Trouble running parabricks fq2bam

Post author
Justin Rhoades

Hello,

I'm trying to run the fq2bam workflow from the Clara-Parabricks workspace provided on Terra. I'm getting an error:
[Parabricks Options Error]: Could not find accessible GPUs. Please make sure the container options enable GPUs

Is there anything special I need to do to be able to utilize GPUs in my workflows? Thanks!

-Justin

Comments

5 comments

  • Comment author
    Samantha (she/her)

    Hi Justin Rhoades,

    Thanks for writing in about this issue. Since the error message is coming from Parabricks, this may end up being an issue better suited for the Nvidia's Developer Forum. However, I'd like to confirm that Terra/GCP are at least provisioning the correct VM with requested GPUs.

    Can you share the workspace where you are seeing this issue with Terra Support by clicking the Share button in your workspace? The Share option is in the three-dots menu at the top-right.

    1. Toggle the "Share with support" button to "Yes"
    2. Click Save

    Please provide us with

    1. A link to your workspace
    2. The relevant submission ID
    3. The relevant workflow ID

    Kind regards,

    Samantha

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  • Comment author
    Justin Rhoades

    Thanks for taking a look, Samantha. I'm a little surprised because we are running the workflow exactly as provided by Nvidia but something appears to be wrong.

    Workspace: https://app.terra.bio/#workspaces/blood-biopsy/test_parabricks_workflows

    submission ID: a589889e-a56e-4ef7-87df-4adde6d4bbff

    workflow ID: ed139533-51c6-40ff-891a-19edd6e1b2de

    -Justin

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  • Comment author
    Justin Rhoades

    Hi Samantha,

    Just wanted to follow up and see if you were able to take a look at this. We're on a bit of a time crunch and I wanted to see if you could identify anything from your end. I've also posted on the Nvidia forum but haven't heard back yet. Thanks for your help!

    -Justin

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  • Comment author
    Samantha (she/her)

    Hi Justin,

    Thanks for following up. I apologize I missed your previous response.

    I took a look at the submission and everything looks fine on the Terra/GCP end. Your workspace Google Project isn't running into any quota issues with GPUs and Terra is able to create a VM with GPUs for your task.

    So it seems like the issue is with Parabricks trying to access those GPUs. I would suggest following up with the Nvidia team regarding this.

    Best,
    Samantha

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  • Comment author
    Justin Rhoades

    Hi Samantha,

    Thanks for taking a look. Sounds like I need to discuss with Nvidia to figure out what's going on.

    -Justin

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