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| Original file line number | Diff line number | Diff line change |
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| # Summary | ||
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| ## Next steps | ||
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| - Q/A session | ||
| - Exercises for the interested. | ||
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| ## Today's topics | ||
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| - **Overview of UPPMAX systems** | ||
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| - NAISS-SENS | ||
| - Several clusters, like | ||
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| - Bianca | ||
| - Rackham | ||
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| - Login and compute nodes | ||
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| - **Legal and administrative aspects** | ||
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| - Sensitive personal data | ||
| - Pseudonymisation and anonymisation | ||
| - Apply for project | ||
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| - **Transferring files** | ||
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| - The ``wharf`` works like a dock at the harbour. | ||
| - There are several ways to use the ``wharf`` to transfer files | ||
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| - copy | ||
| - transit server | ||
| - rsync, scp/sftp | ||
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| - **Introduction to compute nodes** | ||
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| - Submitting jobs | ||
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| - Slurm, sbatch, the job queue | ||
| - Jobs | ||
| - Slurm parameters | ||
| - Interactive jobs | ||
| !!!- info "Learning objectives" | ||
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| - Repeat seeing the overview of topics discussed today | ||
| - Share confidence on having learned the topics discussed today | ||
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| ???- question "For teachers" | ||
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| - allows you to work interactively with command line and your tools but on a compute node. | ||
| Prerequisites are: | ||
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| - None | ||
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| Preparations are: | ||
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| - Copy the learning objectives in the shared document | ||
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| Teaching goals are: | ||
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| - Learners have again seen an overview of topics discussed today | ||
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| Lesson plan: | ||
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| ```mermaid | ||
| gantt | ||
| title Summary | ||
| dateFormat X | ||
| axisFormat %s | ||
| Monologue: 0, 5s | ||
| ``` | ||
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| ## Overview of today | ||
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| Copied from [Introduction](intro.md): | ||
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| ```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 | ||
| ``` | ||
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| ## Learning objectives | ||
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| Most are copied from their respective pages: | ||
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| - [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 | ||
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| ### Exercise | ||
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| Share your confidence on having learned the topics discussed today, | ||
| by going thought the list on the shared document. | ||
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| Although it will be messy, between `[ ]`, add a number for confidence: | ||
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| 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! | ||
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| This may result in a measurement like this: | ||
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| - `[00101000111201]`: most learners have low confidence | ||
| - `[44345454545454]`: most learners have high confidence | ||
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| - How compute nodes are moved between project clusters | ||
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| - Other Slurm tools | ||
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| - **Software and package installation** | ||
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| - Install software yourself | ||
| - Packages and libraries to scripting programs | ||
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| - Conda | ||
| - Python packages with pip | ||
| - R packages | ||
| - Julia packages | ||
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| - "Containers" | ||
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| - Singularity | ||
| - Docker | ||
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| - Build from source | ||
| - Summary about the Bianca Hardware | ||
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| - **IDE:s on Bianca** | ||
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| - RStudio | ||
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| - Run in interactive session | ||
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| - Jupyter | ||
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| - Run in interactive session | ||
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| - VSCodium | ||
| ## Next steps | ||
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| - Run in interactive session | ||
| - Evaluation | ||
| - Optional Q/A session |