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Modeling Environment Setup

This repository provides a step-by-step guide to set up a conda environment for neural modeling.

Prerequisites

Install Miniconda

First, download Miniconda:

wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh

Change the permissions to make the installer executable:

chmod +x Miniconda3-latest-Linux-x86_64.sh

Run the installer:

bash Miniconda3-latest-Linux-x86_64.sh

After installation, close any open terminals. If using SSH, close the window. If local, restart your computer.

Environment Setup

Create the Conda Environment

Create a new conda environment named NME (Neural Modeling Environment) with Python 3.12:

conda create -n NME python=3.12 -y

Activate the Environment

Activate the environment:

conda activate NME

Load Required Modules (HPC Systems)

Before installing packages, ensure GCC and MPI modules are loaded. This varies by HPC system.

For Hellbender:

module load openmpi/4.1.5_gcc_12.3.0

For Expanse:

module purge
module load slurm
module load cpu/0.17.3b
module load gcc/10.2.0/npcyll4
module load openmpi/4.1.1

For lab server:

module load mpich-x86_64-nopy

For other systems, check available modules:

module avail

Look for modules with names like openmpi, intel_mpi or mpich.

Package Installation

Install the required packages using pip:

I recommand running this command first and then the next pip command. I think this is the most stable neuron version.

pip install neuron==8.2.4 
pip install jupyter pandas==2.3.3 mpi4py bmtk bmtool scipy seaborn

Notes on Packages

  • BMTK: The pip install may not always be the most up-to-date. For the latest version, install from GitHub.
  • BMTOOL: If you plan to make changes to bmtool, install from the repository.

This setup provides a good starting point with all necessary packages for neural modeling.