single virtual systems for life and material sciences

8/13/2019 Single Virtual Systems for Life and Material Sciences

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SINGLE VIRTUAL SYSTEMFORLIFE AND MATERIAL SCIENCES


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Small groups of scientists: experts in their domain,

not in computer science

The more compute power, the more simulationsreflect the real world

Many different types of applications, some parallel,some sequential, some requiring vast amounts ofmemory

Research relies on commercially available

applications as well as in-house development

The faster the simulations, the faster results arepublished, the faster new products hit their market.

KEY ISSUES IN LIFE ANDMATERIAL SCIENCES


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APPLICATIONS SEGMENTATION

(*) QSPR: Quantitative Structure Property Relationship

CAN ONE COMPUTING ARCHITECTURE

RUN BOTH?

Compute

Memory

andData

Systems Biology Monte Carlo Simulations

Stochastic Dynamics

Genetics

Image processing and Analysis

Sequence Analysis Genomics

Proteomics

Picture Archiving

Docking

Molecular Analysis

QSPR(*)

Lab Data Management

Quantum Chemistry Molecular Dynamics

Molecular Mechanics

Quantum Chemistry Whole Genomics

In Memory Database

Searching

High Throughput Large Simulation

Cluster

Codes

SMPCodes


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1 Operating System

1.6 TeraFLOPS

128-cores

2.3TB RAM

19TB Internal Storage


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SCALEMP AT A GLANCE


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NEW SERVER VIRTUALIZATIONPARADIGMENTERPRISEAPPLICATIONS HIGH PERFORMANCECOMPUTING


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SERVER VIRTUALIZATIONAGGREGATION


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VSMP FOUNDATION AGGREGATIONPLATFORM


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VSMP FOUNDATION AGGREGATIONPLATFORM


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1

0

VSMP FOUNDATION FOR SMPDIRECT CONNECT 2


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VALUE PROPOSITIONS

Overcoming the

challenges of

applications and

end users

Overcoming thechallenges of IT

administration


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HOW IT WORKS


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BEHIND THE SCENES


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DELL SUPPORTED HARDWARE

PowerEdge M1000e with

M600/M610/M710 blades

Aggregation of 2 to 16 systems

Highest x86 shared-memory supercomputer

Dell Rack-Mount Servers

PE1950III/R410/R610/R710

Up to 32 Nehalem Processors (128 cores) and 2.3TB of Shared Memory


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SINGLE VIRTUAL SYSTEM

Typical Applications

Gaussian

VASP

AMBER

Schrdinger Jaguar

Schrdinger Glide

NAMDDOCK

GAMESS

GOLD

mpiBLAST

GROMACS

MOLPRO

OpenEye FRED

OpenEye OMEGASCM ADF

HMMER.

.

.

Single Operating System

One Large Shared Memory

Hidden InfiniBand Infrastructure

Simplified Storage

Simplified Management

MANAGEABLE PERFORMANCE

Focusing on Science not Computer Science


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EXAMPLE OF A GENERAL PURPOSELMS FAT NODE IMPLEMENTATION


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COMPUTATIONAL CHEMISTRY


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MOLECULAR DYNAMICS


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VSMPROFILE:PERFORMANCE TUNINGCOMPLETE SYSTEM VIEWBefore After

FOR APPLICATIONS DEVELOPERS:

Points to line of code causing performance inefficiencies

Eliminates performance optimization guesswork

Significantly reduces application tuning time

Not available on other architectures


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Small groups of scientists: experts in their domain,

not in computer science

The more compute power, the more simulationsreflect the real world

Many different types of applications, some parallel,some sequential, some requiring vast amounts ofmemory

Research relies on commercially available

applications as well as in-house development

The faster the simulations, the faster results arepublished, the faster new products hit their market.

KEY ISSUES IN LIFE ANDMATERIAL SCIENCES SOLVED


21/21

Thank you

single virtual systems for life and material sciences

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