vivarium-cluster-tools
Tools for running Vivarium simulations on IHME's Slurm cluster
Science Score: 36.0%
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Low similarity (11.2%) to scientific vocabulary
Last synced: 10 months ago
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Tools for running Vivarium simulations on IHME's Slurm cluster
Basic Info
Statistics
- Stars: 1
- Watchers: 9
- Forks: 4
- Open Issues: 0
- Releases: 53
Created over 7 years ago
· Last pushed 11 months ago
Metadata Files
Readme
Changelog
License
Codeowners
Zenodo
README.rst
Vivarium Cluster Tools
=======================
.. image:: https://badge.fury.io/py/vivarium-cluster-tools.svg
:target: https://badge.fury.io/py/vivarium-cluster-tools
.. image:: https://github.com/ihmeuw/vivarium_cluster_tools/actions/workflows/build.yml/badge.svg?branch=main
:target: https://github.com/ihmeuw/vivarium_cluster_tools
:alt: Latest Version
.. image:: https://readthedocs.org/projects/vivarium-cluster-tools/badge/?version=latest
:target: https://vivarium-cluster-tools.readthedocs.io/en/latest/?badge=latest
:alt: Documentation Status
Vivarium cluster tools is a python package that makes running ``vivarium``
simulations at scale on a Slurm cluster easy.
Installation
------------
You can install this package with
.. code-block:: console
pip install vivarium-cluster-tools
In addition, this tool needs the redis client. This must be installed using conda.
.. code-block:: console
conda install redis
A simple example
----------------
If you have a ``vivarium`` model specifcation file defining a particular model,
you can use that along side a **branches file** to launch a run of many
simulations at once with variations in the input data, random seed, or with
different parameter settings.
.. code-block:: console
psimulate run /path/to/model_specification.yaml /path/to/branches_file.yaml
The simplest branches file defines a count of input data draws and random seeds
to launch.
.. code-block:: yaml
input_draw_count: 25
random_seed_count: 10
This branches file defines a set of simulations for all combinations of 25
input draws and 10 random seeds and so would run, in total, 250 simulations.
You can also define a set of parameter variations to run your model over. Say
your original model specification looked something like
.. code-block:: yaml
plugins:
optional: ...
components:
vivarium_public_health:
population:
- BasePopulation()
- Mortality()
disease.models:
- SIS('lower_respiratory_infections')
my_lri_intervention:
components:
- GiveKidsVaccines()
configuration:
population:
population_size: 1000
age_start: 0
age_end: 5
lri_vaccine:
coverage: 0.2
efficacy: 0.8
Defining a simple model of lower respiratory infections and a vaccine
intervention. You could then write a branches file that varied over both
input data draws and random seeds, but also over different levels of coverage
and efficacy for the vaccine. That file would look like
.. code-block:: yaml
input_draw_count: 25
random_seed_count: 10
branches:
lri_vaccine:
coverage: [0.0, 0.2, 0.4, 0.8, 1.0]
efficacy: [0.4, 0.6, 0.8]
The branches file would overwrite your original ``lri_vaccine`` configuration
with each combination of coverage and efficacy in the branches file and launch
a simulation. More, it would run each coverage-efficacy pair in the branches
for each combination of input draw and random seed to produce 25 * 10 * 5 * 3 =
3750 unique simulations.
To read about more of the available features and get a better understanding
of how to correctly write your own branches files,
`Check out the docs!
Owner
- Name: Institute for Health Metrics and Evaluation
- Login: ihmeuw
- Kind: organization
- Email: ihme@healthdata.org
- Location: Seattle, WA
- Website: http://www.healthdata.org/
- Repositories: 152
- Profile: https://github.com/ihmeuw
Open source public health tools and research projects created by teams at the IHME.
GitHub Events
Total
- Release event: 14
- Delete event: 24
- Issue comment event: 5
- Push event: 107
- Pull request review comment event: 29
- Pull request review event: 80
- Pull request event: 52
- Create event: 36
Last Year
- Release event: 14
- Delete event: 24
- Issue comment event: 5
- Push event: 107
- Pull request review comment event: 29
- Pull request review event: 80
- Pull request event: 52
- Create event: 36
Committers
Last synced: over 3 years ago
All Time
- Total Commits: 471
- Total Committers: 15
- Avg Commits per committer: 31.4
- Development Distribution Score (DDS): 0.493
Top Committers
| Name | Commits | |
|---|---|---|
| James Collins | c****k@u****u | 239 |
| Cody | c****t@u****u | 88 |
| Kate Wilson | k****7@u****u | 40 |
| Matthew Kappel | m****l@u****u | 32 |
| Rajan Mudambi | 1****i@u****m | 28 |
| Kjell Swedin | k****s@u****u | 12 |
| Steve Bachmeier | s****i@u****u | 7 |
| Kate Wilson | 3****n@u****m | 6 |
| halfhorst | c****2@g****m | 4 |
| Michelle Park | h****3@u****u | 4 |
| Hussain Jafari | h****i@g****m | 4 |
| kwilson7 | k****1@g****m | 4 |
| Hussain Jafari | h****i@u****u | 1 |
| michaella21 | h****3@c****u | 1 |
| Abraham Flaxman | a****e@a****u | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 11 months ago
All Time
- Total issues: 0
- Total pull requests: 221
- Average time to close issues: N/A
- Average time to close pull requests: 8 days
- Total issue authors: 0
- Total pull request authors: 10
- Average comments per issue: 0
- Average comments per pull request: 0.12
- Merged pull requests: 197
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 54
- Average time to close issues: N/A
- Average time to close pull requests: 2 days
- Issue authors: 0
- Pull request authors: 5
- Average comments per issue: 0
- Average comments per pull request: 0.11
- Merged pull requests: 44
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
Pull Request Authors
- albrja (55)
- stevebachmeier (46)
- patricktnast (41)
- collijk (39)
- mattkappel (38)
- rmudambi (28)
- hussain-jafari (8)
- KjellSwedin (6)
- aflaxman (1)
- halfhorst (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
-
Total downloads:
- pypi 857 last-month
- Total dependent packages: 0
- Total dependent repositories: 6
- Total versions: 73
- Total maintainers: 6
pypi.org: vivarium-cluster-tools
A set of tools for running simulation using vivarium on cluster.
- Homepage: https://github.com/ihmeuw/vivarium_cluster_tools
- Documentation: https://vivarium-cluster-tools.readthedocs.io/
- License: bsd-3-clause
-
Latest release: 2.1.18
published 11 months ago
Rankings
Dependent repos count: 6.0%
Dependent packages count: 10.1%
Average: 15.9%
Forks count: 16.8%
Downloads: 18.6%
Stargazers count: 27.8%
Last synced:
11 months ago
Dependencies
setup.py
pypi
- click *
- drmaa *
- loguru *
- numpy *
- pandas *
- psutil *
- pyyaml >=5.1
- redis *
- requests *
- rq *
- tables *
- vivarium >=0.10.16
.github/workflows/build.yml
actions
- actions/checkout v3 composite
- actions/setup-python v4 composite
.github/workflows/deploy.yml
actions
- actions/checkout v3 composite
- actions/setup-python v4 composite
pyproject.toml
pypi