Terascaling Applications on HPCx: The First 12 Months Mike Ashworth HPCx Terascaling Team HPCx...

Terascaling Applications on HPCx: The First 12 Months

Mike Ashworth

HPCx Terascaling TeamHPCx Service

CCLRC Daresbury Laboratory

UK

[email protected]

http://www.hpcx.ac.uk/

210th December 2003HPCx Annual Seminar

Outline

• Terascaling Objectives• Case Studies

– DL-POLY– CRYSTAL– CASTEP– AMBER– PFARM– PCHAN– POLCOMS

• Efficiency of Codes• Summary

Application, and notH/W driven


Terascaling Objectives


Terascaling Objectives

• The primary aim of the HPCx service is Capability Computing

• Key objective that user codes should scale to O(1000) cpus

• Largest part of our science support is the Terascaling Team

• Understanding performance and scaling of key codes

• Enabling world-leading calculations (demonstrators)

• Closely linked with Software Engineering Team and Applications Support Team

Jobs which use>= 50% of cpus


HPCx Terascaling

Team

Strategy for Capability Computing

• Performance Attributes of Key ApplicationsTrouble-shooting with Vampir & Paraver

• Scalability of Numerical AlgorithmsParallel eigensolvers. FFTs etc

• Optimisation of Communication Collectivese.g., MPI_ALLTOALLV and CASTEP

• New TechniquesMixed-mode programming

• Memory-driven Approachese.g., “In-core” SCF & DFT, direct minimisation & CRYSTAL

• Migration from replicated to distributed datae.g., DL_POLY3

• Scientific drivers amenable to Capability Computing- Enhanced Sampling Methods, Replica Methods


Case Studies


Molecular Simulation

DL_POLY W. Smith and T.R. Forester, CLRC Daresbury Laboratory

• General purpose molecular dynamics simulation package

http://www.cse.clrc.ac.uk/msi/software/DL_POLY/


DL_POLY3 Coulomb Energy Performance

Number of CPUs

DL_POLY3216,000 ions, 200 time steps, Cutoff=12Å

0

1

2

3

4

5

6

7

32 64 128 256

IBM SP/Regatta-H

AlphaServer SC ES45/1000 SGI Origin 3800/R14k-500

Performance Relative to the Cray T3E/1200E

• Distributed Data• SPME, with revised FFT Scheme


Measured Time (seconds)

Number of CPUs

Gramicidin in water;Gramicidin in water;rigid bonds + SHAKE:rigid bonds + SHAKE:792,960 ions, 50 time steps

0

0.5

1

1.5

2

2.5

32 64 128 256

IBM SP/Regatta-H

AlphaServer SC ES45/1000

Performance Relative to the SGI Origin 3800/R14k-500

749

312

176

115

396

200

11673

349

189

11477

0

200

400

600

800

32 64 128 256

SGI Origin 3800/R14k-500

AlphaServer SC ES45/1000

IBM SP/Regatta-H

Number of CPUs

DL_POLY3 Macromolecular Simulations


Materials Science

CRYSTAL

• calculate wave-functions and properties of crystalline systems

• periodic Hartree-Fock or density functional Kohn-Sham Hamiltonian

• various hybrid approximations

http://www.cse.clrc.ac.uk/cmg/CRYSTAL/


Crystal

• Electronic structure and related properties of periodic systems

• All electron, local Gaussian basis set, DFT and Hartree-Fock

• Under continuous development since 1974

• Distributed to over 500 sites world wide

• Developed jointly by Daresbury and the University of Turin


Properties Energy Structure Vibrations (phonons) Elastic tensor Ferroelectric polarisation Piezoelectric constants X-ray structure factors Density of States / Bands Charge/Spin Densities Magnetic Coupling Electrostatics (V, E, EFG classical) Fermi contact (NMR) EMD (Compton, e-2e)

Crystal Functionality

• Basis Set– LCAO - Gaussians

• All electron or pseudopotential• Hamiltonian

– Hartree-Fock (UHF, RHF)– DFT (LSDA, GGA)– Hybrid funcs (B3LYP)

• Techniques– Replicated data parallel– Distributed data parallel

• Forces – Structural optimization

• Direct SCF• Visualisation

– AVS GUI (DLV)


Benchmark Runs on Crambin

• Very small protein from Crambe Abyssinica - 1284 atoms per unit cell

• Initial studies using STO3G (3948 basis functions)

• Improved to 6-31G * * (12354 functions)

• All calculations Hartree-Fock

• As far as we know the largest Hartree-Fock calculation ever converged


Scalability of CRYSTAL for crystalline Crambin

faster, more stable version of the parallel

Jacobi diagonalizer replaces ScaLaPack

HPCxvs.

SGI Origin

Increasing the basis set size increases the

scalability0

10

20

30

0 256 512 768 1024

Number of Processors

Pe

rfo

rma

nc

e (

arb

itra

ry)

Ideal

6-31G** IBM p690

6-31G IBM p690

STO-3G IBM p690

6-31G SGI Origin

STO-3G SGI Origin


Crambin Results – Electrostatic Potential

• Charge density isosurface coloured according to potential• Useful to determine possible chemically active groups


Futures - Rusticyanin

• Rusticyanin (Thiobacillus Ferrooxidans) has 6284 atoms (Crambin was 1284) and is involved in redox processes

• We have just started calculations using over 33000 basis functions

• In collaboration with S.Hasnain (DL) we want to calculate redox potentials for rusticyanin and associated mutants


Materials Science

CASTEPCAmbridge Serial Total Energy Package

http://www.cse.clrc.ac.uk/cmg/NETWORKS/UKCP/


What is Castep?

• First principles (DFT) materials simulation code– electronic energy – geometry optimization– surface interactions– vibrational spectra

• materials under pressure, chemical reactions

– molecular dynamics

• Method (direct minimization)– plane wave expansion of valence electrons– pseudopotentials for core electrons


Castep 2003 HPCx performance gain

0

1000

2000

3000

4000

5000

6000

7000

8000

Job

tim

e

80 160 240 320

Total number of processors

Al2O3 120 atom cell, 5 k- points

Jan-03

Current 'Best'

Bottleneck:• Data Traffic in

3D FFT and MPI_AlltoAllV


Castep 2003 HPCx performance gain

0

2000

4000

6000

8000

10000

12000

14000

16000

Job

Tim

e

128 256 512

Total number of processors

Al2O3 270 atom cell, 2 k- points

Jan-03

Current 'Best'


Molecular Simulation

AMBER(Assisted Model Building with Energy Refinement)Weiner and Kollman, University of California, 1981

• Widely used suite of programs particularly for biomolecules

http://amber.scripps.edu/


AMBER - Initial Scaling

0

2

4

6

8

10

12

0 32 64 96 128Number of Processors

Sp

ee

d-u

p

• Factor IX protein with Ca++ ions – 90906 atoms


Current developments - AMBER

• Bob Duke– Developed a new version of Sander on HPCx– Originally called AMD (Amber Molecular Dynamics)– Renamed PMEMD (Particle Mesh Ewald Molecular Dynamics)

• Substantial rewrite of the code– Converted to Fortran90, removed multiple copies of

routines,…– Likely to be incorporated into AMBER8

• We are looking at optimising the collective communications – the reduction / scatter


Optimisation – PMEMD

0

50

100

150

200

250

300

0 32 64 96 128 160 192 224 256Number of Processors

Tim

e (

se

co

nd

s)

PMEMD

Sander7


Atomic and Molecular Physics

PFARMQueen’s University Belfast, CLRC Daresbury

Laboratory

• R-matrix formalism to treat applications such as the description of the edge region in Tokamak plasmas (fusion power research) and for the interpretation of astrophysical spectra


Peigs vs. ScaLapack in PFARM

0

4000

8000

12000

16000

20000

0 64 128 192 256

Processors

Tim

e (

se

cs

)

Peigs total

ScaLapack total

Peigs diag

ScaLapack diag

Bottleneck:Matrix Diagonalisation


ScaLapack diagonalisation on HPCx

0

50

100

150

200

250

300

0 64 128 192 256


Tim

e (s

ecs)

Dim=7194,PDSYEV

Dim=7194,PDSYEVD

Dim=3888, PDSYEV

Dim=3888,PDSYEVD


0

1000

2000

3000

4000

Tim

e (

se

cs

)

32 64 128 256


Peigs

Scalapack D&C

Projected Sc'k

Stage 1 (Sector Diags) on HPCx

• Sector Hamiltonian matrix size 10032 (x 3 sectors)


Computational Engineering

UK Turbulence ConsortiumLed by Prof. Neil Sandham, University of Southampton

• Focus on compute-intensive methods (Direct Numerical Simulation, Large Eddy Simulation, etc) for the simulation of turbulent flows

• Shock boundary layer interaction modelling - critical for accurate aerodynamic design but still poorly understood

http://www.afm.ses.soton.ac.uk/


Direct Numerical Simulation: 3603 benchmark

0.0

10.0

20.0

30.0

40.0

0 128 256 384 512 640 768 896 1024Number of processors

Per

form

ance

(m

illi

on

ite

rati

on

po

ints

/sec

)

IBM Regatta (ORNL)

Cray T3E/1200E

IBM Regatta (HPCx)

Scaled from 128 CPUs


Environmental Science

Proudman Oceanographic Laboratory Coastal Ocean

Modelling System (POLCOMS)

• Coupled marine ecosystem modelling

http://www.pol.ac.uk/home/research/polcoms/


Coupled Marine Ecosystem Model

Physical Model

Pelagic Ecosystem Model

Benthic Model

Wind Stress

Heat FluxIrradiation

Cloud Cover

C, N, P, Si Sediments

oC

oC

River Inputs

OpenBoundary


0

20

40

60

80

100

120

140

0 128 256 384 512 640 768 896 1024

Number of processors

Pe

rfo

rma

nc

e (

M g

rid

-po

ints

-tim

es

tep

s/s

ec

)

Ideal IBM

1 km IBM

2 km IBM

3 km IBM

6 km IBM

12 km IBM

POLCOMS resolution b/m : HPCx


POLCOMS 2 km b/m : All systems

0

20

40

60

80

100

120

0 128 256 384 512 640 768 896 1024


Pe

rfo

rma

nc

e (

M g

rid

-po

ints

-tim

es

tep

s/s

ec

)

Ideal IBM

IBM p690

Cray T3E

Origin 3800


Efficiency of Codes


Motivation and Strategy

• Scalability of Terascale applications is only half the story• Absolute performance also depends on

single cpu performance• Percentage of peak is seen as an

important measure• Comparison with other systems e.g. vector machines

• Run representative test cases on small numbers of processors for applications and some important kernels

• Use IBM’s hpmlib to measure Mflop/s • Other hpmlib counters can help to understand

performancee.g. memory bandwidth, cache miss rates, FMA count, computational intensity etc.

Scientific output is the key measure


Matrix-matrix multiply kernel

0

10

20

30

40

50

60

0 8 16 24 32


% o

f p

ea

k


PCHAN small test case 1203

0

5

10

0 32 64 96 128


% o

f p

ea

k

0

500

1000

1500

Me

mo

ry b

an

dw

idth

(M

B/s

)

% of peak

Memory bandwidth


Summary of percentage of peak

DLPOLY

PCHAN

AMBER

NAMD

CRYSTAL

GAMESS

H2MOL

CASTEP

PRMAT

DIAG

MXM

POLCOMS

0 10 20 30 40 50 60

% of peak


• HPCx Terascaling Team– Mike Ashworth– Mark Bull– Ian Bush– Martyn Guest– Joachim Hein– David Henty

• IBM Technical Support– Luigi Brochard et al.

• CSAR Computing Service Cray T3E ‘turing’,Origin 3800 R12k-400 ‘green’

• ORNL IBM Regatta ‘cheetah’• SARA Origin 3800 R14k-500• PSC AlphaServer SC ES45-1000

Acknowledgements

– Adrian Jackson– Chris Johnson– Martin Plummer– Gavin Pringle– Lorna Smith– Kevin Stratford– Andrew Sunderland


The Reality of Capability Computing on HPCx

•The success of the Terascaling strategy is shown by the Nov 2003 HPCx usage

•Capability jobs (512+ procs) account for 48% of usage

•Even without Teragyroid it is 40.7%8

0.2%161.9%

325.1%

647.3%

12815.8%

25621.4%

Capability48.0%


Summary

• HPCx Terascaling team is addressing scalability for a wide range of codes

• Key Strategic Applications Areas– Atomic and Molecular Physics, Molecular Simulation, Materials

Science, Computational Engineering, Environmental Science

• Reflected by take up of Capability Computing on HPCx– In Nov ’03, >40% of time used by jobs with 512 procs and

greater

• Key challenges– Maintain progress with Terascaling– Include new applications and new science areas– Address efficiency issues esp. with single processor performance– Fully exploit the phase 2 system: 1.7 GHz p690+, 32 proc

partitions, Federation interconnect

Terascaling Applications on HPCx: The First 12 Months Mike Ashworth HPCx Terascaling Team HPCx...

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