BIG Setup

Installation/Settings for new Linux Workstations at University of Massachusett's Medical School.

Our group uses Fedora with KDE as the desktop for our workstations, which is why you will see yum as the package manager.

Repositories

RPMFusion Repositories

rpm -Uvh http://download1.rpmfusion.org/free/fedora/rpmfusion-free-release-stable.noarch.rpm
rpm -Uvh http://download1.rpmfusion.org/nonfree/fedora/rpmfusion-nonfree-release-stable.noarch.rpm

Adobe Repository

rpm -Uvh http://linuxdownload.adobe.com/adobe-release/adobe-release-i386-1.0-1.noarch.rpm

And/Or

[adobe-linux-x86_64]
name=Adobe Systems Incorporated
baseurl=http://linuxdownload.adobe.com/linux/x86_64/
enabled=1
gpgcheck=1
gpgkey=file:///etc/pki/rpm-gpg/RPM-GPG-KEY-adobe-linux

Skype Repository

vi /etc/yum.repos.d/skype.repo

[skype]
name=Skype Repository
baseurl=http://download.skype.com/linux/repos/fedora/updates/i586/
gpgkey=http://www.skype.com/products/skype/linux/rpm-public-key.asc
enabled=1
gpgcheck=0

Google Repository

vi /etc/yum.repos.d/google.repo

[google]
name=Google - i386
baseurl=http://dl.google.com/linux/rpm/stable/i386
enabled=1
gpgcheck=1
gpgkey=https://dl-ssl.google.com/linux/linux_signing_key.pub

vi /etc/yum.repos.d/google64.repo

[google64]
name=Google - x86_64
baseurl=http://dl.google.com/linux/rpm/stable/x86_64
enabled=1
gpgcheck=1
gpgkey=https://dl-ssl.google.com/linux/linux_signing_key.pub

VirtualBox Repository

vi /etc/yum.repos.d/virtualbox.repo

[virtualbox]
name=Fedora $releasever - $basearch - VirtualBox
baseurl=http://download.virtualbox.org/virtualbox/rpm/fedora/$releasever/$basearch
enabled=1
gpgcheck=1
gpgkey=http://download.virtualbox.org/virtualbox/debian/oracle_vbox.asc

yum install libXv.rpm.i686 alsa-lib.rpm.i686 libXScrnSaver.rpm.i686 qt.ii686

Networking

ifcfg-p1p1

DEVICE=p1p1
BOOTPROTO=none
ONBOOT=yes
MASTER=bond0
SLAVE=yes

ifcfg-p1p2

DEVICE=p1p2
BOOTPROTO=none
ONBOOT=yes
MASTER=bond0
SLAVE=yes

ifcfg-bond0

DEVICE=bond0
IPADDR=146.189.76.*
NETMASK=255.255.248.0
DNS1=146.189.197.157
DNS2=146.189.197.70
GATEWAY=146.189.72.1
ONBOOT=yes
BOOTPROTO=none
USERCTL=no
BONDING_OPTS="mode=4 miimon=500"

Note 1: devices changed from eth* to p1p* with Fedora 17.
Note 2: NetworkManager can now be used with devices as long as the ifcfg-rh plugin is used.
Note 3: IS must activate switch to accommodate mode=4 using Dynamic LAG.

From Citrix There are two types of LAGs:

Static LAG: ports have LACP disabled and become automatically active members of the bond. Static LAG is not widely used, as it is often considered obsolete and inferior to dynamic LAG. With static LAG on the switch, the bond mode should be balance-slb rather than lacp. Note that use of static LAG is not supported.
Dynamic LAG: Link Aggregation Control Protocol (LACP) is used for switch-server communication, in order to negotiate dynamically which links should be active and which should be in stand-by mode.

Packages

After upgrading to Fedora 20, groups must be converted to objects.

yum groups mark convert

64 Bit Packages

yum install kernel-devel gimp grace mplayer mencoder mplayer-gui freeglut ffmpeg-libs lame-libs kdesdk clusterssh tcsh
yum install gstreamer-ffmpeg gstreamer-plugins-good  gstreamer-plugins-ugly gcc gpm tcsh kdegraphics kdm google-chrome-stable.x86_64

yum install dkms.noarch

yum groupupdate "KDE Plasma Workspaces" "GNOME Desktop" "Development and Creative Workstation" "Minimal Install" "Basic Desktop"
yum groupupdate "Administration Tools" "Design Suite" "Authoring and Publishing"
yum groupupdate "Editors" "Electronic Lab" "Fedora Eclipse" 
yum groupupdate "Milkymist" "MySQL Database" "Network Servers" 
yum groupupdate "Office/Productivity" "Robotics" "Sound and Video" "System Tools"
yum groupupdate "Text-based Internet" "Window Managers"

After update, Fedora 19 switched from groups to objects, leading to errors that groups don't exist

sudo rm -rf /var/lib/yum/*; yum clean all; yum update

- Flash**

Check here for the latest 64bit flash: [[1]] and then copy it to /usr/lib64/mozilla/plugins/

32 Bit Packages

- Flash**

[[2]]

yum install flash-plugin gtk2-engines.i686 nss_ldap.i686

cp /storage/big1/kdb/linux_setup/libflashplayer.so /usr/lib64/mozilla/plugins/

KDE Settings

yum groupinstall "KDE Software Development" system-switch-displaymanager.noarch

Set default desktop to KDE

echo -e "DESKTOP=\"KDE\"\nDISPLAYMANAGER=\"KDE\"\n" > /etc/sysconfig/desktop

or

system-switch-displaymanager kdm

Change default movie player from Totem to MPlayer, select "System Settings->File Associations", then open video->mpeg. Make sure "MPlayer" is first on the list.

Mail

yum install thunderbird

IMAP Settings

incoming mail server: mail.umassmed.edu  
Port: 993
Security: SSL/TLS

Outgoing mail server: smtp.umassmed.edu
Port: 587
Security: starttls

username: Windows Network Login
password: Windows Network Password

After setting up Thunderbird, you need to turn on SSL for incoming mail and TSL for outgoing mail.

Global LDAP Address Book

host: people.umassmed.edu
port: 50000
DN: ou=people,dc=umassmed,dc=edu

Security

cp /storage/big1/kdb/linux_setup/etc/hosts.allow /etc/
cp /storage/big1/kdb/linux_setup/etc/hosts.deny /etc/

Home directory

vi /etc/default/useradd

Change:

HOME=/storage/big1

Some users are below 1000, so change

vi /etc/login.defs

Firewall

for every computer but out web server"

sudo firewall-cmd --set-default-zone="work"
sudo firewall-cmd --zone=work --change-interface=bond0

web server:

sudo firewall-cmd --set-default-zone="public"

Biomedical Imaging Group Specific Settings

using nfsvers=3 only on Fedora 16 or less because uid/gid seem to be mapping to nobody when using nfsver=4 edit fstab.

mizar:/mnt/VolGroup01-LogVol00     /mnt/mizar/VolGroup01-LogVol00     nfs  bg,defaults
mizar:/mnt/VolGroup02-LogVol00     /mnt/mizar/VolGroup02-LogVol00     nfs  bg,defaults
mizar:/mnt/VolGroup03-LogVol00     /mnt/mizar/VolGroup03-LogVol00     nfs  bg,defaults
mizar:/mnt/VolGroup04-LogVol00     /mnt/mizar/VolGroup04-LogVol00     nfs  bg,defaults

mkdir /storage/; mkdir /mnt/mizar/;mkdir /mnt/mizar/VolGroup01-LogVol00;mkdir /mnt/mizar/VolGroup02-LogVol00
mkdir /mnt/mizar/VolGroup03-LogVol00;mkdir /mnt/mizar/VolGroup04-LogVol00
ln -s  /mnt/mizar/VolGroup03-LogVol00 /storage/big1; ln -s /mnt/mizar/VolGroup04-LogVol00 /storage/big2
ln -s /mnt/mizar/VolGroup01-LogVol00 /storage/big3; ln -s /mnt/mizar/VolGroup02-LogVol00 /storage/big4

yum -y install compat-libf2c-34.i386 compat-libf2c-34.x86_64 glib.i386 fftw.i386 fftw.x86_64  libtiff-tools

mkdir /usr/share/fonts/windows/; cp /storage/big1/kdb/NT/Fonts/* /usr/share/fonts/windows/

Misc

sudo cp libforms.so.0.89 /usr/local/lib/

Disable package kit refresh

sudo vi /etc/yum/pluginconf.d/refresh-packagekit.conf

Change enable=1 to enable=0

This is need for uManager to save global java preferences

sudo chmod a+rwx /etc/.java/.systemPrefs

Play

yum install compat-libf2c-34.i686 libX11.i686 mesa-libGL.i686 mesa-libGLU.i686 libXpm.i686 ffmpeg-libs.i686

DAVE

yum -y install "*8859*" glib glib.i686 libpng.i686 xorg-x11-drv-nvidia-libs.i686

epr_beowulf

sudo iptables -A INPUT -s itchy.umassmed.edu -m state --state NEW -m tcp -p tcp --dport 1022 -j ACCEPT

Super Resolution

yum install tcsh fftw2.i686 libstdc++.i686 compat-libf2c-34.i686 fftw-libs-single.x86_64

Network Time

cp /storage/big1/kdb/linux_setup/etc/ntp.conf /etc/
sudo service ntpd start
sudo service ntpd enable

64 Bit Settings

Set up paths to include additional directories

cp /storage/big1/kdb/linux_setup/etc/big64.sh /etc/profile.d/

32 Bit Settings

Set up paths to include additional directories

cp /storage/big1/kdb/linux_setup/etc/big.sh /etc/profile.d/

User Authentication

cp ~kdb/linux_setup/etc/sssd/sssd.conf /etc/sssd/
cp ~kdb/linux_setup/certs/* /etc/pki/tls/certs/
cp ~kdb/linux_setup/certs/* /etc/openldap/cacerts/
cp ~kdb/linux_setup/etc/nsswitch.conf /etc/
cp ~kdb/linux_setup/etc/ldap.conf /etc/

chkconfig sssd on;service sssd start

SELinux

setsebool -P use_nfs_home_dirs 1

chcon -h system_u:object_r:user_home_dir_t:s0 /storage/big1

echo "/storage/big1    system_u:object_r:user_home_dir_t:s0" >> /etc/selinux/targeted/contexts/files/file_contexts.local

Torque

Server

yum install torque-server.x86_64 torque-scheduler.x86_64
systemctl start pbs_sched.service
systemctl start pbs_server.service
systemctl enable pbs_sched.service
systemctl enable pbs_server.service

pbs_server -t create
# configure manager/operator user
qmgr -c "set server operators += $USER@$HOST"
qmgr -c "set server managers += $USER@$HOST"
# scheduling options
qmgr -c 'set server scheduling = true'
qmgr -c 'set server keep_completed = 300'
qmgr -c 'create queue batch'
qmgr -c 'set queue batch queue_type = execution'
qmgr -c 'set queue batch started = true'
qmgr -c 'set queue batch enabled = true'
qmgr -c 'set queue batch resources_default.walltime = 72:00:00'
qmgr -c 'set queue batch resources_default.nodes = 1'
qmgr -c 'set server default_queue = batch'
qmgr -c 'set server allow_node_submit = True'

edit /etc/sysconfig/iptables and add (change hostname to reflect client machine)

 -A INPUT -s germanium.umassmed.edu -p tcp -m state --state NEW -m tcp --dport 1024:65535 -j ACCEPT

Restart firewall

systemctl restart iptables

Note: Fedora 14 puts everything in /var/lib/torque and not /var/torque

Client

yum install torque torque-mom
echo "m13.umassmed.edu" > /etc/torque/server_name
systemctl start pbs_mom.service
systemctl enable pbs_mom.service

edit /var/lib/torque/mom_priv/config (should be linked to /etc/torque/mom/config)

$pbsserver m13.umassmed.edu
$usecp m13.umassmed.edu:/storage /storage
$usecp m13.umassmed.edu:/mnt/mizar/VolGroup01-LogVol00  /mnt/mizar/VolGroup01-LogVol00
$usecp m13.umassmed.edu:/mnt/mizar/VolGroup02-LogVol00  /mnt/mizar/VolGroup02-LogVol00
$usecp m13.umassmed.edu:/mnt/mizar/VolGroup03-LogVol00  /mnt/mizar/VolGroup03-LogVol00
$usecp m13.umassmed.edu:/mnt/mizar/VolGroup04-LogVol00  /mnt/mizar/VolGroup04-LogVol00
$restricted *.umassmed.edu

edit /etc/sysconfig/iptables and add

-A INPUT -s m13.umassmed.edu -m state --state NEW -m tcp -p tcp --dport 15001:15004 -j ACCEPT

iptables-save >/etc/sysconfig/iptables