ARCHER User Guide
This guide explains how to make use of the ARCHER facility. It is designed with the needs of new users in mind, but will also be a useful reference for everyone.
The following screencast demonstrates how to access help in the ARCHER terminal once you are connected:
An introduction to the ARCHER facility. This includes links to information on the hardware and software installed on the system.
How to access the ARCHER facilities and transfer data to and from ARCHER.
- 2.1 Interactive access
- 2.2 Transferring data to and from ARCHER
- 2.3 Making access more convenient using a SSH Agent
Information on using budgets (for CPU time), the ARCHER filesystems and managing your resources using the ARCHER SAFE.
- 3.1 The ARCHER administration web site (SAFE)
- 3.2 Checking your CPU-time (kAU) quota
- 3.3 ARCHER Filesystems
- 3.4 Disk quotas
- 3.5 File permissions and security
- 3.6 Sharing data with other ARCHER users
- 3.7 Sharing data between systems
- 3.8 File IO Performance Guidelines
- 3.9 Data archiving
- 3.10 Use of /tmp
- 3.11 Backup policies
Using the application development environment on ARCHER: using modules to control compilers and libraries, compiling and linking code, accessing debugging and performance analysis tools.
- 4.1 Information on the available modules
- 4.2 Loading, unloading and swapping modules
- 4.3 Things to watch out for
- 4.4 Compiler wrapper scripts
- 4.5 Available compiler suites
- 4.6 Using dynamic linking/libraries
- 4.7 Compiling for Postprocessing/Serial Nodes
- Switching to older/newer programming environment releases
How to run jobs on ARCHER facilities and more information on the job submission system.
- 5.1 Using PBS Pro
- 5.2 Output from PBS jobs
- 5.3 bolt: Job submission script creation tool
- 5.4 Running Parallel Jobs
- 5.4.1 PBS Submission Options
- 5.4.2 Parallel job launcher aprun
- 5.4.3 Task affinity for "unpacked" jobs
- 5.4.4 Example: job submission script for MPI parallel job
- 5.4.5 Example: job submission script for MPI parallel job on large memory nodes
- 5.4.6 Example: job submission script for OpenMP parallel job
- 5.4.7 Example: job submission script for MPI+OpenMP (mixed mode) parallel job
- 5.4.8 Interactive Jobs
- 5.5 Array Jobs
- 5.6 Sharing Nodes with OpenMP/Threaded Jobs
- 5.7 Python Task Farm
- 5.8 Job Submission System Layouts and Limits
- 5.9 checkScript: Script validation tool
- 5.10 Setting a time limit for aprun
- 5.11 Low Priority Access
- 5.12 Long Queue Access
- 5.13 Short (debug) Queue Access
- 5.14 Reservations
- 5.15 Serial Queues
- 5.16 OOM (Out of Memory) Error Messages
This chapter describes how to use the Python programming language on ARCHER on both the login and post-processing nodes and on the compute nodes.
- 6.1 Deciding which modules to use
- 6.2 Python for data analysis: the Anaconda distributions
- 6.3 Python for HPC: the native distributions
- 6.4 Virtual Environments
This chapter gives some help on using Linux on ARCHER.