readme.md

SONATA for Arbor

Build the example and unit tests

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

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

Generate unit test input (hdf5 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)

$ 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

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

Run the unit tests

$ ./bin/unit

Run the example

$ ./bin/sonata-example ../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