Merge pull request #154 from EPCCed/portal

Jupyterhub and S3 docs
EPCCed · Jun 13, 2024 · cb6eb9c · cb6eb9c
2 parents 6bca58c + 433721c
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diff --git a/docs/bespoke/eddash/index.md b/docs/bespoke/eddash/index.md
diff --git a/docs/bespoke/eddash/jhub-git.md b/docs/bespoke/eddash/jhub-git.md
diff --git a/docs/bespoke/eddash/safe-registration.md b/docs/bespoke/eddash/safe-registration.md
diff --git a/docs/bespoke/eddash/workshops.md b/docs/bespoke/eddash/workshops.md
diff --git a/docs/bespoke/index.md b/docs/bespoke/index.md
diff --git a/docs/images/access/authorize-btn.png b/docs/images/access/authorize-btn.png
diff --git a/docs/images/access/github-authorize.png b/docs/images/access/github-authorize.png
diff --git a/docs/images/access/github-btn.png b/docs/images/access/github-btn.png
diff --git a/docs/images/access/github-invitation-2.png b/docs/images/access/github-invitation-2.png
diff --git a/docs/images/access/github-invitation.png b/docs/images/access/github-invitation.png
diff --git a/docs/images/access/github-signin-btn.png b/docs/images/access/github-signin-btn.png
diff --git a/docs/images/access/github-signin.png b/docs/images/access/github-signin.png
diff --git a/docs/images/access/join-btn.png b/docs/images/access/join-btn.png
diff --git a/docs/images/access/jupyterhub-dashboard.png b/docs/images/access/jupyterhub-dashboard.png
diff --git a/docs/images/access/jupyterhub-login.png b/docs/images/access/jupyterhub-login.png
diff --git a/docs/images/access/jupyterhub-select-server.png b/docs/images/access/jupyterhub-select-server.png
diff --git a/docs/images/access/jupyterhub-startup.png b/docs/images/access/jupyterhub-startup.png
diff --git a/docs/images/access/jupyterlab-dashboard.png b/docs/images/access/jupyterlab-dashboard.png
diff --git a/docs/images/access/portal-s3-accounts.png b/docs/images/access/portal-s3-accounts.png
diff --git a/docs/images/access/portal-s3-keys.png b/docs/images/access/portal-s3-keys.png
diff --git a/docs/images/access/rstudio-server-screen-2.png b/docs/images/access/rstudio-server-screen-2.png
diff --git a/docs/images/access/rstudio-server-screen.png b/docs/images/access/rstudio-server-screen.png
diff --git a/docs/services/cs2/index.md b/docs/services/cs2/index.md
@@ -1,5 +1,5 @@
 # Cerebras CS-2
 
-[Get Access](./access/)
+[Get Access](./access.md)
 
-[Running codes](./run/)
+[Running codes](./run.md)
diff --git a/docs/services/cs2/run.md b/docs/services/cs2/run.md
@@ -6,7 +6,7 @@ The Cerebras CS-2 Wafer-scale cluster (WSC) uses the Ultra2 system as a host sys
 
 ## Connecting to the cluster
 
-To gain access to the CS-2 WSC you need to login to the host system, Ultra2. See the [documentation for Ultra2](../ultra2/run.md#login).
+To gain access to the CS-2 WSC you need to login to the host system, Ultra2. See the [documentation for Ultra2](../ultra2/connect.md#login).
 
 ## Running Jobs
 

diff --git a/docs/services/datacatalogue/docs.md b/docs/services/datacatalogue/docs.md
diff --git a/docs/services/datacatalogue/index.md b/docs/services/datacatalogue/index.md
@@ -1,9 +1,3 @@
 # EIDF Data Catalogue Information
 
-[QuickStart](./quickstart/)
-
-[Tutorial](./tutorial/)
-
-[Documentation](./docs/)
-
-[Metadata information](./metadata/)
+[Metadata information](./metadata.md)
diff --git a/docs/services/datacatalogue/quickstart.md b/docs/services/datacatalogue/quickstart.md
diff --git a/docs/services/datacatalogue/tutorial.md b/docs/services/datacatalogue/tutorial.md
diff --git a/docs/services/index.md b/docs/services/index.md
@@ -2,18 +2,20 @@
 
 ## Computing Services
 
-[Data Science Virtual Desktops](./virtualmachines/)
+[Data Science Virtual Desktops](./virtualmachines/index.md)
 
-[Managed File Transfer](./mft/)
+[Managed File Transfer](./mft/index.md)
 
-[Managed JupyterHub](./jhub/)
+[Notebooks](./jhub/index.md)
 
-[Cerebras CS-2](./cs2/)
+[Cerebras CS-2](./cs2/index.md)
 
-[Ultra2](./ultra2/)
+[Ultra2](./ultra2/index.md)
 
-[Graphcore Bow Pod64](./graphcore/)
+[Graphcore Bow Pod64](./graphcore/index.md)
 
-## Data Management Services
+## Data Services
 
-[Data Catalogue](./datacatalogue/)
+[S3](./s3/index.md)
+
+[Data Catalogue](./datacatalogue/index.md)
diff --git a/docs/services/jhub/docs.md b/docs/services/jhub/docs.md
diff --git a/docs/services/jhub/index.md b/docs/services/jhub/index.md
@@ -1,7 +1,8 @@
-# EIDF Jupyterhub
+# EIDF Notebook Service
 
-[QuickStart](./quickstart/)
+The EIDF Notebook Service is a scalable Jupyterhub deployment in the EIDF Data Science Cloud.
 
-[Tutorial](./tutorial/)
+The Notebook Service is open to all EIDF users and offers a selection of data science environments
+and user interfaces, including Jupyter notebooks, Jupyter Lab and RStudio.
 
-[Documentation](./docs/)
+Follow [Quickstart](./quickstart.md) to start using the EIDF Notebook Service.
diff --git a/docs/services/jhub/quickstart.md b/docs/services/jhub/quickstart.md
@@ -2,6 +2,58 @@
 
 ## Accessing
 
-## First Task
+Access the EIDF Notebooks in your browser by opening [https://notebooks.eidf.ac.uk/](https://notebooks.eidf.ac.uk/). You must be a member of an active EIDF project and have a user account to use the EIDF Notebook Service.
 
-## Further information
+![JupyterHub Login Page](../../images/access/jupyterhub-login.png)
+
+Click on "Sign In with SAFE". You will be redirected to the SAFE login page.
+
+Log into the SAFE if you're not logged in already.
+If you have more than one account you will be presented with the form "Approve Token" and a choice of user accounts for the Notebook Service.
+This account is the user in your notebooks and you can share data with your DSC VMs within the same project.
+
+Select the account you would like to use from the dropdown "User Account" at the end of the form. Then press "Accept" to return to the EIDF Notebook Service where you can select a server environment.
+
+![JupyterHub Login Page](../../images/access/jupyterhub-select-server.png)
+
+Select the environment that you would like to use for your notebooks and press "Start". Now your notebook container will be launched. This may take a little while.
+
+![JupyterHub Login Page](../../images/access/jupyterhub-startup.png)
+
+## First Notebook
+
+You will be presented with the JupyterLab dashboard view when the container has started.
+
+![JupyterHub Login Page](../../images/access/jupyterhub-dashboard.png)
+
+The availability of launchers depends on the environment that you selected.
+
+For example launch a Python 3 notebook or an R notebook from the dashboard. You can also launch a terminal session.
+
+## Python packages
+
+Note that Python packages are installed into the system space of your container by default.
+However this means that they are not available after a restart of your notebook container which may happen when your session was idle for a while.
+We recommend specifying `--user` to install packages into your user directory to preserve installations across sessions.
+
+To install python packages in a notebook use the command:
+
+```jupyter
+!pip install <package> --user
+```
+
+or run the command in a terminal:
+
+```bash
+pip install <package> --user
+```
+
+## Data
+
+There is a project space mounted in `/project_data`. Only project accounts have permissions to view and write to their project folder in this space. Here you can also share data with DSC VMs in your project. Please contact the helpdesk if you would like to mount this project space to one of your VMs. Data placed in `/project_data/shared` is shared with other notebook users outside your project.
+
+## Limits
+
+Note that there are limited amounts of memory and cores available per user. Users do not have sudo permissions in the containers so you cannot install any system packages.
+
+Currently there is no access to GPUs. You can submit jobs to the EIDF GPU Service but you cannot run your notebooks on a GPU.
diff --git a/docs/services/jhub/tutorial.md b/docs/services/jhub/tutorial.md
diff --git a/docs/services/rstudioserver/docs.md b/docs/services/rstudioserver/docs.md
diff --git a/docs/services/rstudioserver/index.md b/docs/services/rstudioserver/index.md
diff --git a/docs/services/rstudioserver/quickstart.md b/docs/services/rstudioserver/quickstart.md
diff --git a/docs/services/rstudioserver/tutorial.md b/docs/services/rstudioserver/tutorial.md