Merge branch 'dev' of github.com:deNBI/simplevm-user-docs into dev

config.yml

@@ -108,10 +108,12 @@ extra:
 nav:
   - 'Home' : index.md
   - 'Group Permissions': simple_vm/permissions.md
-  - 'Create Instance': simple_vm/create_instance.md
-  - 'Instance overview': simple_vm/instance_overview.md
-  - 'Instance details': simple_vm/instance_detail.md
-  - 'Cluster' :
+  - 'VM Management':
+    - simple_vm/Instance/index.md
+    - 'Create Instance': simple_vm/Instance/create_instance.md
+    - 'Instance overview': simple_vm/Instance/instance_overview.md
+    - 'Instance details': simple_vm/Instance/instance_detail.md
+  - 'Cluster Management' :
     - simple_vm/Cluster/index.md
     - 'New cluster': simple_vm/Cluster/new_cluster.md
     - 'Cluster overview': simple_vm/Cluster/cluster_overview.md

config_local.yml

@@ -32,13 +32,16 @@ markdown_extensions:
 nav:
   - 'Home' : index.md
   - 'Group Permissions': simple_vm/permissions.md
-  - 'Create Instance': simple_vm/create_instance.md
-  - 'Instance overview': simple_vm/instance_overview.md
-  - 'Instance details': simple_vm/instance_detail.md
-  - 'Cluster' :
-      - 'Cluster': simple_vm/Cluster/index.md
-      - 'New cluster': simple_vm/Cluster/new_cluster.md
-      - 'Cluster overview': simple_vm/Cluster/cluster_overview.md
+  - 'VM Management':
+    - simple_vm/Instance/index.md
+    - 'Create Instance': simple_vm/Instance/create_instance.md
+    - 'Instance overview': simple_vm/Instance/instance_overview.md
+    - 'Instance details': simple_vm/Instance/instance_detail.md
+  - 'Cluster Management' :
+    - simple_vm/Cluster/index.md
+    - 'New cluster': simple_vm/Cluster/new_cluster.md
+    - 'Cluster overview': simple_vm/Cluster/cluster_overview.md
+    - 'Cluster detail': simple_vm/Cluster/cluster_detail.md
   - 'SSH keys and sharing access': simple_vm/keypairs.md
   - 'Volumes': simple_vm/volumes.md
   - 'Images/Snapshots': simple_vm/snapshots.md
@@ -52,18 +55,4 @@ nav:
     - 'Tutorials': Tutorials/index.md
     - 'Access a SimpleVM with Mosh' : Tutorials/Mosh/index.md
     - 'SimpleVM File Transfer' : Tutorials/File_Transfer_Methods/index.md
-  - 'FAQ' : 'FAQ.md'
-  - 'Compute Center Specific' :
-    - 'Giessen' : Compute_Center/Giessen.md
-    - 'Bielefeld' : Compute_Center/Bielefeld.md
-    - 'Heidelberg Uni' : Compute_Center/Heidelberg.md
-    - 'Heidelberg DKFZ' : Compute_Center/Heidelberg-DKFZ.md
-    - 'Tuebingen' : Compute_Center/Tuebingen.md
-    - 'Freiburg' : Compute_Center/Freiburg.md
-    - 'Berlin' : Compute_Center/Berlin.md
-    - 'EMBL' : Compute_Center/EMBL.md
-  - 'Cloud Admin':
-    - 'Configure OpenStack to use Elixir AAI via OpenID Connect': cloud_admin/elixir_OIDC.md
-    - 'Register your identity provider for ELIXIR': cloud_admin/identity_provider.md
-    - 'News management': cloud_admin/news_management.md
-    - 'Vault management': cloud_admin/vault_admin.md
+  - 'FAQ' : 'FAQ.md'

wiki/Tutorials/Mosh/index.md

@@ -31,11 +31,11 @@ sudo apt install mosh
 #### Install Mosh on your Virtual Machine
 You have two ways of installing Mosh on your virtual machine:
 
-1. By having it installed on vm creation, [see](../../simple_vm/create_instance.md#mosh-udp-ports).
+1. By having it installed on vm creation, [see](../../simple_vm/Instance/create_instance.md#mosh-udp-ports).
 
 2. Installing it manually:  
 For this Tutorial we chose Ubuntu 18.04 LTS as the image running on our virtual machine.
-First, connect to your VM. Information on how to connect can be cound on the [instance overview](../../simple_vm/instance_overview.md#8-how-to-connect) and on the [instance detail page](../../simple_vm/instance_detail.md#general-information)
+First, connect to your VM. Information on how to connect can be cound on the [instance overview](../../simple_vm/Instance/instance_overview.md#8-how-to-connect) and on the [instance detail page](../../simple_vm/Instance/instance_detail.md#general-information)
 In our case we need to use ssh:
 ```
 ssh -i /path/to/your/ssh/private/key [email protected] -p 30024

wiki/index.md

@@ -17,7 +17,7 @@ Start and manage virtual machines with ease and let SimpleVM take care of variou
 :    SimpleVM runs in a pre-configured network setup. You don't have to set up anything, start your VM with just some 
 clicks. Afterward, you only need to install the tools you need to work on your project.
 Even then, SimpleVM might already offer to do it for you.
-See [Create Instance](simple_vm/create_instance.md) for more details.
+See [Create Instance](simple_vm/Instance/create_instance.md) for more details.
 
 `SSH access`
 :    SimpleVM configures the SSH access for you and provides you with all appropriate commands for SSH access.
@@ -49,7 +49,7 @@ See [Cluster](simple_vm/Cluster/index.md) for more details.
 `Machine management`
 :    Manage your virtual machines with SimpleVM. You can stop, reboot, manage volume attachments, 
 and delete your vms on one page.
-See [Instance overview](simple_vm/instance_overview.md) for more details.
+See [Instance overview](simple_vm/Instance/instance_overview.md) for more details.
 
 `Workshop management`
 :    Manage your workshops with SimpleVM. You can create workshops, 

wiki/simple_vm/Cluster/index.md

@@ -1,6 +1,6 @@
 # Cluster
 
-Besides single machines, SimpleVM users can start entire clusters.
+Besides [single machines](../Instance/index.md), SimpleVM users can start entire clusters.
 Since the cluster feature is still in the development phase,
 only selected projects can use it.
 Contact [[email protected]](mailto:[email protected]) if you want the cluster feature

wiki/simple_vm/create_instance.md → wiki/simple_vm/Instance/create_instance.md

@@ -21,7 +21,7 @@ Some of the inputs are necessary, others are optional.
 The information that is mandatory for starting a machine is, in addition to the selection of the project in which the machine is to be started, the name of the machine, a flavor and an image.
 The available options are listed and explained below.
 
-![create-instance-part1](./img/create_instance/create-instance-part1.png)
+![create-instance-part1](../img/create_instance/create-instance-part1.png)
 
 ### 1. Selected project
 
@@ -53,15 +53,15 @@ Further, snapshotting a vm doesn't persist data from an ephemeral.<br>
 Therefore, you should use ephemeral storage for temporary data that often changes
 (e.g. cache, buffers, or session data) or data often replicated across your environment.
 If you need to persist data from an ephemeral, create a backup on a volume.
-See the [Best practices for data backup](./backup.md) wiki page for more information.<br>
+See the [Best practices for data backup](../backup.md) wiki page for more information.<br>
 Use [Volumes](#8-volumes) for data that must persist.
 
 ???+ danger "Backup important data from an ephemeral"
     Ephemeral storage is a fleeting storage. 
     All data will be irretrievably lost when you delete your vm.
-    If you need to persist any data from an ephemeral, [create a backup on a volume](./backup.md).
+    If you need to persist any data from an ephemeral, [create a backup on a volume](../backup.md).
 
-![create-instance-part2](./img/create_instance/create-instance-part2.png)
+![create-instance-part2](../img/create_instance/create-instance-part2.png)
 
 
 ### 5. Image selection
@@ -71,31 +71,31 @@ An image includes the operating system and tool packages installed on your vm.<b
 You may choose between base images provided by de.NBI, pre-build images containing a Research Environment
 provided by de.NBI, or one of your snapshots.
 Click on a tab to switch between them or use the filter to search by name.<br>
-For more information about images and snapshots, see [Images and Snapshots](./snapshots.md).
-
-![create-instance-part3](./img/create_instance/create-instance-part3.png)
+For more information about images and snapshots, see [Images and Snapshots](../snapshots.md).
+.
+![create-instance-part3](../img/create_instance/create-instance-part3.png)
 
 ### 6. Research Environments
 
 In case you have chosen an base image, you are able to choose Research Environment to be installed on your machine manually.
 It will take longer than choosing an image with an preinstalled Research Environment.
-Find more information on Browser-based Research Environments [here](./customization.md#research-environments).
+Find more information on Browser-based Research Environments [here](../customization.md#research-environments).
 
-![create-instance-part4](./img/create_instance/create-instance-part4.png)
+![create-instance-part4](../img/create_instance/create-instance-part4.png)
 
 ### 7. Conda tools
 
 You may choose conda, bioconda, and anaconda tools, which install on your machine at launch.
 To add a tool, you may filter by name, and click the green plus button.<br>
-For more information, see the [customization wiki page](./customization.md#conda).
+For more information, see the [customization wiki page](../customization.md#conda).
 
-![create-instance-part5](./img/create_instance/create-instance-part5.png)
+![create-instance-part5](../img/create_instance/create-instance-part5.png)
 
 ### 8. Volumes
 
 Create, attach, and mount a new volume or attach and mount an already existing volume to the machine.
 When creating a new volume you can choose the name, the path it gets mounted to and a volume size in GB.
-If you want to know more about volumes, see the [Volumes](./volumes.md) wiki page.
+If you want to know more about volumes, see the [Volumes](../volumes.md) wiki page.
 You will see a selection of volumes which are queued for creation and existing volumes you have chosen for attachment below. 
 
 
@@ -132,4 +132,4 @@ In order to meet all project requirements of all projects that use SimpleVM as c
 
 Please bear this in mind for all resources, regardless of the limitation:
 Only use them for as long as you need them. If a machine is not needed, for example because it is idle, create a snapshot of the machine and delete it.
-You can then use the snapshot to start a new machine when the resource is needed again. This prevents unnecessary use of resources. When deleting machines, please also consider the notes on [backups and persistence of data](./backup.md).
+You can then use the snapshot to start a new machine when the resource is needed again. This prevents unnecessary use of resources. When deleting machines, please also consider the notes on [backups and persistence of data](../backup.md).

wiki/simple_vm/Instance/index.md

@@ -0,0 +1,16 @@
+# Instances
+
+SimpleVM allows machines to be started quickly, easily and without extensive background knowledge of cloud computing.
+
+## Start and manage your machines
+
+Virtual machines are started using a specially developed form.
+A detailed explanation of all steps and selection options can be found under [Create Instance](./create_instance.md).
+
+The management of your machines is possible in the [Instance Overview](./instance_overview.md), which displays all your machines, which you are allowed to handle.
+The [Instance Detail](./instance_detail.md) page of each machine holds more detailed information and additional configuration and management options.
+
+## Clusters
+
+In SimpleVM, you use clusters similarly to your usual virtual machines.
+Take a look at the [Cluster](../Cluster/index.md)-page for more information on this feature.

wiki/simple_vm/instance_detail.md → wiki/simple_vm/Instance/instance_detail.md

@@ -7,7 +7,7 @@ The detail page offers more information about a virtual machine and extra action
 The overview of the instance detail page shows the most important information of the machine.
 This section is devided into several parts
 
-![general](./img/instance_detail/detail_general.png)
+![general](../img/instance_detail/detail_general.png)
 ### General Information
 This part shows:
  - The state of the VM, i.e. whether it is active or shut down, for example.
@@ -24,7 +24,7 @@ This part shows:
       machine.
   - **Create Snapshot**<br>
       Take a snapshot of the virtual machine. 
-      See [here](snapshots.md) for more information.
+      See [here](../snapshots.md) for more information.
   - **Delete VM**<br> 
       Delete the virtual machine. Any attached volume gets detached but not deleted.
   - **Resume/Restart VM**<br> 
@@ -44,30 +44,35 @@ Shows the image the VM runs on.
 
 ## Volumes
 
-![volumes](./img/instance_detail/detail_volume.png)
+![volumes](../img/instance_detail/detail_volume.png)
 
 This tab shows which volumes are attached to the machine and allows actions like detaching, renaming or deleting the volume.
 For each volume, the unique OpenStack ID, the storage capacity, and the status is shown. 
-For more information on volumes, see the [volume](./volumes.md) wiki page.
+For more information on volumes, see the [volume](../volumes.md) wiki page.
 
 
 ## Ports
 
-When enabled for the project your machine is running in, you are able to configure port ranges for the vm, so it allows connections on these ports when sending requests from machines in the same network. In the case of SimpleVM, all machines in a project are located in the same network. Machines outside this network cannot access these ports. 
+When enabled for the project your machine is running in, you are able to configure port ranges for the vm, so it allows connections on these ports when sending requests from machines in the same network. 
+In the case of SimpleVM, all machines in a project are located in the same network. Machines outside this network cannot access these ports. 
 You can open port ranges from port 1024 to 65535.
 The Ethernet type, the IP protocol and the start and end of the range can be specified for each range. This setting can be added to a machine with **Add**. Released port ranges can be removed again in the list below with **Remove**. 
 
-![ports](./img/instance_detail/detail_ports.png)
+Within the same network you are able to reach the machine using the **private IP address** shown.
+The IP cannot be used to reach the machine from outside the project's own network.
+
+
+![ports](../img/instance_detail/detail_ports.png)
 
 ???+ warning "Safety-critical"
     As this is potentially a safety-critical feature, these authorisations should be used with caution.
 
 ## Research environment
 
-![resenv](./img/instance_detail/detail_resenv.png)
+![resenv](../img/instance_detail/detail_resenv.png)
 
 This tab delivers information about the installed browser-based research environment.
-For more information on Research Environments, see the [customization](./customization.md#research-environments) wiki page.
+For more information on Research Environments, see the [customization](../customization.md#research-environments) wiki page.
 This includes the chosen environment itself and the URL to access it via browser.
 You are able to copy the link, view the logs of the research environment setup and to renew the backend or delete it.
 Deleting the backend of the research environment will make the research environment unaccessible.
@@ -81,11 +86,11 @@ To grant access, a user has to be a member of the project.
     This doesn't automatically enable concurrent sessions, i.e., your session terminates
     once another user logs in with the same credentials.
     For information on concurrent sessions, see the specific 
-    section of the [research environment](customization.md#research-environments).
+    section of the [research environment](../customization.md#research-environments).
 
 ## Conda
 
-![conda](./img/instance_detail/detail_conda.png)
+![conda](../img/instance_detail/detail_conda.png)
 
 The conda tab shows which conda packages got installed on the machines during startup.
 Below a log of the installation can be viewed and downloaded as a `PDF` or `.txt`-file

wiki/simple_vm/instance_overview.md → wiki/simple_vm/Instance/instance_overview.md

@@ -2,7 +2,7 @@
 
 On the “Instance Overview” you can list virtual machines, get more information, and manage them.
 
-![layout](./img/instance_overview/instance_overview_general.png)
+![layout](../img/instance_overview/instance_overview_general.png)
 
 ## Layout
 
@@ -47,7 +47,7 @@ The header of the component shows the following information on first glance:
 #### Further Details and actions
 
 
-![actions](./img/instance_overview/instance_overview_actions.png)  
+![actions](../img/instance_overview/instance_overview_actions.png)  
 
 
 By clicking on the header of a specific machine listed, a more detailed description of the machine is shown.

wiki/simple_vm/customization.md

@@ -34,14 +34,14 @@ After choosing your tools and packages, you need to read and confirm the proceed
 
 ??? info "Minoconda3"
     Miniconda3 will install, which is a lightweight package manager.
-    We decided against the full Anaconda sFet of tools due to its size with over 1500 packages.<br>
+    We decided against the full Anaconda set of tools due to its size with over 1500 packages.<br>
     If you wish to install Anaconda, you will have to choose it from the list of packages.
 
 We create a temporary private and public key pair to access your virtual machine at launch, and to
 install your selection with [Ansible](https://docs.ansible.com/ansible/latest/index.html).
 At the end of the installation process we remove the temporary key from your vm and copy your public key onto it,
 regardless of whether the installation of your selection succeeds or fails.<br>
-You may download the installation logs as a PDF or TXT file. See [Instance Detail](./instance_detail.md#ansible-logs) 
+You may download the installation logs as a PDF or TXT file. See [Instance Detail](./Instance/instance_detail.md#ansible-logs) 
 for more information.
 
 ### Environment
@@ -92,8 +92,8 @@ This name appears in the unique URL used to access your research environment.
 
 ### Find your research environment URL
 
-To access your research environment, follow the Link you find on the [instance overview](./instance_overview.md) 
-or on the [detail page](./instance_detail.md) of your virtual machine.
+To access your research environment, follow the Link you find on the [instance overview](./Instance/instance_overview.md) 
+or on the [detail page](./Instance/instance_detail.md) of your virtual machine.
 
 ![resenv_link](./img/instance_detail/detail_resenv.png)
 
@@ -159,7 +159,7 @@ Now you can work with RStudio by web browser.
 #### Multiple users and concurrent sessions
 
 To grant other users access to your research environment, add them to the allowed list of users.
-You may find the list on the [detailed page](./instance_detail.md#user-management).
+You may find the list on the [detailed page](./Instance/instance_detail.md#user-management).
 
 ???+ warning "Concurrent sessions"
     This doesn't automatically allow for concurrent sessions, i.e., your session terminates 
@@ -210,7 +210,7 @@ Now you can work with Apache Guacamole by web browser.
 #### Multiple users and concurrent sessions
 
 To grant other users access to your research environment, add them to the allowed list of users.
-You may find the list on the [detailed page](./instance_detail.md#user-management).
+You may find the list on the [detailed page](./Instance/instance_detail.md#user-management).
 
 ???+ warning "Concurrent sessions"
     This doesn't automatically allow for concurrent sessions, i.e., your session terminates

wiki/simple_vm/guacamole.md

@@ -7,7 +7,7 @@ you need to add them first by following these steps.
 ## Add user to research environment
 
 If you haven't already done so, add the user to your research environment in the
-[instance detail page](./instance_detail.md#user-management).
+[instance detail page](./Instance/instance_detail.md#user-management).
 
 ![user_management](./img/instance_detail/user_management.png)  
 

wiki/simple_vm/rstudio.md

@@ -7,7 +7,7 @@ you need to add them first by following these steps.
 ## Add user to research environment
 
 If you haven't already done so, add the user to your research environment on the
-[instance detail page](./instance_detail.md#user-management).
+[instance detail page](./Instance/instance_detail.md#user-management).
 
 ![user_management](./img/instance_detail/user_management.png)