Skip to content

Latest commit

 

History

History
336 lines (273 loc) · 16.4 KB

README.md

File metadata and controls

336 lines (273 loc) · 16.4 KB
Raw


ClimaArtifacts

FAQs

Pre-processing pipelines for the input data used by the CliMA project and Artifacts.toml entry to use those artifacts.

Each folder (except for ClimaArtifactsHelper.jl) contains everything that is needed to produce and use an artifact for CliMA:

  • A readme to describe the details,
  • Project.toml and a Manifest.toml files that describe the version of packages required,
  • A create_artifact.jl Julia script to do the per-processing, optionally retrieving the data and creating an Artifact.toml entry,
  • A OutputArtifacts.toml entry that contains the code needed to use that artifact. This is produced by the create_artifact.jl script.

To use an artifact, copy the content of the OutputArtifacts.toml to your Artifacts.toml.

To recreate an artifact, cd into the desired folder and run julia --project create_artifact.jl.

The ClimaArtifactsHelper.jl contains shared functions used across the various artifacts.

Artifacts available

The ultimate guide to ClimaArtifacts

Last update: 26 September 2024

What is an artifact?

Sometimes, Julia packages require external piece of binary data to work. This might be a compiled library, a binary blob, or anything else. At CliMA, we use Julia artifacts to define and manage external data required to run our models (e.g., the surface albedo of the globe as a function of time).

Important: While we refer to data as artifacts, technically, Julia artifacts are always folders and not single files.

As a developer, how do I use an existing artifact?

You can find the list of artifacts associated to a package by looking at its Artifacts.toml file.

Let us consider an example Artifacts.toml.

[era5_static_example]
git-tree-sha1 = "9e0fa7970c5ade600867f5afe737bc3ab6930204"

    [[era5_static_example.download]]
    sha256 = "6c2c3312ff49776ab4d3db7e84ba348dc8e3ffad2d3cb5e77e35039bdeec1610"
    url = "https://caltech.box.com/shared/static/pdsre5tumpc04qbomzjduw07ryd3emwj.gz"

[era5_example]
git-tree-sha1 = "c08d3035085c3c2969d1d9fb6f299686bad8d253"
very_important = "yes"

[socrates]
git-tree-sha1 = "43563e7631a7eafae1f9f8d9d332e3de44ad7239"
lazy = true

    [[socrates.download]]
    url = "https://github.com/staticfloat/small_bin/raw/master/socrates.tar.gz"
    sha256 = "e65d2f13f2085f2c279830e863292312a72930fee5ba3c792b14c33ce5c5cc58"

This Artifacts.toml defines three distinct artifacts named era_static_example, era5_example, and socrates. The name is local to this package and there could be packages with artifacts that share the same names.

Let us focus on the first one,

[era5_static_example]
git-tree-sha1 = "9e0fa7970c5ade600867f5afe737bc3ab6930204"

    [[era5_static_example.download]]
    sha256 = "6c2c3312ff49776ab4d3db7e84ba348dc8e3ffad2d3cb5e77e35039bdeec1610"
    url = "https://caltech.box.com/shared/static/pdsre5tumpc04qbomzjduw07ryd3emwj.gz"

In the brackets, we have the name of the artifact, era5_static_example. This is how we access this artifact from the code in this package (see below). Next, we have the git-tree-sha1, this is a cryptographic hash used to verify the integrity of the artifact. When the artifact is downloaded, Julia checks that the hash of the downloaded folder corresponds to one in the Artifacts.toml. The hash is also used to identify the same artifact across different packages (even if they might have different names), allowing for reuse. The subsequent section, [[era5_static_example.download]], specifies how to obtain the artifact.

Now that we have a sense of how an artifact is specified, let us see how to use it in the code. If we use directly the Julia infrastructure, we can simply import Artifacts:

using Artifacts
println(artifact"era5_static_example")
# ~/.julia/artifacts/9e0fa7970c5ade600867f5afe737bc3ab6930204

Note that artifact"era5_static_example"is the path of a folder. The folder could contain one or multiple files, but it is up to the user to specify which one they want to access. Suppose this artifact only contains one file, era5.nc, the code to access that file would look like

using Artifacts
era5_data = joinpath(artifact"era5_static_example", "era5.nc")
# ~/.julia/artifacts/9e0fa7970c5ade600867f5afe737bc3ab6930204/era4.nc

This is not the preferred way to access artifacts. Instead, we use ClimaUtilities.ClimaArtifacts. This module is MPI safe and allows us to keep track of what artifacts are being used. When the ClimaComms context is not available or relevant, ClimaUtilities.ClimaArtifacts provides a drop-in replacement for artifact:

using ClimaUtilities.ClimaArtifacts
era5_data = joinpath(@clima_artifact("era5_static_example"), "era5.nc")
# ~/.julia/artifacts/9e0fa7970c5ade600867f5afe737bc3ab6930204/era4.nc

If the context is available, it is always best to pass it to (as in clima_artifact("era5_static_example", context)). This ensures that the acquiring the artifact is MPI-safe.

Let us now look at the second block,

[era5_example]
git-tree-sha1 = "c08d3035085c3c2969d1d9fb6f299686bad8d253"
very_important = "yes"

This second block does not contain a download section. This makes the artifact undownloadable. This means that Julia will not try to download the artifact. Instead, the folder has to be acquired in a different way and the path specified using the Overrides mechanism (more on this below). Large artifacts (> 500 MB) should be marked as undownlodable. If you are using the Caltech cluster, all the undownloadable artifacts have been handled for you and there is nothing else you have to do. You can use undownloadable artifacts exactly in the same way you would use downlodable one (ie, with @clima_artifacts).

This second block also has an additional tag, very_important = "yes". We are free to add any extra information to the Artifacts.toml.

Finally, the last block introduces us to a new tag, lazy = true. This annotation marks the artifact as lazy: instead of being downloaded upon instantiation, it is downloaded the first time is used. To use this we must pass the ClimaComms context and also load the LazyArtifacts package.

using LazyArtifacts
using ClimaUtilities.ClimaArtifacts
socrates = joinpath(@clima_artifact("socrates"), "apology.txt")

How to download an undownloadable artifact?

If you are on the Caltech cluster, some has already downloaded and configured everything for you (see below on how this is done in practice). If you are using a different machine, you will have to create a file Overrides.toml in the artifacts folder of your depot (typically ~/.julia). The Overrides.toml provides a map between git-tree-sha1s to paths. The simplest Overrides.toml might look like

c08d3035085c3c2969d1d9fb6f299686bad8d253 = "/path/to/era5folder"

This Overrides.toml binds the artifact with id c08d3035085c3c2969d1d9fb6f299686bad8d253 to a specific folder on your machine. Now, it is up to you to fill the folder with the correct files. You should add bindings for all the undownloadable artifacts you want to use in your simulations.

As a developer, how do I add a new ClimaArtifact?

CliMA artifacts must be reproducible, respect the licenses under which original data is released, and be consistent across different repositories. The ClimaArtifacts repository collects the pipelines and environments used to produce data, as well as tools to help creating Julia artifacts. In ClimaArtifacts, we focus on artifacts that are important for a full Earth System Model, especially those that might be shared across components.

To create a new artifact in ClimaArtifacts:

  1. Clone the ClimaArtifacts repository
  2. Create a new folder with the name of your artifact, e.g., dormouse1819
  3. Create a new Julia project with the script that acquires and processes the data. The script should save all the new data files into a new folder. Such folder will become the artifact (remember, Julia artifacts are always folder)
  4. At the end of your script, call create_artifact_guided(folder_path; artifact_name = basename(@__DIR__))
  5. The create_artifact_guided starts a guided process that gives you the string to put in your Artifacts.toml files.

If you are creating multiple artifacts from the same file, consider adding append = true to ensure that the OutputArtifacts.toml has all the information.

If your artifact is tied to your particular module, you may elect to add it to your repository instead. To do so, follow the same steps above with the exception that you have to create a new artifacts folder (if one does not already exist) and create dormouse1819 in there. You can obtain ClimaArtifactsHelper.jl with:

using Pkg
Pkg.develop(url="https://github.com/CliMA/ClimaArtifacts.git", subdir="ClimaArtifactsHelper.jl")

The other steps are the same.

The create_artifact_guided behaves differently depending on the size of the artifact. For small artifacts, it creates and archive, prompt you to upload the archive to the correct place, computes the hash, and validates that the archive can be correctly downloaded and corresponds to the hash.

For large artifacts, we rely on the Overrides.toml mechanism described in the previous section. In this case, you will have to copy the data to the /groups/esm/ClimaArtifacts/artifacts folder on the cluster and add a new entry to the Overrides.toml that lives there. Add a line of comment to tell others about your new artifact and where it is used.

To test that your artifact works, create a new folder, e.g., /tmp/mynewfolder, create an Artifacts.toml file in it, the content of which has to be the OutputArtifacts.toml file created by the create_artifact_guided function. Then, call julia --project -e 'using Artifacts; println(artifact"AAAAAA")' from that folder, where AAAAAA is the name of your artifact. It should print /groups/esm/ClimaArtifacts/artifacts/AAAAAA, where AAAAAA is the folder you just uploaded.

How to upload on the Caltech Box?

Go to Caltech Box. Navigate to your favorite folder and upload your data. Once the data is uploaded, you have to make it shareable. Click on the sharing icon on the right, the following screen will pop up:

screenshot1

Change from "Invited people only to" "People with link"

screenshot2

If the screen says that you don't have permission, go back and check that you selected "People with link" in the previous step.

Next, go on "Link Settings", and disable "Disable Shared Link on". Copy the Direct Link at the bottom

screenshot3

How are artifacts managed on the Caltech cluster?

We do not want to keep downloading the same artifacts over and over, especially when they are large in size. So, on the Caltech cluster, we store them in a folder and point the Artifacts system to that folder. This section describes how this is accomplished.

The implementation of the system that allows a centrally-managed artifact system relies on the ClimaModules. We install and maintain our version of Julia, which is accessible to users via ClimaModules. This allows us to execute code upon startup to customize the behavior of Julia for all our users. This is accomplished by editing the /etc/julia/startup.jl file. In particular, we are going to add a new entry to the Base.DEPOT_PATH vector to point to /groups/esm/ClimaArtifacts. So, we add a new line to the shared startup.jl:

push!(Base.DEPOT_PATH, "/groups/esm/ClimaArtifacts")

This adds /groups/esm/ClimaArtifacts as depot with lowest priority. In/groups/esm/ClimaArtifacts, there is a folder artifacts, which contains the data and contains a Overrides.toml that is loaded by all users. In this way, every user will automatically have access to all the artifacts available on the system.

Q: Why are we using the startup.jlinstead of using system-wide depot?

A: Typically, Base.DEPOT_PATH contains two depots that are "system-wide" (ie, meant to be managed by the system administrators). Unfortunately, changing the JULIA_DEPOT_PATH resets Base.DEPOT_PATH, so that the system depots are ignored. We use JULIA_DEPOT_PATH extensively in slurm-buildkite.

Frequently Asked Questions

ClimaArtifactsHelper is not able to load my artifact

One of the most common reasons for that is malformed Box links. Your Box link should look something like

https://caltech.box.com/shared/static/pdsre5tumpc04qbomzjduw07ryd3emwj.gz

It has to have a /shared/static portion and an extension. If that's not the case, chances are you copied the link from the wrong page. Make sure you are in the "Link Settings" page (see screenshot above).

I just want to create an artifact with one file

If you want to create an artifact with only one file, you can use the crate_artifact_guided_one_file function.

For example:

using ClimaArtifactsHelper

const FILE_URL = "https://svn-ccsm-inputdata.cgd.ucar.edu/trunk/inputdata/lnd/clm2/surfdata_map/surfdata_0.9x1.25_hist_17pfts_nocft_CMIP6_simyr1700_c230809.nc"
const FILE_PATH = "surfdata_0.9x1.25_hist_17pfts_nocft_CMIP6_simyr1700_c230809.nc"

create_artifact_guided_one_file(FILE_PATH; artifact_name = basename(@__DIR__), file_url = FILE_URL)

Credits

The logo contains elements designed by Adrien Coquet.