mdrun crashes with GPU settings on a machine with GPU

[ndonyapour]

Hello,

I am trying to run MD using the quay.io/biocontainers/biobb_md:3.7.2--pyhdfd78af_0 docker with GPU settings on a machine with 4 GPUS, but it crashes with the following error:

Fatal error:
Cannot run short-ranged nonbonded interactions on a GPU because there is none detected.

I would be grateful for any insight you can provide.

Thank you,
Nazanin

[PauAndrio]

Hi @ndonyapour,

As far as I know: "The Docker engine doesn’t natively support NVIDIA GPUs as it uses specialized hardware that requires the NVIDIA driver to be installed.". Even thought, there are some methods to allow docker containers access the system's GPUs link here we do not support them.

However, If you want to use the GPUs I recommend installing, the last version of biobb_gromacs (biobb_md is deprecated) and a GPU enabled GROMACS (gromacs==2022.3=nompi_cuda_ha81c2ac_0) preferably using Anaconda.

Regards,
Pau

[ndonyapour]

Hi @PauAndrio

Thank you for your response. I believe we can run MDs with GPU-enabled docker containers, and here shows an example of running MD on GPUs with containers. I tried nvcr.io/hpc/gromacs:2021 Gromacs container, and it worked on my machine.

Thank you!
Nazanin

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This issue was closed because it has been inactive for 14 days since being marked as stale.

[PauAndrio]

Sorry @ndonyapour, enable GPU usage in the biobb_gromacs docker is not a priority for our team right now.