Difference between revisions of "Debian installation"

Revision as of 11:26, 7 February 2012

(Part of the Software documentation of biowikifarm.)

This is a record of the installation and later updates of a Debian system (originally in version 4, later upgraded, see "Debian upgrade 4 to 5"). The page is intended to help running or repeating the server setup. In parts it may be outdated by subsequent configuration changes and software updates. Some notes may be updated, others not. However, much of the fundamental setup will remain evident from this document.

We use XenServer Express (see Server virtualization) and installed the Xen template for Debian 4.0 (kernel modified for paravirtualization) with the standard setup. This is a documentation of the steps performed to get the Debian server working. These notes are meant to enable non-Linux people to reproduce the setup, and Linux experts to spot problems or errors. A highly useful reference was [1].

Basics

The server can be reached at 160.45.63.55 with ssh enabled. Settings for ssh:

/etc/ssh/ssh_config default settings for ssh when used as client
/etc/ssh/sshd_config default settings for ssh as server
- use nano /etc/ssh/sshd_config to change PermitRootLogin yes to no, disallowing root access through ssh.
- use nano /etc/pam.d/common-password to increase minimum password length
- check lastlog to see last login of users

Current port and firewall situation: See Server ports and shorewall installation.

Memo on other IPs: 10 = base, 11, 41 = xencenter, and 56 = dev

Partitioning and formatting additional storage

NOTE: Info below refers to older setup, newer setup

Xen will partition and format the first two hard drives (system and swap), but any additional, medium needs to be partitioned manually. The name of the third virtual hard disk under XEN is xvdc. Run:

fdisk /dev/xvdc
#  type n for new partition, p for primary, 1 for first partition, 
#  accept defaults for size, type w to write out new partition. 
# To format with ext3 filesystem:
mkfs.ext3 /dev/xvdc1
# repeat the above for a temp and backup disk (/dev/xvde + /dev/xvde1), then
# To label partitions:
e2label /dev/xvda1 root
e2label /dev/xvdc1 storage
e2label /dev/xvde1 dump

Note that the fourth hard disk (used for dispensible content like logs or backup duplicates) had been xvde, with xvdd being fixed to the DVD device.

Correct function of partitioning can be tested, e.g. using webmin (Hardware, Partitions on Local disks). To permanently mount, add the following line to "/etc/fstab" (nano /etc/fstab):

/dev/xvdc1      /mnt/storage    ext3    rw,noatime      0       0
/dev/xvde1      /mnt/dump       ext3    rw,noatime      0       0
# to mount temporarily use something like:  "mount /dev/xvdc1 /mnt/temp"

During Xen-Debian install, the swap partition had been changed from 512 to 1024, however, to actually use more than 512 one needs to issue:

mkswap /dev/xvdb1 -L swap
swapon /dev/xvdb1

Check with

cat /proc/swaps
free

Resizing virtual disks

The disk needs to be deactivated in XenCenter before resizing.
Resizing the virtual storage unit does not change the size of the partition under Linux!
Method 1 (manual): if the disk contains only relatively easily migrated data (no dev/ports, etc.), copy all content to another disk using cp -pr (preserving owner, permission, recursive) or tar -p -s. Use fdisk as above, delete and recreate partition, format and label disk. Copy all back, delete temporary copy.
Method 2 (better, tip Manol, not yet tested):
- install parted: apt-get install parted or gparted (graphical frontend)
- unmount partition and check with parted
- OR: install apt-get install dump (dump - 4.4bsd dump and restore for ext2 filesystems) and use this to store and

Network, Hostname and IP address

First installation

Hostnames are in several places, especially important when renaming a server:

sudo nano /etc/hostname # entered: biowikifarm
sudo nano /etc/mailname # entered: biowikifarm.net
sudo nano /etc/hosts    # 160.45.63.55 biowikifarm.net biowikifarm

Open "nano /etc/network/interfaces" and enter:

# Used by ifup(8) and ifdown(8). See the interfaces(5) manpage or
# /usr/share/doc/ifupdown/examples for more information.
# The loopback network interface
auto lo
iface lo inet loopback

# The primary network interface
auto eth0
iface eth0 inet static
  address 160.45.63.55
  netmask 255.255.255.0
  network 160.45.63.0
  broadcast 160.45.63.255
  gateway 160.45.63.1
  dns-nameservers 160.45.8.8 160.45.10.12

# The following lines are desirable for IPv6 capable hosts
::1     ip6-localhost ip6-loopback
fe00::0 ip6-localnet
ff00::0 ip6-mcastprefix
ff02::1 ip6-allnodes
ff02::2 ip6-allrouters
ff02::3 ip6-allhosts

(Note: 160.45.8.8 and 160.45.10.12 are FU DNS)

Reboot now (first command) and run the following commands (the two hostname commands verify that the hostname setting is ok):

sudo reboot
hostname     # verify
hostname -f  # verify
sudo apt-get update
sudo apt-get upgrade
sudo apt-get dist-upgrade

It may be good to repeat this, some updates came only in second round. Finally, we may want to do some cleanup:

sudo apt-get autoclean

After doing this, the ssh fingerprints may have to be changed on all machines trying to access the new Debian by ssh (security issues fixed). Remove the keys for the previously opened IPs in the following file:

nano /root/.ssh/known_hosts

Related: Reconfiguring a copied virtual machine

Before starting a copied VM check the MAC adress in XEN to avoid running accidentially two servers under the same IP. A copied VM may use other interfaces instead of eth0, e.g., eth2. Thus first use ifconfig -a to find the name of the interface, then change interface name AND IP-number in network AND shorewall interface files. Also edit hostname and hosts, and restart shorewall:

sudo ifconfig -a | more
sudo nano /etc/network/interfaces # interface and IP
sudo nano /etc/shorewall/interfaces # (interface at the bottom, check, update if necessary)
sudo nano /etc/hostname
sudo nano /etc/hosts
sudo /etc/init.d/shorewall restart

(Note: if due to a misconfiguration the shorewall continuously displays blocking messages on the console, try Alt-F2, user name and password. Type blindly, despite repeated shorewall messages. "shorewall stop" will stop shorewall (type blindly).)

sudoers

Add to /etc/sudoers:

%sudo   ALL=(ALL) ALL

This lets all users of group sudo run any command as root without knowing the root password.

Adding repositories to package manager

It is possible to add further repositories to the package manager by editing the repository file: "nano /etc/apt/sources.list". One important addition is the backports (needed for OpenID further down), and we also expanded the scope from "main" to "main non-free contrib":

deb http://ftp.debian.org/debian/ etch main non-free contrib
deb http://www.backports.org/debian etch-backports main 
wget -O - http://backports.org/debian/archive.key | apt-key add -
# perhaps redundant to above (but working, adding keyring security data):
apt-get install debian-backports-keyring
# Necessary for webmin:
deb http://download.webmin.com/download/repository sarge contrib

The last command adds a gpg security key for the backport repository. (Documentation of further testing: We also tested the Google repository as an example. Using root console, we first had to get a pgp key (note: the original google instructions requested using https, but only http worked): wget -q http://dl-ssl.google.com/linux/linux_signing_key.pub -O- | apt-key add -, and add deb http://dl.google.com/linux/deb/ stable non-free.)

JAVA

Debian does not normally install Sun Java, but a slower "free Java". It is possible to install sun software after modifying the repository sources to include non-free software and backports (see here for more information: http://www.debian.org/doc/manuals/debian-java-faq/ch6.html):

apt-get install sun-java6-jre

The install location is /usr/lib/jvm/java-6-sun/. Sun recommends to update the Debian "alternatives system" to have Sun's tools as the default:

update-java-alternatives -s java-6-sun

Then edit /etc/profile (as user root), add:

export JAVA_HOME=/usr/lib/jvm/java-6-sun/
export JRE_HOME=/usr/lib/jvm/java-6-sun/jre
PATH=$JAVA_HOME/bin:$PATH

(The last line before "export PATH"; this export is probably only necessary (e.g. for Tomcat, see below) if an earlier version of Java is still running and is located in a path that is looked up first by the system.)

Log out and log back in again (this may also be another user) and then confirm that these settings are in effect by:

echo $JAVA_HOME
echo $JRE_HOME
echo $PATH

NOTES: apt-get suggested these packages (not installed):

 binfmt-support sun-java6-demo sun-java6-doc sun-java6-source sun-java6-plugin ia32-sun-java6-plugin sun-java6-fonts
 ttf-baekmuk ttf-unfonts ttf-unfonts-core ttf-kochi-gothic ttf-sazanami-gothic ttf-kochi-mincho ttf-sazanami-mincho
 ttf-arphic-uming libmyodbc odbc-postgresql libct1

apt-get recommended packages (not installed):

 libasound2 libnss-mdns gsfonts-x11

NOT DONE, TOMCAT WOULD BE REMOVED: The gcj packages were then removed:

NOT DONE, TOMCAT WOULD BE REMOVED:  apt-get remove ecj-bootstrap-gcj gcj-4.1-base java-gcj-compat libgcj-bc libgcj-common libgcj7-0 libgcj7-jar

Alternatively (and initially on this server, only later changed to apt-get!, following instructions at Sun/Java plus instructions [http://www.cs.wcupa.edu/rkline/netbeans-lin.html here) a downloaded Sun distribution may be manually installed: move downloaded file: "mv /home/vncroot/Desktop/jdk-6u6-linux-i586.bin /usr/local/". Run: "chmod +x jdk-6u6-linux-i586.bin" to make executable. Go to /usr/local/, run the file as: ./jdk-6u6-linux-i586.bin, remove the downloaded file (rm jdk-6u6-linux-i586.bin). -- With manual install in usr/local, to make installations version-independent, issue the following command: cd /usr/local/; ln -s jdk1.6.0_06 jdk (success is not returned, check whether in addition to the jdk1.6.0_06 a new jdk folder is present in /usr/local). Test with /usr/local/jdk/jre/bin/java -version, returns version number if all works. Later (2008-11), for safety, /usr/local/jdk was linked to /usr/lib/jvm/java-6-sun/

MySQL, Apache PHP, etc.

General installations

apt-get install gcc cpp libtool binutils make autoconf automake1.9 flex
apt-get install zip unzip rar unrar p7zip p7zip-full
apt-get install librsvg2-2 librsvg2-bin

The librsvg2-2/librsvg2-bin is an svg-renderer used by MediaWiki (requiring some extra work in settings files though). In our installation, it was already installed with a previous package.

To use MediaWiki with high traffic, a memcached memory cache should be installed prior to installing MediaWiki:

apt-get install memcached php5-memcache

Without further configuration, a single memcached daemon on default port 11211 will be active, limited to localhost (testing from outside with telnet 160.45.63.55 11211 confirmed this), using up to 64 MB of your RAM. This can not be changed by editing /etc/init.d/memcached, but /etc/memcached.config must be modified. We increased size: -m 128 = 128 MByte, user: -u www-data (run under same user as Apache) and -l 127.0.0.1 = listen only on local loopback interface.

Note: At the time of this writing, a fairly old version of memcached (1.1.12) is installed by apt-get of Debian 4 and No backports are available.

Update: at present, memcached has been de-installed because PHP-APC is used as object cache instead (single-machine setup).

MySQL

Installation

 apt-get install mysql-server mysql-client libmysqlclient15-dev
 nano /etc/mysql/my.cnf
 # ... and change port to "port = 8088" and comment out: "#bind-address = 127.0.0.1" 
 # so that mysql can be reached from outside. Then restart:
 /etc/init.d/mysql restart

Console commands

Test with netstat (debian seems to report 8088 as omniorb) and set a password for root (otherwise anybody can access your MySQL database!):

 netstat -tap
 # -u = login as this user
 mysqladmin -u root password (ThePassword)

New users can be created and granted privileges inside the mysql console:

 # enter the mysql console (asks for passwort):
 mysql -u root -p

 -- within the console (mysql> ):
 grant all privileges on *.* to 'username'@'localhost' identified by 'PASSWORD' with grant option;
 grant all privileges on *.* to 'username'@'%' identified by 'PASSWORD' with grant option;
 -- to exit the mysql console type:
 exit

Notes: a) grant will create a user if it does not exist yet. b) username, hostname, PASSWORD must be quoted with '. c) the '%' allows the user to log in from any other host except localhost; an explicit grant for localhost is thus required in addition to the '%'.

Changing password for existing users:

 # enter the mysql console (asks for passwort):
 mysql -u root -p

 -- within the console (mysql> ):
 set password = PASSWORD('NEW-PASSWORD-HERE');
 -- Alternative, for a different user:
 set password FOR 'name'@'localhost' = PASSWORD('NEW-PASSWORD-HERE');

Some other mysql console commands are:

 show databases;
 use mysql; Select * from user;
 drop user root@OudemansD;

Important note: entering mysql command line with "mysql -u wikiuser -p" will ask for password; if you want to include the password (e.g. when using pipe into) do not add a blank between p and the password. Also, when using the -h host option, only -hlocalhost, but not -hlocalhost:8088 will work! The host can usually be omitted. See the following examples:

 mysql -uwikiuser -pTHEPASSWORD
 mysql -hlocalhost -u wikiuser -pTHEPASSWORD < openid_table.sql

Copying or importing a MySQL database

Unlike MS SQL Server, you cannot reliably move a MySQL database by detaching, moving, and attaching binary files in the MySQL directory. You must dump the mysql database to a sql/text file using the mysqldump command. The SQL commands can then re-create the tables and contents. To use the file, start the mysql command interface, create and use the database and give the command "source your_filename" which reads and executes the commands from the dump file.

Over the web, myphpadmim offers backup (which works) and restore (which does not work for any reasonably sized database, despite uploading as zip file, we are getting out of memory errors). So we have to use command line programming. Note that the dump created by myphpadmin includes a database create statement; to copy to a different database name you need to modify this (extremely long lines may become corrupted in some editors!); the mysqldump does not contain database statements and is easier to reuse.

To dump a database:

 mysqldump -u root -p wikidb > /var/backups/wikis/wikidb.sql

This writes the database into a file called sample.sql. To create or import it into a new database called xxx, creating tables with their inserts that were present in the former wikidb, use:

 mysql -u root -pMySecretPW

 -- DROP DATABASE IF EXIST `xxx`;
 CREATE DATABASE `xxx`;
 -- for a wiki:
 CREATE DATABASE metawiki DEFAULT CHARACTER SET utf8 COLLATE utf8_general_ci;
 USE `xxx`;
 -- load from a file:
 SOURCE /var/backups/wikis/wikidb.sql;

You can also copy directly a database from one server to another or the same server. The second database must have been created however,

 mysql -u root -p

 CREATE DATABASE metawiki DEFAULT CHARACTER SET utf8 COLLATE utf8_general_ci;
 exit;

 mysqldump -u root -p(ThePassword) --opt wikidb | mysql -u root -p(ThePassword) --host=localhost -C metawiki

Here wikidb is copied to "localhost" (–C tells mysqldump to use data compression if both servers support it). "localhost" can be replaced by the IP address of any local or remote computer.

Note: a wiki-backup script has been started in /var/backups/scripts

Execute sql from command line:

 mysql -u root -p --database=orowiki < /var/www/v-orowiki/w/media/orowiki.sql

Performance tuning and unicode:

In /etc/mysql/my.cnf we changed:

key_buffer      = 64M  # was 16M
sort_buffer     =  8M  # did not exist
max_connections = 2000 # was 100
table_cache     =  256 # was 64
# utf8
init-connect='SET NAMES utf8'
character-set-server=utf8
collation-server=utf8_unicode_ci

We include three-letter words in the full text index:

ft_min_word_len=3

(Note: after changing this, run "REPAIR TABLE searchindex QUICK;" in mysql/myadmin on each affected database.)

Updating passwords

mysqladmin -u root -p'theOLDpassword' password 'theNEWpassword'

Apache

apt-get install apache2 apache2-doc apache2-mpm-prefork apache2-utils libexpat1 ssl-cert
nano /etc/apache2/mods-available/dir.conf
# add more values to DirectoryIndex:
#    index.html index.htm index.shtml index.cgi index.php index.php3 index.pl index.xhtml
nano /etc/apache2/ports.conf
# add ssl port to the existing "Listen 80" on new line: Listen 443

Now we have to enable some Apache modules (SSL, rewrite, suexec, and include) and execute the last command restart:

sudo a2enmod ssl
sudo a2enmod rewrite
sudo a2enmod suexec
sudo a2enmod include
sudo /etc/init.d/apache2 force-reload

Apache config is in /etc/apache2/apache2.conf, the virtual host configurations are included from: /etc/apache2/sites-enabled/ which are links pointing to /etc/apache2/sites-available/. The command sudo a2ensite name enables an available site.

By default, the www-root (DocumentRoot) is /var/www/.

To test the configuration, use sudo /usr/sbin/apache2 -t

SSL: We use a self-signed certificate, using the OpenSSL command:

sudo openssl req -new -x509 -days 2190 -nodes -out /etc/ssl/certs/ssl-cert-XXXX.pem -keyout /etc/ssl/certs/ssl-cert-XXXX.key

To enable SSL, link in sites-enabled to /etc/apache2/sites-available/default-ssl, modify default-ssl by pointing to the new pem and key files and enable the directive "NameVirtualHost *:443".

Restart: sudo /etc/init.d/apache2 reload. (Note: forgetting the sudo, will result in cryptic messages like: "httpd not running, trying to start / (13)Permission denied: make_sock: could not bind to address [::]:80 / (13)Permission denied: make_sock: could not bind to address 0.0.0.0:80 / no listening sockets available, shutting down / Unable to open logs".)

Logrotation: sudo nano /etc/logrotate.d/apache2 - change any settings, e.g. daily or weekly, "create 640" to "create 660". logrotate has not problems with softlinks, but if moving the path, rights have to be observed. Test with sudo logrotate --debug /etc/logrotate.d/apache2 &> logrotate_debug_log.txt since logrotate writes to standard error, not standard out!

Subversion

apt-get install subversion libapache2-svn
# (note: modules are automatically enabled, no a2enmod necessary)

Tested with MediaWiki svn download (see below)
Potential additional instructions (not used): Configuring Subversion

Special commands:

svn update -rXXXX # update to specific revision (XXXX being an integer revision number)
svn revert filename # revert a modified file to its original state, so future updates will refresh the file again
cd /usr/share/mediawiki; svn status phase3 # show locally modified files (potentially no longer updated)

Later, a local repository was installed, see Configuring the subversion repository

PHP

Instructions for PHPMyAdmin: http://www.debianhelp.co.uk/phpmyadmin.htm, downloading not necessary, apt will do this.

apt-get install libapache2-mod-php5 php5 php5-common php5-curl php5-dev php5-gd php5-idn php-pear php5-imagick php5-imap php5-json php5-mcrypt php5-mhash php5-ming php5-mysql php5-ps php5-pspell php5-recode php5-snmp php5-sqlite php5-tidy php5-xmlrpc php5-xsl
apt-get install phpmyadmin

Enable php after installing:

a2enmod php5

This creates symbolic links from /etc/apache2/mods-available/php5.conf and /etc/apache2/mods-available/php5.load to /etc/apache2/mods-enabled.

As long as all php runs on a single server, APC is better than memcached. Recommended reading: http://www.mediawiki.org/wiki/User:Robchurch/Performance_tuning it is recommended to use:

apt-get install php-apc

Check phpinfo.php, section apc for success. Note: Initially we did not configure the APC user cache for the mediawiki object cache ($wgMainCacheType = CACHE_ACCEL), but use memcached for this ($wgMainCacheType = CACHE_MEMCACHED) to simplify transition to multiserver setup without APC. However, we have since moved the entire cache action to memcached.

PECL extensions

See http://www.jejik.com/articles/2008/07/howto_build_and_install_the_intl_pecl_extension_for_php5_in_debian/

# check whether gpg keys available:
sudo  gpg --list-secret-keys
# if fail, then: sudo  gpg --gen-key
sudo apt-get install php5-dev dh-make-php fakeroot libicu38 libicu-dev xsltproc
# download, extract, build:
cd ~/php-intl-1.1.2
sudo dh-make-pecl --depends libicu38 --build-depends libicu-dev --only 5 --maintainer 'YOUR_GPGName_and_EMAIL'  intl 
cd php-intl-1.1.2
dpkg-buildpackage -rfakeroot

(was build and installed by manol)

php.ini

For MediaWiki, uploading must be enabled. The php.ini file used by apache is at /etc/php5/apache2/php.ini and already contains file_uploads = On and register_globals was already Off. However several settings were changed:

max_execution_time = 120  ; DEFAULT WAS 30; Maximum execution time in seconds of each script
max_input_time = 90       ; Maximum amount of time in seconds each script may spend parsing request data
memory_limit = 100M       ; Maximum amount of memory a script may consume (default 16MB) ## gallery2 install requires at least 34 
upload_max_filesize = 50M ; was just 2
post_max_size =52M ; was 5, affects file upload and must be larger fileupload!
allow_call_time_pass_reference = Off  ; was On

max_execution_time = 120 was increased because certain admin queries on wikis take more than the default 30 seconds allotted.

The ini file for command-line scripts is at /etc/php5/cli/php.ini; this is separate from the one used for the apache php module.

Syntax errors: The log files are relatively silence if a syntax error exists in php.ini. All values will be used with their defaults; thus this situation can be detected by checking Special:Upload whether it displays an upload limit of 2 MB. To manually check php.ini for syntax errors use:

php --info --php-ini /etc/php5/apache2/php.ini

Important for inserting utf-8 text into mysql:

Although a mysql table may be set to CHARACTER SET utf8, the mysql client's standard charset may still be Latin1. So when inserting utf-8 data with PHP, the client's charset may have to be changed to utf-8 after creating the connection:

$conn = mysql_connect($MySQL_Host, $MySQL_User,$MySQL_Passwd);
mysql_query("SET NAMES utf8", $conn);

apc.ini

This is in /etc/php5/conf.d/apc.ini

The status can be viewed by looking at apc_1417869461139.php in the www root.

Our content is (size increased from 30 to 60, especially for mediawiki user-cache usage):

extension=apc.so
# apc.shm_segments=3
apc.enabled=true
# default: apc.shm_size=30 # i.e. 30 MB
apc.shm_size=60

PHPMyAdmin

To enable phpmyadmin, edit: /etc/apache2/apache2.conf and add at end of file:

# Enable PHPMyAdmin
Include /etc/phpmyadmin/apache.conf

(Test with "http://biowikifarm.net/phpmyadmin" - or any current port)

Mediawiki

Mediawiki installation information is available separately: Mediawiki_installation

Gallery 2

Using apt-get install gallery2, Debian 4 (Etch) installs only the obsolete Gallery2.1. For Drupal 6 integration we need Gallery2.3, so this is not an option. Instead, we used subversion-based installation:

cd /usr/share/; https://gallery.svn.sourceforge.net/svnroot/gallery/trunk/gallery2
cd /var/www; ln -s /usr/share/gallery2
# Create a folder for gallery data (non-standard name):
mkdir /var/gallery2data
chmod 777 /var/gallery2data
# Create the config file and make sure the webserver can write it:
cd /var/www/gallery2/
touch config.php 
chmod 666 config.php

The Gallery subversion installation can later be updated with:

cd /usr/share/gallery2/; svn update

The database must have already been created (with utf8!), but we use the mediawiki wikidb and the wikiuser for gallery2 as well to simplify backup and maintenance. Install by navigating e.g. to http://160.45.63.55:8087/gallery2. Install is well prompted. For host use localhost (NOT localhost:8088; non-TCP/IP connection???). During normal install, a memory error may appear, in php.ini the default "memory_limit = 16M" must be increased to "memory_limit = 40M".

The admin user was set to WikiSysop with same password (but they are unconnected).

We selected a wide spectrum of plugins (but not gallery 1 update or shopping modules). Activation notes:

The Ffmpeg module was installed, but needs configuration to be activated
The ImageMagick module was installed, but needs configuration to be activated
The Jpegtran module was installed, but needs configuration to be activated
The URL Rewrite module was installed, but needs configuration to be activated

TODO: Followed recommendation from http://codex.gallery2.org/Gallery2:Security#Short_Check_List

Important modules are:

Link Item - allows external URLs (as well as albums). Link allows to link an external webpage or image (both optionally with an algorithmic thumbnail generation using khtml2png, which, however, is difficult to set up and Linux only)
Major problem: if web-page thumbnail generation is not active, a "chain" image is used as thumbnail. The thumbnail can be manually set, but NOT to a URL, it seems only to local files!
MultiLang = content metadata like title, description in multiple languages!

The gallery configuration created by the install process is </code>/var/www/gallery2/config.php</code>, data are stored in </code>/var/gallery2data/</code> outside of www-root. Some security recommendations [2] were applied, e.g.:

chmod 755 /usr/share/gallery2/
chmod 644 /usr/share/gallery2/config.php

Tomcat

Important: to get Tomcat5.5 running after installing, it is necessary that the environment variables JAVA_HOME and JRE_HOME are set correctly and that JDK 5 or higher is used.

# NOTE: native tomcat no longer used:
# apt-get install tomcat5.5 tomcat5.5-admin tomcat5.5-webapps
apt-get install libapache2-mod-jk

In /etc/default/tomcat5.5 remove comment markers from TOMCAT_USER=tomcat55 (default), or another user, and do the same for JAVA_HOME with the correct path (peferably a symbolic link to current version, e.g. JAVA_HOME=/usr/lib/jvm/java-6-sun). The other options only need to be uncommented if you want to override the defaults (which are set in /etc/init.d/tomcat5.5).

Edit /etc/profile (as user root), add:

## For debian standard: export CATALINA_HOME=/usr/share/tomcat5.5
## Instead, for fedora-tomcat:
export CATALINA_HOME=/usr/share/fedora-3.1/tomcat

To make Tomcat work with Apache edit /etc/libapache2-mod-jk/workers.properties and set the two lines (using your correct paths):

workers.tomcat_home=/usr/share/fedora-3.1/tomcat
workers.java_home=/usr/local/jdk

At the end of /etc/apache2/apache2.conf add:

# Enable libapache2-mod-jk
Include /usr/share/doc/libapache2-mod-jk/httpd_example_apache2.conf

--- Presently, the tomcat used is the one supplied with Fedora, inside the Fedora folder. The main tomcat access is fedora.keytonature.net. However, Lia Veja has installed a secondary point

 http://species-id.net/services/

L. Veja writes "it needs some edits in web.xml file for every application you will put there".

Restart Apache and Tomcat.

/etc/init.d/apache2 restart
/etc/init.d/tomcat5.5 restart

Fedora

See FEDORA Installation, FEDORA Batch Import

For manual Fedora 3.1 start method see section further below under "Stop services / demons"

Note: Fedora does not install the log folder in the log path of debian. GSearch logs become quickly very large (Gigabytes), so it is important to move them. The following code copies existing logs (assuming /var/log/fedora/ already created) and creates symbolic links. THIS NEEDS TO BE REPEATED WITH EVERY UPDATE OF FEDORA TO A NEW VERSION!

cp -pr /usr/share/fedora/server/logs/* /var/log/fedora/ # destination may be /mnt/dump/var/log/fedora
/usr/share/fedora/tomcat/bin/shutdown.sh
rm -r /usr/share/fedora/server/logs
ln -s /mnt/dump/var/log/fedora /usr/share/fedora/server/logs
/usr/share/fedora/tomcat/bin/startup.sh

Note 2009-09:

http://fedora.keytonature.net/x/x.jpg

links to /var/lib/tomcat5.5/webapps/x/x.jpg with /usr/share/tomcat5.5/webapps/ being a link to /var/lib/tomcat5.5/webapps/. However the root of http://fedora.keytonature.net/ links to webapps/ROOT, but on 2009-09 was misconfigured to link to fedora-3.1/tomcat/webapps... folder.

Fedora Rebuild Index

In several situations it may be necessary to rebuild the Fedora indices:

Recovering from inconsistencies and/or corruption of the indexes.
Upgrading from a previous version of Fedora when the SQL database or Resource Index changed significantly between releases
Migrating from one SQL database product to another in an existing Fedora installation. Such migration can be done by modifying /usr/share/fedora-3.XXX/server/config/fedora.fcfg to point to a properly-configured <datastore..>

The batch service fedora-rebuild.sh must be started as follows:

* Stop the Fedora server (if using Fedora-Tomcat, this can be done with the /usr/share/fedora/tomcat/bin ./shutdown.sh command)
* Run /usr/share/fedora/server/bin ./fedora-rebuild.sh 
* Select option "1" in order to rebuild indexes
* Confirm this procedure with "1" 
* Restart the Fedora server (if using the Fedora-Tomcat, this can be done with the /usr/share/fedora/tomcat/bin ./startup.sh command)

Webmin

Webmin is a web-based system configuration tool for Linux. With it you can configure many operating system internals, such as users, disk quotas, services, configuration files etc., as well as modify and control many open source apps, such as the Apache HTTP Server, PHP, MySQL etc. It has it's own web server and a self-signed SSL Certificate Authority. Later configuration of own SSL Certificate is necessary for increased security.

To install, first /etc/apt/sources.list needs to contain the line deb http://download.webmin.com/download/repository sarge contrib". Then:

sudo apt-get update; sudo apt-get install webmin

You will be asked if you wish to install the package without verification. Select yes. After install is complete, webmin's web service runs by default on port 10000 secure. To configure a different port:

sudo nano /etc/webmin/miniserv.conf
# change port AND listen options from 10000 to 8010 and restart:
sudo /etc/init.d/webmin restart

To login under https://160.45.63.55:8010/

Any user that can execute sudo can login with their usual password. Help for the standard modules used by Webmin can be found here: http://doxfer.com/Webmin/Modules. A wiki page for webmin can be found here: http://doxfer.com/Webmin

mc (midnight commander) und jed (editor)

Midnight commander is the Linux equivalent of the Norton Commander. Anyone familiar with Norton Commander should feel right at home. Very useful for browsing through the file system. It has an integrated FTP client, editor and file viewer, and supports the use of a mouse inside an ssh window! Similarly, jed is an editor that supports the use of mouse in ssh. Install both with

sudo apt-get install mc jed

No configuration necessary. Run with

mc
jed

cronjobs

sudo crontab -u root -e  # edit roots cron jobs

crontab uses jed as editor. Format at start of each line is: minutes, hour, day, etc. One can use * for every (hour, day, month, year). Output is normally sent by email. To suppress this redirect output to ">/dev/null 2&>1"

Always add a comment after each line: # explain what this does and who installed it.

Security, virus protection, rootkit hunter

rootkit hunter:

sudo apt-get install rkhunter
sudo rkhunter --update
sudo rkhunter --checkall

clamav:

sudo apt-get install clamav
/etc/init.d/clamav-freshclam start
# or: stop, restart, etc.

rest not sure. clamav, clamscan etc. don't work. Was not asking for configuration. -> ?

http://www.debianadmin.com/clamav-installation-and-configuration.html looks good, but did not help

General: use on files or folders to change group and rights:

sudo chgrp -R mw-extension-writers crossdomain*; sudo chmod -R 664 crossdomain*;
# or if containing folders:
sudo chgrp -R mw-extension-writers /var/www/tools/mediaIBIS; sudo chmod -R 775 /var/www/tools/mediaIBIS

Tips for simple access of Debian file from remote Windows

Install WinSCP, which will allow to browse the Debian server almost like a Windows explorer (or a graphical Midnight commander). It allows to easily and securely (using sftp, we do not use ftp) create folders, copy files within the server, or upload/download files to your machine.

WinSCP also very nicely integrates with PuTTY, a ssh client. To make this as simple as possible, do the following:

You can either
- install PuTTY (copy all files from the zip with all executables and help) into the Putty subfolder of WinSCP
- Or (perhaps already) have installed it anywhere else
In any event go in WinSCP to the menu: Options/Preferences, then in the Dialog box: integration/applications and check the path. It should be something like "%PROGRAMFILES%\PuTTY\putty.exe" if putty has been installed in that folder.
In the same dialog, turn on Remember... and Automatically...
Now whenever you open WinSCP, a second window with ssh will automatically be opened.
To change the display options in PuTTY, go to the Window menu (top left), Change settings (e. g. Window, Color, Use System colors will use black-on-white text if you have set you Windows command window that way). Under Window increase Columns (e.g. to 120), Rows (e.g. to 63), and scrollback (e.g. to 900) to suit your taste. On "Session" itself select "Default" and click "Save" to preserve your changes.

Reversely, adding NTFS support to Debian: In our case this was desirable to add read/write support for NTFS-Formatted USB-disks. Provided backports are installed for apt-get (as instructed above), one can install:

aptitude install ntfs-3g

To temporarily mount from command line use (assuming the usb-disk is xvdf, check in Xen Center)

mount -t ntfs-3g /dev/xvdf1 /mnt/usb-disk
# (if disk is fat32, use: mount -t auto /dev/xvdf1 /mnt/usb-disk)

To mount the NTFS during boot add the following to the end of the /etc/fstab file:

/dev/xvdf1 /mnt/usb-disk ntfs-3g defaults 0 0

See ntfs-3g manual for further information. Some note mention that "To mount files with non-ASCII characters one may have to give the option -o locale=XXX to the mount options of ntfs-3g; see http://ntfs-3g.org/support.html#locale for further information." We did not do so far, using UTF-8 seems to work.

@@ Line 22: / Line 22: @@
 === Partitioning and formatting additional storage ===
+NOTE: Info below refers to older setup, newer setup
 Xen will partition and format the first two hard drives (system and swap), but any additional, medium needs to be partitioned manually. The name of the third virtual hard disk under XEN is xvdc. Run: