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CentOS 4 Installation Personal Notes

Personal notes for CentOS4 installations, additional installations, settings, adjustments, etc.

CentOS is a linux distribution derived from sources freely provided to the public by the RedHat Co. CentOS4 is a clone package of RHEL4, which is based on the Fedora Core 3. Although advanced features are less than the Fedora Core, the Cent OS is more stable and has long-term support of software updating. The CentOS4 is more capable of installing on various architectures. The way to install CentOS4 is quite the same as the Fedora Core 3.

CentOS4 Installation and initial settings
Backup of user's data | Getting iso images of CentOS4 | Burning CD or DVD iso images | Installation of CentOS4 | Changing the user's shell to tcsh | Setting Yum, a software to manage packages | Management of packages by a graphical interface | Setting Up2date | Useful symbolic links | Settings for using drivers of nVidia video cards | MS core fonts | Installation of gv | Installation of auctex | Using wheel mouse in Acrobat Reader etc. | Installation of Java runtime | Accessing to NTFS and MS Windows files | Improve the speed of connection to Web sites | Settings of Apache HTTPD server | Handling MP3 files | Installation of MPlayer | Installation of Mozilla Plugins | Cabextract | Switching desktops by 3D visualization | Desktop Accessory | Necessary procedures when the kernel is updated
Settings in user's directory
SSH public keys | GNOME desktop design | Toolbars | FireFox Design | User Agent Switcher |
Installation under /usr/local
Installation and settings of Gnubiff | Installation of Azureus | Installation of xdiskusage | Installation of Netscape | Installation of RealPlayer | Installation of Acrobat Reader | Installation of dvipdfmx | Installation of Feynmf | Installation of PGPLOT | Installation of Intel Fortran etc. | Installation of sitecopy | Installation of SL

CentOS 4 Installation and initial settings

Backup of user's data

User's data and files should be saved to a secure disk (computer users should regularly do this). The file ".emacs" will be overwritten in course of the installation, rename this file, for example,

% cp .emacs .emacs.bkup

Getting iso images of CentOS4

Riken's site is recommendable in Japan.

You can also get iso images by BitTorrent:
i386 CDs:
i386 DVD:
x86_64 CDs:
x86_64 DVD:

Check the downloaded files:

% md5sum --check MD5SUM-CDS
% md5sum --check MD5SUM-DVD

Burning CD or DVD iso images

Installation CDs or DVD should be made, K3b can be used in Linux systems. In MS Windows, a free software DeepBurner is an alternative.

In Linux systems, xcdroast is another option to make installation CDs. Using dvd+rw-tools is yet another option to make an install DVD by DVD+RW device. When the device name of DVD+RW is /dev/hdc,

# dvd+rw-format /dev/hdc
# growisofs -Z /dev/hdc=CentOS-4.0-i386-bin.DVD.iso

Installation of CentOS4

An example of partitioning(1):

/boot      : 128MB
/          :  15GB
/usr/local :  15GB
/home      : rest of the HD
/swap      : size of the RAM or larger (if the size of the RAM is less
than 256MB, two times the size of the RAM or larger)

Another example of partitioning(2):

/boot      : 512MB
/          :   5GB
/usr	   :  40GB
/usr/local :  40GB
/var       :  20GB
/tmp	   :   5GB
/home      :  rest of the HD
/swap      :  size of the RAM or larger (if the size of the RAM is less
than 256MB, two times the size of the RAM or larger)
/backup    : allocated to the second HD
(Second example has a lot of margin. 1/4 times smaller for each partition is still OK. If you choose the packages, they can even be even smaller than this.) It is convenient to keep /usr/local, /home, /backup without formatting so that the existing data and softwares can survive the OS installation.

The partitions /boot, /, /usr, /var, /tmp should be formatted. The clean installation is recommended. Systems with clean installation are more stable than upgrade installation. By using the custom install, all the necessary softwares should be chosen. If you have a plenty of disk spaces, installing everything is an easy option.

Changing the user's shell to the tcsh

[Applications] -> [System Settings] -> [Users and Groups]
change user's shell from bash to tcsh.

setting example:

umask 022
limit coredumpsize 0

# aliases are set in .alias
if -f ~/.alias source ~/.alias

set path = (. ~/bin $path)
set manpath = ("man -w")

set prompt="%m:%~ %h %% "

setenv EDITOR emacs 
setenv LANG ja_JP.UTF-8
setenv TEXINPUTS .:~/tex/macros:

In the above example, aliases are set by ~/.alias

# aliases
alias       h       history
alias       rm      'rm -i'
alias       mv      'mv -i'
alias       cp      'cp -i'
alias       dir     'ls -al'
alias       ls      'ls -F'

Setting Yum, a software to manage packages

The yum is a software to manage packages and to keep your system updated. These settings are critical for installing various softwares below.

Setting the third-party repository(Dag.wieers).

Add the following lines in /etc/yum.conf

name=Dag RPM Repository for Red Hat Enterprise Linux

Install GPG public keys:

# rpm --import
# rpm --import

Next, update softwares (At the first time, you need a lot of time to complete the following commands):

# yum update

To have the software automatically updated, turn on the yum service. Logs are written in /var/log/yum.log

Management of packages by a graphical interface

[Settings needed in advance: Setting Yum, a software to manage packages]

Use apt + synaptic

# yum install apt
# apt-get update
# apt-get upgrade
# apt-get install synaptic

Setting Up2date

To use the Update Notification, add the following lines in /etc/sysconfig/rhn/sources
### Dag RPM Repository for Red Hat Enterprise Linux
yum DAG-RPM-Repository$ARCH/dag
#yum DAG-RPM-Repository$ARCH/dag

Useful symbolic links

When the softwares are manually installed, the following symbolic links are convenient for installations with minimum modifications of sources:

# ln -s /usr/local /opt
# ln -s /usr/bin/perl /usr/local/bin/perl

Settings for using nVidia video cards

Even when the video cards are recognized, the screen can be unstable, and 3D support is not effective. It is desirable to install nVidia drivers (when you have an nVidia card).

Download a driver for your own card from
To turn off X, type

# /sbin/init 3
and log in as root. Move to the directory where the driver is put, then type
# sh ./
and the driver is installed. Then, type
# cp /etc/X11/xorg.conf /etc/X11/       
and edit /etc/X11/xorg.conf to rewrite Driver "nv" as Driver "nvidia", and remove Load "dri". Make sure that the line Load "glx" exists, and if the line Load "GLcore" is there, remove it. Type
# /sbin/init 5
and X starts again. If you see the logo of NVidia, the driver is successfully installed.

Each time you update the kernel, you need to repeat the installation of the driver.

(information of the nVidia on Linux: NVIDIA Linux Forum)

MS core fonts

From get msttcorefonts-1.3-3.noarch.rpm and type

# rpm -ivh msttcorefonts-1.3-3.noarch.rpm
# /etc/init.d/xfs restart

Installation of gv

If you prefer gv to ggv as ps previewer, the rpm package of gv for FC3 can be installed:

Installation of auctex

Auctex enables to edit, compile, and preview tex documents in Emacs windows.

Download the newest version of auctex-*.tar.gz from and install it as:

% tar xvfz auctex-11.55.tar.gz
% ./configure
% make
% make contrib
# make install
# make install-contrib

Using wheel mouse in Acrobat Reader etc.

To use the wheel mouse in Acrobat Reader, install the imwheel.

Download the newest version of imwheel-*.tar.gz from

% tar xvfz imwheel-1.0.0pre12.tar.gz
% cd imwheel-1.0.0pre12
% ./configure
% make
# make install
Open /etc/X11/xorg.conf as a root user. In Section "InputDevice", Identifier "Mouse0", add the following line
       Option	    "Buttons" "3"
(when you use a 3 button mouse). Make a file ~/.imwheelrc in a user's directory, and write the following lines:
None, Up, Up, 5
None, Down, Down, 5
Shift_L, Up, Page_Up
Shift_L, Down, Page_Down
Restart X-window, and type
% imwheel
to make it work. Use
[Applications] -> [Preferences] -> [More Preferences] -> [Sessions]
to make the imwheel automatically start.

Installation of Java runtime

Self-extracting file is available at
# sh ./jre-1_5_0_01-linux-i586-rpm.bin
Add the following lines in ~/.tcshrc:
setenv JAVA_HOME /usr/java/j2re1.5.0_01
setenv PATH /usr/java/j2re1.5.0_01/bin:$PATH

Accessing to NTFS and MS Windows files

Make a mount point:

# mkdir /winxp

Add the following in /etc/fstab:

/dev/hda5 /winxp ntfs defaults,uid=500 0 0
     ^^^^                          ~~~
Here, ^^^ should be replaced by the name of win partition, and ~~~ by the number of a user who can access to NTFS in addition to the root. Next, type
% uname -r -p
to know the version of kernel and the type of processor, and get the correct rpm for your environment from
# mount /winxp
or reboot the system to access to the NTFS.

Every time the kernel is updated, the rpm installation should be repeated.

Improve the speed of connection to Web sites

The reason why the resolution of the name of web sites take long time is that the Mozilla is forced to try IPv6 first. Since the IPv6 is rarely used, turn off it. At the end of /etc/modprobe.conf, add
# Turn off IPv6
alias net-pf-10 off
alias ipv6 off
and reboot.

Settings of Apache HTTPD server

Settings to locally use the web server without make it public.

Permissions and directory for www files:

% chmod 701 ~
% mkdir -m 705 ~/public_html
If the Apache HTTPD is not installed, install it by yum install httpd. Edit the setting file "/etc/httpd/conf/httpd.conf". The lines to edit are the followings (each line is considerably separated, so you need to use the search command in your editor):
#UserDir disable
UserDir public_html
<Directory /home/*/public_html>
    AllowOverride All
    Options All
AddHandler cgi-script .cgi
#AddDefaultCharset UTF-8
The fisrt line is important to prohibit accesses from outside. Start the httpd, and set the program to automatically start next time:
# /sbin/service httpd start
# /sbin/chkconfig --level 35 httpd on
Now, you can access to the files under ~/public_html/ by the address http://localhost/~[username]/ and you can run cgi's

If you see "403 Forbidden", make sure you have correct permissions. If SELINUX block the files, move to the user's home directory and type

% chcon -R -h -t httpd_sys_content_t public_html

(note) When the ServerName is set by your machine address and the port 80 is open, the web pages are made public. However, it decreases the security of your machine. Some time ago, a student run the httpd on his own machine, which is placed in a university building, and the machine was attacked by a network cracker, resulting in a big damage of network systems in a whole section of the university. That was a big problem.

Handling MP3 files

[Settings needed in advance: Setting Yum, a software to manage packages]

To play MP3 in XMM:

# yum install xmms-mp3

Installation of MPlayer

[Settings needed in advance: Setting Yum, a software to manage packages]

Installation of the MPlayer and related softwares:

# yum install mplayer*

Installation of Mozilla Plugins

[Settings needed in advance: Setting Yum, a software to manage packages]

Installation of Flash, Java, and Mplayer plug-ins used by the Mozilla:

# yum install mozilla-flash mozilla-j2re mplayerplug-in


A tool to melt compressed files of cabinet format used in MS Windows

# yum install cabexract

Switching desktops by 3D visualization

[Settings needed in advance: Settings for using drivers of nVidia video cards]

A tool to switch the virtual desktops by 3D visualization. One needs a 3D-supported graphic card with an OpenGL driver such as nVidia etc.

# yum install 3ddesktop
Check the usage by typing "3ddesk --help"

Desktop Accessory

[Settings needed in advance: Settings for using drivers of nVidia video cards]

# yum install gdesklets*

Usage: First, type

% gdesklets start
to run the program.
To automatically start the program when you login, click
[Applications] -> [Preferences] -> [More Preferences] -> [Sessions]
and open [programs to start automatically], and add "gdesklets start" command.

Displays & Sensors can be found at
[Applications] -> [Accessories] -> [gDesklets]
and use Drag & Drop to install.

(note) Some Display doesn't work.

Necessary procedures when the kernel is updated

Settings in user's directory

The settings below affect only the user's directory.

SSH public keys

The SSH public keys are changed, so the new keys should be set to use the ssh connections without typing password. First, generate the key by

% ssh-keygen -t dsa
The new key is written in ".ssh/" of the client computer (the computer you just installed the CentOS). Add the whole text in this file to the file ".ssh/authorized_keys2" of the host computer (The computer you want to connect to).

Remove the old information in the file ".ssh/known_hosts" of the host computer.

GNOME desktop design

Download your favorite Theme and Background from
[Application] -> [Preferences]
and Drag & Drop.


The icons in the toolbars are too wide. You can change the style of the toolbar:

[Applications] -> [Preferences] -> [Menus and Toolbars]
Change the style of toolbars to [labels beside icons].

FireFox Design

To change the design of FireFox, download Themes from

User Agent Switcher

There are terrible websites that do not allow even the Netscape and only allow Internet Explorer. To access to those websites, an extension tool that can personate the browsers. Open the FireFox, and go to Click an xpi file of User Agent Switcher Extension, then this extension is installed. For the first time, you should allow the installation by the message bar that appears when the extension is clicked.

Installation under /usr/local

The following softwares are installed under /usr/local. If the partition of this directory is separated by the OS partition, the following installations do not need to be repeated when the new OS is installed.

In the following, /opt is a symbolic link to /usr/local. I assume users have permissions to write files in the directory /usr/local/src and all its subdirectories.
General users can execute commands following %
Only root can execute commands following #
In the following settings, the initial directory is assumed to be /usr/local/src

Installation and settings of Gnubiff

A penguin notifies newly arrived mails. It sounds like old xbiff refined. Download the newest version of gnubiff-*.tar.gz from Then install it as
% tar xvfz gnubiff-2.1.1.tar.gz
% cd gnubiff-2.1.1
% ./configure --prefix=`pkg-config libpanelapplet-2.0 --variable=prefix`
% make
# make install
The software is installed in /usr/local by default. Type "gnubiff" to make settings according to your mail server.

This program can be added to desktop panels. If you prefer to use as a GTK application, use
[Applications] -> [Preferences] -> [Other Preferences] -> [Sessions]
and choose [Startup Programs] tab, add a command,

gnubiff -n

Installation of Azureus

[Settings needed in advance: Installation of Java runtime]

Azureus is a file exchange program using Java application and BitTorrent. Recently, the BitTorrent is a major way to distribute Linux packages.

First, install Java runtime according to the above. Download the software for a Linux_GTK platform from Then

% tar jxf Azureus_2.2.0.2_linux.GTK.tar.bz2
# mv azureus /usr/local/.

Add the following lines in ~/.tcshrc:

# Azureus
setenv PATH /usr/local/azureus:$PATH
Type /usr/local/azureus/azureus to make settings. The selection buttons seems to be outside the screen, so click inside the box and select with up-down cursor keys.
[Applications] -> [System Settings] -> [Security Levels]
and select [FireWall Options] tag. In [Other Port], write "6881:tcp" (or appropriate port number you set). Make settings of your router and open corresponding port.

Installation of xdiskusage

Disk usages by every directories and files are graphically displayed by xdiskusage. It's convenient when you want to put the disk in order. It is like "du > xdu" refined.

You need the FLTK (Fast Light Tool Kit): From FLTK homepage download fltk-1.1.6-source.tar.gz and install as

% tar xvfz fltk-1.1.6-source.tar.gz
% cd fltk-1.1.6
% ./configure
% make
# make install
Then from xdiskusage homepage download xdiskusage-1.48.tgz and install as
% tar xvfz xdiskusage-1.48.tgz
% cd xdiskusage-1.48
% ./configure
% make
# make install

Installation of Netscape

There are websites that do not allow browsers other than IEと Netscape to access.

Download an installer from, and install it. Make a symbolic link as

# ln -s /usr/local/netscape/netscape /usr/local/bin/netscape

Installation of RealPlayer

There is an installer at

Installation of Acrobat Reader

A software to read PDF files.

Download the newest version from

% mkdir /usr/local/src/acroread
% cd /usr/local/src/acroread
% wget
% tar zxvf linux-5010.tar.gz
# installers/INSTALL
# ln -s /usr/local/Acrobat5/bin/acroread /usr/local/bin/acroread

Installation of dvipdfmx

A software to transform DVI files to PDF files.

Download the newest version of dvipdfmx-*.tar.gz from

% tar xvfz dvipdfmx-*.tar.gz
% cd dvipdfmx-*
% ./configure
% make 
# make install

Example of preamble of LaTeX source:

Sample: /usr/local/src/dvipdfm/latex-support/sample.tex A program to make html files from LaTeX sources.

Installation of Feynmf

With this software, the Feynman diagrams can be drawn in LaTeX using MetaFont.

# mkdir -p /usr/local/share/texmf/tex/latex/feynmf
# cd /usr/local/share/texmf/tex/latex/feynmf
# wget 
# wget
# ptex feynmf.ins
# mkdir -p /usr/local/share/texmf/fonts/source/feynmf
# cd /usr/local/share/texmf/fonts/source/feynmf
# cp /usr/local/share/texmf/tex/latex/feynmf/ .
# mktexlsr


Example of using the above sample:

% latex template
% mf '\mode:=localfont; input fmftempl'
% latex template
Here, "fmftempl" is a name of a graph defined in the sample. The mf command should be repeated for every graphs defined in the files.

Reference: (Japanese)

Installation of PGPLOT

Excellent plotting tool. It consists of subroutines that can be called from Fortran and C. The author of this program, Tim Pearson, is an astronomer.

Download pgplot5.2.tar.gz from

% mv pgplot5.2.tar.gz /usr/local/src/.
% cd /usr/local/src
% tar xvfz pgplot5.2.tar.gz
# mkdir /usr/local/pgplot
# cd /usr/local/pgplot
# cp /usr/local/src/pgplot/drivers.list .
Open /usr/local/pgplot/drivers.list by your favorite editor, and delete the comment marks of, for example, /GIF, /VGIF, /NULL, /PS, /VPS, /CPS, /VCPS, /XWINDOW, /XSERVE that you want to use.
# cd /usr/local/pgplot
# /usr/local/src/pgplot/makemake /usr/local/src/pgplot linux g77_gcc
# make
# make clean
When you are using x86_64 CPU, you should edit makefile before make command above. Replace the line
LIBS=-L/usr/X11R6/lib -lX11
LIBS=-L/usr/X11R6/lib64 -lX11

Back to an user's right, open ~/.tcshrc and add the following lines:

setenv PGPLOT_DIR /usr/local/pgplot/
setenv PGPLOT_DEV /xwin
setenv LD_LIBRARY_PATH /usr/local/pgplot[:$LD_LIBRARY_PATH]
Here, inside of [...] in the third line should be added only when the same variable is defined in a previous line (the square brackets should not be added).

The manuals of subroutines are found in
Optionally, you can install manuals of html and LaTeX-PS formats. First, modify the first lines of both /usr/local/src/pgplot/makehtml and /usr/local/src/pgplot/maketex to be

# cd /usr/local/pgplot
# make pgplot.html
# make pgplot-routines.tex
# latex pgplot-routines
# dvips pgplot-routines -o
If needed, you can print the manuals:
% lpr /usr/local/pgplot/

In case of Fortran programs with PGPLOT subroutines, the compile options are, for example,
[i386 CPU case]

% g77 example.f -o example.exe -lpgplot -lX11 -L/usr/local/pgplot -L/usr/X11R6/lib -fno-backslash
[x86_64 CPU case]
% g77 example.f -o example.exe -lpgplot -lX11 -L/usr/local/pgplot -L/usr/X11R6/lib64 -fno-backslash

Examples of programs by PGPLOT are in /usr/local/src/pgplot/examples/ The executables of these examples are in /usr/local/pgplot/

Installation of Intel Fortran etc.

Powerful compilers optimized to Intel processors, Intel Compiler (Fortran, C++) and Math Kernel Library are available with free (non-commercial use only):
Following instructions, you get the download site and license file by E-mail. Save them.

Installation of Intel Fortran:

% tar xvfz l_fc_pu_8.1.021.tar.gz
# sh ./l_fc_pu_8.1.021/
On the way, the path to the license file is asked. In ~/.tcshrc, add
# Intel Fortran
setenv PATH /opt/intel_fc_80/bin:$PATH
setenv MANPATH /opt/intel_fc_80/man:[$MANPATH]
setenv LD_LIBRARY_PATH /opt/intel_fc_80/lib[:$LD_LIBRARY_PATH]
setenv INTEL_LICENSE_FILE /opt/intel_fc_80/licenses[:$INTEL_LICENSE_FILE]
Manuals and documents are in /opt/intel_fc_80/doc

Installation of Math Kernel Library:

% tar xvfz l_mkl_p_7.2.1.003.tar.gz
# ./l_mkl_p_7.2.1.003/install
In ~/.tcshrc, add
# Math Kernel Library
setenv INCLUDE /opt/intel/mkl721/include[:$INCLUDE]
setenv LD_LIBRARY_PATH /opt/intel/mkl721/lib/32[:$LD_LIBRARY_PATH]
The meaning of [...] is the same as above.

Intel Fortran Compiler Manual:
Intel C++ Compiler manual:
Math Kernel Library Manual:

Programming examples using MKL are found in /opt/intel/mkl721/examples/

Example of Fortran optimization and linking to MKL:

% ifort -ftz -ip -O3 -parallel -tpp7 -I/opt/intel/mkl721/include/ -L/opt/intel/mkl721/lib/32/ -lmkl -lguide -lpthread -lm -lvml [source filename] -o [executable filename]
The usage of options affects the speed of calculation by factor of 2-3. You should choose appropriate options according to your CPU architecture and nature of your calculations.

Installation of sitecopy

Mirroring tool with FTP. Some Web servers only allow FTP to upload the files. If your Web server allow to login, rsync is better. Download the newest version of sitecopy-*.tar.gz from then install as

% tar xvfz sitecopy-0.14.3.tar.gz
% cd sitecopy-0.14.3
% ./configure
% make
# make install
% cd ~
% mkdir -m 700 .sitecopy
% touch .sitecopyrc
% chmod 600 .sitecopyrc
and open ~/.sitecopyrc and write settings, for example,
site [site identity] (any name, not overlapped)
  server [server name] (example:
  protocol ftp
  username [account name]
  password [password]
  remote [remote directory] (example: ~/public_html/)
  local [local directory] (example: ~/wwwfiles/foosite/)
  url [website URL] (example:
  checkmoved # when local files are moved, the server files will be moved.
  permissions all
  symlinks follow # symbolic links are transfered as files
  exclude *.bak
  exclude *.old
  exclude *~
  exclude "#*#"
See man pages for details of settings. First, tell the program the status of local and remote sites by
% sitecopy -c [site identity]
When you change the local file(s), type
% sitecopy -u [site identity]
to update remote files.

(note) FTP cannot make a symbolic link. In the above settings, the files the symbolic links refer to will be transfered.

Installation of SL

When you fail to type ls, you can take breath by this program: (

% wget
% tar xvf sl.tar
% cd sl
% make
# mv sl /usr/local/bin/


CentOS Home Page

2ch Linux Beginners-CentOS

Linux Tips

Fedora pages are also useful:

2ch Linux Beginners-Fedora Core

Unofficial Fedora FAQ


Fedora Core 3 Linux Installation Notes by Stanton Finley

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