Deployment

The purpose of this section is to describe deployment from a Linux system with internet connection (machine 1) to a second similar Linux system without internet connection (machine 2).

Use a virtual environment. A virtual environment is a self-contained directory that holds a specific Python interpreter and its own set of installed libraries. It allows you to create isolated project spaces, preventing conflicts between dependencies for different projects.

Prerequisites

Both machines must have compatible versions of Python 3.11. The use of anaconda3/2023.09 is illustrated below:

On Machine 1

1. Create a virtual environment:

# see what modules are available
module avail

# activate a version that uses Python 3.11, for example:
module load anaconda3/2023.09

# verify Python 3.11 is loaded
python --version

# create the virtual virtual environment called recon3d_env
python3.11 -m venv recon3d_env

The recon3d_env folder will contain the virtual environment.

2. Activate the virtual environment:

source recon3d_env/bin/activate

3. Update pip:

pip install --upgrade pip

4. Install recond3d:

pip install recon3d

5. Deactivate and zip the virtual environment:

deactivate
tar -czf recon3d_env.tar.gz recon3d_env

6. Transfer to machine 2. Move the zip file using a USB drive, SCP, or equivalent method:

scp recon3d_env.tar.gz user@second_machine:/path/to/destination

On Machine 2

6. Extract and then use

tar -xzf recon3d_env.tar.gz
module load anaconda3/2023.09
source recon3d_env/bin/activate
recon3d