galform-execution 0.1.0__tar.gz

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  1. galform_execution-0.1.0/LICENSE +21 -0
  2. galform_execution-0.1.0/PKG-INFO +86 -0
  3. galform_execution-0.1.0/README.md +70 -0
  4. galform_execution-0.1.0/galform_execution/__init__.py +5 -0
  5. galform_execution-0.1.0/galform_execution/__main__.py +4 -0
  6. galform_execution-0.1.0/galform_execution/config/dust_params.json +26 -0
  7. galform_execution-0.1.0/galform_execution/config/models.json +57 -0
  8. galform_execution-0.1.0/galform_execution/config/run_flags.json +16 -0
  9. galform_execution-0.1.0/galform_execution/config/simulations/colibre_family.json +40 -0
  10. galform_execution-0.1.0/galform_execution/config/simulations/dove_family.json +42 -0
  11. galform_execution-0.1.0/galform_execution/config/simulations/eagle_family.json +62 -0
  12. galform_execution-0.1.0/galform_execution/config/simulations/flamingo_family.json +21 -0
  13. galform_execution-0.1.0/galform_execution/config/simulations/millennium_family.json +134 -0
  14. galform_execution-0.1.0/galform_execution/config/simulations/nifty_family.json +22 -0
  15. galform_execution-0.1.0/galform_execution/submit_galform_job.py +1300 -0
  16. galform_execution-0.1.0/galform_execution.egg-info/PKG-INFO +86 -0
  17. galform_execution-0.1.0/galform_execution.egg-info/SOURCES.txt +22 -0
  18. galform_execution-0.1.0/galform_execution.egg-info/dependency_links.txt +1 -0
  19. galform_execution-0.1.0/galform_execution.egg-info/entry_points.txt +2 -0
  20. galform_execution-0.1.0/galform_execution.egg-info/top_level.txt +1 -0
  21. galform_execution-0.1.0/pyproject.toml +31 -0
  22. galform_execution-0.1.0/setup.cfg +4 -0
  23. galform_execution-0.1.0/tests/test_submit_galform_job.py +664 -0
  24. galform_execution-0.1.0/tests/test_submit_job.py +67 -0
galform_execution-0.1.0/LICENSE ADDED
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+ MIT License
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+
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+ Copyright (c) 2026 Oscar Hickman
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+
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+ Permission is hereby granted, free of charge, to any person obtaining a copy
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+ of this software and associated documentation files (the "Software"), to deal
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+ in the Software without restriction, including without limitation the rights
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+ to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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+ copies of the Software, and to permit persons to whom the Software is
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+ furnished to do so, subject to the following conditions:
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+
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+ The above copyright notice and this permission notice shall be included in all
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+ copies or substantial portions of the Software.
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+
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+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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+ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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+ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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+ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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+ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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+ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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+ SOFTWARE.
galform_execution-0.1.0/PKG-INFO ADDED
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+ Metadata-Version: 2.4
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+ Name: galform_execution
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+ Version: 0.1.0
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+ Summary: GALFORM execution helper utilities
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+ Author: Oscar Hickman
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+ License: MIT
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+ Project-URL: Homepage, https://github.com/OscarHickman/galform_execution
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+ Keywords: astronomy,galform,slurm,submission
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+ Classifier: Programming Language :: Python :: 3
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+ Classifier: License :: OSI Approved :: MIT License
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+ Classifier: Operating System :: POSIX :: Linux
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+ Requires-Python: >=3.8
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+ Description-Content-Type: text/markdown
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+ License-File: LICENSE
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+ Dynamic: license-file
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+
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+ # galform_execution
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+
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+ [![CI](https://github.com/OscarHickman/galform_execution/actions/workflows/ci.yml/badge.svg)](https://github.com/OscarHickman/galform_execution/actions/workflows/ci.yml)
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+ [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
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+
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+ A Python-based utility to manage GALFORM N-body simulation submissions to SLURM on COSMA.
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+
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+ `galform_execution` automates the generation and submission of SLURM batch scripts for GALFORM runs. It handles environment setup, parameter injection into `.input.ref` files, and conditional post-processing (NETA, LUM_FUN, etc.), providing a robust and reproducible workflow for large-scale galaxy formation simulations.
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+
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+ ## Key Features
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+
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+ - **Dynamic Script Generation**: Generates self-contained `tcsh` scripts with resolved simulation and model parameters.
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+ - **Config-Driven**: Manage simulations, models, and dust parameters via JSON configurations.
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+ - **SLURM Optimized**: Automatic job array support and remapping of high subvolume indices.
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+ - **Robustness**: Built-in retries with exponential backoff for transient scheduler errors.
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+
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+ ## Prerequisites
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+
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+ - **Environment**: Access to the **COSMA** HPC cluster (Durham University).
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+ - **Tooling**: [uv](https://github.com/astral-sh/uv) is recommended for fast installation and dependency management.
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+
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+ ## Installation
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+
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+ ```bash
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+ # Clone the repository
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+ git clone https://github.com/OscarHickman/galform_execution.git
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+ cd galform_execution
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+
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+ # Install the package and its dependencies using uv
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+ uv pip install -e .
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+ ```
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+
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+ ## Quick Start
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+
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+ ### 1. Identify your GALFORM directory
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+ You need a compiled version of GALFORM with the standard directory structure (containing `build/galform2`, `*.input.ref`, etc.).
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+
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+ ### 2. Preview a submission (Dry Run)
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+ Check the generated SLURM script without submitting to the queue:
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+ ```bash
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+ submit-galform-job /path/to/your/galform --nbody-sim Mill2 --model lc16 --iz 40 --nvol 1-64 --dry-run
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+ ```
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+
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+ ### 3. Submit a job array
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+ ```bash
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+ submit-galform-job /path/to/your/galform --nbody-sim Mill2 --model lc16 --iz 40 --nvol 1-64 --output-folder-name MyProject
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+ ```
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+
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+ ## Configuration
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+
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+ Configurations are stored in `galform_execution/config/`:
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+ - `simulations/`: JSON files defining N-body simulation parameters (tree paths, cosmology).
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+ - `models.json`: Maps model names to base input files and dust profiles.
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+ - `redshift_lists/`: Redshift mappings for various simulations.
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+
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+ ## Development
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+
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+ ### Running Tests
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+ ```bash
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+ uv run pytest tests
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+ ```
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+
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+ ### Linting
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+ ```bash
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+ uv run ruff check galform_execution
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+ ```
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+
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+ ## License
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+
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+ Distributed under the MIT License. See `LICENSE` for more information.
galform_execution-0.1.0/README.md ADDED
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+ # galform_execution
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+
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+ [![CI](https://github.com/OscarHickman/galform_execution/actions/workflows/ci.yml/badge.svg)](https://github.com/OscarHickman/galform_execution/actions/workflows/ci.yml)
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+ [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
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+
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+ A Python-based utility to manage GALFORM N-body simulation submissions to SLURM on COSMA.
7
+
8
+ `galform_execution` automates the generation and submission of SLURM batch scripts for GALFORM runs. It handles environment setup, parameter injection into `.input.ref` files, and conditional post-processing (NETA, LUM_FUN, etc.), providing a robust and reproducible workflow for large-scale galaxy formation simulations.
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+
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+ ## Key Features
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+
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+ - **Dynamic Script Generation**: Generates self-contained `tcsh` scripts with resolved simulation and model parameters.
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+ - **Config-Driven**: Manage simulations, models, and dust parameters via JSON configurations.
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+ - **SLURM Optimized**: Automatic job array support and remapping of high subvolume indices.
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+ - **Robustness**: Built-in retries with exponential backoff for transient scheduler errors.
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+
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+ ## Prerequisites
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+
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+ - **Environment**: Access to the **COSMA** HPC cluster (Durham University).
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+ - **Tooling**: [uv](https://github.com/astral-sh/uv) is recommended for fast installation and dependency management.
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+
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+ ## Installation
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+
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+ ```bash
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+ # Clone the repository
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+ git clone https://github.com/OscarHickman/galform_execution.git
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+ cd galform_execution
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+
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+ # Install the package and its dependencies using uv
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+ uv pip install -e .
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+ ```
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+
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+ ## Quick Start
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+
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+ ### 1. Identify your GALFORM directory
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+ You need a compiled version of GALFORM with the standard directory structure (containing `build/galform2`, `*.input.ref`, etc.).
37
+
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+ ### 2. Preview a submission (Dry Run)
39
+ Check the generated SLURM script without submitting to the queue:
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+ ```bash
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+ submit-galform-job /path/to/your/galform --nbody-sim Mill2 --model lc16 --iz 40 --nvol 1-64 --dry-run
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+ ```
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+
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+ ### 3. Submit a job array
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+ ```bash
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+ submit-galform-job /path/to/your/galform --nbody-sim Mill2 --model lc16 --iz 40 --nvol 1-64 --output-folder-name MyProject
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+ ```
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+
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+ ## Configuration
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+
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+ Configurations are stored in `galform_execution/config/`:
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+ - `simulations/`: JSON files defining N-body simulation parameters (tree paths, cosmology).
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+ - `models.json`: Maps model names to base input files and dust profiles.
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+ - `redshift_lists/`: Redshift mappings for various simulations.
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+
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+ ## Development
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+
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+ ### Running Tests
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+ ```bash
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+ uv run pytest tests
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+ ```
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+
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+ ### Linting
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+ ```bash
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+ uv run ruff check galform_execution
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+ ```
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+
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+ ## License
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+
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+ Distributed under the MIT License. See `LICENSE` for more information.
galform_execution-0.1.0/galform_execution/__init__.py ADDED
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+ """
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+ galform_execution: Python-based utility to manage GALFORM N-body simulation submissions to SLURM.
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+ """
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+
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+ __version__ = "0.1.0"
galform_execution-0.1.0/galform_execution/__main__.py ADDED
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+ from galform_execution.submit_galform_job import main
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+
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+ if __name__ == "__main__":
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+ main()
galform_execution-0.1.0/galform_execution/config/dust_params.json ADDED
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+ {
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+ "baugh05": {
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+ "beta2_burst": 1.6,
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+ "beta2_disk": 2.0,
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+ "dustfile": "Data/dust/dust_MW_hz1.0.dat",
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+ "emdustfile": "0",
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+ "fcloud": 0.25,
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+ "lambda_break_burst": 100.0,
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+ "lambda_break_disk": 10000.0,
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+ "rfacburst": 1.0,
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+ "tesc_burst": 0.001,
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+ "tesc_disk": 0.001
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+ },
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+ "lacey16": {
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+ "beta2_burst": 1.5,
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+ "beta2_disk": 2.0,
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+ "dustfile": "Data/dust/dust_MW_hz1.0.dat",
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+ "emdustfile": "0",
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+ "fcloud": 0.5,
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+ "lambda_break_burst": 100.0,
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+ "lambda_break_disk": 10000.0,
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+ "rfacburst": 1.0,
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+ "tesc_burst": 0.001,
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+ "tesc_disk": 0.001
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+ }
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+ }
galform_execution-0.1.0/galform_execution/config/models.json ADDED
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+ {
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+ "b06": {
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+ "base_inputs_file": "Bower06_Nbody_MilliMil.input.ref",
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+ "dust_params": null,
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+ "dust_profile": "baugh05",
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+ "extra_replacements": {}
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+ },
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+ "gp14": {
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+ "base_inputs_file": "Gonzalez13_Nbody_MillGas.input.ref",
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+ "dust_params": null,
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+ "dust_profile": "baugh05",
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+ "extra_replacements": {}
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+ },
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+ "gp14.satf": {
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+ "base_inputs_file": "Gonzalez13_Nbody_MillGas.input.ref",
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+ "dust_params": null,
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+ "dust_profile": "baugh05",
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+ "extra_replacements": {
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+ "Saturate_Feedback": ".true.",
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+ "thresholdVcirc": "65.0"
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+ }
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+ },
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+ "gp18": {
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+ "base_inputs_file": "Gonzalez13_Nbody_MillGas.input.ref",
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+ "dust_params": null,
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+ "dust_profile": "baugh05",
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+ "extra_replacements": {}
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+ },
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+ "lc16": {
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+ "base_inputs_file": "Lacey16_Nbody_MillGas.input.ref",
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+ "dust_params": null,
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+ "dust_profile": "lacey16",
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+ "extra_replacements": {}
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+ },
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+ "lc16.newSMBH": {
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+ "base_inputs_file": "Lacey16_Nbody_MillGas.input.ref",
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+ "dust_params": null,
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+ "dust_profile": "lacey16",
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+ "extra_replacements": {}
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+ },
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+ "lc16.newmg": {
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+ "base_inputs_file": "Lacey16_newmg_Nbody_L800.input.ref",
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+ "dust_params": null,
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+ "dust_profile": "lacey16",
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+ "extra_replacements": {}
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+ },
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+ "lc16.newmg.kenn83.vhot": {
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+ "base_inputs_file": "Lacey16_newmg_Nbody_L800.input.ref",
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+ "dust_params": null,
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+ "dust_profile": "lacey16",
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+ "extra_replacements": {
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+ "nmf": "1",
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+ "vhotburst": "290",
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+ "vhotdisk": "290"
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+ }
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+ }
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+ }
galform_execution-0.1.0/galform_execution/config/run_flags.json ADDED
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+ {
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+ "compile": false,
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+ "galform": true,
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+ "neta": true,
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+ "dust_props": false,
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+ "lum_fun": true,
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+ "samp_z0": false,
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+ "cosmicsed": false,
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+ "lum_fun_burst": false,
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+ "samp2_z0": false,
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+ "sedfit": false,
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+ "agn": false,
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+ "sed_agn": false,
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+ "samp_mah": false,
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+ "study_stellar_mass_function": true
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+ }
galform_execution-0.1.0/galform_execution/config/simulations/colibre_family.json ADDED
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+ {
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+ "COLIBRE-L100m6": {
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+ "aquarius_particle_file": "/cosma8/data/dp004/jch/COLIBRE/HBT/L100_m6/DMO/trees/particle_lists/particle_list_127",
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+ "aquarius_tree_file": "/cosma8/data/dp004/jch/COLIBRE/HBT/L100_m6/DMO/trees/tree_127",
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+ "data_filesystem": "cosma8",
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+ "h0": 0.681,
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+ "iz0": 127,
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+ "iz_list": [127, 102, 92],
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+ "lambda0": 0.693922,
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+ "lbox": 68.1,
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+ "mpart": 7847050.0,
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+ "nbody_trees_dir": "/cosma8/data/dp004/jch/COLIBRE/HBT/L100_m6/DMO/trees",
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+ "nvol_range": "1-64",
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+ "omega0": 0.306078,
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+ "omegab": 0.0486,
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+ "pk_file": "Power_Spec/pk_FLAMINGO_DMO_FIDUCIAL.dat",
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+ "sigma8": 0.807,
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+ "snapshot_file": "COLIBRE-L100m6.txt",
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+ "volume": 315821.241
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+ },
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+ "COLIBRE-L400m7": {
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+ "_note": "GALFORM-format aquarius trees not yet built from COLIBRE DMO. dhalo trees at /cosma7/data/dp004/jch/COLIBRE/L400_m7/DMO/dhalo_trees/ (not yet in GALFORM aquarius format). Update tree paths and iz0/iz_list/nvol_range before submitting.",
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+ "aquarius_particle_file": "/cosma5/data/jch/Galform/Merger_Trees/COLIBRE/L400_m7/particle_lists/particle_list_TBD",
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+ "aquarius_tree_file": "/cosma5/data/jch/Galform/Merger_Trees/COLIBRE/L400_m7/treedir_TBD/tree_TBD",
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+ "h0": 0.681,
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+ "iz0": null,
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+ "iz_list": [],
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+ "lambda0": 0.6939,
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+ "lbox": 272.4,
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+ "mpart": null,
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+ "nbody_trees_dir": "/cosma5/data/jch/Galform/Merger_Trees/COLIBRE/L400_m7",
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+ "nvol_range": "1-64",
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+ "omega0": 0.3046,
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+ "omegab": 0.0486,
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+ "pk_file": "Power_Spec/pk_COLIBRE_norm.dat",
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+ "sigma8": 0.8159,
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+ "snapshot_file": "/cosma5/data/jch/Galform/Merger_Trees/COLIBRE/L400_m7/redshift_list.txt",
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+ "volume": null
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+ }
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+ }
galform_execution-0.1.0/galform_execution/config/simulations/dove_family.json ADDED
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+ {
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+ "DoveCDM": {
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+ "aquarius_particle_file": "/cosma5/data/jch/Galform/Merger_Trees/Dove/CDM/trees/particle_lists/particle_list_159",
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+ "aquarius_tree_file": "/cosma5/data/jch/Galform/Merger_Trees/Dove/CDM/trees/treedir_159/tree_159",
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+ "h0": 0.704,
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+ "iz0": 159,
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+ "iz_list": [
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+ 159
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+ ],
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+ "lambda0": 0.728,
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+ "lbox": 70.4,
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+ "mpart": 6195595.0,
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+ "nbody_trees_dir": "/cosma5/data/jch/Galform/Merger_Trees/Dove/CDM/trees",
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+ "nvol_range": "1-64",
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+ "omega0": 0.272,
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+ "omegab": 0.0455,
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+ "pk_file": "Data/Power_Spec/pk_MillGas_norm.dat",
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+ "sigma8": 0.81,
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+ "snapshot_file": "/cosma5/data/jch/Galform/Merger_Trees/Dove/CDM/trees/redshift_list",
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+ "volume": 5451.776
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+ },
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+ "DoveWDM.clean": {
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+ "aquarius_particle_file": "/gpfs/data/dph3apc/dove/wdm/trees_cleaned/particle_lists/particle_list_079",
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+ "aquarius_tree_file": "/gpfs/data/dph3apc/dove/wdm/trees_cleaned/treedir_079/tree_079",
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+ "h0": 0.704,
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+ "iz0": 79,
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+ "iz_list": [
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+ 79
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+ ],
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+ "lambda0": 0.728,
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+ "lbox": 70.4,
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+ "mpart": 6195595.0,
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+ "nbody_trees_dir": "/gpfs/data/dph3apc/dove/wdm/trees_cleaned",
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+ "nvol_range": "1-64",
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+ "omega0": 0.272,
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+ "omegab": 0.0455,
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+ "pk_file": "Power_Spec/pk_WDMDove.dat",
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+ "sigma8": 0.81,
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+ "snapshot_file": "/gpfs/data/dph3apc/dove/wdm/trees_cleaned/dovewdmclean_redshift_list",
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+ "volume": 5451.776
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+ }
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+ }
galform_execution-0.1.0/galform_execution/config/simulations/eagle_family.json ADDED
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+ {
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+ "EagleDM": {
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+ "aquarius_particle_file": "/cosma7/data/dp004/jch/Eagle/Merger_Trees/DMONLY/L0100N1504/trees/particle_lists/particle_list_200",
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+ "aquarius_tree_file": "/cosma7/data/dp004/jch/Eagle/Merger_Trees/DMONLY/L0100N1504/trees/treedir_200/tree_200",
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+ "h0": 0.6777,
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+ "iz0": 200,
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+ "iz_list": [
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+ 200
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+ ],
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+ "lambda0": 0.693,
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+ "lbox": null,
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+ "mpart": null,
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+ "nbody_trees_dir": "/cosma7/data/dp004/jch/Eagle/Merger_Trees/DMONLY/L0100N1504",
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+ "nvol_range": "1-128",
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+ "omega0": 0.307,
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+ "omegab": 0.0482519,
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+ "pk_file": "Power_Spec/pk_EAGLE_norm.dat",
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+ "sigma8": 0.8288,
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+ "snapshot_file": "/cosma7/data/dp004/jch/Eagle/Merger_Trees/DMONLY/L0100N1504/eagle_redshift_list",
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+ "volume": 2431.65796432
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+ },
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+ "EagleDM101": {
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+ "aquarius_particle_file": "/cosma7/data/dp004/jch/Eagle/Merger_Trees/DMONLY/L0100N1504/trees_snapnums100/particle_lists/particle_list_101",
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+ "aquarius_tree_file": "/cosma7/data/dp004/jch/Eagle/Merger_Trees/DMONLY/L0100N1504/trees_snapnums100/treedir_101/tree_101",
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+ "h0": 0.6777,
26
+ "iz0": 101,
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+ "iz_list": [
28
+ 101
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+ ],
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+ "lambda0": 0.693,
31
+ "lbox": null,
32
+ "mpart": null,
33
+ "nbody_trees_dir": "/cosma7/data/dp004/jch/Eagle/Merger_Trees/DMONLY/L0100N1504/trees_snapnums100",
34
+ "nvol_range": "1-128",
35
+ "omega0": 0.307,
36
+ "omegab": 0.0482519,
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+ "pk_file": "Power_Spec/pk_EAGLE_norm.dat",
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+ "sigma8": 0.8288,
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+ "snapshot_file": "/cosma7/data/dp004/jch/Eagle/Merger_Trees/DMONLY/L0100N1504/trees_snapnums100/redshift_list",
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+ "volume": 2431.65796432
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+ },
42
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+ }
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galform_execution-0.1.0/galform_execution/config/simulations/flamingo_family.json ADDED
@@ -0,0 +1,21 @@
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+ {
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+ "FLAMINGO-L1000N1800": {
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+ "aquarius_tree_file": "/cosma8/data/dp004/jch/FLAMINGO/HBT/L1000N1800/DMO_FIDUCIAL/trees/tree_077",
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+ "nvol_range": "1-64",
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+ "volume": 315821241.0
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+ }
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galform_execution-0.1.0/galform_execution/config/simulations/millennium_family.json ADDED
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+ {
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+ "L800": {
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+ "aquarius_particle_file": "/cosma5/data/jch/Galform/Merger_Trees/Millennium/new/particle_lists/particle_list_063",
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+ "MilliMil": {
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+ "volume": 30517.578
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+ }
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galform_execution-0.1.0/galform_execution/config/simulations/nifty_family.json ADDED
@@ -0,0 +1,22 @@
1
+ {
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+ "nifty62.5": {
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+ "aquarius_particle_file": "",
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+ "aquarius_tree_file": "/cosma5/data/jch/Galform/Merger_Trees/nifty/62.5/treedir_061/tree_061",
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+ "nvol_range": "1-64",
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+ "snapshot_file": "/cosma5/data/jch/Galform/Merger_Trees/nifty/62.5/redshift_list",
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+ "volume": 1953125.0
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+ }
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+ }