Desktop Linux at compbio

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Michal Guerquin (mikeg@compbio.washington.edu)

October 21, 2007

Guidelines for installing Linux on your desktop at Compbio.

Contents

Introduction

This document serves as a guideline for configuring your desktop workstation in the compbio.washington.edu domain. It is available at http://compbio.washington.edu/local/doc/linux/linux.html. Please do not redistribute outside of the lab.

As usual, the steps involved in performing a full install include backing up your data (if you are installing on an existing system), obtaining the media, installing the system, and configuring it. This is roughly how this document follows.

Backup

(If you are installing on a brand new system, you can skip this step.)

By running an operating system installer, you risk the possibility of making an incorrect selection and losing your data. So, before installing, make a backup of all files important to you. Speak with Michal if you need help with this.

NOTE: One directory that should be very important to you is /etc. It contains global system configuration options. Make a copy of this onto another system:

  [root @ yourmachine /]# tar -zcf /tmp/etc.tar.gz /etc

Copy the file /tmp/etc.tar.gz from your machine to another system for safe keeping until your system is fully configured.

Prepare

You'll need to know some things about your system so when the installer asks you questions, you will have answers.

Obtain the media

Michal can provide you with Redhat Enterprise Linux CD's for your architecture: x86_64 if you are installing on a system with AMD's 64-bit processors, and i386 otherwise.

Disk

Know your disk layout. It should look something like this:

  • hda1 - Swap partition (2x RAM in size)
  • hda2 - / (root) partition (4 or 8GB)
  • hda3 - /spare partition (the rest of the disk)
  • hdb1 - /maxa partition (entire disk)
  • hdd1 - /maxb partition (entire disk)

Network

There are three things to remember about configuring network connectivity.

IP Address

IP addresses are assigned statically. Find out what your IP address (and netmask) is with:

  /sbin/ifconfig eth0 | grep inet

The IP address should be 10.20.10.x and the netmask should be like 255.255.0.0.

Routing

To get to various parts of our network and to the Internet at large, you must know the gateway or router network address. This should be 10.20.1.1. You can verify this by inspecting the Gateway column in the output of:

  netstat -nr

DNS Resolution

We have two local DNS servers. They are: 10.21.10.1 and 10.20.9.1. You should see these in the file /etc/resolv.conf.

Install

This is probably the easiest step. Boot from the install CD, and essentially keep clicking the next button until the installation is over. Here are some points of advice for in between your clicks.

Upgrade or Start fresh?

As you install, you will be asked if you wish to upgrade or start anew. Unless you feel very strongly about upgrading, a clean (fresh) install is the best option to choose. This will entail reformating your hda2 partition.

If you are upgrading a system that used ext2fs on all drives, you need to format your data partitions to ext3fs. This significantly decreasses the fsck delay at bootup time after a system crash.

NOTE: Converting an ext2fs partition to ext3fs is usually safe and painless. That is, your data shouldn't be deleted by doing so. But, this wouldn't be a problem because you backed up all your files anyways. 4.2 Firewall and SELinux

There will be a question asking you to set up a firewall on the machine; choose not to run a firewall.

There will be an option regarding "SELinux"; make sure SELinux is disabled.

Register the system

You might be prompted to "register" the system with the Redhat Network by creating a new account or by entering your existing username and password. Do not perform this step. One of the options should be "Tell me more about why I need to do this", or words to that effect. Choose that option, and at the next screen, you should be allowed to skip RHN registration. You will register the system with the Redhat Network using another mechanism which is outlined later in the document.

Initial package installation

You will select which packages to initially install on your system. This is where you can be creative. However, ensure that you install the following packages:

  • Legacy Network Server: rsh
  • System Tools am-utils

You may be prompted to install or configure your network time. When this happens, you can use the default network time (NTP) servers, or simply use time.u.washington.edu.

Configure

Do not create local users, even if the installer is very persistant. Instead, choose to use Network Login with the NIS domain compbio.washington.edu and the master server as broadcast.

At the first graphical login screen, log in as user root. Once you are fully logged in, you will have to make some minor adjustments to your configuration files.

Administrative Remote Login

Ensure that your /root/.rhosts file contains the following lines:

  zen.compbio.washington.edu root
  karma.compbio.washington.edu root
  fp1.compbio.washington.edu root
  fp2.compbio.washington.edu root
  fp3.compbio.washington.edu root
  ...
  fp158.compbio.washington.edu root
  fp159.compbio.washington.edu root
  fp160.compbio.washington.edu root
   

(Interpolate the ellipsis so every farm machine numbered 1-160 is accounted for.)

Also ensure that your /etc/securetty file contains the following lines in addition to any already in the file:

  rsh
  rlogin
  pts/0
  pts/1
  pts/2
  pts/3
  pts/4
  pts/5
  pts/6
  pts/7
  pts/8
  pts/9
  pts/10
  pts/11
   

Local file systems

This will most likely be correct by default, but ensure that your /etc/fstab file maps the proper drives to the proper logical locations: /dev/hda2 to /, /dev/hda3 to /spare, /dev/hdb1 to /maxa and /dev/hdd1 to /maxb. Therefore, make sure you have the directories /maxa and /maxb in your root directory.

(If this is a brand new installation, you will have to make your own "home" directory in /maxa, /maxb, and /spare as user root. If you're not sure what this means, ask Michal.)

NFS server

Ensure that your /etc/exports file contains only the following lines:

  /      *.compbio.washington.edu(rw,no_root_squash)
  /spare *.compbio.washington.edu(rw,no_root_squash)
  /maxa  *.compbio.washington.edu(rw,no_root_squash)
  /maxb  *.compbio.washington.edu(rw,no_root_squash)
   

Automounter

Ensure that the /etc/amd.conf file contains the following entries, among everything else that is default:

  [ global ]
  auto_dir =              /tmp_mnt
  [ /hosts ]
  map_name =              amd.hosts
   

The [global] section will include many more options; the defaults are OK, except for auto_dir.

There will be a [ /net ] section at the end. Change its name to [ /hosts ] as above and make sure that the map_name field is set correctly as above.

To have a place to automount systems, create the /hosts and /tmp_mnt directories as root.

Rename the /etc/amd.net file to /etc/amd.hosts and ensure that it contains only the following two lines:

  /defaults fs:=${autodir}/${rhost}${rfs};rhost:=${key};type:=host;rfs:=/
  *         opts:=rw,rsize=8192,wsize=8192,hard,intr,nosuid,nodev,timeo=8,retrans=200
   

DNS resolution

Ensure that your /etc/resolv.conf file contains only the following lines:

  search compbio.washington.edu
  nameserver 10.21.10.1
  nameserver 10.20.9.1
   

Others

You should enable various services to be started upon system startup.

In your Gnome interface as user Root, from the main menu choose "System Settings", "Server Settings", "Services". In the window that appears, ensure that the following services have checkboxes beside them:

  • amd
  • nfs
  • nfslock
  • portmap
  • finger
  • rexec
  • rlogin
  • rsh
  • rsync
  • sshd
  • xinetd
  • finger-server

Note: May need to install this seperately after the system is running. Click "Save" and quit. Log out and restart the computer.

Alternatively to restarting your machine you can restart each of the services you put a checkbox beside. Some cannot be restarted because they are dependent on xinetd, so restart this instead.

Printing

There are three printers in the lab to which you can print:

  Name: color-206
  Type: Jetdirect Printer
  IP: printer1.compbio.washington.edu
  Port: 9100
  Driver: HP Color LaserJet 4600 using Postscript driver
  Name: color-b70a
  Type: Jetdirect Printer
  IP: printer2.compbio.washington.edu
  Port: 9100
  Driver: Postscript
  Name: bw-b70c
  Type: Jetdirect Printer
  IP: printer3.compbio.washington.edu
  Port: 9100
  Driver: Postscript
  Name: bw-2fl-commons
  Type: Jetdirect Printer
  IP: 128.208.120.206
  Port: 9100
  Driver: Postscript
  Name: bw-3fl-commons
  Type: Jetdirect Printer
  IP: 128.208.120.59
  Port: 9100
  Driver: Raw Print Queue

The program printconf can be used to configure printer support.

Choose the one closest to your computer as the default, and print to a black-and-white printer when color is not critical.

Register

Registering your machine is a simple process that entitles you use the Redhat Network. This is a Redhat-maintained repository of .rpm packages and system update information. Using it you can keep your system up to date and install new packages. The UW's Computing & Communications department cut a deal with Redhat which gives UW a local copy (a "caching proxy" or "satellite server" if you will) of the Redhat network files so it's (very) fast and easy for us to get to them. To access this proxy, you have to make some configuration changes to your system. Execute these commands:

  wget http://compbio.washington.edu/local/doc/linux/files/UW-CA-CERT -O /usr/share/rhn/UW-CA-CERT
  wget http://compbio.washington.edu/local/doc/linux/files/up2date -O /etc/sysconfig/rhn/up2date
  rhnreg_ks --activationkey=811419de5dbf14b0c415cfbea6f88cfb

This will configure your system to use the C&C Red Hat Network server. You can use the program up2date to keep your system up to date, as well as install packages (with up2date packagename). See the man page of up2date(8) for more options.

Finished

You are finished. Try to log in as yourself to see if everything is working.

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