ubuntu self-upgrade kit for torrent servers · ubuntu self-upgrade kit for torrent servers pub. no....

Ubuntu Self-Upgrade kit for Torrent Servers

Pub. No. MAN0016115 Rev. A

Product informationThe procedure described in this document allows users to upgrade a Torrent Server that is shipped with an Ion PGM™ or Ion Proton™

sequencer that runs the Ubuntu 10.04 Operating system.

Note: The following procedure is a self-upgrade process that requires the user to have proficiency using command-line interface with theUbuntu Operating System. All data on the server must be backed up before starting the upgrade process.

WARNING! Issues arising from this upgrade process are not covered by the standard instrument warranty. If you would like tohave an Ion Torrent™ Service Engineer perform the upgrade for your server, please contact support.

WARNING! This upgrade process will delete all data on Dell Precision™ T7500 servers that shipped with your Ion PGM™

instrument. If you have a Dell™ PowerEdge™T620 server, which shipped with an Ion Proton™ Instrument, this process will preservedata during the upgrade process. In both cases, we recommend backing up any data that needs to be preserved to an externalstorage device.

Note: If this process fails or stops at any point during download, disk creation, or acknowledgement, you will be able to pick up where youleft off by rerunning the most recent command. Please read the on-screen text carefully before proceeding with a y or n response toquestions. When a wrong response is input, the process will exit and you may need to start the process over again.

Requirements for upgrade• USB hard drive larger than 32 Gb: USB drives with a mechanical drive are ideal, as they are faster than most flash drives. Please note

that this USB drive will be formatted during this process.

• A broadband internet connection capable of downloading a 16-GB file

• A Torrent Server running the Ubuntu 10.04 Operating System

• A Keyboard and Monitor for the Torrent Server

Upgrading your server to Ubuntu 14.04Upgrading your server to Ubuntu 14.04 is a two-part process:

• Download the software and create a bootable USB drive with Ubuntu 14.04 and Torrent Suite Software.

• Boot to the USB drive and reimage the Torrent Server.

PRODUCT INFORMATION SHEET

For Research Use Only. Not for use in diagnostic procedures.

Download the software and create a bootable USB

1. SSH to the Torrent Server as the user "ionadmin" via your preferred SSH client. You can also run these commands from the console.

2. Run the command "sudo apt-get update" to fetch the latest package versions available (while typing the command, ignore doublequotes).

2 Ubuntu Self-Upgrade Kit

3. Run the command "sudo apt-get install pv" to install the package "pv". You may be prompted for an acknowledgement to install thepackage.

Ubuntu Self-Upgrade Kit 3

4. Run the command "sudo apt-get install ion-tsosupgrade" to install the package "ion-tsosupgrade". You may be prompted for anacknowledgement to install the package.


5. Run the command "sudo mk_usb_osup_kit" to run the software download script.

6. At this point, you will be prompted multiple times to accept the EULA for downloading the software and creating the bootable USB.You can use the Page up and Page down buttons to review them. You must accept the EULA(s) to continue to the download promptas shown below. At this prompt, enter y to begin the download.


7. You can monitor the download process on the screen. This may take several hours depending on your network bandwidth.

8. When the download is complete, the server will check for the consistency of the downloaded file and you will be prompted to insert aUSB drive on the Torrent Server. Insert a USB drive on the Torrent Server, then enter y to proceed.


9. On the next prompt, you need to select the destination USB drive. All data on this drive will be deleted when you make this selection.Please enter the number corresponding to the drive you would like to use.

10. Once you make the selection, you will be prompted to acknowledge that all data on the drive will be overwritten. Enter y to proceed.


11. The software image install process may take about 25 minutes or longer depending on the USB drive. You can monitor the progress ofthe install on the screen. When the drive is ready, you will see the following message on the screen.

12. This completes the first part of upgrade process. Please proceed with part 2.

Boot from the USB and install Ubuntu 14.04 on the Torrent Server

1. Plug-In the Bootable USB drive that has been created into one of the USB ports on the server.

2. Reboot the server by logging in as "ionadmin" via the console, then type the command "sudo reboot".

3. When the server reboots, press one of the following to select the boot options: Press F11 for a Dell™ PowerEdge™ T620 server or F12 fora Dell Precision™ T7500 server.

For a Dell™ PowerEdge™ T620 server: Proceed to step 4.

For a Dell Precision™ T7500 server: Proceed to step 5.


4. Dell™ PowerEdge™ T620 server:

a. On the next screen, scroll down to select the BIOS boot menu option, then press the enter key.


b. On the next screen, scroll over to the option "Hard Drive C". You will be presented with sub scroll menu as shown below, withan option to boot from the USB device. Note that the name of the device in your case may be different.

c. Proceed to step 6.


5. Dell Precision™ T7500 server:

a. On the next screen, your bootable USB will be listed as the second option. Scroll over to highlight the option as shown in theimage below, then press the enter key to boot from the device.

b. Proceed to step 6.

6. Upon boot, you will be presented with a console screen and a command prompt.


7. Type in the command "sudo os_upgrade", then press the enter key to initiate the upgrade process.


8. Acknowledge that you would like to upgrade your Operating System by entering y at the prompt.


9. You will be prompted a second time to acknowledge the upgrade. Enter y to proceed.


10. When the upgrade is complete, you will see the message following on the screen.

11. Type "sudo reboot" on the console, then press the enter key to reboot the server.

Wait for the server to boot up normally. You have successfully upgraded your server! Proceed to Post-Upgrade verification.

Post-Upgrade verification

1. If the server is no longer accessible with your old IP address, run the command "ifconfig" on the console to check the new IP address.

2. Check access to Torrent Browser and login (for Dell Precision™ T7500 servers, the password would be reset to "ionadmin").

3. If you have a Dell™ PowerEdge™ T620 server, access old reports to ensure that the old data is accessible.

4. Reboot your instrument and ensure that it is connected to the server.

5. You will need to update your instrument software. Please refer to the Torrent Suite™ 5.2 release notes on how to perform thatprocedure.

Important log file locations for troubleshootingThe file "/tmp/mk_usb_osup_kit.log" on the Torrent Server captures the log during download and preparation of the bootable USB drive.

The directory "/home/ionadmin" on the bootable USB will contain a file in the format " os_upgrade_<systemserialnumber>_<date>.log",which captures logs from the OS upgrade process.


The directory "/home/ionadmin" on the bootable USB will contain a subdirectory with the format " os-migration-<systemserialnumber>_<date>.log", which captures settings and log files.

Customer and technical supportVisit thermofisher.com/support for the latest in services and support, including:

• Worldwide contact telephone numbers

• Product support, including:– Product FAQs

– Software, patches, and updates

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• Order and web support

• Product documentation, including:– User guides, manuals, and protocols

– Certificates of Analysis

– Safety Data Sheets (SDSs; also known as MSDSs)

Note: For SDSs for reagents and chemicals from other manufacturers, contact the manufacturer.

The information in this guide is subject to change without notice.

DISCLAIMER: TO THE EXTENT ALLOWED BY LAW, LIFE TECHNOLOGIES AND/OR ITS AFFILIATE(S) WILL NOT BE LIABLE FOR SPECIAL, INCIDENTAL, INDIRECT, PUNITIVE,MULTIPLE, OR CONSEQUENTIAL DAMAGES IN CONNECTION WITH OR ARISING FROM THIS DOCUMENT, INCLUDING YOUR USE OF IT.

Revision history: Pub. No. MAN0016115

Revision Date DescriptionA September 2016 New document

LICENCE: See the End User License Agreement in the software installer for details. You must agree to the terms of the license before installing or using the software.

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12 September 2016

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