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SCLS - I see! (Q&A)

Q1
What are the fields of HPCI ?
A1

HPCI stands for High Performance Computing Infrastructure. The objective of the HPCI project is to interconnect Japan’s high-performance computing devices, including the K computer, in order to offer researchers and technicians a seamless device that operates like one large computer.
In very simple terms, the goal of the various fields in the strategic program is to give concrete answers to questions such as, “What can we learn that we didn’t know before using the HPCI environment” and “What can we do to make the world a better place?”
At present, the five following fields have been set up under the strategic program:

This website is maintained by the researchers participating in strategic field 1, “Supercomputational Life Science.” Our goal is to prepare an R&D infrastructure to ensure that the fullest use is made of the K computer to generate world-class research outcomes that can benefit society.

Q2
What is the supercomputer ? Is it fast?
A2
Today, home computers are faster than ever, and we can now enjoy beautiful graphics and videos at home. The description of a supercomputer has changed over the years, but generally it refers to the most powerful computers available in any given era.
Q3
What is the K computer?
A3
Based on the High Performance Computing Infrastructure project being promoted by the Ministry of Education, Culture, Sports, Science and Technology (MEXT), RIKEN and Fujitsu launched a collaborative development project with the aim to begin public use in 2012. The first pieces of the computer started to be put together in October 2010. The term “K” was selected by RIKEN in July 2010. In Japanese the word kei refers both to 10 to the 16th power (10,000,000,000,000,000), which is the goal set for the speed of the new computer—10 petaflop—as well as to a large gate, indicating that the aim of the project will be open a new “gate” in the field of computer science.
Q4
People replace their standard personal computers about every five years. Will the K computer need to be replaced every five or ten years?
A4

That’s a very good question. It is certain that in five or ten years, the K computer will be inferior compared to what will then be the world’s fastest supercomputer of the day. However, it would be a waste of money to build a completely new one. Building a new one would also include the building that houses it, the power supply, and the cooling equipment.

In terms replacing the inside of the computer, this may be possible. In fact, in 2002 the Japanese Earth Simulator became the world’s top supercomputer. In 2009 its CPU was replaced with one that was 3 times faster. However, even that is 80 times slower than the K computer.

Advancements in supercomputers are rapid and if the next-generation K computer is not planned now, the world will leave us behind.

Q5
Will the specifications of the K computer increase as the physical scale of the equipment increases?
A5
If physical scale refers to the number of compute nodes, in terms of theoretical performance, specifications would increase proportion to the number of compute nodes. However, in addition to theoretical performance, there are various other indices used to measure computer performance, including execution,and these are often topics of debate.

For example, imagine transporting a large volume of goods from A to B by truck. By doubling the number of trucks, the transportation time would be cut in half, wouldn’t it? So if the number of trucks were increased to 10,000, would you be able to transport the cargo 10,000 times faster? That wouldn’t be possible. The highway would become too congested.

In the same way, when building a fast computer for practical use, you not only have to have fast trucks but also a big enough highway for the trucksto travel on. This is one of the difficulties of building a supercomputer.
Q6
What do “K speed” and “Peta” mean?
A6
In Japan, the digits in large numbers are grouped into units of four (myriads) rather than three (thousands). The Japanese system of counting is: tens, hundreds, and thousands, and then tens of thousands (man), hundreds of millions (oku), trillions (cho), and then tens of quadrillions (kei). Thus, “K speed” means ten quadrillion calculations per second (ten petaflop).
Q7
What is the Molecular dynamics method?
A7
This is a method to describe molecular motion based on the hypotheses that each atom constituting a molecule is a point that has no spatial extension but only a mass (this point is called a mass point), and that every mass point moves according to Newton’s laws of motion. This method allows us to describe the movement of individual atoms in a molecule. Let us assume a molecule that is constituted by several atoms. If atom A moves, other atoms also move coordinately. On the other hand, the movement of atom A is affected by other atoms; for example, it may be pulled or pushed by other atoms. Computers are used to calculate these movements.
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