Set up of computers in Belfast.

The PCs in the machine rooms

The operating systems of these workstations is Windows. However, exercises will be run under a SUSE Linux system running within a "virtual machine" (Virtual Box) host by the native Windows system. For all practical purposes the presence of the host system should be transparent and you will be working under a full Linux installation containing all the programs one would expect to be present. The default shell is the bash shell. A Unix Help page is available here. Note that you must sit at the PC whose number corresponds to the number that is part of your user-id. You might loose data or damage someone else's work if you do not do this. What follows is a brief resume of the programs that you will need and are available.

If your host institution’s machine firewall permits it, you will be able to use sftp and ssh from the local Linux PC here to your own computer. The reverse will not be permitted – i.e. you cannot logon to a Queen's machine from outside the firewall.

Loading the Virtual Machine and booting the Linux system

• In order to boot the Windows system press Ctrl+Alt+Del
• Introduce the username and password for the University Network provided in your welcome letter. The start-up might be slow, so give it the necessary time
• Important. If you intend to transfer data to a USB stick, pen drive or external disk, the device must be plugged to the USB-port at this stage
• Go to: Start -> Programs -> Departmental Aps -> Mathematics and Physics -> Oracle VM Virtual Box
  
• Ignore warning about new VBox version (press OK)
• Double click on OpenSuse
• Read information about Auto Capture Keyboard and press OK
• Follow on-screen information about mouse pointer and press OK
• Ignore message about display colour mode (press OK)
• You can now maximize the VBox window and work comfortably under Linux.  In order to open a terminal go to Computer and click on Gnome Terminal or Xterm
• A final but necessary step. The first time you logon you will need to change the browser settings, otherwise you will not be able to access the network
• Go to Computer and start Firefox. Ignore the message on the screen and press OK
• Go to Edit->Preferences->Advanced->Network->Settings and select Autodetect proxy settings

Word processors and spreadsheets are available as part of the Open Office suite.

Browsers

• Mozilla firefox is installed on all machines, access via Computer tab, but you can always drag the icon to the Desktop the first time you logon. You should use this browser to download all the exercises from the CCP5 website. In particular, you will need to use this browser for the DEMOCRITOS tutorial
  

Compilers

The following compilers are available at the Unix prompt

• gcc : the Gnu C-compiler

• gfortran: The Gnu Fortran 95 compiler. Some of the codes may be in fixed format requiring the appropriate flag:

gfortran –ffixed-form

Graphics Packages

• Two graphics packages are available: gnuplot and xmgrace. gnuplot has the greater functionality but xmgrace is easier to use for basic graph plotting

Molecular Graphics Programs

• jmol and rasmol are the basic viewers for use in the summer school. jmol is the viewer to use unless you are familiar with rasmol and prefer it. In order to use jmol type jmol.sh on the command line.
  

• XCrySDen is a visualisation code that can superimpose displays of isosurfaces and contours on molecular structures. You will need this if you take the electronic structure calculations advanced option

Editors

There are several editors that you may use for working with input files. Use whichever you are comfortable with

• vi - the venerable UNIX screen mode editor: use it if you know and love it. Otherwise avoid it.
• emacs – probably the commonest full-screen Unix editor in use

The Exercises

• Do not hesitate to ask questions if you have a problem, attract our attention and we'll try to sort it out. Sometimes you may find a colleague has cracked the problem already, so don't be too shy to ask him or her.
• For most of the exercises you will be provided with the programs you need, though you may be asked to edit the source or even write small supplementary programs yourself. You will also need to compile these programs, so be sure you use the right compiler.
• You are warned that the programs are not necessarily models of good programming or efficiency. That is not their purpose. Our intention has been to make their structure and function clear. If you can find ways of making the codes more compact or efficient, then feel free to try them out. If anything seems unclear, please point it out, so we can change it for everyone's benefit.

Copying Files

• In these workshops you will be required to copy (download) programs and files on to your PC. We have set things up so that you can do this via hyperlinks in the related web pages.
• Click on the hypertextualised name of the file, what happens then will depend on how your internet browser is configured:

1. A file browser will appear, asking you to supply the name of the file you want to save (the name suggested by the file browser will do) and where you want to save it (you should nominate the directory you have created for each day's exercises).
OR

2. The file will appear as a listing in the window of the web browser. (You can of course examine the file there if you wish, or use an editor later.) To save the file, you should go to the File menu of the internet browser and chose the Save As option. This will open the file browser for you to select the name and place of the file as described above. Remember to save the file as a text file (.txt) to prevent the browser inserting HTML keywords.

The Dell machine

This is also a Unix machine which you will use if you take the electronic structure calculations or the biosimulations advanced courses. The username and password are on your letter of introduction. Use the ssh command to access it. The machine address is delllogin.qub.ac.uk. To access the machine, you should issue the command

ssh username@delllogin.qub.ac.uk where username is the user name allocated to you.

Details of the machine can be found on the website http://www.qub.ac.uk/directorates/InformationServices/Research/HighPerformanceComputing/UsingtheSystems/DellCluster. Further details on how to use it will be found in the relevant exercises.

Jobs are submitted through a script and the qsub command. For a parallel job, the script should look like

#!/bin/bash
#PBS -N  job-name
#PBS -q  ccpst
#PBS -l nodes=X:ppn=Y
#PBS -e error.e
#PBS -o output.o
#PBS -l walltime=1:00:00
. /etc/profile.d/modules.sh
. ~/.bashrc
cd /home/your-username/path-to-execution-directory
cat $PBS_NODEFILE > machinefile
module load maui torque
mpirun -machinefile machinefile -np Z /path-to-executable/executable-name 

Where job-name = name of your job, X = number of nodes requested, Y = number of processors per node (8 maximum), walltime = estimated wall time for job completion (maximum 24 hs). Z = (X*Y) = number of processors requested. ccpst is the name of the queue dedicated to CCP5 jobs. Please do not submitt jobs to any other queue. executable-name and path-to-executable will be provided during the exercises. Bear in mind that full pathnames must be used.

This should be submitted with the command qsub myscript where myscript is the name of the file containing the script. Use qstat to check the status of your job and use qdel to kill your job, should this be necessary. Further details will be given with the exercises.