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Opportunities for Biological Consortia on HPC x Code Capabilities and Performance. HPCx and CCP Staff http://www.ccp.ac.uk/ http://www.hpcx.ac.uk/. Welcome to the Meeting. Background HPCx Objectives to consider whether there is a case to bid Agenda Introduction to the HPCx service

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opportunities for biological consortia on hpc x code capabilities and performance

Opportunities for Biological Consortia on HPCxCode Capabilities and Performance

HPCx and CCP Staff



welcome to the meeting
Welcome to the Meeting
  • Background
    • HPCx
  • Objectives
    • to consider whether there is a case to bid
  • Agenda
    • Introduction to the HPCx service
    • Overview of Code Performance
    • Contributed Presentations
    • Invited Presentation -
    • Discussion

HPCx/Biology Discussions

  • Overview of Code Capabilities and Performance
    • Macromolecular simulation
    • Localised basis molecular codes
      • Gaussian, GAMESS-UK, NWChem
    • Local basis periodic code
      • CRYSTAL
    • Plane wave periodic codes
      • CASTEP
      • CPMD (Alessandro Curioni talk)
  • Note - consortium activity is not limited to these codes.

HPCx/Biology Discussions

dl poly background
DL_POLY Background
  • General purpose parallel MD code
  • Developed at Daresbury Laboratory for CCP5 1994-today
  • Available free of charge (under licence) to University researchers world-wide
  • DL_POLY versions:
    • DL_POLY_2
      • Replicated Data, up to 30,000 atoms
      • Full force field and molecular description
    • DL_POLY_3
      • Domain Decomposition, up to 1,000,000 atoms
      • Full force field but no rigid body description.

HPCx/Biology Discussions

dl poly force field
DL_POLY Force Field
  • Intermolecular forces
    • All common van de Waals potentials
    • Sutton Chen many-body potential
    • 3-body angle forces (SiO2)
    • 4-body inversion forces (BO3)
    • Tersoff potential -> Brenner
  • Intramolecular forces
    • Bonds, angle, dihedrals, inversions
  • Coulombic forces
    • Ewald* & SPME (3D), HK Ewald* (2D), Adiabatic shell model, Reaction field, Neutral groups*, Truncated Coulombic,
  • Externally applied field
    • Walled cells,electric field,shear field, etc

* Not in DL_POLY_3

HPCx/Biology Discussions

boundary conditions
Boundary Conditions
  • None (e.g. isolated macromolecules)
  • Cubic periodic boundaries
  • Orthorhombic periodic boundaries
  • Parallelepiped periodic boundaries
  • Truncated octahedral periodic boundaries*
  • Rhombic dodecahedral periodic boundaries*
  • Slabs (i.e. x,y periodic, z nonperiodic)

HPCx/Biology Discussions

algorithms and ensembles
Algorithms and Ensembles


  • Verlet leapfrog
  • Euler-Quaternion*
  • [All combinations]

*Not in DL_POLY_3


  • NVE
  • Berendsen NVT
  • Hoover NVT
  • Evans NVT
  • Berendsen NPT
  • Hoover NPT
  • Berendsen NT
  • Hoover NT

HPCx/Biology Discussions

migration from replicated to distributed data dl poly 3 domain decomposition





Migration from Replicated to Distributed data DL_POLY-3 : Domain Decomposition
  • Distribute atoms, forces across the nodes
    • More memory efficient, can address much larger cases (105-107)
  • Shake and short-ranges forces require only neighbour communication
    • communications scale linearly with number of nodes
  • Coulombic energy remains global
    • strategy depends on problem and machine characteristics
    • Adopt Smooth Particle Mesh Ewald scheme
      • includes Fourier transform smoothed charge density (reciprocal space grid typically 64x64x64 - 128x128x128)

An alternative FFT algorithm has been designed to reduce communication costs

HPCx/Biology Discussions

migration from replicated to distributed data dl poly 3 coulomb energy evaluation
Conventional routines (e.g. fftw) assume plane or column distributions

A global transpose of the data is required to complete the 3D FFT and additional costs are incurred re-organising the data from the natural block domain decomposition.

An alternative FFT algorithm has been designed to reduce communication costs.

the 3D FFT are performed as a series of 1D FFTs, each involving communications only between blocks in a given column

More data is transferred, but in far fewer messages

Rather than all-to-all, the communications are column-wise only

Migration from Replicated to Distributed data DL_POLY-3: Coulomb Energy Evaluation

Plane Block

HPCx/Biology Discussions

dl poly 2 3 differences
DL_POLY_2 & 3 Differences
  • Rigid bodies not in _3
  • MSD not in _3
  • Tethered atoms not in _3
  • Standard Ewald not in _3
  • HK_Ewald not in _3
  • DL_POLY_2 I/O files work in _3 but NOT vice versa
  • No multiple timestep in _3

HPCx/Biology Discussions

dl poly 2 developments
DL_POLY_2 Developments
  • DL_MULTI - Distributed multipoles
  • DL_PIMD - Path integral (ionics)
  • DL_HYPE - Rare event simulation
  • DL_POLY - Symplectic versions 2/3
  • DL_POLY - Multiple timestep
  • DL_POLY - F90 re-vamp

HPCx/Biology Discussions

dl poly 3 on hpcx
  • Test case 1 (552960 atoms, 300Dt)
    • NaKSi2O5 - disilicate glass
    • SPME (1283grid)+3 body terms, 15625 LC)
    • 32-512 processors (4-64 nodes)

HPCx/Biology Discussions

dl poly 3 on hpcx1
  • Test case 2 (792960 atoms, 10Dt)
    • 64xGramicidin(354)+256768 H2O
    • SHAKE+SPME(2563 grid),14812 LC
    • 16-256 processors (2-32 nodes)

HPCx/Biology Discussions

dl poly people
DL_POLY People
  • Bill Smith DL_POLY_2 & _3 & GUI
    • w.smith@dl.ac.uk
  • Ilian Todorov DL_POLY_3
    • i.t.todorov@dl.ac.uk
  • Maurice Leslie DL_MULTI
    • m.leslie@dl.ac.uk
  • Further Information:
    • W. Smith and T.R. Forester, J. Molec. Graphics, (1996), 14, 136
    • http://www.cse.clrc.ac.uk/msi/software/DL_POLY/index.shtml
    • W. Smith, C.W. Yong, P.M. Rodger,Molecular Simulation (2002), 28, 385

HPCx/Biology Discussions

amber namd and gaussian

AMBER, NAMD and Gaussian

Lorna Smith and Joachim Hein

  • AMBER (Assisted Model Building with Energy Refinement)
    • A molecular dynamics program, particularly for biomolecules
    • Weiner and Kollman, University of California, 1981.
  • Current version – AMBER7
  • Widely used suite of programs
    • Sander, Gibbs, Roar
  • Main program for molecular dynamics: Sander
    • Basic energy minimiser and molecular dynamics
    • Shared memory version – only for SGI and Cray
    • MPI version: master / slave, replicated data model

HPCx/Biology Discussions

amber initial scaling
AMBER - Initial Scaling

Factor IX protein with Ca++ ions – 90906 atoms

HPCx/Biology Discussions

current developments amber
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

HPCx/Biology Discussions

optimisation pmemd
Optimisation – PMEMD

HPCx/Biology Discussions

  • NAMD
    • molecular dynamics code designed for high-performance simulation of large biomolecular systems.
    • Theoretical and Computational Biophysics Group, University of Illinois at Urbana-Champaign.
  • Versions 2.4, 2.5b and 2.5 available on HPCx
  • One of the first codes to be awarded a capability incentive rating – bronze

HPCx/Biology Discussions

namd performance
NAMD Performance

Benchmarks from Prof Peter Coveney

TCR-peptide-MHC system

HPCx/Biology Discussions

namd performance1
NAMD Performance

HPCx/Biology Discussions

molecular simulation namd scaling
Molecular Simulation - NAMD Scaling


Parallel, object-oriented MD code

High-performance simulation of large biomolecular systems

Scales to 100’s of processors on high-end parallel platforms


standard NAMD ApoA-I benchmark, a system comprising 92,442 atoms, with 12Å cutoff and PME every 4 time steps.

scalability improves with larger simulations - speedup of 778 on 1024 CPUs of TCS-1 in a 327K particle simulation of F1-ATPase.

Number of CPUs

HPCx/Biology Discussions

performance comparison
Performance Comparison
  • Performance comparison between AMBER, CHARMM and NAMD
  • See: http://www.scripps.edu/brooks/Benchmarks/
  • Benchmark
    • dihydrofolate reductase protein in an explicit water bath with cubic periodic boundary conditions.
    • 23,558 atoms

HPCx/Biology Discussions


HPCx/Biology Discussions

  • Gaussian 03
    • Performs semi-empirical and ab initio molecular orbital calulcations.
    • Gaussian Inc, www.gaussian.com
  • Shared memory version available on HPCx
    • Limited to the size of a logical partition (8 processors)
    • Phase 2 upgrade will allow access to 32 processors
  • Task farming option

HPCx/Biology Discussions

crystal and castep


Ian Bush and Martin Plummer

  • 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

HPCx/Biology Discussions

crystal functionality
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)




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)

HPCx/Biology Discussions

benchmark runs on crambin
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 HF calculation ever converged

HPCx/Biology Discussions

crambin parallel performance
Crambin - Parallel Performance
  • Fit measured data to Amdahl’s law to obtain estimate of speed up
  • Increasing the basis set size increases the scalability
  • About 700 speed up on 1024 processors for 6-31G * *
  • Takes about 3 hours instead of about 3 months
  • 99.95% parallel

HPCx/Biology Discussions

results electrostatic potential
Results – Electrostatic Potential
  • Charge density isosurface coloured according to potential
  • Useful to determine possible chemically active groups

HPCx/Biology Discussions

futures rusticyanin
Futures - Rusticyanin
  • Rusticyanin (Thiobacillus Ferrooxidans) has 6284 atoms 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

HPCx/Biology Discussions

what is castep
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

HPCx/Biology Discussions

hpcx biological applications
HPCx: biological applications
  • Examples currently include:
    • NMR of proteins
    • hydroxyapatite (major component of bone)
    • chemical processes following stroke
  • Possibility of treating systems with a few hundred atoms on HPCx
  • May be used in conjunction with classical codes (eg DL_POLY) for detailed QM treatment of ‘features of interest’

HPCx/Biology Discussions

castep 2003 hpcx performance gain
Castep 2003 HPCx performance gain

HPCx/Biology Discussions

castep 2003 hpcx performance gain1
Castep 2003 HPCx performance gain

HPCx/Biology Discussions

hpcx biological applications1
HPCx: biological applications
  • Castep (version 2) is written by:
    • M Segall, P Lindan, M Probert C Pickard, P Hasnip, S Clark, K Refson, V Milman, B Montanari, M Payne.
    • ‘Easy’ to understand top-level code.
  • Castep is fully maintained and supported on HPCx
  • Castep is distributed by Accelrys Ltd
  • Castep is licensed free to UK academics by the UKCP consortium (contact ukcp@dl.ac.uk)

HPCx/Biology Discussions


Highly efficient and portable MPP computational chemistry package

Distributed Data - Scalable with respect to chemical system size as well as MPP hardware size

Extensible Architecture

Object-oriented design

abstraction, data hiding, handles, APIs

Parallel programming model

non-uniform memory access, global arrays


GA, Parallel I/O, RTDB, MA, …

Wide range of parallel functionality essential for HPCx


Global arrays:

portable distributed data tool:

Used by CCP1 groups (e.g. MOLPRO)


parallel eigensolver,

guaranteed orthogonality of eigenvectors


Physically distributed data

Single, shared data structure

HPCx/Biology Discussions

distributed data scf
Distributed Data SCF

Pictorial representation of the iterative SCF process in (i) a sequential process, and (ii) a distributed data parallel process: MOAO represents the molecular orbitals, P the density matrix and F the Fock or Hamiltonian matrix


Distributed Data

HPCx/Biology Discussions


NWChem Capabilities (Direct, Semi-direct and conventional):

  • RHF, UHF, ROHF using up to 10,000 basis functions; analytic 1st and 2nd derivatives.
  • DFTwith a wide variety of local and non-local XC potentials, using up to 10,000 basis functions; analytic 1st and 2nd derivatives.
  • CASSCF; analytic 1st and numerical 2nd derivatives.
  • Semi-direct and RI-based MP2 calculations for RHF and UHF wave functions using up to 3,000 basis functions; analytic 1st derivatives and numerical 2nd derivatives.
  • Coupled cluster, CCSD and CCSD(T) using up to 3,000 basis functions; numerical 1st and 2nd derivatives of the CC energy.
  • Classical molecular dynamics and free energy simulations with the forces obtainable from a variety of sources

HPCx/Biology Discussions

case studies zeolite fragments
Case Studies - Zeolite Fragments
  • DFT Calculations with Coulomb Fitting

Basis (Godbout et al.)

DZVP - O, Si


Fitting Basis:



  • NWChem & GAMESS-UK

Both codes use auxiliary fitting basis for coulomb energy, with 3 centre 2 electron integrals held in core.

Si8O7H18 347/832

Si8O25H18 617/1444

Si26O37H36 1199/2818

Si28O67H30 1687/3928

HPCx/Biology Discussions

dft coulomb fit nwchem
DFT Coulomb Fit - NWChem

Si26O37H36 1199/2818

Si28O67H30 1687/3928

Measured Time (seconds)

Measured Time (seconds)

Number of CPUs

Number of CPUs

HPCx/Biology Discussions

memory driven approaches nwchem dft lda performance on the ibm sp p690
Memory-driven Approaches: NWChem - DFT (LDA): Performance on the IBM SP/p690

Zeolite ZSM-5

  • DZVP Basis (DZV_A2) and Dgauss A1_DFT Fitting basis:

AO basis: 3554

CD basis: 12713

  • IBM SP/p690)

Wall time (13 SCF iterations):

64 CPUs = 9,184 seconds

128 CPUs= 3,966 seconds

MIPS R14k-500 CPUs (Teras)

Wall time (13 SCF iterations):

64 CPUs = 5,242 seconds

128 CPUs= 3,451 seconds

3-centre 2e-integrals = 1.00 X 10 12

Schwarz screening = 6.54 X 10 9

% 3c 2e-ints. In core = 100%

HPCx/Biology Discussions

gamess uk
  • GAMESS-UK is the general purpose ab initio molecular electronic structure program for performing SCF-, MCSCF- and DFT-gradient calculations, together with a variety of techniques for post Hartree Fock calculations.
    • The program is derived from the original GAMESS code, obtained from Michel Dupuis in 1981 (then at the National Resource for Computational Chemistry, NRCC), and has been extensively modified and enhanced over the past decade.
    • This work has included contributions from numerous authors†, and has been conducted largely at the CCLRC Daresbury Laboratory, under the auspices of the UK's Collaborative Computational Project No. 1 (CCP1). Other major sources that have assisted in the on-going development and support of the program include various academic funding agencies in the Netherlands, and ICI plc.
  • Additional information on the code may be found from links at: http://www.dl.ac.uk/CFS

† M.F. Guest, J.H. Amos, R.J. Buenker, H.J.J. van Dam, M. Dupuis, N.C. Handy, I.H. Hillier, P.J. Knowles, V. Bonacic-Koutecky van Lenthe, J. Kendrick, K. Schoffel & P. Sherwood, with contributions from R.D., W. von Niessen, R.J. Harrison, A.P. Rendell, V.R. Saunders, A.J. Stone and D. Tozer.

HPCx/Biology Discussions

gamess uk features 1
GAMESS-UK features 1.
  • Hartree Fock:
    • Segmented/ GC + spherical harmonic basis sets
    • SCF-Energies and Gradients: conventional, in-core, direct
    • SCF-Frequencies: numerical and analytic 2nd derivatives
    • Restricted, unrestricted open shell SCF and GVB.
  • Density Functional Theory
    • Energies + gradients, conventional and direct including Dunlap fit
    • B3LYP, BLYP, BP86, B97, HCTH, B97-1, FT97 & LDA functionals
    • Numerical 2nd derivatives (analytic implementation in testing)
  • Electron Correlation:
    • MP2 energies, gradients and frequencies, Multi-reference MP2, MP3 Energies
    • MCSCF and CASSCF Energies, gradients and numerical 2nd derivatives
    • MR-DCI Energies, properties and transition moments (semi-direct module)
    • CCSD and CCSD(T) Energies
    • RPA (direct) and MCLR excitation energies / oscillator strengths, RPA gradients
    • Full-CI Energies
    • Green's functions calculations of IPs.
    • Valence bond (Turtle)

HPCx/Biology Discussions

gamess uk features 2
GAMESS-UK features 2.
  • Molecular Properties:
    • Mulliken and Lowdin population analysis, Electrostatic Potential-Derived Charges
    • Distributed Multipole Analysis, Morokuma Analysis, Multipole Moments
    • Natural Bond Orbital (NBO) + Bader Analysis
    • IR and Raman Intensities, Polarizabilities & Hyperpolarizabilities
    • Solvation and Embedding Effects (DRF)
    • Relativistic Effects (ZORA)
  • Pseudopotentials:
    • Local and non-local ECPs.
  • Visualisation: tools include CCP1 GUI
  • Hybrid QM/MM (ChemShell + CHARMM QM/MM)
  • Semi-empirical : MNDO, AM1, and PM3 hamiltonians
  • Parallel Capabilities:
    • MPP and SMP implementations (GA tools)
    • SCF/DFT energies, gradients, frequencies
    • MP2 energies and gradients
    • Direct RPA

HPCx/Biology Discussions

parallel implementation of gamess uk
Parallel Implementation of GAMESS-UK
  • Extensive use of Global Array (GA) Tools and Parallel Linear Algebra from NWChem Project (EMSL)
  • SCF and DFT
    • Replicated data, but …
    • GA Tools for caching of I/O for restart and checkpoint files
    • Storage of 2-centre 2-e integrals in DFT Jfit
    • Linear Algebra (via PeIGs, DIIS/MMOs, Inversion of 2c-2e matrix)
  • SCF and DFT second derivatives
    • Distribution of <vvoo> and <vovo> integrals via GAs
  • MP2 gradients
    • Distribution of <vvoo> and <vovo> integrals via Gas
  • Direct RPA Excited States
    • Replicated data with parallelisation of direct integral evaluation

HPCx/Biology Discussions

gamess uk dft calculations
GAMESS-UK: DFT Calculations


Elapsed Time (seconds)

Valinomycin (DFT HCTH):

Basis: DZVP2_A2 (Dgauss)

(1620 GTOs)

Number of CPUs

Cyclosporin (DFT B3LYP):

Basis: 6-31G*

(1855 GTOs)

Number of CPUs

HPCx/Biology Discussions

dft analytic 2nd derivatives performance ibm sp p690 hp compaq sc es45 1000 and sgi o3800
DFT Analytic 2nd Derivatives PerformanceIBM SP/p690, HP/Compaq SC ES45/1000 and SGI O3800

(C6H4(CF3))2: Basis 6-31G (196 GTO)

Elapsed Time (seconds)

Terms from MO 2e-integrals in GA storage (CPHF & pert. Fock matrices); Calculation dominated by CPHF:


HPCx/Biology Discussions

  • CHARMM (Chemistry at HARvard Macromolecular Mechanics) is a general purpose molecular mechanics, molecular dynamics and vibrational analysis package for modelling and simulation of the structure and behaviour of macromolecular systems (proteins, nucleic acids, lipids etc.)
  • Supports energy minimisation and MD approaches using a classical parameterised force field.
  • J. Comp. Chem. 4 (1983) 187-217
  • Parallel Benchmark - MD Calculation of Carboxy Myoglobin (MbCO) with 3830 Water Molecules.
  • QM/MM model for study of reacting species
    • incorporate the QM energy as part of the system into the force field
    • coupling between GAMESS-UK (QM) and CHARMM.

HPCx/Biology Discussions

parallel charmm benchmark
Parallel CHARMM Benchmark

Benchmark MD Calculation of Carboxy Myoglobin (MbCO) with 3830 Water Molecules: 14026 atoms, 1000 steps (1 ps), 12-14 A shift.

HPCx/Biology Discussions

qm mm applications

T 128 (IBM SP/Regatta-H) = 143 secs

Measured Time (seconds)

Number of CPUs

QM/MM Applications

Triosephosphate isomerase (TIM)

  • Central reaction in glycolysis, catalytic interconversion ofDHAP to GAP
  • Demonstration case within QUASI (Partners UZH, and BASF)
  • QM region 35 atoms (DFT BLYP)
    • include residues with possible proton donor/acceptor roles
  • MM region (4,180 atoms + 2 link)
    • CHARMM force-field, implemented in CHARMM, DL_POLY

HPCx/Biology Discussions

sampling methods












Reaction Co-ordinate

Sampling Methods
  • Multiple independent simulations
  • Replica exchange - Monte Carlo exchange of configurations between an ensemble of replicas at different temperatures
  • Combinatorial approach to ligand binding
  • Replica path method - simultaneously optimise a series of points defining a reaction path or conformational change, subject to path constraints.
    • Suitable for QM and QM/MM Hamiltonians
    • Parallelisation per point
    • Communication is limited to adjacent points on the path - global sum of energy function

Collaboration with Bernie Brooks (NIH) http://www.cse.clrc.ac.uk/qcg/chmguk

HPCx/Biology Discussions

  • Many of the codes used by the community have quite poor scaling
  • Best cases
    • large quantum calculations (Crystal, DFT etc)
    • very large MD simulations (NAMD)
  • For credible consortium bid we need to focus on applications which have
    • acceptable scaling now (perhaps involving migration to new codes (e.g. NAMD)
    • heavy CPU or memory demands (e.g. CRYSTAL).
    • potential for algorithmic development to exploit 1000s of processors (e.g. pathway optimisation, Monte Carlo etc)

HPCx/Biology Discussions