Milos - BioImage Wiki (internal)

This page is obsolete - see http://milos2.zoo.ox.ac.uk/ibrgtech/index.php/Milos_setup

Milos System Notes

This page contains technical notes about the Milos server system (milos1., milos2.zoo.ox.ac.uk).

Contents:

Hardware configuration
Software configuration
Installation notes
Links and more information

1. Hardware configuration

TransTEC server:

SuperMicro 370DL3 motherboard
Dual Pentium 6 866MHz processors
2Gb RAM
Onboard SCSI controller:
- sda: 140Gb Seagate Cheetah, model ST3126707LW (68-pin connector)
- sdb: 70Gb Seagate
- sdc: 36Gb Maxtor Atlas 10k IV, model 8B036L0
IBM RAID controller with connection to EXP300 rack
Onboard ethernet controller (eth0) - Intel 82557/8/9 - 00:30:48:21:4D:3A
Second Ethernet controller card (eth1) - 3COM 3C980C - 00:01:02:74:26:96

2. Software configuration

Operating system: CentOS 5, clone of Redhat Enterprise Linux 5 (RHEL5)

Disks and volumes:

sda (140Gb)
- /dev/sda1 - /boot
- /dev/sda2 - VolGroup00 (136Gb)
  - /dev/VolGroup00/LogVol00 - / (8Gb)
  - /dev/VolGroup00/LogVol01 - swap (4Gb)
sdb (70Gb)
- /dev/sdb1 - /storage1
sdc (36Gb)
- /dev/sdc1 - /var
eth0 - 129.67.24.14 (milos1.zoo.ox.ac.uk)
eth1 - 129.67.24.15 (milos2.zoo.ox.ac.uk)

3. Installation notes

New operating system installation 10-Oct-2007.

Note: to run the system-config-securitylevel script in an SSH session using the SecureCRT (Van Dyke) SSH client, under Options > Session options > Emulation select Linux, and under Options > Session options > Emulation > Advanced select UTF-8 character encoding.

3.1. Base system

Initially ran into problems with installation of the system from CD. It was either hanging or running very slowly. This apears to be a problem with memory over 2Gb, which is fixed by adding mem=2047M@1M to the boot command line.

Network details:
- subnet: 255.255.252.0 (/22)
- gateway: 129.67.27.254
- DNS: 129.67.1.1, 163.1.2.1, 129.67.1.180
- WINS: 163.1.2.52, 129.67.1.52
- NTP: ntp0.oucs.ox.ac.uk
Initial accounts: root, graham, zhaoj
- Also added johnpybus for oucc
Note installation creates a "kickstart" file at /root/anaconda-ks.cfg
YUM update. (Twice.)

Edit /etc/grub.conf, to add mem= line to kernel command, thus:

[root@milos2 etc]# less grub.conf  
# grub.conf generated by anaconda
#
# Note that you do not have to rerun grub after making changes to this file
# NOTICE:  You have a /boot partition.  This means that
#          all kernel and initrd paths are relative to /boot/
#
default=0
timeout=10
splashimage=(hd0,0)/grub/splash.xpm.gz
hiddenmenu
title CentOS (2.6.18-8.1.14.el5)
        root (hd0,0)
        kernel /vmlinuz-2.6.18-8.1.14.el5 ro root=/dev/VolGroup00/LogVol00 rhgb quiet mem=2047M@1M
        initrd /initrd-2.6.18-8.1.14.el5.img
title CentOS (2.6.18-8.el5)
        root (hd0,0)
        kernel /vmlinuz-2.6.18-8.el5 ro root=/dev/VolGroup00/LogVol00 rhgb quiet
        initrd /initrd-2.6.18-8.el5.img

Edit /etc/ssh/sshd_config to contain:

```
PermitRootLogin no 
```

and

```
allowgroups remote 
```

Create new group 'remote', and edit /etc/group to add remote login users to this group. e.g.
- ```
remote:x:85:graham,zhaoj 
```
Install sshblack per http://wiki.oss-watch.ac.uk/InstallingSshblack,

Edit /etc/fstab to include other disks:

/dev/VolGroup00/LogVol00 /                       ext3    defaults        1 1 
/dev/sdb1                /mnt/sdb1               ext3    defaults        0 2
/dev/sdc1                /mnt/sdc1               ext3    defaults        0 2
LABEL=/boot              /boot                   ext3    defaults        1 2
devpts                   /dev/pts                devpts  gid=5,mode=620  0 0
tmpfs                    /dev/shm                tmpfs   defaults        0 0
proc                     /proc                   proc    defaults        0 0
sysfs                    /sys                    sysfs   defaults        0 0
/dev/VolGroup00/LogVol01 swap                    swap    defaults        0 0

Install and activate inetd:

yum install xindetd 
service xinetd start

Check xinetd is running:
- ```
service xinetd status 
```

Configure yum for automatic daily updates. Edit file /etc/yum/yum-updatesd.conf and change the line do_update thus:

[main] 
# how often to check for new updates (in seconds)
run_interval = 3600
# how often to allow checking on request (in seconds)
updaterefresh = 600

# how to send notifications (valid: dbus, email, syslog)
emit_via = dbus
# should we listen via dbus to give out update information/check for
# new updates
dbus_listener = yes

# automatically install updates
do_update = yes
# automatically download updates
do_download = no
# automatically download deps of updates
do_download_deps = no

3.2. Apapche and PHP

Configure and start apache web server.

Edit /etc/httpd/conf/httpd.conf to add the following at the end (to allow virtual hosts configurations to be created separately, in similar fashion to web application .conf files):
- ```
# 
# Load virtual host files from the config directory "/etc/httpd/conf.d".
#
Include conf.d/*.host
```

Activate the HTTPD server, thus:

[root@milos2 conf]# chkconfig httpd on 
[root@milos2 conf]# chkconfig httpd --list
httpd           0:off   1:off   2:on    3:on    4:on    5:on    6:off
[root@milos2 conf]# service httpd start
Starting httpd: [  OK  ]

Server certificate checking

cd /etc/httpd 
grep -R SSLCertificate *
conf.d/ssl.conf:# Point SSLCertificateFile at a PEM encoded certificate.  If
conf.d/ssl.conf:SSLCertificateFile /etc/pki/tls/certs/localhost.crt
conf.d/ssl.conf:SSLCertificateKeyFile /etc/pki/tls/private/localhost.key

This is the default setup, whose certificate contains localhost as its host name.

Create new server certificate (see http://www.madboa.com/geek/openssl/#cert-self):

openssl req -x509 -nodes -days 365 -newkey rsa:1024 -keyout milos2.zoo.ox.ac.uk.key -out milos2.zoo.ox.ac.uk.crt

Update details of key anhd certificate files in /etc/httpd/conf.d/ssl.conf
Restart httpd

3.3. Mail server

Change mail handler to postfix:

yum install postfix 
yum remove sendmail

Edit /etc/aliases to redirect email for root:

# Person who should get root's mail 
root:           graham,graham.klyne@zoo.ox.ac.uk

Then run:

```
[root@milos2 etc]# newaliases 
```

Run postfix:

[root@milos2 etc]# service postfix start 
Starting postfix: [  OK  ]
[root@milos2 etc]# service postfix status
master (pid 7463) is running...

3.3.1. Handling bioimage.org mail

The intent is that all mail for bioimage.org or mail.bioimage.org will be forwarded to a mailing list ( bioimage-exteranal@mail.ontonet.org) on Antiparos. See http://www.postfix.org/VIRTUAL_README.html for more details.

Add this to file /etc/postfix/main.cf:

# POST-INSTALLATION (GK) 
# 
# See: http://www.postfix.org/VIRTUAL_README.html
#
virtual_alias_domains = bioimage.org, mail.bioimage.org
virtual_alias_maps = hash:/etc/postfix/bioimage

Also in mail.cf, check that postfix is listening for external connections:
- ```
inet_interfaces = all 
```
or
- ```
inet_interfaces = $myhostname, localhost 
```
If this parameter is changed, restart postfix thus:
- ```
service postfix restart 
```

Create a new file /etc/postfix/bioimage:

# Virtual mail host alias file for bioimage.org  
postmaster@bioimage.org postmaster
postmaster@mail.bioimage.org postmaster
@bioimage.org bioimage
@mail.bioimage.org bioimage

Run command: postmap /etc/postfix/bioimage. This creates a file /etc/postfix/bioimage.db.

Add this to etc/aliases:

bioimage:       bioimage, bioimage-external@mail.ontonet.org

Run these commands:
- ```
newaliases 
postfix reload
```

3.4. FastCGI

This is for use by TRAC (see later)

Install httpd-devel:
- ```
yum install http-devel 
```
Retrieve FastCGI tow orking directory; note that the most recent non-snapshot release has some symbol definitions missing for use with Apache 2: see http://www.fastcgi.com/archives/fastcgi-developers/2005-December/004060.html.
- ```
wget http://www.fastcgi.com/dist/mod_fastcgi-SNAP-0709231442.tar.gz 
```

Install FastCGI

tar xvfz mod_fastcgi-SNAP-0709231442.tar.gz  
cd mod_fastcgi-SNAP-0709231442
cp Makefile.AP2 Makefile
make top_dir=/usr/lib/httpd
make top_dir=/usr/lib/httpd install
cd ..

Confirm module is present:

[root@milos2 kit]# find /usr/lib -name mod_fastcgi.so  
/usr/lib/httpd/modules/mod_fastcgi.so

The FastCGI installation suggests an httpd.conf directive like this:
- ```
LoadModule fastcgi_module modules/mod_fastcgi.so 
```

3.5. MySQL

Activate MySQL daemon:

[root@milos2 etc]# chkconfig mysqld on 
[root@milos2 etc]# chkconfig --list mysqld
mysqld          0:off   1:off   2:on    3:on    4:on    5:on    6:off
[root@milos2 etc]# service mysqld start
Initializing MySQL database:  Installing all prepared tables
Fill help tables

To start mysqld at boot time you have to copy support-files/mysql.server
to the right place for your system

PLEASE REMEMBER TO SET A PASSWORD FOR THE MySQL root USER !
To do so, start the server, then issue the following commands:
/usr/bin/mysqladmin -u root password 'new-password'
/usr/bin/mysqladmin -u root -h milos2.zoo.ox.ac.uk password 'new-password'
See the manual for more instructions.

You can start the MySQL daemon with:
cd /usr ; /usr/bin/mysqld_safe &

You can test the MySQL daemon with the benchmarks in the 'sql-bench' directory:
cd sql-bench ; perl run-all-tests

Please report any problems with the /usr/bin/mysqlbug script!

The latest information about MySQL is available on the web at
http://www.mysql.com
Support MySQL by buying support/licenses at http://shop.mysql.com
[  OK  ]
Starting MySQL:  [  OK  ]
[root@milos2 etc]# /usr/bin/mysqladmin -u root password '***'
[root@milos2 etc]# /usr/bin/mysqladmin -u root -h milos2.zoo.ox.ac.uk password '***'

Check out MySQL:

[root@milos2 etc]# /usr/bin/mysqladmin -u root --password=*** version 
/usr/bin/mysqladmin  Ver 8.41 Distrib 5.0.22, for redhat-linux-gnu on i686
Copyright (C) 2000 MySQL AB & MySQL Finland AB & TCX DataKonsult AB
This software comes with ABSOLUTELY NO WARRANTY. This is free software,
and you are welcome to modify and redistribute it under the GPL license

Server version          5.0.22
Protocol version        10
Connection              Localhost via UNIX socket
UNIX socket             /var/lib/mysql/mysql.sock
Uptime:                 10 min 38 sec

Threads: 1  Questions: 16  Slow queries: 0  Opens: 0  Flush tables: 1  Open tables: 6  Queries per second avg: 0.025

[root@milos2 etc]# /usr/bin/mysql -u root --password=*** 
Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 12 to server version: 5.0.22

Type 'help;' or '\h' for help. Type '\c' to clear the buffer.

mysql> show databases;
+--------------------+
| Database           |
+--------------------+
| information_schema | 
| mysql              | 
| test               | 
+--------------------+
3 rows in set (0.00 sec)

mysql> quit
Bye
[root@milos2 etc]#

phpMySqlAdmin setup, starting in a wrokign directory:

wget http://kent.dl.sourceforge.net/sourceforge/phpmyadmin/phpMyAdmin-2.11.1-all-languages.tar.gz 
tar xfvz phpMyAdmin-2.11.1-all-languages.tar.gz
mv phpMyAdmin-2.11.1-all-languages /var/www/html/
cd /var/www/html/
ln -s phpMyAdmin-2.11.1-all-languages/ phpMyAdmin
cd /var/www/html/phpMyAdmin/

Create file /var/www/html/phpMyAdmin/config.inc.php to contain something like this:

<?php
$cfg['blowfish_secret'] = '0123456789ABCDEF';  // use here a value of your choice
$i=0;
$i++;
$cfg['Servers'][$i]['auth_type']     = 'cookie';
?>

Now it is possible to browse to http://milos1.zoo.ox.ac.uk/phpMyAdmin/.

3.6. Samba

Activate SAMBA:

chkconfig smb on 
chkconfig --list smb
service smb start
smbpasswd -a (username)
 :
(etc.)

Edit file /etc/samba/smb.conf, to contain:

[global] 
  workgroup = SHOTTON
  netbios name = MILOS
  server string = Milos server
  security = share
  hosts allow = 129.67.24.0/255.255.252.0 127.
  encrypt passwords = Yes
  debug level = 2
  log file = /var/log/samba/%m.log
  max log size = 100
  socket options = TCP_NODELAY SO_RCVBUF=8192 SO_SNDBUF=8192
  dns proxy = No
  cups options = raw

[homes]
   comment = Home Directories
   browseable = no
   writable = yes

[printers]
   comment = All Printers
   path = /usr/spool/samba
   browseable = no
   writable = no
   printable = yes

[storage1]
   comment = Storage 1
   path = /storage1
   revalidate = Yes
   username = (list of usernames...)
   valid users = (list of usernames...)
   writeable = Yes

Bring /storage1 disk (sdb1) online. (This is mounted by /etc/fstab at /mnt/sdb1.)
- ```
ln -s /mnt/sdb1 /storage1 
```

In /storage1/home, change file owners to match new user codes:

cd /storage1/home/ 
chown -R root: *
chown -R (username): (directoryname)
 :

3.7. Printing

Set up printer using the graphical console interface - I'm not sure what files were actually created or modified, but these are the files that appear to have been changed:
- ```
/etc/printcap 
/etc/cups/printers.conf.O
/etc/cups/printers.conf
```

3.8. TSM backup

Instructions at http://www.oucs.ox.ac.uk/hfs/clients/supported/linux/ (note the dependencies listed here).

Install Tivoli backup software, starting in working directory /root/kit:

wget ftp://ftp.hfs.ox.ac.uk/tsm/clients/v5r4/lnx/tsm-client-5.4.0.0-3.i386.rpm 
rpm -i tsm-client-5.4.0.0-3.i386.rpm 
/opt/tivoli/tsm/client/ba/bin/HFSsetup.sh

At this point, I'm getting errors about the HFS registration, so I can't progress further.

Although the installation appears to work, there is a dependency on module libstdc++.so.5, which was not installed by the standard CentOS installation, and whose absence is not detected by the TSM installation. This is rectified by:
- ```
yum install compat-libstdc++-33.i386 
```

Re-running the TSM setup now works:

[root@milos2 ~]# /opt/tivoli/tsm/client/ba/bin/HFSsetup.sh 
Upgrading old TSM config...
No Servername in dsm.sys
Performing a new install
Installing new TSM config...
Please enter your TSM nodename
NODENAME: milos2.zoo
Please enter your TSM password...
(Your input will not echo to the screen.)
PASSWORD: 
Nodename and password validation.
Attempting to find server...
TCP probing dsmb5.ox.ac.uk 1700 ... success.
Contacting TSM server: OX_HFS_B5
Attempting to store password... 
Attempting to connect to TSM server...
TCP probing dsmb1.ox.ac.uk 1500 ... success.
Contacting TSM server: OX_HFS_B1
Attempting to store password... 
Attempting to connect to TSM server...
TCP probing dsmb4.ox.ac.uk 2600 ... success.
Contacting TSM server: OX_HFS_B4
Attempting to store password... 
Attempting to connect to TSM server...
TCP probing dsmb3.ox.ac.uk 1600 ... success.
Contacting TSM server: OX_HFS_B3
Attempting to store password... 
Attempting to connect to TSM server...
TCP probing dsmb2.ox.ac.uk 2500 ... success.
Contacting TSM server: OX_HFS_B2
Attempting to store password... 
Attempting to connect to TSM server...
Server found - password okay.

Server found - TSM configured.
You appear to be using: 65GB of total disk space.
OX_HFS_B2 has a daily backup limit of 100GB
Install TSM client scheduler [yes]: 
Installing the TSM client scheduler daemon: dsmcad.
Starting TSM Scheduler (dsmcad)...done.

Check /var/log/dsm*.log files in a couple of minutes.

An installation log can be found in: /opt/tivoli/tsm/client/ba/bin/tsm-install.log

Initial backups:
- ```
dsmc incr / 
dsmc incr /mnt/
```

3.8.1. Updating TSM software

See: http://www.oucs.ox.ac.uk/hfs/clients/supported/linux/index.xml?ID=upgrade

* Check for installed TSM client:

```
rpm -qa | grep tsm 
```

* Updating TSM software involves something like the following sequence of commands:

rpm -e tsm-client 
wget ftp://ftp.hfs.ox.ac.uk/tsm/clients/v5r4/lnx/tsm-client-5.4.1.2-1.i386.rpm
rpm -i tsm-client-5.4.1.2-1.i386.rpm
/opt/tivoli/tsm/client/ba/bin/HFSsetup.sh

3.9. VMWare server installation

Serial number: 90RH0-YAJ20-25Q44-48LA8

Install and configure VMware from the rpm kit:
- ```
rpm -Uhv VMware-server-1.0.4-56528.i386.rpm  
```
Accept defaults for all options except use of NAT networking, for which specify No. The normal default port for remote console access (902) was unavailable, and an alternative (904) was selected by the install script.
Configure VMWare. Ensure VMWare isn't running before doing this (running service vmware start before this appears to fail, but seems to leave a running servsion of VMWare.
- ```
service vware stop    # precautionary 
/usr/bin/vmware-config.pl
```
Start VMware (first attempt):
- ```
[root@milos2 kit]# service vmware start 
Starting VMware services:
   Virtual machine monitor[FAILED]
   Virtual ethernet[FAILED]
   Bridged networking on /dev/vmnet0[FAILED]
```
The errors seen here, and also the remote console port selection, seem to have been caused by a previous running version of VMWare while performing the configuration. Stopping VMWare and running the configuration script as above seems to work.

Start VMWare (second attempt):

[root@milos2 kit]# service vmware start 
Starting VMware services:
   Virtual machine monitor[  OK  ]
   Virtual ethernet[  OK  ]
   Bridged networking on /dev/vmnet0[  OK  ]

VMWare Management apparently requires libdb.so.3, which is provided by CentOS package compat-db.i386, thus:
- ```
yum install compat-db 
```

Now try installing the management interface, starting in a working directory containing VMware-mui-1.0.4-56528.tar.gz, and no vmware-mui-distrib/ directory:

tar xvfz VMware-mui-1.0.4-56528.tar.gz 
cd vmware-mui-distrib/
./vmware-install.pl

Accept default values for all prompts. Finally, expect to see:

Configuring httpd.conf to run Apache as:  
User: nobody and Group: nobody

Set the number of minutes before a http session times out. (This is the length 
of time before someone connecting to VMware Management Interface will be logged
out) [60] 150

Generating SSL Server Certificate

   Starting httpd.vmware:[  OK  ]
The configuration of VMware Management Interface completed successfully.

Open up ports 902, 8222 and 8333 for incoming TCP connections.
Access the VMWare console by browsing to milos2.zoo.ox.ac.uk and logging in with a system username and password.
Use the supplied link Download VMware Server Console, save the image file and run it to install the VMWare console program.

3.9.1. Transferring a virtual machine

Copy virtual machine files to a working location, e.g.:

[root@milos2 SL44-ImageWeb]# pwd 
/var/lib/vmware/Virtual Machines/SL44-ImageWeb
[root@milos2 SL44-ImageWeb]# ls -al
total 5162248
drwxr-xr-x 2 root root       4096 Oct 17 17:47 .
drwxrwxrwt 3 root root       4096 Oct 17 17:47 ..
-rw-r--r-- 1 root root       8664 Oct 17 15:30 Red Hat Enterprise Linux 4.nvram
-rw-r--r-- 1 root root          0 Nov 21  2006 Red Hat Enterprise Linux 4.vmsd
-rw-r--r-- 1 root root       2004 Oct 17 17:11 Red Hat Enterprise Linux 4.vmx
-rw-r--r-- 1 root root          0 Sep 17 14:54 Red Hat Enterprise Linux 4.vmx.lck
-rwxr--r-- 1 root root 5280890880 Oct 17 15:30 SL-44-root-000004-cl1.vmdk
-rw-r--r-- 1 root root      18220 Oct 17 17:11 vmware.log

Ensure the .vmx file is executable (this is needed to view the console screen through VMWare server console:
- ```
chmod u+x "Red Hat Enterprise Linux 4.vmx" 
```
Run the VMWare server console program installed previously (maybe on another machine).
Select open existing virtual machine and broewse to the directory containing the copied virtual machine files. Select the .vmx file.
Start the VM. A number of tweaks may be required.
Update VMWare tools...

3.10. Extending root file system

Display and extend LVM for root file system:

lvdisplay 
  --- Logical volume ---
  LV Name                /dev/VolGroup00/LogVol00
  VG Name                VolGroup00
  LV UUID                6ZkGLD-UFN7-7OAP-LZcy-2k8m-H9CU-1acGuI
  LV Write Access        read/write
  LV Status              available
  # open                 1
  LV Size                16.00 GB
  Current LE             512
  Segments               2
  Allocation             inherit
  Read ahead sectors     0
  Block device           253:0
   
  --- Logical volume ---
  LV Name                /dev/VolGroup00/LogVol01
  VG Name                VolGroup00
  LV UUID                3R1XZv-szem-JqdK-3qze-oVL3-Wu62-a9aByy
  LV Write Access        read/write
  LV Status              available
  # open                 1
  LV Size                4.00 GB
  Current LE             128
  Segments               1
  Allocation             inherit
  Read ahead sectors     0
  Block device           253:1

lvextend -L16G /dev/VolGroup00/LogVol00

This extends the underlying logical volume to 16Gb. In this configuration, /dev/VolGroup00/LogVol01 is the swap partition.

Extend the file system. This bit is trickier - apparently, attempting to extend a mounted volume is hazardous. ext2online is claimed to be OK, but is not part of the standard CentOS distribution.

For CentOS 5, there is resize2fs:

[root@milos2 ~]# resize2fs /dev/VolGroup00/LogVol00 
resize2fs 1.39 (29-May-2006)
Filesystem at /dev/VolGroup00/LogVol00 is mounted on /; on-line resizing required
Performing an on-line resize of /dev/VolGroup00/LogVol00 to 4194304 (4k) blocks.
The filesystem on /dev/VolGroup00/LogVol00 is now 4194304 blocks long.

[root@milos2 ~]# df -B G
Filesystem           1G-blocks      Used Available Use% Mounted on
/dev/mapper/VolGroup00-LogVol00
                           16G        4G       12G  23% /
/dev/sdb1                  68G       54G       11G  85% /mnt/sdb1
/dev/sdc1                  34G        8G       27G  23% /mnt/sdc1
/dev/sda1                   1G        1G        1G  17% /boot
tmpfs                       1G        0G        1G   0% /dev/shm

3.11. Subversion

Set up subversion repository. The installation for Centos provides subversion client and server software, so the requirement is to set up a repository with all the required features. The example used here is for a repository called FlyData. All repository files are owned by user svn.
- ```
useradd -r -s /bin/nologin svn 
mkdir /var/svn   # base for all repositories
svnadmin create /var/svn/FlyData
chown -R svn: /var/svn
```
Alternatively, use sudo to create a repository with the desired user:
- ```
sudo -H -u svn svnadmin create /var/svn/newrepo 
```

Enable SVN server: create file /etc/xinetd.d/svn:

# Begin /etc/xinetd.d/svn 

service svn
{
        port                    = 3690
        socket_type             = stream
        protocol                = tcp
        wait                    = no
        user                    = svn
        server                  = /usr/bin/svnserve
        server_args             = -i -r /var/svn             
}

# End /etc/xinetd.d/svn

Restart xinetd:
- ```
service xinetd restart 
```

Test checkout to a local directory:

cd /tmp 
svn checkout svn://milos1.zoo.ox.ac.uk/FlyData
# rm -rf FlyData/ to remove files

To access a repository via SVN, add the SVN users to group svn, and use a URI like svn+ssh://graham@milos1.zoo.ox.ac.uk/var/svn/FlyData (note, the full pathname to the repository is given, and the username is part of the URI authority field. Also, ensure the repository is group-writeable
- ```
groupadd svn 
```
(It may be necessary to do some umask setting in a wrapper script to ensure new uploads are also group-writeable - so far, this has not been needed.)
To access a repository using Tortoise SVN ( http://tortoisesvn.tigris.org/) under windows, first create an empty directory to receive the repository content, then perform an SVN checkout in that directory. For example, using Tortoise SVN, specify:
- URL of repository
  
  svn+ssh://graham@milos1.zoo.ox.ac.uk//var/svn/newrepo
  
  Checkout directory
  
  D:\Svn\Milos\newrepo
and enter the repository password when requested. (Unless an SSH password caching utility is being used, the password may be required twice.) Ways to avoid having to type a password each time include: use a keypair without pass phrase protection; use a keypair ion conjunction with SSH agent; create an SSH tunnel then use a simple svn: URI through that tunnel. See also: http://www.tortoisecvs.org/faq.html#sshkeys.
Set up access via HTTP:
- ```
yum install mod_dav_svn 
```

Edit /etc/httpd/conf.d/subversion.conf, e.g.:

# Subversion configuration 
# See also: http://svnbook.red-bean.com/en/1.0/ch06s04.html
LoadModule dav_svn_module     modules/mod_dav_svn.so
LoadModule authz_svn_module   modules/mod_authz_svn.so

<Location /svn>
  DAV svn
  SVNParentPath /var/svn
  SVNAutoversioning on
  ModMimeUsePathInfo on
  # Limit write permission to list of valid users.
  <LimitExcept GET PROPFIND OPTIONS REPORT>
     # Require SSL connection for password protection.
     SSLRequireSSL
     AuthType Basic
     AuthName "IBRG Subversion"
     AuthUserFile conf.d/svn-users
     Require valid-user
  </LimitExcept>
</Location>

The file /etc/httpd/conf.d/svn-users is created and updated using htpasswd, e.g.:
- ```
cd /etc/httpd/conf.d/ 
htpasswd -c svn-users user1    # create new file and add user1; give password when prompted
htpasswd svn-users user2       # add user2; give password when prompted
```
etc. This controls access to update the SVN repository via HTTP and WebDAV. SSH access is handled separately, as described above.

3.12. Install ClearSilver

ClearSilver is an HTML templating system used by TRAC. Details here are from http://www.madboa.com/geek/trac-centos/.

Update YUM configuration, creating a new file /etc/yum.repos/clearsilver.repo:

[dag] 
name=Dag RPM Repository for Red Hat Enterprise Linux
baseurl=http://apt.sw.be/redhat/el$releasever/en/$basearch/dag
gpgcheck=1
gpgkey=http://dag.wieers.com/rpm/packages/RPM-GPG-KEY.dag.txt
enabled=0
includepkgs=clearsilver python-clearsilver trac

[kbs-CentOS-Extras]
name=CentOS.Karan.Org-EL$releasever - Stable
gpgcheck=1
gpgkey=http://centos.karan.org/RPM-GPG-KEY-karan.org.txt
enabled=0
baseurl=http://centos.karan.org/el$releasever/extras/stable/$basearch/RPMS/
includepkgs=python-docutils python-imaging

Install clearsilver and Python bindings:

yum --enablerepo=dag install clearsilver python-clearsilver

3.13. Install Trac

Assumes that FastCGI has been installed (see above). See also: http://www.madboa.com/geek/trac-centos/, http://trac.edgewall.org/wiki/TracFastCgi.

Download and unpack the tar file:
- ```
tar xvfz trac-0.10.4.tar.gz  
```

From the tar file root:

cd trac-0.10.4 
python ./setup.py install

Create a subversion repository for a Trac project:
- ```
svnadmin create /var/svn/ImageWeb 
```

Create a TRAC project:

[root@milos2 trac-0.10.4]# mkdir /var/trac 
[root@milos2 trac-0.10.4]# trac-admin /var/trac/ImageWeb initenv
Creating a new Trac environment at /var/trac/ImageWeb

Trac will first ask a few questions about your environment 
in order to initalize and prepare the project database.

 Please enter the name of your project.
 This name will be used in page titles and descriptions.

Project Name [My Project]> ImageWeb

 Please specify the connection string for the database to use.
 By default, a local SQLite database is created in the environment 
 directory. It is also possible to use an already existing 
 PostgreSQL database (check the Trac documentation for the exact 
 connection string syntax).

Database connection string [sqlite:db/trac.db]> 

 Please specify the type of version control system,
 By default, it will be svn.

 If you don't want to use Trac with version control integration, 
 choose the default here and don't specify a repository directory. 
 in the next question.

Repository type [svn]> 

 Please specify the absolute path to the version control 
 repository, or leave it blank to use Trac without a repository.
 You can also set the repository location later.

Path to repository [/path/to/repos]> /var/svn/ImageWeb

 Please enter location of Trac page templates.
 Default is the location of the site-wide templates installed with Trac.

Templates directory [/usr/share/trac/templates]> 

Creating and Initializing Project
 Installing default wiki pages
 /usr/share/trac/wiki-default/TracSupport => TracSupport
 /usr/share/trac/wiki-default/WikiHtml => WikiHtml
 /usr/share/trac/wiki-default/TracReports => TracReports
 /usr/share/trac/wiki-default/TracChangeset => TracChangeset
 /usr/share/trac/wiki-default/TracInterfaceCustomization => TracInterfaceCustomization
 /usr/share/trac/wiki-default/WikiProcessors => WikiProcessors
 /usr/share/trac/wiki-default/WikiNewPage => WikiNewPage
 /usr/share/trac/wiki-default/TracLinks => TracLinks
 /usr/share/trac/wiki-default/TracTimeline => TracTimeline
 /usr/share/trac/wiki-default/TracBrowser => TracBrowser
 /usr/share/trac/wiki-default/TracRss => TracRss
 /usr/share/trac/wiki-default/TracPlugins => TracPlugins
 /usr/share/trac/wiki-default/CamelCase => CamelCase
 /usr/share/trac/wiki-default/TracRoadmap => TracRoadmap
 /usr/share/trac/wiki-default/TracStandalone => TracStandalone
 /usr/share/trac/wiki-default/TracFastCgi => TracFastCgi
 /usr/share/trac/wiki-default/TracAccessibility => TracAccessibility
 /usr/share/trac/wiki-default/TracModPython => TracModPython
 /usr/share/trac/wiki-default/TracBackup => TracBackup
 /usr/share/trac/wiki-default/TracWiki => TracWiki
 /usr/share/trac/wiki-default/RecentChanges => RecentChanges
 /usr/share/trac/wiki-default/WikiRestructuredText => WikiRestructuredText
 /usr/share/trac/wiki-default/TracInstall => TracInstall
 /usr/share/trac/wiki-default/TracSearch => TracSearch
 /usr/share/trac/wiki-default/WikiMacros => WikiMacros
 /usr/share/trac/wiki-default/TracTicketsCustomFields => TracTicketsCustomFields
 /usr/share/trac/wiki-default/TracUnicode => TracUnicode
 /usr/share/trac/wiki-default/InterMapTxt => InterMapTxt
 /usr/share/trac/wiki-default/TracCgi => TracCgi
 /usr/share/trac/wiki-default/TracGuide => TracGuide
 /usr/share/trac/wiki-default/TracSyntaxColoring => TracSyntaxColoring
 /usr/share/trac/wiki-default/TitleIndex => TitleIndex
 /usr/share/trac/wiki-default/TracNotification => TracNotification
 /usr/share/trac/wiki-default/TracUpgrade => TracUpgrade
 /usr/share/trac/wiki-default/WikiPageNames => WikiPageNames
 /usr/share/trac/wiki-default/TracAdmin => TracAdmin
 /usr/share/trac/wiki-default/WikiFormatting => WikiFormatting
 /usr/share/trac/wiki-default/TracRevisionLog => TracRevisionLog
 /usr/share/trac/wiki-default/WikiRestructuredTextLinks => WikiRestructuredTextLinks
 /usr/share/trac/wiki-default/TracImport => TracImport
 /usr/share/trac/wiki-default/TracPermissions => TracPermissions
 /usr/share/trac/wiki-default/WikiDeletePage => WikiDeletePage
 /usr/share/trac/wiki-default/TracIni => TracIni
 /usr/share/trac/wiki-default/SandBox => SandBox
 /usr/share/trac/wiki-default/TracQuery => TracQuery
 /usr/share/trac/wiki-default/TracTickets => TracTickets
 /usr/share/trac/wiki-default/WikiStart => WikiStart
 /usr/share/trac/wiki-default/InterWiki => InterWiki
 /usr/share/trac/wiki-default/InterTrac => InterTrac
 /usr/share/trac/wiki-default/TracEnvironment => TracEnvironment
 /usr/share/trac/wiki-default/TracLogging => TracLogging
 Indexing repository

---------------------------------------------------------------------
Project environment for 'ImageWeb' created.

You may now configure the environment by editing the file:

  /var/trac/ImageWeb/conf/trac.ini

If you'd like to take this new project environment for a test drive,
try running the Trac standalone web server `tracd`:

  tracd --port 8000 /var/trac/ImageWeb

Then point your browser to http://localhost:8000/ImageWeb.
There you can also browse the documentation for your installed
version of Trac, including information on further setup (such as
deploying Trac to a real web server).

The latest documentation can also always be found on the project
website:

  http://trac.edgewall.org/

Congratulations!

Create configuration file for trac in /etc/http/conf.s/trac.conf:

# Configure access to TRAC via FastCGI 

# Use native Apache serving for static docs
Alias /trac/chrome/common /usr/share/trac/htdocs

<Directory "/usr/share/trac/htdocs">
  Options Indexes MultiViews
  AllowOverride None
  Order allow,deny
  Allow from all
</Directory>

# Use Trac script for the rest 
ScriptAlias /trac /usr/share/trac/cgi-bin/trac.fcgi

#<Location "/trac">
#  SetEnv TRAC_ENV "/path/to/projectenv"
#</Location>

<Location "/trac">
  SetEnv TRAC_ENV_PARENT_DIR "/var/trac"
</Location>

FastCgiConfig -initial-env TRAC_ENV_PARENT_DIR=/var/trac

<LocationMatch /trac/[^/]+/login>
  # Redirect http: to https: for login
  RewriteEngine On
  RewriteCond %{HTTPS} !on
  ReWriteRule ^/(.*) https://%{SERVER_NAME}%{REQUEST_URI} [R]
  # Now force login login
  # SSLRequireSSL
  AuthType Basic
  AuthName "Trac"
  AuthUserFile conf.d/svn-users
  Require valid-user
</LocationMatch>

Create new group for TRAC:
- ```
groupadd -r trac 
```
Add user apache in the group trac, and make all files under /var/trac group-writeable:
- ```
cd /var/trac 
chgrp -R trac *
chgrp -R trac .
chmod -R g+w *
```
Now try Browsing to http://milos1.zoo.ox.ac.uk/trac.

3.13.1. TRAC administration

The web administration interface has not been installed (yet). Thus, administration is performed using the trac-admin utility.

By default, all users have basic access to the system, but cannot do project administration activities like creating or editing milestones. In order to allow a user full access to the TRAC facilities, issue a command in the following form:
- ```
trac-admin /var/trac/ImageWeb/ permission add username MILESTONE_ADMIN MILESTONE_CREATE MILESTONE_DELETE MILESTONE_MODIFY  REPORT_ADMIN REPORT_CREATE REPORT_DELETE REPORT_MODIFY ROADMAP_ADMIN TICKET_ADMIN TICKET_CHGPROP  TRAC_ADMIN WIKI_ADMIN WIKI_DELETE 
```
Logged in users for whom such permissions have been set will see additional controls on displayed web pages, providing access to the additional features.

To view current permission settings, use:

trac-admin /var/trac/ImageWeb/ permission list

3.14. Changes applied by John Pybus for OUCC

Created /etc/httpd/conf.d/oucc.host with all the configuration for OUCC
Added a symlink: /home/oucc -> /mnt/sdb1/home/oucc
Made changes to /etc/httpd/conf/httpd.conf to i) enable virtual hosts on the machine, and ii) change the log format to include the virtual host as well as requested path (matching the log format used in the old milos setup)

Changes is config files are all commented with JPNP.

4. Links and more information

http://www.rayheffer.com/linux%20web%20server.shtml

-- GrahamKlyne 2007-10-10 17:09:45

URL of repository	`svn+ssh://graham@milos1.zoo.ox.ac.uk//var/svn/newrepo`
Checkout directory	`D:\Svn\Milos\newrepo`