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guide:induction1

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guide:induction1 [2020/03/27 09:15]
kevin created 		guide:induction1 [2021/12/09 16:42] (current)
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 ======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=====
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 </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.
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 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:
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   /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}}.
 +
 +
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