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Docker in the Toil appliance container does not know about --gpus #4282

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adamnovak opened this issue Nov 18, 2022 · 1 comment · Fixed by #4290
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Docker in the Toil appliance container does not know about --gpus #4282

adamnovak opened this issue Nov 18, 2022 · 1 comment · Fixed by #4290
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bug good first issue intern

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adamnovak commented Nov 18, 2022 •
edited by unito-bot
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@glennhickey says that you can't use the Docker client we ship in the Toil appliance with the newly-upstreamed --gpus option:

docker run -it --rm --gpus all  nvidia/cuda:11.4.3-runtime-ubuntu20.04 bash
unknown flag: --gpus
See 'docker run --help'.

We should update our Docker client to one that supports this option.

Related to #4199.

┆Issue is synchronized with this Jira Story
┆Issue Number: TOIL-1247
This was referenced Nov 18, 2022
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@adamnovak
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According to ComparativeGenomicsToolkit/cactus#844, Glenn wants this for the next Toil release.

adamnovak added a commit that referenced this issue Nov 29, 2022
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Switch to Ubuntu-provided Docker to fix #4282
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@adamnovak adamnovak mentioned this issue Nov 29, 2022
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Change to new Aventer Mesos URL DataBiosphere/toil
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