SLinstall: Difference between revisions

Revision as of 16:18, 25 November 2015

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

Preparation

save /etc, /var, /root, /opt, (if needed: /usr/local, /tftpboot) by rsync to some data disk (/ladd/data0/root)
check that "/" partition (it will be overwritten) is different from /home1 and /data partitions
note the MAC addresses of all network interfaces, add them to ladd00 dhcpd.conf to enable PXE boot into the SL "network installer"
shutdown

Running SL installer

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)
(NOT AVAILABLE ANYMORE) 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
boot from ladd00 PXE server - after power up, during BIOS POST, press BIOS "boot selection menu" key (F8, F12, etc). The MAC of the network interface should be listed in the ladd00 dhcpd.conf file. In the PXE boot menu, select SL6x-64 kickstart install.
linux will boot into the graphical installer
two questions will be asked: how to partition the disks and the root password. The rest of the installation is automatic.
to partition the disks, select "Custom partioning":
- If using a single SSD (30 or 60 GB), use whole disk for "/" partition (no swap partition)
- If using single HD, create 4 primary partitions (see below)
- If using dual HDs (should be same size), create 4 "RAID1" (see below) (DO NOT USE LVM)
- Use these partition sizes:
  - "/" - 40GB - md0 or sda1
  - swap - 32 GB - md1 or sda2
  - "/home1" - 100 GB - md2 or sda3
  - "/data" - remaining disk space - md3 or sda4
if installer asks questions about boot loader, accept default settings
package installation will proceed automatically
when finished will ask "press button to reboot"
boot newly installed system
if installing without a kickstart, some questions need to be answered:
- Firewall: disabled
- SELinux: disabled
- KDump: disabled
- Date and Time: leave kickstart defaults (should be NTP using TRIUMF time servers)
- Create user: skip - will be handled during post-installation
- The system will reboot again
after the final reboot, login as root and proceed with post-installation.

Configure SSH

(+CentOS7)

Login from the console
restore the SSH keys from backup (/etc/ssh/*key*)
service sshd restart
ssh into the new machine as root
ssh root@localhost, ctrl-C
### this is done later from Konstantin's git repository - scp root@ladd00:/root/authorized_keys ~root/.ssh/
(not needed for SL5.5 kickstart) check that /etc/ssh/ssh_config contains "ForwardX11 yes" and "ForwardX11Trusted yes":

echo "  ForwardX11 yes" >> /etc/ssh/ssh_config
echo "  ForwardX11Trusted yes" >> /etc/ssh/ssh_config

Configure disks, partitions, raid arrays and filesystems

NOTE1: For compatibility with the SL6 installer, use "fdisk -u" when creating new partitions.

NOTE2a: For 2TB disks or bigger, use "gdisk" to create GPT partitions (yum install epel-release; yum install gdisk)

NOTE2c: (SL6) 3TB, 4TB, 6TB disks do not require anything special - proceed with installation as normal.

Typical disk configuration for DAQ use has 2 large disks with system ("/"), swap, home and data partitions, fully mirrored across the 2 disks using RAID1 software raid (MD).

In this fully mirrored configuration, a DAQ system will continue to operate without interruption and without performance degradation when there is a full or partial failure of either of the two disks.

If disks are hot-swappable, the failed or defective disk can then be physically replaced by a spare, the spare disk can be partioned and added to the RAID1 array, restoring full normal operation, without shutting down or rebooting the system or interrupting data taking. (Since SATA, eSATA and USB are always electrically hot-swappable, disk hot-replacement is more of a mechanical issue).

For small disks using traditional partitions (<=2TB) a typical layout looks like this:

[root@ladd06 ~]# fdisk -l  ### use "fdisk -lu" instead!!!

Disk /dev/sdb: 750.2 GB, 750156374016 bytes
...
   Device Boot      Start         End      Blocks   Id  System
/dev/sdb1   *           1        5100    40960000   fd  Linux raid autodetect
/dev/sdb2            5100        9179    32768000   fd  Linux raid autodetect
/dev/sdb3            9179       21927   102399603+  fd  Linux raid autodetect
/dev/sdb4           21928       91201   556443405   fd  Linux raid autodetect

Disk /dev/sda: 750.2 GB, 750156374016 bytes
...
   Device Boot      Start         End      Blocks   Id  System
/dev/sda1   *           1        5100    40960000   fd  Linux raid autodetect
/dev/sda2            5100        9179    32768000   fd  Linux raid autodetect
/dev/sda3            9179       21927   102399603+  fd  Linux raid autodetect
/dev/sda4           21928       91201   556443405   fd  Linux raid autodetect
...
[root@ladd06 ~]# cat /proc/mdstat
Personalities : [raid1] 
md3 : active raid1 sdb4[1] sda4[0]
      556442245 blocks super 1.2 [2/2] [UU]
      bitmap: 0/5 pages [0KB], 65536KB chunk

md2 : active raid1 sdb3[1] sda3[0]
      102398507 blocks super 1.2 [2/2] [UU]
      bitmap: 0/1 pages [0KB], 65536KB chunk

md1 : active raid1 sda2[0] sdb2[1]
      32766908 blocks super 1.1 [2/2] [UU]
      bitmap: 0/1 pages [0KB], 65536KB chunk

md0 : active raid1 sda1[0] sdb1[1]
      40959928 blocks super 1.0 [2/2] [UU]
      bitmap: 1/1 pages [4KB], 65536KB chunk
...
[root@ladd06 ~]# df -kl
Filesystem           1K-blocks      Used Available Use% Mounted on
/dev/md0              40316208   6222676  32045536  17% /
/dev/md2             100790232    192116  95478192   1% /home1
/dev/md3             547709948    202404 519685432   1% /data6
...
[root@ladd06 ~]# swapon -s
Filename                                Type            Size    Used    Priority
/dev/md1                                partition       32766900        0       -1

Typical size of partitions:

/dev/md0 : "/" : 40 Gbytes should be sufficient. SL5 fits into an 8GB "/" and SL6 fits into a 16GB "/".
/dev/md1 : swap : 32 Gbytes. Additional swap space can be added using a swap file located on the data disk.
/dev/md2 : "/home1" : 100 Gbytes. User home directories backed up by the amanda site backup system. Space is limited by the capacity and capability of the backup and archiving system used to protect user data against accidental file deletion, filesystem corruption and disastrous system failures.
/dev/md3 : "/data" : data partition uses the remaining space on the disks.

Usually, the "/" and swap partitions are created through the SL installer program. The /home and /data partitions can be created at the same time.

Otherwise, for traditional partitions (disks <2TB) follow these instructions:

create the partitions using fdisk or similar (this example creates a 60 GB partition):
- fdisk -cu /dev/sda
- Command (m for help): n
- Command action ... p
- Partition number ... 2, 3 or 4 according to what has been defined before
- First cylinder ... default
- Last cylinder ... +60000M or default
- Command action ... t
- Partition number ... : 2, 3 or 4 according to what has been defined before
- Hex code ... : fd
- Command action ... p to check all is correct
- Command (m for help): w
- fdisk /dev/sdb and repeat as above
- Reboot the machine

For GPT partitions (disks >=2TB), do this:

install gdisk: yum install epel-release; yum install gdisk
gdisk /dev/sdX
- if this is a new disk, do "o" to create a blank partition table
- "n" to create new partition:
  - accept default for partition number
  - accept default for first sector
  - for last sector, say "+40G" to create 40 Gbyte partition, accept default to use all remaining disk space
  - for partition type, say "fd00" to create an mdadm raid partition
- "p" to print the partition table
- "d" to delete wrong partition
- "w" to save and exit

Typical GPT layout:

[root@isdaq01 ~]# gdisk -l /dev/sdh
GPT fdisk (gdisk) version 0.8.10

Partition table scan:
  MBR: protective
  BSD: not present
  APM: not present
  GPT: present

Found valid GPT with protective MBR; using GPT.
Disk /dev/sdh: 3907029168 sectors, 1.8 TiB
Logical sector size: 512 bytes
Disk identifier (GUID): D4FCDE83-12BD-4118-ACA2-702F0E2E57C2
Partition table holds up to 128 entries
First usable sector is 34, last usable sector is 3907029134
Partitions will be aligned on 2048-sector boundaries
Total free space is 2014 sectors (1007.0 KiB)

Number  Start (sector)    End (sector)  Size       Code  Name
   1            2048        83888127   40.0 GiB    FD00  Linux RAID
   2        83888128       150996991   32.0 GiB    FD00  Linux RAID
   3       150996992       360712191   100.0 GiB   FD00  Linux RAID
   4       360712192      3907029134   1.7 TiB     FD00  Linux RAID
[root@isdaq01 ~]#

Check the newly created partitions: fdisk -lu /dev/sda; fdisk -lu /dev/sdb
mdadm --create /dev/md2 --metadata=1.0 --bitmap=internal -l 1 -n 2 /dev/sda3 /dev/sdb3
Check the progress of building the RAID with: more /proc/mdstat
When finished: mkfs -t ext4 /dev/md2; tune2fs -i 0 -c 0 /dev/md2
mkdir /home1
Add to /etc/fstab: "/dev/md2 /home1 ext4 defaults 1 2"
Finally mount this new partition: mount -a
Repeat from "mkfs" for each of the data partitions

At this point you should have these disk partitions (single-disk in parenthesis)
- /dev/md0 (/dev/sda1, sdb1) is the system partition, 40 GBytes or more
- /dev/md1 (/dev/sda2, sdb2) is the swap partition, 32 GBytes or more
- /dev/md2 (/dev/sda3, sdb3) is the /home1 partition, 100 GBytes or more
- /dev/md3 (/dev/sda4, sdb4) is the data partition

Add array descriptions to /etc/mdadm.conf:
- mdadm -Ds >> /etc/mdadm.conf
- emacs -nw /etc/mdadm.conf ### remove duplicate entries

Example /etc/mdadm.conf:

MAILADDR root 
AUTO +imsm +1.x -all 
ARRAY /dev/md0 metadata=1.0 name=isdaq01.triumf.ca:0 UUID=055f0455:18401f41:b12abf53:2b23eca0 
ARRAY /dev/md1 metadata=1.0 name=isdaq01.triumf.ca:1 UUID=dde05275:17961aaf:7c864e3a:c51477d6 
ARRAY /dev/md2 metadata=1.0 name=isdaq01.triumf.ca:2 UUID=e430ba44:361f1807:41f0c491:53c10438 
ARRAY /dev/md3 metadata=1.0 name=isdaq01.triumf.ca:3 UUID=a34d8c5b:cb65a435:be8ee01d:7f988927

(SL5.5 or newer) enable raid1 bitmap files, for each /dev/mdX device: mdadm --grow --bitmap=internal /dev/mdX

Restore data from backups

(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: 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.

Post installation

emacs -nw ~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: echo "olchansk@triumf.ca" >> ~root/.forward
emacs -nw /etc/sysconfig/network
- set "HOSTNAME=" (set it to blank to use hostname from DHCP)
- set "NETWORKWAIT=yes"
(not needed for SL6.1, NEEDED for SL6->6.1 update) in /etc/hosts, remove exteraneous entries - only entries for localhost and localhost6 should remain
disable selinux: edit /etc/sysconfig/selinux, change line to read: SELINUX=disabled, reboot later for change to take effect
chmod a+r /var/log/messages

Post installation CentOS7

CentOS 7.1 default installer will be stuck at the "create local user" screen. To proceed without creating fake local users, do:
yum erase gnome-initial-setup
killall Xorg

echo "olchansk@triumf.ca amaudruz@triumf.ca lindner@triumf.ca" >> ~root/.forward
chmod a+r /var/log/messages

Disable "persistent network names" (DO NOT DO THIS)

/bin/touch /etc/udev/rules.d/75-persistent-net-generator.rules
/bin/rm /etc/udev/rules.d/70-persistent-net.rules
#shutdown -r now

Configure NIS master (OPTIONAL)

(do not use SL6.2 for NIS master)

yum install ypserv
domainname DEAP-NIS
cd /var/yp
edit Makefile
- change NOPUSH=false
- change the "all:" entry to read: all: passwd group netgrp shadow auto.master auto.home auto.local ypservers
touch /etc/netgroup /etc/auto.home /etc/auto.local ./ypservers
make
inspect created NIS maps: ls -l DEAP-NIS
chkconfig ypserv on
chkconfig ypxfrd on
chkconfig yppasswdd on
service ypserv start

Configure NIS client

run "authconfig --enablenis --enablepreferdns --nisdomain LADD-NIS --update"
if NIS server is SL6.2, add "--nisserver=ladd00" to above command
(not needed with --enablepreferdns above) 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)
Use "system-config-users" to add local user accounts
NIS: check user accounts: run "ypcat -k passwd"
echo "NISTIMEOUT=5" >> /etc/sysconfig/network
echo "NETWORKWAIT=yes" >> /etc/sysconfig/network

Configure NIS client (CentOS7)

yum -y install ypbind
echo "NISTIMEOUT=5" >> /etc/sysconfig/network
echo "NETWORKWAIT=yes" >> /etc/sysconfig/network
authconfig --enablenis --enablepreferdns --nisdomain LADD-NIS --nisserver ladd00.triumf.ca --update
ypwhich
ypcat -k passwd

On the master NIS node (ladd00), add this new node to /etc/netgroup, and update NIS maps (cd /var/yp; make)
Use "system-config-users" to add local user accounts
enable selinux ssh key login to nfs mounted home directories:

setsebool -P use_nfs_home_dirs 1

Configure NIS secondary server (OPTIONAL)

(do this only if needed)

(do not use SL6.2 for NIS secondary server!)

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
on the NIS master:
- add the new machine to /var/yp/ypservers, run "make -C /var/yp" and also "cd /var/yp; yppush -h newmachine ypservers"
- if using /var/yp/securenets, copy it from NIS master to new NIS secondary server

Configure NIS secondary server (CentOS7) (OPTIONAL)

Enable local NIS server, make local machine use it:

yum install ypserv
/usr/lib64/yp/ypinit -s ladd00 (/usr/lib/yp/ypinit on 32-bit machines)
systemctl enable rpcbind ypserv ypxfrd yppasswdd
systemctl start rpcbind ypserv ypxfrd yppasswdd
edit /etc/yp.conf # change "domain XXX server YYY.triumf.ca" to read "domain XXX server localhost"
systemctl restart ypbind
ypwhich # should say "localhost"

Punch hole in the firewall: (or "make" on NIS master will complain)

echo YPSERV_ARGS=\"-p 800\" >> /etc/sysconfig/network
systemctl restart ypserv
firewall-cmd --add-service rpc-bind --permanent
firewall-cmd --add-port=800/tcp --add-port=800/udp --permanent
firewall-cmd --reload

on the NIS master:
- add the new machine to /var/yp/ypservers, run "make -C /var/yp" and also "cd /var/yp; yppush -h newmachine ypservers"
- if using /var/yp/securenets, copy it from NIS master to new NIS secondary server

Configure AUTOFS

(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 stop; service autofs start"

Configure AUTOFS (CentOS7)

yum -y install autofs
systemctl enable autofs
systemctl start autofs
ls -l /daq/daqshare

Configure time

Verify time and date configuration. Run "ntpstat", it should say "synchronised to NTP server (142.90.x.y). If not:

(SL6.0) rpm -vh --upgrade http://mirror.triumf.ca/rpmindex/fedora/archive/updates/12/i386/python-slip-0.2.13-1.fc12.noarch.rpm (see https://bugzilla.redhat.com/show_bug.cgi?id=720848)
(BROKEN) (SL6.1) rpm -vh --upgrade http://mirror.triumf.ca/rpmindex/fedora/archive/updates/12/i386/python-slip-0.2.13-1.fc12.noarch.rpm http://mirror.triumf.ca/rpmindex/fedora/archive/updates/12/i386/python-slip-dbus-0.2.13-1.fc12.noarch.rpm http://mirror.triumf.ca/rpmindex/fedora/archive/updates/12/i386/python-slip-gtk-0.2.13-1.fc12.noarch.rpm (see above)
(BROKEN) (SL6.1, SL6.2) rpm -vh --upgrade http://mirror.triumf.ca/rpmindex/fedora/archive/updates/13/i386/python-slip-0.2.13-1.fc13.noarch.rpm http://mirror.triumf.ca/rpmindex/fedora/archive/updates/13/i386/python-slip-dbus-0.2.13-1.fc13.noarch.rpm http://mirror.triumf.ca/rpmindex/fedora/archive/updates/13/i386/python-slip-gtk-0.2.13-1.fc13.noarch.rpm
(SL6.2) yum --enablerepo=sl-fastbugs update "*slip*"
run "system-config-date"
- check "use network time"
- enter NTP servers: time1, time2, time3
- say "OK" (if there is an error about writing config files, say "cancel")
chkconfig ntpdate on; chkconfig ntpd on; service ntpd stop; service ntpdate start; service ntpd start

Configure time with chronyd (SL6)

Use chronyd instead of ntpd.

yum -y install chrony
echo server time1 iburst >> /etc/chrony.conf
echo server time2 iburst >> /etc/chrony.conf
echo server time3 iburst >> /etc/chrony.conf
chkconfig --level 123456 ntpd off
chkconfig --level 123456 ntpdate off
service ntpd stop
chkconfig chronyd on
service chronyd restart
chronyc sources
chronyc tracking

if desired, edit /etc/chrony.conf, remove non-triumf time servers

Configure time (CentOS7)

Time server ntpd was replaced by chronyd.

yum -y install chrony
echo server time1 iburst >> /etc/chrony.conf
echo server time2 iburst >> /etc/chrony.conf
echo server time3 iburst >> /etc/chrony.conf
systemctl enable chronyd
systemctl restart chronyd
chronyc sources
chronyc tracking

if desired, edit /etc/chrony.conf, remove non-triumf time servers

Configure system updates

enable kernel updates: sed 's/^EXCLUDE=/#EXCLUDE=/' -i /etc/sysconfig/yum-autoupdate

Configure system updates (CentOS7)

yum install yum-cron
edit /etc/yum/yum-cron.conf, change:
- set apply_updates = yes

Configure system services

chkconfig --list | grep :on | sort (to see enabled services)
disable unwanted 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
chkconfig --level 12345 kdump off
chkconfig --level 12345 libvirt-guests off
chkconfig --level 12345 libvirtd off
chkconfig --level 12345 spice-vdagentd off
chkconfig --level 12345 ksm off
chkconfig --level 12345 ksmtuned off
chkconfig --level 12345 iscsi off
chkconfig --level 12345 iscsid off
chkconfig --level 12345 openct off
chkconfig --level 12345 blk-availability off
chkconfig --level 12345 fcoe off
chkconfig --level 12345 lldpad off

Configure system services (CentOS7)

systemctl list-unit-files | grep enabled | sort ### (to see enabled services)
disable unwanted services:

systemctl disable bluetooth
systemctl disable dm-event
systemctl disable dmraid-activation
systemctl disable iscsid
systemctl disable iscsi
systemctl disable iscsiuio
systemctl disable libvirtd
systemctl disable lvm2-lmetad
systemctl disable lvm2-monitor
systemctl disable ModemManager
systemctl disable multipathd
systemctl disable netcf-transaction
#systemctl disable

Erase unwanted packages

yum erase PackageKit # bugs users about security updates

Erase unwanted packages (CentOS7)

yum erase PackageKit # bugs users about security updates
yum erase perl-homedir # creates $HOME/perl5
yum erase ModemManager # thinks that all USB-attached devices are modems

Configure external package repositories

yum install elrepo-release epel-release

Configure external package repositories (CentOS7)

EPEL: (addtional packages)

yum install epel-release

ELREPO: (kernel drivers)

rpm --import https://www.elrepo.org/RPM-GPG-KEY-elrepo.org
rpm -Uvh https://www.elrepo.org/elrepo-release-7.0-2.el7.elrepo.noarch.rpm
yum -y install yum-plugin-fastestmirror

Install packages needed to continue with installation

(+CentOS7)

(these packages are sometimes missing, they are needed to follow following instructions instructions)

(SL6.5: libotf is a dependancy of emacs - SL6.5 installer fails to install it)

yum install ed patch wget git libotf gdisk emacs

Configure TRIUMF packages

(only for machines on the TRIUMF network)

(TRIUMF kickstart usually installs this automatically)

rpm -vh --install  http://mirror.triumf.ca/triumf/6/x86_64/Packages/triumf-release-1.4-1.noarch.rpm
yum install triumf-ssh triumf-syslog

Configure TRIUMF packages (CentOS7)

(only for machines on the TRIUMF network)

# TL Was rpm -vh --install http://mirror.triumf.ca/triumf/6/x86_64/RPMS/triumf-release-1.4-1.noarch.rpm
rpm -vh --install  http://mirror.triumf.ca/triumf/6/x86_64/Packages/triumf-release-1.4-1.noarch.rpm
yum install triumf-ssh triumf-syslog

Configure Konstantin's scripts

(+Centos7)

mkdir ~root/git
cd ~root/git
git clone http://ladd00.triumf.ca/~olchansk/git/scripts.git
cd scripts
git pull

Configure TRIUMF mirror of yum repositories

(only for machines on TRIUMF network)

if /daq/mirror is available: /bin/cp ~/git/scripts/etc/daq-mirror-SL6.repo /etc/yum.repos.d/
if /triumfcs/mirror is available: /bin/cp ~/git/scripts/etc/triumfcs-mirror-SL6.repo /etc/yum.repos.d/
otherwise: /bin/cp ~/git/scripts/etc/triumf-SL6.repo /etc/yum.repos.d/

Configure trusted ssh keys

(+CentOS7)

ssh localhost
interrupt by Ctrl-C
/bin/cp ~/git/scripts/etc/authorized_keys ~/.ssh/

Configure hardware sensors

yum install lm_sensors kmod-k10temp kmod-coretemp
sensors-detect (accept default answer to all questions - press ENTER)
service lm_sensors restart (to reload the kernel modules)
sensors (to see available sensors)

If no sensors are detected by standard drivers, follow motherboard-specific instructions at the bottom of this page.

Configure coretemp CPU sensors

On some machines, the coretemp driver for Intel CPU temperature sensors is not loaded after the above steps.

sensors | grep coretemp ### number of sensors reported should be the same as the number of CPU cores
if output is blank, add this to /etc/rc.local

emacs -nw /etc/rc.local
modprobe coretemp

Configure IPMI sensors

Some machines support the IPMI interface for monitoring the hardware: fan speeds, temperatures, voltages.

find out if IPMI is supported. Try this:

dmidecode | grep -i ipmi

if output is not blank, IPMI is maybe supported.

install and enable IPMI software:

yum install "OpenIPMI*" ipmitool
service ipmi start
ipmitool sensor ### to confirm IPMI is present. If output is blank, do not go further.
chkconfig ipmi on
chkconfig ipmievd on
service ipmi restart
service ipmievd restart
tail -100 /var/log/messages ### look at messages logged by ipmievd

(CentOS7) install and enable IPMI software:

yum install "OpenIPMI*" ipmitool
systemctl start ipmi
ipmitool sensor ### to confirm IPMI is present. If output is blank, do not go further.
--- unfinished...
chkconfig ipmi on
chkconfig ipmievd on
service ipmi restart
service ipmievd restart
tail -100 /var/log/messages ### look at messages logged by ipmievd

if ipmievd complains about SEL buffer overflow, clear it manually:

ipmitool sel list ### show ipmi messages in raw format
ipmitool sel elist ### show ipmi messages in useful format
ipmitool sel elist > file ### save ipmi messages into a file
ipmitool sel clear  ### clear all accumulated ipmi messages

useful ipmi commands:
- ipmitool sensor -- read hardware sensors
- ipmitool sel elist -- report all accumulated messages

Configure SMARTD (CentOS7)

edit /etc/smartmontools/smartd.conf
in the DEVICESCAN line, remove the "-M exec ..." switch, the file should read something like this:

#DEVICESCAN -H -m root -M exec /usr/libexec/smartmontools/smartdnotify -n standby,10,q 
DEVICESCAN -H -m root -n standby,10,q

edit /etc/smartmontools/smartd_warning.sh
in the line "export SMARTD_SUBJECT", add ":$SMARTD_DEVICE" after "$hostname", it should read something like this:

export SMARTD_SUBJECT="SMART error (${SMARTD_FAILTYPE-[SMARTD_FAILTYPE]}) detected on host: $hostname:$SMARTD_DEVICE"

run: smartd -q onecheck
if there are smart warnings, email should be sent to root (and forwarded according to ~root/.forward)

Enable User Disk Quotas (OPTIONAL)

read http://docs.redhat.com/docs/en-US/Red_Hat_Enterprise_Linux/6/html/Storage_Administration_Guide/ch-disk-quotas.html
emacs -nw /etc/fstab, add "grpquota,usrquota" to filesystem options, e.g.:

[root@isdaq00 home1]# grep quota /etc/fstab
UUID=5a2aefbd-45db-475e-841e-12ec89220fbd /home1 ext4 defaults,grpquota,usrquota 1 2

cd /; umount /home1; mount /home1
quotacheck -cug /home1
quotacheck -avug
quotaon -av
quota system is now active
increase the soft quota time limit from default 7days to 30 or 60 days: edquota -t
set quotas for all users (see below)
setup warnquota:
- create warnquota config file: emacs -nw /etc/warnquota.conf

# values can be quoted:
MAIL_CMD        = "/usr/sbin/sendmail -t"
FROM            = root
SUBJECT         = User %i@%h exceeded allocated disk quota
CC_TO           = "root"
# If you set this variable CC will be used only when user has less than
# specified grace time left (examples of possible times: 5 seconds, 1 minute,
# 12 hours, 5 days)
# CC_BEFORE = 2 days
SUPPORT         = "root"
# Text in the beginning of the mail (if not specified, default text is used)
# This way text can be split to more lines
# Line breaks are done by '|' character
# The expressions %i, %h, %d, and %% are substituted for user/group name,
# host name, domain name, and '%' respectively. For backward compatibility
# %s behaves as %i but is deprecated.
MESSAGE         = User "%i" on "%h" has exceeded the allocated disk quota.||Please delete any unnecessary files on following filesystems or|contact the system administrato
r to increase your quota allocation:|
SIGNATURE       = --|automated email from warnquota

- note that %i@%h in the SUBJECT line do not seem to work
- create cron job: emacs -nw /etc/cron.daily/warnquota

#!/bin/sh
warnquota
#end

- chmod a+x /etc/cron.daily/warnquota
- touch /etc/crontab

Useful commands for managing quotas:

repquota -a | sort -n -k3 ### show quota of all users sorted by disk usage
edquota -u username ### open "vi" editor to change user quotas
repquote -a | grep username ### report quota for given user
setquota -u username 0 0 0 0 /home1 ### disable quotas for given user
setquota -u username 50000000 100000000 0 0 /home1 ### set quotas for 50GB soft and 100GB hard
edquota -t ### change user quota time limits
edquote -tg ### change group quota time limits

Enable NFS server (CentOS7)

create /etc/exports. example:

/home1  @home_export(rw,no_root_squash,async)
/data1  @data_export(rw,no_root_squash,async)

check the netgroup file
- if using NIS: check NIS netgroup: ypcat -k netgroup
- if no NIS, create /etc/netgroup: @daqmachines (deap00,,) (deap01,,) (deap02,,)
- if no NIS, edit /etc/nsswitch.conf, make the netgrooup line read: "netgroup: files"
enable things, start them:

firewall-cmd --permanent --add-service=nfs
firewall-cmd --reload
firewall-cmd --list-all
systemctl enable nfs-server
systemctl start nfs-server
systemctl status nfs

Enable NFS V3 server

edit /etc/hosts.allow, add or uncomment "mountd: 142.90.0.0/255.255.0.0"
create /etc/exports. example:

/home1  @home_export(rw,no_root_squash,async)
/data1  @data_export(rw,no_root_squash,async)

check the netgroup file
- if using NIS: check NIS netgroup: ypcat -k netgroup
- if no NIS, create /etc/netgroup: @daqmachines (deap00,,) (deap01,,) (deap02,,)
- if no NIS, edit /etc/nsswitch.conf, make the netgrooup line read: "netgroup: files"
chkconfig nfs on
chkconfig nfslock on
service nfs restart

Then on ladd00 need to do

ssh to root@ladd00
edit /etc/auto.daq to add new machine...
make -C /var/yp

Enable NFS V4 SERVER (SL6)

if used with NIS, same as NFSv3
if used as standalone, need to edit idmapd.conf - set the "Domain" name to the same value on NFS server and NFS slave (default automagically determined value does not always work). More TBW.

Enable AMANDA backups

AMANDA backups are already enabled by TRIUMF kickstart installs. For non-kickstart installation, follow instructions at [http://amanda/~amanda], or look at "/triumfcs/trshare/olchansk/linux/amanda/amanda-enable.perl". As final step, use [https://helpdesk.triumf.ca] to contact TRIUMF CS to add this new machine to the amanda backup list.

yum install triumf-amanda

Enable DCACHE

DAQ dcache server is mounted as

/daq/pnfs/triumf.ca/data/

This instructions are unnecessary

# mkdir -p /pnfs
# edit /etc/rc.local, add to the end of file: "mount -o intr,rw,noac,hard,nfsvers=3 trdata00:/pnfs /pnfs &"
# . /etc/rc.local

For more information on, see TrdataDcache dcache page.

Configure Ganglia

SL4 Ganglia instructions (KO ganglia-3.2)

cd /triumfcs/trshare/olchansk/linux/ganglia-3.2/SL4-32 #### or SL4-64 for 64-bit machines
rpm -vh --install apr*.rpm
rpm -vh --upgrade lib*.rpm ganglia*.rpm
/bin/rm /etc/gmond.conf
scp ladd00:gmond.conf /etc/ganglia/gmond.conf
chkconfig gmond on
service gmond restart

SL5 Ganglia instructions (KO ganglia-3.2)

cd /triumfcs/trshare/olchansk/linux/ganglia-3.2/SL5-64 #### or SL5-32 for 32-bit machines
yum install libconfuse
rpm -vh --upgrade lib*.rpm ganglia*.rpm
yum erase ganglia
/bin/rm /etc/gmond.conf
scp ladd00:gmond.conf /etc/ganglia/gmond.conf
chkconfig gmond on
service gmond restart

SL6 Ganglia instructions (EPEL6 ganglia-3.1)

/bin/rm /etc/gmond.conf
yum install "*gmond*"
/bin/rm /etc/ganglia/conf.d/ganglia-triumf-daq.conf
cp ~/git/scripts/etc/gmond.conf /etc/ganglia/gmond.conf
chkconfig gmond on
service gmond restart

SL6 Ganglia instructions (EPEL6 ganglia-3.7.1)

/bin/rm /etc/gmond.conf
yum install "*gmond*"
/bin/rm /etc/ganglia/conf.d/ganglia-triumf-daq.conf
/bin/cp -v /dev/null /etc/ganglia/conf.d/multicpu.conf
/bin/cp -v /dev/null /etc/ganglia/conf.d/netstats.conf
/bin/cp ~/git/scripts/etc/gmond.conf /etc/ganglia/gmond.conf
chkconfig gmond on
service gmond restart

Configure Ganglia (Centos7)

CentOS7 Ganglia instructions (EPEL6/KO ganglia-3.7.1)

/bin/rm /etc/gmond.conf
yum -y install libconfuse
#yum install "*gmond*"
# or use http://daqshare.triumf.ca/~olchansk/ganglia-3.7.1/CentOS7
cd /daq/daqshare/olchansk/public_html/ganglia-3.7.1/CentOS7
rpm -vh --install ganglia-3.7.1-1.el7.centos.x86_64.rpm ganglia-gmond-3.7.1-1.el7.centos.x86_64.rpm ganglia-gmond-python-3.7.1-1.el7.centos.x86_64.rpm
/bin/rm /etc/ganglia/conf.d/multicpu.conf
/bin/touch /etc/ganglia/conf.d/multicpu.conf
/bin/cp ~/git/scripts/etc/gmond.conf /etc/ganglia/gmond.conf
systemctl enable gmond
systemctl start gmond
systemctl status gmond

Configure TRIUMF DAQ packages

(+CentOS7)

cd /etc/yum.repos.d
wget http://daq.triumf.ca/~daqweb/yum/triumf-daq.repo

Install Konstantin's packages

(+CentOS7)

yum --disablerepo=\* --enablerepo=triumf-daq --skip-broken install diskscrub emailonreboot monitor_nfs "ganglia-*" triumf_nodeinfo

Install memtest and PXE boot

cd /boot
wget http://ladd00.triumf.ca/tftpboot/memtest86+-5.01.bin.gz
wget http://ladd00.triumf.ca/tftpboot/memtest86+-4.20.bin.gz
wget http://ladd00.triumf.ca/tftpboot/memtest86+-4.10
wget http://ladd00.triumf.ca/tftpboot/gpxe-1.0.1+-gpxe.lkrn

emacs -nw /boot/grub/grub.conf
title memtest86+-5.01
      root (hd0,0)
      kernel /boot/memtest86+-5.01.bin.gz
title memtest86+-4.20
      root (hd0,0)
      kernel /boot/memtest86+-4.20.bin.gz
title memtest86+-4.10
      root (hd0,0)
      kernel /boot/memtest86+-4.10
title pxeboot
      root (hd0,0)
      kernel /boot/gpxe-1.0.1+-gpxe.lkrn

Install node monitoring

(+CentOS7)

yum --disablerepo=\* --enablerepo=triumf-daq --skip-broken install triumf_nodeinfo
/usr/sbin/sendnodeinfo.perl --config ladd00.triumf.ca:8600
emacs -nw /etc/nodeinfo
/usr/sbin/sendnodeinfo.perl ladd00.triumf.ca:8600

Install latest system updates

(+CentOS7)

yum update -y

Configure TRIUMF Printers

chkconfig cups off
service cups stop
yum install triumf-printers

Install packages needed for QUARTUS, ROOT, EPICS and MIDAS DAQ

(+CentOS7)

yum install --skip-broken giflib.x86_64 sysstat "libusb-devel*" unixODBC-devel postgresql-devel libxml2-devel libXpm-devel libgfortran git compat-readline43 "graphviz*" dcap "tigervnc*" telnet glibc"*" strace "fftw*" libpng "freetype*" xpdf "xemacs*" tkcvs xterm mutt "*g77*" joe "libXmu*" dcap-devel gsl-devel pcre-devel h5py gd-devel xorg-x11-fonts"*" minicom xfig"*" perl-BSD-Resource "net-snmp-*" readline-static git-all nasm imake tcl-devel gv xorg-x11-twm expat-devel screen compat-readline5 ImageMagick ImageMagick-devel wget alacarte scipy numpy nedit gnuplot php-cli php-domxml-php4-php5 php-gd php-fpdf php-cli kdebase cmake tcpdump sqlite sqlite-devel kdegraphics gdisk lsof gconf-editor iftop tk-devel mcelog kdm blt itcl lz4 bzip2 pbzip2 apr-devel apr-util-devel

(do not install boost on 32-bit machines)

yum install --skip-broken "boost-*"

(packages for 32-bit software compilation on 64-bit machines. this is optional)

yum install --skip-broken giflib.i386 giflib.i686 compat-libf2c-34.i386 compat-libf2c-34.i686 mysql-devel.i686 openssl-devel.i686 unixODBC-devel.i686 libstdc++-devel.i386 libstdc++-devel.i686 "zlib-*.i686" "libXext-*.i686" "libXtst-*.i686" glibc-static.i686 freetype.i686 fontconfig.i686 libpng.i686 libXrender.i686 glibc-devel.i686 libX11-devel.i686 libXpm-devel.i686 libXft-devel.i686 mysql-devel.i686 dcap-devel.i686 gsl-devel.i686 pcre-devel.i686 fontconfig-devel.i686 freetype-devel.i686 libpng-devel.i686 libjpeg-devel.i686 libgfortran.i686 libxml2-devel.i686 gd-devel.i686 readline-devel.i686 ncurses-devel.i686 libXdmcp.i686 readline-static.i686 compat-readline5.i686

yum install boost-devel.i686

(separately install these packages - they collide with the big bunch above)

yum install rdesktop

yum reinstall urw-fonts

Remove unnecessary packages

This is optional. Only do this if reducing the size of the OS image is very important.

yum erase "texlive*" "java*" "boost*"

Install SMART scripts

(+CentOS7)

ln -sf ~/git/scripts/smart-status/smart-status.perl ~/

Install NTFS drivers

yum install ntfs-3g ntfsprogs (from EPEL)

Install Google Chrome web browser (64-bit SL6)

rpm -vh --install /triumfcs/trshare/olchansk/linux/google-chrome/google-chrome-stable-27.0.1453.110-202711.x86_64.rpm
sed 's/enabled=.*/enabled=0/' -i /etc/yum.repos.d/google-chrome*.repo

Install Google Chrome web browser (64-bit CentOS7)

create yum repo with following contents: emacs -nw /etc/yum.repos.d/google-chrome-64.repo

[google-chrome-64]
name=google-chrome - 64-bit
baseurl=http://dl.google.com/linux/chrome/rpm/stable/x86_64
enabled=1
gpgcheck=1
gpgkey=https://dl-ssl.google.com/linux/linux_signing_key.pub

yum install google-chrome-stable

Enable 100dpi fonts for EPICS

(+CentOS7)

ln -s /usr/share/X11/fonts/100dpi /etc/X11/fontpath.d/

Disable gdm and X11 (OPTIONAL)

initctl stop prefdm
echo "start on never" > /etc/init/prefdm.override
echo "start on never" > /etc/init/splash-manager.override
initctl reload-configuration

then enable login on default console:

echo "plymouth quit" >> /etc/rc.local
echo "X_TTY=xxx/dev/tty1" >> /etc/sysconfig/init

Install JAVAWS (OPTIONAL)

to run Java "web start" jnlp files (EVO, SEEVOGH, etc): javaws Downloads/spider.jnlp
install javaws:
yum install icedtea-web icedtea-web-javadoc

Install firefox java plugin (OPTIONAL, DO NOT DO THIS)

This installs the Oracle Java plugin:

rpm -vh --install ~deap/jdk-7u15-linux-x64.rpm
ls -l /usr/lib64/mozilla/plugins/
ln -s /usr/java/jdk1.7.0_15/jre/lib/amd64/libnpjp2.so /usr/lib64/mozilla/plugins/
start firefox, go edit->preferences->general->manage add-ons->plugins
"java plugin 1.7.0_15" should be listed

Install SKYPE (OPTIONAL)

on SL6
yum install alsa-lib.i686 libXv.i686 libXScrnSaver.i686 glib2.i686 libtiff.i686
ln -s /usr/lib/libtiff.so.3 /usr/lib/libtiff.so.4
download skype_staticQT-4.0.0.8 ("linux static Qt" choice), untar, cd into it
"ldd ./skype" to confirm that all required shared libraries are installed
./skype

Configure USB device permissions

Configure USB device permissions for user access to USB-serial devices, Altera USB Blaster, etc.

create file /etc/udev/rules.d/99-usb-chmod.rules with this contents:

emacs -nw /etc/udev/rules.d/99-usb-chmod.rules
ACTION=="add", SUBSYSTEM=="usb_device", RUN+="/bin/chmod a+wr /dev/%c"
ACTION=="add", SUBSYSTEM=="usb_device", RUN+="/bin/chmod a+wr /proc/%c"
ACTION=="add", ENV{DEVTYPE}=="usb_device", RUN+="/bin/chmod a+wr $env{DEVNAME}"
ACTION=="add", ENV{DEVTYPE}=="usb_device", RUN+="/bin/chmod a+wr $env{DEVICE}"
ACTION=="add", ENV{PHYSDEVBUS}=="usb-serial", RUN+="/bin/chmod a+wr $env{DEVNAME}"
ACTION=="add", ENV{DEVPATH}=="/class/tty/ttyS*", RUN+="/bin/chmod a+wr $env{DEVNAME}"
ACTION=="add", SUBSYSTEM=="tty", DEVPATH=="*ttyUSB*", RUN+="/bin/chmod a+rw $env{DEVNAME}"
ACTION=="add", SUBSYSTEM=="tty", DEVPATH=="*ttyS*", RUN+="/bin/chmod a+rw $env{DEVNAME}"

apply new permissions: udevadm trigger --action=add

Disable modem-manager

The modem-manager will try to talk to any serial devices attached to USB serial ports. It assumes that those devices are modems and will send out modem-specific commands. if the devices are not modems and do not understand or do not like modem commands, well that's too bad. modem-manager is installed by the ModemManager package required by the NetworkManager package, and there is no configuration setting to turn modem-manager off.

One way to disable it is: chmod a= /usr/sbin/modem-manager

Another way to disable it is by forced uninstall: rpm --erase --nodeps ModemManager

Remember to kill the running copy: killall -KILL modem-manager

Caveat: it is not clear if modem-manager would not be resurrected by an update to the NetworkManager or ModemManager packages.

Configure Altera jtagd

(if needed)

mkdir /etc/jtagd
echo 'Password = "123";' > /etc/jtagd/jtagd.conf
cp -pv /triumfcs/trshare/olchansk/altera/11.0/quartus/linux/pgm_parts.txt /etc/jtagd/jtagd.pgm_parts

start local jtagd: /triumfcs/trshare/olchansk/altera/11.0/quartus/bin/jtagd
test local connection: /triumfcs/trshare/olchansk/altera/11.0/quartus/bin/jtagconfig
test remote connection (add this machine to your .jtag.conf, run jtagconfig

For more information, go to Quartus

(OBSOLETE) Configure packages

yum install xpdf "xemacs*" tkcvs xterm mutt "*g77*" joe "libXmu*"
(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
yum update

Configure GRUB boot loader

edit /boot/grub/grub.conf, remove the "quiet" and "rhgb" options
edit /boot/grub/grub.conf, comment out (with "#") the "splashimage=" line
check that GRUB boot loader is installed on all system disks:
- dd if=/dev/sda bs=1 count=1024 2>&1 | strings | grep GRUB
- dd if=/dev/sdb bs=1 count=1024 2>&1 | strings | grep GRUB
if GRUB is not installed, (i.e. on the 2nd disk of machines with mirrored system disk), (but check that /dev/sdb is the right disk):

# grub
grub> device (hd0) /dev/sdb
grub> root (hd0,0)
grub> setup (hd0)

Configure GRUB boot loader (CentOS7)

edit /etc/default/grub, remove the "quiet" and "rhgb" options
(maybe) grub2-install /dev/sda
check that GRUB boot loader is installed on all system disks:
- dd if=/dev/sda bs=1 count=1024 2>&1 | strings | grep GRUB
- dd if=/dev/sdb bs=1 count=1024 2>&1 | strings | grep GRUB
if GRUB is not installed, (--- unfinished)

Disable ELREPO

sed 's/enabled=.*/enabled=0/' -i /etc/yum.repos.d/elrepo_triumf.repo
sed 's/enabled=.*/enabled=0/' -i /etc/yum.repos.d/elrepo.repo

Special hardware settings

ASUS Crosshair mobo

use BIOS version 1207 or newer
(before CentOS7) sensors need these drivers from ELREPO: yum install --noplugins kmod-it87 kmod-k10temp; sensors-detect; service lm_sensors restart; sensors
CentOS7: installs correct drivers automatically

ASUS Crosshair-II mobo

use BIOS version 2607 or newer
for the onboard IDE to work, add "all-generic-ide" to kernel boot options in grub.conf
sensors need these drivers from ELREPO: yum install --noplugins kmod-it87 kmod-k10temp; sensors-detect; service lm_sensors restart; sensors

ASUS P7P55D EVO mobo

use BIOS version 2004 or newer
SL6 - install special driver for on board PCIe GigE network port and disable on board PCI GigE network port:
- yum --enablerepo elrepo install kmod-r8168 kmod-r8169
- # do not do this: sed 's/^blacklist/#blacklist/' -i /etc/modprobe.d/blacklist-r8169.conf
- reboot
- verify that correct drivers are loaded: ethtool -i eth0; ethtool -i eth1
- note: there will be no eth1 - r8169 driver is disabled.

ASUS P6X58-E-WS mobo

BIOS settings
- F1 or DEL to enter BIOS setup, F8 boot menu
- go to POWER->HW mon, confirm CPU temperature is around 30C. (heatsink is installed correctly. Bad heatsink temperature quickly goes up to 50-70C).
- Main menu: Storage config - SATA change IDE->AHCI
- System information: confirm BIOS version 301, CPU type, memory size
- AI Tweak: set DRAM frequency - AUTO->DDR3-1333
- Advanced->Onboard devices: LAN BOOT: enabled
- Power->HW monitor: CPU Q-FAN: enabled
- Boot->Settings: Quick boot: enabled; Full screen logo: disabled; Wait for F1: disabled
- Save and exit

ASUS E35M1-M PRO mobo

http://www.asus.com/Motherboards/E35M1M_PRO/#specifications
use BIOS version 1002 or newer
for CPU temperature: install kmod-k10temp from ELREPO (kmod-k10temp-0.0-4.el6.elrepo.x86_64.rpm)
for Sensors: yum --enablerepo elrepo install kmod-w83627ehf; modprobe w83627ehf; sensors
for Graphics: yum --enablerepo elrepo install kmod-fglrx fglrx-x11-drv
to enable booting from USB3, edit /etc/dracut.conf, change line "add_drivers" to read: add_drivers+="xhci-hcd"
to use multiple monitors, run "aticonfig --initial --heads=2 --adapter=1 --xinerama=on", to change screen layout, edit /etc/X11/xorg.conf. Only dual monitors DVI+HDMI seem to work. Tripple monitors does not seem to work.

Sensors instructions below are obolete (use driver from ELREPO)

for Sensors, install driver for NCT6776F chip from https://github.com/groeck/w83627ehf/archives/master (in the Makefile, change the line "KERNEL_BUILD=" to read: "KERNEL_BUILD:=/usr/src/kernels/$(TARGET)"):

cd ~root
wget http://ladd00.triumf.ca/~olchansk/linux/groeck-w83627ehf-dd3e543/w83627ehf.ko
echo "modprobe hwmon; modprobe hwmon-vid; modprobe k10temp; rmmod w83627ehf; insmod /root/w83627ehf.ko" >> /etc/rc.local

ASUS E45M1-M PRO mobo

https://www.asus.com/Motherboards/E45M1M_PRO/#specifications
use BIOS 1202 or newer
follow the E35M1-M PRO instructions above

ASUS P9X79 WS

http://www.asus.com/Motherboard/P9X79_WS/
use BIOS version 3101, 3401 or newer. If BIOS is 1305 or older, install P9X79-WS-CAP-Converter.ROM (BIOS 2902/3101), then the new BIOS.
for CPU temperature, install coretemp
for sensors, install driver for NCT6776F chip same as E35M1-M above.
BIOS Settings:
- enter "Advanced mode"
- Ai Tweaker -> Ai Overclock Tuner -> Set to "XMP" - this enables DDR3-1600 RAM speed vs DDR3-1333 by default
- Monitor -> CPU fan speed low limit -> Set to "200 RPM" - we are using high efficiency slow turning CPU coolers and the default 600 RPM is right on the edge of firing false warnings
- Boot -> Full screen logo -> Set to "disabled"
- Wait for F1 -> Set to "disabled"

ASUS P8B-M

use BIOS version 6103 or newer
for CPU temperature, install coretemp
for sensors, install driver for NCT6776F chip same as E35M1-M above.

SUPERMICRO

(use "dmidecode | more" to read mobo model number)

X9SCL

yum install kmod-w83627ehf.x86_64 coretemp
xemacs -nw /etc/rc.local, add:

modprobe coretemp
modprobe w83627ehf

ASUS Z87-WS

cd ~root
wget http://ladd00.triumf.ca/~olchansk/linux/nct6775/nct6775.ko

Place the modprobe and insmod lines in /etc/rc.local to load the drivers at boot time

modprobe hwmon-vid
insmod /root/nct6775.ko

ASUS AM1M-A

use BIOS 602 or later
SL6.5 installer cannot use USB2 ports and the network. Use USB3 ports (blue colour) to boot USB installer (memtest, rescue, etc)
SL6.5 kernels require boot option "iommu=soft" or USB2 and network do not work. (USB3 - blue ports - seems okey)
install ATI/AMD video drivers from ELREPO (see below)
sensors chip is ITE IT8623E, use standalone driver from lm_sensors. (2 fans rpm, 2 temperatures):

cd ~root
wget http://ladd00.triumf.ca/~olchansk/linux/it87.ko
echo modprobe hwmon_vid >> /etc/rc.local
echo insmod /root/it87.ko >> /etc/rc.local
sensors-detect
sensors

AMD "Athlon(tm) 5350 APU" graphics supports 2 monitors maximum (mobo has 3 video outputs, only 2 can be used together)

Intel SE7230NH1

front panel header connector pinout is like this:

PWR LED | 1  2|
        | 3  4|
PWR LED | 5  6|
HDD LED | 7  8|
HDD LED | 9 10|
PWR SW  |11 12| NIC1 LED
PWR SW  |13 14| NIC1 LED
RST SW  |15 16|
RST SW  |17 18|
        |19 20|
NMI SW  |21 22| NIC2 LED
NMI SW  |23 24| NIC2 LED
...     |...  |
        |33 34|

Configure X11 graphics

Special settings for DAQ

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

Install NVIDIA drivers

yum --enablerepo=elrepo install nvidia-detect
run: nvidia-detect
as instructed by nvidia-detect, install correct driver:
- yum --enablerepo=elrepo install kmod-nvidia
- yum --enablerepo=elrepo install kmod-nvidia-304xx
- yum --enablerepo=elrepo install kmod-nvidia-173xx
(before SL6.x: if it fails due to conflict with module-init-tools, run "yum --disablerepo \* --enablerepo elrepo update module-init-tools")
yum erase xorg-x11-glamor ### see http://elrepo.org/tiki/kmod-nvidia (search for glamor)
mv /etc/X11/xorg.conf /etc/X11/xorg.conf-xxx
nvidia-xconfig
(SL6) reboot
(SL5) /dev/MAKEDEV nvidia
(SL5) restart the X11 server (Ctrl-Alt-Backspace or "killall Xorg gdm-binary")
observe that X11 server restarts using the NVIDIA driver (big NVIDIA logo on startup)
if needed, login as root and run "nvidia-settings" to setup dual-screen configuration, etc

Install legacy NVIDIA drivers

For old NVIDIA cards:

GeForce FX 5500

wget http://us.download.nvidia.com/XFree86/Linux-x86/173.14.31/NVIDIA-Linux-x86-173.14.31-pkg1.run
sh ./NVIDIA-Linux-x86-173.14.31-pkg1.run

GeForce 6200 - NVIDIA Corporation NV44A [GeForce 6200]

yum install nvidia-x11-drv-304xx-304.121 --enablerepo=elrepo
nvidia-xconfig
rmmod nvidia
killall gdm-binary
login as root
nvidia-settings to setup multiple displays

Install ATI/AMD drivers

yum --enablerepo elrepo install kmod-fglrx fglrx-x11-drv
check that /etc/X11/xorg.conf section "Device" entry "Driver" says "fglrx"
run "amdcccle" as root to configure dual-screens, etc

 Note: 'amdcccle' is a GUI, so you must run this command from within a running X session

killall Xorg

Install Intel drivers for HD4600/Z87

SL6.5 has the required drivers for the socket 1150 machines with Intel HD4600 graphics and Z87 chipset.

ASUS Z87 WS motherboard has these video connections with corresponding Intel video port assignements, as reported by "xrandr":

DisplayPort - DP1/HDMI1
MiniDisplayPort - DP2/HDMI2
HDMI - HDMI3

Due to hardware limitations, 3 HDMI monitors using 2 passive DP-HDMI adapters (and 1 straight HDMI) cannot be used.

To use 3 monitors do this:

1st monitor: DisplayPort - DP-to-HDMI-passive-adapter - HDMI monitor (not tried: DP-to-DP-cable - DisplayPort monitor).
2nd monitor: MiniDisplayPort - MiniDP-to-DP-cable - DisplayPort monitor
3rd monitor: HDMI - HDMI-cable - HDMI monitor

With the monitors I have (Dell 1920x1200 VGA-HDMI-DP), the software thinks that there are 4 monitors: somehow both DP2 and HDMI2 see 1 minitor each, but the hardware cannot drive 4 monitors, so everything goes blank. To fix, disable HDMI2 (xrandr -display :0 --output HDMI2 --off) and enable DP2 (xrandr -display :0 --output DP2 --auto).

How to make this configuration permanent and how to assign monitor locations (left-right, etc), you figure it out.

Manual selection of monitor, video mode and resolution

Automatic selection of monitor and video mode usually works. When it does not, configure it manualls:

physically go to the computer
login as root
run "nvidia-settings" on machines using the NVIDIA driver
run "aticonfig" on machines with the ATI/AMD driver (use "aticonfig --initial" for initial setup, and good luck with anything more complicated)
run "system-config-display".
- In the "hardware" tab, select monitor type: "generic LCD 1280x1024" or "generic LCD 1600x1200".
- In the "settings" 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.

Disable screen saver

If machine is booted without any monitor connected, current video cards to not enable any video outputs. If a monitor is connected later, there is no video image and there is no easy way to get a video image.

This can be solved by configuring X11 to always enable some video output. Because the monitor type is not known when X11 starts, one has to select some standard video mode (i.e. VESA 1280x1024) on some video output (VGA, DVI or HDMI).

Only NVIDIA cards with the NVIDIA driver (from EPEL) is supported by these instructions.

create default xorg.conf: nvidia-xconfig
edit /etc/X11/xorg.conf
add monitor section for the fake monitor:

Section "Monitor"
    Identifier     "Monitor0"
    VendorName     "Unknown"
    ModelName      "Unknown"
    HorizSync       31.0 - 83.0
    VertRefresh     59.0 - 61.0
    Option         "DPMS" "off"
    ModeLine "1280x1024"   108.00   1280 1328 1440 1688   1024 1025 1028 1066 +hsync +vsync
EndSection

add output selection in the "Device" section:

Section "Device"
    Identifier     "Device0"
    Driver         "nvidia"
    VendorName     "NVIDIA Corporation"
    BoardName      "GeForce 210"
    #Option "ConnectedMonitor" "DFP"
    #Option "ConnectedMonitor" "CRT"
    Option "ConnectedMonitor" "CRT-1"
    Option "UseEDID" "no"
EndSection

add fake video mode to the "Screen" section:

Section "Screen"
    Identifier     "Screen0"
    Device         "Device0"
    Monitor        "Monitor0"
    DefaultDepth    24
    SubSection     "Display"
        Depth       24
        Modes       "1280x1024"
    EndSubSection
EndSection

disable screen saver and DPMS power off in the "ServerLayout" or "ServerFlags" section:

Section "ServerLayout"
    Identifier     "Layout0"
    Screen      0  "Screen0" 0 0
    InputDevice    "Keyboard0" "CoreKeyboard"
    InputDevice    "Mouse0" "CorePointer"
    Option         "Xinerama" "0"
    Option         "BlankTime" "0"
    Option         "StandbyTime" "0"
    Option         "SuspendTime" "0"
    Option         "OffTime" "0"
EndSection

Section "ServerFlags" 
    Option         "BlankTime" "0" 
    Option         "StandbyTime" "0" 
    Option         "SuspendTime" "0" 
    Option         "OffTime" "0" 
EndSection

Finish installation

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

Configure large RAID6 arrays

connect the disks
check the disks health
- run smart-status.perl
partition the disks
- yum install gdisk
- gdisk /dev/sdX
- delete all partitions: o
- create new partition: n, enter, enter, enter, fd00 (default sizes, partition type fd00)
- write and exit: w
check presence of all partitions:
- /bin/ls -l /dev/sd*1
prepare to use an external bitmap file
- touch /md6bitmap
- edit /etc/fstab, change entry for root filesystem from: "defaults 1 1" to "defaults 0 0"
- edit /boot/grub/grub.conf, change entry "kernel ... ro ..." to "kernel ... rw ..."
create raid array:
- mdadm --create /dev/md6 --level=6 --bitmap=/md6bitmap --raid-devices=10 /dev/sd[b-k]1
- mdadm -Ds >> /etc/mdadm.conf
- cleanup /etc/mdadm.conf
- echo "echo 16384 > /sys/block/md6/md/stripe_cache_size" >> /etc/rc.local
- echo "echo 1 > /sys/block/md6/md/sync_speed_min" >> /etc/rc.local
- source /etc/rc.local
observe raid array rebuild:
- watch -d -n1 "cat /proc/mdstat"

performance notes

Individual disks:

WDC WD40EZRX-00SPEB0 - write rate: 150->70 Mbytes/sec

Raid arrays:

4xWD40EZRX RAID5 Z87 88SE9230, 88SE9485: raw: read: 420 M/sec, write: ~400 M/s. xfs: read/write: 400->300 M/s (10min avg)
6xWD40EZRX RAID6 Z87 1x88SE9485: raw: .... xfs: write /dev/null 600->300 M/s, 443 M/s ave across 17TB, xfs read: 550->??? M/s, 440 M.s ave across 17TB, strip_cache_size 32k.

Revision as of 15:44, 23 November 2015 (view source) Olchansk (talk \| contribs) m (→‎performance notes) ← Older edit		Revision as of 16:18, 25 November 2015 (view source) Olchansk (talk \| contribs) m (→‎performance notes) Newer edit →
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	* 4xWD40EZRX RAID5 Z87 88SE9230, 88SE9485: raw: read: 420 M/sec, write: ~400 M/s. xfs: read/write: 400->300 M/s (10min avg)		* 4xWD40EZRX RAID5 Z87 88SE9230, 88SE9485: raw: read: 420 M/sec, write: ~400 M/s. xfs: read/write: 400->300 M/s (10min avg)
	* 6xWD40EZRX RAID6 Z87 1x88SE9485: raw: .... xfs: write /dev/null 600->300 M/s, 443 M/s ave across 17TB, xfs read: 550->??? M/s, strip_cache_size 32k.		* 6xWD40EZRX RAID6 Z87 1x88SE9485: raw: .... xfs: write /dev/null 600->300 M/s, 443 M/s ave across 17TB, xfs read: 550->??? M/s, 440 M.s ave across 17TB, strip_cache_size 32k.