#492

garden_ai/app/hpc_notebook.py

@@ -1,5 +1,9 @@
 import logging
 import typer
+import os
+import subprocess
+import tempfile
+import sys
 
 logger = logging.getLogger()
 
@@ -12,13 +16,102 @@ def hpc_notebook():
     pass
 
 
+def start_apptainer(notebooks_dir, container_image):
+    process = None
+    try:
+        with tempfile.TemporaryDirectory() as working_directory:
+            tmp_dir = os.path.join(working_directory, "tmp")
+            os.makedirs(tmp_dir, exist_ok=True)
+
+            # Step 2: Set environment variables
+            os.environ["SINGULARITY_TMPDIR"] = tmp_dir
+            os.environ["APPTAINER_TMPDIR"] = tmp_dir
+            os.environ["JUPYTER_RUNTIME_DIR"] = tmp_dir
+            os.environ["JUPYTER_DATA_DIR"] = tmp_dir
+            os.environ["JUPYTER_CONFIG_DIR"] = tmp_dir
+
+            run_command = [
+                "apptainer",
+                "run",
+                "--bind",
+                f"{notebooks_dir}:/notebooks",
+                container_image,
+                "jupyter",
+                "notebook",
+                "--no-browser",
+                "--ip=0.0.0.0",
+            ]
+            process = subprocess.Popen(run_command)
+            process.wait()
+            logger.info(
+                "Jupyter Notebook started successfully in the Apptainer container."
+            )
+    except KeyboardInterrupt:
+        if process:
+            process.terminate()
+            process.wait()
+        logger.info("Operation cancelled by user (Ctrl-C).")
+        typer.echo("Operation cancelled by user (Ctrl-C).")
+        sys.exit(0)
+
+
 @hpc_notebook_app.command()
-def start():
+def rerun(container_image: str = "hpc-notebook.sif"):
+    current_directory = os.getcwd()
+    notebooks_dir = os.path.join(current_directory, "notebooks")
+
+    if not os.path.exists(container_image):
+        logger.error("Not found.")
+        typer.echo("Not found")
+    else:
+        start_apptainer(notebooks_dir, container_image)
+
+
+@hpc_notebook_app.command()
+def start(container_image: str = "hpc-notebook.sif"):
     """Open a notebook file in HPC."""
-    print("🚧🌱🚧 Under Construction 🚧🌱🚧")
+
+    # Get the absolute path of the definition file located three levels up from the current script's directory
+    definition_file = os.path.abspath(
+        os.path.join(os.path.dirname(__file__), "../../../scripts/Singularity.def")
+    )
+
+    current_directory = os.getcwd()
+    notebooks_dir = os.path.join(current_directory, "notebooks")
+
+    os.makedirs(notebooks_dir, exist_ok=True)
+
+    try:
+        # Ensure the definition file exists
+        if not os.path.isfile(definition_file):
+            logger.error(f"Definition file {definition_file} not found.")
+            typer.echo(f"🚧🌱🚧 Definition file {definition_file} not found 🚧🌱🚧")
+            raise typer.Exit(code=1)
+
+        # Step 3: Build the Apptainer container
+        build_command = ["apptainer", "build", container_image, definition_file]
+        subprocess.run(build_command, check=True)
+        logger.info("Apptainer container built successfully.")
+
+        # Step 4: Run the Apptainer container and start Jupyter Notebook
+        start_apptainer(notebooks_dir, container_image)
+    except subprocess.CalledProcessError as e:
+        logger.error(f"Failed to start Jupyter Notebook: {e}")
+        typer.echo("🚧🌱🚧 Failed to start Jupyter Notebook 🚧🌱🚧")
+    except KeyboardInterrupt:
+        logger.info("Operation cancelled by user (Ctrl-C).")
+        typer.echo("Operation cancelled by user (Ctrl-C).")
+        sys.exit(0)
+    except Exception as e:
+        logger.error(f"An error occurred: {e}")
+        typer.echo("🚧🌱🚧 An unexpected error occurred 🚧🌱🚧")
 
 
 @hpc_notebook_app.command()
 def publish():
     """Publish your hpc-notebook."""
     print("🚧🌱🚧 Under Construction 🚧🌱🚧")
+
+
+if __name__ == "__main__":
+    hpc_notebook_app()

scripts/Singularity.def

@@ -0,0 +1,25 @@
+Bootstrap: docker
+From: python:3.8-slim
+
+%post
+    # install Jupyter Notebook
+    apt-get update && apt-get install -y \
+        python3-pip
+
+    pip install jupyter
+
+    # create notebook directory
+    mkdir /notebooks
+
+%environment
+
+    export PATH=/usr/local/bin:$PATH
+    export HOME=/root
+
+%runscript
+
+    jupyter notebook --notebook-dir=/notebooks --ip 0.0.0.0 --no-browser 
+
+%startscript
+
+    exec /bin/bash -c "jupyter notebook --notebook-dir=/notebooks --ip 0.0.0.0 --no-browser"