Installing Linux

1.  Hardware

  • Check cables etc., especially on old PCs:
    • power splitters are generally unreliable, try not to use them to connect the primary hard disk.
    • a faulty floppy disk may stop grub-install (the post-install phase). If "floppy seek at boot" is disabled in the BIOS, you might not notice until it's too late, so check the cables - or completely disable the floppy in the BIOS.
  • it is better and easier if the hard disk is connected as primary master: check its configuration jumpers;
    • some old disks did have separate "single", "master" and "slave" modes. Newer ones only have "master" and "slave" modes;
    • in general, avoid the "Cable Select" mode: if you change the cabling, the order of the hard disks will change, which might be a very unexpected effect. On old PCs, the cables anyway did not support it. On the other side, "Cable Select" prevents the problem below...
  • With new fast Ultra-ATA hard disks (80-pin cables) make very sure that the master or single disk is at the end of the cable, not in the middle. Otherwise you may have various odd behaviours, and even data corruption. (Why? Because the Ultra-ATA cable behaves like a wave guide - its impedance must be matched at the ends).

2.  Configure the BIOS:

  • temporarily enable boot from CD
  • enable SMART on hard disks
  • disable legacy support for USB

3.  Install Scientific Linux

  • Partitions
    • avoid using LVD on non-server machines. This means do not use automatic partitioning.
    • on large HDs, make a separate partition for system, at least 5GB
    • CERN is using XFS for non system partitions - should we try that ?
    • make a swap partition of twice the size of the RAM - at least 512MB. Make 2GB if you have a fast PC and a decent size hard disk: it's quite common to buy more memory, and quite difficult to repartition a hard disk.
  • Packages
    • Do not forget to include the YUM package !
    • be careful not to install server software that you do not need.
    • make sure you install the development tools, but you will normally not need Gnome and KDE development libraries

4.  UJ configuration

  • you can use system-config-authentication to reconfigure:
    [*] Cache Information
    [*] Use MD5 Passwords
    [*] Use Shadow Passwords
    [*] Local authorization is sufficient

4.1  Config scripts

rmdir /home 
ln -s /nfs/autofs/psi_home /home 
ln -s /nfs/autofs/psi_SCRATCH /SCRATCH 
ln -s /nfs/autofs/psi_SHARED /SHARED 

4.2  additional useful packages:

yum -y install mc xemacs-nox
# for physics
yum -y install cernlib root geant4 geant4-examples
# for mail
yum -y install thunderbird 
# for reading PDF files - better than the default one
yum -y install xpdf 
# for writing LaTeX
yum -y install lyx latex-xft-fonts
# for programming
yum -y install xemacs
yum -y install subversion esvn doxygen doxygen-doxywizard graphviz
# for web pages
yum install nvu 
# for creating CDs
yum -y install k3b

use yum info <package name> to see what they are

5.  Special video modes


$ gtf 1680 1050 60

# 1680x1050 @ 60.00 Hz (GTF) hsync: 65.22 kHz; pclk: 147.14 MHz
  Modeline "1680x1050_60.00"  147.14  1680 1784 1968 2256  1050 1051 1054 1087  -HSync +Vsync

You need to take the line generated by gtf, and add it to your X config file (/etc/X11/xorg.conf). Open it, and find the Monitor section for your monitor. Add the modeline from gtf into that section. Next, go to the Screen section, and add the new resolution into the list of accepted resolutions. Note that the name of the new resolution is "1680x1050_60.00", not "1680x1050". Now, restart X. It should come up in 1680x1050. If it doesn't, have a look at your X logs (/var/log/Xorg.0.log) to see if there were any errors. Also, look at the list of display modes given by xrandr. Even if you couldn't switch to your new mode, it should appear in there somewhere.

But you should remember that it also depends on the video driver; for example the vesa driver in SL4 does not support "widescreen" modes, so you can't do 1680x1050 with vesa.

For Intel graphic or integrated chipsets, you may need to use 915resolution to add the video mode to the VBIOS.

6.  Automatic network: ifplugd

for portables, recognises when a cable is plugged in the ethernet port. The rpm is from the DAG repository.

yum install ifplugd

7.  Upgrading from SL 4.1 to SL 4.3

Upgrading to a minor release can be done simply via YUM. There is a nice HowTo page on SL web site that explains this, but we have to adapt that procedure because we use a local repository:

Please note also that the new PSI-HEP packages have changed the numbering scheme; to get the updated Geant4 [presently version 8.0-p01.0.SL4.WITS, check it with rpm -q geant4] you may have to remove the existing one:

rpm -q geant4
rpm -e geant4 geant4-examples
yum install geant4 geant4-examples

8.  Hard disk performance

  • configure using /etc/sysconfig/harddisks (see man hdparm):
  • test it carefully, some chipsets might not fully support these options and cause data corruption.
    When done with testing , you can change
    to keep the configuration over resets
  • For reference, check the speed: hdparm -t /dev/hda
160GB SATA56.70 MB/sec
80GB UATA (80-wires cable)55.38 MB/sec
20GB ATA (40-wires cable)25.57 MB/sec
20GB ATA (40-wires cable)11.91 MB/sec