NVIDIA Parabricks v4.3.0
  1. What is NVIDIA Parabricks?

    Parabricks is a software tool for speeding up DNA and RNA analysis.

  2. Where does the name come from?

    We started building small components that could be used to speed up computation much like you'd use bricks to build a house. Those "bricks" developed into larger components, which eventually became Parabricks.

  3. What hardware and software do I need?

    For hardware, at least one supported GPU. How much memory you need depends on how many CPU cores you have. See Hardware Requirements for more details.

    For software, Parabricks comes as a Docker container so you'll need nvidia-docker2 and an OS that supports it. You'll also need an NVIDIA driver, version 525.60.13 or later. See Software Requirements for more details.

    That's all - because Parabricks comes as a Docker container no additional software installation is required.

  4. How do I ensure that my Parabricks analysis won't terminate if I lose my SSH connection?

    This is only a problem if you're running on a remote computer - an AWS instance, for example. It's not specific to Parabricks; it can happen with any program being run on the remote computer.

    A simple option is to preface your command with nohup:

    This will run your command in the background in a way that ignores all "hangup" signals (i.e. loss of SSH connection) and saves all output to a file called nohup.out.

    Another option is to use a program that supports persistent sessions such as screen or tmux.

  5. Parabricks does not run when a system is initialized using Singularity containerization; Singularity does not load all nvidia modules.

    Do this if you see an initialization error:

    This is only a concern with versions of Parabricks prior to v4.0.

  6. Can I use Parabricks on my video card?

    Probably not. Parabricks requires at least 16 GB of GPU memory (24 GB for fq2bam, unless you use the --low-memory option), and runs on 'data center' GPUs. See the Hardware Requirements for more details.

  • We're here to help! Please reach out to us on our Developer Forums if you are having trouble using the software.


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