Dates and Times of Workshop

Monday 14th February 2pm - 4pm

Tuesday 15th February 2pm - 4pm

Overview

The purpose of this workshop is to ensure that you have the computational skills needed to undertake the VMD and NAMD workshops (Workshop Parts 2 and 3), using the Centre for Scientific Computing (CSC) linux computing facilities.

Prior to the workshop you should have requested an account on the CSC machines and installed the NX Client on your laptop.

Aims

This workshop is not directly assessed but it is expected that by the end of the workshop you will be able to:

• Competently manipulate files, directories and utilities under the linux operating system;
• Demonstrate a familiarity with the emacs editor;
• Be able to plot data using xmgrace;
• Be able to run jobs on the COW (i.e. submit jobs to the queue).

Exercises

1. Open up the NX client and log on to godzilla.csc.warwick.ac.uk. You will now be able to see your linux desktop.
2. To open up a terminal window click on the green icon on the bottom left of the screen and the click on the terminal icon.
3. For this workshop we will use the material from Session 1 of the CSC MSc module CY900 Foundations in Scientific Computing. Work through the material at your own pace; you do not need to do absolutely everything but you should make sure that you have achieved the aims of the workshop listed above.
4. Follow the steps below to learn how to run jobs on the COW.

Running jobs on the COW

CSC desktops operate together as a Cluster of Workstations (COW) and any computation (job) expected to take more than a few minutes MUST be submitted to the COW.

You should only use godzilla for editing, compiling, and very short interactive runs (seconds, not minutes or hours).

Detailed instructions on using the COW are given at http://www2.warwick.ac.uk/fac/sci/csc/local/desktop/cow/ (you will need your CSC username and password to access the documentation).

Below is a worked example of how to submit a short, test molecular dynamics simulation of a box of water using the NAMD simulation package. The use of NAMD will be covered in detail in Part 3 of the Workshop but for now we will just focus on the practical aspect of running the simulation on the COW.

Make a new directory from which to run the test simulation of a box of water:

mkdir water_box

Navigate to the directory:

cd water_box

Download these input files and save them in the water_box directory. Unzip the files:

unzip water.zip

You will see that there are 4 NAMD input files (all called “water.something”) and a file called job.pbs which is the pbs script that enables you to submit the simulation to the queue. Examine job.pbs using:

cat job.pbs

Comments in the file begin with the # symbol. Commands to the queuing system begin with #PBS. Further explanation of the file format is given at https://rcs.csc.warwick.ac.uk/twiki/bin/view/Main/TorqueUserGuide.

Before you can run the simulation you need to load the NAMD module (this configures your linux environment for running NAMD):

module load namd

There is a dedicated queue (called "ch926") for running the simulations for this module. Now you can submit the test simulation using the qsub command:

qsub -q ch926 job.pbs

You can view the status of the queue using:

qstat

or:

qstat –u username

to view only the jobs that you have submitted.

The output of qstat looks something like this:

Job id         Name        User       Time Use S Queue

-------------- ----------- ---------- -------- - -----

251799.foo     run_01.pbs  mssxxx     85:45:19 R troisi         

251800.foo     run_02.pbs  mssxxx     85:42:46 R troisi         

251802.foo     job.pbs     mssyyy     86:39:21 R nazgul         

251805.foo     volume20    msszzz     85:14:06 R troisi         

251836.foo     protein     mssyyy            0 Q nazgul 

251836.foo     volume30    msszzz            0 Q troisi 

The status of the job is indicated by Q or R (there are also some other possibilities). Q means a job is in the queue but has not started running; R means the job is running.

Note: To delete a job that you have submitted to the queue type:

qdel job_id

where the job_id is the number that appears in the left hand column.

Once your job is complete it will exit the queue and you will see two output files jobname.ejobid and jobhame.ojobid. The .e file will contain any error messages and the .o file will contain any standard output.

For completeness, you can visualise the simulation that you have just run using VMD. Again, we will cover the use of VMD in more detail in Part 2 of the workshop. First load the VMD module:

module load vmd

Then open the output trajectory file using vmd

vmd water.psf water.dcd

The trajectory will load into VMD and you can play it back from the VMD Main window.