Resource Seminar 2007: Introduction to Linux

Eun-seo Choi

Oct 11, 2007

1 Resources

• Senior grads

• System administrators (help@gps.caltech.edu)

• Documents in /home/datalib/Resource Class

• Internet and magazines

– Google, Wikipedia, etc.

– Linux Journal (http://www.linuxjournal.com/), Linux Magazine (http://www.

linux-mag.com/), Linux Format (http://www.linuxformat.co.uk/), and many

others (http://en.wikipedia.org/wiki/List_of_Linux_magazines).

– Source of the up-to-date information.

• http://tldp.org

– The Llinux Documentation Project.

– Guides and FAQs are excellent introductions.

• http://www.ibm.com/developerworks/linux

– Contains a vast collection of toturials on many Linux-related subjects.

– Go to “How do I get started with Linux?” (http://www.ibm.com/developerworks/

linux/newto/#6) to get started with linux.

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2 Accessing a remote linux server

2.1 SSH

ssh is a remote login program, meaning “secure shell”. ssh and the associated programs

such as scp and sftp are the only allowed methods to remotely access division servers.

There are many different ways of using ssh, but a real basic one is

ssh -X -lusername server or ssh -X username @server

For example,

ssh -X -lces74 narsil.gps.caltech.edu

or

ssh -X ces74@narsil.gps.caltech.edu

where -X option forwards X windows programs (running on the remote host) to a local dis-

play.

For more about ssh, type ‘man ssh’ on a terminal’s command line or visit http://www.

openssh.org/manual.html. There are numerous on-line documents including the 3-part tu-

torial on IBM DeveloperWorks (http://www.ibm.com/developerworks/library/l-keyc.

html).

Several ssh clients for MS Windows are available. Putty is quite popular (http://www.

chiark.greenend.org.uk/~sgtatham/putty/).

2.2 X server on Microsft Windows

You might want to have an “X windows system” available on your MS Windows desktop or

laptop. Then, you can keep working as if you locally logged in a linux server.

Let’s imagine a situation where you are wokring on your MS Windows laptop at home

but want to finish up your Ge161 homework using GMT wihtout going back to the office.

Moreover, you left some partially working scripts in your home directory on the division’s

linux system. You can log in the linux server through the normal terminal emulators and

edit the GMT scripts. However, those terminal programs cannot pop up a window showing

the EPS files you made. To see the results in this particular case or to run other X windows

programs, you need an X server running on your local computer.

You can set up an X windows system on MS Windows using Cygwin (http://www.

cygwin.com/), Xming (http://www.straightrunning.com/XmingNotes/), or X-Win32 (http:

//www.starnet.com/products/xwin32/). The first two are free; the latter is commercial

but is freely downloadable from http://software.caltech.edu.

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2.3 Virtual machines and dual booting

Instaling a linux system on your computer is an obvious way of getting a linux-compatible

working environment. You have two options for installing linux while keeping your current

non-linux OS. One is to partition your physical hard drive, install linux on one of the parti-

tions, and use “dual booting”. Further information on dual booting is available on wikipedia

(http://en.wikipedia.org/wiki/Dual_boot). The other is to install linux on a “virtual

machine”. If interested, try out one of these: VMWare (commercial, http://www.vmware.

com/), Parallel Workstation (commercial, http://www.parallels.com), Microsoft Virtual

PC (free, http://www.microsoft.com/windowsxp/virtualpc/). Dual booting can be an-

noying because you need to reboot everytime you want to switch to a different OS, while

the virtual machine softwares suffer performance overhead. These techniques might be an

overkill if you just want to work on linux servers.

3 Frequently used programs

For complete documentation of any of the following programs, try man command , or info command

(‘q’ to quit while reading.)

3.1 Overview of file system

Excerpted from Wikipedia’s “Filesystem Hierarchy Standard” (http://en.wikipedia.org/wiki/Filesystem_Hierarchy_Standard).

[ces74@elendil]/% cd

[ces74@elendil]~% cd /

[ces74@elendil]/% ls

bin/ etc/ lib/ mnt/ proc/ scratch1@ sys/ var/

boot/ export/ lost+found/ net/ root/ selinux/ tmp/

dev/ home/ media/ opt/ sbin/ srv/ usr/

/ Primary hierarchy root and root directory of the entire file system hierarchy.

/bin/ Essential command binaries that need to be available in single user mode; for all

users (e.g., cat, ls, cp).

/boot/ Boot loader files (e.g., kernels, initrd). Often a separate partition.

/dev/ Essential devices (e.g., /dev/null).

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/etc/ Host-specific system-wide configuration files (the name comes from et cetera).

/etc/opt/ Configuration files for /opt/.

/etc/X11/ Configuration files for the X Window System, version 11.

/etc/sgml/ Configuration files for SGML.

/etc/xml/ Configuration files for XML.

/home/ Users’ home directories - containing saved files, personal settings etc. Often a sep-

arate partition.

/lib/ Libraries essential for the binaries in /bin/ and /sbin/.

/media/ Mount points for removable media such as CD-ROMs (appeared in FHS-2.3).

/mnt/ Temporarily mounted filesystems.

/opt/ Optional application software packages.

/proc/ Virtual filesystem documenting kernel and process status as text files (e.g., uptime,

network).

/root/ Home directory for the root user.

/sbin/ Essential system binaries (e.g., init, route, ifup).

/srv/ Site-specific data which is served by the system.

/tmp/ Temporary files (see also /var/tmp).

/usr/ Secondary hierarchy for user data; contains the majority of (multi-)user utilities and

applications.

/usr/bin/ Non-essential command binaries (not needed in single user mode); for all

users.

/usr/include/ Standard include files.

/usr/lib/ Libraries for the binaries in /usr/bin/ and /usr/sbin/.

/usr/sbin/ Non-essential system binaries (e.g. daemons for various network-services).

/usr/share/ Architecture-independent (shared) data.

/usr/src/ Source code (e.g. the kernel source code with its header files).

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/usr/X11R6/ X Window System, Version 11 Release 6.

/usr/local/ Tertiary hierarchy for local data, specific to this host. Typically has fur-

ther subfolders, e.g. bin/, lib/, share/.

/var/ Variable files, such as logs, spool files, and temporary e-mail files.

/var/lock/ Lock files. Files keeping track of resources currently in use.

/var/log/ Log files. Various logs.

/var/mail/ Users’ mail-boxes.

/var/run/ Information about the running system since last boot (e.g. currently logged-

in users and running daemons).

/var/spool/ Spool for tasks waiting to be processed (e.g. print queues and unread

mail).

/var/spool/mail/ Deprecated location for users’ mail-boxes.

/var/tmp/ Temporary files to be preserved between reboots.

3.2 Getting system information

uname : Print system information.

df : Report file system disk space usage.

du : Estimate file space usage.

top : Display Linux tasks. While running, hit ’u’ for a user id; ’k’ to kill a process; ’q’ to

quit.

w : Show who is logged on and what they are doing.

finger : User information lookup program.

date : Print or set the system date and time.

time : Time a simple command or give resource usage.

echoi@echoi-laptop:~$ uname -a

Linux echoi-laptop 2.6.20-16-generic #2 SMP Sun Sep 23 19:50:39 UTC 2007 i686 GNU/Linux

5

echoi@echoi-laptop:~$ df -h

Filesystem Size Used Avail Use% Mounted on

/dev/sda3 38G 18G 19G 49% /

varrun 1013M 144K 1013M 1% /var/run

varlock 1013M 0 1013M 0% /var/lock

procbususb 1013M 120K 1013M 1% /proc/bus/usb

udev 1013M 120K 1013M 1% /dev

devshm 1013M 0 1013M 0% /dev/shm

lrm 1013M 15M 999M 2% /lib/modules/2.6.20-16-generic/volatile

/dev/sda1 67G 42G 26G 62% /media/sda1

/dev/sda2 5.9G 5.1G 808M 87% /media/sda2

echoi@echoi-laptop:~$ du -sh

13G .

echoi@echoi-laptop:~$ top

top - 17:39:06 up 9:58, 5 users, load average: 0.15, 0.16, 0.14

Tasks: 140 total, 2 running, 137 sleeping, 0 stopped, 1 zombie

Cpu(s): 0.0%us, 0.0%sy, 0.0%ni, 99.2%id, 0.0%wa, 0.0%hi, 0.8%si, 0.0%st

Mem: 2074620k total, 970440k used, 1104180k free, 205656k buffers

Swap: 489972k total, 19428k used, 470544k free, 136692k cached

PID USER PR NI VIRT RES SHR S %CPU %MEM TIME+ COMMAND

3606 echoi 15 0 2320 1184 880 R 1 0.1 0:00.04 top

1 root 15 0 2912 1808 488 S 0 0.1 0:01.79 init

2 root RT 0 0 0 0 S 0 0.0 0:00.00 migration/0

3 root 34 19 0 0 0 S 0 0.0 0:00.00 ksoftirqd/0

4 root RT 0 0 0 0 S 0 0.0 0:00.00 watchdog/0

8 root 10 -5 0 0 0 S 0 0.0 0:00.73 events/0

10 root 10 -5 0 0 0 S 0 0.0 0:00.00 khelper

11 root 10 -5 0 0 0 S 0 0.0 0:00.00 kthread

35 root 10 -5 0 0 0 S 0 0.0 0:00.00 kblockd/0

37 root 10 -5 0 0 0 S 0 0.0 0:01.44 kacpid

[ces74@narsil]~% w

17:40:08 up 3 days, 1:40, 4 users, load average: 0.00, 0.00, 0.00

USER TTY FROM LOGIN@ IDLE JCPU PCPU WHAT

danb pts/0 rockpile Wed15 25:04m 0.69s 0.69s -tcsh

carltape pts/1 denali Tue08 2days 0.03s 0.03s -bash

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ces74 pts/2 dhcp-65-221 17:40 0.00s 0.37s 0.00s w

carltape pts/4 denali 06:53 10:45m 0.02s 0.02s -bash

[ces74@narsil]~% finger danb

Login: danb Name: Daniel Bower

Directory: /home/danb Shell: /bin/tcsh

Office: 358 South Mudd

On since Wed Oct 3 15:56 (PDT) on pts/0 from rockpile

1 day 1 hour idle

No mail.

No Plan.

bash-3.1$ date

Sat Oct 6 19:35:42 PDT 2007

bash-3.1$ cat > myprogram

#!/bin/bash

find . -maxdepth 2 -name ’.csh*’

bash-3.1$ chmod +x myprogram

bash-3.1$ time ./myprogram

./.cshrc%

./.cshrc

real 0m1.907s

user 0m0.005s

sys 0m0.022s

3.3 Navigating file system

ls : List directory contents.

cd : Change to another directory.

cd - : Go back to the previous directory.

find : Search for files in a directory hierarchy by file name, modified time, accessed time,

permission, etc.

pwd : Print name of current/working directory.

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cd : Change to another directory.

which : Locate a command.

echoi@echoi-laptop:~$ ls -tl

합계 232

-rw-r--r-- 1 echoi echoi 7 2007-10-04 17:16 cron.log

drwxr-xr-x 5 echoi echoi 4096 2007-09-30 20:00 Desktop

-rw------- 1 echoi echoi 8155 2007-09-20 15:31 walkthrough_detailed_weak.svg

drwxr-xr-x 3 echoi echoi 4096 2007-08-29 17:21 data

drwxr-xr-x 2 echoi echoi 4096 2007-08-27 14:21 roms

drwxr-xr-x 2 echoi echoi 4096 2007-07-02 23:27 Pictures

drwx------ 2 echoi echoi 4096 2007-06-28 15:50 amsn_received

-rw-r--r-- 1 echoi echoi 87423 2007-06-06 10:06 latest_address.ldif

lrwxrwxrwx 1 echoi echoi 26 2007-04-24 06:01 Examples -> /usr/share/example-content

echoi@echoi-laptop:~$ pwd

/home/echoi

echoi@echoi-laptop:~$ cd opt/stgSnac/Snac/

echoi@echoi-laptop:~/opt/stgSnac/Snac$ ls ~-

echoi@echoi-laptop:~/opt/stgSnac/Snac$ echo ~-

/home/echoi

echoi@echoi-laptop:~/opt/stgSnac/Snac$ echo ~+

/home/echoi/opt/stgSnac/Snac

echoi@echoi-laptop:~/opt/stgSnac/Snac$ cd -

/home/echoi

echoi@echoi-laptop:~$

echoi@echoi-laptop:~/opt$ find ~/opt -name ’deal.II’

/home/echoi/opt/deal.II

/home/echoi/opt/deal.II/deal.II

echoi@echoi-laptop:~/opt$ find . -mmin -60

.

./test.sh

echoi@echoi-laptop:~$ find . -size +1G

./opt/Snac_new/tests/hydroPressure.0

./opt/deal.II.projects/vishunu.tar.bz2

echoi@echoi-laptop:~$ which paraview

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/home/echoi/opt/paraview-3.0.2-Linux-x86/bin/paraview

3.4 Manipulating files and directories

cp : Copy files or directories.

rm : Remove files or directories.

mv : Rename or move files or directories to another location.

ln -s : Create a symbolic link to an existing file or directory.

mkdir : Make a directory.

rmdir : Remove a directory.

touch : Change file timestamps. Create file if it does not exist yet.

3.5 Acess permission and mode

Every file or folder in Linux has access permissions. There are three types of permissions

(what allowed to do with a file):

• read access

• write access

• execute access

Permissions are defined for three types of users:

• user (owner).

• group that the owner belongs to.

• other user.

A “mode” is one of the possible combinations of permissions and users.

These commands are used to change the mode and the ownership of files and directories.

chmod : Change the mode.

chown : Change the owner.

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chgrp : Change the group.

ls -l : Print long list including permission.

The following examples are taken from http://www.tldp.org/LDP/intro-linux/html/

sect_03_04.html#sect_03_04_01 .

asim:~> ./hello

bash: ./hello: bad interpreter: Permission denied

asim:~> cat hello

#!/bin/bash

echo "Hello, World"

asim:~> ls -l hello

-rw-rw-r-- 1 asim asim 32 Jan 15 16:29 hello

asim:~> chmod u+x hello

asim:~> ./hello

Hello, World

asim:~> ls -l hello

-rwxrw-r-- 1 asim asim 32 Jan 15 16:29 hello*

asim:~> chmod u+rwx,go-rwx hello

asim:~> ls -l hello

-rwx------ 1 asim asim 32 Jan 15 16:29 hello*

3.6 Viewing and manipulating contents of files

cat : Write each FILE to standard output, first line first.

tac : Write each FILE to standard output, last line first.

less : Displays text one screen at a time. Similar but superior to more. ’q’ to quit.

wc : Print the number of newlines, words, and bytes in files.

paste : Write lines consisting of the sequentially corresponding lines from each file, sepa-

rated by TABs, to standard output.

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→paste puts together two or more files column by column; cat puts together files one

after another.

cut : Remove sections from each line of files.

head : Output the first part of files.

tail : Output the last part of files.

3.7 Manipulating text files with awk and sed

sed : Strem editor. Read a file line by line, manipulate strings in the line, and print them

to standard output.

awk : Pattern scanning and processing language. It is a programming language.

Examples (from /home/datalib/Resource Class/Resource Class 2005/UNIXtips.txt

by Kevin Lewis):

> ls U*.txt

UNIXtips.txt

> ls U*.txt | sed ’s/txt/doc/g’

UNIXtips.doc

> cat UNIXtips.txt | sed ’s/UNIX/Windows/g’ > Windowstips.txt

> cat UNIXtips.txt | sed ’s/\ //g’ > Unixtips_spacedeleted.txt

> seq -s\ 4

1 2 3 4

> seq -s\ 4 | awk ’{print $1","$2","$3","$4}’

1,2,3,4

> seq -s\ 4 | awk ’{print $1*10","$2/10","cos($3)","$4-7}’

10,0.2,-0.989992,-3

3.8 Managing processes

ps : Report a snapshot of the current processes.

kill : Send a signal to a process (to kill it). Ctrl-c for killing a running process.

nice : Run a program with modified scheduling priority.

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top : See Section 3.2.

echoi@echoi-laptop:~/opt$ ps

PID TTY TIME CMD

1331 pts/2 00:00:00 bash

2863 pts/2 00:00:00 ps

echoi@echoi-laptop:~/opt$ ps uxwf | grep emacs

echoi 944 0.0 0.4 13808 9632 pts/1 T 16:22 0:00 | | \_ emacs

echoi 957 0.0 0.4 13796 9616 pts/1 T 16:22 0:00 | | \_ emacs

echoi 2867 0.0 0.0 2988 760 pts/2 S+ 17:18 0:00 | | \_ grep emacs

echoi@echoi-laptop:~/opt$ kill -9 957 944

echoi@echoi-laptop:~/opt$ nice -19 myBigProgram

3.9 Printing

Printing in modern linux systems is as easy as, if not easier than, in MS Windows. In case

you still need to send files to printers on command line, use these programs:

lp : Print a file.

lp -d 366sm hp 2side -n 2 file1 Print 2 copies of le1 to 366sm hp 2side.

lpstat : Check the print queue.

lpstat -p 366sm hp 2side Check the queue of 366sm hp 2side

cancel : Cancel a print job.

cancel 366sm hp 2side-36 Cancel job number 36 on 366sm hp 2side.

cancel -u username : Cancel all your jobs on all the printers.

enscript : Convert a text file to a postscript file.

enscript -2 -r file1 Prints file1 with 2 columns and in landscape mode.

enscript -2 -r file1 -o tmp.ps Prints file1 to tmp.ps with 2 columns and in land-

scape mode.

3.10 Archiving and Compression/Uncompression

• Creating an archive file (.tar) from obj/ directory:

tar -cvf obj.tar obj/

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• Creating an archive file with compression:

tar -czvf obj.tar.gz obj/ compressing with gzip

tar -cjvf obj.tar.bz2 obj/ compressing with bzip2

• Extracting (and uncompressing) an archive file:

tar -xvf obj.tar , tar -xzvf obj.tar.gz , tar -xjvf obj.tar.bz2

• Viewing the contents of an archive file:

tar -tvf obj.tar , tar -tzvf obj.tar.gz , tar -tjvf obj.tar.bz2

4 bash Basics

To learn about bash in a systematic fashion, it is really recommended to read “Bash Ref-

erence Manual” (http://www.gnu.org/software/bash/manual/bashref.html).

The following is a short list of things that are used in the examples of this document

but might look mysterious at first:

. : Current directory. cp test/test.txt .

As a command, equal to source (read and execute).

. .bashrc = source .bashrc

.. : Upper directory by one level. To represent multi-lelvel, ../.., ../../.., etc.

cd .. , mv test.txt ../../../test dir

~ : Equal to /home/username .

cp ~/test.txt ~/test2.txt

; : Commands separated by ; are executed sequentially.

cp ~/test.txt ~/test2.txt; rm /test.txt

& : When put after a command, the process runs in the background.

emacs & = emacs → Ctrl+z → bg

| : When a sequence of commands are separated by ’|’, the standard output of a command

becomes the standard input for the next command.

find ~ -name ’.*’ | grep bash

${} : Variable expansion.

echo ${PATH} , cd ${GMTHOME}

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‘ ‘ (backquotes) or $() : Command substitution.

echoi@echoi-laptop:~$ ls -l $(which python)

lrwxrwxrwx 1 root root 9 2007-05-31 11:05 /usr/bin/python -> python2.5

echoi@echoi-laptop:~$ ls -l ‘which python‘

lrwxrwxrwx 1 root root 9 2007-05-31 11:05 /usr/bin/python -> python2.5

4.1 Redirection

Redirecting outputs can be useful when you want to save or throw away texts printed on

command line by shell commands or programs.

Texts printed on command line have the type of either stdout or stderr. These are two

of the three standard “file descriptor” (see http://en.wikipedia.org/wiki/File_descriptor).

One of the differences between stdout and stderr is that outputs sent to stdout are “buffered”

before acutally shown while outputs sent to stderr are displayed without delay. Integer

value of 1 and 2 are assigned to stdout and stderr.

The following has been excerpted from “BASH Programming - Introduction HOW-TO”

(http://tldp.org/HOWTO/Bash-Prog-Intro-HOWTO-3.html).

1. stdout to file

This will cause the ouput of a program to be written to a file. Note that use of ’>’

will overwrite ls-l.txt if it already exists. To append, use ‘>>’.

to create or overwrite, ls -l > ls-l.txt

to append, ls -l >> ls-l.txt

2. stderr to file

This will cause the stderr ouput of a program to be written to a file.

to create or overwrite, grep da * 2> grep-errors.txt

to append, grep da * 2>> grep-errors.txt

3. stdout to stderr

This will cause the stderr ouput of a program to be written to the same filedescriptor

than stdout.

grep da * 1>&2

4. stderr to stdout

This will cause the stderr ouput of a program to be written to the same filedescriptor

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than stdout.

grep * 2>&1

5. stderr and stdout to file

This will place every output of a program to a file.

rm -f $(find / -name core) &> removedcore.log

This will throw away all the outputs.

rm -f $(find / -name core) &> /dev/null

4.2 Globbing

Globbing is another name for ”filename expansion”. The next examples are from ”Advanced

Bash-Scripting Guide” by Medel Cooper (http://www.faqs.org/docs/abs/HTML/globbingref.

htm).

bash$ ls -l

total 2

-rw-rw-r-- 1 bozo bozo 0 Aug 6 18:42 a.1

-rw-rw-r-- 1 bozo bozo 0 Aug 6 18:42 b.1

-rw-rw-r-- 1 bozo bozo 0 Aug 6 18:42 c.1

-rw-rw-r-- 1 bozo bozo 466 Aug 6 17:48 t2.sh

-rw-rw-r-- 1 bozo bozo 758 Jul 30 09:02 test1.txt

bash$ ls -l t?.sh

-rw-rw-r-- 1 bozo bozo 466 Aug 6 17:48 t2.sh

bash$ ls -l [ab]*

-rw-rw-r-- 1 bozo bozo 0 Aug 6 18:42 a.1

-rw-rw-r-- 1 bozo bozo 0 Aug 6 18:42 b.1

bash$ ls -l [a-c]*

-rw-rw-r-- 1 bozo bozo 0 Aug 6 18:42 a.1

-rw-rw-r-- 1 bozo bozo 0 Aug 6 18:42 b.1

-rw-rw-r-- 1 bozo bozo 0 Aug 6 18:42 c.1

bash$ ls -l [^ab]*

-rw-rw-r-- 1 bozo bozo 0 Aug 6 18:42 c.1

-rw-rw-r-- 1 bozo bozo 466 Aug 6 17:48 t2.sh

-rw-rw-r-- 1 bozo bozo 758 Jul 30 09:02 test1.txt

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bash$ ls -l {b*,c*,*est*}

-rw-rw-r-- 1 bozo bozo 0 Aug 6 18:42 b.1

-rw-rw-r-- 1 bozo bozo 0 Aug 6 18:42 c.1

-rw-rw-r-- 1 bozo bozo 758 Jul 30 09:02 test1.txt

bash$ echo *

a.1 b.1 c.1 t2.sh test1.txt

bash$ echo t*

t2.sh test1.txt

4.3 Shell programming

Good readings to learn bash programming would be ”Bash guide for beginners” (http://

www.tldp.org/LDP/Bash-Beginners-Guide/html/index.html) and ”Advanced bash-scripting

guide” (http://www.tldp.org/LDP/abs/html/index.html) for more advanced techniques.

The example script given below shows how to use a few important and frequently used

features such as processing command line arguments, using a for loop, and command sub-

stitution. Condition test using if/then is also very useful (see the example in Section 4.5).

To run this script, save the boxed code as rename.sh and run ’chmod u+x rename.sh’.

Then, you can run it like a regular program. An easy way of making a text file on command

line is using cat. For example, ’cat > rename.sh’ → ’copy and paste or type the code’ →’Ctrl-d’.

#!/bin/bash

# rename.sh

# Basic file renamer

criteria=$1

re_match=$2

replace=$3

for i in $( ls *$criteria* );

do

src=$i

tgt=$(echo $i | sed -e "s/$re_match/$replace/")

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mv $src $tgt

done

4.4 Hierarchy of setup files

/etc/profile

~/.bash_profile

~/.profile

The above files, if exist, are “sourced” (read and executed) in this order when you log in.

They seldom need touching.

/etc/bashrc

~/.bashrc

These files are sourced whenever you run a new (non-login) interactive shell. You do

not have permission to modify the system files in /etc. So, all your personal settings such

as aliases and environment variables should be put in ${HOME}/.bashrc

4.5 Setting up user environment

You can either put everything in a single, ${HOME}/.bashrc, or divide commands into two

(or more) separate files. To take the latter approach, add the code in the box below whatever

is in your current ${HOME}/.bashrc:

if [ -f ~/.envvars ]; then

. ~/.envvars

fi

if [ -f ~/.aliases ]; then

. ~/.aliases

fi

This style is just a suggestion, but I personally find it convenient because setting a per-

sonal environment is usually composed of two things: Defining aliases and setting environ-

ment variables.

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Now, if you create two files, ${HOME}/.envvars and ${HOME}/.aliases, they will be

sourced everytime you start a new shell. Nothing breaks even if you don’t. In case you al-

ready have many environment-setting commands in the current ${HOME}/.bashrc, you can

simply move all the ’alias ...’ commands to ${HOME}/.aliases and all the ’export ...’ to

${HOME}/.envvars. Be careful to group related commands together. The next section will

clarify what it means.

Setting environment variables

Contents of ${HOME}/.envvars would look like the following:

# GMT

export GMTHOME=/opt/GMT

export PATH=${GMTHOME}/bin:${PATH}

# Matlab

export MATLABDIR=/opt/matlab

export PATH=${MATLABDIR}/bin:${PATH}

# mpich

export CXX=g++

export MPI_DIR=${HOME}/opt/mpich-1.2.7p1

export MPI_BINDIR=${MPI_DIR}/bin

export MPI_INCDIR=${MPI_DIR}/include

export MPI_LIBDIR=${MPI_DIR}/lib

export PATH=${MPI_BINDIR}:${PATH}

export LD_LIBRATY_PATH=${MPI_LIBDIR}:${LD_LIBRATY_PATH}

The environment variables should be “exported” using export, a shell command, so that

all the programs run from the shell can “see” them..

The most important variables are PATH and LD LIBRARY PATH. PATH contains directories

where executables you want to run reside. By maintaining this variable properly, you can

run programs without remembering where they are or typing the whole paths to them ev-

ery time. LD LIBRARY PATH contains directories which a compiler automatically looks into

to find libararies required for building an application. This becomes really important when

you write a big program that depends on codes someone else wrote.

These environment variables have a default values when you log in. For example, PATH

usually include /usr/bin during the login process. That is why you can run commands in

18

/usr/bin like ls, cd, or rm, without adding it to PATH manually. To add new directories

to these variables, you should follow the syntax of export command given in the above

example so as not to overwrite those default values. The same for LD LIBRARY PATH.

Some programs require to export their own set of variables. For example, SAC requires

do the following:

SACAUX = /foo/sac/aux

export SACAUX

So, refer to the program’s documentation when thigns do not work as expected.

Defining aliases

Defining aliases is straight foward. Just follow the syntax in the below example. Note that

“unalias” command is available to temporarily disable an alias.

echoi@echoi-laptop:~$ cat /home/echoi/.aliases

alias ll=’ls -l’

alias la=’ls -A’

alias l=’ls -CF’

alias cp=’cp -i’

alias mv=’mv -i’

alias rm=’rm -i’

alias em=’xemacs’

alias pangu=’\ssh -XA -lces74 pangu.gps.caltech.edu’

alias alfred=’\ssh -XA -lces74 alfred.gps.caltech.edu’

5 Text editors

Whatever your choice is, it is critical for efficient editing to get used to keyboard shorcuts

(see the attached reference cards.)

5.1 vim

Light and fast. Once you get used to its peculiar “mode” concept, any editing job can be

done very efficiently. Best on command line.

19

5.2 Emacs/XEmacs

Powerful in a sense that they are IDE (Integrated Development Environment). In other

words, you can compile, run, and debug programs without going back to a terminal.

5.3 gedit/Kate

Similar to Wordpad of MS Windows, but can do a lot more. Not IDEs, but provide good

support for programming.

6 Other useful applications

Inkscape : SVG (a vector graphics format) editor. Good for drawing cartoons without wor-

rying about resolution. Similar to Adobe Illustrator. Cannot read but can write EPS

files.

ImageMagick, Gimp : Editing images and converting their format.

Thunderbird, KMail, Evolution : Desktop email clients.

OpenOffice : An alternative to MS Office. Can make PDFs of good quality.

LATEX : Can quickly make equation-laden documents with pre-defined formats. Slides and

posters, too.

20

XEm

acsR

eference

Card

(for

versio

n21.0

+)

Startin

gEm

acs

To

enter

XE

macs,

just

type

itsnam

e:xemacs

To

read

ina

file

toed

it,see

Files,

below

.

Leav

ing

Em

acs

susp

end

Em

acs

(or

iconify

fram

eunder

X)

C-z

exit

Em

acs

perm

anen

tlyC-x

C-c

Files

read

afile

into

Em

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C-x

C-f

save

afile

back

todisk

C-x

C-s

save

all

files

C-x

sin

sert

conten

tsofanoth

erfile

into

this

buffer

C-x

irep

lace

this

file

with

the

file

you

really

want

C-x

C-v

write

buffer

toa

specifi

edfile

C-x

C-w

Gettin

gH

elp

The

Help

system

issim

ple.

TypeC-h

and

follow

the

directio

ns.

Ifyou

are

afirst-tim

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typeC-h

tfo

ra

tuto

ria

l.

quit

Help

win

dow

qscro

llH

elpw

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pos:

show

com

mands

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astrin

gC-h

ash

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key

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C-h

cdescrib

ea

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info

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m

Error

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abort

partia

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ped

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gco

mm

and

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shM-x

recover-file

recover

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from

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undo

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change

C-x

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restore

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tsM-x

revert-buffer

redraw

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aged

screenC-l

Increm

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Search

search

forw

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C-s

search

back

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C-r

regula

rex

pressio

nsea

rchC-M-s

reverse

regula

rex

pressio

nsea

rchC-M-r

selectprev

ious

search

string

M-p

selectnex

tla

tersea

rchstrin

gM-n

exit

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rchRET

undo

effect

ofla

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abort

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ineith

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n.

IfE

macs

isstill

search

ing,C-g

cancels

only

the

part

not

done.

c©1998

Fre

eSoftw

are

Foundatio

n,In

c.

Perm

issions

on

back.

v2.0

XEm

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Motion

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kill

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last

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disp

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read-o

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The

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prev

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12

3

XEm

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Card

Buffers

selectanoth

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C-x

blist

all

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C-x

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kill

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gC

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(defun

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Type

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for

more

info

rmatio

n.

Copyrig

ht

c©1998

Fre

eSoftw

are

Foundatio

n,In

c.

desig

ned

by

Ste

phen

Gild

ea,A

pril

1998

v2.0

XEm

acs

for

GN

UEm

acs

versio

n19

on

Unix

syste

ms

Update

dfo

rX

Em

acs

inFebru

ary

1995

by

Ben

Win

g

Perm

ission

isgra

nte

dto

make

and

distrib

ute

copie

sof

this

card

pro

-vid

ed

the

copyrig

ht

notic

eand

this

perm

ission

notic

eare

pre

serv

ed

on

all

copie

s.

For

copie

softh

eG

NU

Em

acs

manual,

write

toth

eFre

eSoftw

are

Foun-

datio

n,In

c.,

59

Tem

ple

Pla

ce

-Suite

330,B

osto

n,M

A02111-1

307,U

SA

.

45

6

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