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script.sh: - remote_pid: - submitted: 1737827924.408376 - finished: 1737827935.101008 diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..85118b7 --- /dev/null +++ b/.gitignore @@ -0,0 +1,2 @@ +.env +*.pyc diff --git a/README.md b/README.md index 83233ba..64d6d5a 100644 --- a/README.md +++ b/README.md @@ -3,48 +3,35 @@ [Project page](https://calkit.io/calkit/example-ssh) | [GitHub repo](https://github.com/calkit/example-ssh) -A [Calkit](https://github.com/calkit/calkit) example project that -executes a command on a remote server using SSH, -automatically copying project files back and forth. +A [Calkit](https://github.com/calkit/calkit) example project that runs one +pipeline stage on another machine over SSH, and the rest locally. -Note this will probably fail if run from Windows for a Unix-like host -because Git will probably -check out files with the wrong line endings and send those over. -This is [configurable](https://docs.github.com/en/get-started/getting-started-with-git/configuring-git-to-handle-line-endings), -however. +The `raw-data` stage collects data in the `py` environment on a remote +host; `plot` then reads that data and makes a figure here. +Calkit moves the project to a workspace on that host, runs the stage there, +and brings the outputs back. -## Setup +## Getting set up and running -### Create an SSH key and add it to the agent - -See [these docs](https://docs.github.com/en/authentication/connecting-to-github-with-ssh/generating-a-new-ssh-key-and-adding-it-to-the-ssh-agent). - -This is only necessary if you haven't done this before. -Optionally, you can create a new key just for this host. -Don't use a passphrase if you want your commands to run without entering -it each time. -This should be okay if your machine is secure. - -### Add your SSH key to the server - -Assuming you've created one and added it to the agent, call: +There isn't a separate setup step. +Run the pipeline and Calkit asks for whatever is missing: ```sh -ssh-copy-id $USER@$HOST +calkit run ``` -If created a unique key for this remote host, -use the `-i` flag to specify that key file. +In a terminal, that prompts for the host and user (saving them to `.env`), +offers to create an SSH key if you don't have one, offers to authorize this +machine on the host with `ssh-copy-id`, and offers to install Calkit there +if it's missing. +Nothing happens without you agreeing to it. -### Fill in the correct environment details - -In `calkit.yaml`, there is an environment called `cluster`. -Replace any relevant values there to match your remote machine. - -## Running the pipeline - -Execute: +To check the setup without running anything, use: ```sh -calkit run +calkit check env -n remote ``` + +Outside a terminal---in CI, say---nothing is prompted for, because there's +nobody to answer. +It fails with the exact commands to run instead. diff --git a/calkit.yaml b/calkit.yaml index d18ea7f..8d7f012 100644 --- a/calkit.yaml +++ b/calkit.yaml @@ -1,13 +1,44 @@ -dependencies: - - calkit>0.16.3 +owner: calkit +name: example-ssh +hub: calkit.io +title: SSH Example +description: An example of running a Calkit pipeline stage on a remote + machine via SSH. + +requirements: + - calkit>=0.44.0 + - kind: env-var + name: CK_SSH_HOST + environments: - cluster: - kind: ssh - host: "10.211.55.12" - user: parallels - wdir: /home/parallels/calkit/example-ssh - key: ~/.ssh/id_ed25519 - send_paths: - - script.sh - get_paths: - - results + remote: + kind: system + host: ${CK_SSH_HOST} + # Choosing a working directory is optional. It says where to put the + # project when it has to be sent here; if you're already on this host, + # stages run in the checkout you're in and this is ignored. The host is + # recognized whether it's written as a name or an address, so running + # from the machine itself skips SSH entirely. + wdir: ~/calkit/example-ssh + py: + kind: uv + path: .calkit/envs/py/pyproject.toml + python: "3.12" + +pipeline: + stages: + raw-data: + kind: python-script + script_path: scripts/collect.py + environment: remote:py + outputs: + - path: data/raw.csv + storage: git + plot: + kind: python-script + script_path: scripts/plot.py + environment: py + inputs: + - data/raw.csv + outputs: + - figures/plot.png diff --git a/data/raw.csv b/data/raw.csv new file mode 100644 index 0000000..96ff90a --- /dev/null +++ b/data/raw.csv @@ -0,0 +1,201 @@ +t,signal +0.0,0.01257302210933933 +0.06314759102693052,0.04989514498354346 +0.12629518205386103,0.19000197011204578 +0.18944277308079155,0.19880167820502184 +0.25259036410772207,0.19634602505419727 +0.3157379551346526,0.3466775373651173 +0.3788855461615831,0.5002852899295606 +0.4420331371885136,0.5224861640231339 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+ md5: 17f4ca0df24b3de27e52f7e3349a6dde + size: 21 + - path: .calkit/envs/py/uv.lock + hash: md5 + md5: 42a6bb483bf62e9c50141357e3f934d6 + size: 111884 + - path: scripts/collect.py + hash: md5 + md5: 5e90799577a974131ba41936a4572a5e + size: 952 + outs: + - path: data/raw.csv + hash: md5 + md5: 0841adb5f537addcefff8632579fbb98 + size: 7804 + plot: + cmd: calkit xenv -n py --no-check -- python scripts/plot.py + deps: + - path: .calkit/envs/py/uv.lock + hash: md5 + md5: 42a6bb483bf62e9c50141357e3f934d6 + size: 111884 + - path: data/raw.csv + hash: md5 + md5: 0841adb5f537addcefff8632579fbb98 + size: 7804 + - path: scripts/plot.py + hash: md5 + md5: 11c2636e9009187d57ca797d6d64bde5 + size: 1016 + outs: + - path: figures/plot.png + hash: md5 + md5: 0cd9cc7514f58a76a516866f163db662 + size: 45260 diff --git a/dvc.yaml b/dvc.yaml index 8e8dc01..b59715f 100644 --- a/dvc.yaml +++ b/dvc.yaml @@ -1,11 +1,24 @@ stages: - # Run a command in the SSH 'cluster' env - # Note that even if we disconnect while running, the results will be awaited - # and collected if the pipeline is run again - run-sim: - cmd: calkit xenv -n cluster -- bash script.sh + raw-data: + cmd: calkit xenv -n remote --no-check -- calkit xenv -n py --no-check + -- python scripts/collect.py deps: - - script.sh + - scripts/collect.py + - .calkit/envs/py/uv.lock + - .calkit/env-locks/remote/info.json outs: - - results: + - data/raw.csv: cache: false + persist: false + desc: Automatically generated from the 'raw-data' stage in calkit.yaml. + Changes made here will be overwritten. + plot: + cmd: calkit xenv -n py --no-check -- python scripts/plot.py + deps: + - scripts/plot.py + - data/raw.csv + - .calkit/envs/py/uv.lock + outs: + - figures/plot.png + desc: Automatically generated from the 'plot' stage in calkit.yaml. + Changes made here will be overwritten. diff --git a/figures/.gitignore b/figures/.gitignore new file mode 100644 index 0000000..1ec03d7 --- /dev/null +++ b/figures/.gitignore @@ -0,0 +1 @@ +/plot.png diff --git a/results/1.txt b/results/1.txt deleted file mode 100644 index 2e8b545..0000000 --- a/results/1.txt +++ /dev/null @@ -1 +0,0 @@ -sup diff --git a/results/2.txt b/results/2.txt deleted file mode 100644 index 039727e..0000000 --- a/results/2.txt +++ /dev/null @@ -1 +0,0 @@ -lol diff --git a/script.sh b/script.sh deleted file mode 100644 index 04625f8..0000000 --- a/script.sh +++ /dev/null @@ -1,5 +0,0 @@ -echo "Hello from the cluster" -mkdir -p results -echo sup > results/1.txt -echo lol > results/2.txt -sleep 10 diff --git a/scripts/collect.py b/scripts/collect.py new file mode 100644 index 0000000..f30a384 --- /dev/null +++ b/scripts/collect.py @@ -0,0 +1,30 @@ +"""Stand in for whatever actually produces this project's raw data. + +This is the stage that runs somewhere else. Its environment in +``calkit.yaml`` is ``remote-machine:py``, which means Calkit sends the +project to a workspace on the remote host, activates the ``py`` environment +there, and runs this script on that machine rather than on yours. + +Deliberately seeded, so re-running produces byte-identical output and the +pipeline can show you a cached stage rather than fresh noise every time. +""" + +import csv +import os +import platform + +import numpy as np + +N_POINTS = 200 + +rng = np.random.default_rng(seed=0) +t = np.linspace(0, 4 * np.pi, N_POINTS) +signal = np.sin(t) + rng.normal(scale=0.1, size=N_POINTS) + +os.makedirs("data", exist_ok=True) +with open("data/raw.csv", "w", newline="") as f: + writer = csv.writer(f) + writer.writerow(["t", "signal"]) + writer.writerows(zip(t, signal)) + +print(f"Collected {N_POINTS} points on {platform.node()}") diff --git a/scripts/plot.py b/scripts/plot.py new file mode 100644 index 0000000..c92d20a --- /dev/null +++ b/scripts/plot.py @@ -0,0 +1,34 @@ +"""Stand in for whatever actually turns this project's data into a figure. + +This stage runs locally, in the ``py`` environment, on the data the +``raw-data`` stage collected remotely. That split is the point of the +example: the work that needs the other machine happens there, and +everything downstream of it carries on here as normal. +""" + +import csv +import os + +import matplotlib + +# No display on a machine running a pipeline, and none needed to write a file +matplotlib.use("Agg") + +import matplotlib.pyplot as plt # noqa: E402 + +t = [] +signal = [] +with open("data/raw.csv") as f: + for row in csv.DictReader(f): + t.append(float(row["t"])) + signal.append(float(row["signal"])) + +os.makedirs("figures", exist_ok=True) +fig, ax = plt.subplots(figsize=(6, 3), layout="constrained") +ax.plot(t, signal, linewidth=1) +ax.set_xlabel("t") +ax.set_ylabel("Signal") +ax.set_title(f"Collected remotely: {len(t)} points") +fig.savefig("figures/plot.png", dpi=150) + +print(f"Plotted {len(t)} points to figures/plot.png")