Download ppt - NAMD Development Goals

NIH Resource for Biomolecular Modeling and Bioinformaticshttp://www.ks.uiuc.edu/

Beckman Institute, UIUC

NAMD Development Goals

L.V. (Sanjay) KaleProfessor

Dept. of Computer Sciencehttp://www.ks.uiuc.edu/Research/namd/



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

• Goals:– High performance– Ease of use:

• configuration and run

– Ease of modification (for us and advanced users)• Maximize reuse of communication and control patterns• Push parallel complexity down into Charm++ runtime

– Incorporation of features needed by Scientists



NAMD 3 New Features

• Software Goal:– Modular architecture to permit reuse extensibility

• Scientific/Numeric Modules:– Implicit solvent models (e.g, generalized Born)– Replica exchange (e.g., 10 on 16 processors)– Self-consistent polarizability with a (sequential) CPU penalty of

less than 100%.– Hybrid quantum/classical mechanics– 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.



Design

• NAMD 3 will be a major rewrite of NAMD– Incorporate lessons learned in the past years– Use modern features of Charm++– Refactor software for modularity– Restructure for supporting planned features– Algorithms that scale to even larger machines



Programmability

• NAMD3 Scientific Modules:– Forces, integration, steering, analysis– Keep code with a common goal together– Add new features without touching old code

• Parallel Decomposition Framework:– Support common scientific algorithm patterns– Avoid duplicating services for each algorithm– Start with NAMD 2 architecture (but not code)



Core CHARM++

Clusters Lemieux Teragrid

Collective communication Load balancer

FFT Fault Tolerance Grid Scheduling

Bonds related Force calculation

Integration Pair-wise Forces calculation

PME

Charm++ modules

NAMD Core

Replica exchange QM Implicit Solvents Polarizable Force Field

MDAPI

…

New Science modules



MDAPI Modular Interface

• Separate “front end” from modular “engine”• Same program or over a network or grid• Dynamic discovery of engine capabilities, no

limitations imposed by interface• Front ends: NAMD 2, NAMD 3, Amber,

CHARMM, VMD• Engines: NAMD 2, NAMD 3, MINDY



Terascale Biology and ResourcesPSC LeMieux

RikenMDGRAPE

NCSATungsten

TeraGrid

ASCI Purple

Red StormThor’s Hammer

CRAY X1



NAMD on Charm++• Active computer science collaboration (since 1992)• Object array - A collection of chares,

– with a single global name for the collection, and– each member addressed by an index– Mapping of element objects to processors handled by the system

A[0] A[1] A[2] A[3] A[..]

A[3]A[0]

User’s view

System view



NAMD3 Features Based on Charm++

• Adaptive load balancing• Optimized communication

– Persistent Communication, Optimized concurrent multicast/reduction• Flexible, tuned, parallel FFT libraries• Automatic Checkpointing• Ability to change the number of processors • Scheduling on the grid• Fault tolerance

– Fully automated restart– Survive loss of a node

• Scaling to large machines– fine-grained parallelism for PME: bonded and nonbonded force

evaluations



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 on 0.003s/step on 64 processors of faster machine, that is

20picosecond/minute

• Flexible use of clusters– Migrating jobs (shrink/expand)– Better utilization when machine is idle



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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