T3 was only tested on Linux (Ubuntu_ 22.04.1 LTS) and MacOS. We don't expect it to work on Windows.
It can be installed on a server, as well as on your local desktop / laptop, in order to submit jobs to the server/s.
Package Manager and Cloning from Github¶
You can install either package.
sudo apt install curl
sudo apt install wget
2. Install compiler¶
Ubuntu or Debian
bash sudo apt install git gcc g++ make
Fedora or Red Hat
bash sudo dnf install git gcc gcc-c++ make
3. Download Python Package Manager¶
curl -L -O "https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-$(uname)-$(uname -m).sh" bash Mambaforge-$(uname)-$(uname -m).sh
wget "https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-$(uname)-$(uname -m).sh" bash Mambaforge-$(uname)-$(uname -m).sh
4. Clone T3 Repository¶
Clone T3's repository by typing the following command in the desired folder (e.g., under ~/Code/):
git clone https://github.com/ReactionMechanismGenerator/T3.git
Setting up Path¶
- To set up T3 to your local path in .bashrc, you have two options:
Terminal Command (NOTE: Make sure to change "~/Path/to/T3/" accordingly"):
echo 'PYTHONPATH=$PYTHONPATH:~/Path/to/T3/' >> ~/.bashrc
Editing .bashrc directly (NOTE: Make sure to change "~/Path/to/T3/" accordingly"):
- In terminal, enter the command:
sudo gedit ~/.bashrc
- Then in the opened file, on a new line, enter the following:
T3 requires RMG-Py, RMG-databse and ARC to function correctly. In order to install the necessary dependencies, you can follow either option below.
Navigate to the T3 folder, depending on where you cloned it to.
Open a terminal in the T3 folder, and type the following:
make install all
Note: This can take some time to finish.
- You have now installed all the required dependencies.
- Install the latest versions of RMG-Py and the RMG-database on the same machine where T3 is installed. Follow the instructions on RMG's Documentation.
Make sure to install RMG's developer version which includes important recent features. Note that the installation instructions suggest Anaconda, but Mambaforge can be used in it's place.
Be sure to add RMG-Py to your PATH and PYTHONPATH as explained in the instructions.
Install the latest version of ARC on the same machine where T3 is installed. Follow the instructions on ARC's documentation
Make sure to add ARC to your PATH and PYTHONPATH, as well as to define your servers as explained in ARC's documentation.
Create the Anaconda/Mambaforge environment for T3 by executing the following command in the T3 folder:
$ mamba env create -f environment.yml INFO: Collecting package metadata (repodata.json): done INFO: Solving environment: done INFO: INFO: Downloading and Extracting Packages INFO: ... INFO: Preparing transaction: done INFO: Verifying transaction: done INFO: Executing transaction: done INFO: # INFO: # To activate this environment, use INFO: # INFO: # $ conda activate t3_env INFO: # INFO: # To deactivate an active environment, use INFO: # INFO: # $ conda deactivate
- Activate the T3 environment every time before running T3:
conda activate t3_env
Add T3 aliases to your .bashrc¶
Some optional yet convenient aliases are listed below
(make sure to change "/Path/to/T3/" accordingly).
Add these to your
.bashrc file, which can be edited by typing, e.g.,
sudo nano ~/.bashrc:
export t3_path=$HOME`/Path/to/T3' alias t3e='conda activate t3_env' alias t3='python $t3_path/T3.py input.yml' alias t3code='cd $t3_path'
Then, after sourcing
.bashrc or restarting the terminal,
t3e will activate the environment,
t3code will change the directory into the T3 repository,
and finally typing
t3 from any folder with
a valid T3 input file will execute T3 in that folder.
The T3 repository is being updated frequently.
Make sure to update your instance of T3 to enjoy new features
and get recent bug fixes. To get the most recent developer version,
execute the following commands (make sure to change
cd ~/Path/to/T3/ git fetch origin git pull origin main
The above will update your main branch of T3.