Shell Scripting

Why Shell Scripting ?

▪ Shell scripts can be used to prepare input

files, job monitoring, and output processing.
▪ Useful to create own commands.
▪ Save lots of time on file processing.
▪ To automate some task of day to day life.
▪ System Administration part can be also
automated.

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 Objectives & Prerequisites

▪ After this workshop, you should be:

• Familiar with UNIX/LINUX, Borne Shell, shell
variables/operators
• Able to write simple shell scripts to illustrate
programming logic
• Able to write scripts for research computing purposes
▪ We assume that you have/know
• An account on the Emerald cluster
• Basic knowledge of UNIX/LINUX and commands
• UNIX editor e.g. vi or emacs
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 History of UNIX/Linux

▪ Unix is a command line operating system developed around

1969 in the Bell Labs
▪ Originally written using C
▪ Unix is designed so that users can extend the functionality
• To build new tools easily and efficiently
• To customize the shell and user interface.
• To string together a series of Unix commands to create
new functionality.
• To create custom commands that do exactly what we
want.
▪ Around 1990 Linus Torvalds of Helsinki University started off a
freely available academic version of Unix
▪ Linux is the Antidote to a Microsoft dominated future
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 What is UNIX/Linux ?
Simply put
▪ Multi-Tasking O/S
▪ Multi-User O/S
▪ Available on a range of Computers
▪ SunOS Sun Microsystems
▪ IRIX Silicon Graphics
▪ HP-UX Hewlett Packard
▪ AIX IBM
▪ Linux ….
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 UNIX/LINUX Architecture

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 What is a “Shell”?

▪ The “Shell” is simply another program on top of the

kernel which provides a basic human-OS interface.
• It is a command interpreter
 Built on top of the kernel
 Enables users to run services provided by the UNIX OS
• In its simplest form, a series of commands in a file is a shell
program that saves having to retype commands to perform
common tasks.

user
Shell
▪ How to know what shell you use
echo $SHELL
user OS

user

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 UNIX Shells

▪ sh Bourne Shell (Original Shell) (Steven Bourne of AT&T)

▪ bash Bourne Again Shell (GNU Improved Bourne Shell)
▪ csh C-Shell (C-like Syntax)(Bill Joy of Univ. of California)
▪ ksh Korn-Shell (Bourne+some C-shell)(David Korn of
AT&T)
▪ tcsh Turbo C-Shell (More User Friendly C-Shell).
▪ To check shell:
• $ echo $SHELL (shell is a pre-defined variable)
▪ To switch shell:
• $ exec shellname (e.g., $ exec bash or simply type $ bash)
• You can switch from one shell to another by just typing the name
of the shell. exit return you back to previous shell.
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 Which Shell to Use?

▪ sh ( Bourne shell) was considered better for programming

▪ csh (C-Shell ) was considered better for interactive work.
▪ tcsh and korn were improvements on c-shell and bourne shell
respectively.
▪ bash is largely compatible with sh and also has many of the nice
features of the other shells
▪ On many systems such as our LINUX clusters sh is symbolically linked to
bash, /bin/sh -> /bin/bash
▪ We recommend that you use sh/bash for writing new shell scripts but
learn csh/tcsh to understand existing scripts.
▪ Many, if not all, scientific applications require csh/tcsh environment
(GUI, Graphics Utility Interface)
▪ All Linux versions use the Bash shell (Bourne Again Shell) as the
default shell
• Bash/Bourn/ksh/sh prompt: $
• All UNIX system include C shell and its predecessor Bourne shell.
• Csh/tcsh prompt: %
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 What is Shell Script?

▪ A shell script is a script written for the

shell

▪ Two key ingredients

• UNIX/LINUX commands
• Shell programming syntax

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 A Shell Script Example
#!/bin/sh

`ls -l *.log| awk '{print $8}' |sed 's/.log//g' > file_list`

cat file_list|while read each_file

do
babel -ig03 $each_file".log" -oxyz $each_file".xyz“

echo '# nosymmetry integral=Grid=UltraFine scf=tight rhf/6-311++g** pop=(nbo,chelpg)'>head

echo ' ' >>head
echo ''$each_file' opt pop nbo chelp aim charges ' >> head
echo ' ' >>head
echo '0 1 ' >>head

`sed '1,2d' $each_file.xyz >junk`

input=./$each_file".com"
cat head > $input
cat junk >> $input
echo ' ' >> $input

done
/bin/rm ./junk ./head ./file_list
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 UNIX/LINUX Commands

File Management and Viewing To understand the working of the

command and possible options
Filesystem Mangement use (man command)
Help,Job/Process Management
Using the GNU Info System
Network Management (info, info command)
System Management Listing a Description of a Program
User Management (whatis command)
Printing and Programming Many tools have a long−style
Document Preparation option, `−−help', that outputs
usage information about the tool,
Miscellaneous including the options and
arguments the tool takes. Ex:
whoami --help

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 File and Directory Management

cd Change the current directory. With no arguments "cd" changes to the users home
directory. (cd <directory path>)
chmod Change the file permissions.
Ex: chmod 751 myfile : change the file permissions to rwx for owner, rx for group
and x for others (x=1,r=4,w=2)
Ex: chmod go=+r myfile : Add read permission for the group and others (character
meanings u-user, g-group, o-other, + add permission,-remove,r-read,w-write,x-exe)
Ex: chmod +s myfile - Setuid bit on the file which allows the program to run with
user or group privileges of the file.
chown Change owner.
Ex: chown <owner1> <filename> : Change ownership of a file to owner1.
chgrp Change group.
Ex: chgrp <group1> <filename> : Change group of a file to group1.
cp Copy a file from one location to another.
Ex: cp file1 file2 : Copy file1 to file2; Ex: cp –R dir1 dir2 : Copy dir1 to dir2

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 File and Directory Management

ls List contents of a directory.

Ex: ls, ls –l , ls –al, ls –ld, ls –R
mkdir Make a directory.
Ex: mkdir <directory name> : Makes a directory
Ex mkdir –p /www/chache/var/log will create all the directories starting from www.
mv Move or rename a file or directory.
Ex: mv <source> <destination>
find Find files (find <start directory> -name <file name> -print)
Ex: find /home –name readme -print
Search for readme starting at home and output full path, “/home" = Search starting at
the home directory and proceed through all its subdirectories; "-name readme" =
Search for a file named readme "-print" = Output the full path to that file
locate File locating program that uses the slocate database.
Ex: locate –u to create the database,
locate <file/directory> to find file/directory

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 File and Directory Management
pwd Print or list the present working directory with full path.
rm Delete files (Remove files). (rm –rf <directory/file>)
rmdir Remove a directory. The directory must be empty. (rmdir <directory>)
touch Change file timestamps to the current time. Make the file if it doesn't exist. (touch
<filename>)
whereis Locate the binary and man page files for a command. (whereis
<program/command>)
which Show full path of commands where given commands reside. (which <command>)

File viewing and editing

emacs Full screen editor.
pico Simple text editor.
vi Editor with a command mode and text mode. Starts in command mode.
gedit GUI Text Editor
tail Look at the last 10 lines of a file.
Ex: tail –f <filename> ; Ex: tail -100 <filename>
head Look at the first 10 lines of a file. (head <filename>)
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 File and Directory Management

File compression, backing up and restoring

compress Compress data.
uncompress Expand data.
cpio Can store files on tapes. to/from archives.
gzip - zip a file to a gz file.
gunzip - unzip a gz file.
tar Archives files and directories. Can store files and directories on tapes.
Ex: tar -zcvf <destination> <files/directories> - Archive copy groups of files. tar –zxvf
<compressed file> to uncompress
zip – Compresses a file to a .zip file.
unzip – Uncompresses a file with .zip extension.
cat View a file
Ex: cat filename
cmp Compare two files.
cut Remove sections from each line of files.
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 File and Directory Management

diff Show the differences between files.

Ex: diff file1 file2 : Find differences between file1 & file2.
echo Display a line of text.
grep List all files with the specified expression.
(grep pattern <filename/directorypath>)
Ex: ls –l |grep sidbi : List all lines with a sidbi in them.
Ex: grep " R " : Search for R with a space on each side
sleep Delay for a specified amount of time.
sort Sort a file alphabetically.
uniq Remove duplicate lines from a sorted file.
wc Count lines, words, characters in a file. (wc –c/w/l <filename>).
sed stream editor, extremely powerful!
awk an extremely versatile programming language for working on files

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 Useful Commands in Scripting

▪ grep
• Pattern searching
• Example: grep ‘boo’ filename
▪ sed
• Text editing
• Example: sed 's/XYZ/xyz/g' filename
▪ awk
• Pattern scanning and processing
• Example: awk ‘{print $4, $7}’ filename

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 Shell Scripting

▪ Start vi [Link] with the line

#!/bin/sh
▪ All other lines starting with # are comments.
• make code readable by including comments
▪ Tell Unix that the script file is executable
$ chmod u+x [Link]
$ chmod +x [Link]
▪ Execute the shell-script
$ ./[Link]

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 My First Shell Script
$ vi [Link]
#! /bin/sh

# The first example of a shell script

directory=`pwd`
echo Hello World!
echo The date today is `date`
echo The current directory is $directory
$ chmod +x [Link]
$ ./[Link]
Hello World!
The date today is Mon Mar 8 15:20:09 EST 2010
The current directory is /netscr/shubin/test

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 Shell Scripts

▪ Text files that contain sequences of UNIX commands ,

created by a text editor
▪ No compiler required to run a shell script, because
the UNIX shell acts as an interpreter when reading
script files
▪ After you create a shell script, you simply tell the OS
that the file is a program that can be executed, by
using the chmod command to change the files’ mode
to be executable
▪ Shell programs run less quickly than compiled
programs, because the shell must interpret each
UNIX command inside the executable script file
before it is executed

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 Commenting
▪ Lines starting with # are comments except the very
first line where #! indicates the location of the shell
that will be run to execute the script.
▪ On any line characters following an unquoted # are
considered to be comments and ignored.
▪ Comments are used to;
• Identify who wrote it and when
• Identify input variables
• Make code easy to read
• Explain complex code sections
• Version control tracking
• Record modifications

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 Quote Characters

There are three different quote characters with different

behaviour. These are:
“ : double quote, weak quote. If a string is enclosed in “ ”
the references to variables (i.e $variable ) are replaced
by their values. Also back-quote and escape \ characters
are treated specially.
‘ : single quote, strong quote. Everything inside single
quotes are taken literally, nothing is treated as special.
` : back quote. A string enclosed as such is treated as a
command and the shell attempts to execute it. If the
execution is successful the primary output from the
command replaces the string.
Example: echo “Today is:” `date`
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 Echo

Echo command is well appreciated when trying to debug

scripts.
Syntax : echo {options} string
Options: -e : expand \ (back-slash ) special characters
-n : do not output a new-line at the end.
String can be a “weakly quoted” or a ‘strongly quoted’
string. In the weakly quoted strings the references to
variables are replaced by the value of those variables
before the output.
As well as the variables some special backslash_escaped
symbols are expanded during the output. If such
expansions are required the –e option must be used.
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 User Input During Shell
Script Execution
▪ As shown on the hello script input from the standard
input location is done via the read command.
▪ Example
echo "Please enter three filenames:”
read filea fileb filec
echo “These files are used:$filea $fileb $filec”
▪ Each read statement reads an entire line. In the above
example if there are less than 3 items in the response
the trailing variables will be set to blank ‘ ‘.
▪ Three items are separated by one space.

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 Hello script exercise
continued…
▪ The following script asks the user to enter his
name and displays a personalised hello.
#!/bin/sh
echo “Who am I talking to?”
read user_name
echo “Hello $user_name”
▪ Try replacing “ with ‘ in the last line to see
what happens.

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 Debugging your shell scripts

▪ Generous use of the echo command will help.

▪ Run script with the –x parameter.

E.g. sh –x ./myscript
or set –o xtrace before running the script.

▪ These options can be added to the first line of the

script where the shell is defined.
e.g. #!/bin/sh -xv

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 Shell Programming

▪ Programming features of the UNIX/LINUX shell:

Shell variables: Your scripts often need to keep values in
memory for later use. Shell variables are symbolic names
that can access values stored in memory
Operators: Shell scripts support many operators, including
those for performing mathematical operations
Logic structures: Shell scripts support sequential logic (for
performing a series of commands), decision logic (for
branching from one point in a script to another), looping
logic (for repeating a command several times), and case
logic (for choosing an action from several possible
alternatives)

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 Variables

▪ Variables are symbolic names that represent values stored in memory

▪ Three different types of variables
• Global Variables: Environment and configuration variables, capitalized, such as
HOME, PATH, SHELL, USERNAME, and PWD.

When you login, there will be a large number of global System variables that are
already defined. These can be freely referenced and used in your shell scripts.

• Local Variables

Within a shell script, you can create as many new variables as needed. Any variable
created in this manner remains in existence only within that shell.

• Special Variables

Reversed for OS, shell programming, etc. such as positional parameters $0, $1 …

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 A few global (environment)
variables
SHELL Current shell
DISPLAY Used by X-Windows system to identify the
display
HOME Fully qualified name of your login directory

PATH Search path for commands

MANPATH Search path for <man> pages

PS1 & PS2 Primary and Secondary prompt strings

USER Your login name

TERM terminal type
PWD Current working directory
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 Referencing Variables

Variable contents are accessed using ‘$’:

e.g. $ echo $HOME

$ echo $SHELL
To see a list of your environment variables:

$ printenv

or:

$ printenv | more

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 Defining Local Variables

▪ As in any other programming language, variables can be defined and

used in shell scripts.
▪ Unlike other programming languages, variables in Shell Scripts are not
typed.
▪ Examples :
a=1234 # a is NOT an integer, a string instead
b=$a+1 # will not perform arithmetic but be the string ‘1234+1’
b=`expr $a + 1 ` will perform arithmetic so b is 1235 now.
Note : +,-,/,*,**, % operators are available.
b=abcde # b is string
b=‘abcde’ # same as above but much safer.
b=abc def # will not work unless ‘quoted’
b=‘abc def’ # i.e. this will work.
IMPORTANT NOTE: DO NOT LEAVE SPACES AROUND THE =
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 Referencing variables
--curly bracket
▪ Having defined a variable, its contents can be referenced by
the $ symbol. E.g. ${variable} or simply $variable. When
ambiguity exists $variable will not work. Use ${ } the
rigorous form to be on the safe side.
▪ Example:
a=‘abc’
b=${a}def # this would not have worked without the{ } as
#it would try to access a variable named adef

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 Variable List/Arrary
▪ To create lists (array) – round bracket
$ set Y = (UNL 123 CS251)

▪ To set a list element – square bracket

$ set Y[2] = HUSKER

▪ To view a list element:

$ echo $Y[2]

▪ Example:
#!/bin/sh
a=(1 2 3)
echo ${a[*]}
echo ${a[0]}
Results: 1 2 3
1
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 Positional Parameters

▪ When a shell script is invoked with a set of command line parameters each
of these parameters are copied into special variables that can be accessed.
▪ $0 This variable that contains the name of the script
▪ $1, $2, ….. $n 1st, 2nd 3rd command line parameter
▪ $# Number of command line parameters
▪ $$ process ID of the shell
▪ $@ same as $* but as a list one at a time (see for loops later )
▪ $? Return code ‘exit code’ of the last command
▪ Shift command: This shell command shifts the positional parameters by
one towards the beginning and drops $1 from the list. After a shift $2
becomes $1 , and so on … It is a useful command for processing the input
parameters one at a time.

Example:
Invoke : ./myscript one two buckle my shoe
During the execution of myscript variables $1 $2 $3 $4 and $5 will contain
the values one, two, buckle, my, shoe respectively.

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 Variables

▪ vi [Link]
#! /bin/sh
echo Total number of inputs: $#
echo First input: $1
echo Second input: $2

▪ chmod u+x [Link]

▪ [Link] HUSKER UNL CSE

Total number of inputs: 3
First input: HUSKER
Second input: UNL

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 Shell Programming

▪ programming features of the UNIX

shell:
Shell variables
Operators
Logic structures

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 Shell Operators

▪ The Bash/Bourne/ksh shell operators are

divided into three groups: defining and
evaluating operators, arithmetic operators,
and redirecting and piping operators

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 Defining and Evaluating

▪ A shell variable take on the generalized form

variable=value (except in the C shell).
$ set x=37; echo $x
37
$ unset x; echo $x
x: Undefined variable.
▪ You can set a pathname or a command to a
variable or substitute to set the variable.
$ set mydir=`pwd`; echo $mydir

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Linux Commands
Pipes & Redirecting

Piping: An important early development in Unix , a way to pass the

output of one tool to the input of another.
$ who | wc −l

By combining these two tools, giving the wc command the output

of who, you can build a new command to list the number of users
currently on the system
Redirecting via angle brackets: Redirecting input and output follows
a similar principle to that of piping except that redirects work with
files, not commands.
tr '[a-z]' '[A-Z]' < $in_file > $out_file
The command must come first, the in_file is directed in by the
less_than sign (<) and the out_file is pointed at by the greater_than
sign (>).

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 Arithmetic Operators

▪ expr supports the following operators:

• arithmetic operators: +,-,*,/,%
• comparison operators: <, <=, ==, !=, >=, >
• boolean/logical operators: &, |
• parentheses: (, )
• precedence is the same as C, Java

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 Arithmetic Operators

▪ vi [Link]
#!/bin/sh
count=5
count=`expr $count + 1 `
echo $count
▪ chmod u+x [Link]
▪ [Link]
6

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 Arithmetic Operators

▪ vi [Link]
#!/bin/sh
a=5.48
b=10.32
c=`echo “scale=2; $a + $b” |bc`
echo $c
▪ chmod u+x [Link]
▪ ./[Link]
15.80

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 Arithmetic operations in
shell scripts

var++ ,var-- , ++var , -- post/pre

var increment/decrement
+ ,- add subtract
*,/,% multiply/divide,
remainder
** power of
!,~ logical/bitwise negation
&,| bitwise AND, OR
&& || logical AND, OR

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 Shell Programming

▪ programming features of the UNIX

shell:
Shell variables
Operators
Logic structures

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 Shell Logic Structures

The four basic logic structures needed for program development

are:

Sequential logic: to execute commands in the order in

which they appear in the program

Decision logic: to execute commands only if a certain

condition is satisfied

Looping logic: to repeat a series of commands for a given

number of times

Case logic: to replace “if then/else if/else” statements when

making numerous comparisons

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 Conditional Statements
(if constructs )

The most general form of the if construct is;

if command executes successfully

then
execute command
elif this command executes successfully
then
execute this command
and execute this command
else
execute default command
fi

However- elif and/or else clause can be omitted.

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 Examples
SIMPLE EXAMPLE:
if date | grep “Fri”
then
echo “It’s Friday!”
fi
FULL EXAMPLE:
if [ “$1” == “Monday” ]
then
echo “The typed argument is Monday.”
elif [ “$1” == “Tuesday” ]
then
echo “Typed argument is Tuesday”
else
echo “Typed argument is neither Monday nor Tuesday”
fi

# Note: = or == will both work in the test but == is better for readability.
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 Tests

▪ string1 = string2 True if strings are identical

▪ String1 == string2 …ditto….
▪ string1 !=string2 True if strings are not identical
▪ string Return 0 exit status (=true) if string is not null
▪ -n string Return 0 exit status (=true) if string is not null
▪ -z string Return 0 exit status (=true) if string is null

▪ int1 –eq int2 Test identity

▪ int1 –ne int2 Test inequality
▪ int1 –lt int2 Less than
▪ int1 –gt int2 Greater than
▪ int1 –le int2 Less than or equal
▪ int1 –ge int2 Greater than or equal

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 Combining tests with logical
operators || (or) and && (and)
Syntax: if cond1 && cond2 || cond3 …
An alternative form is to use a compound statement using the –a
and –o keywords, i.e.
if cond1 –a cond22 –o cond3 …
Where cond1,2,3 .. Are either commands returning a a value or test
conditions of the form [ ] or test …
Examples:
if date | grep “Fri” && `date +’%H’` -gt 17
then
echo “It’s Friday, it’s home time!!!”
fi

if [ “$a” –lt 0 –o “$a” –gt 100 ] # note the spaces around ] and [
then
echo “ limits exceeded”
fi
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 File enquiry operations

-d file Test if file is a directory

-f file Test if file is not a directory
-s file Test if the file has non zero length
-r file Test if the file is readable
-w file Test if the file is writable
-x file Test if the file is executable
-o file Test if the file is owned by the user
-e file Test if the file exists
-z file Test if the file has zero length

All these conditions return true if satisfied and false

otherwise.
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 Decision Logic

▪ A simple example
#!/bin/sh
if [ “$#” -ne 2 ] then
echo $0 needs two parameters!
echo You are inputting $# parameters.
else
par1=$1
par2=$2
fi
echo $par1
echo $par2

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 Decision Logic
Another example:
#! /bin/sh
# number is positive, zero or negative
echo –e "enter a number:\c"
read number
if [ “$number” -lt 0 ]
then
echo "negative"
elif [ “$number” -eq 0 ]
then
echo zero
else
echo positive
fi
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 Loops
Loop is a block of code that is repeated a number
of times.
The repeating is performed either a pre-
determined number of times determined by a
list of items in the loop count ( for loops ) or
until a particular condition is satisfied ( while
and until loops)
To provide flexibility to the loop constructs there
are also two statements namely break and
continue are provided.

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 for loops
Syntax:
for arg in list
do
command(s)
...
done
Where the value of the variable arg is set to the values provided
in the list one at a time and the block of statements
executed. This is repeated until the list is exhausted.
Example:
for i in 3 2 5 7
do
echo " $i times 5 is $(( $i * 5 )) "
done

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 The while Loop

▪ A different pattern for looping is created using the

while statement
▪ The while statement best illustrates how to set up a
loop to test repeatedly for a matching condition
▪ The while loop tests an expression in a manner
similar to the if statement
▪ As long as the statement inside the brackets is true,
the statements inside the do and done statements
repeat

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 while loops
Syntax:
while this_command_execute_successfully
do
this command
and this command
done

EXAMPLE:
while test "$i" -gt 0 # can also be while [ $i > 0 ]
do
i=`expr $i - 1`
done

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 Looping Logic

▪ Example: ▪ Adding integers from 1 to 10

#!/bin/sh #!/bin/sh
for person in Bob Susan Joe Gerry i=1
do sum=0
echo Hello $person
while [ “$i” -le 10 ]
done
do
Output: echo Adding $i into the sum.
Hello Bob sum=`expr $sum + $i `
Hello Susan i=`expr $i + 1 `
Hello Joe done
Hello Gerry echo The sum is $sum.

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 until loops

The syntax and usage is almost identical to the while-

loops.
Except that the block is executed until the test condition
is satisfied, which is the opposite of the effect of test
condition in while loops.
Note: You can think of until as equivalent to not_while
Syntax: until test
do
commands ….
done

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 Switch/Case Logic

▪ The switch logic structure simplifies the

selection of a match when you have a list of
choices

▪ It allows your program to perform one of

many actions, depending upon the value of a
variable

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 Case statements

The case structure compares a string ‘usually contained in a

variable’ to one or more patterns and executes a block of
code associated with the matching pattern. Matching-
tests start with the first pattern and the subsequent
patterns are tested only if no match is not found so far.
case argument in
pattern 1) execute this command
and this
and this;;
pattern 2) execute this command
and this
and this;;
esac
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 Functions
▪ Functions are a way of grouping together commands so that they can later be
executed via a single reference to their name. If the same set of instructions
have to be repeated in more than one part of the code, this will save a lot of
coding and also reduce possibility of typing errors.
SYNTAX:
functionname()
{
block of commands
}
#!/bin/sh
sum() {
x=`expr $1 + $2`
echo $x
}

sum 5 3
echo "The sum of 4 and 7 is `sum 4 7`"
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 Take-Home Message

▪ Shell script is a high-level language that must be

converted into a low-level (machine) language by UNIX
Shell before the computer can execute it
▪ UNIX shell scripts, created with the vi or other text editor,
contain two key ingredients: a selection of UNIX
commands glued together by Shell programming syntax
▪ UNIX/Linux shells are derived from the UNIX Bourne, Korn,
and C/TCSH shells
▪ UNIX keeps three types of variables:
• Configuration; environmental; local
▪ The shell supports numerous operators, including many
for performing arithmetic operations
▪ The logic structures supported by the shell are sequential,
decision, looping, and case

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 To Script or Not to Script

▪ Pros
• File processing
• Glue together compelling, customized testing utilities
• Create powerful, tailor-made manufacturing tools
• Cross-platform support
• Custom testing and debugging

▪ Cons
• Performance slowdown
• Accurate scientific computing

[Link] 64
 Shell Scripting Examples

▪ Input file preparation

▪ Job submission
▪ Job monitoring
▪ Results processing

[Link] 65
 Input file preparation
#!/bin/sh

`ls -l *.log| awk '{print $8}' |sed 's/.log//g' > file_list`

cat file_list|while read each_file

do
babel -ig03 $each_file".log" -oxyz $each_file".xyz“

echo '# nosymmetry integral=Grid=UltraFine scf=tight rhf/6-311++g** pop=(nbo,chelpg)'>head

echo ' ' >>head
echo ''$each_file' opt pop nbo chelp aim charges ' >> head
echo ' ' >>head
echo '0 1 ' >>head

`sed '1,2d' $each_file.xyz >junk`

input=./$each_file".com"
cat head > $input
cat junk >> $input
echo ' ' >> $input

done
/bin/rm ./junk ./head ./file_list
[Link] 66
 LSF Job Submission

$ vi [Link]
#!/bin/sh -f

#BSUB -q week
#BSUB -n 4
#BSUB -o output
#BSUB -J job_type
#BSUB -R “RH5 span[ptile=4]”
#BSUB -a mpichp4

[Link] ./[Link]

exit
$chmod +x [Link]
$bsub < [Link]

[Link] 67
 Results Processing
#!/bin/sh
`ls -l *.out| awk '{print $8}'|sed 's/.out//g' > file_list`
cat file_list|while read each_file
do
file1=./$each_file".out"
Ts=`grep 'Kinetic energy =' $file1 |tail -n 1|awk '{print $4}' `
Tw=`grep 'Total Steric Energy:' $file1 |tail -n 1|awk '{print $4}' `
TsVne=`grep 'One electron energy =' $file1 |tail -n 1|awk '{print $5}' `
Vnn=`grep 'Nuclear repulsion energy' $file1 |tail -n 1|awk '{print $5}' `
J=`grep 'Coulomb energy =' $file1 |tail -n 1|awk '{print $4}' `
Ex=`grep 'Exchange energy =' $file1 |tail -n 1|awk '{print $4}' `
Ec=`grep 'Correlation energy =' $file1 |tail -n 1|awk '{print $4}' `
Etot=`grep 'Total DFT energy =' $file1 |tail -n 1|awk '{print $5}' `
HOMO=`grep 'Vector' $file1 | grep 'Occ=2.00'|tail -n 1|cut -c35-47|sed 's/D/E/g' `
orb=`grep 'Vector' $file1 | grep 'Occ=2.00'|tail -n 1|awk '{print $2}' `
orb=`expr $orb + 1 `
LUMO=`grep 'Vector' $file1 |grep 'Occ=0.00'|grep ' '$orb' ' |tail -n 1|cut -c35-47|sed
's/D/E/g'
echo $each_file $Etot $Ts $Tw $TsVne $J $Vnn $Ex $Ec $HOMO $LUMO $steric >>out
done
/bin/rm file_list
[Link] 68
 Reference Books
▪ Class Shell Scripting
[Link]
▪ LINUX Shell Scripting With Bash
[Link]
[Link]
▪ Shell Script in C Shell
[Link]
▪ Linux Shell Scripting Tutorial
[Link]
▪ Bash Shell Programming in Linux
[Link]
▪ Advanced Bash-Scripting Guide
[Link]
▪ Unix Shell Programming
[Link]
[Link]

[Link] 69
 Questions & Comments
Please direct comments/questions about research computing to
E-mail: research@[Link]
Please direct comments/questions pertaining to this presentation to
E-Mail: shubin@[Link]

The PPT file of this presentation is available here:

[Link]

[Link]
 Hands-on Exercises

1. The simplest Hello World shell script – Echo command

2. Summation of two integers – If block
3. Summation of two real numbers – bc (basic calculator) command
4. Script to find out the biggest number in 3 numbers – If –elif block
5. Operation (summation, subtraction, multiplication and division) of two
numbers – Switch
6. Script to reverse a given number – While block
7. A more complicated greeting shell script
8. Sort the given five numbers in ascending order (using array) – Do loop
and array
9. Calculating average of given numbers on command line arguments – Do
loop
10. Calculating factorial of a given number – While block
11. An application in research computing – Combining all above
12. Optional: Write own shell scripts for your own purposes if time permits

The PPT/WORD format of this presentation is available here:

[Link]
[Link] /afs/isis/depts/its/public_html/divisions/rc/training/scientific/short_courses/ 71