gpu support, rstudio launch, lab by default

.env

@@ -7,6 +7,7 @@
 # are not set in the shell environment.
 
 # To override these values, set the shell environment variables.
+# JUPYTERHUB_VERSION=2.3.1
 JUPYTERHUB_VERSION=1.5.0
 
 # Assign a port for the hub to be hosted on.
@@ -24,7 +25,7 @@ DOCKER_NETWORK_NAME=hub-network
 #DOCKER_NOTEBOOK_IMAGE=jupyter/tensorflow-notebook:4d9c9bd9ced0
 # d0bfe4b38f78: tensorflow==2.4.1 python==3.9.2 lab==3.0.15 notebook==6.3.0 hub==1.4.1
 # 23ac04200f8f: tensorflow==2.6.0 python==3.9.7 lab==3.2.3 notebook==6.4.5 hub==1.5.0
-DOCKER_NOTEBOOK_IMAGE=jupyter/tensorflow-notebook:hub-1.5.0
+DOCKER_NOTEBOOK_IMAGE=jupyter/tensorflow-notebook:hub-${JUPYTERHUB_VERSION}
 
 # the local image we use, after pinning jupyterhub version
 #LOCAL_NOTEBOOK_IMAGE=jupyterhub-user

Dockerfile.jupyterhub

@@ -8,7 +8,7 @@ RUN pip install psycopg2-binary~=2.7 && \
     pip install --no-cache-dir \
         oauthenticator==0.8.*
 
-RUN pip install jupyterhub-hashauthenticator dockerspawner~=12.0
+RUN pip install jupyterhub-hashauthenticator dockerspawner==12.1.0
 RUN pip install jupyterhub-idle-culler
 
 # Copy TLS certificate and key
@@ -19,4 +19,4 @@ RUN pip install jupyterhub-idle-culler
 #RUN chmod 700 /srv/jupyterhub/secrets && \
 #    chmod 600 /srv/jupyterhub/secrets/*
 
-#COPY ./userlist /srv/jupyterhub/userlist
+#COPY ./userlist /srv/jupyterhub/userlist

jupyterhub_config.py

@@ -82,13 +82,17 @@ def create_volume_mount(group_id='group', mode='ro', nb_user='jovyan') -> 'Dict[
 ENABLE_DROPDOWN = True
 IMAGE_WHITELIST= {
     'default': f"{HUB_NAME}-user",
-    'rstudio+shiny': "r-image",
-    'scipy-notebook': "jupyter/scipy-notebook", 
-    'tensorflow-notebook': "jupyter/tensorflow-notebook",
-    'r-notebook': 'jupyter/r-notebook',
-    'base-notebook': "jupyter/base-notebook",
+    'gpu': f"{HUB_NAME}-gpu-user",
+    'RStudio & Shiny': "r-image",
 }
 
+def default_url_fn(handler):
+    user = handler.current_user
+    if user and user.admin:
+        return '/hub/admin'
+    return '/hub/home'
+
+c.JupyterHub.default_url = default_url_fn
 
 # Spawn single-user servers as Docker containers
 from dockerspawner import DockerSpawner
@@ -100,23 +104,70 @@ def start(self):
         #     self.mount_config_files()
         #     self.grant_sudo()
         # self.limit_resources()
-        self.enable_lab()
+        self.update_image_name()
         self.grant_sudo()  # grants sudo to all users!!!
+        self.grant_gpu()
+        # self.enable_lab()
         return super().start()
 
+
+    def update_image_name(self):
+        """
+        Updates the image name from dropdown list (if exists).
+        This is required because the `self.start()` method
+        updates it but we need access to the variable `self.image`
+        prior to startup in order to set extra_host_config (for gpus).
+        NOTE: If the check was based on username rather than image name,
+        this would not be required (but then GPUs are attached per-user)
+        """
+        image = self.user_options.get('image')
+        if image:
+            allowed_images = self._get_allowed_images()
+            if allowed_images:
+                if image not in allowed_images:
+                    raise web.HTTPError(
+                        400,
+                        "Image %s not in allowed list: %s" % (image, ', '.join(allowed_images)),
+                    )
+                else:
+                    image = allowed_images[image]
+
+        self.image = image
+
+        if self.image in (f"{HUB_NAME}-user", f"{HUB_NAME}-gpu-user"):
+            self.environment["VSCODE"] = "1"
+
+        if self.image == "r-image":
+            self.environment["RSTUDIO"] = "1"
+
     def grant_sudo(self):
         """
         Grants sudo permission to current user being spawned.
         """
         self.environment['GRANT_SUDO'] = "1"
-        self.extra_create_kwargs = {'user': 'root'}
-
+        self.extra_create_kwargs.update({"user": "root"})
+
+    def grant_gpu(self):
+        if "gpu" in self.image:
+            import docker
+            self.extra_host_config.update({
+                "device_requests": [
+                    docker.types.DeviceRequest(
+                    count=-1,
+                    capabilities=[["gpu"]],
+                    driver="nvidia",
+                    options={"--gpus":"all"}
+                    )],
+            })
+
     def enable_lab(self):
         """
         Sets Jupyterlab as the default environment which users see.
+        WARNING: Will not work if ~/.jupyter/jupyter_notebook_config.py exists.
         """
         self.environment['JUPYTER_ENABLE_LAB'] = 'yes'
         self.default_url = '/lab'
+        # self.notebook_dir = '/home/jovyan/work'
 
     def update_volumes(self, group_list):
         for group_id in group_list:
@@ -168,7 +219,7 @@ def mount_config_files(self, username='jovyan'):
 # user `jovyan`, and set the notebook directory to `/home/jovyan/work`.
 # We follow the same convention.
 notebook_dir = os.environ.get('DOCKER_NOTEBOOK_DIR') or '/home/jovyan/work'
-#c.DockerSpawner.notebook_dir = notebook_dir
+# c.DockerSpawner.notebook_dir = notebook_dir
 # Mount the real user's Docker volume on the host to the notebook user's
 # notebook directory in the container
 c.DockerSpawner.volumes = { 'hub-user-{username}': notebook_dir }
@@ -185,7 +236,8 @@ def mount_config_files(self, username='jovyan'):
 # User containers will access hub by container name on the Docker network
 c.JupyterHub.hub_ip = HUB_NAME
 # The hub will be hosted at example.com/HUB_NAME/ 
-c.JupyterHub.base_url = u'/%s/'%HUB_NAME
+# c.JupyterHub.base_url = u'/%s/'%HUB_NAME
+c.JupyterHub.base_url = u'/'
 #c.JupyterHub.hub_port = 8001
 
 ## Authentication 
@@ -236,7 +288,7 @@ def mount_config_files(self, username='jovyan'):
 
 
 # https://github.com/jupyterhub/jupyterhub-idle-culler
-if os.environ['CULL_IDLE']:
+if os.environ['CULL_IDLE'] == "true":
     c.JupyterHub.services = [
         {
             "name": "jupyterhub-idle-culler-service",

makefile

@@ -61,6 +61,12 @@ notebook_image: pull singleuser/Dockerfile
 		--build-arg DOCKER_NOTEBOOK_IMAGE=$(DOCKER_NOTEBOOK_IMAGE) \
 		singleuser
 
+gpu_notebook_image: singleuser/Dockerfile.gpu
+	docker build -t $(HUB_NAME)-gpu-user:latest -f singleuser/Dockerfile.gpu \
+		--build-arg JUPYTERHUB_VERSION=$(JUPYTERHUB_VERSION) \
+		--build-arg DOCKER_NOTEBOOK_IMAGE=cschranz/gpu-jupyter:v1.4_cuda-11.2_ubuntu-20.04_slim \
+		singleuser
+
 build: check-files network volumes secrets/oauth.env secrets/postgres.env
 	docker-compose build
 

singleuser/Dockerfile

@@ -3,6 +3,7 @@ FROM $DOCKER_NOTEBOOK_IMAGE
 ARG JUPYTERHUB_VERSION
 
 USER root
+
 RUN apt-get update && \
 	apt-get install -y --no-install-recommends \
 	dvipng \
@@ -25,10 +26,10 @@ COPY install_dev_tools.sh /tmp/
 RUN /tmp/install_dev_tools.sh
 
 # Final cleaning and user customizations
-USER $NB_UID
+# USER $NB_UID
 RUN \
-    fix-permissions $CONDA_DIR && \
-    fix-permissions /home/$NB_USER
+	fix-permissions $CONDA_DIR && \
+	fix-permissions /home/$NB_USER
 
 USER $NB_UID
 # RUN mamba install xeus-python -y
@@ -46,22 +47,6 @@ COPY install_monitoring.sh /tmp/
 COPY install_hugo.sh /tmp/
 COPY install_geckodriver.sh /tmp/
 
-USER root
-## CONFIG
-# Copy over config which creates launcher icons in jupyterlab
-COPY jupyter_notebook_config.py /home/jovyan/.jupyter/
-RUN mkdir -p /home/$NB_USER/.jupyter/lab/workspaces/
-COPY ./jupyterlab_settings /home/$NB_USER/.jupyter/lab/user-settings/@jupyterlab
-RUN chmod -R 777 /home/$NB_USER/.jupyter/lab
-
-USER $NB_UID
-
-# USER SETTINGS
-RUN echo "export EDITOR=/usr/bin/vim" >> /home/$NB_USER/.bashrc
-RUN echo "export PAGER=less" >> /home/$NB_USER/.bashrc
-
-# remember git login credentials
-RUN git config --global credential.helper "cache --timeout 144000"
 
 USER root
 COPY install_vscode.sh /tmp/
@@ -76,3 +61,21 @@ RUN code-server --install-extension eamodio.gitlens
 RUN code-server --install-extension mechatroner.rainbow-csv
 # RUN code-server --install-extension golang.go
 RUN echo '{ "python.defaultInterpreterPath": "conda", "telemetry.enableTelemetry": false, "telemetry.telemetryLevel": "off",}' > /home/$NB_USER/.local/share/code-server/User/settings.json
+
+
+USER root
+## CONFIG
+# Copy over config which creates launcher icons in jupyterlab
+COPY jupyter_notebook_config.py /home/$NB_USER/.jupyter/
+RUN mkdir -p /home/$NB_USER/.jupyter/lab/workspaces/
+COPY ./jupyterlab_settings /home/$NB_USER/.jupyter/lab/user-settings/@jupyterlab
+RUN chown -R $NB_USER:$NB_GUID /home/$NB_USER/.jupyter/lab
+USER $NB_UID
+
+# USER SETTINGS
+RUN echo "export EDITOR=/usr/bin/vim" >> /home/$NB_USER/.bashrc
+RUN echo "export PAGER=less" >> /home/$NB_USER/.bashrc
+
+# remember git login credentials
+RUN git config --global credential.helper "cache --timeout 144000"
+RUN pip install jupyterhub==$JUPYTERHUB_VERSION

singleuser/Dockerfile-R

@@ -102,5 +102,13 @@ RUN conda clean --all -f -y && \
 	fix-permissions $CONDA_DIR && \
 	fix-permissions /home/$NB_USER
 
-USER $NB_UID
 # CMD R
+USER root
+## CONFIG
+# Copy over config which creates launcher icons in jupyterlab
+COPY jupyter_notebook_config.py /home/$NB_USER/.jupyter/
+RUN mkdir -p /home/$NB_USER/.jupyter/lab/workspaces/
+COPY ./jupyterlab_settings /home/$NB_USER/.jupyter/lab/user-settings/@jupyterlab
+RUN chown -R $NB_USER:$NB_GUID /home/$NB_USER/.jupyter/lab
+
+USER $NB_UID

singleuser/Dockerfile.gpu

@@ -0,0 +1,88 @@
+ARG DOCKER_NOTEBOOK_IMAGE
+FROM $DOCKER_NOTEBOOK_IMAGE
+ARG JUPYTERHUB_VERSION
+
+USER root
+RUN apt-key del 7fa2af80 && \
+	cd /tmp/ && \
+	wget https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2004/x86_64/cuda-keyring_1.0-1_all.deb && \
+	dpkg -i cuda-keyring_1.0-1_all.deb && \
+	rm cuda-keyring_1.0-1_all.deb && \
+	sed -i '/developer\.download\.nvidia\.com\/compute\/cuda\/repos/d' /etc/apt/sources.list && \
+	rm -f /etc/apt/sources.list.d/cuda*.list /etc/apt/sources.list.d/nvidia-ml.list
+
+RUN apt-get update && \
+	apt-get install -y --no-install-recommends \
+	dvipng \
+	fonts-lato \
+	fonts-dejavu \
+	gcc \
+	gfortran \
+	ghostscript \
+	imagemagick \
+	lmodern \ 
+	&& \
+	apt-get -qq purge && \
+	apt-get -qq clean && \
+	rm -rf /var/lib/apt/lists/*
+
+
+# Dev tools
+USER root
+COPY install_dev_tools.sh /tmp/
+RUN /tmp/install_dev_tools.sh
+
+# Final cleaning and user customizations
+# USER $NB_UID
+RUN \
+	fix-permissions $CONDA_DIR && \
+	fix-permissions /home/$NB_USER
+
+USER $NB_UID
+# RUN mamba install xeus-python -y
+RUN pip install jupyter_server_proxy
+RUN pip install black flake8 autopep8 isort pre-commit
+
+COPY install_jupyter_nbextensions.sh /tmp/
+# RUN /tmp/install_jupyter_nbextensions.sh
+
+COPY install_language_server.sh /tmp/
+RUN /tmp/install_language_server.sh
+
+COPY install_monitoring.sh /tmp/
+# RUN /tmp/install_monitoring.sh
+COPY install_hugo.sh /tmp/
+COPY install_geckodriver.sh /tmp/
+
+
+USER root
+COPY install_vscode.sh /tmp/
+RUN /tmp/install_vscode.sh
+
+USER $NB_UID
+RUN mkdir -p /home/$NB_USER/.local/share/code-server/User/
+RUN code-server --install-extension ms-python.python
+RUN code-server --install-extension ms-toolsai.jupyter
+RUN code-server --install-extension hookyqr.beautify
+RUN code-server --install-extension eamodio.gitlens
+RUN code-server --install-extension mechatroner.rainbow-csv
+# RUN code-server --install-extension golang.go
+RUN echo '{ "python.defaultInterpreterPath": "conda", "telemetry.enableTelemetry": false, "telemetry.telemetryLevel": "off",}' > /home/$NB_USER/.local/share/code-server/User/settings.json
+
+
+USER root
+## CONFIG
+# Copy over config which creates launcher icons in jupyterlab
+COPY jupyter_notebook_config.py /home/$NB_USER/.jupyter/
+RUN mkdir -p /home/$NB_USER/.jupyter/lab/workspaces/
+COPY ./jupyterlab_settings /home/$NB_USER/.jupyter/lab/user-settings/@jupyterlab
+RUN chown -R $NB_USER:$NB_GUID /home/$NB_USER/.jupyter/lab
+USER $NB_UID
+
+# USER SETTINGS
+RUN echo "export EDITOR=/usr/bin/vim" >> /home/$NB_USER/.bashrc
+RUN echo "export PAGER=less" >> /home/$NB_USER/.bashrc
+
+# remember git login credentials
+RUN git config --global credential.helper "cache --timeout 144000"
+RUN pip install jupyterhub==$JUPYTERHUB_VERSION

singleuser/install_vscode.sh

@@ -4,7 +4,7 @@ apt-get update && \
 	curl && \
 	echo "getting latest install script" && \
 	curl -fsSL https://code-server.dev/install.sh > install.sh && \
-	sh install.sh --version 4.7.0 && \
+	sh install.sh --version 4.5.2 && \
 	rm install.sh && \
 	apt-get -qq purge curl && \
 	apt-get -qq purge && \

singleuser/jupyter_notebook_config.py

@@ -1,20 +1,28 @@
+import os
+
 c.LatexConfig.latex_command = 'pdflatex'
+c.NotebookApp.default_url = '/lab'
+if os.environ.get("VSCODE", None):
+  c.NotebookApp.default_url = '/vscode'
+if os.environ.get("RSTUDIO", None):
+  c.NotebookApp.default_url = '/rstudio'
 
 # Jupyterlab icons can be created here to launch apps
 # that are included in the user's image.
-c.ServerProxy.servers = {
-  'vscode': {
-    'command': [
-		'code-server',
-		'--auth', 'none',
-		'--bind-addr', '0.0.0.0',
-		'--port', '5000'
-	],
-    'port': 5000,
-    'absolute_url': False,
-    'new_browser_tab': True,
-    'launcher_entry': {
-        'title': 'VSCode',
-        },
+if os.environ.get("VSCODE", None):
+  c.ServerProxy.servers = {
+    'vscode': {
+      'command': [
+  		'code-server',
+  		'--auth', 'none',
+  		'--bind-addr', '0.0.0.0',
+  		'--port', '5000'
+  	],
+      'port': 5000,
+      'absolute_url': False,
+      'new_browser_tab': True,
+      'launcher_entry': {
+          'title': 'VSCode',
+          },
+    }
   }
-}