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guide:induction1

CHPC Induction

This is an introduction to the practical aspects of using the CHPC Lengau cluster. This page is an abbreviated overview of the full short course. More details will be delivered by the lecturer.

Links to slides and videos will be added later.

Connecting to Lengau

To connect to the CHPC cluster you will need to use the ssh protocol. This is most easily accomplished with the ssh program on Linux systems. If you do not have Linux on your laptop and are using MS Windows, please see the appropriate section of the Connecting to the CHPC guide.

On your Linux laptop, open a text terminal and type the ssh command:

ssh username@lengau.chpc.ac.za

where you will need to replace username with your user name, of course.

If you do not have an account on Lengau as part of a CHPC research programme then you will be provided with a temporary studentNN account valid for the duration of the workshop only.

For more information on ssh see the Connecting to the CHPC guide.

Linux shell

Once connected to Lengau you will be using the Linux shell command line interface (CLI). To be precise, the default shell is bash. When you successfully connect via ssh you will see a display similar to:

Last login: Mon Feb 24 12:07:46 2020 from 10.128.23.164

Welcome to LENGAU

################################################################################
#                                                                              #
# In order to receive notifications via email from the CHPC all users should   #
# be subscribed to the CHPC user distribution list. If you are not part of the #
# distribution list you can subscribe at the following link:                   #
# https://lists.chpc.ac.za/mailman/listinfo/chpc-users                         #
#                                                                              #
################################################################################ 
login2:~$ 

The first part is a welcome message. Read it first since important announcements will be displayed here: notice of shutdowns, your quota usage, et al.

Please take note of the login2:~$ – this is the shell prompt and it contains important information about your location in the system. The first part, before the colon, login2 indicates that you are on the login2 node of the cluster. This means that the command you type and the directories and files you have access to are not on your computer, they are on the CHPC login node. You are connected remotely to it over the Internet

The part after the colon, and before the $, displays your current working directory. Note, at first login this will just display ~ which is short hand for your home directory path.

Here are a few basic Linux commands which you can use:

pwd

This prints out the current working directory. When you do this for the first time it should display your home directory, e.g.,

/home/username

Note: username will be replaced by your user name. This is the actual full absolute path to your home directory and the ~ short form is equivalent to this.

ls

The ls command lists the files in the current working directory.

cd dir

Change directory to dir.

The lecturer will demonstrate the most commonly used commands.

Work Sheet

The practical portion of this short course uses a worksheet. This includes spaces for you to fill in notes and answer questions.

Interactive Job

The login nodes are not for any substantive computation, including compiling. Instead, request an interactive job through the PBSPro scheduler:

qsub -I 

You will then see (after a short delay) a display similar to:

login2:~$ qsub -I -q serial -l select=1:ncpus=12:mpiprocs=12 -P WCHPC
qsub: waiting for job 2665052.sched01 to start
qsub: job 2665052.sched01 ready

cnode0040:~$ 

Note that you are now connected to a compute node as indicated by the prompt: you are on cnode0004 and all commands you run will execute on this compute node and not on the login2 node.

First Job Script

#!/bin/bash
#PBS -N example01
#PBS -l select=1:ncpus=24:mpiprocs=24
#PBS -P Wchpc
#PBS -q smp
#PBS -l walltime=0:10:00
 
CWD=/mnt/lustre/users/$USER/example
 
 
 
cd $CWD
echo "Working directory is $CWD"
nproc=`cat $PBS_NODEFILE | wc -l`
echo "nproc is $nproc"
echo "Nodes used by this job:"
cat $PBS_NODEFILE
 
echo "Starting run..."
# Insert command to run here:
 
echo "... done."
The lecturer will explain this script and you will be able to write notes in your worksheet.
/var/www/wiki/data/pages/guide/induction1.txt · Last modified: 2020/04/16 19:22 by kevin