We have a Windows 10 Pro Server connected to Nanopore and NextGen Sequencers where we would like to run docker inside WSL2, where we intend to orchestrate bioinformatic pipelines in NextFlow workflows utilizing docker runtimes, and a majority of our tasks utilizing these pipelines will utilize GPU. We are able to use our GeForce ATX GPU with CUDA/drivers installed on the Windows OS utilizing basecalling and other software with windows compiled binaries, and additionally, we have Docker Desktop running on Windows where we have ran post-secondary omics-analysis pipelines in Jupyter R/Python DS notebooks using this Docker for their runtime env. Currently, in trying to run nvdia-smi or benchmark commands using 2x docker images, and the appropriate arguments, with nvidia-docker inside WSL2, errors show these containers will not init. Below are further details:
Our main Windows OS:
| Edition | Windows 10 Pro |
|---|---|
| Version | 20H2 |
| Installed on | 11/16/2021 |
| OS build | 19042.1415 |
| Experience | Windows Feature Experience Pack 120.2212.3920.0 |
Our WSL2 version:
Linux RD-MINION 5.10.60.1-microsoft-standard-WSL2 #1 SMP Wed Aug 25 23:20:18 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
Docker Desktop Version on Windows OS:
Client:
Cloud integration: v1.0.22
Version: 20.10.11
API version: 1.41
Go version: go1.16.10
Git commit: dea9396
Built: Thu Nov 18 00:42:51 2021
OS/Arch: windows/amd64
Context: default
Experimental: true
Server: Docker Engine - Community
Engine:
Version: 20.10.11
API version: 1.41 (minimum version 1.12)
Go version: go1.16.9
Git commit: 847da18
Built: Thu Nov 18 00:35:39 2021
OS/Arch: linux/amd64
Experimental: false
containerd:
Version: 1.4.12
GitCommit: 7b11cfaabd73bb80907dd23182b9347b4245eb5d
runc:
Version: 1.0.2
GitCommit: v1.0.2-0-g52b36a2
docker-init:
Version: 0.19.0
GitCommit: de40ad0
Our WSL2 Docker Version:
nvidia-docker version
NVIDIA Docker: 2.9.1
Client:
Version: 20.10.7
API version: 1.41
Go version: go1.13.8
Git commit: 20.10.7-0ubuntu5~20.04.2
Built: Mon Nov 1 00:34:17 2021
OS/Arch: linux/amd64
Context: default
Experimental: true
Server:
Engine:
Version: 20.10.7
API version: 1.41 (minimum version 1.12)
Go version: go1.13.8
Git commit: 20.10.7-0ubuntu5~20.04.2
Built: Fri Oct 22 00:45:53 2021
OS/Arch: linux/amd64
Experimental: false
containerd:
Version: 1.5.5-0ubuntu3~20.04.2
GitCommit:
runc:
Version: 1.0.1-0ubuntu2~20.04.1
GitCommit:
docker-init:
Version: 0.19.0
GitCommit:
Finally when we run start docker, we must perform dockerd & , systemctl docker start, or service docker start do not work, but dockerd started this way also starts containerd. Other basic images run, and we are able to confirm basic tests of these that they run.
The following fails to run:
docker run -it --gpus=all --rm nvidia/cuda:11.4.2-base-ubuntu20.04 nvidia-smi
time=“2022-03-09T10:54:37.238158000-06:00” level=info msg=“starting signal loop” namespace=moby path=/run/docker/containerd/daemon/io.containerd.runtime.v2.task/moby/4cfc45a62f6b62b9ca836d408c509f800c46086dd8d0456ebe13e78bbeacc026 pid=3148
INFO[2022-03-09T10:54:37.351979600-06:00] shim disconnected id=4cfc45a62f6b62b9ca836d408c509f800c46086dd8d0456ebe13e78bbeacc026
WARN[2022-03-09T10:54:37.352034100-06:00] cleaning up after shim disconnected id=4cfc45a62f6b62b9ca836d408c509f800c46086dd8d0456ebe13e78bbeacc026 namespace=moby
INFO[2022-03-09T10:54:37.352057500-06:00] cleaning up dead shim
WARN[2022-03-09T10:54:37.357752100-06:00] cleanup warnings time=“2022-03-09T10:54:37-06:00” level=info msg=“starting signal loop” namespace=moby pid=3184
ERRO[2022-03-09T10:54:37.357979600-06:00] copy shim log error=“read /proc/self/fd/12: file already closed”
ERRO[2022-03-09T10:54:37.358424900-06:00] stream copy error: reading from a closed fifo
ERRO[2022-03-09T10:54:37.559744400-06:00] 4cfc45a62f6b62b9ca836d408c509f800c46086dd8d0456ebe13e78bbeacc026 cleanup: failed to delete container from containerd: no such container
ERRO[2022-03-09T10:54:37.567389700-06:00] Handler for POST /v1.41/containers/4cfc45a62f6b62b9ca836d408c509f800c46086dd8d0456ebe13e78bbeacc026/start returned error: failed to create shim: OCI runtime create failed: container_linux.go:380: starting container process caused: process_linux.go:545: container init caused: Running hook #0:: error running hook: signal: segmentation fault, stdout: , stderr:: unknown
docker: Error response from daemon: failed to create shim: OCI runtime create failed: container_linux.go:380: starting container process caused: process_linux.go:545: container init caused: Running hook #0:: error running hook: signal: segmentation fault, stdout: , stderr:: unknown.