Bianca In-Depth Hackathon: Improve Your Handling of Sensitive Research Data

Are you already working with sensitive data in your research and feel your workflow can be improved? If yes, welcome to a full day of learning of smarter ways to work on the Bianca UPPMAX cluster.

I am new to Bianca, where do I start?

As a beginner, you are encouraged to start with the basic Bianca course, at here.

You will learn how to login from a terminal (bypassing ThinLinc), do file transfer from a terminal (allowing scripts), advanced SLURM, using IDEs (i.e. RStudio and/or VSCode), and installing custom software and packages.

Tentative schedule

Time	Topic
9.00	Introduction
9.10	NAISS-SENS summary
9.20	Transferring files to and from Bianca
10.00	Coffee break
10.15	Transferring files p2
10.35	Slurm jobs p1
11.00	Break
11.15	Slurm jobs p2
12.00	LUNCH
13.00	Software and packages installation
13.50	break
14.05	IDE:s on Bianca
15.00	Coffee break
15.15	Summary
15.20	Q/A and extra material
15.55	Closing words
16.00	END

Suggested new schedule:

When	Who	What
9:00	?R	Introduction
9:15	P	45 minutes Transferring files to and from Bianca
10:00	.	Break
10:15	P	20 minutes Transferring files p2
10:35	D	25 minutes Slurm jobs p1
11:00	.	Break
11:15	D	45 minutes Slurm jobs p2
12:00	.	Lunch
13:00	B	Software and packages installation
13:45	.	Break
14:00	PR	IDEs on Bianca
14:45	.	Break
15:00	L	NAISS-SENS summary
15:30	?R	Summary
15:35	?R	Evaluation
15:45	All	Optional Q/A and extra material
16:00	.	END

• Who: B: Björn, L: Lars, P: Pavlin, R: Richèl

Changes:

• IDEs changed from 55 -> 45 minutes, as there is a new setup: (1) let learners vote on one IDE, (2) discuss that IDE in detail, (3) mention the others more briefly. If teachers think it would be better to discuss 2 in detail, they may do so
• NAISS-SENS to back, so that (1) learners can dive in immediately, (2) it is a nice easy way to round off the day
• NAISS-SENS duration changed from 10 -> 30 minutes, as this is more realistic
• Introduction duration changed from 5 -> 15 minutes
• Transferring files part 1 duration changed from 40 -> 45 minutes

Q/A collaboration document

• Use the Q/A page for the workshop with your questions.

  • https://hackmd.io/@bclaremar/bianca_hack_dec_2023?both

• Depending on how many helpers there are we’ll see how fast there are answers.

  • Some answers may come after the workshop.

• Create a new line for new questions. Take care if others are editing at the same time.

Overview of courses

%% Direction is top->down
flowchart TD

    %% Give a white background, instead of a transparent one
    classDef node fill:#fff,color:#000,stroke:#000
    classDef focus_node fill:#fff,color:#000,stroke:#000,stroke-width:4px

    subgraph sub_basic_use["Basic use of Bianca"]
      can_login_to_remove_desktop(Can login to remote deskop)
      can_login_to_console(Can login to console)
      can_use_command_line_1(Can use the command line 1)
      can_use_modules(Can use modules)
      can_use_interactive_node(Can use an interactive node):::focus_node
      can_manage_files_using_cli(Can manage files using CLI)
      can_tranfer_files_using_rsync(Can transfer files using rsync):::focus_node
      can_schedule_jobs(Can schedule jobs):::focus_node
      can_create_bash_script_using_cli(Can create a bash script using CLI)
    end
    style sub_basic_use fill:#fcc,color:#000,stroke:#fcc

    subgraph sub_intermediate_use["Intermediate use of Bianca"]
      can_use_command_line_2(Can use the command line 2)
      can_use_custom_software(Can use custom software):::focus_node
      can_monitor_jobs(Can monitor jobs):::focus_node
      can_use_ide(Can use an IDE)
    end
    style sub_intermediate_use fill:#ffc,color:#000,stroke:#ffc

    subgraph sub_non_goal["Not in course"]
      can_tranfer_files_using_gui(Can transfer files using GUI)
      can_create_bash_script_using_gui(Can create a bash script using GUI)
    end
    style sub_non_goal fill:#ccc,color:#000,stroke:#ccc


    %% Basic
    can_login_to_console --> can_tranfer_files_using_rsync
    can_login_to_console --> can_use_command_line_1
    can_login_to_remove_desktop ---> can_use_command_line_1
    can_use_command_line_1 --> can_use_modules
    can_use_command_line_1 --> can_use_interactive_node
    can_use_command_line_1 --> can_use_command_line_2
    can_use_command_line_1 --> can_create_bash_script_using_cli
    can_use_command_line_1 --> can_schedule_jobs
    can_use_command_line_1 --> can_manage_files_using_cli
    can_use_command_line_1 --> can_tranfer_files_using_rsync
    can_use_modules --> can_schedule_jobs
    can_create_bash_script_using_cli --> can_schedule_jobs

    %% Basic -> Intermediate
    can_schedule_jobs --> can_monitor_jobs
    can_use_interactive_node --> can_use_ide
    can_use_modules --> can_use_ide

    %% Make sure Intermediate is below Basic,
    %% using invisible nodes
    can_schedule_jobs ~~~ can_use_command_line_2

    %% Intermediate
    can_use_command_line_2 --> can_use_custom_software

    %% Basic -> None
    %% can_login_to_remove_desktop ---> can_tranfer_files_using_gui
    %% can_tranfer_files_using_gui --> can_use_custom_software
    %% can_login_to_remove_desktop ---> can_create_bash_script_using_gui
    %% can_create_bash_script_using_gui --> can_schedule_jobs

    %% Make sure Non-goals is below Intermediat,
    %% using invisible nodes
    can_use_custom_software ~~~ can_tranfer_files_using_gui