| Name | neurodamus JSON |
| Version |
3.9.0
JSON |
| download |
| home_page | None |
| Summary | A BBP Simulation Control application for NEURON |
| upload_time | 2025-07-23 09:53:59 |
| maintainer | None |
| docs_url | None |
| author | Blue Brain Project, EPFL |
| requires_python | >=3.9 |
| license | Apache License
Version 2.0, January 2004
http://www.apache.org/licenses/
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| keywords |
|
| VCS |
 |
| bugtrack_url |
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| requirements |
numpy
h5py
docopt
libsonata
|
| Travis-CI |
No Travis.
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| coveralls test coverage |
|
|banner|
=============
Neurodamus
=============
.. image:: https://zenodo.org/badge/640796304.svg
:target: https://doi.org/10.5281/zenodo.8075201
Neurodamus is a BBP Simulation Control application for Neuron.
The Python implementation offers a comprehensive Python API for fine tuning of the simulation, initially defined by a BlueConfig file.
Description
===========
Neurodamus is the BBP in-house developed application for setting up large-scale neuronal simulations.
It has traditionally been implemented as a set of extensions to Neuron, in the form of .hoc and .mod files.
The parameters of the simulation are loaded from a configuration file, by default BlueConfig.
To address several limitations of the Hoc implementation, including development effort, the
high-level layers of Neurodamus have been reimplemented in Python.
Such implementation effectively makes available to the user a Python module with a comprehensive
API, suitable to fine control simulation aspects, as well as inspect and eventually adapt the
simulations as intended.
Install
=======
Prerequisites
-------------
- hdf5
- libsonatareport https://github.com/BlueBrain/libsonatareport
- neuron with MPI https://github.com/neuronsimulator/nrn
Install neurodamus
------------------
.. code-block:: sh
git clone https://github.com/BlueBrain/neurodamus.git
cd neurodamus
pip install .
Build special with mod files
----------------------------
Once neuron and neurodamus are installed, you can build `special` with your mod files:
.. code-block:: sh
mkdir mods
cp -r <your-mod-files> mods/
export DATADIR=$(python -c "import neurodamus; from pathlib import Path; print(Path(neurod)mus.__file__).parent / 'data')")
cp -r $DATADIR/mod/* mods/
nrnivmodl -incflags '-I <include-paths-of-our-dependencies>' -loadflags '-L <libs-paths-for-linking>' mods
To use the Blue Brain open models, you can build `neurodamus-models <https://github.com/blueBrain/neurodamus-models>`_.
It will also produce a handy `build_neurodamus.sh` script that calls `nrnivmodl` with all dependencies to compile your future mod files
.. code-block:: sh
build_neurodamus mods/
Examples
========
Once neurodamus is installed, you should be able to find the executable `neurodamus` in your path:
.. code-block::
$ neurodamus
Usage:
neurodamus <ConfigFile> [options]
neurodamus --help
Among the options you will find flags to tune run behavior.
Neurodamus explicitly depends on MPI libraries for parallel execution.
Therefore please use "srun" or "mpiexec" to launch it, according to your platform. If you
don't, complicated error messages may show up. Please remember it.
Even though a `neurodamus` launcher is provided, for production runs we suggest using
`special` instead. This way has proven to take advantage of optimized math libraries.
We hope to bring the same advantages to the launcher script soon.
.. code-block:: sh
export NEURODAMUS_PYTHON=$(python -c "import neurodamus; from pathlib import Path; print(Path(neurod)mus.__file__).parent / 'data')")
export HOC_LIBRARY_PATH=<hoc_files_folder>
srun <srun params> <your_built_special> -mpi -python $NEURODAMUS_PYTHON/init.py <neurodamus params>
An example of a full installation with a simulation run can be found in the workflow test
`simulation_test.yaml <https://github.com/BlueBrain/neurodamus/blob/main/.github/workflows/simulation_test.yml>`__.
Docker container
================
Alternatively, you can start directly a neurodamus docker container where all the packages are built.
With the container, you can build your mod files and run simulations.
See instructions in `docker/README.md <https://github.com/BlueBrain/neurodamus/blob/main/docker/README.md>`_.
Building the docker container
-----------------------------
.. TODO: decide what to do without pipelines
.. The docker container image is built automatically when a new tag is created in the repository, if a container with the specified version doesn't already exist.
.. On manual pipeline runs, the container image is also built but not automatically pushed to docker-hub; you'll have to manually start the job in the pipeline you created if you want this to happen. Keep in mind that this is *optional*, the container image is *always* pushed to the gitlab registry!
The docker images will be built in the `regular github action <https://github.com/openbraininstitute/neurodamus/actions>`_ - if triggered under the right conditions (either manually or through git tag creation) the container jobs will be added to this pipeline.
If you run the pipeline manually, you can also set versions for the dependencies:
* `LIBSONATAREPORT_TAG`: git tag for libsonata-report
* `LIBSONATA_TAG`: git tag for libsonata
* `NEURON_COMMIT_ID`: commit ID for neuron
* `REGISTRY_IMAGE_TAG`: this will be the container version. Must be specified if you specify one of the others.
Acknowledgment
==============
The development of this software was supported by funding to the Blue Brain Project,
a research center of the École polytechnique fédérale de Lausanne (EPFL),
from the Swiss government's ETH Board of the Swiss Federal Institutes of Technology.
Copyright (c) 2005-2023 Blue Brain Project/EPFL
Copyright (c) 2025 Open Brain Institute
.. substitutions
.. |banner| image:: docs/img/neurodamus_banner_230701.png
Raw data
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"_id": null,
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"name": "neurodamus",
"maintainer": null,
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"requires_python": ">=3.9",
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"author": "Blue Brain Project, EPFL",
"author_email": null,
"download_url": "https://files.pythonhosted.org/packages/b7/c4/5bd842e5cb2de16803335cfcecf44b0208887f4e621ebd8204accb427f16/neurodamus-3.9.0.tar.gz",
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"description": "|banner|\n\n=============\nNeurodamus\n=============\n.. image:: https://zenodo.org/badge/640796304.svg\n :target: https://doi.org/10.5281/zenodo.8075201\n\n\nNeurodamus is a BBP Simulation Control application for Neuron.\n\nThe Python implementation offers a comprehensive Python API for fine tuning of the simulation, initially defined by a BlueConfig file.\n\n\nDescription\n===========\n\nNeurodamus is the BBP in-house developed application for setting up large-scale neuronal simulations.\nIt has traditionally been implemented as a set of extensions to Neuron, in the form of .hoc and .mod files.\nThe parameters of the simulation are loaded from a configuration file, by default BlueConfig.\n\nTo address several limitations of the Hoc implementation, including development effort, the\nhigh-level layers of Neurodamus have been reimplemented in Python.\nSuch implementation effectively makes available to the user a Python module with a comprehensive\nAPI, suitable to fine control simulation aspects, as well as inspect and eventually adapt the\nsimulations as intended.\n\nInstall\n=======\n\nPrerequisites\n-------------\n- hdf5\n- libsonatareport https://github.com/BlueBrain/libsonatareport\n- neuron with MPI https://github.com/neuronsimulator/nrn\n\nInstall neurodamus\n------------------\n.. code-block:: sh\n\n git clone https://github.com/BlueBrain/neurodamus.git\n cd neurodamus\n pip install .\n\nBuild special with mod files\n----------------------------\nOnce neuron and neurodamus are installed, you can build `special` with your mod files:\n\n.. code-block:: sh\n\n mkdir mods\n cp -r <your-mod-files> mods/\n export DATADIR=$(python -c \"import neurodamus; from pathlib import Path; print(Path(neurod)mus.__file__).parent / 'data')\")\n cp -r $DATADIR/mod/* mods/\n nrnivmodl -incflags '-I <include-paths-of-our-dependencies>' -loadflags '-L <libs-paths-for-linking>' mods\n\nTo use the Blue Brain open models, you can build `neurodamus-models <https://github.com/blueBrain/neurodamus-models>`_.\nIt will also produce a handy `build_neurodamus.sh` script that calls `nrnivmodl` with all dependencies to compile your future mod files\n\n.. code-block:: sh\n\n build_neurodamus mods/\n\nExamples\n========\nOnce neurodamus is installed, you should be able to find the executable `neurodamus` in your path:\n\n.. code-block::\n\n $ neurodamus\n Usage:\n neurodamus <ConfigFile> [options]\n neurodamus --help\n\nAmong the options you will find flags to tune run behavior.\n\nNeurodamus explicitly depends on MPI libraries for parallel execution.\nTherefore please use \"srun\" or \"mpiexec\" to launch it, according to your platform. If you\ndon't, complicated error messages may show up. Please remember it.\n\nEven though a `neurodamus` launcher is provided, for production runs we suggest using\n`special` instead. This way has proven to take advantage of optimized math libraries.\nWe hope to bring the same advantages to the launcher script soon.\n\n.. code-block:: sh\n\n export NEURODAMUS_PYTHON=$(python -c \"import neurodamus; from pathlib import Path; print(Path(neurod)mus.__file__).parent / 'data')\")\n export HOC_LIBRARY_PATH=<hoc_files_folder>\n srun <srun params> <your_built_special> -mpi -python $NEURODAMUS_PYTHON/init.py <neurodamus params>\n\nAn example of a full installation with a simulation run can be found in the workflow test\n`simulation_test.yaml <https://github.com/BlueBrain/neurodamus/blob/main/.github/workflows/simulation_test.yml>`__.\n\nDocker container\n================\nAlternatively, you can start directly a neurodamus docker container where all the packages are built.\nWith the container, you can build your mod files and run simulations.\nSee instructions in `docker/README.md <https://github.com/BlueBrain/neurodamus/blob/main/docker/README.md>`_.\n\nBuilding the docker container\n-----------------------------\n.. TODO: decide what to do without pipelines\n.. The docker container image is built automatically when a new tag is created in the repository, if a container with the specified version doesn't already exist.\n.. On manual pipeline runs, the container image is also built but not automatically pushed to docker-hub; you'll have to manually start the job in the pipeline you created if you want this to happen. Keep in mind that this is *optional*, the container image is *always* pushed to the gitlab registry!\n\nThe docker images will be built in the `regular github action <https://github.com/openbraininstitute/neurodamus/actions>`_ - if triggered under the right conditions (either manually or through git tag creation) the container jobs will be added to this pipeline.\n\nIf you run the pipeline manually, you can also set versions for the dependencies:\n * `LIBSONATAREPORT_TAG`: git tag for libsonata-report\n * `LIBSONATA_TAG`: git tag for libsonata\n * `NEURON_COMMIT_ID`: commit ID for neuron\n * `REGISTRY_IMAGE_TAG`: this will be the container version. Must be specified if you specify one of the others.\n\n\nAcknowledgment\n==============\nThe development of this software was supported by funding to the Blue Brain Project,\na research center of the \u00c9cole polytechnique f\u00e9d\u00e9rale de Lausanne (EPFL),\nfrom the Swiss government's ETH Board of the Swiss Federal Institutes of Technology.\n\nCopyright (c) 2005-2023 Blue Brain Project/EPFL\nCopyright (c) 2025 Open Brain Institute\n\n.. substitutions\n.. |banner| image:: docs/img/neurodamus_banner_230701.png\n",
"bugtrack_url": null,
"license": "Apache License\n Version 2.0, January 2004\n http://www.apache.org/licenses/\n \n TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION\n \n 1. Definitions.\n \n \"License\" shall mean the terms and conditions for use, reproduction,\n and distribution as defined by Sections 1 through 9 of this document.\n \n \"Licensor\" shall mean the copyright owner or entity authorized by\n the copyright owner that is granting the License.\n \n \"Legal Entity\" shall mean the union of the acting entity and all\n other entities that control, are controlled by, or are under common\n control with that entity. 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For the purposes\n of this License, Derivative Works shall not include works that remain\n separable from, or merely link (or bind by name) to the interfaces of,\n the Work and Derivative Works thereof.\n \n \"Contribution\" shall mean any work of authorship, including\n the original version of the Work and any modifications or additions\n to that Work or Derivative Works thereof, that is intentionally\n submitted to Licensor for inclusion in the Work by the copyright owner\n or by an individual or Legal Entity authorized to submit on behalf of\n the copyright owner. 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