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System Requirements

Supported systems

Instrument Instrument software
Revio® system Instrument software v13.3, all chemistries
Vega™ system Instrument software v1.1.0, all chemistries

Sequel® II systems, Sequel IIe systems, and Sequel systems are not supported.

Operating Systems

Supported Distributions Specification
Rocky Linux 9 & 10
Ubuntu 22.04 & 24.04

Warning

  • SMRT Link is not guaranteed to work on operating system versions that are no longer supported by their vendors.
  • SMRT Link server software cannot be installed on Mac OS or Windows systems.

Hardware configuration

There are three hardware configuration options for on-prem SMRT Link installation:

  1. SMRT Link (multi-node)
  2. SMRT Link (single-node)
  3. SMRT Link Lite

Which configuration option to choose depends on your available compute resources and if you need SMRT Analysis (push-button secondary analysis).

Configuration Option CPU RAM Local Storage Use Cases
SMRT Link
multi-node		 Full SMRT Analysis support
Head Node 8 cores 32 GB 500 GB SSD
Compute Node(s) 64 cores 4 GB/core (256 GB) 100 GB SSD or HDD
SMRT Link
single-node		 16 cores 64 GB 1 TB SSD Limited SMRT Analysis support
SMRT Link Lite 4 cores 16 GB 50 GB SSD No SMRT Analysis

SMRT Link Lite is optimized for non-server hardware by disabling compute-intensive components.

In the SMRT Link single-node configuration, certain workflows may be unsupported or limited by the maximum input file size for a single-node system. Below is a list of recommended input size limits for datasets when performing analysis with a single-node configuration.

Additionally, it is recommended to adjust the concurrent-job-limit in Step 9 of the SMRT Link installation process or manually edit the $SMRT_ROOT/userdata/generated/config/cromwell.conf file to ensure that the number of concurrently running jobs does not exceed the available memory on your single-node system.

Workflow Limit
HiFi Mapping 150 Gb
Read Segmentation no limit
Iso-Seq Analysis 20 M reads
Single cell Iso-Seq Analysis 60 M reads
Target Enrichment no limit but disable variant calling
PureTarget repeat expansion no limit
Variant Calling not supported
Microbial Genome Analysis no limit

Software Dependencies

  • SMRT Link server should run on a dedicated 64-bit Linux host with libc 2.17 or greater.
  • SMRT Link requires the Google Chrome web browser.
  • SMRT Link requires a minimum screen resolution of 1600 by 900 pixels.

If you are installing a full SMRT Link instance and want to use SMRT Analysis to run push-button analyses there are additional software requirements.

Job Management System (JMS)

Configuring SMRT Link with a Job Management System (JMS) is required for SMRT Analysis. Using unsupported JMS may require additional user provided configuration.

  • SLURM (supported)
  • LSF
  • PBS

Singularity

Singularity v3.10.5 or later is required for the Variant Calling and Target Enrichment analysis workflows. Apptainer may be used as a drop-in replacement for Singularity.

  • We recommend installing the Singularity through the package manager (e.g., apt, yum), with the setuid bit enabled (chmod u+s singularity) in the /bin or /usr/bin directory. The singularity binary should then have -rwsrxr-x permissions.
  • Because a SMRT Link server running SMRT Analysis should be configured to run with SLURM, we recommend installing the singularity-ce package on the SMRT Link server, as well as each of the nodes within the relevant partition where you are submitting jobs.
  • Singularity should not be installed in an NFS area of the file system.
  • The singularity binary cannot be installed to any file system area mounted with the nosuid and/or noexec mount options.
  • To run Variant Calling or Target Enrichment, Singularity requires the following Docker images:
    • docker://google/deepvariant:1.6.1
    • docker://google/deepvariant:1.6.1-gpu
    • docker://quay.io/biocontainers/whatshap:1.4--py39hc16433a_1
    • docker://ghcr.io/dnanexus-rnd/glnexus:v1.4.1

To save these images locally, we provide a script, $SMRT_ROOT/admin/bin/fetch-singularity-cache, which uses the root account to download the images, using /tmp as a temporary file space, before depositing the .sif files into $SMRT_ROOT/userdata/singularity and changing ownership to the requesting user. We recommend running this script after installing SMRT Link.

Note

DeepVariant 1.9.0 is the newest model and trained on SPRQ sequencing chemistry. It is not yet available for use with SMRT Link but is available in our GitHub PacBio WGS Variant (WDL) Pipeline (for advanced users).

Server environment

Definitions and variables

  • $SMRT_USER: Dedicated service account to install and run SMRT Link
    • Recommend username: smrtanalysis
  • $SMRT_ROOT: The SMRT Link installation root directory
    • Recommended install location: /opt/pacbio/smrtlink
  • smrtlinkhost.mydomain.com: The fully-qualified domain name of the SMRT Link Install Host.
  • smrtlinkhost: The short host name of the SMRT Link Install Host.

We recommend setting SMRT_USER and SMRT_ROOT in your shell profile to avoid having to type them repeatedly.

export SMRT_USER=smrtanalysis
export SMRT_ROOT=/opt/pacbio/smrtlink

Note

  • The base directory /opt/pacbio/ should be created prior to installation and owned by $SMRT_USER with read/write/execute permissions.
  • The smrtlink/ directory should not exist prior to installation as it will be created during installation
  • db_datadir, jobs_root, and tmp_dir can be modified during installation or using $SMRT_ROOT/admin/bin/smrt_reconfig scripts.

Warning

Do not install SMRT Link as the root user!

Associated install directories

Directory name Description Default Permissions Servers requiring access via the same PATH
$SMRT_ROOT SMRT Link installation directory /opt/pacbio/smrtlink rwx for $SMRT_USER SMRT Link server and all compute nodes (NFS)
db_datadir SMRT Analysis database directory
During installation, a symbolic link is set from $SMRT_ROOT/userdata/db_datadir to the desired location.		 $SMRT_ROOT/userdata/db_datadir.default rwx for only $SMRT_USER SMRT Link server only (not NFS)
jobs_root SMRT Analysis workflow output/results directory
During installation a symbolic link is set from $SMRT_ROOT/userdata/jobs_root to the desired location.		 $SMRT_ROOT/userdata/jobs_root.default rwx for $SMRT_USER SMRT Link server and all compute nodes (NFS)
tmp_dir SMRT Analysis temporary directory used for fast I/O operations
During installation a symbolic link is set in $SMRT_ROOT/userdata/tmp_dir to the desired location for this database		 /tmp/smrtlink rwx for $SMRT_USER SMRT Link server only (not NFS)

Note

Storage Considerations: Job storage requirements depend on utilization and analyses performed. jobs_root is unrelated to storage requirements related to instrument data transfer.

  • For the Revio system: Up to 78 TB/year, assuming ~60 GB of HiFi data per SMRT Cell and 1,300 SMRT Cells per year.
  • For the Vega system: Up to 6 TB/year, assuming ~30 GB of HiFi data per SMRT Cell and 200 SMRT Cells per year.

Other environment considerations

  • No other daemons/services processes are bound to the same ports as the SMRT Link services. Ideally, the SMRT Link server should be dedicated to only running SMRT Link services.
  • PacBio highly recommends that the system clock be synchronized to a domain or public NTP time server.
  • The $SMRT_USER service account must have both the nofile and nproc soft user limits set to a minimum of 8192. (See the ulimit and limits.conf Linux man pages for more information).
  • The host operating system must provide the en_US.UTF-8 locale/character set.
  • SMRT Link and SMRT Link Lite are not designed to handle changes in the hostname. If you are using them to connect to a Revio or Vega instrument you should ensure that the configured hostname is and will remain accessible across the network.

Network Configuration

Firewall Settings: Ensure ports are open and not blocked by firewalls. No other daemons/services processes can be bound to the same ports as the SMRT Link services.

Source Destination Port Description
Customer laptop/PC SMRT Link Server 8243/tcp SMRT Link web services and GUI https and communication from instrument
Customer laptop/PC SMRT Link Server 9443/tcp SMRT Link administration
Disabled by default in SMRT Link services
Must be manually enabled using --enable-keycloak-console
Revio/Vega system SMRT Link Server 8243/tcp Communication from instrument to SMRT Link
SMRT Link Server Revio/Vega system 9243/tcp Communication from SMRT Link to instrument
SMRT Link Server PacBio Event server
(https://smrtlink-eve.pacbcloud.com)		 443/tcp Optional reporting of server metrics to PacBio Tech support
SMRT Link Server PacBio Update server
(https://smrtlink-update.pacbcloud.com)		 443/tcp Downloading chemistry updates
SMRT Link server Shared Network File System (NFS) NFS ports (may vary depending on configuration) Shared file system (NFS) storage for analysis data
HPC nodes Shared Network File System (NFS) storage¹ NFS ports (may vary depending on configuration) Shared file system (NFS) storage for analysis data

If you are connecting SMRT Link to an instrument, please be aware of these additional ports that may need to be opened in your firewall to enable the instrument to communicate with SMRT Link, transfer data, and connect to PacBio for remote support.

Source Destination Port Description
Revio/Vega system PacBio SecureLink Servers (see below) 22/tcp, 80/tcp, or 443/tcp Communication for remote support (PacBio Insight)
Revio/Vega system Storage (cloud or local) SSH: 22/tcp
Cloud: 80/tcp or 443/tcp depending on protocol		 Data transfer from instrument to customer storage
Revio and Vega system Customer or external NTP servers 123/udp Used for updating machine time. Defaults to pool.ntp.org
Revio and Vega system Customer server 53/udp or 53/tcp Nameservers

PacBio SecureLink Servers

Region Servers Ports Required
US securelink-us.pacificbiosciences.com (34.228.163.151)
securelink-us-001.pacificbiosciences.com (34.228.163.151)
securelink-us-002.pacificbiosciences.com (18.207.27.182)		 22, 80, or 443/TCP
EMEA securelink-emea.pacificbiosciences.com (3.122.45.57)
securelink-emea-001.pacificbiosciences.com (3.122.45.57)
securelink-emea-002.pacificbiosciences.com (3.121.132.217)		 22, 80, or 443/TCP
APAC securelink-apac.pacificbiosciences.com (3.0.254.58)
securelink-apac-001.pacificbiosciences.com (3.0.254.58)
securelink-apac-002.pacificbiosciences.com (13.251.34.130)		 22, 80, or 443/TCP

Full Network Diagram

User Authentication (Optional)

SMRT Link supports integration with LDAP for user login authentication, as well as using local Keycloak users that exist only within SMRT Link. SMRT Link can also leverage Single Sign-On (SSO) when configured through Keycloak, allowing users to authenticate once and access multiple systems seamlessly.

If you are interested in configuring SMRT Link integration with your organization’s LDAP or SSO setup, PacBio recommends consulting your LDAP or identity administrator to determine the correct settings.

See Advanced Topics for more information on configuring LDAP and SSO in Keycloak.

SSL/TLS Certificate (Optional)

SMRT Link uses SSL/TLS to encrypt logins and data transmitted via HTTPS. SMRT Link includes an authentication server (Keycloak), which can integrate with LDAP/AD or Single Sign-On (SSO) to enable secure user authentication with your organization’s credentials. To ensure a secure connection between the SMRT Link server and your browser, a domain-specific SSL certificate can be installed after SMRT Link installation.

See Advanced Topics for more information on installing an SSL certificate for SMRT Link.