About Ubuntu

AAA

Ubuntu version

lsb_release -a
uname -a

Ubuntu installer

download the latest Ubuntu LTS desktoip installer iso image
dd the image to a USB key
boot from USB key in legacy mode (NOT UEFI - may have to select this in the BIOS boot menu - F8 for ASUS, F11 for Supermicro)
follow the instruction
create user "wheel" with the usual root password
run through the installation, reboot
login as user wheel
open terminal, run "sudo /bin/bash", enter the root password, you now have the root shell
run nm-connection-editor to configure the network
after network is up (can ping ladd00), continue with post-installation steps below

Install instructions

prepare

apt-get update
apt-get upgrade

install time synchronization

apt-get -y install chrony
echo server time1 iburst >> /etc/chrony/chrony.conf
echo server time2 iburst >> /etc/chrony/chrony.conf
echo server time3 iburst >> /etc/chrony/chrony.conf
systemctl disable systemd-timesyncd.service
systemctl stop systemd-timesyncd.service
systemctl disable ntp
systemctl stop ntp
systemctl enable chrony
systemctl restart chrony
chronyc sources
chronyc tracking

install email server

dpkg-reconfigure postfix ### or
apt-get install postfix ### select "satellite system", enter full hostname "xxx.triumf.ca", enter "smtp.triumf.ca"
echo olchansk@triumf.ca >> ~root/.forward
mailx root
test
^D

install missing packages

yes | apt-get -y install ssh
yes | apt-get -y install git subversion g++
yes | apt-get -y install libz-dev sqlite sqlite3 libsqlite3-dev libmysqlclient-dev unixodbc-dev
yes | apt-get -y install sqliteman
yes | apt-get -y install libssl-dev
yes | apt-get -y install sysstat smartmontools # also installs postfix
yes | apt-get -y install emacs xemacs21
yes | apt-get -y install mutt # email client
yes | apt-get -y install liblz4-tool pbzip2
yes | apt-get -y install libc6-dev-i386 # otherwise no /usr/include/sys/types.h
yes | apt-get -y install libreadline-dev
yes | apt-get -y install chromium-browser chromium-codecs-ffmpeg-extra
yes | apt-get -y install ubuntu-mate-themes
yes | apt-get -y install minicom
yes | apt-get -y install screen
yes | apt-get -y install rsync strace net-tools
yes | apt-get -y install emacs xemacs21

install ganglia

yes | apt-get -y install ganglia-monitor
systemctl enable ganglia-monitor
cd ~root/git/scripts
git pull
cp etc/gmond-ubuntu.conf /etc/ganglia/gmond.conf
systemctl restart ganglia-monitor
systemctl status ganglia-monitor
ps -efw | grep gmond

install gonodeinfo

go to https://bitbucket.org/dd1/gonodeinfo follow instructions:

yes | apt-get -y install golang
mkdir ~/git
cd ~/git
git clone https://bitbucket.org/dd1/gonodeinfo.git
cd gonodeinfo
git pull
make
make install # install gonodeinfo agent
cd ~ # this is important

edit /etc/gonodeinfo.conf
change "Description", "Location", "User" and "Administrator" as appropriate (or delete them)
change "Servers" to read: Servers: ladd00.triumf.ca:8601
run gonodeinfo
if error is "connection refused". go to the nodeinfo server to add this client to the access control list:
on the gonodeinfo server: run gonodereceive -a daq13
try gonodeinfo again, there should be no error
on the gonodeinfo server: run gonodereport, look at the web pages, the new machine should be listed now

install libz.so.1 for CentOS compatibility

yes | apt-get -y install zlib1g
yes | apt-get -y install zlib1g:i386 libc6:i386 libgcc1:i386 gcc-6-base:i386

install libpng12.so.0 for Quartus compatibility

(does not work anymore!!!)

wget http://ftp.ca.debian.org/debian/pool/main/libp/libpng/libpng12-0_1.2.50-2+deb8u2_amd64.deb
dpkg --install libpng12-0_1.2.50-2+deb8u2_amd64.deb

install packages for building ROOT

apt-get -y install libx11-dev libxpm-dev libxft-dev libxext-dev libpng-dev libjpeg-dev xlibmesa-glu-dev libxml2-dev libgsl-dev cmake

install desktop environments

install MATE desktop

yes | apt-get -y install ubuntu-mate-core ubuntu-mate-desktop
yes | apt-get -y install ubuntu-mate-themes

install Cinnamon desktop

### not needed 18.04 LTS ### add-apt-repository ppa:embrosyn/cinnamon
yes | apt update
yes | apt-get -y install cinnamon

install KDE desktop

yes | apt-get -y install kubuntu-desktop

install Lxqt desktop

yes | apt-get -y install lxqt

install Xfce4 desktop

yes | apt-get -y install xfce4

install ROOT

Please install ROOT per instructions at http://root.cern.ch.

NOTE1: The ROOT package available from Ubuntu repositories is severely out of date and cannot be used with MIDAS and ROOTANA. ### DO NOT DO THIS! apt-get install root-system

NOTE2: as of 2017-Jan-09, ROOT binary kits for Ubuntu do not work (use GCC 5 instead of GCC6), build from source instead.

Install x2go

x2go instructions, thanks to Art O.

add-apt-repository ppa:x2go/stable
apt-get update
apt-get install x2goserver x2goserver-xsession

Post installation

setup hostname

xemacs -nw /etc/hostname ### add .triumf.ca to the hostname if it is missing

install Konstantin's scripts

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

enable root login from ladd00

ssh localhost
CTRL-C
/bin/cp ~root/git/scripts/etc/authorized_keys ~root/.ssh/

enable automatic updates 1

sudo apt-get install unattended-upgrades
xemacs -nw /etc/apt/apt.conf.d/50unattended-upgrades ### uncomment "-updates", uncomment "::Mail "root"", uncomment allowed-origins -security and -updates

enable automatic updates 2

add this to: xemacs -nw /etc/apt/apt.conf.d/10periodic

APT::Periodic::Update-Package-Lists "1";
APT::Periodic::Download-Upgradeable-Packages "1";
APT::Periodic::AutocleanInterval "7";
APT::Periodic::Unattended-Upgrade "1";

NIS instructions

apt-get -y install portmap nis ### will ask for NIS domain (LADD-NIS)
ypwhich -m
edit /etc/default/nis
- set "NISSERVER=slave"
- set "YPSERVARGS=-p800"
edit /etc/yp.conf", comment-out everything, add "domain LADD-NIS server localhost"
/usr/lib/yp/ypinit -s ladd00
systemctl restart nis
ypwhich -m
ypcat -k passwd
apt-get -y install autofs
systemctl enable autofs
vi /etc/nsswitch.conf ### add the automount line, modify the passwd, group and shadow lines to read this:

passwd: files nis
group: files nis
shadow: files nis
automount:  files nis

systemctl restart autofs
enable hourly update of NIS maps

cd ~/git/scripts/etc
git pull
ln -s $PWD/ypxfr-cron-hourly /etc/cron.hourly

### NOT NEEDED sudo vi /etc/idmapd.conf ### add line: "Domain = triumf.ca"
reboot

Fix systemd NIS breakage

there is a delay in ssh logins for normal users. "ssh -v" shows the delay is after "pledge...". this fix removes the delay.

systemd developers think that we should not use NIS and made sure there are problems if we do. To give them credit, they do offer a workaround. Read this: https://github.com/poettering/systemd/commit/695fe4078f0df6564a1be1c4a6a9e8a640d23b67

mkdir /etc/systemd/system/systemd-logind.service.d
echo -e "[Service]\nIPAddressDeny=\n" > /etc/systemd/system/systemd-logind.service.d/local.conf
systemctl daemon-reload
systemctl cat systemd-logind.service

Install sddm display manager (DO NOT DO THIS)

apt-get install sddm
apt-get install sddm-theme-"*"
create sddm.conf:

root@daqubuntu:~# more /etc/sddm.conf
[Theme]
Current=maldives
root@daqubuntu:~#

dpkg-reconfigure lightdm (select sddm)
reboot

Configure lightdm display manager

enable it

systemctl disable gdm
systemctl disable sddm
systemctl enable lightdm

make the MATE desktop as default

cd ~root/git/scripts/
git pull
/bin/cp -v etc/lightdm_default_mate.conf /etc/lightdm/lightdm.conf.d/

enable login by NIS users

/bin/cp -v etc/lightdm_enable_nis_login.conf /etc/lightdm/lightdm.conf.d/

restart lightdm

systemctl restart lightdm

Install libpng12.so.0

Quartus 16 needs libpng12:

wget http://mirrors.kernel.org/ubuntu/pool/main/libp/libpng/libpng12-0_1.2.54-1ubuntu1_amd64.deb
dpkg --install libpng12-0_1.2.54-1ubuntu1_amd64.deb

Install google-chrome

Instructions from here: https://www.ubuntuupdates.org/ppa/google_chrome?dist=stable

wget -q -O - https://dl-ssl.google.com/linux/linux_signing_key.pub | apt-key add -
sh -c 'echo "deb [arch=amd64] http://dl.google.com/linux/chrome/deb/ stable main" >> /etc/apt/sources.list.d/google.list'
apt-get update
apt-get install google-chrome-stable

Disable unwanted services

systemctl disable mpd
systemctl disable snapd
systemctl disable ModemManager

Install apache httpd proxy for midas and elog

This will configure the HTTPS/SSL certificate using "certbot" and "letsencrypt" and configure an HTTPS web server using apache2.

First, configure apache2:

execute these commands:

apt install apache2
cd /etc/apache2

create new file conf-available/ssl-daq14.conf # use actual hostname instead of daq14

SSLSessionCache         shmcb:/run/httpd/sslcache(512000)
SSLSessionCacheTimeout  300
SSLRandomSeed startup file:/dev/urandom  256
SSLRandomSeed connect builtin
SSLCryptoDevice builtin

create new file sites-available/daq14-ssl.conf # use actual hostname instead of daq14

<IfModule mod_ssl.c>
    <VirtualHost *:443>
        ServerName daq14.triumf.ca
        DocumentRoot /var/www/html
        ErrorLog /var/log/apache2/daq14.log
        SSLEngine on
        # note SSLProtocol, SSLCipherSuite and some other settings are overwritten by /etc/letsencrypt/options-ssl-apache.conf
        SSLProtocol all -SSLv2 -SSLv3
        SSLCipherSuite HIGH:MEDIUM:!aNULL:!MD5:!SEED:!IDEA:!RC4
        ## use port specified in elogd.cfg
        #ProxyPass /elog/ http://localhost:8082/ retry=1 
        ## use mhttpd port
        #ProxyPass /      http://localhost:8080/ retry=1 
        Header always set Strict-Transport-Security "max-age=31536000; includeSubDomains"
        <Location />
            SSLRequireSSL
            AuthType Basic
            AuthName "DAQ password protected site"
            Require valid-user
            # create password file: touch /etc/apache2/htpasswd
            # to add new user or change password: htpasswd /etc/apache2/htpasswd username
            AuthUserFile /etc/apache2/htpasswd
        </Location>
    </VirtualHost>
</IfModule>

stop apache2 from listening on port 80: edit /etc/apache2/ports.conf, comment-out the line "Listen 80"
stop apache2 from listening on port 80: edit /etc/apache2/ports.conf, comment-out the line "Listen 80"
enable ssl module
enable new configurations
check that there are no syntax problems

a2enmod ssl
a2enmod headers
a2enmod proxy
a2enmod proxy_http
a2enconf ssl-daq14
a2ensite daq14-ssl
apache2ctl configtest

enable and start apache2:

systemctl enable apache2
systemctl restart apache2
systemctl status apache2

apache2 may fail to start, look in /var/log/apache2/error.log and /var/log/apache2/daq14.log
if it says "Failed to configure ... certificate", proceed to the step for setting certbot.
try to access https://daq14.triumf.ca
- you should see a complaint about self-signed certificate
- you should see a request for password (do not login yet)
- if you get "connection refused", HTTPS port 443 may need to be enabled in the local firewall, look at documentation for ufw.

Second, configure certbot:

(Note: as of 2018-01-18 certbot requires use of http port 80 to get the initial https certificate, renewal can continue to use the https port 443)

(Note: as of 2019-01-?? certbot requires use of port 80 for renewals)

check that port 80 is not used by anything:
netstat -an | grep LISTEN | grep ^tcp | grep 80
lsof -P | grep -i tcp | grep LISTEN | grep 80
if lsof reports that apache2 is listening on port 80, follow the apache2 instructions above (remove "listen 80" from apache2.conf

install certbot (if necessary open tcp port 80 in the firewall, see documentation for ufw):

apt install certbot python3-certbot-apache
certbot certonly --standalone --installer apache

then answer questions:
"activate HTTPS for daq14.triumf.ca" - say ok
"enter email address" - enter your own email address
"please read terms..." - read the terms and say "agree"
it will take a few moments...
"congratulations..." - say ok.

certbot install --apache --cert-name daq14.triumf.ca

then answer questions:
"choose redirect..." - say "1" (no redirect)
look inside /etc/apache2/sites-enabled/ssl-daq14.conf to see that SSLCertificateFile & co point to certbot certificates in

/etc/letsencrypt/live/daq14.triumf.ca/

to check current renewal and to update the certbot config file in /etc/letsencrypt/renewal, run this:

certbot renew --standalone --installer apache --force-renewal

NOTE: this certificate will expire in 3 months, automatic renewal should work with current version of certbot

Third, activate password protection:

as shown in the config file above, create password file and initial user: (replace "midas" with specific username)

touch /etc/apache2/htpasswd
htpasswd /etc/apache2/htpasswd midas

restart apache2

systemctl restart apache2
systemctl status apache2

From here:

enable proxy for MIDAS mhttpd - uncomment redirect in the config file above
enable proxy for ELOG - ditto

a2enmod proxy
a2enmod proxy_http
apache2ctl configtest
systemctl restart apache2

From here:

enable proxy for MIDAS mhttpd - uncomment redirect in the config file above
enable proxy for ELOG - ditto

a2enmod proxy
a2enmod proxy_http
apache2ctl configtest
systemctl restart apache2

try accessing MIDAS https://daq14.triumf.ca/ (make sure mhttpd is running)
if it's not working, check odb setting FIXME!
try accessing ELog https://daq14.triumf.ca/elog/ (make sure elogd is running)
if it's not working, check elogd.cfg file and make sure

SSL                  = 0

NOTE: if certbot fails with errors about 'module' object has no attribute 'pyopenssl', try this: pip install requests==2.6.0

Update packages

apt-get update # update package list
apt-get dist-upgrade # install updated packages and update "kept back" packages
apt-get autoremove # remove packages that apt thinks should be removed

Finish installation

reboot

shutdown -r now

Install ZFS

!!! after installing all the packages, after updating the system, after updating the linux kernel, after rebooting into latest kernel !!!

apt-get install zfsutils-linux

Follow generic ZFS instructions: ZFS

Update to new version of Ubuntu

vi /etc/update-manager/release-upgrades # set "Prompt=normal"
do-release-upgrade

Ubuntu package manager

apt-get install xxx # install package xxx
apt-get update
apt-get upgrade
apt-get dist-upgrade
apt-get autoremove # remove automatically installed packages required by a removed package
apt-get remove xxx # remove package xxx
apt-cache search . # list all available packages
apt-cache show "." | grep ^Package # list al available packages
apt-cache madison root-system # show all available versions of package root-system
apt list # list all installed packages
dpkg --listfiles libpng16-16 # list all files from this package
apt list --installed # list all installed packages

Ubuntu grub boot loader

edit /etc/default/grub
grub-mkconfig -o /boot/grub/grub.cfg
update-initramfs -v -u
grub-install /dev/sda

Setup ubuntu as gateway to private network

Steps to do

assign network numbers to the private network, i.e. 192.168.1.x, 192.168.2.x, etc
(on the gateway machine, each private network interface has to have a different network number)
(each network interface can have multiple networks attached, via VLANs or via eth0:0, eth0:1 constructs)
assign IP addresses on the private network, save them in /etc/hosts i.e. "hvps 192.168.1.10"
(for simplicity, assign 192.168.1.1 to the gateway machine itself)
(IP addresses 192.168.1.0 and 192.168.1.255 are "special", do not use them)
setup DNS server (dnsmasq) to serve contents of /etc/hosts via DNS (otherwise, many programs will see inconsistent name to IP address mapping)
setup DHCP server (ISC dhcpd or dnsmasq) to give out the IP addresses
setup tftp, pxelinux and NFS for diskless booting
setup time server (chronyd) to provide common time to all devices
setup NAT so machines on private network can access the internet (to get OS updates, etc)
setup NIS and NFS so machines on the private network can use common home directories
setup rsync backup of machines on the private network

setup hosts

edit /etc/hosts

192.168.1.101 dsfe01
... and so forth

setup dns and dhcp

apt-get install dnsmasq
edit /etc/dnsmasq.conf

# /etc/dnsmasq.conf
# DNS settings
#port=0 # disable DNS function
port=53
domain-needed
bogus-priv
no-resolv
server=142.90.100.19
# DHCP settings
interface=enp1s0f0 # DHCP interface
#dhcp-range=192.168.1.50,192.168.1.150,infinite
dhcp-range=192.168.1.0,static
dhcp-boot=pxelinux.0
#dhcp-host=ac:1f:6b:9e:7f:4a,192.168.1.100,10m
dhcp-host=ac:1f:6b:9e:7f:4a,dsfe01,infinite
# TFTP settings
enable-tftp
tftp-root=/zssd/tftpboot

mkdir /zssd/tftpboot ### per tftp-root
systemctl enable dnsmasq
systemctl restart dnsmasq

setup chronyd

enable ntp server:
configure and enable chronyd per instructions above
emacs -nw /etc/chrony/chrony.conf
- add "allow 192.168.1.0/24" at the end
systemctl restart chronyd
chronyc tracking ### wait until time is synchronized (a few seconds)

setup diskless network booting

setup pxelinux

cd ~
wget https://www.kernel.org/pub/linux/utils/boot/syslinux/4.xx/syslinux-4.03.tar.bz2
tar xjvf syslinux-4.03.tar.bz2
cd syslinux-4.03
cp -pv ./core/pxelinux.0 ./com32/hdt/hdt.c32 ./memdisk/memdisk ./com32/menu/menu.c32 /zssd/tftpboot/

cd /zssd/tftpboot

wget http://ladd00.triumf.ca/tftpboot/memtest86+-4.20.iso.zip
wget http://ladd00.triumf.ca/tftpboot/memtest86+-5.01.iso.gz
wget http://ladd00.triumf.ca/tftpboot/modules.alias
wget http://ladd00.triumf.ca/tftpboot/modules.pcimap
wget http://ladd00.triumf.ca/tftpboot/pci.ids

mkdir pxelinux.cfg
emacs -nw pxelinux.cfg/default

default menu.c32
prompt 0

menu title Welcome to the DSVSLICE PXE boot menu

timeout 50

label hdt
  kernel hdt.c32

label memtest86+-5.01 
  kernel memdisk iso initrd=memtest86+-5.01.iso.gz 

label memtest86+-4.20
  kernel memdisk iso initrd=memtest86+-4.20.iso.zip

label vmlinuz-5.3.0-26-generic
  menu default
  kernel vmlinuz-5.3.0-26-generic
  append initrd=initrd.img-5.3.0-26-generic boot=nfs root=/dev/nfs netboot=nfs nfsroot=192.168.1.1:/zssd/nfsroot/dsfe01 toram ip=dhcp panic=60 BOOTIF=enp1s0f0

#end

setup linux kernel

copy the kernel files

cd /boot
rsync -av config* initrd* System.map* vmlinuz* /zssd/tftpboot/

cd /zssd/tftpboot
chmod a+r *

setup nfs

apt-get install nfs-kernel-server
emacs -nw /etc/exports

/zssd/nfsroot/dsfe01 dsfe01(rw,no_root_squash,async,no_subtree_check)

enable services

systemctl enable nfs-server
systemctl enable nfs-mountd
systemctl enable nfs-idmapd

setup userland

zfs create zssd/nfsroot
zfs set dedup=verify zssd/nfsroot ### enable deduplication to save disk space because most linux images have mostly identical files
clone ubuntu

mkdir /zssd/nfsroot/dsfe01
cd /
rsync -avx . /zssd/nfsroot/dsfe01

edit config files:
cd /zssd/nfsroot/dsfe01
emacs -nw etc/hostname ### change to dsfe01
emacs -nw etc/fstab ### add this

192.168.1.1:/zssd/nfsroot/dsfe01 / nfs defaults,nolock 0 0

emacs -nw etc/chrony/chrony.conf
- comment-out all "pool" and "server" entries
- add entry "server 192.168.1.1 iburst"

After dsfe01 is booted:

disable services:

systemctl disable apache2
systemctl disable dnsmasq
systemctl disable zfs-import-cache

To setup additional machines, clone dsfe01 instead of cloning the gateway machine

setup shared home directory

on the gateway machine

define netgroups
emacs -nw /etc/netgroup

dsfe (dsfe01,,) (dsfe02,,)

emacs -nw /etc/nsswitch.conf ### edit the netgroup line to read:

netgroup: files

export the home directories:
emacs -nw /etc/exports ### add this:

/zssd/home1 @dsfe(rw,no_root_squash,async,no_subtree_check)

exportfs -rc

on the frontend machine

mkdir /home
emacs -nw /etc/fstab ### add this:

192.68.1.1:/zssd/home1 /home defaults 0 0

mount -a

Ubuntu