HEC 3.0 Documentation

This documentation is a guide to using the HEC 3.0 test bed, in particular the SLURM job scheduler which will replace the current SGE job scheduler. The structure of this guide is broadly similar to the current official HEC user guide so you can easily compare the two.

• HEC 3.0 Testbed - check here for the current status

Note

The HEC 3.0 test bed is under development, so check back regularly to see what changes have been made to best practice.

Contents

Overview of the HEC

• Introduction
• How the HEC Works
• Applying for HEC access

HEC Basics

• Logging in to the HEC
• Learning Linux/Unix
• Using Filestore on the HEC
• Using environment modules

Job submission and monitoring

• Job Submission on the HEC
• Monitoring jobs on the HEC
• Running large memory jobs on the HEC
• Job arrays - Submitting multiple similar jobs

Parallel job submission

• Overview of Parallel jobs
• Message Passing Interface (MPI) parallel jobs
• OpenMP parallel jobs
• Requesting specific node types
• GPU Jobs

Job templates for popular software

• Introduction
• Using C and Fortran compilers on the HEC
• ANSYS
• The COMSOL Multiphysics Package
• CP2K
• CST
• GROMACS
• The GNU Scientific Library (GSL)
• The LAMMPS molecular dynamics simulator
• The NAMD molecular dynamics simulator
• The Open Cognitive Environment (Open-CE) Software Suite
• The R Stats Package
• Stata and StataMP
• Turbomole