Illumina DRAGEN Server v4
Site Prep and Installation Guide

DRAGEN v4 Server

ILLUMINA PROPRIETARY
Document #200015717 v03
January 2023
For Research Use Only. Not for use in diagnostic procedures.

This document and its contents are proprietary to Illumina, Inc. and its affiliates (“Illumina”), and are intended solely for the contractual use of its customer in connection  with the use of the product(s) described herein and for no other purpose. This document and its contents shall not be used or distributed for any other purpose and/or  otherwise communicated, disclosed, or reproduced in any way whatsoever without the prior written consent of Illumina. Illumina does not convey any license under its  patent, trademark, copyright, or common- law rights nor similar rights of any third parties by this document.
The instructions in this document must be strictly and explicitly followed by qualified and properly trained personnel in order to ensure the proper and safe use of the  product(s) described herein. All of the contents of this document must be fully read and understood prior to using such product(s).
FAILURE TO COMPLETELY READ AND EXPLICITLY FOLLOW ALL OF THE INSTRUCTIONS CONTAINED HEREIN MAY RESULT IN DAMAGE TO  THE PRODUCT(S), INJURY TO PERSONS, INCLUDING TO USERS OR OTHERS, AND DAMAGE TO OTHER PROPERTY, AND WILL VOID ANY WARRANTY APPLICABLE TO THE PRODUCT(S).
ILLUMINA DOES NOT ASSUME ANY LIABILITY ARISING OUT OF THE IMPROPER USE OF THE PRODUCT(S) DESCRIBED HEREIN (INCLUDING  PARTS THEREOF OR SOFTWARE).
© 2023 Illumina, Inc. All rights reserved.
All trademarks are the property of Illumina, Inc. or their respective owners. For specific trademark information, refer to www.illumina.com/company/legal.html.
Document #200015717 v03
For Research Use Only. Not for use in diagnostic procedures.

Revision History

installation
Updated 10 GB SFP+ port interface name
Added the following information:
• Steps to activate the DRAGEN software license
• Steps to verify and install the
DRAGEN software
Updated steps to install the server license
Updated offline server commands
Removed reference to remote assistance
Removed the set server time section
200015717 v02| August 2022| Internal process change. No content changes.
200015717 v01| July 2022| Updated the server specifications. Added the server weight.

Updated the UPS recommendations. Renamed Install the Server Racks to Mount Server.

200015717 v00| June 2022| Initial Release

Overview

This resource provides instructions for setting up the Illumina® DRAGEN Server™, including preparing your site for installation and operation.
The CentOS Project will discontinue support of CentOS 7 on June 30, 2024. As a result, support for CentOS 7 on the DRAGEN Servers will end. Upgrade the operating  system to Oracle 8 to use future versions of the DRAGEN Server software. Refer to the Upgrade to Oracle 8 instructions on support.illumina.com/bulletins.html. Contact  Illumina Technical Support for additional help.
Use the following specifications and guidelines to prepare your facility:

• Space requirements
• Electrical requirements
• Environmental considerations
• Computing requirements
• Network considerations

Site Preparation

This section provides specifications and guidelines for preparing your site for installation and operation of the DRAGEN Server.

• Laboratory space requirements
• Electrical requirements
• Environmental considerations

Delivery and Setup
The DRAGEN Server is unpacked and installed by the customer. The space must be ready before delivery.
Box Dimensions
Use the following dimensions to determine transport, setup, and storage plans.

Shipping Box Components
The DRAGEN Server and components are shipped in one box. The following components are included:

• Power cord, country- specific
• DRAGEN Server license USB key
• Rack mount rails – 80 cm (31.5 in) length
• Rack mount screws
• Two SFP+ transceivers

Facility Requirements
Use the specifications and requirements provided in this section to set up your lab space.
Equipment Dimensions

Rack Requirements

If the rack is shorter than the length of the server (29.9 in) or the rails (31.5 in), the server and rails will extend beyond the length of the rack. To avoid interference with power and cable management, and to make sure the rack closes properly, use a rack with a depth of at least 29 in.
Placement Requirements
Position the DRAGEN Server to allow proper ventilation, access to one power outlet, and access for servicing.

• Allow a rack height of at least 2U.
• Make sure that there is one standard pocket outlet within 3 m (10 ft) of the server.
• Position the instrument so personnel can quickly disconnect the power cords from the outlets.

Electrical Requirements
Power Specifications

For 100–240 Volts AC, your facility must be wired with a minimum 15 amp grounded line with proper voltage. An electrical ground is required. If the voltage fluctuates more  than 10%, a power line regulator is required.
The server must be connected to a dedicated circuit that must not be shared with any other equipment.
Receptacles
Your facility must be wired with the following receptacles:

• For 100–110 Volts AC—Two 10 amp grounded, dedicated lines with proper voltage and electrical ground.
• For 220–240 Volts AC—Two 6 amp grounded lines with proper voltage and electrical ground.
• North America and Japan—NEMA 5–15.
• If the voltage fluctuates more than 10%, power line regulators are required.

Protective Earth
The DRAGEN Server has a connection to protective earth through the enclosure.
The safety ground on the power cord returns protective earth to a safe reference.
The protective earth connection on the power cord must be in good working condition when using this device.
Power Cords
The instrument comes with an international standard IEC 60320 C20 receptacle, and is shipped with a region- specific power cord. To obtain equivalent receptacles or power  cords that comply with local standards, consult a third- party supplier such as Interpower Corporation (www.interpower.com). All power cords are 2.5 m (8 ft) in length.
Hazardous voltages are removed from the instrument only when the power cord is disconnected from the AC power source. Position the server so that you can quickly  disconnect the power cord from the outlet.
To avoid power surges, use an extension cord to connect the instrument to a power supply.
Fuses
The server contains no user- replaceable fuses.

Environmental Considerations
The following table specifies temperature, humidity, and other environmental considerations for safely housing the instrument.

temperature is the operating temperature of the  DRAGEN Server. Do not allow the ambient temperature to vary by more than ±2°C.
Humidity| Maintain a noncondensing relative humidity between 10–85%.
Altitude| Locate the DRAGEN Server at an altitude below 2,000 m (6,500 ft).
Air Quality| Operate the server in a data center environment with air filtration per ISO 14644- 1 Class 8 with a 95%  upper confidence limit.
Ventilation| Consult your facilities department for ventilation requirements sufficient for the level of heat output  expected from the DRAGEN Server.
Location| Operate the server in an indoor environment only. The server is not suitable for use in locations where  children are likely to be present. The server is intended for use in a server room.

Uninterruptible Power Supply
Illumina recommends using a user- supplied uninterruptible power supply (UPS).
Illumina is not responsible for data loss caused by interrupted power, regardless of whether the DRAGEN Server is connected to a UPS. Standard generator- backed power is often not uninterruptible, so a brief power outage occurs before power resumes. This power outage interrupts analysis and data transfer.
The following table shows three example recommended UPS models for the DRAGEN Server.

Specification| North America APC Model # SMT3000RM2U| **Japan APC Model

SMT3000RMJ2U| International APC Model

**SMT3000RMI2U

---|---|---|---
Maximum Output Capacity| 2700 W 2880 VA| 2400 W 2400 VA| 2700 W 3000 VA
Input Voltage (Nominal)| 120 VAC| 100 VAC| 230 VAC
Input Frequency| 50/60 Hz| 50/60 Hz| 50/60 Hz
Input Connection| NEMA L5-30P| NEMA L5-30P| BS1363A British IEC 320 C20 Schuko CEE 7 / EU1- 16P
Built-In UPS Output Receptacles| 3xNEMA 5-15R 3xNEMA 5-20R 1xNEMA L5-30R| 3xNEMA 5-15R 3xNEMA 5-20R 1xNEMA L5-30R| 8xIEC 320 C13 3xIEC Jumpers 1xIEC 320 C19
Dimensions| 8.5 cm x 43.2 cm x 66.7 cm (3.35 in x 17.01 in x 26.26 in)| 8.7 cm x 43.2 cm x 66.7 cm| 8.6 cm x 48 cm x 68.3 cm
Rack Height| 2U| 2U| 2U
Weight| 38.45 kg (84.77 lb)| 39 kg| 44.28 kg
Typical Run Time (at 500 Watt Average Draw)| 58 minutes| 40 minutes| 38 minutes

Safety & Compliance

This section provides important safety information pertaining to the installation and operation of the DRAGEN Server. This section includes product compliance and  regulatory statements. Read this section before performing any procedures on the server.
The country of origin and date of manufacture of the server are printed on the server label.
Safety Considerations and Markings
This section identifies potential hazards associated with installing, servicing, and operating the DRAGEN Server. Do not operate or interact with the DRAGEN Server in a  manner that exposes you to any of these dangers.
General Safety Warnings
Make sure that all personnel are trained in the correct operation of the DRAGEN Server and any potential safety considerations.
Follow all operating instructions when working in areas marked with this label to minimize risk to personnel or the DRAGEN Server.
Electrical Safety Warnings
Do not remove the outer panels from the DRAGEN Server. There are no user- serviceable components inside. Operating the DRAGEN Server with any of the panels  removed creates potential exposure to line voltage and DC voltages.
Compliance and Regulatory Markings
The DRAGEN Server is labeled with the following compliance and regulatory markings.
Waste Electrical & Electronic Equipment (WEEE)
This label indicates that the instrument meets the WEEE Directive for waste.
Visit support.illumina.com/certificates.html for guidance on recycling your equipment.

Set Up the DRAGEN Server

This section provides information on installing the DRAGEN Server. Before beginning, make sure that you have all the components and your facility meets the requirements.
The following components are not included with the DRAGEN Server and are required to set up the server:

• Monitor with a VGA input
• VGA cable
• Keyboard with a USB input

Mount the Server
Use the following instructions to mount the DRAGEN Server to your server rack.
Attach Mounting Bracket to Server

1. Pull the mounting bracket rail out from the rail assembly until you reach the safety lock.

2. Press the yellow rail lock lever up, and then remove the mounting bracket rail from the rail assembly.
   

3. Align the key slots to the T studs on the sides of the server, and then slide the mounting bracket back to lock into place.
   

4. Repeat to attach the mounting bracket on the other side.

Mount the Rail Assemblies in Rack

1. Press down on the rail assembly mechanism to unlock the rear rail assembly lock.

2. Align the rail assembly into the desired server rack brackets, and then push forward to lock into place.
   An audible click indicates that the rail assembly is in place.

3. Release the yellow locking latch and push the slider forward to the rear of the rail assembly.

4. Align the rail assembly into the desired front server rack brackets, and then flip the lock mechanism forward to lock the rail assembly into place.

5. Repeat for the other rail.
   

Install the Server in the Rack
Two people are recommended for moving the server.

1. Facing the front of the rack, align the mounting brackets on the server with the slide rails inside the rack.
2. Slide the mounting brackets into the slide rails until you reach the safety locks.
3. Press both safety lock triggers down simultaneously, and then slide the server forward until it rests against the server rack.
4. Insert the required cables.
5. Insert screws into the rectangular window on the front of each lock mechanism.

Server Ports
The following figure indicates the port location on the rear of the server for each cable required when installing the Illumina DRAGEN Server.

A. VGA port (monitor)
B. 1 GB Ethernet port with interface name enp5s0 (BMC)
C. 1 GB Ethernet port with interface name enp4s0
D. 10 GB Ethernet port with interface name enp26s0f1
E. 10 GB Ethernet port with interface name enp26s0f0
F. 10 GB SFP+ port with interface name enp134s0f0
G. 10 GB SFP+ port with interface name enp134s0f1
H. Power supply inlets

Insert Cables

1. Using the VGA cable, attach the VGA monitor to the server VGA port.
2. Attach the USB keyboard to any open USB port.
3. Attach network cable RJ45 to network port D or E.

Install the Illumina DRAGEN Server
You can activate the DRAGEN Server by installing the USB license key as follows. You must activate the server before proceeding.

1. Locate the USB license key in the delivery box.
2. Plug the USB license key into any USB port on the back of the server.
3. Connect the power cord to the power supply inlet, and then to the wall outlet.
4. Connect your monitor to the DRAGEN Server using the VGA port.
5. Connect your keyboard to the DRAGEN Server using any unoccupied USB port.
6. Press the power button to turn on the server.

The DRAGEN Server performs an additional boot cycle when first turned on. The boot cycle unlocks the drive. Allow the DRAGEN Server to perform the boot cycle  without user input.
Shut Down the Server
You can shut down the DRAGEN Server directly from the command line.

1. Log in as root.
2. To initiate system shutdown, enter the following command:
   power off
   Wait a few minutes until the server comes to a complete shutdown.

Configure Settings

You can configure the following settings for the DRAGEN Server:

• Security

• Networking

• Baseboard management controller
  Security and Safety
  The DRAGEN Server is designed to resist attacks. Supplement this design with the following security recommendations:

• A secure internal LAN to prevent the distribution of data to all web browsers.

• Limited access to the DRAGEN Server to prevent the removal of the RAID controller, disk drives, and access to data. Booting in single- user mode allows access to the  whole system.

• The DRAGEN Server is designed to analyze sequencing data. Do not consider it a general- purpose computer. Refer to User Behavior on page 14 for more information on appropriate use.

Antivirus Software
Illumina does not recommend running any virus scanners on the DRAGEN Server. Virus scanners often impact the performance of High- Performance Computing (HPC) systems.

Restricted Ports and Authentication

Stack Overflow Protection
Modern processors disable coded execution in data sections of the program to address stack overflow attacks. By default, this feature is enabled.
User Behavior
The DRAGEN Server is designed for analyzing sequencing data. For quality and security reasons, the server should not be used for general- purpose computing such as web  browsing, checking email, or running third- party software. These activities can result in degraded performance or data loss. Users should also avoid storing files on the  scratch drive as it can impede the proper operation of the server.

Network Considerations
Before running tests, make sure that your network contains the required components and meets the network connection recommendations.
DRAGEN Server setup requires the following network components:

• Default gateway address

•  DNS Server IP address

• IP addresses (2)

• Subnet mask for the IP addresses
  The following operations require an external internet connection using TCP on ports 80 and 443:

• Updating the Operating System

• Access to license server

Network Connections
Use the following recommendations to install and configure a network connection:

• Recommended bandwidth for a connection is 10 Gb per second.

• Switches and other network equipment must have a minimum of 10 Gb per second.
  – Calculate the total capacity of the workload on each network switch. The number of connected instruments and ancillary equipment, such as a printer, can impact capacity.

• For 10 Gb connections, SFP+ and RJ45 connections are supported. If using SFP+ ports, twinax cables or SFP+ transceivers are required. Validated transceivers include  Intel and Finisar.

• Ask your IT professional to review network maintenance activities for potential compatibility risks with the system.

Configure the Server Network
Use the Network Manager Text User Interface (NMTUI) to configure the IP address, gateway, DNS server, and additional options for your connection.

1. Log in as root using the default password: Hello@Illumina!. The system prompts users to reset the password upon first login.

2. Enter: nmtui

3. Use the keyboard to navigate the NMTUI.

4. Select Activate a connection to view the active Ethernet connection.
   The active Ethernet connection shows an asterisk in front of the connection name.

5. Select Back.

6. Select Edit a connection.

7. Navigate to the active connection, and then select Edit.

8. Select Show next to IPv4 Configuration or IPv6 Configuration.

9. Select Automatic to choose one of the following IP configurations:
   • To remove the IP configuration, select Disabled.
   • To automatically obtain your IP address from DHCP, select Automatic.
   • To manually set your IP address, select Manual.

10. Set the following network settings:
    • IP address and subnet mask
    • Gateway
    • DNS server
    • [Optional] Search domain
    • [Optional] Select additional routing settings depending on your routing configuration.

11. Select how users can access the connection.
    • Automatically connection—The connection acts as the default connection for all users.
    • Available to all users—All users can access this connection. Disabling this option removes the connection from the list of available connections for users.

12. Select OK.

Set Server Time
Synchronize Server Time to NTP Server

1. Log in as root.

2. Check if chrony daemon is running. Enter: systemctl status chronyd

3. If the result from the previous command shows inactive or dead, enable the chrony daemon. Enter: systemctl enable chronyd

4. To start the daemon, enter: systemctl start chronyd

5. Edit /etc/chrony.conf using vi. Enter: vi/etc/chrony.conf

6. Replace the default NTP server settings to the local NTP server.
   Original default settings:
   server 0.centos.pool.ntp.org iburst
   server 1.centos.pool.ntp.org iburst
   server 2.centos.pool.ntp.org iburst
   server 3.centos.pool.ntp.org iburst
   Settings to use local NTP server(s):
   server 192.168.1.1 iburst
   server 192.168.1.2 iburst

7. To save the file, enter: :wq!

8. To restart the chrony daemon, enter: systemctl restart chronyd

9. Check the health of the local time server as follows.
   timedatectl

10. To make sure that DRAGEN Server can synchronize with the local NTP server, use one of the following commands:
    • chronyc tracking (Manual)
    • ntpdate (Automatic)
    The following is an example command: ntpdate -q 192.168.1.1

Configure BMC
You can connect to the Baseboard Management Controller (BMC) to provide remote monitoring and control for Illumina Technical Support. Refer to Server Ports on page  12 for the proper port to use.

1. Log in as root user using the root password provided in the DRAGEN Server welcome email. If you have not received your sign in credentials, contact Illumina  Customer Service.

2. If signing in for the first time, reset your password.
   Passwords must contain at least 10 alphanumeric characters and two special characters.

3. To use a static IP address, do as follows.
   a. Enter the following command:
   ipmitool lan set 1 ipsrc static
   b. To set the IP address, enter the following command: ipmitool lan set 1 ipaddr
   c. To set the netmask, enter the following command: ipmitool lan set 1 netmask

   d. To set the default gateway, enter the following command: ipmitool lan set 1 defgw ipaddr

4. Enter the IP address into the web browser. You can sign in as an admin using the password printed on the back of the DRAGEN Server.

Access the Server Remotely
To access your DRAGEN Server from a remote location, you must set your firewall zone to public and allow root login from SSH connections.
Configuring remote access allows any device on the network to access your server and exposes your server to security risks.
Set Firewall Zone
By default, the firewall is enabled and blocks all incoming connections. To allow remote SSH connections, run the following script:
/usr/local/bin/mfg_enable_network.sh
This script accomplishes the following steps:

• Sets firewall zone to public.
• Sets network interfaces to automatically start when the server is turned on.
• Allows users to log in via SSH.
• Reloads the SSHD configuration.
• Restarts the network manager service.

Allow Root Log in by SSH
To access the Illumina DRAGEN Server remotely, you must enable root log in by SSH connections. By default, root log in attempts from SSH connections are blocked.

1. Log in as root.
2. Open /etc/ssh/sshd_config.
3. Set PermitRootLogin to yes.
4. Restart sshd as follows.
   systemctl restart sshd

Activate the DRAGEN Software License

The Illumina DRAGEN Server ships with temporary short- term software licenses. The license activation process differs depending on whether the server is connected to  the internet or is offline. Root/sudo access is required to run the commands below. For assistance with the various command line options, email Illumina Technical Support.
Use the following instructions to activate your licenses.
Online Servers
For servers connected to the internet, activate your DRAGEN software license as follows.

1. Test and confirm that the server is connected to the internet.
   Example:
   ping www.illumina.com

2.  To activate the license, enter:/opt/edico/bin/dragen_lic -i auto
   3. Confirm that the license has been updated. Enter:/opt/edico/bin/dragen_lic

Offline Servers
For servers not connected to the internet, Illumina Customer Service provides the necessary license files to activate the license on the server locally. If you have not received  these license files, email Illumina Technical Support.
After you have the necessary license files, activate your DRAGEN Software license as follows.

1. Copy the license files to the server.

2. Run the following commands: rm /var/lib/edico/*.gbin sudo /opt/edico/bin/dragen_lic -i license_Genome.bin sudo /opt/edico/bin/dragen_lic -i  license_JointGenotype.bin sudo /opt/edico/bin/dragen_lic -i license_Transcriptome.bin sudo /opt/edico/bin/dragen_lic -i license_Somatic.bin sudo  /opt/edico/bin/dragen_lic -i license_CNV.bin sudo /opt/edico/bin/dragen_lic -i license_TSO500Combined.bin sudo /opt/edico/bin/dragen_lic -i license_Compression.bin (if applicable)
   sudo /opt/edico/bin/dragen_lic dragen_lic -i license_TSO500_HRD.bin (if applicable)
   sudo /opt/edico/bin/dragen_lic dragen_lic -P {Board Serial}_license.dat

3. Confirm that the license has been updated. Enter: /opt/edico/bin/dragen_lic

Running the System Check
After turning on the server, make sure that your Illumina DRAGEN Server is functioning properly by running the following self- test script: /opt/edico/self_test/self_test.sh
The self- test script performs the following actions:

• Automatically indexes chromosome M from the hg19 reference genome.
• Loads the reference genome and index.
• Maps and aligns a set of reads.
• Saves the aligned reads in a BAM file.
• Asserts that the alignments exactly match the expected results.
  Each server ships with the test input FASTQ data for this script, which is located in /opt/edico/selftest. The system check takes approximately 25–30 minutes.
  The following example shows how to run the script and the output from a successful test.

[root@edico2 ~]# /opt/edico/self_test/self_test.sh
——————————–test hash creating test hash created
——————————–reference
loading /opt/edico/self_test/ref_data/chrM/hg19_chrM reference loaded
——————————–real0m0.640s user0m0.047snot
properly paired and unmapped input records percentages: PASS
md5sum check dbam sorted: PASS
——————————–SELF
TEST COMPLETED
SELF TEST RESULT : PASS

If the output BAM file does not match the expected results, the last line of the previous text displays the following text:
SELF TEST RESULT : FAIL
If you receive a FAIL result after running the test script immediately after turning on your Illumina DRAGEN Server, contact Illumina Technical Support.

Verify and Install the DRAGEN software

Verify the DRAGEN Software Version
If you are already running the latest version of the software, refer to the llumina DRAGEN Bio- IT Platform User Guide on the DRAGEN Bio- IT Platform support page  for information on running system checks and self- tests.
Use the following commands to query the current version of the DRAGEN software and server.

• To view the current version of only the DRAGEN software, enter the following command: dragen –version
• To view the current versions of both the DRAGEN software and hardware, enter the following command: dragen_info -b

Install the DRAGEN Software

1. Download the software package from the DRAGEN Bio- IT Platform support page.
2. Enter the following command to use the self- extracting *.run file: sudo sh dragen-4.0.3-8.el7.x86_64.run
3. If prompted to switch to a new hardware version, enter y. If the hardware upgrade process is interrupted, perform the software install steps again. If the DRAGEN  software is not functional after the second install attempt, contact Illumina Technical Support.
4. Use the following halt command to power the server off and on: sudo ipmitool chassis power cycle A reboot command does not update the hardware version.

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For Research Use Only. Not for use in diagnostic procedures.
© 2023 Illumina, Inc. All rights reserved.

References

• Technical Bulletins
• Regulatory and Quality Information
• Illumina | Sequencing and array solutions to fuel genomic discoveries
• Legal | Legal Information for this website
• Interpower Website
• Illumina DRAGEN Bio-IT Platform Support
• Technical Bulletins

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