Todays Practical Experience'

1
Todays Practical Experience.

• You will be able to have a go at the following
• Creating your own submit files
• Submitting some jobs
• Monitoring your jobs and the pool
• Removing your jobs
• Using the basic web tools

2
Initial admin stuff

• You are all in front of a computer. Some may have
  to share.
• Login/Password as per instructions on sheet in
  front of the PC.
• Open up PuTTY- The location of the program is on
  the white-board.
• Enter the Host Name in the top box.
• Host Name chinon.geol.ucl.ac.uk
• Hit open at the bottom of the GUI.
• When the shell terminal opens, enter the
  following and hit enter
• Loginguest
• Password guest!
• Pwd You should be in /usr/people/guest.
• This directory contains 30 subdirectories. Your
  PC has been assigned one- its on the sheet. Once
  issued, cd to that directory, and pwd to check.
• THIS IS YOUR DIRECTORY FOR THE DURATION OF THE
  SESSION, AND WILL PREVENT YOU FROM OVERWRITING
  OTHER PEOPLES WORK!

3
Task 1 create a simple submit file

• There are 4 files in your directory. They are the
  input files for Abinit.exe
• Note The primary input file (files.abi) MUST BE
  SPECIFIED AS SUCH IN THE SUBMIT FILE.
• The location of the abinit executable is as
  follows
• /home4/arnaud/bin/abinit.exe
• You will need to specify a log file, an error
  file and an output file.
• You will have to use vi to create the submit
  file. If you dont know how, ask us!
• Create an input file which submits one single
  abinit job and returns the results to your
  working directory. This submit file is simpler
  than the one I showed you earlier.
• For help go to http/slamdunk.geol.ucl.ac.uk/pwil
  son, where you will find links to the power point
  presentation from earlier today, and the UCL
  condor documentation. Or, go to
  http//www.cs.wisc.edu/condor and look at the
  manuals submitting a job section.
• ASK US FOR HELP!

4
Task 2 create a multi-job submit file

• The task
• You are asked to run 6 abinit programs.
• Each needs the four input files.
• Each requires a slightly edited version of
  input.abi
• How are you going to do this?
• Its similar to the metadise example I gave
  earlier, but a bit more complicated by the fact
  that it has 4 input files, one of which
  (files.abi) IS THE primary input and must be
  specified as such using the field ltINPUT
  filenamegt in addition to the transfer_input_files
  field.
• Give it a go! Use the previous example as a base
  submit file.
• When you have your files sorted into the right
  places, edit the input.abi files using the vi
  editor, by changing the value of the ecut line
  from its default of 45 to something bigger or
  smaller, so that your 6 jobs each take a
  different length of time to complete. Its the
  line in red on the next page

5

• Bulk MgO, 2 atoms
• KPTS
• kptopt 1 Option for the automatic
  generation of k points,
• nshiftk 1
• shiftk 0.0 0.0 0.0 These shifts will be the
  same for all grids
• ngkpt 4 4 4
• Definition of the unit cell
• acell 34.21 angstroem
• rprim 0.0 0.5 0.5
• 0.5 0.0 0.5
• 0.5 0.5 0.0
• Definition of the atom types
• ntype 2 There are two types of
  atom
• zatnum 12 8 The keyword "zatnum"
  refers to the atomic number of the
• possible type(s) of
  atom. The pseudopotential(s)
• mentioned in the "files"
  file must correspond
• to the type(s) of atom.
  Here, type 1 is the Aluminum,
• type 2 is the Arsenic.