l Running CASTEP on the QUB Dell Cluster

Running CASTEP on the QUB Dell Cluster

The First Principles course practical sessions will involve using a powerful parallel computer clusters which runs a Red Hat version of the linux operating system.

Logging on to Dell and transferring files.

Dell is accessed using the SSH protocol, initially in command-line mode.

ssh <username>@delllogin.qub.ac.uk

Your Dell username and password are given on the School registration pack information. For convenience it is worth setting up an easy shortcut for login and file transfer to the Dell. Create/edit a file on the School linux virtual machine called ~/.ssh.config with contents

ControlMaster auto ControlPath ~/.ssh/master-%r@%h:%p host delllogin delllogin.qub.ac.uk hostname delllogin.qub.ac.uk user<your username>
ForwardAgent yes ForwardX11 yes

This will simplify the login command to

ssh delllogin

Furthermore if you start one login session, future login and file copy commands will not require a password.

To transfer files from the Linux virtual machine to the Dell use the scp command, e.g.

scp myfile dellogin:

See the tutorial on ssh and scp for more detailed instructions.

Setting up your Dell environment to access the tools

Edit your login setup file ~/.bash_profile (using any text editor) to set up your paths

Change the line setting the PATH variable from

PATH=$PATH:$HOME/bin

PATH=$PATH:$HOME/bin:/home/ccpst1/bin

and log out and in again. This will make the School software available to your account.

Running CASTEP on the Dell

The Dell system uses a batch job submission system of the kind that all simulation scientists must deal with. To avoid wasting time editing job scripts, I have set up a simple command to submit CASTEP jobs. CASTEP requires several input files to run. I have set up a very simple example for you of the mineral Forsterite. First create and change to a suitable working directory, for example

mkdir -p Work cd Work

Now unpack the test files:

tar xvfz /home/ccpst1/CCP5SS/Exercise_0.tar.gz

This will create a subdirectory named "Exercise_0". Briefly examine the contents of the files. The .cell and .param files are the two CASTEP input files describing the structure and the calculation, and the ".usp" files contain the pseudopotentials. Then invoke the script to submit a CASTEP job

castepsub -n 8 forsterite

This submits a batch job to run CASTEP on the files forsterite.cell and forsterite.param and requests a parallel run on 8 processors. You may monitor the progress of the job using the qstat command.

qstat -u my-userid

You may examine the output file forsterite.castep, to monitor the progress to SCF convergence. The run should take around 40 seconds.

Another castepsub option you will need later is

castepsub -n 8 -W 02:00:00 forsterite

to increase the job time limit to 2 hours.

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