RHEL 6 Install Info
Bios Settings on HPZ420
Enter BIOS and change the following settings:
Storage
Storage options
SATA Mode ==> IDE
Boot Order
UEFI Boot Sources ==> Disable All
Legacy Boot Sources ==> Enable All
Installing RHEL 6.3
Prerequisites
You will need:
The RHEL 6.3 Installation DVD and license from RedHat (you need the Workstation version)
The preinstall script, VnmrJLinuxInstallSupport.tbx2 (available on the Agilent website or service)
The VnmrJ3.2 Media Kit or VnmrJ3.2_MI media kit
**These directions should also work for upgrading a Dell to RHEL 6.1 as well.
RHEL DVD Install
- Turn computer on and put the Linux 6.1 DVD in the drive.
Use ctrl-alt-del to reboot the computer. - Choose Install or Upgrade an Existing system
- Skip Test Next
- Choose language Next
- Choose keyboard Next
- Keep the default Basic Storage Devices Next
- Enter hostname (Note: Do not use names that only contain
capital letters and numbers. For example, NMR600 is not
okay, but nmr600 is okay) Next - Choose time zone Next
- Enter root password and confirm Next
- Type of installation, choose Use All Space. Next
- Choose both drives under the data storage and click the Forward arrow to move them to Install Target Device. Do not change the Boot Loader. Next
- Choose write changes to disk from pop-up GUI
- Wait for formatting to finish.
- Choose Desktop for Default Installation and
- Choose customize now Next
- Choose all packages including optional. (Hint-select top option, hold down shift, select bottom option- right click mouse and choose select all optional packages.
- Do this for everything in the list: Base System, Servers, …….., Development.
Once you get to Languages, pick whatever you want. - Once OS is done loading, remove the RHEL DVD and select Reboot.
- There are a few more questions to answer on boot-up. Forward
- Agree to license. Forward
- Register at a later time. Forward
- Select, No Thanks, I’ll connect later. Forward
- Create a User Skip this Forward
- Set the Date and Time Forward
- Un-check the kdump option, choose yes in the GUI pop-up window, and Reboot.
- When the login screen appears, select “other”
- Username root
- Enter root’s passwd
- Close the window warning of the damages to the system that root can cause
Configure Network eth1:
You can check which port is eth1 by issuing the following command:
ethtool –p eth1 20
In /etc/sysconfig/network-scripts/ifcfg-eth1, make sure that
ONBOOT=yes
BOOTPROTO=static
IPADDR=172.16.0.1 (If the main network has a 172 IP address, use 10.0.0.1)
NOTE: You must restart the network before running setacq. As root, in a terminal window
# /etc/init.d/network restart (rebooting works as well)
Configure Network eth0:
Things you will need:
a. For DHCP, you will need a hostname.
b. For static IP address, you will need a hostname, IP address, DNS servers, gateway, and domain name.
Agilent-NMR is our sample hostname. Remember to make sure your hostname does not consist of only capital letters and numbers such as 600NMR. 600nmr is okay.
For DHCP:
In /etc/hosts, the line starting with 127.0.0.1 needs to contain the hostname
For example,
127.0.0.1 localhost.localdomain Agilent-NMR (delete the localhost4 localhost4.localdomain4 entries from this line)
Comment out the next line starting with ::1 localhost……localhost6 (Do not delete this line)
In /etc/sysconfig/network, make sure
HOSTNAME=Agilent-NMR (or DHCP_HOSTNAME=Agilent-NMR)
In /etc/sysconfig/network-scripts/ifcfg-eth0, make sure
BOOTPROTO=dhcp
ONBOOT=yes
If there is a HOSTNAME or DHCP_HOSTNAME it must match what is in the host file and network file. A hostname does not have to be in this file.
NOTE: You must restart the network before running setacq. As root, in a terminal window
# /etc/init.d/network restart (rebooting works as well)
For Static IP:
In /etc/hosts, make sure there is a line containing the hostname and the static IP address. For example,
123.123.123.123 Agilent-NMR (not on the 127.0.0.1 line)
In /etc/sysconfig/network, make sure
HOSTNAME=Agilent-NMR
In /etc/sysconfig/network-scripts/ifcfg-eth0, make sure
BOOTPROTO=none (or static)
ONBOOT=yes
If there is a HOSTNAME or DHCP-HOSTNAME it must be correct. It does not need to exist.
IPADDR= (this should be the static IP address of the host computer)
GATEWAY= This should be set to the gateway IP address.
DNS1= dns server address
DNS2= dns server address
In /etc/resolv.conf, make sure there is a line with your domain name. For example,
search=scs.agilent.com
(The DNS servers will automatically be written to this file from the entries in ifcfg-eth0)
NOTE: You must restart the network before running setacq. As root, in a terminal window
# /etc/init.d/network restart (rebooting works as well)
Install the VnmrJLinuxInstallSupport.tbz2 Script
- As root, copy the VnmrJLinuxInstallSupport.tbz2 script to /tmp
- Untar and run the script
In a terminal window,
# cd /tmp
# tar xvf VnmrJLinuxInstallSupport.tbz2
# cd preinstall
# ./installpkgs
- A window will pop up saying to hit the Enter key once the RHEL6.1 DVD has mounted. If the RHEL 6.1 DVD is not in the drive, put the DVD in the drive now, and hit enter once the drive is mounted.
- Once the packages have been installed, remove the RHEL6.1 DVD from the drive.
- Reboot the computer.
- There will be a log file written to /tmp/preinstall. The file will be named pkgInstall.log_date_time.
Configuring RHEL for VnmrJ Install
- Turn off firewall
# chkconfig iptables off
# service iptables stop
(To check the status of the service type: chkconfig | grep iptables)
- Disable selinux
edit /etc/selinux/config and change SELINUX=disabled
(to check status type: sestatus)
- Reboot
Lilly Modifications
DNS Settings
In /etc/resolv.conf, add DNS Search path
search am.lilly.com d51.lilly.com d48.lilly.com d50.lilly.com d52.lilly.com)
System Settings
- SystemèAdministrationèServices turn on the following services
gssftp, klogin, krb5-telnet, nfs, rexec, rlogin, rsh, telnet, tftp
- Edit /etc/xinetd.d/gssftp and remove the “-a” option in the server_args field
- Create daily cron job to remove unnecessary temporary files
# su
# vi /etc/cron.daily/tmpwatch
add the following line to the tmpwatch file before the for ; do statment
/usr/sbin/tmpwatch 120 /vnmr/tmp /var/spool/cups
close file (:wq)
- Reboot
- Login as root
- edit /etc/group and change GID of gopher to 31
- edit /etc/passwd and change UID of cyrus to 86
- chown –R cyrus /var/lib/imap
- Under SystemèAdministration èUsers and Groups
- Edit/ Preferences – hide system groups – de-select
- Edit gopher user and re-select gopher as a group for user gopher and then select gopher as the primary group for gopher
- Add new group “nmr” with manual assigned GID of 30
- Add new user “nmruser” w/ UID 76, group “nmr”, default terminal /bin/csh, default home of /home/nmruser and appropriate password. You will have to re-edit this user to select the box next to ‘group=nmr’ and then select the pulldown and assign the primary group to be “nmr”
- Add new user “vnmr1” w/ UID 501, group “nmr”, default terminal /bin/csh, default home of /home/vnmr1 and appropriate password You will have to re-edit this user to select the box next to ‘group=nmr’ and then select the pulldown and assign the primary group to be “nmr”
Pre-VJ Installation Tasks
7. Take care of ownership issues in these accounts
- chown –R vnmr1:nmr /home/vnmr1
- chown –R nmruser:nmr /home/nmruser
- chmod a+rx /home/vnmr1
- chmod a+rx /home/nmruser
Loading VnmrJ3.2 (VNMRS, DD2, 400-MR, 400-MR-DD2)
- Turn on the computer.
- At the login screen, choose other
- Username is root
- Enter password
- A warning window will pop up warning about the damage root can do. Close this window.
- Place the VnmrJ3.2 DVD in the CDROM drive or mount ISO image as follows where /path_of_iso/vj.iso is the location of the ISO image:
# mkdir /mnt/vnmrj
# mount –o loop /path_of_iso/vj.iso /mnt/vnmrj
- Open a terminal window (right click on the desktop)
- In the terminal window
#cd /media/ G5028-60002
# ./load.nmr
- If a window appears saying that some linux files are missing, follow the directions in the window. You will need your RH 6.1 kickstart DVD.
- Once the VnmrJ Install GUI appears, select VNMRS, DD2, 400MR, or 400MR-DD2.
- Enter the passwords for any passworded items that have been purchased. These options may also be loaded at a later time. (DOSEY 3.2 gm-ppb)
- Select DONE when the installation is complete
- Eject the VnmrJ 3.2 disk. (You may have to close all terminal windows before the DVD will eject.)
- Run makeuser on any existing users.
- Install any patches at this time.
Running setacq
- If this computer is connected to a spectrometer, type su in a terminal window to become root.
#/vnmr/bin/setacq
- Choose yes to blink the eth1 port, and check to make sure that the console is plugged into this port. The blinking times out in 20 seconds.
- The software will download 13 files. Note that only the RF controllers will contain 14 files (the 13 downloaded files plus boot.ini). The other controllers will only have 11 files.
- Once setacq has completed, you will need to reboot the computer.
- Login as vnmr1.
- Run config. It is under Edit> System Settings > System Configuration. This is under Tools > System Settings on imaging systems.
- The user acqproc will need to be created if this is the first time VnmrJ has been installed on this computer:
In a terminal window, as root, type
#/vnmr/bin/makesuacqproc
NOTE: The console, by default, uses eth1.
#ethtool –p eth1 20
Will make the eth1 port blink for 20 seconds.
Loading VnmrJ3.2 (Inova, Mercury Plus, MercuryVX)
- Place the VnmrJ3.2 DVD in the CDROM drive or mount ISO image as follows where /path_of_iso/vj.iso is the location of the ISO image:
# mkdir /mnt/vnmrj
# mount –o loop /path_of_iso/vj.iso /mnt/vnmrj
- Open a terminal window (right click on the desktop)
- In the terminal window
# cd /media/VnmrJ32A (may differ)
# ./load.nmr
- If a window appears saying that some linux files are missing, follow the directions in the window. You will need your RH 6.3 DVD. This will most likely not happen.
- Once the VnmrJ Install GUI appears, select Inova or Mercury (both Mercury VX and Mercury Plus use Mercury)
- Enter the passwords for any passworded items that have been purchased. These options may be loaded at a later time. (DOSEY 3.2 gm-ppb)
- Select DONE when the installation is complete
- Eject the VnmrJ 3.2 disk. (You may have to close all terminal windows before the DVD will eject.)
Running setacq
NOTE: If this is an Inova, the system will boot up with a PPC or Motorola CPU without modifying any files.
- Log in as vnmr1
- If this computer is connected to a spectrometer, type su in a terminal window to become root.
# /vnmr/bin/setacq
- Choose yes to blink the eth1 port, and check to make sure that the console is plugged into this port. The blinking times out in 20 seconds.
- Reboot the console when prompted.
- Then hit the enter key.
- The console software will download
- The user acqproc will need to be created if this is the first time VnmrJ has been installed on this computer:
- In a terminal window, as root, type
# /vnmr/bin/makesuacqproc
- Run config. It is under Editè System Settings è System Configuration. Choose Use Console Data
NOTE: The console, by default, uses eth1.
# ethtool –p eth1 20
Will make the eth1 port blink for 20 seconds.
NOTE2: If you are upgrading from 6.1B or earlier, make sure that both the shims and the VT are plugged into the MSR card and not the CPU (Inova). The shim cable goes to port #1 on the MSR, and the VT cable goes to port #2 on the MSR.
Passworded Options may be loaded at any time by entering
vnmrjOptions
on the vnmrj command line. You must be vnmr1 to do this. This is also the only way to load passworded options on the Mac and Windows data station versions of VnmrJ3.2.
Lilly VnmrJ Post Install
- Log in as root
- Open a terminal window
- cd /vnmr/bin
- ./makeuser vnmr1
- ./makeuser nmuser
- ./sudoins
- ./makesuacqproc
Note: if eth0 is configured, it must be connected to network to do a dbsetup
- Enter cd and eject the VnmrJ CD if inserted
- Log out of root
- Log in as vnmr1
- In terminal window type dbsetup
- reboot
- Login as vnmr1
- Launch vnmrj adm
- Add nmruser as new user – Configure/Users/Convert Users
- run dbsetup
- Install all current Linux related patches for VnmrJ. (i.e. patchinstall <patch>.tar.Z)
- As root, vi the files /etc/mail/submit.cfand /etc/mail/sendmail.cfso that the line starting with DS appears as:
DSsmtp-z1-mta.lilly.com
- Test email by setting emailaddr=’lzollars@lilly.com’ then typing eplot
- Edit /etc/fstab and add lines as follows:
nmrnas.am.lilly.com:/nmrdata/nmruser /nmrserverdata nfs bg,soft 0 0
gulf.d51.lilly.com:/nmrtransport/nmrtransport/raw /atpfiles nfs bg,soft 0 0 *
icux3100.am.lilly.com:/icux3100_export/nmr1 /NMR_dataserver1 nfs bg,soft 0 0 **
* LZ systems
** SB Systems
- mkdir /nmrserverdata /atpfiles /NMR_dataserver1
- Set system proxy for web. Under System=>Preferences=>Network Proxy=> set to:
LCC-http-proxy.d48.lilly.com 9000
LCC-security-proxy.d48.lilly.com 9000
LCC-ftp-proxy.d48.lilly.com 9000
Configuring TurboVNC
TurboVNC is installed by VnmrJ by default in /opt/TurboVNC. This will need to be added to the login path. To do so edit the file ~/.login
set path=($path /usr/sbin /opt/TurboVNC/bin $HOME/bin /etc)
You will then need to log out and log back in for this to take effect.
Next, you can start a vnc server session by typing the command vncserver followed by the display number (note: you will only be asked to configure the password the first time you start vncserver. After that you can change it via the command vncpasswd):
nmruser 84>vncserver :1
You will require a password to access your desktops.
Password: password
Verify: password
Would you like to enter a view-only password (y/n)? n
New ‘X’ desktop is Agilent-NMR: 1
Creating default startup script /home/nmruser/.vnc/xstartup.turbovnc
Starting applications specified in /home/nmruser/.vnc/xstartup.turbovnc
Log file is /home/nmruser/.vnc/Agilent-NMR:1.log
You can now use a vnc viewer to login to the server at display :1
To kill the server you will need to type the command vncserver –kill followed by the display number:
nmruser 85>vncserver -kill :1
Killing Xvnc process ID 5670
We can also start up a vnc session at different resolutions, etc.
For example the following command will start a desktop at 1600×1200 on display 33:
nmruser 93>vncserver :33 -geometry 1600×1200
New ‘X’ desktop is Agilent-NMR:33
Starting applications specified in /home/nmruser/.vnc/xstartup.turbovnc
Log file is /home/nmruser/.vnc/Agilent-NMR:33.log
To start a vnc server on display 33 at 1600×1200 resolution:
vncserver :33 –geometry 1600×1200
To kill vnc server on display 33
vncserver –kill :33
To change the vncserver password
vncpasswd
Disabling the ‘Packagekit Update Applet’
It is possible to disable the Packagekit Update Applet, thus also preventing the popup. Here the update options in the GUI will stay available to the user. To disable the applet:
- In the Gnome GUI go to System > Preferences > Startup Applications
- Uncheck ‘Packagekit Update Applet’ from the list
Disabling ESC
ESC is Enterprise Security Client Smart Card client. It is a tool which enables you to configure, control and monitor smart cards and personal security certificates on your system. If you go into system monitor, and look at processes, you might see multiple instances of esc running, with some as zombies. Kill off the zombies.
Once all instances of esc are killed, from the terminal, run esc and look at the gui. If you don’t have any certs on your system, you can always:
# yum remove esc
DBUS_SESSION_BUS_ADDRESS error
If you are trying to access VNC locally from the GDI you will need to edit the ~/.vnc/xstartup.turbovnc file as follows:
Typical use by customer is to create a VNC server locally and then login locally to that VNC server. Because the server has an issue detecting its hostname when loged in this way the file ~/.vnc/xstartup.turbovnc has to add the following line (in RED) to work:
#!/bin/sh
unset SESSION_MANAGER
unset DBUS_SESSION_BUS_ADDRESS
OS=`uname -s`
if [ $OS = ‘Linux’ ]; then
case “$WINDOWMANAGER” in
*gnome*)
if [ -e /etc/SuSE-release ]; then
PATH=$PATH:/opt/gnome/bin
export PATH
fi
;;
esac
fi
Chempack 5 Install
- Login as vnmr1
- Copy CP5.tgz to /vnmr/userlib/chempack
- Then type:
cd /vnmr/userlib
./extract chempack/CP5
- Answer yes to questions (Install as vnmr1)
Upgrading if Current Version of VnmrJ is not 2.3A, 3.0, or 3.1:
If the current version of VnmrJ is 2.2C with the 107 patch, install the 3.2AbinLNXall304.tar.Z patch before running setacq. Once the 3.2ApsgLNXall102.tar.Z patch is released, just install the 102 patch.
Patches can be downloaded from:
Customers running 2.2C without the 107 patch, need to install the 2.2CallLNXall107.tar.Z 1 patch and run setacq before installing VnmrJ3.2.
Customers running 2.1B should contact service or AskTAC for directions to upgrade their VnmrJ.
http://tac2.cos.agilent.com/ (AskTAC )