Guide to Running ATK in Parallel
Introduction
Atomistix ToolKit
Guide to running in parallel
Version
12.2.0
Copyright © 2008–2012 QuantumWise A/S
Legal Notice
Table of Contents
Introduction
Quick guide
Prerequisites
How to run
Test the parallel setup
How many MPI processes to use?
Additional parallelization via OpenMP threading (for multi-core machines)
Detailed parallel guide
System requirements
Hardware considerations
Library requirements
License considerations
Launching a parallel job using MPICH2
How many nodes to run on?
Useful MPICH2 tips
Controlling threading
Resource allocation via queue systems
Parallelization strategies
Definitions
Cores, sockets, and nodes
Parallelization technologies
Which parts of ATK are parallelized?
MPI
OpenMP threading
How to choose a parallelization strategy
Balancing MPI and threading
Parallelization strategies for different systems
Summary
Appendix
Simple bash script for launching mpiexec
Advanced bash script for launching mpiexec
Simple PBS script
Longer PBS script
mpdboot
MPI safety in I/O operations
