Shell_Scripting.pdf

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AICT High Performance Computing Workshop

Shell Scripting

With Applications to

HPC

Edmund Sumbar

research.support@ualberta.ca

Shell Scripting

High performance computing environment (1)

batch job

head node

execution nodes

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Shell Scripting

High performance computing environment (2)

• Portable Batch System (PBS)

• Batch job described by a PBS script

• PBS script is a shell script

• Therefore, a batch job is a shell script

• Also, shell scripts for utility purposes

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Shell Scripting

What is a shell (1)

Internet

head node

desktop

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Shell Scripting

What is a shell (2)

• ssh client (on desktop) connects to ssh server (on head node)

• User authentication (login)

• A “shell” program is launched on head node (login shell)

• Local ssh client displays the results from the shell

• Allows you to execute commands interactively on the head node

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Shell Scripting

Two major shell program variants

• Bourne-like shells

•

ksh

•

bash

• C-like shells

•

csh

•

tcsh

• Look for your

CCID

/etc/passwd

•

echo $SHELL

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Shell Scripting

Very little difference for basic interactive use

Non-interactive use

• Execute a sequence of commands contained in a file (script)

• More advanced usage

• Differences in shell syntax become important

Focus on the bash shell

Reference documentation

•

man bash

•

info bash

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Shell Scripting

Example commands (* internal command)

•

cd*

•

mkdir

•

cat

•

diff

•

find

•

grep

•

read*

•

chmod

•

awk

•

kill*

•

sleep

•

echo*

•

exit*

•

qsub

•

qstat

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Shell Scripting

Types of commands

• Simple

•

ls ~/src > filelist

•

test -e mhd.c

• Pipeline (sequence of one or more simple commands)

•

cat mhd.c | grep MPI | grep -v Bcast

• List (sequence of one or more pipelines)

•

cd ~/src ; test -e mhd.c && cp mhd.c mhd2.c &

• Compound commands (act on lists)

•

if ! grep MPI mhd.c ; then echo serial code ; fi

•

for f in * ; do test –L $f && rm $f ; done

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Shell Scripting

Three ways to execute a script

• If script syntax is appropriate for current shell, set executable bit

on the file (chmod), and run script file directly

• Run shell program with script file as argument

(bash

scriptfile)

• Specify the path to the shell program on the first line, set the

executable bit, and execute the script directly (#!/bin/bash same

effect as

/bin/bash scriptfile)

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Advanced-bash-shell-scripting-guide.pdf (2677 KB)
Pro Bash Programming.pdf (5903 KB)
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