The HECToR Service is now closed and has been superceded by ARCHER.

10. Software on HECToR

10.1 Simulation Software Packages

There are a number of third party applications and libraries supported on the service:

Amber/PMEMD A package of molecular simulation programs and analysis tools.
CASINO A code for quantum Monte Carlo electronic structure simulations of finite and periodic systems.
CASTEP A software package which uses density functional theory to provide a good atomic-level description of all manner of materials and molecules.
CP2K A freely available program to perform atomistic and molecular simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and classical pair and many-body potentials.
CPMD A parallelised plane wave/pseudopotential implementation of Density Functional Theory, particularly designed for ab initio molecular dynamics.
DL_POLY A general purpose molecular dynamics simulation package.
GAMESS GAMESS is a program for ab initio molecular quantum chemistry. Briefly, GAMESS can compute SCF wavefunctions ranging from RHF, ROHF, UHF, GVB, and MCSCF. Correlation corrections to these SCF wavefunctions include Configuration Interaction, second order perturbation Theory, and Coupled-Cluster approaches, as well as the Density Functional Theory approximation.
GROMACS GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. It is primarily designed for biochemical molecules like proteins, lipids and nucleic acids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers.
GS2 A package to study gyro-kinetic turbulence in fusion experiments and astrophysical plasmas.
LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) a classical molecular dynamics code.
NAMD A parallel molecular dynamics application designed to simulate large bio-molecular systems. It is developed and maintained by the University of Illinois at Urbana-Champaign.
NWChem NWChem aims to provide its users with computational chemistry tools that are scalable both in their ability to treat large scientific computational chemistry problems efficiently, and in their use of available parallel computing resources from high-performance parallel supercomputers to conventional workstation clusters. The NWChem software can handle: Biomolecules, nanostructures, and solid-state; From quantum to classical, and all combinations; Gaussian basis functions or plane-waves; Scaling from one to thousands of processors; Properties and relativity.
R/SPRINT R is a free software environment for statistical computing and graphics. SPRINT provides an easy access to high performance computing for the analysis of high throughput post genomic data using the statistical programming language R.
SIESTA (Spanish Initiative for Electronic Simulations with Thousands of Atoms) is a program to perform electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids.
VASP A package for ab initio, quantum-mechanical, molecular dynamics simulations.

We are currently adding documentation on how to use the centrally installed software to the website. So the list above is work in progress. Please check the HECToR User Wiki for more information on the packages available and how to access and run them.

Information on the latest versions of modules and upcoming changes is also available at:

10.2 HECToR System Software

Operating System

Cray Linux Environment (CLE) is the operating system in use on HECToR. It consists of two main components: Compute Node Linux (CNL) for the compute nodes and a fully featured Linux distribution for the service nodes. The service nodes include the login, I/O and system nodes.

The Compute Node Linux kernel deployed on the compute nodes is a stripped down version of Linux, designed to be extremely lightweight to limit the number of interruptions to the compute process by the operating system. The benefits are excellent scalability to extremely large process counts and minimal variations of application run time. On the other hand this leads to some services, which a very limited number of applications expect from a fully featured OS, being unavailable on the compute nodes.

9. Tools | Contents | 11. Grid computing