current research projects ath the hlrs from drug...

03.12.2013 :: ::

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::

Current Research Projects ath the HLRS from Drug Production over Green-IT to Medical Simulations

Uwe Wössner, HLRS

SEAIP 2013

03.12.2013 :: ::

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::

THE HLRS SYSTEMS

SEAIP 2013

Stuttgart

NEC Nehalem (1400x4/8)

Cray XC30, XK6, XD1 SUN Fire 2900 (48x2)

Ulm

NEC Asama (64)

CAVE

IBM x3755

(144x2)

IBM HSM > 2 PB

NEC SX-9 (156)

Hermit Cray XE6(7000x16)

Dalco Vis-Cluster (24*8+16*4)

NEC Sandybridge (576x8)

03.12.2013 :: ::

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::

NEW HLRS SYSTEM (CRAY XE6 „HERMIT“)

SEAIP 2013

• 2011

– AMD Interlagos

• @ 2.3GHz 16 Cores

– 113.000 Cores

– 1 PF/s Peak

– 250-300 TF/S application performance

– 100 TB main memory

– 2.7 PB storage

03.12.2013 :: ::

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:: SEAIP 2013

03.12.2013 :: ::

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::

INDUSTRIAL USAGE

SEAIP 2013

• Bertrandt

• BTB

• Daimler

• Kärcher

• Mahle

• Porsche

• RECOM

• Transsolar

• Stellba

• Optima Pharma

03.12.2013 :: ::

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::

NEW FIVE SIDED CAVE

SEAIP 2013

03.12.2013 :: ::

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::

Go

• 5 ProjectionDesign

F35 AS3D

• 1920x1200

• Single chip DLP

• 0.8/1 wide angle lens

CAVE PROJECTORS

SEAIP 2013

03.12.2013 :: ::

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:: SEAIP 2013

03.12.2013 :: ::

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::

Go

• 22 Nodes + 8 Nodes

• 2 Intel Sandybridge CPUs/Node

• NVIDIA K5000 / NVIDIA K6000 GPUs

• 256 GB,32 GB Head nodes/Render nodes

• QDR Infiniband

• External NICs: 10GigE

• Closed loop water cooled rack by

Schäfer/Stulz

• 1LNET Router to Cray fs

CAVE CLUSTER

SEAIP 2013

03.12.2013 :: ::

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::

Go

• 9 UE 55A 3D LCD Displays

• 1920x1080 Full HD 3D (HDMI

1.4a)

• 11 K5000 GPUs

3D TILED DISPLAY

SEAIP 2013

03.12.2013 :: ::

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:: SEAIP 2013

Product development/Optimization

Construction Physical Prototype Analysis

Construction Simulation Analysis

V i r t u a l P r o t o t y p e s

H y b r i d P r o t o t y p e s

03.12.2013 :: ::

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::

BUILDING BLOCKS OF A WORKSPACE

SEAIP 2013

Virtual Reality (VR) Augmented Reality (AR)

Hybrid Prototypes

VR Userinterface (VRUI)

Tablet-PC (TabletUI)

Tangible Interface

Visualization Simulation

Multi Touch

Desktop

User Interface

Workspace

Tools

03.12.2013 :: ::

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::

COLLABORATIVE ENVIRONMENTS

SEAIP 2013

Virtual Reality (VR) Augmented Reality (AR)

Hybrid Prototypes

VR Userinterface (VRUI)

Tablet-PC (TabletUI)

Tangible Interface

Visualization Simulation

Multi Touch

Desktop

User Interface

Workspace

Tools

Virtual Reality (VR) Augmented Reality (AR)

Hybrid Prototypes

VR Userinterface (VRUI)

Tablet-PC (TabletUI)

Tangible Interface

Visualization Simulation

Multi Touch

Desktop

User Interface

Workspace

Tools

Virtual Reality (VR) Augmented Reality (AR)

Hybrid Prototypes

VR Userinterface (VRUI)

Tablet-PC (TabletUI)

Tangible Interface

Visualization Simulation

Multi Touch

Desktop

User Interface

Workspace

Tools

Virtual Reality (VR) Augmented Reality (AR)

Hybrid Prototypes

VR Userinterface (VRUI)

Tablet-PC (TabletUI)

Tangible Interface

Visualization Simulation

Multi Touch

Desktop

User Interface

Workspace

Tools

03.12.2013 :: ::

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::

COVISE COLLABORATIVE VISUALIZATION AND SIMULATION ENVIRONMENT

SEAIP 2013

03.12.2013 :: ::

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:: SEAIP 2013

Virtual Reality

03.12.2013 :: ::

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COAL PARTICLE VISUALIZATION

SEAIP 2013

03.12.2013 :: ::

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::

OPENCOVER COVISE VIRTUAL ENVIRONMENT RENDERER

SEAIP 2013

Features:

– Flexible plugin system

– Support for projection based VR, tiled Displays and HMDs

– Augmented Reality

– CSCW

– Volume rendering

– VRML97

– 3D VR GUI (VRUI)

– Parallel rendering

covise_lib

OpenCOVER

VRUI

VRBClient

OpenSceneGraph

Volumen- Rendering

render_lib

Vic

ARToolKit

Plugin- Support

VRML97

Tracker

Simulation and Visualization of the Airflow in Clean Rooms Bärbel Große-Wöhrmann, Uwe Wössner, High Performance Computing Center Stuttgart (HLRS)

Ralph Eisenschmid, OPTIMA pharma GmbH

03.12.2013 :: ::

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::

WHY SIMULATING THE AIRFLOW IN CLEAN ROOMS?

Pharma Forum 2013

Design:

How to avoid the

• pollution of vails?

• contamination of staff?

Testing and justification

03.12.2013 :: ::

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::

WHY SIMULATING THE AIRFLOW IN CLEAN ROOMS?

Pharma Forum 2013

03.12.2013 :: ::

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::

OPENFOAM® - A TOOLBOX FOR CFD

Pharma Forum 2013

Mesh generation (SnappyHexMesh)

Initial and boundary conditions

Surface data in STL format

Solver

Post-processing

03.12.2013 :: ::

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::

OPENFOAM® - A TOOLBOX FOR CFD

Pharma Forum 2013

Mesh generation

Initial and boundary conditions

Solver

Post-processing

/*--------------------------------*- C++ -*-------------------------*\

| ========= | |

| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |

| \\ / O peration | Version: 2.1.1 |

| \\ / A nd | Web: www.OpenFOAM.org |

| \\/ M anipulation | |

\*------------------------------------------------------------------*/

FoamFile

{

version 2.0;

format ascii;

class volScalarField;

object p;

}

// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //

dimensions [0 2 -2 0 0 0 0];

internalField uniform 0;

boundaryField

{

inlet

{

type zeroGradient;

}

outlet

{

type fixedValue;

value $internalField;

}

03.12.2013 :: ::

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::

OPENFOAM® - A TOOLBOX FOR CFD

Pharma Forum 2013

Mesh generation

Initial and boundary conditions

Solver

Post-processing

/*--------------------------------*- C++ -*-------------------------*\

| ========= | |

| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |

| \\ / O peration | Version: 2.1.1 |

| \\ / A nd | Web: www.OpenFOAM.org |

| \\/ M anipulation | |

\*------------------------------------------------------------------*/

FoamFile

{

version 2.0;

format ascii;

class dictionary;

object controlDict;

}

// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //

application simpleFoam;

startFrom startTime;

startTime 0;

stopAt endTime;

endTime 500;

deltaT 1;

writeControl timeStep;

writeInterval 100;

Steady-state solver for incompressible, turbulent flow

03.12.2013 :: ::

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::

OPENFOAM® - A TOOLBOX FOR CFD

Pharma Forum 2013

Mesh generation

Initial and boundary conditions

Solver

Post-processing

03.12.2013 :: ::

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::

OPENFOAM® - RUNNING IN PARALLEL

Pharma Forum 2013

Parallel solver

Domain decomposition

Parallel mesh generation

Reconstruction

Block Mesh

03.12.2013 :: ::

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::

OPENFOAM® - RUNNING IN PARALLEL

Pharma Forum 2013

Parallel solver

Domain decomposition

Parallel mesh generation

Reconstruction

Mesh generation

20 min

20 min

Serial tools: 40 min

Clean room simulations example, one run: • 12 million mesh cells • Memory requirement: 96 GByte • 64 compute cores • Queuing time: 5 ... 600 minutes

03.12.2013 :: ::

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:: SEAIP 2013

03.12.2013 :: ::

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::

VR VISUALIZATION OF A CAPPER

SEAIP 2013

Capper Bottle

03.12.2013 :: ::

::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: :::::

::

INTERACTIVE SIMULATIONS

SEAIP 2013

Mesh generation

Geometry generation

Domain decomposition

Simulation

Post Processing

Visualization

Geometry modification

Mesh refinement

Number of domains / algorithm

Boundary condition

Interactive visualization

< 1

Min

ute

03.12.2013 :: ::

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::

SIMULATION COUPLING

SEAIP 2013

Code Type Coupling mode

StarCD CFD SimLib, Fortran user subroutine, Loose

CFX CFD SimLib, Fortran user subroutine, Loose

Fluent CFD SimLib, C user subroutine, Loose

OpenFoam CFD SimLib, C++ user subroutine, Loose

Fidap CFD Script, Black-Box, Loose

Fenfloss CFD SimLib, C Plugin, Loose

Diablo Diffusion in metal alloys Script, Black-Box, Loose

Trans3D Laser ablation COVISE Modul C++, Tight

Uranus CFD Socket interface, coupling module, C++, Loose

SunFace Radiation COM/DCOM, coupling module, C++, Hybrid

03.12.2013 :: ::

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INTERACTIVE SIMULATION IN COVISE

SEAIP 2013

Grid generation

Domain decomposition Simulation

Post processing

Rendering

03.12.2013 :: ::

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VIRTUAL WATER TURBINE TEST-BED

SEAIP 2013

Simulation of the river power

station Kiebingen, Neckar

Through interactive simulation,

the output could be increased by

30%, simply by substituting the

runner and wicked gate

03.12.2013 :: ::

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::

VIRTUAL TURBINE TEST-BED

SEAIP 2013

03.12.2013 :: ::

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::

• EU-Projekt: FP7 ICT Call 7

• Budget: 3,614,210€ (funded: 2,645,000€)

• Duration: 30 Months

• Start: Oktober 2011

• Consortium

34 CoolEmAll – eine Einführung

03.12.2013 :: ::

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::

GOAL AND MAIN RESULTS

35 2nd Review Meeting, Brussels, 13.11.2013

Goal: To enable data centre designers and operators to reduce its

energy impact combining optimization of IT, cooling and

workload management

Main Results:

• ComputeBox Blueprints and Data Centre Efficiency Building Blocks (DEBBs)

abstracting IT infrastructure on different granularity level n

Levels: node, node-group (RECS), ComputeBox1 (rack), ComputeBox2 (DC)

• SVD-Toolkit allowing analysis and optimisation of modular IT infrastructure

(level n+1) built of DEBBs (level n), taking into account (input parameters):

• HW-Models (represented by DEBBs on level n)

• Workloads and Application Models

• Workload- & Resource Management Policies

• Cooling methods and environmental conditions

• To be achieved by combining:

(i) coupled simulations of various workloads and applications,

(ii) CFD simulation to analyze airflow and heat transfer in a data centres

(iii) visualization of results

03.12.2013 :: ::

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::

Deep insight

into workload

execution and

hw behaviour

Adequate

metrics

Savings

potential

36

Depending on a use case:

• Rack re-arrangement: 25% for racks cooled by CRAC

• Capacity management: 20% + performance gains

• Free cooling: 30% for free cooling, up to 4% per 0.5C increase

Workload and Resource Simulation

CFD Simulation

Metrics Calculation

260

280

300

320

340

360

380

400

420

440

460

10:58 10:59 10:59 11:00 11:00 11:01 11:01 11:02 11:02

Po

we

r u

se

d

Date\nTime

Linpack 4c

Daemon outputReal output

03.12.2013 :: ::

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Comparison of real

measurements with

simulation models

Definition of open Data

Center Efficiency

Building Blocks

USE OF PREDICTABLE TRENDS USING DCIM AND MODELING TOOLS

37 Simulations based on real measurements and re-usable building blocks

03.12.2013 :: ::

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The best rather

than just highest

utilisation

Minimizing

utilisation along

with smart

resource

mamagement

Hierarchical

monitoring and

aggregation of

metrics

EFFICIENT MONITORING AND INTELLIGENT WORKLOAD AND RESOURCE MANAGEMENT

38

CPU-intensive Application

Data-intensive Application

Web Server Application

CR

AC

C

RA

C

03.12.2013 :: ::

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PROJECT HIGHLIGHTS IN 2013

SEAIP 2013

• Specification and simulation of node groups

03.12.2013 :: ::

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SVD - Toolkit

COVISE / Simulation Workflow

CO

VIS

E Simulation

Post-Processing

Web

Serv

ice Visualisation

Pipeline

•Modules•Parameters•Links

•Events

Even

t Q

ueu

es

•Web Server

DEBB

Airthroughput

Powerusage

CF

D S

olv

er

(Op

en

Fo

am

/

An

sy

s C

FX

)

Data Center Workload

and Resource

Management

Simulator

Sample points

histogram

Data

(1)

(2) (3)

Airthroughput

Powerusage(4) (4)

(5)

(6)

Simulation

parameters

Simulation

results

(8)

Interaction

(9)

(10)

(11)

(7)

Metrics Calculator

MO

P G

UI

CoolEmAll Web GUI

Simulation

Interaction &

Visualisation

(COVISE)

(MOP) Database

Simulation Workflow (COVISE)

- Components

- Power profile

- Air thr. profile

- ge

om

etry

- po

sitio

n

DEBB

Repository

Workload

Repository

Application

Profile

Repository

Application

(with Paremeters)

Application

ProfilerRepository

(1)

(1)

(0)

(10)

(8)

(12)

DC

-WO

RM

S GU

I

CFD Simulator - Integrate CFX as second CFD Solver

COVISE -integrated post processing

THE SVD TOOLKIT COMPONENTS

SEAIP 2013 MOP GUI Web GUI DB integration

DEB

B co

nfigu

rator

03.12.2013 :: ::

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::

2ND RELEASE OF THE SVD TOOKIT

SEAIP 2013

• CoolEmAll WEB-GUI – advanced Visualisation Tool

• Web based GUIs to all components easy usage of SVD

Toolkit

• DEBB configuration, definition

• Selection of Application Profiles, Workloads

• View workload simulation

• Interact and view CFD simulation

• MOP-GUI

• Report GUI

03.12.2013 :: ::

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::

2ND RELEASE OF THE SVD TOOKIT

SEAIP 2013

• CFD Simulation using COVISE

• Rack rearrangement in Compute-Room

• interactive simulation

• Remote steering

03.12.2013 :: ::

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AUGMENTED REALITY

SEAIP 2013

Mixed Reality

03.12.2013 :: ::

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::

DEEP DRAWING OF A CUP

SEAIP 2013

Flange

03.12.2013 :: ::

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::

COMPUTATIONAL ELECTRODYNAMICS

SEAIP 2013

03.12.2013 :: ::

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:: SEAIP 2013

CoolEmAll

03.12.2013 :: ::

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::

MODELL WIND TUNNEL AT THE FKFS

SEAIP 2013

03.12.2013 :: ::

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::

WIND TUNNEL AT FKFS

SEAIP 2013

03.12.2013 :: ::

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::

FREIGHTLINER CASCADIA (SC11)

SEAIP 2013

03.12.2013 :: ::

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::

ABDOMINAL AORTIC ANEURYSM (AAA)

SEAIP 2013

• AAA can be found at 2% of the older population

• Diagnosis is difficult and discovery of existence of an AAA occurs mostly by chance

• There is a substantial risk of burst which typically ends deadly (Albert Einstein, April 18th 1955)

• Two forms: saccular and tube-like

• Dimensions:

– Diameter: 2-4 inches (normally 1)

– Volume: 120-280 cm (norm. 22-30)

• Ralf Schneider, Björn Sander, Peter Lammers, Daniela Pless, Thorsten Fleiter

03.12.2013 :: ::

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::

WORKFLOW FOR BLOOD FLOW SIMULATIONS

SEAIP 2013

03.12.2013 :: ::

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::

INTERACTIVE VISUALIZATION OF AN AAA

SEAIP 2013

03.12.2013 :: ::

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::

INTERACTIVE VISUALIZATION OF AN AAA

SEAIP 2013

03.12.2013 :: ::

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::

BONE IMPLANT SYSTEMS

SEAIP 2013

• Patient specific FE simulations of bone-implant-systems within 2h

• Realistic and patient specific modeling of

• Bone geometry

• Bone tissue

• Muscle forces

• Implant placement

• Simulations fully based on clinical imaging techniques like CT, MRI and US

• Support of diagnostic decisions with respect to:

• Implant Type

• Positioning of Implant

• Prediction of healing process

03.12.2013 :: ::

::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: :::::

::

• Absolute stress results for implant structure

PRESENTATION FOR DOCTORS/PATIENTS

SEAIP 2013

Development of von Mises equivalence stresses in Targon PF implant during slow step Load situation: person of 76.5kg bodyweight, Reduced set of Muscle forces, Fracture A2.3 according to AO

03.12.2013 :: ::

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::

CSI@HLRS STATE OFFICE OF CRIMINAL INVESTIGATION

SEAIP 2013

03.12.2013 :: ::

::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: :::::

::

EFFICIENT VISUALIZATION OF BEE HIVES

SEAIP 2013

03.12.2013 :: ::

::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: ::::: :::::

::

THE HLRS VIS-TEAM

SEAIP 2013

• Martin Aumüller – Parallel Rendering;Parallel Visualization,Remote Rendering (CRESTA)

• Nico Eichhorn – Cloud Visualization, Virtualization of Graphics hardware, Remote Rendering(GAIA-Cloud)

• Andreas Gottlieb – Automatic optimization (Daimler CFD)

• N.N. – Interactive Simulation, Air conditioning; (CoolEmAll)

• Jutta Sauer – Video streaming; Video Conferencing; COVISE Dev.; 3D Modeling

• Jörg Scheurich – Virtual Reality, VRML, X3D

• Wolfgang Schotte – Virtual Reality, CSI-Stuttgart (VISIONAIR);

• Aihong Yin – Web services, Web GUIs, (GAIA-Cloud)

• Uwe Zimmat – Video service

Aumueller-eichhorn-gottlieb-rathgeb-sauer-scheurich-schotte-woessner-yin-zimmat@hlrs.de