NAMD Development Goals

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NAMD Development Goals

• L.V. (Sanjay) Kale
• Professor
• Dept. of Computer Science
• http//www.ks.uiuc.edu/Research/namd/

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NAMD Vision

• Make NAMD a widely used MD program
• For large molecular systems,
• Scaling from PCs, clusters, to large parallel
  machines
• For interactive molecular dynamics
• Specific Goals for NAMD 3
• High performance
• Ease of use Easy to configure, set-up, and run
• Ease of modification (for us and advanced users)
• Incorporation of features needed by Scientists

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NAMD 3 New Features

• Scientific/Numeric Modules
• Implicit solvent models (e.g, generalized Born)
• Replica exchange (e.g., 10 on 16 processors)
• Hybrid quantum/classical mechanics
• Self-consistent polarizability
• with a (sequential) CPU penalty of less than
  100.
• Fast nonperiodic (and periodic) electrostatics
• using multiple grid methods.
• A Langevin integrator that permits larger time
  steps
• by being exact for constant forces
• An integrator module that computes shadow energy.

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Terascale Biology and Resources
PSC LeMieux
TeraGrid
CRAY X1
NCSA Tungsten
ASCI Purple
Riken MDGRAPE
Red Storm Thors Hammer
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NAMD on Charm

• NAMD uses these diverse resources using Charm
• Active computer science collaboration (since
  1992)
• Object array - A collection of objects,
• Mapping of objects to processors handled by the
  system

Users view
A0
A1
A2
A3
A..
System view
A3
A0
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Namd 3 Features Based on Charm

• Adaptive load balancing
• Optimized communication
• Flexible, tuned, parallel FFT libraries
• Ability to change the number of processors
• Automatic Checkpointing
• Scheduling on the grid
• Fault tolerance
• Fully automated restart
• Surviving loss of a node
• Scaling to large machines
• fine-grained parallelism

1.02 TeraFLOPs
ATPase synthase
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Design for Programmability

• Software Goal
• Modular architecture to permit reuse and
  extensibility
• NAMD 3 will be a major rewrite of NAMD
• Incorporate lessons learned in the past years
• Use modern features of Charm
• Re-factor software for modularity
• Separate physics modules from parallel framework
• Restructure for supporting planned features
• Algorithms that scale to even larger machines

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MDAPI
New Science modules
Replica exchange
QM
Implicit Solvents
Polarizable Force Field
Bonds related Force calculation
Integration
Pair-wise Forces calculation
PME
NAMD Core
Charm modules
FFT
Fault Tolerance
Grid Scheduling
Collective communication
Load balancer
Core CHARM
Clusters
Lemieux
Teragrid

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MDAPI Modular Interface
Dynamic discovery of engine capabilities
Front End Input/Output User Interface
Linked Executable
Engine Force Computation Integration, ..
LAN
VMD
Grid
Namd
Namd 2
Namd 3
Amber
MINDY
Charm
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Efficient Parallelization for IMD

• Characteristics
• Limited parallelism on small systems
• Real time response needed
• Fine grained parallelization
• Improve speedups on 4K-30K atom systems
• Time/step goal
• Currently 0.2s/step for BrH on single processor
  (P4 1.7GHz)
• Targeting 3ms/step on 64 processors (20 ps/min)
• Flexible use of clusters
• Timeshare background and interactive jobs

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Integration with CHARMM/Amber?

• Goal NAMD as parallel simulation engine for
  CHARMM/Amber
• Generate input files in CHARMM/Amber
• NAMD must read native file formats
• Run with NAMD on parallel computer
• Need to use equivalent algorithms
• Analyze simulation in CHARMM/Amber
• NAMD must generate native file formats

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Proud to be Programmers!