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- 2013 - 3D Structures of Biological Macromolecules Floating Point Operations and Benchmarking of Computer Performance. Jürgen Sühnel jsuehnel@fli-leibniz.de. Leibniz Institute for Age Research, Fritz Lipmann Institute, Jena Centre for Bioinformatics Jena / Germany.

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slide1

- 2013 -

3D Structuresof Biological Macromolecules

Floating Point Operations

and Benchmarking of Computer Performance

Jürgen Sühnel

jsuehnel@fli-leibniz.de

Leibniz Institute for Age Research, Fritz Lipmann Institute,

Jena CentreforBioinformatics

Jena / Germany

Supplementary Material: http://www.fli-leibniz.de/www_bioc/3D/

slide2

Floating Point Operation

- A Floating Point Operation is a mathematical operation with floating point numbers.

- Floating point number: 23.452 = 23452 x 10-3

significant digits x base exponent

- They cover easily extremely large number ranges between astronomy

and particle physics.

- A Floating Point Unit is a part of a computer system specifically designed to carry out

operations on floating point numbers.

- FLOPS is in computing to a measure of computer performance -

-floating point operations per second (note plural and per second).

slide4

Floating Point Operation – Theoretical Peak Performance

GFLOPS =

(CPU-Takt in GHz) ×

(Anzahl der CPU-Kerne) ×

(CPU-Instruktionen pro Takt) ×

(Anzahl der CPU im Rechnerknoten)

Beispiel: Zwei Sockel-Server mit 8 Kernen und einer Taktfrequenz von 2.6 GHz

und 8 Instruktionen per Zyklus (z.B. Intel E5-2600-Reihe)

GFLOPS = 2.6 x 8 x 8 x 2 = 332.8 GFLOPS

Adjusted Peak Performance is significantly lower.

slide5

Benchmarking

LINPACK – software library for performing numerical linear algebra on computers,

is now widely used for measuring computer performance

Linpack Benchmark - Java Version´- (http://www.netlib.org/benchmark/linpackjava/)

The problem solved is a dense 500x500 system of linear equations with one right hand side, Ax=b.

The matrix is generated randomly and the right hand side is constructed so the solution has all components

equal to one.

800 – 1100 Mflops/s

slide6

TOP500 List

Measured in Pflops.