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[BUG] - Permission denied error when activating environments in terminal #1859

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kcpevey opened this issue Jul 13, 2023 · 5 comments
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impact: high 🟥 This issue affects most of the nebari users or is a critical issue type: bug 🐛 Something isn't working

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@kcpevey
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kcpevey commented Jul 13, 2023

Describe the bug

When I activate an environment in the Jupyter Terminal or in the VS Code terminal, I get a permission denied error regarding a symlink.

Expected behavior

conda activate ... shouldn't throw an error or warning.

OS and architecture in which you are running Nebari

Nebari deployment on AWS

How to Reproduce the problem?

From a terminal on Nebari, run:
conda activate nebari-git-dask

Command output

kcpevey:~ 
11:24 $ conda activate nebari-git-dask 
mkdir: cannot create directory ‘/home/conda/nebari-git/envs/nebari-git-dask/share/gdb/auto-load//home/conda/nebari-git/envs’: Permission denied
ln: failed to create symbolic link '/home/conda/nebari-git/envs/nebari-git-dask/share/gdb/auto-load//home/conda/nebari-git/envs/nebari-git-dask/lib/libarrow.so.1000.1.0-gdb.py': No such file or directory
/home/conda/nebari-git/envs/nebari-git-dask/etc/conda/activate.d/libarrow_activate.sh ERROR: Failed to create symlink from '/home/conda/nebari-git/envs/nebari-git-dask/share/gdb/auto-load/replace_this_section_with_absolute_slashed_path_to_CONDA_PREFIX/lib/libarrow.so.1000.1.0-gdb.py' to '/home/conda/nebari-git/envs/nebari-git-dask/share/gdb/auto-load//home/conda/nebari-git/envs/nebari-git-dask/lib/libarrow.so.1000.1.0-gdb.py'
(nebari-git-dask) kcpevey:~ 
11:24 $ 


### Versions and dependencies used.

This happens on:
Nebari: v2023.5.2.dev20+g596083a6 running on AWS
Nebari: https://github.com/nebari-dev/nebari/tree/nfs-pd-ssd (2023.5.1 plus one commit for SSDs) on GCP

This does not happen on:
Nebari: v2023.5.1 running on GCP

All of these are running conda-store 0.4.14

### Compute environment

AWS

### Integrations

_No response_

### Anything else?

_No response_
@kcpevey kcpevey added type: bug 🐛 Something isn't working impact: high 🟥 This issue affects most of the nebari users or is a critical issue labels Jul 13, 2023
@kcpevey
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kcpevey commented Jul 13, 2023

This was originally reported as a discussion topic by @gzt5142 here. The issue notes as reported here are my own personal observations.

@kcpevey
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kcpevey commented Jul 25, 2023

Confirmed this is still an issue with the 2023.7.1 release

@dharhas
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dharhas commented Jul 25, 2023

This is specific to conda environments that include packages with a post activation hook that tries to write to the readonly conda folder.

upstream issue opened - conda-forge/arrow-cpp-feedstock#1126

@iameskild
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@kcpevey it looks like this issue was resolved upstream, can you confirm that this has been resolved?

@pavithraes
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can you confirm that this has been resolved?
I just verified on Nebari - works. :)

Closing as resolved!

@github-project-automation github-project-automation bot moved this from New 📬 to Done 💪🏾 in 🪴 Nebari Project Management Jul 31, 2023
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Labels
impact: high 🟥 This issue affects most of the nebari users or is a critical issue type: bug 🐛 Something isn't working
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