Frequently Asked Questions

:local:

Quick, friendly answers to the most common questions we get from users. All commands are meant to be run inside a compute container (or via an interactive shell on the node).

(If you can’t find an answer, see Support & Contact.)

File-management & trash

Q: I deleted a bunch of files through the UI (“Move to trash”). My quota is still full. Why?

A: The UI only moves the files into a hidden .Trash-<uid> directory; the data stays on disk until it is physically removed.

Step

What to do

Example command

Locate your trash folder

~/workspace/Storage/<username>/persistent/.Trash-1000

ls -l ~/workspace/Storage/$SCISERVER_USER_NAME/persistent/.Trash-1000

Empty the trash

Delete the contents with rm

rm -r ~/workspace/Storage/$SCISERVER_USER_NAME/persistent/.Trash-1000/*

Verify quota

use the “Current storage use” command below

du -sh ~/workspace/Storage/$SCISERVER_USER_NAME

Only a true rm (or unlink) frees the blocks; the UI’s “trash” is just a convenience folder.

Conda vs. Mamba

Q: I see both conda and mamba in the containers. Which one should I use?

A:

  • conda works and is the classic tool.

  • mamba is a drop-in replacement that is ~5-10× faster for solving environments.

All Sciserver images ship with mamba pre-configured to use the conda-forge channel, so you get the same packages with a much quicker install.

Bottom line

  • Use mamba for new environment creation or when you need a quick solve.

  • conda remains available for legacy scripts, but you’ll rarely need it.

# Example – create an environment with mamba
mamba create -n myenv python=3.13 numpy pandas
# Activate using either mamba or conda (both conda and mamba share the same env files)
conda activate myenv

How can I see how much storage am I using right now?

Q: I’m not sure how much of my quota is already taken. Is there a quick command?

A: Yes – a couple of du one-liners give you a snapshot of the two main storage areas.

# Persistent storage quota
du -h --max-depth=2 ~/workspace/Storage/*/ > storage-$(date +'%d%m%Y-%H%M%S').log

# Temporary (scratch) area
du -h --max-depth=2 ~/workspace/Temporary/*/ > temporary-$(date +'%d%m%Y-%H%M%S').log

  • The files storage-<timestamp>.log and temporary-<timestamp>.log are created in your current working directory; open them with less or cat to see a per-folder breakdown.

  • If you just want a summary:

du -sh ~/workspace/Storage
du -sh ~/workspace/Temporary

Knowing which sub-folders consume the most space makes it easier to clean up or request extra quota if needed.