Using Singularity for the docker image

Healthcare Parabricks
1

Running the Parabricks docker image using Singularity doesn’t get me the Singularity terminal. Has it been tested yet?

2

Hey @tnnandi,

Are you running the latest Parabricks 4.0 container? Which version of Parabricks are you running?

Thanks!

3

Yes, I’m using 4.0.0-1 from Nvidia Clara Parabricks | NVIDIA NGC. FYI: I’m using the same Singularity installation to load GATK4 images so I don’t think Singularity is the issue. Also, I’m having the same problem for other NVIDIA containers too, e.g. RAPIDS.

4

Thanks, I could resolve the issue related to the container: I had to first check out a GPU node on the cluster before executing “run singularity shell --nv image_name.img”.

5

Hey @tnnandi,

I’m glad you were able to figure it out. Let us know if you have any other questions!

Thanks,