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Introduction

Our website is powered by PlutoSliderServer.jl. Before reading the document below, be sure to read the README of PlutoSliderServer first!

Our server is running on DigitalOcean, in the margo + pluto organization. The server is currently called margo-interactive-2.

How to update/add/remove notebooks

Our server is set up to automatically run the notebooks from the main branch. So to update one of the notebooks on the website, simply edit the notebook file and commit to the main branch. To add or remove notebooks from the website, add or remove notebook files in the repository.

Notebooks

See PlutoSliderServer for more information!

Excluding notebooks from the slider server

The file pluto-deployment-environment/PlutoDeployment.toml can be used to configure the HTML export process ([Export]), and the slider server ([SliderServer]). When this file is edited (on main), the server will automatically reboot. This means that all notebooks restart (with the new settings).

You can use the exclude setting to control which notebooks are exported, or which notebooks are running on the live slider server.

How to update the version of Pluto or PlutoSliderServer

We pinned the version of Pluto and PlutoSliderServer using pluto-deployment-environment/Manifest.toml. To use newer versions, you need to update manually using the pkg REPL. Use Julia 1.8.

➜  ~ cd Documents/margo-interactive 
➜  margo-interactive git:(main) ls
LICENSE                      introduction.jl
Procfile                     pluto-deployment-environment
README.md
➜  margo-interactive git:(main) cd pluto-deployment-environment 
➜  pluto-deployment-environment git:(main) julia --project
               _
   _       _ _(_)_     |  Documentation: https://docs.julialang.org
  (_)     | (_) (_)    |
   _ _   _| |_  __ _   |  Type "?" for help, "]?" for Pkg help.
  | | | | | | |/ _` |  |
  | | |_| | | | (_| |  |  Version 1.8.0
 _/ |\__'_|_|_|\__'_|  |  Official https://julialang.org/ release
|__/                   |

(pluto-deployment-environment) pkg> st
      Status `~/Documents/margo-interactive/pluto-deployment-environment/Project.toml`
  [2fc8631c] PlutoSliderServer v0.2.5 `https://github.com/JuliaPluto/PlutoSliderServer.jl.git#main`

(pluto-deployment-environment) pkg> up
    Updating registry at `~/.julia/registries/General.toml`
    Updating git-repo `https://github.com/JuliaPluto/PlutoSliderServer.jl.git`
  Downloaded artifact: Git
┌ Warning: The active manifest file at `/Users/fons/Documents/margo-interactive/pluto-deployment-environment/Manifest.toml` has an old format that is being maintained.
│ To update to the new format run `Pkg.upgrade_manifest()` which will upgrade the format without re-resolving.
└ @ Pkg.Types /Users/julia/buildbot/worker/package_macos64/build/usr/share/julia/stdlib/v1.7/Pkg/src/manifest.jl:287
    Updating `~/Documents/margo-interactive/pluto-deployment-environment/Project.toml`
  [2fc8631c] ~ PlutoSliderServer v0.2.5 `https://github.com/JuliaPluto/PlutoSliderServer.jl.git#main` ⇒ v0.3.3 `https://github.com/JuliaPluto/PlutoSliderServer.jl.git#main`
    Updating `~/Documents/margo-interactive/pluto-deployment-environment/Manifest.toml`
  [1520ce14] + AbstractTrees v0.3.4
  [c9fd44ac] + BetterFileWatching v0.1.4
  [5218b696] ↑ Configurations v0.16.4 ⇒ v0.16.6
  [55351af7] ↑ ExproniconLite v0.6.10 ⇒ v0.6.13
  [ff7dd447] ↑ FromFile v0.1.1 ⇒ v0.1.2
  [d7ba0133] + Git v1.2.1
  [6b79fd1a] ↑ GitHubActions v0.1.3 ⇒ v0.1.4
  [cd3eb016] ↑ HTTP v0.9.14 ⇒ v0.9.17
  [692b3bcd] + JLLWrappers v1.4.1
  [1d6d02ad] + LeftChildRightSiblingTrees v0.1.3
  [69de0a69] ↑ Parsers v2.0.4 ⇒ v2.2.1
  [c3e4b0f8] ↑ Pluto v0.16.1 ⇒ v0.17.7
  [2fc8631c] ~ PlutoSliderServer v0.2.5 `https://github.com/JuliaPluto/PlutoSliderServer.jl.git#main` ⇒ v0.3.3 `https://github.com/JuliaPluto/PlutoSliderServer.jl.git#main`
  [21216c6a] + Preferences v1.2.3
  [33c8b6b6] + ProgressLogging v0.1.4
  [d1efa939] - TableIOInterface v0.1.6
  [bd369af6] ↑ Tables v1.5.2 ⇒ v1.6.1
  [5d786b92] + TerminalLoggers v0.1.5
  [04572ae6] + Deno_jll v1.16.3+0
  [2e619515] + Expat_jll v2.2.10+0
  [78b55507] + Gettext_jll v0.21.0+0
  [f8c6e375] + Git_jll v2.34.1+0
  [94ce4f54] + Libiconv_jll v1.16.1+1
  [458c3c95] + OpenSSL_jll v1.1.13+0
  [02c8fc9c] + XML2_jll v2.9.12+0
  [e66e0078] + CompilerSupportLibraries_jll
  [4536629a] + OpenBLAS_jll
  [efcefdf7] + PCRE2_jll
  [8e850b90] + libblastrampoline_jll
┌ Warning: The active manifest file is an older format with no julia version entry. Dependencies may have been resolved with a different julia version.
└ @ ~/Documents/margo-interactive/pluto-deployment-environment/Manifest.toml:0
Precompiling project...
  9 dependencies successfully precompiled in 6 seconds (33 already precompiled)

(pluto-deployment-environment) pkg> 
➜  pluto-deployment-environment git:(main) ✗ # now commit this to git
➜  pluto-deployment-environment git:(main) ✗ git add .
➜  pluto-deployment-environment git:(main) ✗ git commit -m "Update pluto deployment"
[main 9c1a6cd] Update pluto deployment
 1 file changed, 127 insertions(+), 27 deletions(-)
➜  pluto-deployment-environment git:(main) git push

DigitalOcean

You can log in to digitalocean.com to access our server. Note: on Nov 7 2022, I moved the server to a new Team, "MIT Julia Lab Pluto". I sent Henri an invite email to join the team. https://github.com/fonsp, https://github.com/pankgeorg and https://github.com/edelman also have access.

Monitoring

With Graphs, you can view the current CPU and memory usage. (Tip: if the memory graph shows a regular (sawtooth) pattern, this means that we are out of memory.)

image

Resize

If we need to change the amount of CPU cores or memory of the server, use the Resize tab.

Schermafbeelding 2022-02-04 om 16 29 49

To resize:

  1. Shut down the server using to top-right button
  2. Choose a new size. (Don't resize the disk unless needed. You can only scale the disk up, never down (locking you in a high price))
  3. Click Resize
  4. When done, start the server using to top-right button
  5. (Because the server is using a systemctl service, it automatically runs PlutoSliderServer on boot.)

About CPU types:

  • AMD vs Intel vs "Basic" is mostly marketing
  • Dedicated CPU vs Shared CPU does make a big difference. Dedicated CPU is about 2x faster in launching notebooks and running bond requests. (It's also 2x as expensive.)
  • 2 cores is enough (even with 20+ notebooks), PlutoSliderServer is almost always memory-limited.

Domain name

Our domain is margo.plutojl.org, which currently points to 104.248.124.165, the IP of our digitalocean server. To change this, ask someone from the Pluto team to change the DNS in the plutojl.org cloudflare account.

Advanced: Log in to the server

If your SSH key is added to the server, you can log in like so:

ssh fons@104.248.124.165

The sudo password is the same as the username: fons. The server has Julia 1.7.1 installed.

How to view status & logs

# To see quick status (running/failed and memory):
systemctl -l status pluto-server

# To browse the logs:
sudo journalctl -u pluto-server

How to update the launch script

(You should not need to do this.)

FYI: This server was set up following these instructions: https://github.com/JuliaPluto/PlutoSliderServer.jl#sample-setup-given-a-repository-start-a-plutosliderserver-to-serve-static-exports-with-live-preview Read those first!

# To edit the service file:
sudo nano /etc/systemd/system/pluto-server.service

# To edit the launch script:
sudo nano /usr/local/bin/pluto-slider-server.sh

And then enable&run the new scripts:

sudo systemctl daemon-reload
sudo systemctl start pluto-server