SL5 Linux installation and upgrade instructions

Instructions for installing SL5 on DAQ machines

Notes:

these instructions are periodically updated to include items needed for older/newer versions of Linux. They are marked like this: (SL4.2+) means Scientific Linux 4.2 and newer; (SL4 is equivalent to FC3). (FC5 only) means Fedora Core 5; etc.
obsolete items are marked by the "#" sign at the beginning of the line and sometimes have a comment about the reason for removal.
typically, we do not "upgrade" machines using the Red Hat "upgrade" function. Instead, we save critical files from the old installation and do a "fresh install" from scratch

Upgrade procedure

save /etc, /var, /root, /usr/local, /opt and /tftpboot (tar and scp to another machine or use either of: /triumfcs/trshare/midas/Disks/rsync_all_NIS.csh or /triumfcs/trshare/midas/Disks/rsync_all_noNIS.csh)
NIS only: ascertain NIS domain name (use authconfig) e.g. "DAQ-NIS","MUSR-NIS" etc.
check existing partition sizes on machine: df -hl, fdisk -l
note which are the /home1 and /data partitions
if /home1 is inside the "/"partition you must save it also
shutdown
Start installation of the new system:
IMPORTANT: if you have WDC "advanced partitioning disks" (4kB sectors), disks have to be repartitioned before use, see special instructions (TBW) (note: use fdisk -H 224 -S 56 /dev/sdx)
boot from latest "SL5 kickstart" CD from Kelvin Raywood or PXE boot the latest SL installation image
after the system enters graphical mode, one can remove the CD- the installation is running over the network
two questions will be asked: how to partition the disks and the root password. The rest of the installation is automatic.

select "Custom partioniong". You can create either simple normal partitions if you have only one disk or RAID 1(mirror) for / and /home1 if you have two disks.

   <strong>For the case of one disk only</strong>: - no "/boot" filesystem,
   - allocate at least 20 GBytes for "/" filesystem (primary partition, hda1)
   - allocate at least 8 GBytes for swap (primary partition, hda2)
   - allocate the rest as /home1 and /data (primary partitions hda3 and hda4)

<strong>For the case of two or more disks:</strong>
- If there are already some partitions on the disks, consider DELETING them all 
- Click New, select software RAID for /dev/sda, 20000MB (20 GB) and Force primary partition
- Same as above for /dev/sdb
- Click RAID, select create a RAID device /dev/md0, mount point /, RAID Level1 (mirror)
- Repeat for the swap partition (/dev/md1, make it at least 8 Gbytes)
- Leave the rest of the disks free. The other RAID partitions will be created AFTER installation.

enter the root password for the new system
continue with installation, at the very end, the system will ask you to reboot
boot newly installed system and answer the few questions for SL5
Firewall: Leave it disabled; SELinux: choose Disabled; KDump: Leave it disabled; Date and Time: Leave kickstart defaults (should be NTP using TRIUMF time servers)
Create user: not necessary if you are using NIS; Sound card: ignore possibly.
The system will reboot again.
Login from the console, restore the SSH keys from backup (/etc/ssh/*key*), "service sshd restart"
ssh into the new machine as root
If you created only one mirror partitions, it is time to create the others: Create one 60 GB primary partition on each disks for /home1 and another one using the remainder of space.

<strong>fdisk /dev/sda</strong>
...
Command (m for help): <strong>n</strong>
Command action ...   <strong>p</strong>
Partition number ... <strong>2, 3 or 4</strong> according to what has been defined before
First cylinder ... default
Last cylinder ...  <strong>+60000M</strong>  or default
Command action ...   t
Partition number ... : <strong>2, 3 or 4</strong> according to what has been defined before
Hex code ... : fd if you intend to include this into a RAID array
Command action ...   <strong>p to check all is correct</strong>
Command (m for help): <strong>w
.... </strong>The new table will be used at the next reboot.<strong>
</strong><strong><strong>fdisk /dev/sdb  </strong></strong>and repeat as above
<strong><em>-  Reboot the machine  ---
</em></strong>Check the newly created partitions: <strong>fdisk -l /dev/sda; fdisk -l /dev/sdb
mdadm --create /dev/md2 -a yes  -l 1 -n /dev/sda3 /dev/sdb2</strong>
Check the progress of building the RAID with <strong>more /proc/mdstat
</strong>When finished:<strong> mkfs -j -L /home1 /dev/md2; tune2fs -i 0 -c 0 /dev/md2; mkdir /home1</strong>
Add a line to /etc/fstab: 
<strong>/dev/md2                /home1                  ext3    defaults        1 2</strong>
Finally mount this new partition: <strong>mount -a</strong>
Repeat from <strong>mkfs</strong>  for each of the data partitions.

At this point you should have these disk partitions (single-disk in parenthesis)

/dev/md0 (/dev/hda1) is the system partition, 20 GBytes or more
/dev/md1 (/dev/hda2) is the swap partition, 8 GBytes or more
/dev/md2 (/dev/hda3) is the /home1 partition, 60 GBytes or more
/dev/md3 or /dev/sda4 (/dev/hda4), etc are the data partitions

check that /etc/ssh/ssh_config contains:

        ForwardX11 yes
        ForwardX11Trusted yes

(on midm15/midm9b/midm20 only) install correct ethernet driver eepro100 not e100
restore /home (non-NIS) or /home1 (NIS) and other required user directories from backup.
(Can use /triumfcs/trshare/midas/Disks/rsync_back.csh ).
if needed, for non-NIS only, make a softlink for /home1 (NIS automounts /home).
ln -s /home /home1
Restore users accounts (non-NIS and NIS master only):
- edit /etc/passwd and /etc/shadow
Append users' login info to the end of these files from the backup versions.
edit ~root/.forward
(create file if not present, or restore from backup) In file add email address of the person(s) to receive root's email - always include Konstantin - olchansk@triumf.ca)
cleanup network setup (or postfix would not work):

check that /etc/sysconfig/network has the entry "HOSTNAME=xxx.triumf.ca" (fully qualified domain name)
check that /etc/hosts has only the entry for "localhost".

###run "system-config-authentication", check "select NIS support", click on "configure NIS", set NIS domain, leave NIS server field blank.
run "authconfig --enablenis --nisdomain LADD-NIS --update"
run "sed 's/^hosts:.*/hosts: files dns/' -i /etc/nsswitch.conf" (to undo a mistake from authconfig)
On the master NIS node (ladd00), add this new node to /etc/netgroup, and update NIS maps (cd /var/yp; make)
(if needed) To setup NIS slave server:

check if /usr/lib64/yp exists. If not, run "yum install ypserv"
/usr/lib64/yp/ypinit -s ladd00 (/usr/lib/yp/ypinit on 32-bit machines)
chkconfig ypserv on
service ypserv start
service ypbind restart
add the new machine to /var/yp/ypservers on the NIS master, run "make -C /var/yp" and also "cd /var/yp; yppush -h newmachine ypservers"
If using securenets on the NIS master, remember to copy this file to the new slave server in /var/yp

(if NIS master or standalone) check /etc/auto.* against backups, particularly auto.master if NIS master
(if needed) add "+auto.master" at the end of /etc/auto.master
restart autofs to use the newly configured NIS maps: "service autofs restart"
Verify time and date configuration. Run "ntpstat", it should say "synchronised to NTP server (142.90.x.y). If not, run "system-config-time", check "use network time", enter NTP servers: time1, time2, time3
(If needed) enable automatic system updates: run "/triumfcs/trshare/olchansk/linux/triumf-update/yum-setup.perl -o"
(If needed) enable automatic kernel updates: run "/triumfcs/trshare/olchansk/linux/triumf-update/yum-setup.perl -k -o"

disable unwanted services, use "chkconfig --list | grep on | sort" to see what is enabled. SL4- disable unnecessary services:

(only if amanda is not used) -> chkconfig --level 12345 xinetd off
chkconfig --level 12345 canna off
chkconfig --level 12345 FreeWnn off
chkconfig --level 12345 hpoj off
chkconfig --level 12345 ip6tables off
chkconfig --level 12345 iptables off
chkconfig --level 12345 isdn off
chkconfig --level 12345 pcmcia off
chkconfig --level 12345 rhnsd off
chkconfig --level 12345 spamassassin off
chkconfig --level 12345 bluetooth off
chkconfig --level 12345 apmd off
chkconfig --level 12345 iiim off
chkconfig --level 12345 fenced off
chkconfig --level 12345 ccsd off
chkconfig --level 12345 cpuspeed off
chkconfig --level 12345 pcp off
chkconfig --level 12345 pmie off
chkconfig --level 12345 yum-updatesd off
chkconfig --level 12345 clvmd off
chkconfig --level 12345 cman off
chkconfig --level 12345 lvm2-monitor off
chkconfig --level 12345 modclusterd off
chkconfig --level 12345 yum-updateonboot off
chkconfig --level 12345 cmirror off
chkconfig --level 12345 lock_gulmd off
chkconfig --level 12345 firstboot off
chkconfig --level 12345 ricci off
chkconfig --level 12345 gfs off
chkconfig --level 12345 scsi_reserve off
chkconfig --level 12345 openibd off
chkconfig --level 12345 arptables_jf off
chkconfig --level 12345 auditd off
chkconfig --level 12345 avahi-daemon off
chkconfig --level 12345 hplip off
chkconfig --level 12345 iscsi off
chkconfig --level 12345 iscsid off
chkconfig --level 12345 mcstrans off
chkconfig --level 12345 pcscd off
chkconfig --level 12345 restorecond off
chkconfig --level 12345 setroubleshoot off
chkconfig --level 12345 xend off
chkconfig --level 12345 xendomains off
chkconfig --level 12345 kudzu off
#chkconfig --level 12345 yum-cron off

configure hardware sensors:

run "yum install lm_sensors"
run "sensors-detect", accept default answer to all questions (press ENTER)
run "service lm_sensors restart" to load the kernel modules
run "sensors", observe the sensors data

if sensors reports "General parse error", do "cp /triumfcs/trshare/olchansk/linux/lm_sensors/lm_sensors-3.0.1/prog/sensors/sensors /usr/bin/sensors" and try again.

ssh root@localhost, ctrl-C
scp root@ladd00:/root/authorized_keys ~root/.ssh/
Use "system-config-users" to add local user accounts
NIS: check user accounts: run "ypcat -k passwd"

to enable NFS:

edit /etc/hosts.allow, add or uncomment "mountd: 142.90.0.0/255.255.0.0"
create /etc/exports, e.g. "/home1  @daqmachines(rw,no_root_squash,async)"
chkconfig nfs on
chkconfig nfslock on
service nfs restart

(already done by SL5 kickstart) to enable amanda, see <a href="http://amanda/~amanda">http://amanda/~amanda</a> or run "/triumfcs/trshare/olchansk/linux/amanda/amanda-enable.perl"
contact TRIUMF CS to add this new machine to the amanda backup list
mount the dCache partition (if needed): "mkdir -p /pnfs/triumf.ca", edit /etc/rc.local, add the line " mount -o intr,rw,noac,hard,nfsvers=2 trdata00:/pnfsdoors /pnfs/triumf.ca", execute the line above.

(not needed for SL5.5 kickstart) erase unwanted packages: yum erase logwatch mailman mrtg inn inn-devel cyrus-imapd cyrus-imapd-devel cyrus-imapd-murder cyrus-imapd-nntp webalizer squirrelmail rhn-applet yumex-applet apt-autoupdate SL_enable_serialconsole tog-pegasus kernel-largesmp kernel-hugemem kernel-largesmp-devel spamassassin slrn-pull openafs kernel-module-openafs openafs-debug openafs-devel openafs-kernel-source kernel-largesmp kernel-hugemem kernel-hugemem-devel xen kernel-xen bash-completion
install xemacs (from EPEL): yum install "xemacs*"

install ganglia:

scp ladd00:/etc/gmond.conf /etc/gmond.conf
yum install ganglia ganglia-gmond
chkconfig gmond on
service gmond restart

install misc stuff

cd /triumfcs/trshare/olchansk/linux/misc-rpms
rpm -vh --install triumf-ko-ganglia-*
rpm -vh --install emailonreboot-*
rpm -vh --install monitor_nfs-*
rpm -vh --install /triumfcs/trshare/olchansk/public_html/diskscrub/download/diskscrub*

install memtest86: "yum install memtest86+", "ls -1 /boot/* | grep memtest" to find out the name of the memtest boot file to use on the "kernel" line of the incantation to be added at the end of /boot/grub/grub.conf:

cat >> /boot/grub/grub.conf

title memtest
      root (hd0,0)
      kernel /boot/memtest86+-1.65

yum install tkcvs

install node monitoring

cd /triumfcs/trshare/olchansk/linux/misc-rpms
rpm -vh --install triumf_nodeinfo.noarch.rpm
/usr/sbin/sendnodeinfo.perl --config ladd00:8600
edit /etc/nodeinfo
/usr/sbin/sendnodeinfo.perl ladd00:8600

(before FC5) remove the fancy screen savers

rm -f /usr/X11R6/lib/xscreensaver/*
rm -f /usr/bin/*.kss

chmod a+r /var/log/messages
(before FC5) edit /etc/updatedb.conf, set "DAILY_UPDATE=yes"
cd ~; yum update
install packages needed for ROOT & DAQ: yum install giflib.i386 giflib.x86_64 compat-libf2c-34.i386 mysql-devel sysstat "libusb-devel*" unixODBC-devel postgresql-devel libxml2-devel libXpm-devel libgfortran libstdc++-devel.i386
install xpdf (from EPEL, on SL5): yum install xpdf
(if desired) install all missing packages: /triumfcs/trshare/olchansk/linux/triumf-update/yum-everything.perl
(SL5) If yum complains about unsigned java packages: cd ~; rpm -vh --upgrade /triumfcs/mirror/scientificlinux.org/5x/i386/updates/security/jdk*rpm /triumfcs/mirror/scientificlinux.org/5x/i386/updates/security/java*rpm
(SL5.5 or newer) enable raid1 bitmap files, for each /dev/mdX device, run "mdadm --grow --bitmap=internal /dev/mdX". In /proc/mdstat, verify that there is a "bitmap" entry. This will fail if the md device reconstruction is in progress.
edit /boot/grub/grub.conf, remove the "quiet" and "rhgb" options
edit /boot/grub/grub.conf, comment out (with "#") the "splashimage=" line
for machines with mirrored system disk, configure booting from 2nd system disk: (but check that /dev/sdb is the right disk)
```
# grub
grub> device (hd0) /dev/sdb
grub> root (hd0,0)
grub> setup (hd0)
```
ssh as root
add the following at the end of /etc/X11/xorg.conf. The enables Ctrl-Alt-KP-/ and Ctrl-Alt-KP-* to unlock the keyboard after Altera Quartus crash

Section "ServerFlags"
        Option "AllowDeactivateGrabs" "true"
        Option "AllowClosedownGrabs" "true"
EndSection

configure NVidia video card (if installed) (SL5.5+)

yum install nvidia-x11-drv kmod-nvidia
(if above fails due to conflict with module-init-tools, run "yum --disablerepo \* --enablerepo elrepo update module-init-tools")
mv /etc/X11/xorg.conf /etc/X11/xorg.conf-xxx
nvidia-xconfig
reboot to enable the nvidia driver
after reboot, login as root
run "nvidia-settings" to setup dual-screen configuration, etc

(not needed for SL5.5+) configure X11:

physically go to the computer
login as root
run "system-config-display".
In the "hardware" tab, select monitor type: "generic LCD 1280x1024" or "generic LCD 1600x1200".
In the "settigs" tab, select "1280x1024" or "1600x1200" and "Thousands of colors".
Press "ok", the display settings application should close.
Logout, the new login window should use the new settings.

logout and reboot the computer to have all the changes to take effect

SLinstall

Contents

SL5 Linux installation and upgrade instructions

Instructions for installing SL5 on DAQ machines

Notes:

Upgrade procedure

Navigation menu

SLinstall

SL5 Linux installation and upgrade instructions

Instructions for installing SL5 on DAQ machines

Notes:

Upgrade procedure

Navigation menu

Search