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MiV Simulator Case Studies

References

  • Gfluct3
    • Destexhe, A et al. “Fluctuating synaptic conductances recreate in vivo-like activity in neocortical neurons.” Neuroscience vol. 107,1 (2001): 13-24. doi:10.1016/s0306-4522(01)00344-x
How to install?

Suggested setup

  1. Install uv
curl -LsSf https://astral.sh/uv/install.sh | sh
  1. Update uv environment variables
# SSL certificate for Python OpenSSL
export SSL_CERT_FILE=/etc/pki/tls/cert.pem
export REQUESTS_CA_BUNDLE=/etc/pki/tls/cert.pem

# UV cache directories
export UV_TOOL_DIR=$SCRATCH/uv/tools
export UV_TOOL_BIN_DIR=$SCRATCH/uv/bin
export UV_PYTHON_INSTALL_DIR=$SCRATCH/uv/python
export UV_CACHE_DIR=$SCRATCH/uv/cache
  1. Load MPI and HDF5 modules, e.g.
module load gcc/13.2.0 phdf5/1.14.3 impi/21.9.0
module save default
  1. Sync the project

Clone repository into $SCRATCH, cd into it, and run uv sync. This will create a virtualenv in .venv that you can use

  1. If using neuroh5, clone into $SCRATCH and build
git clone https://github.com/iraikov/neuroh5.git
cd neuroh5
cmake .
make

Then add the build binaries to PATH:

export PATH=$SCRATCH/neuroh5/bin:$PATH