendo 64. In the PC world, notable failed first tries for low-cost 3D graphics chips were the S3 ViRGE, ATI Rage, and Matrox Mystique. These chips were essentially previous-generation 2D accelerators with 3D features bolted on. Many were even pin-compatible with the earlier-generation chips for ease of implementation and minimal cost. Initially, performance 3D graphics were possible only with discrete boards dedicated to accelerating 3D functions (and lacking 2D GUI acceleration entirely) such as the 3dfx Voodoo. However, as manufacturing technology continued to progress, video, 2D GUI acceleration, and 3D functionality were all integrated into one chip. Rendition’s Verite chipsets were the first to do this well enough to be worthy of note.

NVidia’s GPU chips contain hundreds of simple processing units, each driving a display region on the monitor. NVidia later added a set of APIs to allow users program those chips and use them for general purpose computing. Please check General-purpose computing on graphics processing units (GPGPU) for more details.


Above debates about architecture and programming language would be unnecessary, if everyone could built a computer chip customized for his task and then program it to fine-tune the performance. Unfortunately, fabricating a custom chip is very expensive.

FPGA technology from Xilinx and Altera removes the fabrication problem by designing generic chips customizable through hardware level programming. FPGAs contain gates and building blocks, whose connections are reprogrammed by passing electric signals into them. The reprogrammed chip can then be used just like a Intel chip. Pretty cool, eh?

Please do not forget that you will do diddly squat, if we give you an Intel chip. The chip needs to come in a board (motherboard) with memory and other useful units before we can start talking. For grandmas and most python programmers, the board needs to come packaged within a large and generally trouble free box.

The same is true for FPGA chips. You need to get them in the form of cards or complete boxes. The process can be ad maddening as trying to select a shampoo from the supermarket isle given how many variations of FPGA chips and boards are around.


Written by M. //