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UK Research Data Facility (UK-RDF) Guide

  • 1. Introduction
  • 2. Interactive access to UK-RDF
  • 3. UK-RDF File Systems
  • 4. Transferring Data to/from UK-RDF
  • 5. Using the UK-RDF Data Analytic Cluster (DAC)
  • User Guides & Documentation
  • Essential Skills
  • Quick Start Guide
  • ARCHER User Guide
  • ARCHER Best Practice Guide
  • Scientific Software Packages
  • UK Research Data Facility Guide
  • Knights Landing Guide
  • Data Management Guide
  • SAFE User Guide
  • ARCHER Troubleshooting Guide
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  • Screencast Videos

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UK Research Data Facility (UK-RDF) Guide

The UK Research Data Facility (UK-RDF), funded by EPSRC and NERC, is collocated with ARCHER and is housed at the ACF facility.

The Research Councils' vision behind the RDF:

  • Provide a high capacity robust file store;
  • Easily extensible in size and number of hosts - degree of future proofing and potential for increasing local post processing activities;
  • Operates independently of any one vendor's offering for compute;
  • Remotely accessible via an Edinburgh host - not restricted to through login nodes;

This guide describes the UK-RDF and provides information on how to use the facility.

If you have any questions about the RDF, please contact the ARCHER Helpdesk.

Contents

1. Introduction

An introduction to the UK-RDF facility. This includes information on the hardware.

  • 1.1 Acknowledging UK-RDF
  • 1.2 Disk Hardware
  • 1.3 Data Transfer Nodes (DTNs)
  • 1.3 Data Analytic Cluster (DAC)

2. Interactive access to UK-RDF

How to open an interactive connection to the UK-RDF resources

  • 2.1 Access via ARCHER
  • 2.2 Access via the Data Transfer Nodes (DTNs)
  • 2.2 Access via the Data Analytic Cluster
  • 2.4 Making access more convenient using a SSH Agent
    • 2.4.1 Setup a SSH key pair protected by a passphrase
    • 2.4.2 Copy the public part of the key to the remote host
    • 2.4.3 Enabling the SSH Agent
    • 2.4.4 Adding access to other remote machines
    • 2.4.5 SSH Agent forwarding

3. UK-RDF File Systems

Overview of the file systems on the UK-RDF

  • 3.1 ARCHER File Systems: /epsrc, /nerc, /general

4. Transferring Data to/from UK-RDF

Best practice for transferring data to/from UK-RDF

  • 4.1 Data Management Guide

5. Using the UK-RDF Data Analytic Cluster (DAC)

How to get use the UK-RDF data analytic cluster (DAC). All nodes on the DAC have high-bandwidth, direct Infiniband connections to the UK-RDF disks.

  • 5.1 Accessing the Data Analytic Cluster
  • 5.2 System Software
  • 5.3 OMP_NUM_THREADS
  • 5.4 Compiling Code
    • 5.4.1 Serial Compilation
    • 5.4.2 MPI Compilation
    • 5.4.3 Build Tools
  • 5.5 Running Jobs
    • 5.5.1 Example job submission scripts: standard compute nodes
    • 5.5.2 Example job submission scripts: high memory compute nodes
    • 5.5.3 Interactive Jobs
  • 5.6 Using Python
    • 5.6.1 Python 3
  • 5.7 Installed Software
    • 5.7.1 Paraview
    • 5.7.2 VisIt
    • 5.7.3 R
    • 5.7.4 NetCDF
    • 5.7.6 HDF5
    • 5.7.7 FFTW 3
    • 5.7.8 BLAS and LAPACK
    • 5.7.9 ScaLAPACK

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