LAMP Programming For Professionals

Designed for beginners, intermediate and professional developers, this book provides genuine domain knowledge to learn web based, application development, usingApache as the Web server, PHP as the programming language, MySQL as the data store, all mounted on the Linux OS. It delves deeply into the core of the MySQL and PHP providing a sound understanding of both.

This book also demonstrates a step-by-step guide to developing a few Webapplications [using PHP 6 & MySQL 5.4 under Apache 2.2] which re-enforces all the learning that takes place throughout the book. 

This book uses the learning by doing pattern with a lot of ready-to-use examples. This pattern has proven to be the best approach for learning a new technology. Most [if not all] of the concepts that you will find in this book are demonstrated using well described and easy to understand examples, yet sophisticated enough to demonstrate LAMP Programming in a real-world context.

Additionally, a special chapter covering the virtual installation of Linux is included. This provides an opportunity to create a Virtual LAMP Framework on MS Windows. 

What You’ll Learn? 

Installing and Setting Up LAMP
Working with the MySQL Database 
Working with the PHP programming language
o    Basics – Variables, Operators, Control Structures, Functions
o    Regular Expression [PCRE]
o    Using MySQLnd, the new native driver
o    Using MySQL, MySQLi and PDO extensions
o    Cookies and Sessions
o    Object Oriented Programming
o    Debugging And Error Handling
o    Web Services Using SOAP
Building Web Based Applications
o    Contact Management System
o    Uses jQuery and Ajax
o    Uses SendMail to dispatch reminder emails for birthdays and anniversaries
o    RSS Widget
o    Uses MagpieRSS [RSS parser for PHP]
o    Uses JavaScript to provide Drag and Drop functionality
o    Newsletter Delivery System
o    Uses SendMail to dispatch newsletter
o    An Automatic Email Dispatcher 
o    Uses CronJob to schedule email dispatch
o    Uses SendMail to dispatch emails
o    Using The Model View Controller Architecture
Setting Up Linux On A Virtual Machine Over MS Windows 
Using phpMyAdmin – A Web based MySQL Administration tool

ISBN 10: 81-8404-843-8

ISBN 13: 978-81-8404-843-8
Edition: First
Downloads

Sample Chapter                                                      TOC

THE TOPICS COVERED IN THE BOOK

All About The L.A.M.P. Framework
Introduction to Linux, Apache, MySQL and PHP. How the L.A.M.P. framework works.

Setting Up The L.A.M.P. Environment
Installing Cent OS, Apache, PHP and MySQL. Configuring the Development Environment.

Understanding The MySQL Database
Db Storage Engines, Db Administration, SQL Elements, Table Creation, Working With Table Data, Tables And Its Structure, Operators And Regular Expression, Grouping Data, Joins, Views, Functions, Data Constraints, Subquery, Union, Indexes, Stored Procedures, Transactions, Cursors

Understanding The PHP Language
Mixing PHP And HTML, Variables And Operators, Control Structures, Functions, Regular Expressions, Working With Database using MySQL, MySQLi and PDO, Cookies, Sessions, Object Oriented Programming, Debugging And Error Handling, Web Services Using SOAP

Application Development
Contact Management, RSS Widget, Newsletter Delivery System, Automatic Email Dispatcher, Programming Using The Model View Controller Architecture    

Linux On Virtual Machine
Installing CentOS On Sun VirtualBox

Appendix
phpMyAdmin – A web based MySQL Db Administration tool

CONTENTS OF THE CD-ROM

Setup files for Apache Web Server 2.2.13
MySQL 5.4
PHP 6.0 [Development Snapshot]
ICU 4.2.1
PHP 5.3 [Stable Release]
phpMyAdmin 3.2.2
Video Footage covering LAMP Installation
Source code for the examples covered in this book   

THE TOPICS COVERED IN THE BOOK

All About The L.A.M.P. Framework
Introduction to Linux, Apache, MySQL and PHP. How the L.A.M.P. framework works.

Setting Up The L.A.M.P. Environment
Installing Cent OS, Apache, PHP and MySQL. Configuring the Development Environment.

Understanding The MySQL Database
Db Storage Engines, Db Administration, SQL Elements, Table Creation, Working With Table Data, Tables And Its Structure, Operators And Regular Expression, Grouping Data, Joins, Views, Functions, Data Constraints, Subquery, Union, Indexes, Stored Procedures, Transactions, Cursors

Understanding The PHP Language
Mixing PHP And HTML, Variables And Operators, Control Structures, Functions, Regular Expressions, Working With Database using MySQL, MySQLi and PDO, Cookies, Sessions, Object Oriented Programming, Debugging And Error Handling, Web Services Using SOAP

Application Development
Contact Management, RSS Widget, Newsletter Delivery System, Automatic Email Dispatcher, Programming Using The Model View Controller Architecture    

Linux On Virtual Machine
Installing CentOS On Sun VirtualBox

Appendix
phpMyAdmin – A web based MySQL Db Administration tool

CONTENTS OF THE CD-ROM

Setup files for Apache Web Server 2.2.13
MySQL 5.4
PHP 6.0 [Development Snapshot]
ICU 4.2.1
PHP 5.3 [Stable Release]
phpMyAdmin 3.2.2
Video Footage covering LAMP Installation
Source code for the examples covered in this book

1. Install nginx on centos using cyberciti’s tutorial
2. update default iptables to allow http traffic:

   # ref: http://www.cyberciti.biz/faq/redhat-fedora-ip6tables-firewall-configuration/
   # ref: http://wiki.zimbra.com/index.php?title=Firewall_Configuration
   # Firewall configuration written by system-config-securitylevel
   # Manual customization of this file is not recommended.
   *filter
   :INPUT ACCEPT [0:0]
   :FORWARD ACCEPT [0:0]
   :OUTPUT ACCEPT [0:0]
   :RH-Firewall-1-INPUT - [0:0]
   -A INPUT -j RH-Firewall-1-INPUT
   -A FORWARD -j RH-Firewall-1-INPUT
   -A RH-Firewall-1-INPUT -i lo -j ACCEPT
   -A RH-Firewall-1-INPUT -p icmp --icmp-type any -j ACCEPT
   -A RH-Firewall-1-INPUT -p 50 -j ACCEPT
   -A RH-Firewall-1-INPUT -p 51 -j ACCEPT
   -A RH-Firewall-1-INPUT -p udp --dport 5353 -d 224.0.0.251 -j ACCEPT
   -A RH-Firewall-1-INPUT -p udp -m udp --dport 631 -j ACCEPT
   -A RH-Firewall-1-INPUT -p tcp -m tcp --dport 631 -j ACCEPT
   -A RH-Firewall-1-INPUT -m tcp -p tcp --dport 80 -j ACCEPT
   -A RH-Firewall-1-INPUT -m state --state ESTABLISHED,RELATED -j ACCEPT
   -A RH-Firewall-1-INPUT -m state --state NEW -m tcp -p tcp --dport 22 -j ACCEPT
   -A RH-Firewall-1-INPUT -j REJECT --reject-with icmp-host-prohibited
   COMMIT
   

3. install mochiweb using BeeBole’s tutorial.  For ease of use while testing, launch dev server using separate screen, as the mochiweb shell will own the terminal used to launched it by default, and add the following line to iptables so we can hit the server directly:

   -A RH-Firewall-1-INPUT -m tcp -p tcp --dport 8000 -j ACCEPT # allow access to mochiweb
   

   Test that mochiweb is available to localhost by running the following from the command line on the server:

   curl http://127.0.0.1:8000
   

   You should get something back like:

   <html>
   <head>
   <title>It Worked</title>
   </head>
   <body>
   MochiWeb running.
   </body>
   </html>

4. Configure nginx to proxy api calls to mochiweb.  Put this in /etc/nginx/nginx.conf:

   user              nginx;
   worker_processes  1;
   error_log         /var/log/nginx/error.log;
   pid               /var/run/nginx.pid;
   events {
       worker_connections  1024;
   }
   http {
       include       /etc/nginx/mime.types;
       default_type  application/octet-stream;
       log_format  main  '$remote_addr - $remote_user [$time_local] $request '
                         '"$status" $body_bytes_sent "$http_referer" '
                         '"$http_user_agent" "$http_x_forwarded_for"';
       access_log  /var/log/nginx/access.log  main;
       sendfile        on;
       keepalive_timeout  65;
       include /etc/nginx/conf.d/*.conf;
       server {
           listen       80;
           server_name  localhost;
           location ~ api { # <-- pass requests for 'api...' to mochiweb
                   proxy_pass      http://127.0.0.1:8000;
           }
           location / {
               root   /usr/share/nginx/html;
               index  index.html index.htm;
           }
           error_page  404              /404.html;
           location = /404.html {
               root   /usr/share/nginx/html;
           }
           error_page   500 502 503 504  /50x.html;
           location = /50x.html {
               root   /usr/share/nginx/html;
           }
       }
   }
   

   As per BeeBole’s tutorial, edit the mochiweb request handler to handle requests for ‘api’:

   %% @author author <author@example.com>
   %% @copyright YYYY author.
   
   %% @doc Web server for myapp.
   
   -module(myapp_web).
   -author('author <author@example.com>').
   
   -export([start/1, stop/0, loop/2]).
   
   %% External API
   
   start(Options) ->
       {DocRoot, Options1} = get_option(docroot, Options),
       Loop = fun (Req) ->
                      ?MODULE:loop(Req, DocRoot)
              end,
       mochiweb_http:start([{name, ?MODULE}, {loop, Loop} | Options1]).
   
   stop() ->
       mochiweb_http:stop(?MODULE).
   
   loop(Req, DocRoot) ->
       "/" ++ Path = Req:get(path),
       case Req:get(method) of
           Method when Method =:= 'GET'; Method =:= 'HEAD' ->
               case Path of
                   "api" -> Req:ok({"text/html", [],["<h1>Congratulation</h1>"]}); % <-- the 'api' request handler
                   _ -> Req:serve_file(Path, DocRoot)
               end;
           'POST' ->
               case Path of
                   _ ->
                       Req:not_found()
               end;
           _ ->
               Req:respond({501, [], []})
       end.
   
   %% Internal API
   
   get_option(Option, Options) ->
       {proplists:get_value(Option, Options), proplists:delete(Option, Options)}.
   

   As per James Gardner’s post Streaming File Upload with Erlang and Mochiweb Multipart Post, rebuild the request handler by running make in the myapp directory. The mochiweb server will automatically restart

5. confirm the proxy is working by hitting http://domain/ and http://domain/api.  The former should return the nginx install confirmation page, and the latter should return the simple “Congratulation” page.

Have you ever wrestled with a problem for far too long, before realizing that the solution was actually really simple?  I love to point and laugh when this happens to other people, but yesterday it happened to me.

A long time ago (on a server far, far away), I installed Lighttpd, and set up a very simple site.  The config file was only a few lines long – it pointed at the index page, and had the required mime-types for PHP and HTML.  For what I wanted at the time, that was fine.

I left the server for a long time, and completely forgot about how it was set up.

I decided to change the page that was on the server to a more useful wiki.  I installed MediaWiki, and everything looked OK until the installer completed, and I was greeted with an un-styled front page.

My first thought was that the paths were wrong.  I checked to make sure that there were no .htaccess rules that would affect how the page looked.  Lighttpd stores URL rewriting rules in config files (lighttpd.conf, or a mysite.conf file for each site), rather than in .htaccess, so checking that you’ve converted all the rules over to Lighttpd’s syntax is a good first step.

As far as I could see, everything was correct.  So, to me, the next obvious issue was folder permissions.  Everything in the /www folder should, in theory be owned by the wwwdata group and www user.  However, in this case I had used wget to download MediaWiki while logged in as an unrelated user, and I had chgrp / chown-ed the folders afterwards.  I thought that I may have made a mistake with the file permissions.

That turned out not to be the case.  After that, my troubleshooting skills failed me.  I tried re-installing Media Wiki, I even re-set up the site in Lighttpd – basically anything but checking that one darn config file.

Of course, after wasting far too much time on the problem, I went back to basics, and guess what – adding the mime information for .css files fixed the problem.  Yes, you can point and laugh now!

So, the moral of today’s story is – sometimes the most obvious things are worth looking at.

Some Background Talk:

It was way back when I first got my hand on linux in 2002. It was a Red-hat. My neighbour Zakir Uncle introduced it to me. He told me at that time, linux holds gr8 features and u can do so many things with it. But all I did was ( cd .. / cd. / mkdir / touch / ).  I removed linux after 1month cause it was boring( what do u expect from a 3month old experienced computer user? ). Later, I experiment with different linux versions ( fedora, mandrake); and did able to make it popular enough that my late cousin (she died in 2008), my little sister and even my aunt used linux. Just to play Shishanshu and Mahjong.

In February, 2009 jhoroTEK configured the network server at Skyinnova (experimental work), where we configured a central server with Fedora Core 10 and squid. Adnan made it a success. [ He was suppose to write an article on it. Hopefully he will put it sooner.] My  friend Harun-ur Rashid who is a B/W  re-seller in our area was using squid as a proxy server and tc for traffic shaping.  No visual admin section and no DHCP.  So I got the perfect opportunity to experiment at his place.

For the Reader:

It’s not a complete tutorial on Configuring a network Server using CENT OS rather an experience sharing.  If you can take the clues and see the rose line u will find the destiny .  My task is still on-going;  if you have better suggestion then drop a comment.

If you want more details or consultancy then contact me.

Follow me on twitter  @neotohin  to see which step i am right now and some tips .

Things in my hand:

1. An 1 mbps B/W from ISP provider
2. A Core-2-duo Machine ( server ), A Pentium 4 client Machine)
3. 1 switch,  1 hub
4. CentOS 5.2

Task :

1. Share the B/W with clients in sub-network
2. Traffic Shaping Each client will have different kind of B/W plan like  16KB to 64KB shared.
3. DHCP Server + MAC binding [ future PPP ]
4. Proxy Server
5. FTP, WEB server ( Simple extensions )
6. More interesting things to come

Let the Journey Begin ====================================

Few steps to get apt on CentOS 5

$wget http://dag.wieers.com/rpm/packages/rpmforge-release/rpmforge-release-0.3.6-1.el5.rf.i386.rpm
$wget http://dag.wieers.com/rpm/packages/apt/apt-0.5.15lorg3.2-1.el5.rf.i386.rpm
$sudo rpm -Uvh rpmforge-release-0.3.6-1.el5.rf.i386.rpm apt-0.5.15lorg3.2-1.el5.rf.i386.rpm
$sudo apt-get update
$sudo apt-get install git


How to install flash plugin for firefox on centos/redhat

I have been setting up and integrating an LDAP authentication system into our infrastructure over the past few days. This is just one small “got-cha” that I ran into. The default setting in the OpenLDAP configuration (/etc/ldap.conf) is to continuously try reconnecting to the LDAP server on failure. This is definitely not what I want to happen if we loose LDAP. In this scenario, when connecting to the server via SSH, the session will hang and eventually timeout. This even removes the ability to login with a local system account.
Example of the timeout when LDAP server is down:

testuser@workstation4-l:~$ ssh test123@ldapclientsrv
Connection closed by 172.16.0.192

To begin, lets look at a typical error that you would get on the system if LDAP communication was down.

Dec 13 12:52:58 ldapServer sshd[15965]: nss_ldap: failed to bind to LDAP server ldap://127.0.0.16: Can't contact LDAP server
Dec 13 12:52:58 ldapServer sshd[15965]: nss_ldap: reconnecting to LDAP server (sleeping 4 seconds)...
Dec 13 12:53:02 ldapServer sshd[15965]: nss_ldap: failed to bind to LDAP server ldap://127.0.0.16: Can't contact LDAP server
Dec 13 12:53:02 ldapServer sshd[15965]: nss_ldap: reconnecting to LDAP server (sleeping 8 seconds)...
Dec 13 12:53:10 ldapServer sshd[15965]: nss_ldap: failed to bind to LDAP server ldap://127.0.0.16: Can't contact LDAP server
Dec 13 12:53:10 ldapServer sshd[15965]: nss_ldap: reconnecting to LDAP server (sleeping 16 seconds)...

As noted before, I was unable to login with a local account. Turns out that the problem was with the default “bind_policy” in /etc/ldap.conf.  Per the document:

# Reconnect policy: hard (default) will retry connecting to
# the software with exponential backoff, soft will fail
# immediately.
#bind_policy hard

This was changed to:

bind_policy soft

Once this was changed, I brought up the firewall on the LDAP server and refused connections. Ability to login via LDAP was gone, but the server did fail back to local system authentication

Note(s): When failing back to local authentication, there is no error sent back to the client trying to login, only errors go to /var/log/secure file. The server will just keep rejecting the users login until LDAP is back up. At least this gives you the ability to get in with a local system account in an emergency.

Example error to /var/log/secure when LDAP server is down and local authentication is rejecting the LDAP user received from the client:

Dec 13 12:59:59 ldapServer sshd[2588]: pam_unix(sshd:auth): authentication failure; logname= uid=0 euid=0 tty=ssh ruser= rhost=172.16.0.22

Sau khi cài Subverion trên server mọi thứ có vẻ hoạt động tốt nhưng khi dùng lệnh svn status hoặc cũng command khác của svn thì nhận được thông báo:

[root@server ncs]# svn status
svn: warning: cannot set LC_CTYPE locale
svn: warning: environment variable LANG is en_US.UTF-8
svn: warning: please check that your locale name is correct

Tìm trên mạng thấy khắc phục như vầy,

>>> export LC_ALL = C

Short & sweet — if you’re server is connected to a network which is advertising both IPv4 and IPv6 information, you may sometimes get back the information in one format when you want it in another (application specific) that can cause problems. A simple way to tune that is the file:

/etc/gai.conf

Do a ‘man gai.conf‘ to get the details and some simple examples – not hard to understand, it’s how you can set a precedence list for network information (think like DNS MX precedence format) to be retrieved by getaddrinfo().

So kann man bei den verschiedenen Distributionen IPV6 ausschalten:

Debian / Sidux / Ubuntu / Linux-Mint:

Als root die Datei /etc/modprobe.d/aliases öffnen
und die Zeile

alias net-pf-10 ipv6
in
alias net-pf-10 off
ändern.

Um das manuelle Laden des ipv6-Moduls zu verhindern kann noch die Zeile alias ipv6 off angehängt werden.

Archlinux

In der Datei /etc/modprobe.d/modprobe.conf die Zeilen

#Laden von IPV6-Modul verhindern
alias net-pf-10 off

einfügen.

Fedora 12 (gilt vermutlich auch für RedHat Enterprise 6 + CentOS 6)

In die Datei /etc/modprobe.d/blacklist.conf folgende Zeilen eintragen:

# ipv6 deaktiviert
blacklist ipv6
install ipv6 /bin/true

OpenSuse 11.2

Da IPV6 fest in den Kernel kompiliert wurde und sich über Yast nicht deaktivieren lässt, muss man bei Grub
/boot/grub/menu.lst die Parameter ipv6.disable=1 anhängen.

Firefox / Iceweasel

Damit auch bei Firefox IPV6 deaktiviert ist muss man inder Adresszeile about:config eingeben, anschließend den Wert des Strings network.dns.disableIPv6 auf true setzen

At work I have been given the task of coming up with a procedure of bare metal restore of redhat servers. There were two requirments.

1) Hot backing up
2) Remote restore

After some researching this is the procedure I came up with. Please bear in mind this procedure has only been tested in model enviroment and do your own homework before using this as your DR plan.

A) Backup

Backup the mbr and the bootloader. First 512 bytes of the primary HD contains the partion table and the bootloader. Here is the command for that.

dd if=/dev/sda of=/backup/mbr.img bs=512 count=1

Ensure that you have the backup directory and correct HD.

Now we need to backup the filesystem. Linux is dynamically creating the following directories. So no need to take the backup of them.

1) /sys
2) /proc
3) /var/run
4) /lost+found
5) /tmp

You need to exclude the backup directories. You can use tar or rsync to take the backup, however if you use rsync ensure you preserve symlinks and file permissions. Here is the command to create the tar archive.

tar cvfpz /backup/root.tar.gz –exclude=sys –exclude=proc –exclude=var/run –exclude=tmp –exclude=lost+found –exclude=backup /

Take a backup of the /etc/fstab and partion table info from the following command.

fdisk -l > /backup/fdisk.txt

B) Restore

Okay before restore lets crash the HD. Please beware this command shall ruin your HD, do not run this in the production enviroment.

dd if=/dev/random of=/dev/sda bs=512 count=100

Okay let’s start restoring.

You need a lInux live cd. Well I prefer a knoppix since it has all the useful tools.

Boot the server with the knoppix cd and restore the partion table. Since I am soundf this remotely I will be using iLo virtual media to mount the knoppix live cd.

dd if=/backup/mbr.img of=/dev/sda bs=512 count=1

Linux will not identify the HD until you reboot, however you can do the following as well. Run fdisk and write the partion table by pressing ‘w’.

Okay now let’s format the partions. This is where the copy of fstab helps. You can run the following command for each partion.

mkfs.ext3 /dev/sda2 -L /
mkfs.ext3 /dev/sda1 -L /boot

Now your partions are ready for the data. Let’s mount the devices. First create the mount point by running the following command. I am killing two birds with one command. I am creating rootfs and boot directories.

mkdir -p /rootfs/boot

Okay change directories, into cd /rootfs

Let’s extract the archive

tar xvzp /backup/root.tar.gz

Okay now we need to create the following directories.

mkdir /sys; mkdir /tmp; mkdir /lost+found; mkdir /proc; mkdir /var/run

Okay now you need to chroot into the /rootfs

mount -t proc /proc /rootfs/proc
mount -o loop /dev /rootfs/dev

chroot /rootfs -c /bin/bash

Now you have mounted the filesystem. Run the following command to reinstall grub

grub-install /dev/sda

Okay fingers cross you have recovered your crashed server. Reboot the box you have resurrected your Linux box.

Things you need to know. This won’t work if you have a LVM. If your fstab has uid rather than block devices, you need to change it to block devices.

If you have grub2 grub reinstallation might change a bit.
I will cover that in another post.

Okay something you might notice that I didn’t cover the backup directory. You have several options here. You can use a nfs or samba mount for that. Please keep in mind if you are using rsync as your backup method you cannot have the symlinks in a samba mount. So you need to use tar if you are using the samba option.

If you have a better way or see a mistake please comment.

If you decide to use InnoDB in your MySQL, be aware that the default on Red Hat / CentOS is to lump everything together into one big massive file (/var/lib/mysql/ibdata1 by default). At first glance you may not thing there’s anything wrong with this…until you read a design decision by the developers (arguably a deficiency, as I believe it to be) that you can not reclaim disk space from the physical file after the data inside it has been deleted.

Set in your /etc/my.cnf this before you set any of your databases up (if it’s already running, you’ll probably want to rebuild it from scratch by mysqldump’ing it to a file, erasing the DB, then re-importing the data – plan your actions well!):

  [mysqld]
  innodb_file_per_table = 1

The result is that each table in a database will now have it’s own discrete IDB (InnoDB) file in a subdirectory of the database name. When the files are unique, you can run an ‘OPTIMIZE LOCAL TABLE FOOBAR;’ on it and it will in fact shrink in size, sometimes quite drastically. The Optimize process basically reads the records from the real file, writes them to a temporary file next to the real one, then when it’s done replaces the old real file with the new temporary one written.

A real case scenario is that we have a database that has a table which records “job complete” status, but only needs to retain that data for a short period of time (maybe 30 days) and then it can be purged. Regardless of the internal purging, if we were using the default “all innodb inside one file” setting that ‘ibdata1′ would grow to huge proportions and could never shrink.

  1543503872  job_completion_log_item.ibd
   176160768  job_completion_log_item.ibd

That is a real result from just this morning — this aforementioned log tablespace was 1.5gig IDB file; we deleted 75% of the records not needed and it shrunk to a mere 175meg in size after running an OPTIMIZE on it. And that’s just one table alone, imagine your savings when you work on all of them.

A developer had some issues connecting to a MySQL server running on a RHEL/CentOS 5 machine with the PHP 5.3 software that’s included/installed in the new OS X 10.6 Snow Leopard; it turns out there’s an issue with PHP being unable to connect if the MySQL server has accounts using the old_passwords scheme set to TRUE (old_passwords = 1 in your /etc/my.cnf for instance, the Red Hat 5 default).

A quick fix that won’t affect other things running is to dynamically turn off old_passwords and create your user a new account with the needed privileges on the database(s) in question; the two styles can coexist peacefully in your database. As your properly enabled root/admin MySQL account the scenario is:

set OLD_PASSWORDS = FALSE;
grant ALL privileges on DATABASENAME.* to 'NEWUSER'@'HOSTNAME' identified by 'PASSWORD';
flush privileges;

That’s all there is to it, no harm no foul. Replace above values as necessary for your particular installation (perhaps you only want to grant SELECT, UPDATE, INSERT, DELETE to them) and you’re off and running. A more complete transition might simply involve updating the needed password to the newer schema, just be sure that you won’t break any of the other running code/tools first.

Sometime ago within my post entitled vSphere ESX4: Hot Add Memory for Linux Guests, I promised to blog about hot add CPU support to the same VM.  As you may have guessed, I didn’t get around to writing it, and have subsequently found the area well covered elsewhere.

wila has knocked together a very clear procedure here http://communities.vmware.com/docs/DOC-10493 which kinda makes my post unecessary.

My earlier post has been referenced as a resource by lamw for his helpful guide here: http://communities.vmware.com/docs/DOC-10492

TAR – Tape Archive  (application/x-tar)

TAR - svnlabs

A common archive format used on Unix-like systems. Generally used in conjunction with compressors such as gzip, bzip2, compress or xz to create .tar.gz, .tar.bz2, .tar.Z or tar.xz files.

# tar -cvvf foo.tar foo/ –exclude=”/home/svnlabs”

# tar -cvzpP –file=/home/backup.tar.gz –exclude={/dev/*,/proc/*,/sys/*,/tmp/*} /

tar work with directory “/” except for /dev, /proc, /sys, /tmp

La siguiente versión del diagrama de flujo que desarrollé está mal!! ya que hay puntos que han cambiado para el mapeo de los reads de 25bp hacia el genoma de referencia.

–Edit.
Originally, I had run into the issue of trying to determine the *nix distribution – a command that would tell me the distribution and the build and everythign else I wanted to know. After reviewing some of the awesome comments left behind, here’s the updated perl script to determine the distribution (in Perl).

#!/usr/bin/env perl
use strict;
use warnings;

my ( $distro );
$distro = `lsb_release -i -s`;
chomp $distro;

my %installCmd = (
"Fedora" => \&fedora,
"Ubuntu" => \&ubuntu,
);

&test();

sub test {
if ( exists $installCmd{$distro} ) {
$installCmd{$distro}->();
} else {
print "Supported Distributions are: ". join(', ' , keys %installCmd) . ".\n";
exit;
}
}


sub fedora { print "Hello from the Fedora Family!"; }
sub ubuntu { print "Hello from UBUNTU!!!"; }

Deciding which Linux distribution to install is more of a personal choice. You should install a few of them to see which version do you like. However, there are some characteristics that could identify among the different distribution. The most popular Linux distribution is Fedora and Ubuntu.

Ubuntu

If you are new in Linux, Ubuntu is the only choice. Ubuntu is design for people who are migrating from Windows or Mac. It is novice friendly and easy to use. Its documentation is very rich and clear. Ubuntu also has a very large support community. Furthermore, Ubuntu focus its feature enhancement more on the desktop experience. Compare to Fedora, Ubuntu is more concern of stability and therefore it won’t adopt any new technology that is too new and unstable.

If you want a stable and user-friendly desktop experience, Ubuntu is the choice. If you do not like to tinker with operating system and just want to use it for normal usage, choose Ubuntu.

Fedora

Fedora, however, is the most technically advanced distribution. Any new technology will be adopted by Fedora first.  If you want the latest and most advanced technology, use Fedora. Therefore, Fedora is not as stable as Ubuntu. Sometime you would get a problematic kernel update which forces you to switch back to older kernel for a while. Fedora is more suitable for season Linux user who wants to try out the latest. You must not be afraid of tinkering with the operating system when using Fedora. If you are technically inclined but new to Linux, you could try Fedora. The support community for Fedora is good.

For feature enhancement, Fedora is more concern of security and it may include enterprise feature which might not benefit you. Fedora is the test bed for trying out new technology before such technology is adopted by its sponsor Linux Red Hat in their enterprise operating system. If you are an IT professional considering adopting a new skills in Linux administration, Fedora is the choice. By learning Fedora, you will be sure that Linux Red Hat would adopt some of the technology eventually. For anyone who would like to learn some system administration that could help in their career in IT, Fedora is he choice.

Enterprise: Linux Red Hat and CentOS

In the enterprise market, Linux Red Hat is the most popular open source distribution. However, Linux Red Hat is not free. You can download Red Hat for a free trial. After which, you have to pay for any updates and support. For those looking to learn the skills in administering Linux Red Hat, you could use Fedora or CentOS. CentOS is very similar to Linux Red Hat. In fact, what CentOS did is to get the source code from Linux Red Hat, remove its trade mark and marketed as CentOS.

Please bear in mind that CentOS is not 100% compatible with Linux. CentOS is trying to be as similar to Red Hat as possible. I could say that CentOS is 99% compatible with Linux Red Hat. For those who want to learn Red Hat administration, CentOS is the choice because you can download it for free. In the enterprise market, some companies try out CentOS before adopting Linux Red Hat. There are some companies who would not like to pay for updates and support would use CentOS operationally.

Mobile Distribution: Knoppix and DSL

Beside the two popular desktop distributions Fedora and Ubuntu, I would like to introduce you to some light weight and mobile distribution. Such distribution is not rich in software but it is good enough for simple usage. Knoppix contains in a bootable CD with a collection of GNU/Linux software. There is no need to install Knoppix to the hard disk as you can boot it up from CD.

Another mobile distribution is DSL (Damn Small Linux). It is derived from Knoppix and it is much smaller in size. It contains only 50MB and could be stored in a thumb drive. Mobile distribution could be used for demonstrative or educational purpose. However, Linux administrator uses it frequently for hardware troubleshooting or repair.

Distribution for Hardcore Geek: Gentoo and LFS

Gentoo Linux was designed for power users. Its installation could be cumbersome although recently it includes an installer to simplify the installation. If you would like to modify your operating system to your liking, Gentoo could be your choice. Gentoo also got a good support community with comprehensive documentation.  Gentoo users are more technically inclined. In fact, Gentoo forum provide a lot of the highly technical solution to the common problem in other distribution.

If you want to build Linux from scratch, you should consider LFS project. Linux From Scratch (LFS) is a project that provides you with the steps necessary to build your own custom Linux system. The most important reason for using LFS is to learn how a Linux system works internally. Building an LFS system teaches you about all that makes Linux tick, how things work together, and depend on each other. Along the way you could customize it to your own taste and needs.

Debian

Finally, I would like to mention Debian. Before Ubuntu arrives, Debian got the largest support community with a large collection of software. Debian also got the largest group of developers working on the project. The existence of Ubuntu, which uses the base code of Debian, split up the manpower and resource from Debian. In fact, a lots of other Linux distribution are derived from Debian.

Usage

With all the different Linux distributions mentioned above. I would like to highlight that the usage between these distributions can be very different especially in the area of software installation and distribution. We can categorize most Linux distribution into 2 classes.

The first class is the Red Hat class of distributions. Red Hat uses rpm files to package their software and it uses yum for software update and distribution. Red Hat class distribution includes Linux Red Hat, Fedora and CentOS.

The other class, is the Debian class of distributions. Obviously, these distributions use the base code of Debian. Debian uses deb package for software packaging and it uses apt-get for updates and distributions. Debian class of Linux includes Ubuntu, Kubuntu, Knoppix and DSL (via Knoppix).

I hope the analysis above will help you to make up your mind on which Linux distribution to choose.

When not using NFS, Linux administrators generally move files from one server to the next via SFTP or FTP. This can sometimes be a headache when needing to move large amounts of files between the systems. This is where I like GVFS (GNOME Virtual File System). This subsystem allows you to mount remote systems via the following protocols to a local directory tree:

user01@LinuxDesk:~$ cd ~/.gvfs

user01@LinuxDesk:~/.gvfs$ gvfs-mount ssh://user05@SftpServer02
Enter password
Password:

user01@LinuxDesk:~/.gvfs$ ls
sftp for user05 on SftpServer02

user01@LinuxDesk:~/.gvfs$ cd sftp\ for\ user05\ on\ SftpServer02/

user01@LinuxDesk:~/.gvfs/sftp for user05 on SftpServer02$ ls
app  boot  etc   hs_err_pid15240.log  lib         media  mnt  opt   relay  sbin     srv  tmp  var
bin  dev   home  hs_err_pid8660.log   lost+found  misc   net  proc  root   selinux  sys  usr

user01@LinuxDesk:~/.gvfs/sftp for user05 on SftpServer02$ cd home/user05/

user01@LinuxDesk:~/.gvfs/sftp for user05 on SftpServer02/home/user05$ echo "asdfasdf" > asdf
user01@LinuxDesk:~/.gvfs/sftp for user05 on SftpServer02/home/user05$ cat asdf
asdfasdf

user01@LinuxDesk:~$ gvfs-mount -l
Mount(0): sftp on SftpServer02 -> sftp://SftpServer02/
  Type: GDaemonMount

user01@LinuxDesk:~$ gvfs-mount -l
Drive(0): USB Drive
  Type: GProxyDrive (GProxyVolumeMonitorHal)
  Volume(0): 4.1 GB Media
    Type: GProxyVolume (GProxyVolumeMonitorHal)
    Mount(0): 4.1 GB Media -> file:///media/disk
      Type: GProxyMount (GProxyVolumeMonitorHal)
Mount(0): sftp on SftpServer02 -> sftp://SftpServer02/
  Type: GDaemonMount

user01@LinuxDesk:~/.gvfs$ gvfs-mount -u ssh://user05@SftpServer02

user01@LinuxDesk:~/.gvfs$  ps -ef | grep gvfsd-sftp
user01  8022     1  0 10:34 ?        00:00:00 /usr/lib/gvfs/gvfsd-sftp --spawner :1.8 /org/gtk/gvfs/exec_spaw/21

Requirements: net-snmp, net-snmp-utils, mrtg, lighttpd

mrtg : Multi Router Traffic Grapher

net-snmp and net-snmp-utils : SNMP (Simple Network Management Protocol) is a protocol used for network management. The NET-SNMP project includes various SNMP tools. net-snmp package contains the snmpd and snmptrapd daemons, documentation, etc. You also want to install the net-snmp-utils package, which contains NET-SNMP utilities.

Install the packages

# yum install mrtg net-snmp net-snmp-utils

Configure snmpd.conf

# cp /etc/snmpd/snmpd.conf /etc/snmpd/snmpd.conf.factory-default

# vi /etc/snmpd/snmpd.conf

Comment out the contents, append: (http://www.sofee.cn/blog/2006/10/21/49/)

##############################################################
# Added by Justin
## sec.name source community
com2sec local   localhost       public
com2sec lan     192.168.1.0/24  public

## group.name sec.model sec.name
group   MyRWGroup       v1      local
group   MyRWGroup       v2c     local
group   MyRWGroup       usm     local
group   MyROGroup       v1      lan
group   MyROGroup       v2c     lan
group   MyROGroup       usm     lan

view all    included  .1                               80
#view mib2   included  .iso.org.dod.internet.mgmt.mib-2 fc

## context sec.model sec.level prefix read write notif
access MyROGroup ""      any       noauth    exact      all    none   none
access MyRWGroup ""      any       noauth    exact      all    all    all
rocommunity  public
disk / 100000
disk /mnt/share 500000
##############################################################

Save and close the file

# chkconfig snmpd on
# service snmpd restart

Make sure you see interface IP, by running the following command:

# snmpwalk -v 1 -c public localhost IP-MIB::ipAdEntIfIndex

Sample Outputs:

IP-MIB::ipAdEntIfIndex.123.xx.yy.zzz = INTEGER: 2
IP-MIB::ipAdEntIfIndex.127.0.0.1 = INTEGER: 1

Configure MRTG

# vi /etc/mrtg/mrtg.cfg

OR

# /usr/bin/cfgmaker –global ‘WorkDir: /var/www/mrtg’ –output /etc/mrtg/mrtg.cfg public@127.0.0.1

Create the html file

# indexmaker --output=/var/www/mrtg/index.html /etc/mrtg/mrtg.cfg

Configure Lightttpd

# vi /etc/lighttpd/lighttpd.conf

Add a new alias:

alias.url + ( "/mrtg" => "/var/www/mrtg/www" )

or Append the alias:

alias.url += ( "/mrtg" => "/var/www/mrtg/www" )

Please read the followings for detailed tutorials or documentation.

English Tutorials:

http://www.cyberciti.biz/faq/centos-fedora-linux-multi-router-traffic-grapher-tutorial/

Chinese Tutorials:

http://lincf0315.blogspot.com/2007/04/mrtgcentos.html

http://forum.icst.org.tw/phpbb/viewtopic.php?t=14871

http://www.lslnet.com/linux/f/docs1/i05/big5132597.htm

http://www.sofee.cn/blog/2006/10/21/49/

Official documentation:

http://oss.oetiker.ch/mrtg/doc/mrtg-reference.en.html

http://oss.oetiker.ch/mrtg/doc/mrtg-unix-guide.en.html

CentOS adalah sebuah distribusi linux yang merupakan turunan dari RedHatEntherprise (RHEL)

semua yang ada pada centos baik fitur, command dan aplikasi sama persis dengan RHEL,,jdi bagi yang sudah familiar dengan centos pasti bisa menggunakan RHEL, nah sekarang redhat telah menghentikan distrubusi redhat linux itu sendiri dan menggantikannya dengan fedora linux,, fedora bisa dikatakan sebagai model untuk ujicoba untuk dikeluarkannya RHEL versi terbaru…..

centos dapat kita download dari situs www.centos.org yang saat ini memiliki versi terakhir 5.4,, centos mendukung tipe processor mulai i386,ppc,amd_64 dan sparc.

Introduction

Landing in a new startup company has its cons and pros.
The pros being:

1. You can do almost whatever you want

The cons:

1. You have to do it from scracth!

The Developers

Linux developers are not dumb. They can’t be. If they were dumb, they couldn’t have developed anything on Linux. They might have been called developers on some other platforms.
I was opted quite early about the question of:
“Am I, as a SysAdmin, going to give those Linux developers root access on their machines?”

Why not:

1. They can cause a mess and break their system in a second.
   A fellow developer (the chowner) who ran:

   
   # chown -R his_username:his_group *
   

   He came to me saying “My Linux workstation stopped working well!!!”
   Later on I also discovered he was at /, when performing this command!
   For his defence he added: “But I stopped the command quickly! after I saw the mistake!”

2. And there’s no 2, I think this is the only main reason, given that these are actually people I generally trust.

Why yes:

1. They’ll bother me less with small things such as mounting/umounting media.
2. If they need to perform any other administrative action – they’ll learn from it.
3. Heck, it’s their own workstation, if they really want, they’ll get root access, so who am I to play god with them?

Choosing the former and letting the developers rejoice with their root access on their machines, I had to perform some proactive actions in order to avoid unwanted situations I might encounter.

Installation

Your flavor of installation should be idempotent, in terms of letting the user destroy his workstation, but still be able to reinstall and get to the same position.
Let’s take for example the chowner developer. His workstation was ruined. I never even thought of starting to change back permissions to their originals. It would cause much more trouble in the long run than any good.
We reinstalled his workstation and after 15 minutes he was happy again to continue development.

Automatic network installations are too easy to implement today on Linux. If you don’t have one, you must be living in the medieval times or so.
I can give you one suggestion though about partitioning – make sure your developers have a /home on a different partition. It’ll be easier when reinstalling to preserve /home and remove all the rest.

Consolidating software

I consider installing non-packaged software םn Linux a very dirty action.
The reasons for that are:

1. You can’t uninstall it using standard ways
2. You can’t upgrade it using standard ways
3. You can’t keep track of it

In addition to installing packaged software, you must also have all your workstations and server synchronize against the same software repositories.
If user A installs software from repository A and user B from repository B, they might run into different behavior on their software.
Have you ever heard: “How come it works on my computer and doesn’t work on yours??”
As a SysAdmin, you must eliminate the possibilities of this to happen to a zero.

How do you do it?
Well, using CentOS – use a YUM repository and cache whatever packages you need from the various internet repositories out there.
Debian? – just the same – just with apt.

Remember – if you have any software on workstations that is not well packaged or not well controlled – you’ll run into awkward situations very soon.

Today

Up until today Linux developers in my company still posses their root access, but they barely use it. To be honest I don’t think they even really need it. However, they have it. It is also about educating the developers that they are given the root access because they are being trusted. If they blew it, it’s mostly their fault, not yours.

I’ll continue to let them be root when needed. They have proved worthy so far.
And I’ll ask you another question – do you really think that someone who can’t handle his own workstation be a good developer? – think again!

Wicd can be installed on CentOS 5.4 with the following commands.

$ wget http://downloads.wicd.net/pkgs/stable/1.6.x/1.6.2/CentOS_5/wicd-1.6.2-2.1.i386.rpm
$ wget http://packages.sw.be/python-urwid/python-urwid-0.9.8.2-1.el5.rf.i386.rpm
# rpm -Uvh python-urwid-0.9.8.2-1.el5.rf.i386.rpm wicd-1.6.2-2.1.i386.rpm

Installation:

1. CD ROM – you can take 1of6.iso file (later you can use yum to install rest)

or

2. Making a DVD ( making a DVD whill show sometimes this error)

Unable to find boot image: linux
boot:

Note: i just saw kind of bug with few BIOS and SYSTEMS (in my case TravelMate 290 laptop didnt worked)

or

3. PXE Boot

What i need?

a. TFTP (non secure ftp server)

b. DHCP server (basic)

or

b. DHCP server (advanced)

If you own a Router which can handle the dd-wrt firmware you don’t have to disable the dhcp service in the router. Just open the ‘Administration’->’Services’ tab and enable ‘DNSMasq’ and in the ‘Additional DNS Options’ input field enter ‘dhcp-boot=pxelinux.0,tfptd-hostname,tftpd-ip‘. Replace tfptd-hostname with the hostname of your tftpd machine and tftpd-ip with the ip-address of you tfptd. Thats all. Nice articel. Can’t wait until the next comes out, which handles the PXE and NFS-Root.

c. centOS stored somewhere

Note: http://www.debian-administration.org/articles/478

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