k8hertweck
commented
4 years ago From discussion with community member:
General comments:
Overall I feel like it is information overload. What I think may help me understand the pages better is a search tree-like structure. E.g.
“What do you want to do?”
- Use an existing docker image
- Run docker locally
- Run docker on the cluster
- Info on singularity
- Run docker in the cloud
- Build my own docker image
Specific comments:
On the computing environments and containers page:
- Using Docker at Fred Hutch section: what is LBL?
- I’m not sure whether the words of wisdom are adding to my confusion or understanding
On the singularity page:
- Is the ubuntu-python.sif container automatically available to me?
- I assume the python script is the script I want to run? What if I don’t have a python script I want to run? Do not use on Rhino part:
- How can I batch process lots of files then? I have several hundred files I need to run through the pipeline
- Does the ‘singularity build docker://ubuntu:latest’ command build docker or a particular image?
On accessing /fh/fast or /fh/scratch
- I don’t understand what this sentence means: ‘Please create these empty directories inside your docker container before you pull it using singularity’. How do I do this?
- What would help me tremendously here is an example case of how I can get a docker image set up of an existing image, access my data on the scratch drive and run the commands on the data
On the using docker at fred hutch page:
- I would start this section with the running pre-made docker images sections
- The other parts of this page seem to not be relevant to my situations since I’m not trying to build my own image
vortexing
URL of existing content (a rendered, sciwiki.fredhutch.org link)
https://sciwiki.fredhutch.org/scicomputing/compute_environments/
Specific information requests or concerns, or specific region on page of content to refresh.