Introduction to Bianca: Handling Sensitive Research Data

Bianca Castafiore, the Tintin character the cluster is named after.

Prefer a video?

In case you prefer a video over reading, watch this YouTube video (6 minutes long)

Notes for teachers

Teaching goals:

• The learners have heard the topics of this course

Schedule:

gantt
  title Lesson plan Introduction and Logging in
  dateFormat X
  axisFormat %s
  section Introduction
  Prior knowledge: prior_1, 0, 5s
  Theory : theory_1, after prior_1, 5s
  section Logging In
  Prior knowledge: prior_2, after theory_1, 5s
  Theory: theory, after prior_2, 5s
  Exercises: crit, exercise, after theory, 30s
  Feedback: feedback, after exercise, 10s

Introduction

Are you starting to work with your sensitive data in your research?

If yes, welcome to a full day introduction to handling sensitive data on the UPPMAX cluster, Bianca!

You will learn how to login to Bianca, upload and download files, using pre-installed software and how to run your code.

Schedule

When	Who	What
9:00	R	Introduction (this page), login, log in to remote desktop, use the remote desktop
10:00	.	Break
10:15	R	Log in to console environment, command line
11:00	.	Break
11:15	R	Create an executable script, use modules
12:00	.	Lunch
13:00	P	Transferring files to and from Bianca
13:55	.	Break
14:05	B	Compute nodes and SLURM, including interactive nodes
14:55	.	Break
15:10	L	Legal aspects of sensitive data
15:30	R	Summary and anonymous evaluation
15:45	All	Optional Q&A

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

Useful pages:

• The project name
• The shared document

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
    classDef basic_node fill:#fdd,color:#000,stroke:#f00
    classDef basic_extra_node fill:#ffd,color:#000,stroke:#ff0
    classDef intermediate_node fill:#dfd,color:#000,stroke:#0f0

    %% subgraph sub_basic_use[Basic use of Bianca]
      understand_login(Understand login, has 2FA):::basic_node
      can_login_to_remove_desktop(Can login to remote deskop):::basic_node
      can_login_to_console(Can login to console):::basic_extra_node
      can_navigate_filesystem_using_gui(Can navigate filesystem using GUI):::basic_node
      can_navigate_filesystem_using_cli(Can navigate filesystem using CLI):::basic_extra_node
      can_find_wharf(Can find the wharf):::basic_node
      can_use_command_line_1(Can use the command line 1):::basic_node
      can_use_modules(Can use modules):::basic_node
      can_use_interactive_node(Can use an interactive node):::basic_node
      can_manage_files_using_cli(Can manage files using CLI):::basic_extra_node
      can_schedule_jobs(Can schedule jobs):::basic_node
      can_create_bash_script_using_cli(Can create a bash script using CLI):::basic_node
      can_tranfer_files_using_gui(Can transfer files using GUI):::basic_node
    %% end
    %% style sub_basic_use fill:#fcc,color:#000,stroke:#fcc

    %% subgraph sub_intermediate_use[Intermediate use of Bianca]
      can_tranfer_files_using_rsync(Can transfer files using rsync):::intermediate_node
      can_use_command_line_2(Can use the command line 2):::intermediate_node
      can_use_custom_software(Can use custom software):::intermediate_node
      can_use_custom_python_pip(Can use custom Python packages using pip):::intermediate_node
      can_use_custom_python_conda(Can use custom Python packages using conda):::intermediate_node
      can_use_custom_r(Can use custom R packages):::intermediate_node
      can_use_container(Can use a container):::intermediate_node
      can_build_from_source(Can build software from source):::intermediate_node

      can_monitor_jobs(Can monitor jobs):::intermediate_node
      can_use_gpus(Can use GPUs):::intermediate_node
      can_use_partitions(Can use partitions):::intermediate_node
      can_use_ide(Can use an IDE):::intermediate_node
    %% end
    %% style sub_intermediate_use fill:#ffc,color:#000,stroke:#ffc


    %% Basic
    understand_login --> can_login_to_remove_desktop
    can_login_to_remove_desktop --> can_login_to_console
    can_login_to_remove_desktop --> can_use_command_line_1
    can_login_to_remove_desktop --> can_navigate_filesystem_using_gui
    can_navigate_filesystem_using_gui --> can_find_wharf
    can_login_to_console --> can_navigate_filesystem_using_cli
    can_navigate_filesystem_using_cli --> can_find_wharf
    can_find_wharf --> can_tranfer_files_using_gui
    understand_login --> can_login_to_console
    can_login_to_console --> 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_navigate_filesystem_using_cli --> can_manage_files_using_cli
    can_use_modules --> can_schedule_jobs
    can_create_bash_script_using_cli --> can_schedule_jobs

    %% Basic -> Intermediate
    can_manage_files_using_cli --> can_tranfer_files_using_rsync
    can_find_wharf --> can_tranfer_files_using_rsync
    can_schedule_jobs --> can_monitor_jobs
    can_schedule_jobs --> can_use_gpus
    can_schedule_jobs --> can_use_partitions
    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_1 --> can_tranfer_files_using_rsync
    can_use_command_line_2 --> can_use_custom_software

    can_use_custom_software --> can_use_custom_python_pip
    can_use_custom_software --> can_use_custom_python_conda
    can_use_custom_software --> can_use_custom_r
    can_use_custom_software --> can_build_from_source
    can_use_custom_software --> can_use_container

Overview of the courses. Red nodes: Intro to Bianca. Yellow node: Intro to Bianca extra material. Green node: Intermediate Bianca.