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README.rst

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@@ -101,29 +101,14 @@ You'll find six directories inside the main
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data or process outputs.
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Running Simulations
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-------------------
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Before running a simulation, you should have a model specification file.
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A model specification is a complete description of a vivarium model in
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a yaml format. An example model specification is provided with this repository
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in the ``model_specifications`` directory.
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With this model specification file and your conda environment active, you can then run simulations by, e.g.::
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(vivarium_profiling) :~$ simulate run -v /<REPO_INSTALLATION_DIRECTORY>/vivarium_profiling/src/vivarium_profiling/model_specifications/model_spec.yaml
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The ``-v`` flag will log verbosely, so you will get log messages every time
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step. For more ways to run simulations, see the tutorials at
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https://vivarium.readthedocs.io/en/latest/tutorials/running_a_simulation/index.html
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and https://vivarium.readthedocs.io/en/latest/tutorials/exploration.html
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Profiling and Benchmarking
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---------------------------
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This repository provides tools for profiling and benchmarking Vivarium simulations
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to analyze their performance characteristics.
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to analyze their performance characteristics. See the tutorials at
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https://vivarium.readthedocs.io/en/latest/tutorials/running_a_simulation/index.html
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and https://vivarium.readthedocs.io/en/latest/tutorials/exploration.html for general instructions
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on running simulations with Vivarium.
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Configuring Scaling Simulations
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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