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

2. 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

3. Load MPI and HDF5 modules, e.g.

module load gcc/13.2.0 phdf5/1.14.3 impi/21.9.0
module save default

4. 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

5. 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