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ARCHER White Papers

White Papers produced by the ARCHER Service.

Parallel I/O Performance Benchmarking and Investigation on Multiple HPC Architectures

Version 1.1, May 10, 2017

Andy Turner, Xu Guo, Dominic Sloan-Murphy, Juan Rodriguez Herrera, EPCC, The University of Edinburgh
Bryan Lawrence, Met Office, United Kingdom
Chris Maynard, The University of Reading

Solving the bottleneck of I/O is a key consideration when optimising application performance, and an essential step in the move towards exascale computing. Users must be informed of the I/O performance of existing HPC resources in order to make best use of the systems and to be able to make decisions about the direction of future software development effort for their application. This paper therefore presents benchmarks for the write capabilities for ARCHER, comparing them with those of the COSMA, UK-RDF DAC, and JASMIN systems, using MPI-IO and, in selected cases, the HDF5 and NetCDF parallel libraries.

Full white paper (PDF)

Source code (GitHub)

Using Dakota on ARCHER

Version 1.0, March 22, 2017

Gordon Gibb, EPCC, The University of Edinburgh

Dakota[1] is a toolkit that automates running a series of simulations whose input param- eters can be varied in order to determine their effects on the simulation results. In par- ticular, Dakota can be used to determine optimal parameter values, or quantify a model’s sensitivity to varying parameters.

This white paper describes how to use Dakota on ARCHER.

Full white paper (PDF)

UK National HPC Benchmarks

Version 1.0, March 16, 2017

Andy Turner, EPCC, The University of Edinburgh

This paper proposes an updated set of benchmarks for the UK National HPC Service based on historical use patterns and consultations with users.

Full white paper (PDF)

Implementation of Dual Resolution Simulation Methodology in LAMMPS

Version 1.2, October 19, 2016

Iain Bethune, EPCC, The University of Edinburgh
Sophia Wheeler, Sam Genheden and Jonathan Essex, The University of Southampton

This white paper describes the implementation in LAMMPS of the Dual Resolution force-field ELBA. In particular, symplectic and time-reversible integrators for coarse-grained beads are provided for NVE, NVT and NPT molecular dynamics simulations and a new weighted load balancing scheme allows for improved parallel scaling when multiple timestepping (r-RESPA) is used. The new integrators are available in the 30th July 2016 release of LAMMPS and the load balancer in the lammps-icms branch. A version of LAMMPS with all of this functionality has been installed on ARCHER as the module 'lammps/elba' and is available to all users.

Full white paper (PDF)

Invertastic: Large-scale Dense Matrix Inversion

Version 1.0, June 15, 2016

Alan Gray, EPCC, The University of Edinburgh

This white paper introduces Invertastic, a relatively simple application designed to invert an arbitrarily large dense symmetric positive definite matrix using multiple processors in parallel. This application may be used directly (e.g. for genomic studies where the matrix represents the genetic relationships between multiple individuals), or instead as a reference or template for those wishing to implement large-scale linear algebra solutions using parallel libraries such as MPI, BLACS, PBLAS, ScaLAPACK and MPI-IO. The software is freely available on GitHub and as a centrally available package on ARCHER (at /work/y07/y07/itastic)

Full white paper (PDF)

VOX-FE: New functionality for new communities

Version 1.1, June 10, 2016

Neelofer Banglawala and Iain Bethune, EPCC, The University of Edinburgh
Michael Fagan and Richard Holbrey, The University of Hull

This white paper describes new functionality implemented in the VOX-FE finite element bone modelling package funded by ARCHER eCSE project 04-11. In particular, we describe new features in the GUI for setting up realistic muscle-wrapping boundary conditions, improvements to the performance of the solver by using ParMETIS to generate optimal partitioning of the model, and better automation for the dynamic remodelling process. The VOX-FE code is freely available from https://sourceforge.net/projects/vox-fe/ under a BSD licence.

Full white paper (PDF)

Using NETCDF with Fortran on ARCHER

Version 1.1, January 29, 2016

Toni Collis, EPCC, The University of Edinburgh

This paper explains one particular approach to parallel IO based on the work completed in an ARCHER funded eCSE on the TPLS software package [2]: using NetCDF. There are multiple resources available online for using NetCDF, but the majority focus on software written in C. This guide aims to help users of ARCHER who have software written in modern Fortran (90/95 onwards) to take advantage of NetCDF using parallel file reads and writes.

Full white paper (PDF)

Voxel-based finite element modelling with VOX-FE2

Version 1.0, 20 May 2015

Neelofer Banglawala and Iain Bethune, EPCC, The University of Edinburgh
Michael Fagan and Richard Holbrey, The University of Hull

This white paper summarises the work of an ARCHER eCSE project to redevelop the VOX-FE voxel finite element modelling package to improve its capabilities, performance and usability. We have developed a new GUI, implemented as a Paraview plugin, a new solver which uses PETSc and demonstrated how iterative remodelling simulations can be run on ARCHER.

Full white paper (PDF)

Parallel Software usage on UK National HPC Facilities

Version 1.0, 23 Apr 2015

Andy Turner, EPCC, The University of Edinburgh

Data and analysis of parallel applications on UK National HPC facilities HECToR and ARCHER including:

Trends in application usage over time: which applications have declined in use and which have become more important to particular research communities; and why might this be?
Trends in the sizes of jobs: which applications have been able to increase their scaling properties in line with architecture changes and which have not? Can we identify why this is the case?
Changes in research areas on the systems: which areas have appeared/increased and which have declined?

Full white paper (PDF)

Supplementary Data

Using RSIP Networking with Parallel Applications on ARCHER Phase 2

Version 1.0, 7 Apr 2015

Iain Bethune, EPCC, The University of Edinburgh

Instructions on how to use RSIP to enable TCP/IP communications between parallel jobs on the compute nodes and the login nodes (and beyond). Two case study applications are shown: Parallel visualisation using ParaView, and Path Integral Molecular Dynamics with i-PI and CP2K.

Full white paper (PDF)