ARCHER White Papers

White Papers produced by the ARCHER Service.

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 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)

Monitoring the Cray XC30 Power Management Hardware Counters

Version 1.3, 19 Dec 2014

Michael Bareford, EPCC, The University of Edinburgh

Monitoring code power usage using the Cray XC30 hardware counters. Impact of compiler and parallel programming model on power consumption on ARCHER.

Full white paper (PDF)

Performance of Parallel IO on ARCHER

Version 1.1, 15 Jun 2015

David Henty, Adrian Jackson, EPCC, The University of Edinburgh
Charles Moulinec, Vendel Szeremi, STFC, Daresbury

Performance benchmarchs and advice for parallel IO on ARCHER. This is work in progress and will be continually updated.

Full white paper (PDF)

Source code

What's with all this Python import scaling, anyhow?

Version 1.0, 17 Dec 2014

Nick Johnson, EPCC, The University of Edinburgh

Addressing the issue of poor scaling performance on Python import. This is work in progress and will be continually updated.

Full white paper (PDF)