> For the complete documentation index, see [llms.txt](https://help.connected.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.connected.illumina.com/dragen/dragen-v4.6/reference/dragen-multi-cloud.md). # DRAGEN FPGA Mode ## Overview DRAGEN FPGA Mode runs DRAGEN secondary analysis with a FPGA card. Mapping and alignment, variant calling, and zip and unzip of FASTQ and BAM files are accelerated on the card. You can run this mode on a DRAGEN Server or on a supported FPGA-enabled cloud instance. Use FPGA Mode when you have FPGA hardware and you need the shortest turnaround time. To compare FPGA Mode with [Software Mode](/dragen/dragen-v4.6/reference/software-mode.md), and for all deployment choices, see [Deployment Options](/dragen/dragen-v4.6/overview/deployment-options.md). {% hint style="success" %} DRAGEN FPGA Mode produces exactly the same bit-exact output as DRAGEN Software Mode. {% endhint %} ## Requirements | Requirement | Value | | --------------------- | ------------------------------------------------------------------------------------------------------------------------ | | Operating system | Red Hat Enterprise Linux (RHEL) 8.x or 9.x, and RHEL-compatible Enterprise Linux distributions. | | FPGA hardware | A DRAGEN FPGA card in a DRAGEN Server, or an FPGA-enabled AWS instance. AWS `f2.6xlarge` is recommended. | | Architecture | x86-64 | | Local storage | Fast local storage, ideally NVMe or SSD, on the compute node. Network-attached storage is supported but not recommended. | | Licensing and network | Depends on the deployment. See [DRAGEN Pricing and Licensing](/dragen/dragen-v4.6/reference/licensing.md). | FPGA Mode requires FPGA hardware. If the node has no DRAGEN FPGA card, install and run [DRAGEN Software Mode](/dragen/dragen-v4.6/reference/software-mode.md) instead. ### Network connectivity Network connectivity requirements depend on the deployment. See [DRAGEN Pricing and Licensing](/dragen/dragen-v4.6/reference/licensing.md). ## Obtain and Install How you obtain FPGA Mode DRAGEN depends on the platform. {% tabs %} {% tab title="On-premises server" %} Install the `.run` installer for your DRAGEN version from the [DRAGEN Software Support Site](https://support.illumina.com/sequencing/sequencing_software/dragen-bio-it-platform/downloads.html). Root privileges are required. ```bash sudo sh ``` The installer places application files under `/opt/dragen/` (v4.3 and later) and FPGA bitstream files under `/opt/bitstream/`. For single-version and multi-version install behavior, see [Getting Started](/dragen/dragen-v4.6/product-guides/dragen-v4.6/getting-started.md). For hardware site preparation, see [DRAGEN Server](/dragen/dragen-v4.6/reference/platform-maintenance.md). For licensing, see [DRAGEN Server Licensing](/dragen/dragen-v4.6/reference/licensing/onprem_licensing.md). {% endtab %} {% tab title="AWS" %} Build a custom AMI and install the DRAGEN RPMs on an FPGA-enabled instance. See [Building your own DRAGEN AMI](/dragen/dragen-v4.6/reference/dragen-multi-cloud/dragen-on-aws.md#building-your-own-dragen-ami). For launch, storage, and data-flow steps, see [DRAGEN on AWS](/dragen/dragen-v4.6/reference/dragen-multi-cloud/dragen-on-aws.md). For batch workloads, see [DRAGEN on AWS Batch](/dragen/dragen-v4.6/reference/dragen-multi-cloud/dragen-on-aws-batch.md). For licensing, see [BioInsight Platform Licensing](/dragen/dragen-v4.6/reference/licensing/api_key_licensing.md). {% endtab %} {% endtabs %} ### Confirm the installation Run the system check, `self_test.sh`, which exercises the FPGA card: ```bash /self_test/self_test.sh ``` A `PASS` result confirms that the FPGA card, bitstream, and software are operating. See [Running the System Check](/dragen/dragen-v4.6/product-guides/dragen-v4.6/getting-started.md#running-the-system-check). ## Performance and Tuning ### Threads FPGA Mode does not default `--num-threads` to all available cores. Host CPU threads still run stages that are not offloaded to the FPGA card. | Option | Type | Description | | --------------- | ---- | -------------------------------------------------------------- | | `--num-threads` | INT | Number of processor threads to use. Must be a positive number. | Set `--num-threads` only when you share a node or when you want to reserve cores for other work. ### Local storage DRAGEN analysis is I/O intensive, and disk throughput can limit performance. * Use fast local storage, ideally NVMe or SSD on the compute node, for inputs, outputs, and temporary files. * Keep the reference directory on local storage. Every node reads it on every run. Network-attached storage is supported but not recommended. On AWS, if local instance storage is insufficient, attach about 2 TB of EBS using four 500 GB gp3 volumes in RAID 0. See [DRAGEN on AWS](/dragen/dragen-v4.6/reference/dragen-multi-cloud/dragen-on-aws.md). ### Cloud storage * Input streaming of FASTQ files from S3 or Azure Blob Storage is supported. * Output streaming of temporary files and output files to S3 or Azure Blob Storage is not supported. * Cloud instances must use attached storage such as EBS for temporary and output files. ## Platform Guidance Use the pages in this section for cloud instance types, marketplace images, storage layout, and batch schedulers. Use [DRAGEN Server](/dragen/dragen-v4.6/reference/platform-maintenance.md) for on-premises hardware maintenance. Note: Azure FPGA instances are not available in DRAGEN 4.6. For Azure, use [DRAGEN Software Mode](/dragen/dragen-v4.6/reference/software-mode.md).
TitleTarget
DRAGEN on AWSDRAGEN on AWS
DRAGEN on AWS BatchDRAGEN on AWS Batch
DRAGEN ServerDRAGEN Server
For general DRAGEN troubleshooting, see [Troubleshooting](/dragen/dragen-v4.6/reference/troubleshooting.md). For help from Illumina, see [Support](/dragen/dragen-v4.6/reference/technical-assistance.md). --- # Agent Instructions This documentation is published with GitBook. GitBook is the documentation platform designed so that both humans and AI agents can read, navigate, and reason over technical content effectively. Learn more at gitbook.com. ## Querying This Documentation If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question. Perform an HTTP GET request on the current page URL with the `ask` query parameter, and the optional `goal` query parameter: ``` GET https://help.connected.illumina.com/dragen/dragen-v4.6/reference/dragen-multi-cloud.md?ask=&goal= ``` `ask` is the immediate question: it should be specific, self-contained, and written in natural language. `goal` is optional and describes the broader end goal you are ultimately trying to accomplish on behalf of the user. GitBook uses it to tailor the answer towards what is most useful for that goal. The response will contain a direct answer to the question and relevant excerpts and sources from the documentation. Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.