Cannot Uninstall SLEAP, Not Recognized as Conda Environment

[Asolee24]

Hello,

I am trying to run SLEAP on a cluster at my institution in order to run trainings faster and because my computer does not have a NVIDA GPU. I navigated onto the cluster and was able to properly install miniforge3 and activate conda. I went to install sleap and most everything got installed, but I got kicked off the cluster towards the end and things didn't setup properly. I am able to activate the sleap environment with conda activate sleap, but when I go to try and uninstall it (from my base environment) it says

EnvironmentLocationNotFound: Not a conda environment: /scratch/zt1/project/angueyra-lab/shared/sleap/miniforge3/envs/sleap

I have tried different paths of just in miniforge3, also I noticed in my envs folder there is nothing there, but somehow I am able to still activate sleap. Any advice of how to uninstall so I call properly install things, or advice on what I may be missing that I could just run to finish the SLEAP setup would be greatly appreciated. I cannot share the file setup beyond screenshots as it is a closed cluster for my institution. If there is anything else I could add that would be helpful let me know.

Background of my goals for sleap and this issue:

When I run sh files for centroid and centered instance (see attached markdowns) sleap-train is not able to be identified so my jobs continue to fail. I was told to also change my beginning of my sh files to be by my IT department:

In the submit script, you are doing an 'eval' of a bash hook but you don't specify the full path to 'conda' and 'shell.bash'. I recommend you remove the 'eval' line in your submit script and replace it with these two lines:

source /scratch/zt1/project/angueyra-lab/shared/sleap/miniforge3/etc/profile.d/conda.sh
conda activate sleap

Ultimately, I want to be able to run trainings and export the predictions from my cluster back into sleap and repeat the process until the sleap.ai learns how to track my organisms.

train-centered-instance-setup.md
train-centroid-setup.md

Thank you,

Autumn Lee

[talmo]

Hi @Asolee24,

I see you closed the thread -- were you able to resolve this issue?

If you're getting the EnvironmentLocationNotFound error, usually it's because the environment uninstall failed, which is typically because the binaries are still in use by a running process.

The solution is to just delete the directory where the environment was installed, e.g.:

rm -rf /scratch/zt1/project/angueyra-lab/shared/sleap/miniforge3/envs/sleap

Let us know if you run into any issues!

Cheers,

Talmo