feat: added note on vscode R on compute nodes #1
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SilviaRaineri
requested changes
Jul 2, 2024
docs/dangpu/R_vscode.md
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| ssh user@danhead01fl.unicph.domain | ||
| tmux new-session | ||
| srun -c 2 --mem=30gb --time=0-10:00:00 -w dancmpn02fl --pty bash | ||
| source ~/.bash_profile |
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This can be removed, move all the bashrc profile logic to bashrc instead.
See example below
$ cat .bashrc
### Source standard KU IT's global bashrc
if [ -f /etc/bashrc ]; then
. /etc/bashrc
fi
### Source DanGPU definitions
if [ -f /maps/projects/dan1/apps/etc/bashrc ]; then
. /maps/projects/dan1/apps/etc/bashrc
fi
### Source Brickman definitions
if [ -f /maps/projects/dan1/data/Brickman/config/brickman.bashrc ]; then
. /maps/projects/dan1/data/Brickman/config/brickman.bashrc
fi
docs/dangpu/R_vscode.md
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| **IMPORTANT!** When using `code tunnel` the connection between your local VScode instance and the compute node is bridged by a Microsoft server. This means `code tunnel` should not be used to work with sensitive human data. However, the connection is secured and authenticated using your Microsoft account and all data is encrypted during transit. | ||
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| ## code-server |
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Make this more clear, no one will know what is the code-server
docs/dangpu/R_vscode.md
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| ## Downloads | ||
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| Do only once to make modules |
docs/dangpu/R_vscode.md
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| ### VScode CLI | ||
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| ```bash | ||
| curl -Lk 'https://code.visualstudio.com/sha/download?build=stable&os=cli-alpine-x64' --output vscode_cli.tar.gz | ||
| tar -xf vscode_cli.tar.gz | ||
| ``` |
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Put this under installation
docs/dangpu/R_vscode.md
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| ### VScode code-server | ||
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| ```bash | ||
| curl -fL https://github.com/coder/code-server/releases/download/v4.90.2/code-server-4.90.2-linux-amd64.tar.gz | tar -C /maps/projects/dan1/data/Brickman/shared/modules/software/code-server/4.90.2 -xz | ||
| ``` |
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Same as above, different heading structure would make this easier to read
docs/dangpu/R_vscode.md
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| - Open the link and enter the given code to authenticate | ||
| - Chose your KU microsoft account and click continue | ||
| - Open the link in your web browser and accept the connection | ||
| - ALTERNATIVELY: Open your VScode desktop app, click `open a remote window` in bottom left corner, choose connect to tunnel > microsoft account > tunnel name and accept connection |
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Suggested change
| - ALTERNATIVELY: Open your VScode desktop app, click `open a remote window` in bottom left corner, choose connect to tunnel > microsoft account > tunnel name and accept connection | |
| - **ALTERNATIVELY**: Open your VScode desktop app, click `open a remote window` in bottom left corner, choose connect to tunnel > microsoft account > tunnel name and accept connection |
docs/dangpu/R_vscode.md
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| - Chose your KU microsoft account and click continue | ||
| - Open the link in your web browser and accept the connection | ||
| - ALTERNATIVELY: Open your VScode desktop app, click `open a remote window` in bottom left corner, choose connect to tunnel > microsoft account > tunnel name and accept connection | ||
| - You can now run R interactively on the chosen compute node using VScode |
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Suggested change
| - You can now run R interactively on the chosen compute node using VScode | |
| - Go back to terminal and hit ENTER on questions about tunnel name | |
| - go to vsc > settings > Rterm:Linux and paste the following `/opt/software/R/4.3.1/bin/R` |
| A solution to run R scripts on computing nodes dancmpn01fl and dancmpn02fl using VScode code tunnel | ||
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| This is much faster than the current RStudio solution, and frees up danGPU for those who actually need GPU resources :) | ||
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Maybe here we should add that the first time you open R in vsc you will most likely have to re-install all your libraries
docs/dangpu/R_vscode.md
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| tmux new-session | ||
| srun -c 2 --mem=30gb --time=0-10:00:00 -w dancmpn02fl --pty bash | ||
| source ~/.bash_profile | ||
| module load vscode_cli |
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Suggested change
| module load vscode_cli | |
| module load vscode_cli gcc/11.2.0 R/4.3.1 |
Co-authored-by: Silvia_R <silvia.rnr@gmail.com>
Co-authored-by: Silvia_R <silvia.rnr@gmail.com>
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