Tutorials

Location: The tutorials are located at the Collegium Conference Center.

Further questions: If you have any questions, please contact Patrick Norman.

Tutorials:

1. Using Linux Clusters at NSC
   09:00-12:00 tutorial session (Room Vitelius 2)
2. NorduGrid tutorial
   09:00-12:00 tutorial session (Room Vitelius 1)
3. GAMESS-UK—Chemistry on the Computer
   08:30-12:30 tutorial session (Room Lyceum 1)
   15:30-17:30 hands-on session
4. Beowulfs—Design and Installation, an Introduction
   09:00-12:00 tutorial session (Room Lyceum 2)

Using Linux Clusters at NSC

Purpose:
The purpose with this tutorial is to give the participant a crash course in how to use linux clusters. Even though the tutorial will focus on the NSC Cluster Environment (NCE) it will also include a fair amount of generic information.

Topics:

• Logging in and security
• Software environment overview
• Compilers
• Available MPI implementations
• The Maui scheduler
• Understanding system load
• Compiling MPI applications
• Running interactively
• Running in batch

Relevant web-links:
National Supercomputer Centre

Prerequisites:
In order to fully appreciate this tutorial a basic knowledge of Unix is required.

NorduGrid tutorial

Purpose:
The intent of this tutorial is to introduce basic concepts of grid computing, demonstrate the basic use and some more exotic applications of NorduGrid ARC grid middleware and computing environment, and to give the audience the basic skills needed to submit calculations to NorduGrid.

Topics:

• Grids in general
• Grid computing vs. local clusters and batch queue systems
• NorduGrid
• NorduGrid ARC middleware
• Scientific computing in NorduGrid

Relevant web-links:
Nordugrid
Grid workshop (organized by CSC in Espoo, Finland)

Prerequisites:
In order to fully appreciate this tutorial a basic knowledge of scientific computing, batch queue systems and Linux is required. The latter half of the lecture consists of hands-on tutorial material. We encourage the participants to bring their personal laptops with working wireless lan (WLAN) to the lecture. The NorduGrid ARC client software can be installed on Linux machines during the hands-on tutorial. An SSH connection to a machine with pre-installed NorduGrid client software is provided for both Linux and Windows users. However, don't hesitate to sign up even if you don't have a laptop. You can go through the hands-on exercises together with some other participant who has one.

GAMESS-UK—Chemistry on the Computer

Purpose:
Computational chemistry and Quantum Chemistry in particular, aims at solving chemically related problems by means of calculation. Many aspects of chemistry are addressed by such computations; the equilibrium configuration of molecules, the making or breaking of molecules to make or dissociate chemical bonds, the excitation or ionization of molecular species analysed experimentally by spectroscopy, and the treatment of molecular properties. All of these issues are of immediate concern in a wide range of applications, and provide the ability of the computational chemist to make a major impact in the field. The goal of the computational chemist is thus to understand and predict chemistry and chemical properties in terms of electronic structure. This tutorial should provide the appropriate background and experience of, (i) the variety of popular computational electronic structure methods that underpin such computations, and the associated chemical accuracy available from these methods, (ii) the application of these methods, in particular using a standard electronic structure program called GAMESS-UK.

Topics:
Two 2-hour tutorial sessions on GAMESS-UK are presented, the first an introduction and description of the program basics, the second dealing with more advanced options available within the program. Both sessions are intended to provide some insight into the range of chemical problems amenable to study. The first session provides an overview of quantum chemistry methods and associated functionality within GAMESS-UK; here we provide details of specifying the molecular geometry, the basis set, and undertaking self consistent Hartree Fock (SCF) calculations and corresponding studies using Density Functional Theory (DFT).
In the second tutorial session we first describe the variety of options available for analysing the wavefunctions computed using the code; molecular properties, graphics and visualisation. The computation of stationary points on potential energy surfaces is considered, both equilibrium geometries and transition states, followed by an overview of the variety of available post Hartree Fock methods for the treatment of electron correlation. Consideration is given to the available methods for performing valence-only calculations and for computing solvation energies, and a description given of the variety of interfaces to other analysis packages: NBO and AIMPAC. We also consider the variety of QM/MM methods available for dealing with macromolecular systems too large for ab initio treatments alone. Finally we consider the functionality and performance of the parallel code, and provide trouble-shooting advice intended to help the user in recognising and dealing with potential problems.

In the practical, hands on session, we apply the theory of electronic structure to a variety of problems through a number of worked examples using the electronic structure program, GAMESS-UK. A Graphical User Interface (GUI) will be demonstrated and made available for the session. For further details on the program, click [here] to find details on the functionality of the code, documentation, and its usage in a variety of chemical applications.

Relevant web-links:
Computing for Science Ltd (developers of GAMESS-UK)

Prerequisites:
A suitable background for you as a participant is that you have at least passed a course in Modern Physics or Chemistry, have an interest or potential interest in the field of computational chemistry, and have some acquaintance with the associated techniques.

Beowulfs—Design and Installation, an Introduction

Purpose:
This tutorial is an introduction for anyone who are going to accuire and install a beowulf for high performance computing. It will cover both the time before the purcase and the initial installation after.

Installation and execution of application software is no covered in this tutorial.

Practial issues will, of natural reasons, be slightly coloured by our experience of Beowulfs at National Supercomputer Centre.

Topics:
The tutorial consist of two parts. In the first part we focus on the process of creating the hardware specification of a Beowulf system for high performance computing. We will have the cost of solution in mind when we address the questions.

• Why Beowulf—a short motivation
• Typical configurations
• Performance requirements
• A glimpse of current processor architectures
• Interconnects (Ethernet, SCI, Myrinet, Infiniband, others)
• Benchmarking
• Floorspace, Power and Cooling
• Reliablity, Accessibility, Serviceability

• Open source vs. commercial solutions
• Installation procedure
• The Linux operating system and distributions
• Job management, queuing systems, scheduling
• Compilers, MPI, libraries
• Managing nodes and users
• Monitoring
• Security issues

Relevant web-links:
Beowulf.org

Prerequisites:
A basic knowledge of PC hardware architecture is assumed. To fully appreciate the tutorial a knowledge of Linux on administration level is required.