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Deeplabcut Software Installation Procedure #843

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Premas opened this issue Oct 28, 2024 · 3 comments
Open

Deeplabcut Software Installation Procedure #843

Premas opened this issue Oct 28, 2024 · 3 comments
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fabric: cheaha Docs related to Cheaha platform feat: article New article or section request

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@Premas
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Premas commented Oct 28, 2024

What would you like to see added?

Based on multiple requests regarding the installation process for DeepLabCut on Cheaha, we propose creating a dedicated section in our docs.

The section will cover the following topics,

  1. Installation of Deeplabcut on Cheaha
  2. Known issues related to the software:
  • Enabling GUI mode functionality
  • Resolving library linking errors
@Premas Premas self-assigned this Oct 28, 2024
@Premas Premas added fabric: cheaha Docs related to Cheaha platform feat: article New article or section request labels Oct 28, 2024
@Premas
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Premas commented Oct 28, 2024

Installed DeepLabCut using the conda environment provided on their GitHub page.
Encountered the following error when using Deeplabcut.
ImportError: /lib64/libstdc++.so.6: version `GLIBCXX_3.4.20' not found (required by /home/prema/.conda/envs/DEEPLABCUT/lib/python3.10/site-packages/zmq/backend/cython/../../../../../libzmq.so.5)

To resolve this issue, update the LD_LIBRARY_PATH to include the path to libstdc++.so.6, which can be found in the lib folder of the Conda environment. Execute the following command in the terminal:

export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$HOME/.conda/envs/env_name/lib

@Premas
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Premas commented Nov 15, 2024

We have created a community container for DeepLabCut software in our RC Gitlab page.

The reported GLIBC error does not occur when using this container.

@Premas
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Premas commented Nov 19, 2024

Installing DeepLabCut Software and User Guide

  1. The DeepLabCut Software is available as a container in RC gitlab repo under communtiy containers here, https://gitlab.rc.uab.edu/rc-data-science/community-containers/deeplabcut/container_registry.
  2. Pull the Docker Container in your cloud VM terminal using the command below,
docker pull docker://gitlab.rc.uab.edu:4567/rc-data-science/community-containers/deeplabcut:latest
  1. After the image is pulled successfully, you can verify it using command,
docker images

And, the output looks like it is shown below,

REPOSITORY                                                               TAG       IMAGE ID       CREATED      SIZE

gitlab.rc.uab.edu:4567/rc-data-science/community-containers/deeplabcut   latest    288c22a0ae1b   4 days ago   9.59GB
  1. Now you can run the docker image to open up the DeepLabCut GUI using the following commands,
xhost +local:
docker run --env DISPLAY=$DISPLAY -v /tmp/.X11-unix:/tmp/.X11-unix --rm -it -v /home/ubuntu:/home gitlab.rc.uab.edu:4567/rc-data-science/community-containers/deeplabcut:latest

Note that the cloud VM's /home/ubuntu path is bind inside the container's /home.

  1. After running the docker run command successfully, you will be inside the container,
root@ed6c6cbb30b6:/app/DeepLabCut#

Now activate the Virtual environment, where DeepLabCut and their dependencies, are installed,

source deepenv/bin/activate

Run the DeepLabCut software using

python3 -m deeplabcut

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