From 56df6ce682f97c1e1c410e2e1100dcab293d7837 Mon Sep 17 00:00:00 2001 From: Matheus Tosta Date: Thu, 24 Oct 2024 17:12:34 -0400 Subject: [PATCH] PENG-2414 implement the whole functionality required to initiate the project (#1) * PENG-2414 implement the whole functionality required to initiate the project * PENG-2414 fix the *help* target in the Makefile * PENG-2414 attempt to fix CI workflow by adjusting the order of the steps * PENG-2414 PR review modifications * PENG-2414 omit empty fields in the metadata.yaml * PENG-2414 add icon url to the cfd-openfoam-motorbike job script --- .github/PULL_REQUEST_TEMPLATE.md | 5 + .github/workflows/catalog-cd.yaml | 92 ++ .github/workflows/pr-ci.yaml | 47 + .gitignore | 133 +++ .python-version | 1 + .tool-versions | 2 + Makefile | 37 + README.md | 188 ++++ builder/__init__.py | 0 builder/cache.py | 34 + builder/config.py | 84 ++ builder/context.py | 14 + builder/exceptions.py | 63 ++ builder/format.py | 32 + builder/logging.py | 15 + builder/main.py | 44 + builder/schemas.py | 16 + builder/subapps/__init__.py | 6 + builder/subapps/apptainer.py | 70 ++ builder/subapps/catalog.py | 91 ++ builder/subapps/files.py | 50 + builder/subapps/helpers.py | 253 +++++ builder/subapps/settings.py | 49 + builder/tools.py | 41 + builder/types.py | 6 + cdk.json | 6 + cfd-openfoam-motorbike/.dockerignore | 1 + cfd-openfoam-motorbike/Dockerfile | 18 + cfd-openfoam-motorbike/README.md | 35 + cfd-openfoam-motorbike/job-script.sh | 80 ++ cfd-openfoam-motorbike/metadata.yaml | 7 + infra/__init__.py | 0 infra/app.py | 21 + infra/catalog_bucket.py | 58 + infra/website.py | 114 ++ poetry.lock | 1500 ++++++++++++++++++++++++++ pyproject.toml | 48 + 37 files changed, 3261 insertions(+) create mode 100644 .github/PULL_REQUEST_TEMPLATE.md create mode 100644 .github/workflows/catalog-cd.yaml create mode 100644 .github/workflows/pr-ci.yaml create mode 100644 .gitignore create mode 100644 .python-version create mode 100644 .tool-versions create mode 100644 Makefile create mode 100644 builder/__init__.py create mode 100644 builder/cache.py create mode 100644 builder/config.py create mode 100644 builder/context.py create mode 100644 builder/exceptions.py create mode 100644 builder/format.py create mode 100644 builder/logging.py create mode 100644 builder/main.py create mode 100644 builder/schemas.py create mode 100644 builder/subapps/__init__.py create mode 100644 builder/subapps/apptainer.py create mode 100644 builder/subapps/catalog.py create mode 100644 builder/subapps/files.py create mode 100644 builder/subapps/helpers.py create mode 100644 builder/subapps/settings.py create mode 100644 builder/tools.py create mode 100644 builder/types.py create mode 100644 cdk.json create mode 100644 cfd-openfoam-motorbike/.dockerignore create mode 100644 cfd-openfoam-motorbike/Dockerfile create mode 100644 cfd-openfoam-motorbike/README.md create mode 100644 cfd-openfoam-motorbike/job-script.sh create mode 100644 cfd-openfoam-motorbike/metadata.yaml create mode 100644 infra/__init__.py create mode 100644 infra/app.py create mode 100644 infra/catalog_bucket.py create mode 100644 infra/website.py create mode 100644 poetry.lock create mode 100644 pyproject.toml diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md new file mode 100644 index 0000000..8917db7 --- /dev/null +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -0,0 +1,5 @@ +#### What +Provide a full detailed description of the pull request. It should include detialed explanations about the proposed changes. Keep this section as much technical as possible. + +#### Why +Explain why the proposed change is necessary. Skip if it is already explained on any task related to the pull request. \ No newline at end of file diff --git a/.github/workflows/catalog-cd.yaml b/.github/workflows/catalog-cd.yaml new file mode 100644 index 0000000..bc40ab9 --- /dev/null +++ b/.github/workflows/catalog-cd.yaml @@ -0,0 +1,92 @@ +name: Build and Publish Job Scripts + +on: + workflow_dispatch: + inputs: + job-script-names: + description: Comma-separated list of job script names to build and publish + required: true + type: string + +jobs: + catalog-cd: + runs-on: ubuntu-24.04 + steps: + - name: Checkout code + uses: actions/checkout@v3 + + - uses: actions/setup-node@v4 + with: + node-version: '22.8.0' + + - name: Set up Python + uses: actions/setup-python@v4 + with: + cache: 'poetry' + + - name: Install Poetry + uses: Gr1N/setup-poetry@v8 + with: + poetry-version: 1.8.0 + + - name: Install CDK + run: | + npm install -g aws-cdk@2.162.1 + + - name: Cache cdk.out + uses: actions/cache@v4 + with: + path: cdk.out + key: cdk-out + + - name: Setup AWS credentials + uses: aws-actions/configure-aws-credentials@v4 + with: + aws-access-key-id: ${{ secrets.AWS_ACCESS_KEY_ID }} + aws-secret-access-key: ${{ secrets.AWS_SECRET_ACCESS_KEY }} + aws-region: ${{ vars.S3_BUCKET_REGION }} + + - name: Install Python packages + run: | + poetry install --with=infra + + - name: Install Apptainer + run: | + sudo apt install -y software-properties-common + sudo add-apt-repository -y ppa:apptainer/ppa + sudo apt-update + sudo apt install -y apptainer + + - name: Configure settings + run: | + poetry run builder settings set \ + --aws-access-key-id ${{ secrets.AWS_ACCESS_KEY_ID }} \ + --aws-secret-access-key ${{ secrets.AWS_SECRET_ACCESS_KEY }} \ + --s3-bucket ${{ vars.S3_BUCKET }} \ + --s3-bucket-region ${{ vars.S3_BUCKET_REGION }} + + - name: Build job scripts images + run: | + job_script_names="${{ github.event.inputs.job-script-names }}" + job_script_names_spaced=$(echo $job_script_names | sed 's/,/ /g') + poetry run builder --verbose apptainer build $job_script_names_spaced + + - name: Publish job scripts images + run: | + job_script_names="${{ github.event.inputs.job-script-names }}" + job_script_names_spaced=$(echo $job_script_names | sed 's/,/ /g') + poetry run builder --verbose apptainer publish $job_script_names_spaced + + - name: Publish job scripts artifacts + run: | + job_script_names="${{ github.event.inputs.job-script-names }}" + job_script_names_spaced=$(echo $job_script_names | sed 's/,/ /g') + poetry run builder --verbose files publish $job_script_names_spaced + + - name: Generate the catalog.yaml file + run: | + poetry run builder --verbose catalog generate + + - name: Publish the catalog.yaml file + run: | + cdk deploy --require-approval never VantageJobsCatalogWebsite \ No newline at end of file diff --git a/.github/workflows/pr-ci.yaml b/.github/workflows/pr-ci.yaml new file mode 100644 index 0000000..c9a344e --- /dev/null +++ b/.github/workflows/pr-ci.yaml @@ -0,0 +1,47 @@ +name: 'Test' + +on: + push: + branches: + - main + - release/** + pull_request: + +jobs: + qa: + name: Code Quality Assurance + runs-on: ubuntu-24.04 + + steps: + - name: Checkout code + uses: actions/checkout@v3 + + - uses: actions/setup-node@v4 + with: + node-version: '22.8.0' + + - name: Install Poetry + uses: Gr1N/setup-poetry@v8 + with: + poetry-version: 1.8.0 + + - name: Set up Python + uses: actions/setup-python@v4 + with: + cache: 'poetry' + + - name: Cache Ruff + uses: actions/cache@v4 + with: + path: .ruff_cache + key: ${{ runner.os }}-ruff-${{ hashFiles('.ruff_cache/CACHEDIR.TAG') }} + + - name: Cache Mypy + uses: actions/cache@v4 + with: + path: .mypy_cache + key: ${{ runner.os }}-mypy-${{ hashFiles('.mypy_cache/CACHEDIR.TAG') }} + + - name: Run QA + run: | + make qa diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..a20a974 --- /dev/null +++ b/.gitignore @@ -0,0 +1,133 @@ +# Byte-compiled / optimized / DLL files +__pycache__/ +*.py[cod] +*$py.class + +# C extensions +*.so + +# Distribution / packaging +.Python +build/ +develop-eggs/ +dist/ +downloads/ +eggs/ +.eggs/ +lib/ +lib64/ +parts/ +sdist/ +var/ +wheels/ +pip-wheel-metadata/ +share/python-wheels/ +*.egg-info/ +.installed.cfg +*.egg +MANIFEST + +# PyInstaller +# Usually these files are written by a python script from a template +# before PyInstaller builds the exe, so as to inject date/other infos into it. +*.manifest +*.spec + +# Installer logs +pip-log.txt +pip-delete-this-directory.txt + +# Unit test / coverage reports +htmlcov/ +.tox/ +.nox/ +.coverage +.coverage.* +.cache +nosetests.xml +coverage.xml +*.cover +*.py,cover +.hypothesis/ +.pytest_cache/ + +# Translations +*.mo +*.pot + +# Django stuff: +*.log +local_settings.py +db.sqlite3 +db.sqlite3-journal + +# Flask stuff: +instance/ +.webassets-cache + +# Scrapy stuff: +.scrapy + +# Sphinx documentation +docs/_build/ + +# PyBuilder +target/ + +# Jupyter Notebook +.ipynb_checkpoints + +# IPython +profile_default/ +ipython_config.py + +# pipenv +# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control. +# However, in case of collaboration, if having platform-specific dependencies or dependencies +# having no cross-platform support, pipenv may install dependencies that don't work, or not +# install all needed dependencies. +#Pipfile.lock + +# PEP 582; used by e.g. github.com/David-OConnor/pyflow +__pypackages__/ + +# Celery stuff +celerybeat-schedule +celerybeat.pid + +# SageMath parsed files +*.sage.py + +# Environments +.env +.venv +env/ +venv/ +ENV/ +env.bak/ +venv.bak/ + +# Spyder project settings +.spyderproject +.spyproject + +# Rope project settings +.ropeproject + +# mkdocs documentation +/site + +# mypy +.mypy_cache/ +.dmypy.json +dmypy.json + +# Pyre type checker +.pyre/ + +# Apptainer images +*.sif + +catalog.yaml + +cdk.out \ No newline at end of file diff --git a/.python-version b/.python-version new file mode 100644 index 0000000..871f80a --- /dev/null +++ b/.python-version @@ -0,0 +1 @@ +3.12.3 diff --git a/.tool-versions b/.tool-versions new file mode 100644 index 0000000..ca1efb6 --- /dev/null +++ b/.tool-versions @@ -0,0 +1,2 @@ +poetry 1.8.0 +nodejs 22.8.0 diff --git a/Makefile b/Makefile new file mode 100644 index 0000000..4c02928 --- /dev/null +++ b/Makefile @@ -0,0 +1,37 @@ +SHELL:=/bin/bash +ROOT_DIR:=$(shell dirname $(shell pwd)) + +.PHONY: install +install: ## Install Python packages + poetry install + +.PHONY: lint +lint: install ## Lint the project using ruff + poetry run ruff check builder infra + +.PHONY: mypy +mypy: install ## Run mypy on the project + poetry run mypy builder --pretty + +.PHONY: qa +qa: lint mypy ## Run the quality assurance check + echo "All tests pass! Ready for deployment" + +.PHONY: format +format: install ## Format the code using ruff + poetry run ruff format builder infra + +.PHONY: clean +clean: ## Clean all files/folders created by the project + @find . -iname '*.pyc' -delete + @find . -iname '__pycache__' -delete + @find . -type d -name '.mypy_cache' -exec rm -rf {} + + @find . -type d -name '.ruff_cache' -exec rm -rf {} + + @find . -type d -name '.venv' -exec rm -rf {} + + @find . -iname '*.sif' -delete + @find . -iname 'catalog.yaml' -delete + @find . -type d -name 'cdk.out' -exec rm -rf {} + + +.PHONY: help +help: ## Print the targets and their descriptions + @grep -E '^[a-zA-Z_-]+:.*?## .*$$' $(MAKEFILE_LIST) | awk 'BEGIN {FS = ":.*?## "}; {printf "\033[36m%-30s\033[0m %s\n", $$1, $$2}' \ No newline at end of file diff --git a/README.md b/README.md index 43f5005..5f3ae2b 100644 --- a/README.md +++ b/README.md @@ -1,2 +1,190 @@ # vantage-jobs-catalog A git store of prepared job scripts that can be imported into Vantage and submitted to a cluster. + +## Overview + +This repository serves as a centralized catalog of job scripts designed for seamless execution on HPC clusters managed through Vantage. It provides a curated collection of ready-to-use scripts for various common HPC workloads, simplifying job submission and execution using Vantage. + +Currently, the following job scripts are available: + +* **OpenFOAM Motorbike**: A CFD workflow for simulating the flow around a motorcycle. + +## Job Catalog Definition + +The job catalog is defined by the `catalog.yaml` file generated by the builder program. This YAML file provides a structured definition of each available job script, including: + +* **Entry Point File**: The primary script responsible for executing the job. +* **Suppoting Files**: Any auxiliary scripts or data files required by the job. +* **Apptainer Image URI**: The URI of the Apptainer image containing the necessary software and dependencies for the job. + +## Contributing + +Feature requests and bug reports are always welcome. If you find a bug in any of the job scripts in the catalog, be sure +to mention the specific job script name. + +New jobs can be added to the repository if they meet the following acceptance criteria: + +1. The job script folder must have a name that describes the job script it contains, e.g. `cfd-openfoam-motorbike`. +2. The job script folder must contain: + * A `README.md` file + a. It must explain the computation that the job script performs. + b. It must explain the HPC app(s) that the job script uses to run the computation, e.g. OpenFOAM. + c. It must explain how to examine the results of the job. + * A job script entrypoint file + a. It must either be a shell script or a python source file. + b. It must have a descriptive name. + c. It should use Apptainer to run job-specific HPC app(s): + i. It must pull the apptainer image that it needs to the shared file system at `/nfs` + * The image name must be prefixed by `vantage-jobs-catalog`. + * The image name must include the name of the job script folder. + * Example of the resulting name: `vantage-jobs-catalog-cfd-openfoam-motorbike`. + d. It must execute its HPC app(s) within the Apptainer container. + * Any supporting files needed by the job script. + * An optional `Dockerfile` that can be used to build the Apptainer image. + * A `metadata.yaml` file that includes: + a. `summary` (required): A very brief summary describing the catalog entry. + b. `icon-url` (optional): An icon URL for the catalog entry. + c. `entrypoint` (entrypoint): The entrypoint job script file. + d. `supporting-files` (optional): The supporting files for the job script. + e. `image-source` (optional): The source to use when building the Apptainer image. This may be a `Dockerfile` in the job script folder, a URL to a Docker image hosted somewhere + f. `image-tags` (optional): The tags to apply to the image upon publication. If omitted, it should be assumed `latest`. Each entry must follow the semantic versioning pattern. + +Example: +```yaml +# metadata.yaml +summary: Compute steady flow around a motorcycle +entrypoint: job-script.sh +image-source: Dockerfile +image-tags: +- "1.0.0" +- "latest" +``` + +## CLI + +The project is integrated with a CLI tool for assisting in the process of building and publishing the artifacts. + +The requirements are: +* Python >= 3.12 +* Poetry 1.8.0 +* Apptainer 1.3.4 + +Start by installing the dependencies: + +```bash +poetry install --only main +``` + +The entrypoint of the CLI is called by running `poetry run builder`. You can increase the verbosity by adding the +`--verbose` flag, e.g. + +```bash +poetry run builder --verbose +``` + +### Configure the settings + +Before building or publishing any artifact, you need to configure the settings for the CLI. The settings are described +with the following command: + +```bash +poetry run builder settings set --help +``` + +#### Note + +In case you want to use temporary AWS credentials, run the following command to issue them: + +```bash +aws sts assume-role --role-arn --role-session-name jobCatalogBuilder --no-cli-pager --region us-east-1 +``` + +Substitute the placeholder `` for the role you want to assume. Independently if you are assuming a role or using your own credentials, you must have the following AWS permissions: + +* **ecr-public:GetAuthorizationToken** +* **ecr-public:DescribeRegistries** +* **ecr-public:GetRepositoryCatalogData** +* **ecr-public:PutImage** +* **ecr-public:UploadLayerPart** +* **ecr-public:CompleteLayerUpload** +* **ecr-public:BatchCheckLayerAvailability** +* **ecr-public:InitiateLayerUpload** +* **s3:UploadFile** +* **s3:PutObjectAcl** + +### Build a job script image + +To build a job script's Apptainer image, run the following command: + +```bash +poetry run builder --verbose apptainer build +``` + +Substitute the `` placeholder by the paths of the jobs scripts. You can build more than one +concurrently. Here is an example builder command: + +```bash +poetry run builder --verbose apptainer build ./foo/ ./boo/ ./qux/ +``` + +To see what the command will do without actually executing the build process, you can add a `--dry-run` flag. + +### Publish a job script image + +To publish a job script's Apptainer image, run the following command: + +```bash +poetry run builder --verbose apptainer publish +``` + +Similarly to building the image, substitute the placeholder by passing as many job scripts paths as you need to: + +```bash +poetry run builder --verbose apptainer publish ./foo/ ./boo/ ./qux/ +``` + +### Publish a job script artifact + +To publish the job script's artifacts to S3 (i.e. the entry point and the supporting files), run the command: + +```bash +poetry run builder --verbose files publish +``` + +Substitute the placeholder `` by the paths of the job scripts whose artifacts will be uploaded. + +### Build the `catalog.yaml` file + +To build the `catalog.yaml` file, run the command: + +```bash +poetry run builder catalog generate +``` + +A file `catalog.yaml` will be generated at the root of the directory. + +## Create the artifact bucket + +To create the S3 bucket that will store the job script entry points and supporting files, you need CDK installed. +This deployment is verified with node 22.8.0 and CDK 2.162.1. To create the bucket, run: + +```bash +cdk deploy VantageJobsCatalogArtifacts +``` + +Configure the GitHub repository to use this bucket in automatic deployments using the GitHub CLI and the AWS CLI: + +```bash +BUCKET_NAME=$(aws cloudformation list-exports \ +--region us-east-1 \ +--query 'Exports[?Name==`VantageJobsCatalogArtifactsBucketName`].Value[] | [0]' \ +--no-cli-pager \ +--output text) +BUCKET_REGION=$(aws cloudformation list-exports \ +--region us-east-1 \ +--query 'Exports[?Name==`VantageJobsCatalogArtifactsBucketRegion`].Value[] | [0]' \ +--no-cli-pager \ +--output text) +gh variable set S3_BUCKET --body "$BUCKET_NAME" --repos omnivector-solutions/vantage-jobs-catalog +gh variable set S3_BUCKET_REGION --body "$BUCKET_REGION" --repos omnivector-solutions/vantage-jobs-catalog +``` diff --git a/builder/__init__.py b/builder/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/builder/cache.py b/builder/cache.py new file mode 100644 index 0000000..f7e87f3 --- /dev/null +++ b/builder/cache.py @@ -0,0 +1,34 @@ +"""Core module for cache related operations.""" + +from __future__ import annotations + +from functools import wraps +from pathlib import Path + +from builder.exceptions import Abort + +cache_dir: Path = Path.home() / ".local/share/vantage-jobs-catalog" + + +def init_cache(func): + """Return a decorator to initialize the cache directory.""" + + @wraps(func) + def wrapper(*args, **kwargs): + try: + cache_dir.mkdir(exist_ok=True, parents=True) + info_file = cache_dir / "info.txt" + info_file.write_text("This directory is used by Vantage Jobs Catalog CLI for its cache.") + except Exception: + raise Abort( + f""" + Cache directory {cache_dir} doesn't exist, is not writable, or could not be created. + + Please check your home directory permissions and try again. + """, + subject="Non-writable cache dir", + log_message="Non-writable cache dir", + ) + return func(*args, **kwargs) + + return wrapper diff --git a/builder/config.py b/builder/config.py new file mode 100644 index 0000000..e1a8178 --- /dev/null +++ b/builder/config.py @@ -0,0 +1,84 @@ +"""Configuration management for the Vantage Jobs Catalog CLI.""" + +import json +from functools import wraps +from typing import Optional + +import snick +import typer +from loguru import logger +from pydantic import BaseModel, ValidationError + +from builder.cache import cache_dir +from builder.exceptions import Abort + +settings_path = cache_dir / "builder.json" + + +class Settings(BaseModel): + """Settings for the Vantage Jobs Catalog CLI.""" + + aws_access_key_id: str + aws_secret_access_key: str + aws_session_token: Optional[str] = None + s3_bucket: str + s3_bucket_region: str + + +def init_settings(**settings_values): + """Initialize the settings object.""" + try: + logger.debug("Validating settings") + return Settings(**settings_values) + except ValidationError as err: + raise Abort( + snick.dedent( + f""" + A configuration error was detected. + + Details: + + [red]{err}[/red] + """ + ), + subject="Configuration Error", + log_message="Configuration error", + ) + + +def attach_settings(func): + """Return a decorator to attach settings to the CLI context.""" + + @wraps(func) + def wrapper(ctx: typer.Context, *args, **kwargs): + try: + logger.debug(f"Loading settings from {settings_path}") + settings_values = json.loads(settings_path.read_text()) + except FileNotFoundError: + raise Abort( + f""" + No settings file found at {settings_path}! + + Run the *settings set* sub-command first to establish the settings. + """, + subject="Settings file missing!", + log_message="Settings file missing!", + ) + logger.debug("Binding settings to CLI context") + ctx.obj.settings = init_settings(**settings_values) + return func(ctx, *args, **kwargs) + + return wrapper + + +def dump_settings(settings: Settings): + """Dump the settings to a file.""" + logger.debug(f"Saving settings to {settings_path}") + settings_values = json.dumps(settings.model_dump()) + settings_path.write_text(settings_values) + + +def clear_settings(): + """Clear the saved settings.""" + logger.debug(f"Removing saved settings at {settings_path}") + settings_path.unlink(missing_ok=True) diff --git a/builder/context.py b/builder/context.py new file mode 100644 index 0000000..986109c --- /dev/null +++ b/builder/context.py @@ -0,0 +1,14 @@ +"""Context for the CLI application.""" + +from typing import Optional + +from pydantic import BaseModel + +from builder.config import Settings + + +class CliContext(BaseModel, arbitrary_types_allowed=True): + """Context model for the CLI application.""" + + settings: Optional[Settings] = None + verbose: bool = False diff --git a/builder/exceptions.py b/builder/exceptions.py new file mode 100644 index 0000000..c9af4d6 --- /dev/null +++ b/builder/exceptions.py @@ -0,0 +1,63 @@ +"""Custom exceptions for the Vantage Jobs Catalog CLI.""" + +from functools import wraps +from sys import exc_info + +import buzz +import snick +import typer +from loguru import logger +from rich import traceback +from rich.console import Console +from rich.panel import Panel + +# Enables prettified traceback printing via rich +traceback.install() + + +class Abort(buzz.Buzz): + """Custom exception to handle aborting the CLI.""" + + def __init__( # noqa: D107 + self, + message, + *args, + subject=None, + log_message=None, + warn_only=False, + **kwargs, + ): + self.subject = subject + self.log_message = log_message + self.warn_only = warn_only + (_, self.original_error, __) = exc_info() + super().__init__(message, *args, **kwargs) + + +def handle_abort(func): + """Return a decorator to handle Abort exceptions.""" + + @wraps(func) + def wrapper(*args, **kwargs): + try: + func(*args, **kwargs) + except Abort as err: + if not err.warn_only: + if err.log_message is not None: + logger.error(err.log_message) + + if err.original_error is not None: + logger.error(f"Original exception: {err.original_error}") + + panel_kwargs = dict() + if err.subject is not None: + panel_kwargs["title"] = f"[red]{err.subject}" + message = snick.dedent(err.message) + + console = Console() + console.print() + console.print(Panel(message, **panel_kwargs)) + console.print() + raise typer.Exit(code=1) + + return wrapper diff --git a/builder/format.py b/builder/format.py new file mode 100644 index 0000000..99ff35e --- /dev/null +++ b/builder/format.py @@ -0,0 +1,32 @@ +"""Core module for defining format functions when rendering to the terminal.""" + +import json +from typing import Any + +import snick +from rich.console import Console +from rich.panel import Panel + + +def terminal_message(message, subject=None, color="green", footer=None, indent=True): + """Render a message to the terminal using rich.""" + panel_kwargs = dict(padding=1) + if subject is not None: + panel_kwargs["title"] = f"[{color}]{subject}" + if footer is not None: + panel_kwargs["subtitle"] = f"[dim italic]{footer}[/dim italic]" + text = snick.dedent(message) + if indent: + text = snick.indent(text, prefix=" ") + console = Console() + console.print() + console.print(Panel(text, **panel_kwargs)) + console.print() + + +def render_json(data: Any): + """Render a JSON object to the terminal using rich.""" + console = Console() + console.print() + console.print_json(json.dumps(data)) + console.print() diff --git a/builder/logging.py b/builder/logging.py new file mode 100644 index 0000000..42169d2 --- /dev/null +++ b/builder/logging.py @@ -0,0 +1,15 @@ +"""Core module for logging definitions and initializations.""" + +import sys + +from loguru import logger + + +def init_logs(verbose=False): + """Initialize logging for the CLI application based on the verbosity.""" + logger.remove() + + if verbose: + logger.add(sys.stdout, level="DEBUG") + + logger.debug("Logging initialized") diff --git a/builder/main.py b/builder/main.py new file mode 100644 index 0000000..f3395eb --- /dev/null +++ b/builder/main.py @@ -0,0 +1,44 @@ +"""Main module for the Vantage Jobs Catalog CLI app.""" + +import snick +import typer + +from builder.context import CliContext +from builder.exceptions import handle_abort +from builder.format import terminal_message +from builder.logging import init_logs +from builder.subapps import apptainer_app, catalog_app, files_app, settings_app + +app = typer.Typer(name="Vantage Jobs Catalog") +app.add_typer(settings_app, name="settings") +app.add_typer(apptainer_app, name="apptainer") +app.add_typer(files_app, name="files") +app.add_typer(catalog_app, name="catalog") + + +@app.callback(invoke_without_command=True) +@handle_abort +def main( + ctx: typer.Context, + verbose: bool = typer.Option(False, help="Enable verbose logging to the terminal"), +): + """Welcome to the Vantage Jobs Catalog CLI!. + + More information can be shown for each command listed below by running it with the + --help option. + """ + if ctx.invoked_subcommand is None: + terminal_message( + snick.dedent( + f""" + No command provided. Please check [bold magenta]usage[/bold magenta] + + [yellow]{ctx.get_help()}[/yellow] + """ + ), + subject="Need a command", + ) + raise typer.Exit() + + init_logs(verbose=verbose) + ctx.obj = CliContext(verbose=verbose) diff --git a/builder/schemas.py b/builder/schemas.py new file mode 100644 index 0000000..53b05bc --- /dev/null +++ b/builder/schemas.py @@ -0,0 +1,16 @@ +"""Core module for defining schemas and constants.""" + +from pathlib import Path + +from pydantic import BaseModel, Field + + +class JobScriptMetadata(BaseModel): + """Metadata for a job script.""" + + summary: str + icon_url: str | None = Field(None, alias="icon-url") + entrypoint: Path + supporting_files: list[Path] | None = Field(None, alias="supporting-files") + image_source: str | None = Field(None, alias="image-source") + image_tags: list[str] | None = Field(None, alias="image-tags") diff --git a/builder/subapps/__init__.py b/builder/subapps/__init__.py new file mode 100644 index 0000000..5888543 --- /dev/null +++ b/builder/subapps/__init__.py @@ -0,0 +1,6 @@ +from builder.subapps.settings import app as settings_app +from builder.subapps.apptainer import app as apptainer_app +from builder.subapps.files import app as files_app +from builder.subapps.catalog import app as catalog_app + +all = ["settings_app", "apptainer_app", "files_app", "catalog_app"] \ No newline at end of file diff --git a/builder/subapps/apptainer.py b/builder/subapps/apptainer.py new file mode 100644 index 0000000..c6ac874 --- /dev/null +++ b/builder/subapps/apptainer.py @@ -0,0 +1,70 @@ +"""App for apptainer related operations.""" + +import asyncio +from pathlib import Path +from typing import Annotated, Optional + +import typer + +from builder.config import attach_settings +from builder.context import CliContext +from builder.exceptions import handle_abort +from builder.format import terminal_message +from builder.subapps.helpers import ( + build_image, + check_existing_paths, + check_sif_exists, + find_job_scripts, + publish_image, + run_tasks_concurrently, +) + +app = typer.Typer() + + +@app.command(name="build") +@handle_abort +def build( + job_scripts: Annotated[ + Optional[list[Path]], + typer.Argument( + ..., help="Paths of the job scripts to build. If None, all job scripts will be built." + ), + ] = None, + dry_run: bool = typer.Option(False, help="Do not build the images, only print the commands."), +): + """Build an Apptainer .sif file from a Dockerfile for each job script imputed.""" + job_scripts = find_job_scripts(job_scripts) + check_existing_paths(job_scripts) + tasks = [build_image(job_script_path, dry_run) for job_script_path in job_scripts] + asyncio.run(run_tasks_concurrently(tasks)) + terminal_message("Built Apptainer images successfully", "Process Complete") + + +@app.command(name="publish") +@handle_abort +@attach_settings +def publish( + ctx: typer.Context, + job_scripts: Annotated[ + Optional[list[Path]], + typer.Argument( + ..., help="Paths of the job scripts to publish. If None, all job scripts will be published." + ), + ] = None, + dry_run: bool = typer.Option(False, help="Do not publish the images, only print the commands."), +): + """Publish the built Apptainer .sif files for each job script supplied.""" + ctx_obj = ctx.obj + assert isinstance(ctx_obj, CliContext) + settings = ctx_obj.settings + assert settings is not None + + job_scripts = find_job_scripts(job_scripts) + + check_sif_exists(job_scripts) + tasks = [ + publish_image(job_script_path, settings, dry_run, ctx_obj.verbose) for job_script_path in job_scripts + ] + asyncio.run(run_tasks_concurrently(tasks)) + terminal_message("Published Apptainer images successfully", "Process Complete") diff --git a/builder/subapps/catalog.py b/builder/subapps/catalog.py new file mode 100644 index 0000000..f77c2d5 --- /dev/null +++ b/builder/subapps/catalog.py @@ -0,0 +1,91 @@ +"""App for managing the catalog.yaml file.""" + +import typer +import yaml +from loguru import logger + +from builder.config import attach_settings +from builder.context import CliContext +from builder.exceptions import handle_abort +from builder.format import render_json, terminal_message +from builder.subapps.helpers import find_job_scripts, load_job_script_metadata +from builder.types import JobScriptCatalog + +app = typer.Typer() + + +@app.command(name="generate") +@handle_abort +@attach_settings +def generate_catalog_file( + ctx: typer.Context, + dry_run: bool = typer.Option( + False, + help=( + "Do not generate the catalog file, only print the commands. " + "Use in conjunction with the --verbose flag for enhanced debugging." + ), + ), +): + """Generate a catalog.yaml file.""" + ctx_obj = ctx.obj + assert isinstance(ctx_obj, CliContext) + settings = ctx_obj.settings + assert settings is not None + + job_scripts_paths = find_job_scripts() + logger.debug(f"Found {len(job_scripts_paths)} job scripts: {[path.name for path in job_scripts_paths]}") + + catalog: JobScriptCatalog = {"job-scripts": []} + + for job_script_path in job_scripts_paths: + metadata = load_job_script_metadata(job_script_path) + + apptainer_image_urls: list[str | None] + if metadata.image_source is None: + logger.warning(f"No image source found for {job_script_path.name}") + apptainer_image_urls = [None] + elif metadata.image_source == "Dockerfile": + if metadata.image_tags is None: + apptainer_image_urls = [ + f"oras://public.ecr.aws/omnivector-solutions/{job_script_path.name}:latest" + ] + else: + apptainer_image_urls = [ + f"oras://public.ecr.aws/omnivector-solutions/{job_script_path.name}:{tag}" + for tag in metadata.image_tags + ] + else: + apptainer_image_urls = [metadata.image_source] + + supporting_files_urls = ( + [ + f"s3://{settings.s3_bucket}/files/{job_script_path.name}/{supporting_file.name}" + for supporting_file in metadata.supporting_files + ] + if metadata.supporting_files + else [] + ) + + catalog_item = { + "name": job_script_path.name, + "summary": metadata.summary, + "icon-url": metadata.icon_url, + "description": job_script_path.joinpath("README.md").read_text(), + "entrypoint-file-url": f"s3://{settings.s3_bucket}/files/{job_script_path.name}/{metadata.entrypoint.name}", + "supporting-files-urls": supporting_files_urls, + "apptainer-image-urls": apptainer_image_urls, + } + catalog["job-scripts"].append(catalog_item) + logger.debug(f"Added {job_script_path.name} to the catalog") + + catalog_path = "catalog.yaml" + if ctx_obj.verbose: + logger.debug("Generated catalog:") + render_json(catalog) + + if not dry_run: + with open(catalog_path, "w") as catalog_file: + yaml.dump(catalog, catalog_file, indent=2) + + terminal_message(f"Catalog file generated at {catalog_path}.", "Process Complete") diff --git a/builder/subapps/files.py b/builder/subapps/files.py new file mode 100644 index 0000000..3e918e3 --- /dev/null +++ b/builder/subapps/files.py @@ -0,0 +1,50 @@ +"""App for file related operations, such as upload supporting files to S3.""" + +import asyncio +from pathlib import Path +from typing import Annotated, Optional + +import typer + +from builder.config import attach_settings +from builder.context import CliContext +from builder.exceptions import handle_abort +from builder.format import terminal_message +from builder.subapps.helpers import ( + check_metadata_exists, + find_job_scripts, + publish_files, + run_tasks_concurrently, +) + +app = typer.Typer() + + +@app.command(name="publish") +@handle_abort +@attach_settings +def publish( + ctx: typer.Context, + job_scripts: Annotated[ + Optional[list[Path]], + typer.Argument( + ..., help="Paths of the job scripts to publish. If None, all job scripts will be published." + ), + ] = None, + dry_run: bool = typer.Option(False, help="Do not publish the images, only print the commands."), +): + """Publish the built Apptainer .sif files for each job script imputed.""" + ctx_obj = ctx.obj + assert isinstance(ctx_obj, CliContext) + settings = ctx_obj.settings + assert settings is not None + + job_scripts = find_job_scripts(job_scripts) + + check_metadata_exists(job_scripts) + tasks = [publish_files(job_script_path, settings, dry_run) for job_script_path in job_scripts] + asyncio.run(run_tasks_concurrently(tasks)) + terminal_message( + f"Published auxiliary files to the bucket {settings.s3_bucket}", + "Process Complete", + ) diff --git a/builder/subapps/helpers.py b/builder/subapps/helpers.py new file mode 100644 index 0000000..f24d4df --- /dev/null +++ b/builder/subapps/helpers.py @@ -0,0 +1,253 @@ +"""Core module for defining auxiliary functions of the commands.""" + +import asyncio +import base64 +from pathlib import Path +from typing import Any, AsyncGenerator, Coroutine, Iterable + +import boto3 +import docker +import yaml +from loguru import logger +from mypy_boto3_ecr_public.client import ECRPublicClient +from mypy_boto3_s3.client import S3Client + +from builder.config import Settings +from builder.exceptions import Abort +from builder.format import render_json, terminal_message +from builder.schemas import JobScriptMetadata +from builder.tools import run_command, run_command_logged + + +def check_existing_paths(paths: list[Path]) -> bool: + """Check if the given paths exist.""" + with Abort.check_expressions( + f"Some of the paths in {[path.name for path in paths]} do not exist", + raise_kwargs={ + "subject": "Path does not exist", + "log_message": "Some of the paths do not exist", + }, + ) as checker: + for path in paths: + checker(path.exists(), f"{path.name} does not exist") + return True + + +def check_sif_exists(paths: list[Path]) -> bool: + """Check if the given parent paths have a child .sif file in them.""" + return check_existing_paths([path.joinpath("output.sif") for path in paths]) + + +def check_metadata_exists(paths: list[Path]) -> bool: + """Check if the given parent paths have a child metadata.yaml file in them.""" + return check_existing_paths([path.joinpath("metadata.yaml") for path in paths]) + + +def find_job_scripts(paths: list[Path] | None = None) -> list[Path]: + """Check if the input is None. If so, return a list containing all job scripts.""" + if paths is None: + # search of folder in the current execution directory + # and return the ones with a metadata.yaml file + paths = list(Path(".").glob("*")) + paths = [path for path in paths if path.joinpath("metadata.yaml").exists()] + return paths + + +def load_job_script_metadata(job_script_path: Path) -> JobScriptMetadata: + """Load the metadata.yaml file from a job script.""" + with open(job_script_path / "metadata.yaml") as metadata_file: + metadata_dict = yaml.safe_load(metadata_file) + metadata = JobScriptMetadata(**metadata_dict) + return metadata + + +async def run_tasks_concurrently(tasks: list[Coroutine[Any, Any, Any]]): + """Run tasks concurrently.""" + await asyncio.gather(*tasks) + + +async def create_async_generator(iterable: Iterable[Any]) -> AsyncGenerator: + """Create an async generator from an iterable.""" + for item in iterable: + yield item + + +async def build_image(job_script_path: Path, dry_run: bool = False): + """Build an Apptainer image from a Dockerfile.""" + with Abort.handle_errors( + "Failed to build Docker image", + raise_kwargs={ + "subject": "Build error", + "log_message": f"Failed to build Docker image from {job_script_path}", + }, + ): + logger.debug(f"Building local docker image from {job_script_path}") + docker_client = docker.from_env() + tag = f"{job_script_path.name}:latest" + if not dry_run: + docker_client.images.build( + path=str(job_script_path), + tag=tag, + rm=True, + ) + docker_image_source = f"docker-daemon://{tag}" + logger.debug(f"Built local docker image {tag}") + + with Abort.handle_errors( + "Failed to build Apptainer image", + raise_kwargs={ + "subject": "Build error", + "log_message": f"Failed to build Apptainer image from {job_script_path}", + }, + ): + logger.debug(f"Building Apptainer image from {docker_image_source}") + output_path = job_script_path / "output.sif" + if not dry_run: + command = f"apptainer build {output_path} {docker_image_source}" + run_command_logged(command) + final_message = f"Built Apptainer image {output_path}" + logger.debug(final_message) + terminal_message(final_message, "Image Built Successfully") + + +async def publish_image( + job_script_path: Path, settings: Settings, dry_run: bool = False, verbose: bool = False +): + """Publish an Apptainer image to a remote registry.""" + logger.debug(f"Loading metadata.yaml from {job_script_path}") + metadata = load_job_script_metadata(job_script_path) + logger.debug("Metadata loaded successfully:") + if verbose: + render_json(metadata.model_dump(mode="json")) + + logger.debug("Examining the metadata to identify the image source") + image_source = metadata.image_source + + logger.debug(f"Using {image_source=} as the image source") + if image_source is None: + logger.debug("No image source defined. Skipping the publish process") + terminal_message("No image source defined. Skipping the publish process", "Publish Skipped") + return + elif image_source == "Dockerfile": + logger.debug("The image source is 'Dockerfile'. Starting the publish process") + image_name = job_script_path.stem + logger.debug(f"Using {image_name=} as the image name") + + logger.debug("Getting ECR client for region us-east-1") + ecr: ECRPublicClient = boto3.client( + "ecr-public", + region_name="us-east-1", + aws_access_key_id=settings.aws_access_key_id, + aws_secret_access_key=settings.aws_secret_access_key, + aws_session_token=settings.aws_session_token, + ) + + logger.debug("Fetching authorization token and extracting username and password") + auth_token_response = ecr.get_authorization_token() + token = auth_token_response["authorizationData"]["authorizationToken"] + (username, password) = base64.b64decode(token).decode().split(":") + logger.debug(f"Got authorization token for user {username}") + + logger.debug("Describing registries on ECR Public") + registry_response = ecr.describe_registries() + registry_list = registry_response["registries"] + Abort.require_condition( + len(registry_list) == 1, + "Did not find one and only one registry", + raise_kwargs=dict( + subject="Publish failed", + log_message=f"Found {len(registry_list)} registries instead of one", + ), + ) + registry_data = registry_list[0] + registry_id = registry_data["registryId"] + registry_uri = registry_data["registryUri"] + registry_domain = registry_uri.split("/")[0] + + try: + ecr.get_repository_catalog_data( + registryId=registry_id, + repositoryName=image_name, + ) + except ecr.exceptions.RepositoryNotFoundException: + raise Abort( + f"There is no repository for {image_name=}", + subject="Publish failed", + log_message=f"There is no repository for {image_name=}", + ) + + logger.debug("Logging into the ECR Public registry via Apptainer") + command = ( + "apptainer registry login " + f"--username={username} " + f"--password={password} " + f"oras://{registry_domain}" + ) + run_command(command) + + logger.debug("Fetching image tags from the metadata") + tags = metadata.image_tags + # if no tag is defined, use "latest" + # if a tag is present, make sure it has the latest as well + if tags is None or len(tags) == 0: + tags = ["latest"] + logger.debug(f"No tag defined for the image {image_name=}, using {tags=}") + elif "latest" not in tags: + tags = list(set(tags + ["latest"])) + logger.debug("Added the 'latest' tag to the image tags") + else: + logger.debug(f"Using tags {tags=} for the image {image_name=}") + + async for tag in create_async_generator(tags): + logger.debug(f"Publishing Apptainer image from {job_script_path}") + publish_url = f"oras://{registry_uri}/{image_name}:{tag}" + output_path = job_script_path / "output.sif" + if not dry_run: + command = f"apptainer push {output_path} {publish_url}" + run_command_logged(command) + logger.debug(f"Published Apptainer image {output_path} to {registry_uri}/{image_name}:{tag}") + else: + logger.debug("The image source is an external registry. Skipping the publish process") + terminal_message( + "The image source is an external registry. Skipping the publish process", "Publish Skipped" + ) + + +async def publish_files(job_script_path: Path, settings: Settings, dry_run: bool = False): + """Publish the auxiliary files for a job script to a remote S3 bucket.""" + logger.debug(f"Loading metadata.yaml from {job_script_path}") + metadata = load_job_script_metadata(job_script_path) + logger.debug("Metadata loaded successfully:") + render_json(metadata.model_dump(mode="json")) + + logger.debug("Examining the metadata to identify the files to publish") + files_paths = [metadata.entrypoint] + if metadata.supporting_files: + files_paths.extend(metadata.supporting_files) + logger.debug(f"Using {[path.name for path in files_paths]} as the files to publish") + + if not all(job_script_path.joinpath(path).exists() for path in files_paths): + raise Abort( + f"Some of the files in {[path.name for path in files_paths]} do not exist", + subject="File does not exist", + log_message="Some of the files do not exist", + ) + + async for file_path in create_async_generator(files_paths): + logger.debug(f"Publishing {file_path} to the bucket {settings.s3_bucket}") + s3: S3Client = boto3.client( + "s3", + region_name=settings.s3_bucket_region, + aws_access_key_id=settings.aws_access_key_id, + aws_secret_access_key=settings.aws_secret_access_key, + aws_session_token=settings.aws_session_token, + ) + if not dry_run: + s3.upload_file( + Filename=str(job_script_path / file_path), + Bucket=settings.s3_bucket, + Key=f"files/{job_script_path.name}/{file_path}", + ) + logger.debug( + f"Published {file_path} to the bucket s3://{settings.s3_bucket}/files/{job_script_path.name}" + ) diff --git a/builder/subapps/settings.py b/builder/subapps/settings.py new file mode 100644 index 0000000..d350182 --- /dev/null +++ b/builder/subapps/settings.py @@ -0,0 +1,49 @@ +"""App for managing configuration settings commands.""" + +import typer + +from builder.cache import init_cache +from builder.config import attach_settings, clear_settings, dump_settings, init_settings +from builder.exceptions import handle_abort +from builder.format import render_json + +app = typer.Typer() + + +@app.command(name="set") +@init_cache +def set_config( + aws_access_key_id: str = typer.Option(..., help="The access key id used by authenticating against AWS"), + aws_secret_access_key: str = typer.Option( + ..., help="The secret access key used by authenticating against AWS" + ), + aws_session_token: str = typer.Option(None, help="The session token used by authenticating against AWS"), + s3_bucket: str = typer.Option(..., help="The S3 bucket where job scripts will be uploaded to"), + s3_bucket_region: str = typer.Option(..., help="The region of the S3 bucket"), +): + """Set the configuration for the CLI.""" + settings = init_settings( + aws_access_key_id=aws_access_key_id, + aws_secret_access_key=aws_secret_access_key, + aws_session_token=aws_session_token, + s3_bucket=s3_bucket, + s3_bucket_region=s3_bucket_region, + ) + dump_settings(settings) + + +@app.command(name="show") +@handle_abort +@init_cache +@attach_settings +def show_config(ctx: typer.Context): + """Show the current config.""" + render_json(ctx.obj.settings.model_dump()) + + +@app.command(name="clear") +@handle_abort +@init_cache +def clear_config(): + """Show the current config.""" + clear_settings() diff --git a/builder/tools.py b/builder/tools.py new file mode 100644 index 0000000..c436a73 --- /dev/null +++ b/builder/tools.py @@ -0,0 +1,41 @@ +"""Core module for bash command related operations.""" + +import shlex +import subprocess + +from loguru import logger + + +def run_command(command) -> tuple[str | None, str | None]: + """Run a command and return the stdout and stderr.""" + proc = subprocess.run(shlex.split(command), stdout=subprocess.PIPE, stderr=subprocess.PIPE) + (stdout, stderr) = (proc.stdout.decode(), proc.stderr.decode()) + return (stdout, stderr) + + +def run_command_logged(command): + """Execute a shell command while logging its output and errors. + + This function runs a given shell command as a subprocess, captures its + standard output and standard error streams, and logs the output in real-time. + If the subprocess returns a non-zero exit code, a RuntimeError is raised with + the last line of the error output. + """ + logger.debug(f"Issuing subprocess {command=}") + proc = subprocess.Popen( + shlex.split(command), + stdout=subprocess.PIPE, + stderr=subprocess.PIPE, + ) + proc_name = proc.args[0] + last_err_line = "" + while proc.poll() is None: + while True: + stderr_line = proc.stderr.readline().decode() + if stderr_line: + last_err_line = stderr_line + logger.debug(f"Subprocess {proc_name} => {stderr_line}") + else: + break + if proc.returncode != 0: + raise RuntimeError(f"Subprocess {proc_name} error: {last_err_line}") diff --git a/builder/types.py b/builder/types.py new file mode 100644 index 0000000..5ae775f --- /dev/null +++ b/builder/types.py @@ -0,0 +1,6 @@ +"""Core module for defining types.""" + +from typing import TypeAlias + +# type alias for the job script catalog structure +JobScriptCatalog: TypeAlias = dict[str, list[dict[str, list[str | None] | list[str] | str | None]]] diff --git a/cdk.json b/cdk.json new file mode 100644 index 0000000..b95da39 --- /dev/null +++ b/cdk.json @@ -0,0 +1,6 @@ +{ + "app":"poetry run python infra/app.py", + "context":{ + "@aws-cdk/core:newStyleStackSynthesis":true + } +} \ No newline at end of file diff --git a/cfd-openfoam-motorbike/.dockerignore b/cfd-openfoam-motorbike/.dockerignore new file mode 100644 index 0000000..f59ec20 --- /dev/null +++ b/cfd-openfoam-motorbike/.dockerignore @@ -0,0 +1 @@ +* \ No newline at end of file diff --git a/cfd-openfoam-motorbike/Dockerfile b/cfd-openfoam-motorbike/Dockerfile new file mode 100644 index 0000000..9f36b42 --- /dev/null +++ b/cfd-openfoam-motorbike/Dockerfile @@ -0,0 +1,18 @@ +FROM ubuntu:22.04 + +ENV DEBIAN_FRONTEND=noninteractive + +RUN apt update \ + && apt install -y software-properties-common wget + +RUN wget -O - https://dl.openfoam.org/gpg.key > /etc/apt/trusted.gpg.d/openfoam.asc \ + && add-apt-repository http://dl.openfoam.org/ubuntu + +RUN apt update +RUN apt install -y openfoam11 + +RUN bash -c "source /opt/openfoam11/etc/bashrc" + +EXPOSE 8080 + +CMD ["/bin/bash"] \ No newline at end of file diff --git a/cfd-openfoam-motorbike/README.md b/cfd-openfoam-motorbike/README.md new file mode 100644 index 0000000..ef362f1 --- /dev/null +++ b/cfd-openfoam-motorbike/README.md @@ -0,0 +1,35 @@ +# Motorbike Simulation with OpenFOAM + +This job script performs an aerodynamic simulation of a motorbike using OpenFOAM, an open-source +computational fluid dynamics (CFD) software package. It leverages Apptainer (formerly Singularity) +to encapsulate the OpenFOAM environment and ensure reproducibility. + +## Simulation Steps + +The script performs the following steps: + +1. **Clone OpenFOAM**: Clones the OpenFOAM-11 source code from GitHub if it's not already available. +2. **Create Working Directory**: Creates a unique working directory within the shared NFS filesystem. +3. **Fetch Apptainer Image**: Downloads the OpenFOAM Apptainer image from an S3 bucket if it doesn't exist. +4. **Load OpenFOAM Environment**: Sources the OpenFOAM environment script to set up necessary variables. +5. **Copy Tutorial Files**: Copies the `motorBike` tutorial files from the OpenFOAM source code. +6. **Clean Previous Results**: Cleans any previous simulation results. +7. **Copy Geometry**: Copies the motorbike geometry file. +8. **Define Surface Features**: Defines surface features for mesh generation. +9. **Generate Mesh**: Generates the mesh for the simulation domain. +10. **Decompose Mesh**: Decomposes the mesh for parallel processing. +11. **Mesh Refinement**: Refines the mesh around the motorbike using `snappyHexMesh`. +12. **Patch Summary**: Generates a summary of boundary conditions. +13. **Potential Flow Calculation**: Solves for the velocity potential. +14. **Turbulent Flow Simulation**: Performs a steady-state simulation of turbulent flow using `simpleFoam`. +15. **Reconstruct Results**: Reconstructs the simulation results from parallel execution. + +## HPC Application + +This script utilizes the following HPC application: + +* **OpenFOAM:**: A widely-used open-source CFD software package for simulating fluid flow phenomena. + +The Apptainer image for OpenFOAM is pre-built with all necessary dependencies and configurations, simplifying +execution and ensuring reproducibility across different HPC environments. For more details regarding the +Apptainer image, check the [Dockerfile](./Dockerfile). \ No newline at end of file diff --git a/cfd-openfoam-motorbike/job-script.sh b/cfd-openfoam-motorbike/job-script.sh new file mode 100644 index 0000000..b06a13e --- /dev/null +++ b/cfd-openfoam-motorbike/job-script.sh @@ -0,0 +1,80 @@ +#!/bin/bash +#SBATCH --partition compute +#SBATCH --nodes=2 +#SBATCH --ntasks=2 +#SBATCH -J motorbike +#SBATCH --output=/nfs/R-%x.%j.out +#SBATCH --error=/nfs/R-%x.%j.err +#SBATCH -t 1:00:00 + +# clone OpenFOAM-11 if it is not available yet +OPENFOAM_DIR=/nfs/OpenFOAM-11 +if [[ ! -d $OPENFOAM_DIR ]] +then + echo "Cloning OpenFOAM-11" + cd /nfs/ + git clone https://github.com/OpenFOAM/OpenFOAM-11 +else + echo "Skipping clone process...we already have the OpenFOAM-11 source code" +fi + +# create a working folder inside the shared directory +WORK_DIR=/nfs/$SLURM_JOB_NAME-Job-$SLURM_JOB_ID +mkdir -p $WORK_DIR +cd $WORK_DIR + +# path to the openfoam singularity image +export APPTAINER_IMAGE=/nfs/openfoam11.sif + +# download the openfoam v11 singularity image if it is not available yet +if [[ ! -f $APPTAINER_IMAGE ]] +then + echo "Pulling the singularity image for OpenFOAM-11" + apptainer pull $APPTAINER_IMAGE oras://public.ecr.aws/omnivector-solutions/cfd-openfoam-motorbike:latest +else + echo "Skipping the image fetch process...we already have the singularity image" +fi + + +# copy motorBike folder +cp -r $OPENFOAM_DIR/tutorials/incompressibleFluid/motorBike . + +# enter motorBike folder +cd motorBike + +# clear any previous execution +apptainer exec --bind $PWD:$HOME $APPTAINER_IMAGE ./Allclean + +# copy motorBike geometry obj +cp $OPENFOAM_DIR/tutorials/resources/geometry/motorBike.obj.gz constant/geometry/ + +# define surface features inside the block mesh +apptainer exec --bind $PWD:$HOME $APPTAINER_IMAGE surfaceFeatures + +# generate the first mesh +# mesh the environment (block around the model) +apptainer exec --bind $PWD:$HOME $APPTAINER_IMAGE blockMesh + +# decomposition of mesh and initial field data +# according to the parameters in decomposeParDict located in the system +# create 6 domains by default +apptainer exec --bind $PWD:$HOME $APPTAINER_IMAGE decomposePar -copyZero + +# mesh the motorcicle +# overwrite the new mesh files that are generated +srun apptainer exec --bind $PWD:$HOME $APPTAINER_IMAGE snappyHexMesh -overwrite -parallel + +# write field and boundary condition info for each patch +srun apptainer exec --bind $PWD:$HOME $APPTAINER_IMAGE patchSummary -parallel + +# potential flow solver +# solves the velocity potential to calculate the volumetric face-flux field +srun apptainer exec --bind $PWD:$HOME $APPTAINER_IMAGE potentialFoam -parallel + +# steady-state solver for incompressible turbutent flows +srun apptainer exec --bind $PWD:$HOME $APPTAINER_IMAGE simpleFoam -parallel + +# after a case has been run in parallel +# it can be reconstructed for post-processing +apptainer exec --bind $PWD:$HOME $APPTAINER_IMAGE reconstructParMesh -constant +apptainer exec --bind $PWD:$HOME $APPTAINER_IMAGE reconstructPar -latestTime \ No newline at end of file diff --git a/cfd-openfoam-motorbike/metadata.yaml b/cfd-openfoam-motorbike/metadata.yaml new file mode 100644 index 0000000..8f6ff6b --- /dev/null +++ b/cfd-openfoam-motorbike/metadata.yaml @@ -0,0 +1,7 @@ +summary: Compute steady flow around a motorcycle +icon-url: https://upload.wikimedia.org/wikipedia/commons/4/48/OpenFOAM_logo.svg +entrypoint: job-script.sh +image-source: Dockerfile +image-tags: +- "1.0.0" +- "latest" diff --git a/infra/__init__.py b/infra/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/infra/app.py b/infra/app.py new file mode 100644 index 0000000..e7dff3b --- /dev/null +++ b/infra/app.py @@ -0,0 +1,21 @@ +#!/usr/bin/env python3 +"""Core module for setting up the AWS CDK application for the Vantage Jobs Catalog. + +It defines the environment, tags, and stacks for the application, including: +- WebsiteStack: The stack for the Vantage Jobs Catalog website. +- ArtifactBucket: The stack for the artifact storage bucket. +""" + +import aws_cdk as cdk + +from infra.catalog_bucket import ArtifactBucket +from infra.website import WebsiteStack + +tags = {"project": "Vantage"} + +env = cdk.Environment(region="us-east-1") + +app = cdk.App() +WebsiteStack(app, "VantageJobsCatalogWebsite", env=env, tags=tags) +ArtifactBucket(app, "VantageJobsCatalogArtifacts", env=env, tags=tags) +app.synth() diff --git a/infra/catalog_bucket.py b/infra/catalog_bucket.py new file mode 100644 index 0000000..1e135b2 --- /dev/null +++ b/infra/catalog_bucket.py @@ -0,0 +1,58 @@ +"""S3 infrastructure for the job scripts artifacts of the Vantage Jobs Catalog.""" + +import aws_cdk as cdk +from aws_cdk import ( + App, + Stack, +) +from aws_cdk import ( + aws_iam as iam, +) +from aws_cdk import ( + aws_s3 as s3, +) + + +class ArtifactBucket(Stack): + """Stack for the S3 bucket for the job scripts artifacts.""" + + def __init__(self, app: App, id: str, **kwargs): # noqa: D107 + super().__init__(app, id, **kwargs) + + bucket = s3.Bucket( + self, + "ArtifactBucket", + bucket_name="vantage-jobs-catalog-artifacts", + removal_policy=cdk.RemovalPolicy.RETAIN, + block_public_access=s3.BlockPublicAccess( + block_public_acls=True, + block_public_policy=False, + ignore_public_acls=True, + restrict_public_buckets=False, + ), + ) + + bucket.add_to_resource_policy( + iam.PolicyStatement( + actions=["s3:GetObject"], + effect=iam.Effect.ALLOW, + principals=[iam.StarPrincipal()], + resources=[bucket.arn_for_objects("files/*")], + ) + ) + + cdk.CfnOutput( + self, + "BucketName", + value=bucket.bucket_name, + description="The name of the S3 bucket for the job scripts artifacts.", + export_name="VantageJobsCatalogArtifactsBucketName", + ) + + cdk.CfnOutput( + self, + "BucketRegion", + value=self.region, + description="The region of the S3 bucket for the job scripts artifacts.", + export_name="VantageJobsCatalogArtifactsBucketRegion", + ) diff --git a/infra/website.py b/infra/website.py new file mode 100644 index 0000000..9e0057d --- /dev/null +++ b/infra/website.py @@ -0,0 +1,114 @@ +"""Website infrastructure for the Vantage Jobs Catalog.""" + +import aws_cdk as cdk +import yaml +from aws_cdk import App, Stack +from aws_cdk import aws_certificatemanager as cm +from aws_cdk import aws_cloudfront as cloudfront +from aws_cdk import aws_route53 as route53 +from aws_cdk import aws_route53_targets as targets +from aws_cdk import aws_s3 as s3 +from aws_cdk import aws_s3_deployment as s3_deploy + + +class WebsiteStack(Stack): + """Stack for the Vantage Jobs Catalog website.""" + + def __init__(self, app: App, id: str, **kwargs): # noqa: D107 + super().__init__(app, id, **kwargs) + + site_domain = "catalog.vantagehpc.io" + + hosted_zone = route53.HostedZone.from_hosted_zone_attributes( + self, + "HostedZone", + hosted_zone_id="Z063993623YJJ3OLAC1Z6", + zone_name="vantagehpc.io", + ) + + distribution_oai = cloudfront.OriginAccessIdentity( + self, "CloudFrontOAI", comment=f"OAI for stack {id}" + ) + + bucket = s3.Bucket( + self, + "HostBucket", + bucket_name=site_domain, + website_index_document="index.html", + website_error_document="index.html", + removal_policy=cdk.RemovalPolicy.DESTROY, + cors=[ + s3.CorsRule( + allowed_origins=["*"], + allowed_methods=[s3.HttpMethods.GET, s3.HttpMethods.HEAD], + allowed_headers=["*"], + ) + ], + ) + + bucket.grant_read(distribution_oai) + + certificate = cm.Certificate( + self, + "Certificate", + domain_name=site_domain, + validation=cm.CertificateValidation.from_dns(hosted_zone=hosted_zone), + ) + + distribution = cloudfront.CloudFrontWebDistribution( + self, + "Distribution", + origin_configs=[ + cloudfront.SourceConfiguration( + behaviors=[ + cloudfront.Behavior( + is_default_behavior=True, + max_ttl=cdk.Duration.seconds(0), + min_ttl=cdk.Duration.seconds(0), + default_ttl=cdk.Duration.seconds(0), + ) + ], + s3_origin_source=cloudfront.S3OriginConfig( + s3_bucket_source=bucket, + origin_access_identity=distribution_oai, + ), + ), + ], + price_class=cloudfront.PriceClass.PRICE_CLASS_ALL, + viewer_protocol_policy=cloudfront.ViewerProtocolPolicy.REDIRECT_TO_HTTPS, + viewer_certificate=cloudfront.ViewerCertificate.from_acm_certificate( + certificate=certificate, + aliases=[site_domain], + security_policy=cloudfront.SecurityPolicyProtocol.TLS_V1_2_2021, + ssl_method=cloudfront.SSLMethod.SNI, + ), + error_configurations=[ + cloudfront.CfnDistribution.CustomErrorResponseProperty( + error_code=404, + error_caching_min_ttl=0, + response_code=200, + response_page_path="/index.html", + ) + ], + ) + + route53.ARecord( + self, + "ARecord", + target=route53.RecordTarget.from_alias(targets.CloudFrontTarget(distribution=distribution)), + zone=hosted_zone, + record_name=site_domain, + ) + + with open("catalog.yaml", "r") as f: + catalog_content = 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