1/13/23 feedback

[avahoffman]

@carriewright11 fyi

[avahoffman]

Is this something you'd want to make avail. for every lab?
What would you like to see next?

questions that came up?

Liked the definitions? Explaining what gizmo and rhino is!
My issue was that I don't generally code. I do need to run code to generate a plot.

Who uses the cluster section maybe ?
Where to go from here?

Could be cool to play around with some data on the cluster

What kind of analysis do you do / what would you like to do?

Image processing. That would be a lot.

Have instructions on How to create an sh file? What is that all about? More about this?

Be more clear that we're not supposed to install our own software

I find the biggest barrier for batch processing and comp cluster computing is finding the files and calling them. How to manage the data flow! More about data systems? How to get to data from login page.

Thinking about when to upload a file versus when to have an interactive session [ we're taking that out ]

Also, if you run through sbatch, can you turn your computer off and still have it run?

yes- when a jobs batched up and sent, you don't need to stay connected

some discussion of file paths. issue I've run into with using different image programs is that the data input path can be confusing.

What is the computing structure for the cluster?

spend? Does my internet at home affect my speeds on rhino?

when you see the terminal window and see list of files. Does that mean tehre's a folder on a hard drive dedicated just for you?

you are accessing a computer somewhere with a hard drive and folder dedicated to your work.

Cartoons and text helpful

Trailer of what you can do with this! Idea of what you can do as the end product, with maybe some papers?

Connections to WDL 101 , transition is abrupt

Course took roughly half an hour. could be longer. could have more examples to solidify learning.

How long does it take to run a batch script / job?

adding a thing about plain text editors to the end. How to open that script file and edit it.

[carriewright11]

Some of this might be redundant with @avahoffman's notes :P:

• leanpub didn't load for one of the students
• want reassurance about costs and not breaking things
• Physically where are my files?
• drop down about text editors when you edit the sh file would be helpful
• estimate on how long jobs make take
• class took about 30 min but could be longer with examples (maybe these could be optional?)
• WDL course: resources about what to do before the class would help, also: what a workflow is, why you would use one, what does WDL stand for
• trailers for our courses - after this course you will be able to do this - or take these other courses to do this
• people want github help - examples of recent papers and work people did using resources or tools in the course
• have people walk through there code to show how their work is done as examples
• maybe add a working from home section and describe costs etc how this works
• how to transfer large files
• image analysis example
• when to install or not- how to reach out to get something installed
• what you can access on Rhino
• when to do interactive or not- examples of both
• what level of resources might be too much
• what happens when you turn off your machine
• FIJI/ImageJ on cluster example
• data input paths are confusing - where am I on the cluster
• explanation of ls -l (shows where things are)
• Nextflow with singularity class would be of interest
• If I am still logged in overnight - cause I ran a job overnight what happens