Installation - Remote

On this page, specific information is presented for using readDiag on virtual machines (e.g., Itapemirim and Ilópolis) and Egeon at CPTEC. If you want to install readDiag on a local machine, use the instructions on the Local Installation page.

Itapemirim/Ilopolis

The Ilopolis machine has a Jupyter server that can be used to run readDiag. This server is accessible at http://ilopolis.cptec.inpe.br/. Follow the instructions below to create a readDiag kernel for use within this Jupyter server.

Installing the readDiag Environment

Warning

In this section, it is assumed that the user will create the readDiag environment and install the package within the environment so the user can make modifications to the code.

1. Download the readDiag code (in your $HOME):

   gh repo clone GAD-DIMNT-CPTEC/readDiag
   

   or

   git clone https://github.com/GAD-DIMNT-CPTEC/readDiag.git
   

2. Inside the readDiag directory, create the environment, activate it, and install readDiag:

   cd readDiag
   conda env create -f environment.yml
   conda activate readDiag
   pip install -e .
   

   or,

   cd readDiag
   python -m venv readDiag-env
   source readDiag-env/bin/activate
   pip install -r requirements.txt
   pip install -e .
   

   Note

   By creating the environment, the readDiag will be installed automatically. It is important to note that by running pip install -e ., the readDiag released version of readDiag from PyPi will be uninstalled, and the repository version will be installed in edit (or development) mode. This way, modifications made to the code will be readly available without the need to reinstall the package.

3. Install the readDiag environment kernel within Jupyter:

   python -m ipykernel install --user --name readDiag --display-name "readDiag"
   

4. Access the host http://ilopolis.cptec.inpe.br/ and navigate to the $HOME/readDiag/notebooks directory and click on the readDiag_tutorial_complete-en_us.ipynb file;

5. In the Jupyter interface, change the kernel to readDiag. This step is necessary to execute the code.

Reusing the readDiag Environment

Warning

In this section, it is assumed that the user will reuse the readDiag environment with the package already installed previously. In this case, it is not necessary to create an environment or install readDiag.

1. Download the readDiag code (in your $HOME) - to access the readDiag usage example notebooks:

   gh repo clone GAD-DIMNT-CPTEC/readDiag
   

   or

   git clone https://github.com/GAD-DIMNT-CPTEC/readDiag.git
   

2. Activate the readDiag environment:

   source /share/das/miniconda3/envs/readDiag/bin/activate
   

3. Install the readDiag environment kernel within Jupyter:

   python -m ipykernel install --user --name readDiag --display-name "readDiag"
   

4. Access the host http://ilopolis.cptec.inpe.br/ and navigate to the $HOME/readDiag/notebooks directory and click on the readDiag_tutorial_complete-en_us.ipynb file;

5. In the Jupyter interface, change the kernel to readDiag. This step is necessary to execute the code.

Egeon

To use readDiag on Egeon, follow the instructions below:

1. Perform steps 1 and 2 described in the Installing the readDiag Environment section;

2. Activate the readDiag environment:

   source /home/carlos.bastarz/.conda/envs/readDiag/bin/activate
   

3. Execute the following command - note the port on which Jupyter is being run, e.g., jupyter:8889:

   jupyter-notebook --ip='*' --NotebookApp.token='' --NotebookApp.password='' --no-browser
   

4. On your computer, run the following command to open Jupyter locally - where localhost:XXXX should be a port on your computer, e.g., localhost:8820:

   ssh -N -f -L  localhost:XXXX:localhost:8889 <username>@egeon.cptec.inpe.br
   

5. On your computer, open the browser and access the address localhost:8820.

Warning

If it is necessary to terminate Jupyter or restart the process, run the following commands - identify the process corresponding to the executed ssh command and terminate it:

ps -ef | grep ssh
kill -9 PID