Installation of
Scientific Linux 3
UNIX at SLAC
Linux at SLAC
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Installation of
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SLAC Computing UNIX at SLAC Linux at SLAC |
| Updated: 19 Jun 2008 |
Note: These are not complete Scientific Linux installation instructions; go to the Scientific Linux page for more complete information.
This procedure does a "clean install", not an upgrade. If you follow SCCS recommendations against storing permanent data on a workstation's system disk, this should not be a problem. If you do have some data you want to preserve on this disk, but it is all stored in a non-system partition, e.g., /u1, you might be OK, providing your system partitions are large enough to accommodate Scientific Linux 3 with sufficient room for future updates (see Disk Partitions, below). Otherwise, it is your responsibility to backup your data before beginning the installation. If you must restore it to a local filesystem after the installation, we strongly urge you to buy a second disk and keep permanent data off the system disk.
It may be helpful to work next to a machine with a web browser displaying the information on this web page.
To make a bootable CDROM for installing SL3, you will need to burn an ISO 9660 image file onto CD-R (or CD-RW) media. On Linux, you can use an application like Xcdroast (requires X Windows) or cdrecord (a command-line tool). Mac OSX can successfully create bootable CDROMs using the CDROM burning utility.
To create an installation boot CDROM under Linux, using the cdrecord utility:
Find the ISO 9660 disc image for an installation boot CDROM for the current SL3 Update level:
cd /afs/slac/package/SciLinux/SL3/cur/i386/images/SL
ls boot.iso
cdrecord -scanbus dev=/dev/hdc
You'll get a line that includes some text identifying your
specific CDROM device, along with the device address; for example:
1,0,0 100) '_NEC ' 'CD-RW NR-9300A ' '105B' Removable CD-ROM
The first field in this example, "1,0,0", is your CDROM device
address. This is the information you'll need.
cdrecord -v -speed=2 dev=1,0,0 -eject -data boot.iso
On some systems you may need to prefix the device address with a
transport layer indicator, such as 'ATA:' or
'ATAPI:', or you may need additional options on the cdrecord
command line. See the man page for cdrecord for details.
If you haven't burned any CDROMs before, it's a good idea to run some tests first by adding the '-dummy' option to the cdrecord command line.
You might also want to consider burning a "rescue disc" for use in case of problems with the system on your hard disk. The procedure is similar to the above and you can find the appropriate image in the directory, /afs/slac/package/SciLinux/SL3/cur/iso/i386 Look for a file ending in "...-i386-disc1.iso" and including the current SL3 update level, e.g., for update level 305, the appropriate image is "SL.305.072605.i386.disc1.iso". Incidentally, it should also be possible to install from a rescue disk, but you'll need to add the 'askmethod' argument to the command line when the installation program starts up.
Stick the CDROM in the drive and reboot your machine.
If your machine ignores the CDROM at boot time, and simply reboots the existing system on the hard disk, there is most likely a problem with the boot order in the BIOS. You can usually get into the BIOS by pressing a function key (usually F2) early in the boot process. The various BIOS screens vary quite a bit, even within a single vendor's products. However, there is usually a place where you can specify the order in which the BIOS should look for a bootable device. You should make sure it looks at the CDROM drive before the hard disk.
When the Scientific Linux page is displayed, you can choose between
installing in graphical or text mode. Unless you have
an older monitor or video card, it should be OK to just press the
Enter key and run the installation in graphical mode. To run in text
mode, type linux text and press the Enter key.
It will take a minute or two to load. Once you are in the install program, follow the directions until you get to the question about Installation Method.
N.B. There may be some variations in the order of the screens in the installation program depending on your exact hardware configuration and/or the choices you make, so it's probably a good idea to read through the rest of this section before proceeding.
Also N.B. When installing in graphical mode, we saw at least one instance of a mis-sized screen panel that covered the Next and Back buttons at the bottom of the screen. If this should happen, you should still be able to use the Alt-N or Alt-B key combinations to navigate.
Next, you will be asked to configure TCP/IP. Uncheck Use dynamic IP configuration (BOOTP/DHCP) and enter the IP Address, Netmask, Default gateway and Primary nameserver information given to you by SCCS when you requested your node name and IP address.
WARNING:Please be careful to enter this information accurately, since errors can disrupt the network.
Note that the Scientific Linux install program will try to guess your Default gateway and Primary nameserver after you enter your IP address and Netmask, and will set these up as defaults. These Scientific Linux supplied values are most likely wrong. If you don't know one or more of these values, please ask the Help Desk or unix-admin -- do not use the Scientific Linux supplied values.
Next you will be asked for NFS setup information.
The NFS server name is
afsnfs2
and the SL directory is
/afs/slac/package/SciLinux/SL3/cur/i386.
If the directory can't be mounted, try using afsnfs2's IP
address, 134.79.19.29, instead of its name.
Continue with the prompts.
Choose Custom for the Installation Type.
At the Disk Partitioning Setup screen, select Manually partition with Disk Druid. The default partitioning scheme used by the Automatically partition option is not suitable for use in the SLAC environment.
The table below shows suggested partitioning schemes for two different size disks, representing typical sizes of disks available on older hardware still in service here at SLAC. Newer systems usually have substantially larger system disks.
Make sure to give Linux at least a 4.5GB root partition. If your root partition is less than about 6.0 GB, you should omit installing some of the software package groups recommended below, in order to allow room for future upgrades and security patches. Similarly, if you install more package groups than suggested below, you will probably need a larger root partition -- perhaps 7-8 GB if you install nearly everything. Small root partitions can make it difficult or impossible to install required security patches later on. Systems that cannot apply required security patches in a timely fashion may be denied access to the SLAC network.
You should also create a swap partition at least as large as the memory (twice the main memory is a good rule of thumb for the size of the swap partition).
If there is sufficient space, we recommend that you allocate
an /scswork partition of 1 GB,
to be reserved for the exclusive use of SCCS.
Use the rest for scratch space;
for example, you might want to create a larger /tmp
or add a separate /scratch directory.
Note that older files in /tmp are periodically removed
but files in /scratch will remain until removed by
you unless the system is re-installed.
Always choose to format your Linux partitions. Use the new, ext3 filesystem type on all partitions except for the /usr/vice/cache and swap partitions. Use ext2 for the /usr/vice/cache partition since ext3 and AFS cache partitions do not get along (at least as of May 2002). ext3 is a journaling filesystem and will permit much faster recovery following crashes.
WARNING! You should not allocate any partitions on the system disk for permanent data. Because of the large sizes of currently available disks, you may be strongly tempted to ignore this warning. However, it is very risky to do so, because:
The best way to make use of extra space on your system disk is to allocate a large /tmp or /scratch partition. If you need additional permanent space, please contact unix-admin@slac.stanford.edu; we will do our best to help you acquire reliable, backed-up storage at a reasonable cost. If you ignore this warning, it will be your responsibility to save and restore your data the next time your system needs to be re-installed.
Note that partition names and numbers, and the order of the partitions, are assigned automatically by Disk Druid. Also, the actual sizes of allocated partitions may vary a little bit from what you request via Disk Druid's GUI interface. This may make it difficult to allocate every last block on the disk.
| Partition Mount Point |
Partition Type |
Partition Size | |
|---|---|---|---|
| 7 GB disk | 17 GB or larger disk | ||
| / | ext3 | 5 GB | 8 GB |
| swap | swap | 1 x memory or at least 512 MB |
2 x memory or at least 1 GB |
| /var | ext3 | 512 MB | 1 GB |
| /usr/vice/cache | ext2 | 512 MB | 1 GB |
| /tmp | ext3 | 512 MB | 1 GB |
| /scswork | ext3 | omit | 1 GB |
| /scratch (or extra /tmp space) | ext3 | omit | remainder |
We recommend that you use the default boot loader, GRUB, and accept the defaults for the other options on this screen.
The Network Devices area of this screen should show the same information you entered above in the TCP/IP Setup when requesting an NFS installation. For Set the hostname:, select manually and enter your hostname.
If you will be using your system within the SLAC environment, you will need to select No firewall on the Firewall Configuration screen. However, if you are installing a stand-alone system, e.g., for use from your home, or a laptop that will be connected to the Internet from outside SLAC's firewall, you may want to learn more about the firewall facilities in Scientific Linux in order to better protect your system. Please refer to the firewall documentation at IPTables for more information.
You can select the default, English (USA). If you wish, select one or more additional languages.
Select the time zone, either by location or UTC offset (e.g., by clicking on a nearby city, such as Los Angeles, on the map or by selecting UTC-08 plus daylight savings time on the UTC Offset tab). You should not check the "System clock uses UTC" box on dual-booted machines (note that SCCS strongly discourages dual boot machines).
Choose a
good root password and DON'T FORGET IT!
SLAC's post-installation tool taylor will override this password.
You may select package groups or individual packages to be installed. The default package groups are probably a pretty good starting point for most users:
| Scientific Linux Default |
SCCS Recommendation |
Package Groups |
|---|---|---|
| Desktops | ||
[*] |
[*] |
X Window System |
[*] |
[*] |
GNOME Desktop Environment |
[ ] |
[*] |
KDE Desktop Environment |
| Scientific Linux Additional Choices | ||
[ ] |
[?] |
Packages added to Scientific Linux |
[ ] |
[?] |
Developer Suite |
| Applications | ||
[*] |
[*] |
Editors |
[ ] |
[*] |
Engineering and Scientific |
[*] |
[*] |
Graphical Internet |
[*] |
[*] |
Text-based Internet |
[*] |
[*] |
Office/Productivity |
[*] |
[*] |
Sound and Video |
[ ] |
[*] |
Authoring and Publishing |
[*] |
[*] |
Graphics |
| Servers (Please see SCCS before installing) | ||
[ ] |
[ ] |
Server Configuration Tools |
[ ] |
[ ] |
Web Server |
[ ] |
[ ] |
Mail Server |
[ ] |
[ ] |
Windows File Server |
[ ] |
[ ] |
DNS Name Server |
[ ] |
[ ] |
SQL Database |
[ ] |
[ ] |
MySQL Database |
[ ] |
[ ] |
News Server |
[ ] |
[ ] |
Network Servers |
[ ] |
[ ] |
Legacy Network Server |
| Development | ||
[*] |
[*] |
Development Tools |
[ ] |
[ ] |
Kernel Development |
[ ] |
[?] |
X Software Development |
[ ] |
[ ] |
Gnome Software Development |
[ ] |
[?] |
KDE Software Development |
[ ] |
[ ] |
Legacy Software Development |
| System | ||
[*] |
[*] |
Administration Tools |
[ ] |
[ ] |
System Tools |
[*] |
[*] |
Printing Support |
| Miscellaneous | ||
[ ] |
[ ] |
Everything |
[ ] |
[ ] |
Minimal |
2210 |
2421 |
Space Consumed (MB) |
In addition to the Scientific Linux defaults, we recommend adding the following groups:
The section titled Scientific Linux Additional Choices contains two groups of packages that do not correspond to packages in Red Hat Enterprise Linux. None of these packages is selected by default, but a few of them might be of interest to some SLAC users. Examples include back-level compatibility versions of the ncurses and readline packages, the icewm window manager, gv and sndconfig for systems with older sound cards. To see what's in each group, check the box to select the group and then click on the Details link that appears.
Please do not install servers unless you really know what you are doing and okay it with SCCS first. And please don't select "Everything" which would also install the servers.
To find out exactly what's included in a group, click on Details (you'll have to select the group first if it is not already selected). Some groups have optional parts; in the Details screen you can select or unselect these options.
Note that selecting "Minimal" will override your previous selections, but unselecting it will restore them.Note that the last row in the above table simply shows the sum of the package sizes, and is really only intended to give you a rough idea of relative sizes for different collections of packages. You must allocate a root partition significantly larger than these minimums to get a workable system and to reserve space to install package updates (especially security updates).
Don't worry too much about getting every package you might ever want -- you can always add additional packages later.
It may take 15 minutes to over an hour to install the packages depending on the speed of your machine and network.Configuration tools have become much better at probing the hardware and correctly deducing the video modes that can be supported. It is fairly safe to proceed with whatever has been selection by the installer. Nevertheless, it is a good idea to gather in advance the following information about your video hardware:
The installation program will probe your monitor to determine its capabilities and you can choose what it selects. If it cannot deduce the particular vendor and model in order to look it up in its database, it will be identified as "Unprobed monitor". It may still be in the database, however, so try to look it up by hand. If you cannot find your particular model in the list, but you know the horizontal and vertical sync ranges from the documentation, enter them in the boxes at the bottom of the screen. Be careful when entering these values; if you enter values that fall outside the capabilities of your equipment, you can cause damage to your display. If you are unsure, it is probably safe to click "Restore original values" and use the program's conservative guesses, or you can click "Back" to return to the video card configuration screen and check the "Skip X configuration" box for now.
On this screen, you can select your desired color depth and screen resolution. If your video memory is limited, you may need to give up some color depth to get higher resolution, or vice versa. Unless you need to manipulate photographic images, 16 bit color is probably all you need (one caveat, however: one application, Framemaker, is known to fail when trying to display on an X server with 16 bit color).
If the range of available color depths and resolutions does not include video modes that you know are supported, e.g. from previous experience under Windows or an earlier version of Linux, the installation program has probably not been able to determine how much video memory you have and has guessed a conservative value. At this point, you can go back to the "Graphical Interface (X) Configuration" screen and try specifying a larger value for your video memory.
For more information about setting up X Windows, see the sections on configuring your video card and monitor in the RHEL 3 Installation Guide.
Once you click "Next" on the "Customize Graphics Configuration" screen, your Scientific Linux installation is complete and you will not be able to go back and change anything. The next step is to boot into your new system.
Be sure to remove any floppy disk still remaining in the drive and press Enter to reboot the system.
If you skipped the X configuration during installation, or if you have problems
with the resulting X Windows setup, you can try running the X Configuration
Tool now by running the command, redhat-config-xfree86.
If you can't get a satisfactory X configuration using this tool then you will
have to fiddle with the /etc/X11/XF86Config file. See the
XF86Config(5x) man page for information on the format of this file and it's
many device-independent options. There are also device-specific man pages for
the various supported video drivers -- see the SEE ALSO section of
XF86Config(5x) for some of the driver names. Do not increase
the refresh rate ranges on your monitor unless you are absolutely sure it is
supported!
If your sound card was not automatically configured by the installation
program or during the initial boot (by a program called "kudzu"), you can try
running (as root) the Sound Card Configuration Tool. You can also run this
tool by entering redhat-config-soundcard on the command line, or
by choosing Main Menu => System Settings => Soundcard Detection. Note that
this tool requires that you have an X server running. For more information,
see the section on
Problems with Sound Configuration in the RHEL 3 Installation Guide. If
you have an unusual sound card, you may also have to search the web for
detailed help on configuring it.
WARNING: This is not (yet) for laptop users.
Taylor is the tool used by SCCS for administering the very large number of UNIX (including Linux) systems for which we are responsible. It can be run after the Scientific Linux installation program to automatically configure your new system to be integrated into the SLAC environment. It normally installs a cronjob which will maintain your system automatically.
Some of the things Taylor does include:
/usr/local to point to
SLAC AFS /usr/local for Linux.For additional information, see the Taylor Web page.
Taylor uses a configuration file, /etc/taylor.opts,
to control its actions.
If you don't have this file the first time you run Taylor,
it will install one with a reasonable set of defaults.
However, you may want to set some of these options
before you run Taylor the first time,
since the root password you set during installation
will otherwise be overridden at this point.
If your machine was previously taylored, you will most likely
want to restore most or all of the options from your old
taylor.opts file
(you did print a copy
before beginning, right?).
If your machine is connected to a
non-autonegotiating (fixed speed) 100 MB/s port,
it is particularly important to include the option,
ethernet=100mb.
If you are not sure, omit this option or check with net-admin.
If your machine has not been previously taylored,
look in
/afs/slac/package/taylor/taylor.opts
for a sample taylor.opts file.
In particular, this file includes commented out examples examples showing how to:
For a more complete list of options,
type man taylor.opts.
After running Taylor the first time,
if you subsequently need an option changed
and can no longer modify /etc/taylor.opts yourself,
contact one of your Linux Desktop Support people
or send mail to
unix-admin.
To install and run Taylor, execute the following command:
elinks -source http://www/comp/unix/linux/go-taylor | sh
You will be asked whether to use the version of /usr/local
maintained by SCCS or set up a private /usr/local. We highly
recommend that you use the central one.
Taylor will probably take several minutes to complete its work. If there is
an error and you can see how to fix the problem, it is safe to rerun
taylor afterward. If you have an error you cannot understand
or fix, send email to
unix-admin to request help. If possible, paste the error
messages from Taylor into the email.
If you receive your email via the UNIX mail spool
rather than SLAC's Exchange server,
you'll need access to
/nfs/mailspool/mail/<your_UID>.
Some users may also want to access
other central NFS file servers from their Linux workstations.
Access to NFS is not automatic;
for security reasons you must submit a request to SCCS
for permission to mount our central servers.
There is a simple
NFS Access form for this purpose
if you do not need any superuser privileges on the machine.
If you also need privileges, see the next section.
If you need superuser privileges
(i.e., the root password and/or sudo ALL)
on your machine, you will need to carefully read the
Superuser/NFS Privileges page,
then fill out and submit the form you'll find there.
If you also need NFS access, you must request it via this same form.
SLAC maintains a mirror of the Scientific Linux 3 distribution at
/afs/slac/package/SciLinux/SL3. The mirror is updated nightly.
Within this directory, you can find a complete set of RPMs from the currently recommended update level of Scientific Linux at:
/afs/slac/package/SciLinux/SL3/cur/i386/SL/RPMS/
This is sometimes referred to as the base area or directory. RPMs with security fixes since the current recommended update level can be found in the following directory:
/afs/slac/package/SciLinux/SL3/cur/i386/errata/SL/RPMS
Under the ".../errata/" directory therey may also be a directory or directories named 'bugfix' and/or 'fastbugs' with non security patches since the current recommended update level (SL's naming conventions are a bit of a moving target).
The application, yum, is used to update packages. See the
yum man page for detail on the command.
Look in our RPM repository for additional RPMS that you might want to install (be sure to always check the updates area as well as the quarterly base directory in case there have been any recent security updates). To read the description of one of these packages, change to the appropriate directory of the repository and use the rpm program as in the following example:
rpm -qip enscript-1.6.1-24.i386.rpm
There are some known issues with Scientific Linux 3.
3Com NICs.
Two network interface cards (NICs) from 3Com,
3c905 (Boomerang) and 3c905B (Cyclone),
have a problem under SL at least through 3.0.3.
Following a successful installation (even a network
installation) they sometimes come up configured to the wrong
speed or duplex setting, making network connections extremely
slow or impossible. The problem does not always occur, but if
it does the work-around is to disable kudzu and reboot.
To do so, issue the command "chkconfig kudzu off" as root;
you can turn kudzu back on temporarily if you add a new device
to your machine and need to get it configured. A fix is
expected in 3.0.4.
Missing drivers.
A number of third party drivers and other kernel modules that
are not supported by Scientific Linux have been moved to separate RPMs
that are no longer installed by default. If you are missing a
driver for some device in your system, try installing the
appropriate version (depending on your kernel) of the
kernel-unsupported or
kernel-smp-unsupported RPM in
our RPM repository.
Note that none of the kernel*unsupported
RPMs actually contain kernels -- they are simply collections
of kernel modules.
Please also report such missing drivers to
unix-admin
so that
we can give feedback to Scientific Linux about which legacy hardware is
still important to us at SLAC.
Missing ACPI support. ACPI stands for Advanced Configuration and Power Interface, a power management specification which is particularly important for laptops. Although ACPI support was included in some earlier Linux distributions, it is not included in Scientific Linux 3 (or Red Hat Enterprise Linux 3), probably because the version for the 2.4 series kernel is not yet considered "production quality". It is hoped that some support for ACPI will be available in SL4. In the meantime, laptop users might want to try using the Fedora Core 1 kernel along with the rest of the SL3 distribution.
The default setting for the LANG environment variable is "en_US.UTF-8". However, some problems have been reported when using the UTF-8 encoding; for example, if you use less as your pager, you may see some special characters displayed as hex characters enclosed in angle brackets, like this (from man man):
...
manpath - determine user&<80><99>s search path for man pages
...
Setting LANG to just "en_US" appears to solve this problem. You
can put this in your $HOME/.i18n file, for example:
...
LANG="en_US"
...
subscribe linux-l".If you need more information, please have a look at our Linux Resources page.