From 48841766a71df6a5e9d116d991fe6bd4cde2518a Mon Sep 17 00:00:00 2001 From: richelbilderbeek Date: Tue, 21 May 2024 14:20:37 +0200 Subject: [PATCH] Summary is a summary, #21 --- docs/intermediate/intro.md | 2 +- docs/intermediate/summary.md | 246 ++++++++++++++++++++++++----------- 2 files changed, 172 insertions(+), 76 deletions(-) diff --git a/docs/intermediate/intro.md b/docs/intermediate/intro.md index e7761aea..c5f2a2ad 100644 --- a/docs/intermediate/intro.md +++ b/docs/intermediate/intro.md @@ -91,7 +91,7 @@ Time |Topic When | Who | What -----|------|------------------------- -9:00 | R | [Introduction](https://uppmax.github.io/bianca_workshop/intermediate/intro/) +9:00 | R | [Introduction](https://uppmax.github.io/bianca_workshop/intermediate/intro/) 9:15 | R | 45 minutes [Transferring files to and from Bianca](https://uppmax.github.io/bianca_workshop/intermediate/transfer/) 10:00| . | Break 10:15| R | 20 minutes [Transferring files p2](https://uppmax.github.io/bianca_workshop/intermediate/transfer/) diff --git a/docs/intermediate/summary.md b/docs/intermediate/summary.md index 27166a5c..2d1c13fb 100644 --- a/docs/intermediate/summary.md +++ b/docs/intermediate/summary.md @@ -1,80 +1,176 @@ # Summary -## Next steps - -- Q/A session -- Exercises for the interested. - -## Today's topics - -- **Overview of UPPMAX systems** - - - NAISS-SENS - - Several clusters, like - - - Bianca - - Rackham - - - Login and compute nodes - -- **Legal and administrative aspects** - - - Sensitive personal data - - Pseudonymisation and anonymisation - - Apply for project - -- **Transferring files** - - - The ``wharf`` works like a dock at the harbour. - - There are several ways to use the ``wharf`` to transfer files - - - copy - - transit server - - rsync, scp/sftp - -- **Introduction to compute nodes** - - - Submitting jobs - - - Slurm, sbatch, the job queue - - Jobs - - Slurm parameters - - Interactive jobs +!!!- info "Learning objectives" + + - Repeat seeing the overview of topics discussed today + - Share confidence on having learned the topics discussed today + +???- question "For teachers" - - allows you to work interactively with command line and your tools but on a compute node. + Prerequisites are: + + - None + + Preparations are: + + - Copy the learning objectives in the shared document + + Teaching goals are: + + - Learners have again seen an overview of topics discussed today + + Lesson plan: + + ```mermaid + gantt + title Summary + dateFormat X + axisFormat %s + Monologue: 0, 5s + ``` + +## Overview of today + +Copied from [Introduction](intro.md): + +```mermaid +%% Direction is top->down +flowchart TD + + 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) + can_manage_files_using_cli(Can manage files using CLI) + can_tranfer_files_using_rsync(Can transfer files using rsync) + can_schedule_jobs(Can schedule jobs) + can_create_bash_script_using_cli(Can create a bash script using CLI) + end + + 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) + can_monitor_jobs(Can monitor jobs) + can_use_ide(Can use an IDE) + can_tranfer_files_using_rsync2(Can transfer files using rsync) + end + + subgraph sub_non_goal["Not in courses"] + can_tranfer_files_using_gui(Can transfer files using GUI) + can_create_bash_script_using_gui(Can create a bash script using GUI) + end + + + %% 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_tranfer_files_using_rsync --> can_tranfer_files_using_rsync2 + can_schedule_jobs --> can_monitor_jobs + can_use_interactive_node --> can_use_ide + can_use_modules --> can_use_ide + can_tranfer_files_using_rsync2 -.-> |extra| can_tranfer_files_using_gui + + %% 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 +``` + +## Learning objectives + +Most are copied from their respective pages: + +- [Introduction](https://uppmax.github.io/bianca_workshop/intermediate/intro/) + - [ ] See an overview of topics discussed today + - [ ] See the link to the shared document + - [ ] See the schedule +- [Transferring files to and from Bianca](https://uppmax.github.io/bianca_workshop/intermediate/transfer/) + - [ ] Explore the UPPMAX documentation + - [ ] Understand what the wharf is + - [ ] Understand what the Transit server allows + - [ ] Mount the wharf on Transit + - [ ] Transfer files to/from Bianca using rsync + - [ ] Transfer files to/from Bianca using FileZilla +- [Slurm jobs](https://uppmax.github.io/bianca_workshop/intermediate/slurm_intermed/) + - [ ] Understand what Slurm is + - [ ] Understand some Slurm parameters + - [ ] Understand what sbatch is + - [ ] Understand what the job queue is + - [ ] Start jobs + - [ ] See job CPU and memory usage + - [ ] Can start an interactive job + - [ ] Understand how compute nodes are moved between project clusters + - [ ] Have used other Slurm tools +- [Software and packages installation](https://uppmax.github.io/bianca_workshop/intermediate/install/) + - [ ] Understand how to install software yourself + - Understand how to use Packages and libraries for scripts + - [ ] ... using Conda + - [ ] ... using Python packages with pip + - [ ] ... using R packages + - [ ] ... using Julia packages + - [ ] Understand what containers are + - [ ] Understand what Singularity is + - [ ] Understand what Docker is + - [ ] Understand how to build from source +- [IDEs on Bianca](https://uppmax.github.io/bianca_workshop/intermediate/ides/) + - [ ] Understand what an IDE is + - [ ] Have heard that RStudio, Jupyter, VSCodium are IDEs + - [ ] Understand that there are IDEs that can run on Bianca + - [ ] Have run the voted-for IDE on Bianca +- [NAISS-SENS](https://uppmax.github.io/bianca_workshop/sens_project_short/) + - [ ] Understand what sensitive personal data is + - [ ] Understand the difference between pseudonymisation and anonymisation + - [ ] Know where to apply for project + + +### Exercise + +Share your confidence on having learned the topics discussed today, +by going thought the list on the shared document. + +Although it will be messy, between `[ ]`, add a number for confidence: + +Grade|Description +-----|------------------------------------ +`0` |I have no idea what this is about +`1` |I have no confidence I can do this +`2` |I have low confidence I can do this +`3` |I have some confidence I can do this +`4` |I have good confidence I can do this +`5` |I absolutely can do this! + +This may result in a measurement like this: + +- `[00101000111201]`: most learners have low confidence +- `[44345454545454]`: most learners have high confidence - - How compute nodes are moved between project clusters - - - Other Slurm tools - -- **Software and package installation** - - - Install software yourself - - Packages and libraries to scripting programs - - - Conda - - Python packages with pip - - R packages - - Julia packages - - - "Containers" - - - Singularity - - Docker - - - Build from source - - Summary about the Bianca Hardware - -- **IDE:s on Bianca** - - - RStudio - - - Run in interactive session - - - Jupyter - - - Run in interactive session - - - VSCodium +## Next steps - - Run in interactive session +- Evaluation +- Optional Q/A session