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workshops:hpcprac2

Practical 2: OpenMP & Using CHPC

Aim: to launch a parallel job on the CHPC cluster Lengau.

Slides

The slides for the OpenMP lecture on Linux will be posted.

Logging in

Download and install putty-ssh and connect to lengau.chpc.ac.za using the username (studentNN) and password provided.

User Guide

Documentation for the CHPC systems starts with the CHPC Quick Start Guide. Read it, but note the differences below which are specific to the studentNN accounts you are using.

Student Accounts

  • Your user name is: studentNN
  • Your project is: Wchpc
  • Your queue is: R522145
  • Your PBS group is: training

Interactive Session

A user can not simply ssh onto a compute node because you don't know which ones are not in use by a currently running job. But the PBSPro scheduler does know. So we ask the scheduler for an interactive job which gives us a login shell on a compute node:

qsub -I -P Wchpc -q R522145 -W group_list=training

Note:

  • -I selects an interactive job
  • you must specify the project Wchpc
  • the queue is R522145
  • you need to specify the training group.

Advanced options:

  • -l select=1:ncpus=24:mpiprocs=24:nodetype=haswell_reg
  • interactive jobs only get one node: select=1
  • you can request all the cores on the node: ncpus=24
  • you can run MPI code: indicate how many ranks you want with mpiprocs=

If you find your interactive session timing out too soon then add -l walltime=4:0:0 to the above command line to request the maximum 4 hours.

OpenMP Part I

To carry out the exercises in the first OpenMP practical you must run the examples on a compute node and not the login node.

After logging on to lengau, the first thing you will do is request an interactive session on a compute node:

qsub -I -P Wchpc

Your prompt will change to something like:

[student00@cnode0004 ~]$

Remember, this is a login shell so you can change the environment as before, for example, change the prompt with

export PS1='\h:\w\$ '

and now see

cnode0004:~$ 

Practical 2 Worksheet

Download and follow the worksheet.

Copy the OpenMP_Tut.tar.gz file from the student00 home directory to your home directory.

cp ~/../student00/OpenMP_Tut.tar.gz ~/lustre

cd ~/lustre

Then untar (unpack) it.

tar -zxvf OpenMP_Tut.tar.gz

And then go into the OpenMP/ tut directory and start the practical. Have fun!

OpenMP Part II

Job Script

Most of the prac can be done in an interactive session.

/var/www/wiki/data/pages/workshops/hpcprac2.txt · Last modified: 2017/07/05 09:27 by kevin