SONATA for Arbor: ☕ Arbata

This project builds ☕ Arbata: it executes Sonata models with the Arbor simulator. Point arbata at a simulation_config.json and let us know what happened 😄.

Build the runner and unit tests

Optional: Clone and build the arbor library in the install-arbor directory

Have Arbor installed somewhere, e.g. /home/you/.local. Alternatively:

$ cd install-arbor
$ ./install-local.sh

Generate unit test input (hdf5 files)

Make sure you have h5py installed. Make sure to delete existing files if regenerating, otherwise you seem to end with corrupted h5 files.

$ cd test/unit/inputs
$ python generate/gen_edges.py
$ python generate/gen_nodes.py
$ python generate/gen_spikes.py

Generate example input (hdf5 files)

Make sure you have h5py installed. Make sure to delete existing files if regenerating, otherwise you seem to end with corrupted h5 files.

$ cd example/network
$ python generate/gen_edges.py
$ python generate/gen_nodes.py
$ cd ../inputs
$ python generate/gen_spikes.py

Enter the correct paths

• The paths have to be hard coded (for now)
• The following files need to be modified
  • example/circuit_config.json
  • example/network/edge_types.csv
  • example/network/node_types.csv
  • example/simulation_config.json

Build the sonata library, unit tests and example

Make sure you have an hdf5 development package installed, e.g. libhdf5-dev.

$ mkdir build && cd build
$ cmake .. -Darbor_DIR=/absolute/path/to/install-arbor/install/lib/cmake/arbor -DCMAKE_BUILD_TYPE=release && make -j4

Run the unit tests

$ ./build/bin/unit

Run the example

$ ./build/bin/arbata example/simulation_config.json

Expected outcome of running the example:

• 2492 spikes generated
• Output spikes report: output_spikes.h5
• Voltage and current probe reports: voltage_report.h5 and current_report.h5

Code org

• sonata/
  • contains the library, also libsonata.
• test/
  • Unit tests for libsonata
• arbata/
  • contains the ☕ Arbata application.
• example/
  • contains an example Sonata simulation.

Developer notes

• class sonata_recipe: public arb::recipe, in sonata_recipe.hpp

  • takes as arg
  • main entry point to setting up a Sonata simulation, see example.cpp.

• class sonata_cell -> arb::cable_cell, in sonata_cell.hpp

  • not meant for direct use.

• class model_desc, in data_management_lib.hpp

  • member of sonata_recipe
  • place where most parsing takes place.

• arbata.cpp

  • An example user of libsonata and the end-user tool for Sonata-on-Arbor simulation.