illumina DRAGEN v3 User manual

Illumina DRAGEN Server v3
Site Prep and Installation Guide
Introduction 1
Delivery and Setup 1
Facility Requirements 2
Electrical Requirements 2
Environmental Considerations 3
Network Considerations 4
Security and Safety 5
Set Up the DRAGEN Server 6
Configure BMC 10
Configure the Server Network 11
Set Server Time 12
Configure External Storage 13
Activate DRAGEN Software License 14
Install the DRAGEN Software 16
Access the Server Remotely 16
Shut Down the Server 17
Advanced Exchange 17
Server Specifications 20
Document # 1000000097923 v02
September 2020
ILLUMINA PROPRIETARY
For Research Use Only. Not for use in diagnostic procedures.

Revision History 21
Technical Assistance 22
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Illumina DRAGEN Server v3 Site Prep and Installation Guide

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).
© 2020 Illumina, Inc. All rights reserved.
All trademarks are the property of Illumina, Inc. or their respective owners. For specific trademark information, see
www.illumina.com/company/legal.html.
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Illumina DRAGEN Server v3 Site Prep and Installation Guide

Introduction
This guide provides instructions for setting up the Illumina® DRAGEN™ Server, including preparing your site
for installation and operation. You can use the following specifications and guidelines included to prepare your
facility:
uSpace requirements
uElectrical requirements
uEnvironmental considerations
uComputing requirements
uNetwork considerations
Safety Considerations
See the DRAGEN Bio-IT Platform Safety and Compliance Guide (document # 1000000096716) for important
information about safety considerations.
Additional Resources
The DRAGEN Bio-IT Platform support pages on the Illumina website provide additional system resources.
These resources include software, training, compatible products, and the following documentation. Always
check support pages for the latest versions.
Resource Description
DRAGEN Bio-IT Platform Safety and
Compliance Guide (document #
1000000096716)
Provides information about operational safety considerations, compliance
statements, and labeling.
llumina DRAGENBio-ITPlatform User Guide
(document # 1000000070494)
Provides an overview of the platform and associated procedures. Instructions
for use, maintenance, and troubleshooting procedures are included.
Delivery and Setup
The DRAGEN Server v3 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.
Measurement Dimension
Height 41.0 cm (16.0 in)
Width 85.1 cm (33.5 in)
Depth 62.2 cm (24.5 in)
Weight 33.1 kg (73 lb)
Shipping Box Components
The DRAGEN Server v3 and components are shipped in one box. The following components are included:
uPower cord, country-specific
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uDRAGEN License USBkey
uRack mount rails
uRack mount screws
Facility Requirements
Use the specifications and requirements provided in this section to set up your lab space.
Equipment Dimensions
Measurement Dimension
Height 8.8 cm (3.5 in)
Width 47.8 cm (19 in)
Depth 49.32 cm (19.4 in)
Weight 16.10 kg (35 lbs)
Placement Requirements
Position the DRAGEN Server v3 to allow proper ventilation, access to one power outlet, and access for
servicing.
uAllow a rack height of at least 2U.
uMake sure that there is one standard pocket outlet within 10 ft (3 m) of the server.
uPosition the instrument so personnel can quickly disconnect the power cords from the outlets.
Electrical Requirements
Power Specifications
Power Specification
Power Supply Rating 1574 Watts at 100%. Maximum power draw under load
800 W
Input Voltage 100–240 V AC at 50/60 Hz, autoranging
Receptacles
Your facility must be wired with the following receptacles:
uFor 100–110 Volts AC—Two 10 amp grounded, dedicated lines with proper voltage and electrical
ground.
uFor 220–240 Volts AC—Two 6 amp grounded lines with proper voltage and electrical ground.
uNorth America and Japan—NEMA 5-15.
uIf the voltage fluctuates more than 10%, power line regulators are required.
Protective Earth
The 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.
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Power Cords
The DRAGEN Server v3 has international standard IEC 60320 C13 receptacles and is shipped with one
region/country-specific power cords.
Hazardous voltages are removed from the DRAGEN Server v3 only when the power cords are disconnected
from the AC power source.
To obtain equivalent receptacles or power cords that comply with local standards, consult a third-party
supplier such as Interpower Corporation (www.interpower.com).
CAUTION
Never use an extension cord to connect the DRAGEN Server v3 to a power supply.
Fuses
The DRAGEN Server v3 contains no user-replaceable fuses.
Environmental Considerations
The following table specifies temperature, humidity, and other environmental considerations for safely housing
the instrument.
Element Specification
Temperature Maintain a server room temperature of 0°C to 40°C. This temperature is the operating
temperature of the DRAGEN Server v3. Do not allow the ambient temperature to vary by
more than ±2°C.
Humidity Maintain a noncondensing relative humidity between 10–95%.
Altitude Locate the DRAGEN Server v3 at an altitude below 2,000 meters (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 v3.
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.
Heat Output
Measured Power Thermal Output
1100 Watts 4100 BTU/hr
Noise Output
A measurement of ≤ 70 dB is within the level of a normal conversation at a distance of approximately 1 meter
(3.3 feet).
Acoustical Performance Noise Output (dB)
Idle at 25°C Ambient 36
Max. Loading at 35°C Ambient <75
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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 v3 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 v3.
Specification Japan
APC Model
# SMX1500RMJ2U
North America
APC Model
# SMX1500RM2UNC
International
APC Model
# SMX1500RMI2UNC
Maximum
Output
Capacity
1200 W 1500 VA 1200 W 1440 VA 1200 W 1500 VA
Input Voltage
(Nominal)
100 VAC 120 VAC 230 VAC
Input
Frequency
50/60 Hz 50/60 Hz 50/60 Hz
Input
Connection
NEMA 5–15P NEMA 5–15P IEC-320 C14
Schuko CEE7/EU1-16P
British BS1363A
Built-In UPS
Output
Receptacles
Six NEMA 5–-15 R (battery backup) Eight NEMA 5–15R (battery
backup)
Eight IEC 320 C13 (battery
backup)
Dimensions 8.9 cm × 43.2 cm × 46.8 cm 8.9 cm × 43.1 cm × 49.0 cm
(3.5 in × 17.0 in × 19.3 in)
8.9 cm × 43.2 cm × 49.0 cm
Weight 27.8 kg 24.8 kg (54.6 lb) 24.8 kg
Typical Run
Time (at 500
Watt Average
Draw)
19.5 minutes 22.9 minutes 22.9 minutes
Table 1 Region-Specific UPS Recommendations
Network Considerations
Before running tests, make sure that your network contains the required components and meets the network
connection recommendations.
DRAGEN Server v3 setup requires the following network components:
uDefault gateway address
uDNS Server IP address
uIP addresses (2)
uSubnet mask for the IP addresses
The following operations require an external internet connection using TCP on ports 80 and 443:
uUpdating the software
uRemote assistance from Illumina Technical Support
uAccess to license server
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Network Connections
Use the following recommendations to install and configure a network connection:
uRecommended bandwidth for a connection is as follows.
u10 Gb per second connection to storage.
uSwitches and other network equipment must have a minimum of 10 Gb per second.
uCalculate 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.
uFor 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.
uAsk your IT professional to review network maintenance activities for potential compatibility risks with the
system.
Third-Party Software
DRAGEN Server v3 does not support software beyond what is provided at installation. Do not install any
software that was not provided with the DRAGEN Bio-IT Platform. Third-party software is untested and can
interfere with performance and security.
User Behavior
The DRAGEN Server v3 is designed to analyze sequencing data. Do not consider it a general-purpose
computer. For quality and security reasons, do not use the computer for web browsing, checking email,
reviewing documents, or other unnecessary activity. These activities can result in degraded performance or
loss of data.
Security and Safety
The DRAGEN Server v3 is designed to resist attacks. Supplement this design with the following security
recommendations:
uA secure internal LAN to prevent the distribution of data to all web browsers.
uLimited access to the DRAGEN Server v3 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.
Antivirus Software
Illumina does not recommend running any virus scanners on the DRAGEN Server v3. Virus scanners often
impact the performance of High-Performance Computing (HPC) systems.
Restricted Ports and Authentication
Outbound Connections lus.edicogenome.com port 80
Inbound Connections SSH: TCP port 22
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.
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Set Up the DRAGEN Server
This section provides information on installing the DRAGEN Server v3. Before beginning, make sure that you
have all the components and your facility meets the necessary requirements. For more information, see
Shipping Box Components on page 1 and Facility Requirements on page 2.
The following components are not included with the DRAGEN Server v3 and required to set up the sever:
uMonitor with a HDMI input
uHDMI cable
uKeyboard with a USB input
uMouse with a USB input
uTwo USB cables
Install the Server Racks
Use the following instructions to mount the DRAGEN Server v3 to your server rack.
1 Pull the mounting bracket rail out from the rail assembly until you reach the safety lock.
2 Press the safety lock trigger down, and then remove the mounting bracket rail from the rail assembly.
3 Release the sliding lock on both ends of the rail assembly.
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4 Extend the slide rail out from the rail assembly.
5 Insert the rail assembly end that was not extended into the server rack brackets.
An audible click indicates that the rail assembly is in place.
6 Push the rail assembly forward to secure.
7 Insert the other end of the rail assembly into the server rack brackets.
An audible click indicates that the rail assembly is in place.
8 Push the sliding locks forward to secure.
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9 Install the other rail assembly.
10 Insert screws into each rail assembly to secure the rail assembly to the mounting bracket.
11 Position the mounting bracket so the green edge is located at the front of the server.
12 Line up the threaded holes on the server with the corresponding holes on the mounting bracket.
13 Insert the screws.
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14 Make sure that all screws are fully seated.
15 Extend the slide rails out from the rail assembly.
16 Facing the front of the rack, lift the server between the slide rails.
17 Slide the mounting brackets into the slide rails until you reach the safety locks.
18 Press both safety lock triggers down simultaneously.
19 Slide the server forward until it rests against the server rack.
20 Insert the required cables. See Insert Server Cables on page 9.
21 Insert screws into each corner of the server to secure the server to the mounting bracket.
Insert Server Cables
The following figure indicates the port location for each cable required when installing the DRAGEN Server v3.
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Figure 1 Rear of DRAGEN Server v3
A Power supply inlet
B RJ45 10 GB Port 2
C RJ45 10 GB Port 1
D 10 GB SFP+ Port 2
E 10 GB SFP+ Port 1
F BMC
G HDMI Port (monitor)
Install the DRAGEN Server v3 License
You can activate the DRAGEN Server v3 by installing the USB license key as follows. You must activate the
server before proceeding.
1 Connect the power supply to the AC inlet, and then to a wall outlet.
2 Locate the USBlicense key in the delivery box.
3 Plug the USBlicense key into any USB port on the back of the server.
4 Connect the power cord to the power supply inlet, and then to the wall outlet.
The server powers on automatically.
5 Connect your monitor to the DRAGEN Server v3 using the HDMI port.
6 Connect your keyboard to the DRAGEN Server v3 using any unoccupied USB port.
Configure BMC
You can connect to the Baseboard Management Controller (BMC) to provide remote monitoring and control
for Illumina Technical Support.
1 Log in as root.
2 Enter the root password provided in the DRAGEN welcome email. If you have not received your sign in
credentials, contact Illumina Customer Service.
3 If signing in for the first time, reset your password.
Passwords must contain at least 10 alphanumeric characters and two special characters.
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4 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:
ipmitool lan set 1 ipaddr <IP address>
c To set the netmask, enter:
ipmitool lan set 1 netmask <netmask ID>
d To set the default gateway, enter:
ipmitool lan set 1 defgw ipaddr <gateway ID>
5 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 v3.
Configure the Server Network
Using the Network Manger Text User Interface (NMTUI), you can configure the IP address, gateway, DNS
server, and additional options for your connection.
1 Enter the user name and password information included in your Welcome email.
2 Enter:
nmtui
3 Use your keyboard to navigate the NMTUI.
4 Select Activate a connection to view your 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 your 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:
uTo remove the IP configuration, select Disabled.
uTo automatically obtain your IP address from DHCP, select Automatic.
uTo manually set your IP address, select Manual.
10 Set the following network settings:
uIP address and subnet mask
uGateway
uDNS server
u[Optional] Search domain
11 [Optional] Select additional routing settings depending on your routing configuration.
12 Select how users can access the connection.
uAutomatically connection—The connection acts as the default connection for all users.
uAvailable to all users—All users can access this connection. Disabling this option removes the
connection from the list of available connections for users.
13 Select OK.
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Set Server Time
Set Server Time to Local Time Zone
1 Log in as root.
2 Check if the current server time reflects the local time zone using the date command. Enter:
date
3 Check for a nearby city with the correct time zone using the timedatectl list-timezones
command.
For example, use the following command to find time zones in Asia:
timedatectl list-timezones | grep Asia
4 Change the server time to local time using the timedatectl set-timezone command.
Example:
timedatectl set-timezone Asia/Singapore
5 To make sure that the server time has changed, enter:
date
ls -l /etc/localtime
Synchronize Server Time to NTP Server
1 Log in as root.
2 Check if chrony daemon is running. Enter:
systemctl enable 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.
Example:
<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:
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:wq!
8 To restart the chrony daemon, enter:
systemctl restart chronyd
9 Check the health of the local time server. Enter:
timedatectl
10 Make sure that DRAGEN can synchronize with the local NTPserver using the ntpdate command.
Example:
ntpdate -q 192.168.1.1
Configure External Storage
The DRAGEN Server v3 storage uses PCIe NVMe: Micron 9300 max series 6.4TB NVMe U.2 SSD and SATA
III SSD: Transcend 2.5“ 256GB SATAIII SSD. Use the instructions in this section to mount an external storage
server.
Mount NFS on DRAGEN Server
1 Locate your NFS server and share name.
Example:
uServer: 192.168.100.100
uShare name: /share
2 Use server:/share name for the mount location.
Example:
192.168.100.100:/share.
3 To map this share to /mnt on the DRAGEN Server v3, run the following command as root on your
system:
mount -t nfs 192.168.100.100:/share /mnt
4 Share is mounted at 192.168.100.100:/share to the local file system under /mnt.
Mount SMB/CIFS on DRAGEN Server
1 Locate your SMB/CIFS server and share name.
Example:
uServer: 192.168.100.100
uShare name: /share
2 Locate the user name and password required to access this share (if applicable).
Example:
uUser name: sbsuser
uPassword: sbs123
3 Use //server/share name as the mount location.
Example:
//192.168.100.100/share.
4 To map this share to /mnt on the DRAGEN Server v3, run the following command as root on your local
system:
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mount -t cifs -o user=sbsuser //192.168.100.100/share /mnt
5 Enter password when prompted.
6 Share is mounted at //192.168.100.100/share to the local file system under /mnt.
Add NFS or SMB mount to /etc/fstab
1 Add the network share to /etc/fstab so that the mount is permanent across reboots.
Using the previous examples in Mount NFS on DRAGEN Server on page 13 and Mount SMB/CIFS on
DRAGEN Server on page 13, the following is an example basic entry for a NFS or SMB mount:
NFS:
192.168.100.100:/share /mnt nfs rsize=8192,wsize=8192 0 0
SMB:
//192.168.100.100/share /mnt cifs user=sbsuser,pass=sbs123 0 0
Activate DRAGEN Software License
The DRAGEN Server v3 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 at [e-mail]. 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:
uping 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
CustomerService at [e-mail].
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:
sudo rm /var/lib/edico/*.gbin
sudo /opt/edico/bin/dragen_lic -i license_genome.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 -P license.dat
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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 DRAGEN Server v3 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:
uAutomatically indexes chromosome M from the hg19 reference genome.
uLoads the reference genome and index.
uMaps and aligns a set of reads.
uSaves the aligned reads in a BAM file.
uAsserts 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/self_test. 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, then 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 DRAGEN Server v3,
contact Illumina Technical Support.
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Install the DRAGEN Software
If you are already running the latest version of the software, see the llumina DRAGENBio-ITPlatform User
Guide (document # 1000000070494) for information on running system checks and self-tests.
1 Use the following commands to query the current version of the DRAGEN software and server.
uTo view the current version of only the Local Analysis Software, enter the following command:
dragen --version
uTo view the current versions of both the Local Analysis Software and hardware, enter the following
command:
dragen_info -b
2 Download the software package from theDRAGEN Bio-IT Platform support page.
3 Enter the following command to use the self-extracting .run file:
sudo sh dragen-3.3.7.el7.x86_64.run
4 If prompted to switch to a new hardware version, enter y.
CAUTION
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.
5 Use the following halt command to power the server off and on:
A reboot command does not update the hardware version.
sudo ipmitool chassis power cycle
Access the Server Remotely
To access your DRAGEN Server v3 from a remote location, you must set your firewall zone to public and allow
root log in from SSH connections.
CAUTION
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, the
firewall zone must be set to public.
1 Log in as root.
2 Set the default firewall zone to public. Enter:
firewall-cmd --set-default-zone=public
Allow Root Log in by SSH
To access the DRAGEN Server v3 remotely, you must enable root log in by SSH connections. By default, root
log in from SSH connections are blocked.
1 Log in as root.
2 Open /etc/ssh/sshd_config.
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3 Set PermitRootLogin to yes.
4 Restart sshd. Enter:
systemctl restart sshd
Shut Down the Server
You can shut down the DRAGEN Server v3 directly from the command line.
1 Log in as root.
2 To initiate system shutdown, enter:
poweroff
3 Wait a few minutes until the server comes to a complete shutdown.
Advanced Exchange
Because the DRAGEN Server v3 has no serviceable parts, Illumina uses an Advanced Exchange replacement
model to rectify issues that cannot be resolved remotely.
Advanced Exchange replaces a damaged or defective DRAGEN Server v3 with a replacement server. To
minimize downtime, you receive the replacement system before shipping back the original. The time it takes
to ship the replacement can vary by region.
Regional Applicability
Advanced Exchange is available in all regions.
Receive a Replacement System
1 After a system check and other troubleshooting efforts have failed, email Illumina Technical Support at
[e-mail].
uMake system check results available to Technical Support.
2 If Technical Support cannot resolve the issue remotely, a return is initiated and an order is placed for a
replacement system.
3 When you receive the replacement server:
u Save all the packaging . The packaging is used to return the original server.
uSet aside the return documents, which include a UPSreturn label and commercial invoice (for
international shipments).
uVerify receipt and condition of the server.
Return the Original Server
Shut Down and Disconnect
1 If the DRAGEN Server v3 is turned on, do as follows.
a Back up all your data.
b Delete any files and folders you do not want to share with Illumina.
c Make sure that the server is not being used.
d Shut down the server. For instructions, see Shutting Down the Server on page 1.
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