BIG Setup

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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.

- Disk should be partitioned with the default filesystem: LVM.

- All additional packages from KDE should be deselected, packages should be installed in a second time with yum.

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
Dropbox
https://www.dropbox.com/install?os=lnx
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

Only for machine that have bond interface

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 gimp grace mplayer mencoder mplayer-gui imagej freeglut ffmpeg ffmpeg-libs lame-libs kdesdk clusterssh tcsh
yum install gcc gpm tcsh kdegraphics kdm google-chrome-stable.x86_64
yum install gstreamer-plugins-bad-free.x86_64 gstreamer-ffmpeg gstreamer-plugins-good  gstreamer-plugins-ugly 
yum install gstreamer1-plugins-bad-free.x86_64 gstreamer1-plugins-bad-freeworld.x86_64 gstreamer1-plugins-base.x86_64 
yum install gstreamer1-plugins-good.x86_64 gstreamer1-plugins-ugly.x86_64 zsh

yum install dkms.noarch

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

[devel] 

yum groupupdate "Development and Creative Workstation" "Fedora Eclipse" "MySQL Database"

[optional] 

yum groupupdate "GNOME Desktop"

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/

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. 

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

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

yum -y install compat-libf2c-34.i686 compat-libf2c-34.x86_64 glib.i686 compat-libstdc++-33.i686 
yum -y install fftw.i686 fftw.x86_64  libtiff-tools

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

KDE Settings

only if GNOME install previously 


yum groupinstall "KDE Software Development" switchdesk-gui

Set default desktop to KDE 

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

or 

switchdesk kde


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/

Firewall

for every computer but out web server" 

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

IF BOND 

sudo firewall-cmd --zone=work --change-interface=bond0

IF NOT 

sudo firewall-cmd --zone=work --change-interface=em1

web server: 

sudo firewall-cmd --set-default-zone="public"
sudo firewall-cmd --permanent --add-service=http

Home directory

vi /etc/default/useradd

Change: 

HOME=/storage/big1

Some users are below 1000, so change 

vi /etc/login.defs

where and how?

Updating

sudo yum erase Packagekit gnome-packagekit apper
sudo systemctl disable packagekit-offline-update

nVidia

yum install kmod-nvidia xorg-x11-drv-nvidia dracut

mv /boot/initramfs-$(uname -r).img /boot/initramfs-$(uname -r)-nouveau.img

## Create new initramfs image ##
dracut /boot/initramfs-$(uname -r).img $(uname -r)

uname has to be replaced with username??

Misc

sudo cp /storage/big1/kdb/linux_setup/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

Software

Play

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

DAVE

yum -y install "*8859*" glib glib.i686 libpng.i686 xorg-x11-drv-nvidia-libs.i686 libpng12.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

Additional settings

Remote Desktop

yum install xrdp
firewall-cmd --permanent --add-port=3389/tcp
service xrdp start
systemctl enable xrdp.service

bug 

sudo chcon --type=bin_t /usr/sbin/xrdp*

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/

are this file on big1 or karl local? 


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

Restart firewall 

systemctl restart iptables.service

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

File Servers

yum install sendmail xauth openldap openldap-servers openldap-clients 
yum groupinstall "GNOME Desktop" "Infrastructure Server" "Minimal Install"

Openldap

copy database from backup to /var/lib/ldap

copy configuration 

cp -a /<backup>/etc/openldap/slapd.d/* slapd.d/

cd /var/lib/ldap/
db_recover -v -h . *.bdb
db_upgrade -v -h . *.bdb
db_checkpoint -v -h . -1

cd /var/lib/ldap/accesslog
db_recover -v -h . *.bdb
db_upgrade -v -h . *.bdb
db_checkpoint -v -h . -1

firewall-cmd --permanent --zone=work --add-service=ldap
firewall-cmd --permanent --zone=work --add-service=ldaps

systemctl start slapd.service
systemctl enable slapd.service

NFS

systemctl enable nfs-lock.service
systemctl enable nfs-server.service

systemctl start  nfs-lock.service
systemctl start  nfs-server.service

cat >/etc/firewalld/services/mountd.xml <<EOD
<?xml version="1.0" encoding="utf-8"?>
<service>
<short>mountd</short>
<description>Mount Lock Daemon</description>
<port protocol="tcp" port="20048"/>
<port protocol="udp" port="20048"/>
</service>
EOD

cat >/etc/firewalld/services/rpc-bind.xml <<EOD
<?xml version="1.0" encoding="utf-8"?>
<service>
<short>rpc-bind</short>
<description>Remote Procedure Call Bind</description>
<port protocol="tcp" port="111"/>
<port protocol="udp" port="111"/>
</service>
EOD

restorecon /etc/firewalld/services

firewall-cmd --permanent --zone work --add-service mountd
firewall-cmd --permanent --zone work --add-service rpc-bind
firewall-cmd --permanent --zone work --add-service nfs
firewall-cmd --reload
firewall-cmd --list-all

Samba

restorecon /etc/samba/smb.conf

semanage fcontext -a -t samba_share_t "/mnt/alcor/VolGroup01-LogVol00(/.*)?"
restorecon -R -v /mnt/alcor/VolGroup01-LogVol00/

semanage fcontext -a -t samba_share_t "/mnt/alcor/VolGroup02-LogVol00(/.*)?"
restorecon -R -v /mnt/alcor/VolGroup02-LogVol00/

semanage fcontext -a -t samba_share_t "/mnt/alcor/VolGroup03-LogVol00(/.*)?"
restorecon -R -v /mnt/alcor/VolGroup03-LogVol00/

semanage fcontext -a -t samba_share_t "/mnt/alcor/VolGroup04-LogVol00(/.*)?"
restorecon -R -v /mnt/alcor/VolGroup04-LogVol00/

setsebool samba_create_home_dirs=true
setsebool samba_enable_home_dirs=true
setsebool samba_export_all_rw=true
setsebool samba_share_nfs=true

firewall-cmd --zone=work --add-service=samba
firewall-cmd --permanent --zone=work --add-service=samba

firewall-cmd --zone=work --add-service=mdns
firewall-cmd --permanent --zone=work --add-service=mdns

systemctl start  smb.service
systemctl enable smb.service
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