Warning

The Blue Brain Project concluded in December 2024, so development has ceased under the BlueBrain GitHub organization. Future development will take place at: https://github.com/openbraininstitute/o1v5-workflows

O1v5-workflows

Workflow configurations and extensions for setting up and running simulation campaigns using the O1v5 circuit

Folder organization:

• /blob_stim_replication
  Code and config files for setting up and running replication experiments of the BlobStim experiment (proj32) using the converted O1v5-SONATA circuit [NSETM-1222] with original TC (BlobStim) projections under various connectome manipulations.

• /simplified_connectome_models
  Code and config files for setting up and running replication experiments of the BlobStim experiment (proj32) using the converted O1v5-SONATA circuit [NSETM-1222] with original TC (BlobStim) and simplified connectomes.

• /project_cleanup
  Code and workflows for project cleanup, i.e., moving simulation campaigns to other folder locations, etc.

Requirements:

• bbp-workflow CLI

How to set up and run simulation campaigns:

1. Register a new circuit (only once, if not yet registered in Nexus)
bbp-workflow launch --follow --config workflows/RegisterCircuit__xxx.cfg bbp_workflow.circuit.task RegisterDetailedCircuit

To be specified in RegisterCircuit__xxx.cfg:

• Circuit name, type, description, and additional information
• Circuit config

2. Set up simulation campaign
bbp-workflow launch --follow --config workflows/GenerateCampaign__xxx.cfg bbp_workflow.simulation GenerateSimulationCampaign

To be specified in GenerateCampaign__xxx.cfg:

• Campaign name and description
• Circuit URL
• Coordinates (parameters that are varied throughout the campaign)
• Attributes (fixed parameters, including campaign path and BlueConfig template)
• Parameter processors (e.g., user target generation, stimulus generation, ...)

3. Generate (human-readable) symbolic links
bbp-workflow launch --follow --config workflows/GenerateSymLinks__xxx.cfg bbp_workflow.simulation SimCampaignInfo generate-symlinks

To be specified in GenerateSymLinks__xxx.cfg:

• Campaign URL

4. Launch simulation campaign
bbp-workflow launch --follow --config workflows/LaunchCampaign__xxx.cfg bbp_workflow.simulation SimulationCampaign

To be specified in LaunchCampaign__xxx.cfg:

• Campaign URL
• Project account for SLURM allocation
• Simulation type
• Hardware resources and allocation time

ℹ️ Note: Adding benchmark=True at the end of the launch command will only run the last simulation in a campaign, which can be useful for benchmarking.

5. Analyze/visualize simulation campaigns
Analysis launcher workflow on GitLab

IMPORTANT:

• Unless --workflows-dir is specified, bbp-workflow ... must be launched from the root folder containing ./workflows as a subfolder!
• The Nexus instance (staging or production) can be selected in the [DEFAULT] section in the config files!

Funding & Acknowledgment

This development is 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 © 2024 Blue Brain Project/EPFL