User Tools

Site Tools


guide:induction1

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Next revision
Previous revision
guide:induction1 [2020/03/27 09:15]
kevin created
guide:induction1 [2020/04/16 19:22]
kevin [Connecting to Lengau]
Line 1: Line 1:
 ======CHPC Induction====== ======CHPC Induction======
  
-This is an introduction to the practical aspects of using the CHPC //Lengau// cluster.+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===== =====Connecting to Lengau=====
Line 12: Line 14:
 </​code>​ </​code>​
 where you will need to replace ''​username''​ with //your// user name, of course. 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 ''​student''​NN account valid for the duration of the workshop only.
  
 For more information on **ssh** see the //​[[guide:​connect|Connecting to the CHPC]]// guide. For more information on **ssh** see the //​[[guide:​connect|Connecting to the CHPC]]// guide.
Line 37: Line 41:
 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.// 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:​~$''​ -- this is the shell //prompt// and it contains important information about your //​location//​+Please take note of the ''​login2:​~$''​ -- 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: Here are a few basic Linux commands which you can use:
Line 47: Line 53:
   /​home/​username   /​home/​username
  
-Note: ''​username''​ will be replaced by //your// user name. +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   ls
   ​   ​
 The ''​ls''​ command lists the files in the current working directory. 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 {{:​guide:​worksheet.pdf|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:
 +
 +<​code>​
 +qsub -I 
 +</​code>​
 +
 +You will then see (after a short delay) a display similar to:
 +
 +<​code>​
 +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:​~$ ​
 +</​code>​
 +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=====
 +
 +<code bash>
 +#!/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."
 +</​code>​
 +
 +> The lecturer will explain this script and you will be able to write notes in your {{:​guide:​worksheet.pdf|worksheet}}.
 +
 +
/var/www/wiki/data/pages/guide/induction1.txt · Last modified: 2020/04/16 19:22 by kevin