docs/NRP/index.md

+---
+title: The National Research Platform
+summary: "How to utilize the National Research Platform (NRP)."
+weight: 8
+---
+
+### What is the National Research Platform (NRP)?
+
+The [National Research Platform](https://nationalresearchplatform.org) is a partnership of more than 50 institutions, led by researchers at UC San Diego, University of Nebraska-Lincoln, and UC Berkeley and includes the National Science Foundation, Department of Energy, and multiple research universities in the US and around the world.
+
+The major resource of NRP is a heterogenous globally distributed, open system that fetures a variety of CPUs, GPUs and storage, arranged into a Kubernetes cluster called [Nautilus](https://docs.pacificresearchplatform.org). 
+
+The map below shows the National Research Platform resources located across the world.
+
+<iframe
+  src="https://dash.nrp-nautilus.io/map"
+  style="width:100%; height:600px; border:1px solid black"
+></iframe>
+
+This help document covers these topics:
+
+- [Quick Start](quick_start)
+- [Basic Kubernetes](basic_kubernetes)
+- [GPU Pods](gpu_pods)
+- [Batch Jobs](batch_jobs)
+- [Deployments](deployments)
+- [Storage](storage)
+- [JupyterHub Services](jupyterhub)
+
+The full documentation of the NRP Nautilus Cluster can be found at https://docs.pacificresearchplatform.org.
+To get help regarding using the NRP Nautilus Cluster, please refer to the [Contact page](https://docs.pacificresearchplatform.org/userdocs/start/contact/)

docs/NRP/jupyterhub.md

+---
+title: JupyterHub Service
+summary: "JupyterHub Service"
+weight: 70
+---
+
+### [JupyterHub](https://jupyterhub-west.nrp-nautilus.io) on Nautilus
+
+[JupyterHub](https://jupyterhub-west.nrp-nautilus.io) service is provided on the Nautilus Cluster, which is great
+if you need to quickly run your workflow and do not want to learn any
+kubernetes. Simply follow the link to [https://jupyterhub-west.nrp-nautilus.io](https://jupyterhub-west.nrp-nautilus.io), click the **Sign in With CILogon** button, and use your institutional credentials to login using CILogon. After authentication, choose the hardware specs to spawn your instance. An example of the specs selection is shown as below:
+
+<img src="/images/nrp-jupyterhub-options.png">
+
+Your persistent home folder initially will be limited to 5GB. If you need more, you can request it to be extended.
+You can also request for [cephFS storage](https://docs.pacificresearchplatform.org/userdocs/storage/ceph/)  that is mounted to a shared disk space. All these requests can be made by **contacting NRP admins through [Matrix](https://docs.pacificresearchplatform.org/userdocs/start/contact/)**.
+Please use this to store all the data, code and results that you would need for long experiments.
+
+
+**NOTE:** Your jupyter container will shut down 1hr after your browser disconnects from it. If you need your job to keep running, don't close the browser window.
+You could either use a desktop with a persistent Internet connection or only use this for testing your code.
+
+**NOTE:** Available images are described in the [scientific images section](https://docs.pacificresearchplatform.org/userdocs/running/sci-img/).
+
+If you need to use an image that is not provided by NRP, proceed to [Step by Step Tensorflow with Jupyter](https://docs.pacificresearchplatform.org/userdocs/jupyter/jupyter-pod). If you prefer a customized JupyterHub, follow the guide to [Deploy JupyterHub](https://docs.pacificresearchplatform.org/userdocs/jupyter/jupyterhub/) to deploy your own JupyterHub instance on the Nautilus Cluster.
+
+!!! tip "Deploying your own JupyterHub instance"
+    Instructions on how to create and customize your own instance of JupyterHub are available on the [Deploy JupyterHub]({{ nrp.docs_url }}/userdocs/jupyter/jupyterhub/) documentation page. 

docs/NRP/quick_start.md

+---
+title: Quick Start
+summary: "Quick Start"
+weight: 10
+---
+
+The Nautilus Cluster is a globally distrubuted [Kubernetes](https://kubernetes.io) cluster. 
+
+The general guide of getting access to the Nautilus Cluster can be found [here](https://docs.pacificresearchplatform.org/userdocs/start/get-access/). The guidance in this page is tailored to NU users:
+
+### Get access to the Nautilus cluster
+
+1. Point your browser to the [Nautilus Portal](https://portal.nrp-nautilus.io)
+2. On the portal page click on "Login" button at the top right corner
+   <img src="/images/nautilus-portal-login.png" height="50">
+3. You will be redirected to the "CILogon" page
+4. On this page, select "University of Nebraska-Lincoln" as the Identity Provider from the menu and Click "Log On" button to use your UNL credentials to login. For users from other NU campuses, select the institution of the NU system that you are affilicated with.
+   <img src="/images/cilogon-unl.png">
+5. After a successful authentication you will login on the portal.
+
+    _On first login you become a **guest**.  Any admin user can 
+    validate your guest account,  promote you to **user** and add your account to their **namespace**. You need to be assigned to at least one namespace (usually  a group project but can be your new namespace)._
+ 
+   - To get access to a namespace, please contact its owner (usually email). Once you are granted the user role in the cluster and are added to the namespace, you will get access to all namespace resources.
+
+   - If you're starting a new project and would like to have your own namespace, either for yourself or for your group, you can request to be promoted to the admin by **contacting NRP admins through [Matrix](https://docs.pacificresearchplatform.org/userdocs/start/contact/)**.
+
+         This will give you permission to create any number of namespaces and invite other users to your namespace(s). Please note, **you'll be the one responsible for all activity happening in your namespaces**.
+
+
+6. Once you are made either a user or admin of a namespace, you'll need to accept the **Acceptable Use Policy (AUP)** on the portal page \(as shown in the screenshot below\) in order to get access to the cluster.
+<img src="/images/nrp-aup.png" height="50">
+
+7. Please review [Policies](https://docs.pacificresearchplatform.org/userdocs/start/policies/) before starting any work on the Nautilus Cluster.
+
+### Configure a client to use the Nautilus Cluster
+
+Now you have been given access to the Nautilus Cluster. To interact with the cluster, you need to configure a client with the `kubectl` command-line tool. A client can be your desktop or laptop computer, a virtual machine, or a terminal environment.
+
+1. [Install][1] the kubectl tool
+
+2. Login to [NRP Nautilus portal][2] 
+    <img src="/images/nautilus-portal-login.png" height="50">
+3. Click the **Get Config** link on top right corner of the page to get your configuration file.
+    <img src="/images/nrp-get-config.png" height="50">
+
+4. Save the file as **config** and put the file in your \<home\>/.kube folder. 
+    This folder may not exist on your machine, to create it execute from a terminal:
+
+    ```
+    mkdir ~/.kube
+    ```
+5. Test kubectl can connect to the cluster using a command line tool: 
+
+    ```
+    kubectl get pods -n your_namespace
+    ```
+
+    It's possible there are no pods in your namespace yet. If you've got `No resources found.`, this indicates your namespace is empty and you can start running in it.
+
+
+[1]: https://kubernetes.io/docs/tasks/tools/install-kubectl/
+[2]: https://portal.nrp-nautilus.io

docs/NRP/storage.md

+---
+title: Storage
+summary: "Storage"
+weight: 60
+---
+
+### Using Storage
+
+Different Kubernetes clusters will have different storage options available.
+Let’s explore the most basic one: emptyDir. It will allocate local scratch volume, which will be gone once the pod is destroyed.
+
+You can copy-and-paste the lines below.
+
+###### strg1.yaml:
+
+```yaml
+apiVersion: apps/v1
+kind: Deployment
+metadata:
+  name: test-storage
+  labels:
+    k8s-app: test-storage
+spec:
+  replicas: 1
+  selector:
+    matchLabels:
+      k8s-app: test-storage
+  template:
+    metadata: 
+      labels:
+        k8s-app: test-storage
+    spec:
+      containers:
+      - name: mypod
+        image: alpine
+        resources:
+           limits:
+             memory: 100Mi
+             cpu: 100m
+           requests:
+             memory: 100Mi
+             cpu: 100m
+        command: ["sh", "-c", "apk add dumb-init && dumb-init -- sleep 100000"]
+        volumeMounts:
+        - name: mydata
+          mountPath: /mnt/myscratch
+      volumes:
+      - name: mydata
+        emptyDir: {}
+```
+
+Now let’s start the deployment:
+
+```
+kubectl create -f strg1.yaml
+```
+
+Now log into the created pod, create
+
+```
+mkdir /mnt/myscratch/username
+```
+
+then store some files in it.
+
+Also put some files in some other (unrelated) directories.
+
+Now kill the container: `kill 1` wait for a new one to be created, then log back in.
+
+What happened to the files?
+
+You can now delete the deployment.
+
+### Using outer persistent storage
+
+In our cluster we have ceph storage connected, which allows using it for real data persistence.
+
+To get storage, we need to create an abstraction called PersistentVolumeClaim. By doing that we "Claim" some storage space - "Persistent Volume". There will actually be PersistentVolume created, but it's a cluster-wide resource which you can not see.
+
+Create the file:
+
+###### pvc.yaml:
+
+```yaml
+apiVersion: v1
+kind: PersistentVolumeClaim
+metadata:
+  name: test-vol
+spec:
+  storageClassName: rook-ceph-block
+  accessModes:
+  - ReadWriteOnce
+  resources:
+    requests:
+      storage: 1Gi
+```
+
+We're creating a 1GB volume and formatting it with XFS.
+
+Look at its status with `kubectl get pvc test-vol`. The `STATUS` field should be equal to `Bound` - this indicates successful allocation.
+
+Now we can attach it to our pod. Create one:
+
+```yaml
+apiVersion: v1
+kind: Pod
+metadata:
+  name: test-pod
+spec:
+  containers:
+  - name: mypod
+    image: centos:centos7
+    command: ["sh", "-c", "sleep infinity"]
+    resources:
+      limits:
+        memory: 100Mi
+        cpu: 100m
+      requests:
+        memory: 100Mi
+        cpu: 100m
+    volumeMounts:
+    - mountPath: /examplevol
+      name: examplevol
+  volumes:
+    - name: examplevol
+      persistentVolumeClaim:
+        claimName: test-vol
+```
+
+In volumes section we're attaching the requested persistent volume to the pod (by its name!), and in volumeMounts we're mounting the attached volume to the container in specified folder.
+
+### Exploring storageClasses
+
+Attaching persistent storage is usually done based on storage class. Different clusters will have different storageClasses, and you have to read the [documentation](https://docs.pacificresearchplatform.org/userdocs/storage/intro) on which one to use. Some are restricted and you need to contact admins to ask for permission to use those.
+
+Note that the one we used is the default - it will be used if you define none.
+
+### Cleaning up
+
+After you've deleted all the pods and deployments, delete the volume claim:
+
+```
+kubectl delete pvc test-vol
+```
+
+Please make sure you did not leave any running pods, deployments, volumes.
+

docs/OSG/.nav.yml

+title: The OSG Consortium

content/OSG/characteristics_of_an_osg_friendly_job.md → docs/OSG/characteristics_of_an_osg_friendly_job.md

-+++
-title = "Characteristics of an OSG friendly job"
-description = "Characteristics of an OSG friendly job"
-weight=10
-+++
-
-The OSG is a Distributed High Throughput Computing (DHTC) environment,
-which means that users can access compute cores on over 100 different
-computing sites across the nation with a single job submission.  This
-also means that your jobs must fit a set of criteria in order to be
+---
+title: Characteristics of an OSG friendly job
+summary: "Characteristics of an OSG friendly job"
+weight: 10
+---
+
+Any researcher performing Open Science in the US can become an [OSPool](https://osg-htc.org/services/open_science_pool.html) user. The OSPool provides its users with fair-share access (no allocation needed!) to processing and storage capacity contributed by university campuses, government-supported supercomputing institutions and research collaborations. Using state-of-the-art distributed computing technologies the OSPool is designed to support High Throughput workloads that consist of large ensembles of independent computations.
+
+Your jobs must fit a set of criteria in order to be
 eligible to run on OSG.  The list below provides some rule of thumb
 characteristics that can help us make a decision if using OSG for a
 given job is a viable option. 
 
 
-| Characteristics of an OSG friendly job |
-| -------------------------------------- |
 
+!!! tip "**Characteristics of an OSG friendly job**"
     | Variable                                      | Suggested Values                                                                      |
     | --------------------------------------        | ------------------------------------------------------------------------------------- |
-| Memory/Process                                | <= 2GB                                                                                |
+    | Memory/Process                                | <= 40 GB                                                                                |
     | Type of job                                   | serial (i.e. mostly single core)                                                      |
     | Network traffic<br>(input or output files)    | <= 2GB each side                                                                      |
-| Running Time                                  | Ideal time is 1-10 hours - max is 72  |
+    | Running Time                                  | Ideal time is 1-10 hours - max is 40  |
     | Runtime Disk Usage                            | <= 10GB                                                                               |
-| Binary Type                                   | Portable RHEL6/7                                                                      |
+    | Software                                   | Non-licensed, pre-compiled binaries, containers                                                                      |
     | Total CPU Time (of job workflow)              | Large, typically >= 1000 hours                                                        |
 
 ### OSG Job Runtime
@@ -36,5 +34,4 @@ over from the beginning.  For this reason, it is good practice to build
 automatic checkpointing into your job, or break a large job into
 multiple small jobs if it is at all possible.
 
-Next: [How to submit an OSG Job with HTCondor]({{< relref "how_to_submit_an_osg_job_with_htcondor" >}})
 

docs/OSG/index.md

+---
+title: The OSG Consortium
+summary: "How to utilize the OSG."
+weight: 9
+---
+
+If you find that you are not getting access to the volume of computing
+resources needed for your research through HCC, you might also consider
+submitting your jobs to the OSG. 
+
+### What is the OSG?
+
+The [OSG](https://osg-htc.org/) advances
+science through open distributed computing. Established in 2005, the OSG Consortium operates a fabric of distributed High Throughput Computing (dHTC) services in support of the National Science & Engineering community. The research collaborations, campuses, national laboratories, and software providers that form the consortium are unified in their commitment to advance open science via these services. The Holland Computing Center is proud member of the OSG Consortium. If you are interested in hearing more about OSG or utilizing its resources for your research, please email hcc-support.unl.edu.
+
+The map below shows the Open Science Grid sites located across the U.S.
+
+<img src="/images/17044917.png">
+
+
+- [Characteristics of an OSG friendly job](characteristics_of_an_osg_friendly_job)

docs/accounts/.nav.yml

+title: Creating an Account

content/accounts/how_to_change_your_password.md → docs/accounts/how_to_change_your_password.md

-+++
-title = "Changing Your Password"
-description = "How to change your HCC password"
-weight = "30"
-+++
+---
+title: Changing Your Password
+summary: "How to change your HCC password"
+---
 
 How to change your password
 ---------------------------
 
-{{% notice info%}}
-**Your account must be active with Duo authentication setup in order for
-the following instructions to work.**
-{{% /notice %}}
+!!! info
+    **Your account must be active with Duo authentication setup in order for the following instructions to work.**
 
+
+- [How to change your password](#how-to-change-your-password)
   - [HCC password requirements](#hcc-password-requirements)
   - [Changing a known HCC password](#changing-a-known-hcc-password)
     - [Change your password via the command line](#change-your-password-via-the-command-line)
@@ -20,7 +19,7 @@ the following instructions to work.**
   - [Tutorial Video](#tutorial-video)
 
 Every HCC user has a password that is same on all HCC machines
-(Crane, Rhino, Anvil). This password needs to satisfy the HCC
+(Swan, Anvil). This password needs to satisfy the HCC
 password requirements.
 
 ### HCC password requirements
@@ -51,13 +50,13 @@ any HCC cluster and use the ***passwd*** command:
 
 **Change HCC password**
 
-{{< highlight bash >}}
+```bash
 $ passwd
 Changing password for user <username>.
 Current Password:
 New password:
 New password:
-{{< /highlight >}}
+```
 
 With this command, the user is first prompted for his/her old password.
 If the "*Current Password*" is correct, then the user is asked twice for
@@ -70,12 +69,12 @@ needs to fulfill the HCC password requirements.
     with your HCC credentials.
 2.  Click **Update Account** in the top menu  
     
-    {{< figure src="/images/35326617.png" height="150" >}} 
+    <img src="/images/35326617.png" height="150">
          
 3.  Enter your new password in the **Password** and **Retype Password**
     boxes and click **Modify** to save
 
-    {{< figure src="/images/35326618.png" height="150" >}}
+    <img src="/images/35326618.png" height="150">
 
 ### Resetting a forgotten HCC password
 
@@ -83,7 +82,7 @@ To reset your password, navigate to the [myHCC User Portal](https://hcc.unl.edu/
 
 Click the link to reset your forgotten password
 
-{{< figure src="/images/35326619.png" height="400" >}}
+<img src="/images/35326619.png" height="400">
 
 Fill in the requested information (your HCC user name and email
 associated with your account) and click **Reset Password**. A reset link
@@ -92,4 +91,4 @@ onscreen prompts to set a new password.
 
 ### Tutorial Video
 
-{{< youtube eaTW6FDhpsM >}}
+{{ youtube('eaTW6FDhpsM') }}

content/accounts/_index.md → docs/accounts/index.md

-+++
-title = "Creating an Account"
-weight = "20"
-+++
+---
+title: Creating an Account
+weight: 2
+---
 
-Anyone affiliated with the Unveristy of Nebraska system can request an account on
+Anyone affiliated with the University of Nebraska (NU) system can request an account on
 and use HCC shared resources for free.
 
 How to create an HCC account:
 
 1. **Identify or Setup a Group:** All HCC accounts must be associated 
-with an HCC group. Usually, user's HCC group the research group owned by their advisor 
+with an HCC group **owned by NU faculty**. Usually, user's HCC group is the research group owned by their advisor 
 but it may also be a class group owned by the course instructor. To establish a new 
-group, please complete a [new group request](https://hcc.unl.edu/new-group-request).
+group, please complete a [new group request](https://hcc.unl.edu/new-group-request) if you are NU faculty.
 
 2. **Request an Account:** All accounts must be associated with an HCC group. 
 Your group will usually be owned by your advisor, however, it could also be a 
@@ -19,16 +19,13 @@ class group owned by your instructor. Once you know the group your account will
 be associated with, please complete a [new user request](http://hcc.unl.edu/new-user-request/). 
 
 3. **Setup Two Factor Authentication:** Once your account has been approved, you will recieve an email
-with login instructions. To finish activating your account, you will need to visit HCC
-offices in person with your photo ID in order to [activate Two Factor Authentication]
-({{< relref "setting_up_and_using_duo.md" >}}).
+with login instructions. To finish activating your account, you will need to either have phone number registered with TrueYou or join our [Remote Open Office hours](https://hcc.unl.edu/OOH) or schedule another remote session and show your photo ID in order to [activate Two Factor Authentication](setting_up_and_using_duo.md).
 
 4. **Reset your Temporary Password:** To maintain the security of your account, please
-[change your password]({{< relref "how_to_change_your_password.md" >}}) as soon as
+[change your password](how_to_change_your_password.md) as soon as
 your account is active.
 
 Once the above steps are complete, your account is now active and you are ready to 
-[connect to HCC resources]({{< ref "/connecting" >}}) and 
-[begin submitting jobs]({{< ref "/submitting_jobs" >}}). If you 
-have any questions or would like to setup a consultation meeting, please [contact us]
-({{< ref "/contact_us" >}}).
+[connect to HCC resources](/connecting) and 
+[begin submitting jobs](/submitting_jobs). If you 
+have any questions or would like to setup a consultation meeting, please [contact us](/contact_us/).

content/accounts/setting_up_and_using_duo.md → docs/accounts/setting_up_and_using_duo.md

-+++
-title = "Setting Up and Using Duo"
-description = "Duo Setup Instructions"
-weight = "8"
-+++
+---
+title: Setting Up and Using Duo
+summary: "Duo Setup Instructions"
+---
+
+!!! note
+    The information here only pertains to using Duo with Holland Computing Center accounts.
+For help with your general University (i.e. TrueYou) account and Duo, contact
+the [Huskertech Help Center](https://its.unl.edu/helpcenter/) via email at [support@nebraska.edu](mailto:support@nebraska.edu).
+
 
 ##### **Use of Duo two-factor authentication (https://www.duosecurity.com) is required for access to HCC resources.**
 
@@ -26,16 +31,20 @@ If you *are not* currently using Duo with your TrueYou account:
 
 1.  Install the free **Duo Mobile** application from the
     [Google Play Store](https://play.google.com/store/apps/details?id=com.duosecurity.duomobile), [Apple App Store](https://itunes.apple.com/us/app/duo-mobile/id422663827), or [Microsoft Store](https://www.microsoft.com/en-us/store/apps/duo-mobile/9nblggh08m1g)
-2.  Visit one of the following locations.  **Bring your smartphone and a valid photo ID** such as your university ID card or drivers license.
-    1.  Visit either HCC location [118 Schorr Center, UNL](http://www1.unl.edu/tour/SHOR) | 
-        [152 Peter Kiewit Institute, UNO](http://pki.nebraska.edu/new/pages/about-pki/maps-directions-and-parking) in-person anytime from 9am-5pm to enroll.
-    2.  Visit Information Technology Services [115 Otto Olsen, UNK](http://www.unk.edu/campus-map/?q=m15)
-        in-person and ask for HCC identity verification.
+2.  ~~Visit one of the following locations.  **Bring your smartphone and a valid photo ID** such as your university ID card or drivers license.~~
+    1.  ~~Visit either HCC location [118 Schorr Center, UNL](http://www1.unl.edu/tour/SHOR) |
+        [152 Peter Kiewit Institute, UNO](http://pki.nebraska.edu/new/pages/about-pki/maps-directions-and-parking) in-person anytime from 9am-5pm to enroll.~~
+    2.  ~~Visit Information Technology Services [115 Otto Olsen, UNK](http://www.unk.edu/campus-map/?q=m15)
+        in-person and ask for HCC identity verification.~~
+
+    **Due to current health and safety concerns, Duo activation is entirely remote.** Join one of [HCC's Remote Open Office hours](https://hcc.unl.edu/OOH)
+    sessions every Tues/Thurs from 2-3PM CST to activate Duo. Contact [hcc-support@unl.edu](mailto:hcc-support@unl.edu) for alternate
+    times if you are not able to attend.
 
     Faculty/staff members with a verified NU telephone number can enroll by
     phone. If you would like an HCC staff member to call your NU telephone
     number to enroll, please email
-    {{< icon name="envelope" >}}[hcc-support@unl.edu](mailto:hcc-support@unl.edu)
+    [hcc-support@unl.edu](mailto:hcc-support@unl.edu)
     with a time you will be available.
 
 If you *are* currently using Duo with your TrueYou account:
@@ -59,23 +68,22 @@ U2F use.
 Example login using Duo Push
 ----------------------------
 
-This demonstrates an example login to Crane using the Duo Push method.
+This demonstrates an example login to Swan using the Duo Push method.
 Using another method (SMS, phone call, etc.) proceeds in the same way.
  (Click on any image for a larger version.)
 
 First, a user connects via SSH using their normal HCC username/password,
 exactly as before.
 
-{{< figure src="/images/5832713.png" width="600" >}}
-
-{{% notice warning%}}**Account lockout**
+<img src="/images/duo_login_pass.png" width="600">
 
+!!!warning "**Account lockout**"
     After 10 failed authentication attempts, the user's account is
 disabled. If this is the case, then the user needs to send an email to
 [hcc-support@unl.edu](mailto:hcc-support@unl.edu)
 including his/her username and the reason why multiple failed
 authentication attempts occurred.  
-{{% /notice %}}
+
 
 After entering the password, instead of completing the login, the user
 will be presented with the Duo prompt. This gives the choice to use any
@@ -84,21 +92,20 @@ this example, the choices are Duo Push notification, SMS message, or
 phone call. Choosing option 1 for Duo Push, a request to verify the
 login will be sent to the user's smartphone.
 
-{{< figure src="/images/5832716.png" height="350" >}}
+<img src="/images/duo_app_request.png" height="350">
 
 Simply tap `Approve` to verify the login.
 
-{{< figure src="/images/5832717.png" height="350" >}}
+<img src="/images/duo_app_approved.png" height="350">
+
+!!! warning
+    **If you receive a verification request you didn't initiate, deny the request and contact HCC immediately via email at[hcc-support@unl.edu](mailto:hcc-support@unl.edu)**
 
-{{% notice warning%}}**If you receive a verification request you didn't initiate, deny the 
-request and contact HCC immediately via email at
-[hcc-support@unl.edu](mailto:hcc-support@unl.edu)**
-{{% /notice %}}
 
 In the terminal, the login will now complete and the user will logged in
 as usual.
 
-{{< figure src="/images/5832714.png" height="350" >}}
+<img src="/images/duo_login_successful.png" height="350">
 
 
 Duo Authentication Methods
@@ -107,7 +114,7 @@ Duo Authentication Methods
 ### Duo Push 
 ##### [[Watch the Duo Push Demo]](https://www.duosecurity.com/duo-push)
 
-{{< figure src="/images/5832709.png" height="350" caption="Photo credit: https://duosecurity.com" >}}
+<img src="/images/5832709.png" height="350" caption="Photo credit: https://duosecurity.com">
 
 For smartphone or tablet users (iPhone, Android, Blackberry, Windows
 Phone), the Duo Mobile app is available for free. A push notification
@@ -116,7 +123,7 @@ one tap.
 
 ### Duo Mobile Passcodes
 
-{{< figure src="/images/5832711.png" height="350" caption="Photo credit: https://duosecurity.com" >}}
+<img src="/images/5832711.png" height="350" caption="Photo credit: https://duosecurity.com">
 
 The Duo Mobile app can also be used to generate numeric passcodes, even
 when internet and cell service is unavailable.  Press the key icon to
@@ -126,7 +133,7 @@ prompt to complete authentication.
 ### SMS Passcodes
 
 
-{{< figure src="/images/5832712.png" height="350" >}}
+<img src="/images/5832712.png" height="350">
 
 For non-smartphone users, Duo can send passcodes via normal text
 messages which are entered manually to complete login. Please note since
@@ -143,9 +150,12 @@ entered manually to complete the login.
 ### YubiKey
 ##### [[Yubico]](http://www.yubico.com/)
 
-{{< figure src="/images/5832710.jpg" height="200" caption="Photo credit: Yubico" >}}
+<img src="/images/5832710.jpg" height="200" caption="Photo credit: Yubico">
 
 YubiKeys are USB hardware tokens that generate passcodes when pressed.
+With HCC clusters, there is no prompt to press on the YubiKey. When the DUO prompt
+appears in the terminal, press the YubiKey and it will output a string to the terminal
+to authenticate you.
 They appear as a USB keyboard to the computer they are connected to, and
 so require no driver software with almost all modern operating systems.
 YubiKeys are available from the Husker Tech store at UNL. Users may also purchase them directly from

docs/anvil/.nav.yml

+title: "Anvil: HCC's Cloud"

content/anvil/adding_ssh_key_pairs.md → docs/anvil/adding_ssh_key_pairs.md

-+++
-title = "Adding SSH Key Pairs"
-description = "How to add key pairs to your OpenStack account."
-+++
+---
+title: Adding SSH Key Pairs
+summary: "How to add key pairs to your OpenStack account."
+---
 
 If you have not already generated your key pairs and need help doing so,
 please see the documentation that relates to your operating system:
 
-- [Creating SSH key pairs on Mac]({{< relref "creating_ssh_key_pairs_on_mac" >}})
-- [Creating SSH key pairs on Windows]({{< relref "creating_ssh_key_pairs_on_windows" >}})
+- [Creating SSH key pairs on Mac](../creating_ssh_key_pairs_on_mac/)
+- [Creating SSH key pairs on Windows](../creating_ssh_key_pairs_on_windows/)
+
+!!! note
+    This guide assumes you are either accessing Anvil from on-campus, or are connected to the [Anvil VPN](../connecting_to_the_anvil_vpn/).
 
-{{% notice info %}}
-This guide assumes you are either accessing Anvil from on-campus, or are
-connected to the [Anvil VPN]({{< relref "connecting_to_the_anvil_vpn" >}}).
-{{% /notice %}}
 
 Log into the Anvil web dashboard at **https://anvil.unl.edu** using
 your HCC credentials.  On the left-hand side navigation menu,
 click *Access & Security*.
 
-{{< figure src="/images/13599031.png" >}}
+<img src="/images/13599031.png">
 
 Choose the *Key Pairs* tab in the main window section.
 
-{{< figure src="/images/13599033.png" >}}
+<img src="/images/13599033.png">
 
 Open your **public** key file, select the entire text, and copy it.  On
 the right-hand side, click the *Import Key Pair* button.
 
-{{< figure src="/images/13599036.png" >}}
+<img src="/images/13599036.png">
 
 In the pop-up window, fill in the *Key Pair Name* field with a
 convenient name.  Paste the copied public key text in the larger *Public
 Key* box.
 
-{{< figure src="/images/13599039.png" width="650" >}}
+<img src="/images/13599039.png" width="650">
 
 Click the *Import Key Pair* button to close the pop-up and save the key.
  You should then see an entry with the saved key (the fingerprint value
 will be different than the example below).
 
-{{< figure src="/images/13599043.png" >}}
+<img src="/images/13599043.png">
 
 The key pair can now be associated with any newly created instances.
 

content/anvil/anvil_instance_types.md → docs/anvil/anvil_instance_types.md

-+++
-title = "Anvil Instance Types"
-description = "Details on the available instance types (flavors)"
-+++
+---
+title: Anvil Instance Types
+summary: "Details on the available instance types (flavors)"
+---
 
 Anvil provides many instance types that are optimized for different
 usage patterns.

docs/anvil/available_images.md

+---
+title: Available images
+summary: "HCC-provided images for Anvil"
+---
+
+HCC provides pre-configured images available to researchers.  Below is a
+list of available images.
+
+{% include "static/markdown/anvil-images.md" %}
+
+
+
+Additional images can be produced by HCC staff by request at [hcc-support@unl.edu](mailto:hcc-support@unl.edu).
+ 

content/anvil/connecting_to_linux_instances_from_mac.md → docs/anvil/connecting_to_linux_instances_from_mac.md

-+++
-title = "Connecting to Linux Instances from Mac"
-description = "How to connect to Linux-based instance from a Mac" 
-+++
+---
+title: Connecting to Linux Instances from Mac
+summary: "How to connect to Linux-based instance from a Mac" 
+---
 
-{{% notice info %}}
+!!! note
     This guide assumes you associated your SSH Key Pair with the instance
-when it was created, and that you are connected to the [Anvil VPN]({{< relref "connecting_to_the_anvil_vpn" >}}).
-{{% /notice %}}
+    when it was created, and that you are connected to the [Anvil VPN](../connecting_to_the_anvil_vpn/).
+
 
 Access to Linux instances is via standard SSH, however SSH keys are used
 as opposed to entering a username and password.  
@@ -14,39 +14,41 @@ as opposed to entering a username and password.
 Start the built-in *Terminal* application, located in the *Utilities*
 folder under *Applications.*
 
-{{< figure src="/images/13599111.png" width="598" height="67" >}}
+<img src="/images/13599111.png" width="598" height="67">
 
 Login into the web dashboard atn https://anvil.unl.edu.
 From the left-hand side menu, choose *Instances.*
 
-{{< figure src="/images/13599115.png" width="226" height="374" >}}
+<img src="/images/13599115.png" width="226" height="374">
 
 This will show a table with the running instances and a few details
 about them.  Take note of the *IP address* entry; this is the address
 that will be used to connect.
 
-{{< figure src="/images/13599117.png" width="1064">}}
+<img src="/images/13599117.png" width="1064">
 
 In this example, the private key file is assumed to be on the desktop,
 and named `anvil_key`.  Depending on which Linux OS you're using in your
 instance, the username to use will be different.  See the 
-[Available Images]({{< relref "available_images" >}})
+[Available Images](../available_images/)
 page for a table with the username to use for each OS.  
 In the *Terminal* application, run the command:
 
-{{< highlight bash >}}ssh -i ~/Desktop/anvil_key centos@<ip address> {{< /highlight >}}
+```bash
+ssh -i ~/Desktop/anvil_key centos@<ip address> 
+```
 
 substituting the IP address of your instance.  For the example here, it would look
 like:
 
-{{< figure src="/images/13599205.png" >}}
+<img src="/images/13599205.png">
 
 The first time you connect, you will get a warning; type `yes` and hit
 Enter to continue connecting.  Subsequent connections will not show this
 warning.
 
-{{< figure src="/images/13599208.png" >}}
+<img src="/images/13599208.png">
 
 You will now be logged into your instance and can use it.
 
-{{< figure src="/images/13599212.png" width="592" >}}
+<img src="/images/13599212.png" width="592">

content/anvil/connecting_to_linux_instances_from_windows.md → docs/anvil/connecting_to_linux_instances_from_windows.md

-+++
-title = "Connecting to Linux Instances from Windows"
-description = "How to connect to Linux-based instance from Windows"
-+++
+---
+title: Connecting to Linux Instances from Windows
+summary: "How to connect to Linux-based instance from Windows"
+---
 
-{{% notice info %}}
+!!! note
     This guide assumes you associated your SSH Key Pair with the instance
-when it was created, and that you are connected to the [Anvil VPN]({{< relref "connecting_to_the_anvil_vpn" >}}).
-{{% /notice %}}
+    when it was created, and that you are connected to the [Anvil VPN](../connecting_to_the_anvil_vpn/).
 
-If do not already have the PuTTY package installed, download and install
-it from [this link](https://the.earth.li/~sgtatham/putty/latest/w32/putty.exe).
+
+If do not already have the PuTTY package installed, download and install the PuTTY package (64-bit x86 .msi installer) 
+from [this link](https://www.chiark.greenend.org.uk/~sgtatham/putty/latest.html).
 Once installed, start PuTTY.
 
 Login into the web dashboard at https://anvil-beta.unl.edu/.
 From the left-hand side menu, choose *Instances*.
 
-{{< figure src="/images/13599115.png" width="226" height="374" >}}
+<img src="/images/13599115.png" width="226" height="374">
 
 This will show a table with the running instances and a few details
 about them.  Take note of the *IP address* entry; this is the address
 that will be used to connect.
 
-{{< figure src="/images/13599117.png" width="1064" >}}
+<img src="/images/13599117.png" width="1064">
 
 In this example, the private key file is assumed to be
 named `anvil_key.ppk` and saved on the desktop.  In PuTTY window, click
 the '+' icon next to *SSH* under *Connection* to expand the menu.
 
-{{< figure src="/images/13599229.png" width="450" >}}
+<img src="/images/AnvilLinux-Win10.png" width="450">
 
 Next, click the *Auth* menu item.
 
-{{< figure src="/images/13599231.png" width="450" >}}
+<img src="/images/AnvilLinux-Win10Auth.png" width="450">
+
+!!! note
+    Since PuTTY version 0.78, the *Private key file for authentication* field has been moved under **Auth -> Credentials**, so please select this to upload the key when using PuTTY version 0.78 and above.
+
 
 Click the *Browse* button and the select the `anvil_key.ppk `file.
 
-{{< figure src="/images/13599236.png" width="450" >}}
+<img src="/images/AnvilLinux-Win10Key.png" width="450">
 
 With the private key selected, click the *Session* menu option at the
 top to return to the original PuTTY window.
 
-{{< figure src="/images/13599239.png" width="450" >}}
+<img src="/images/AnvilLinux-Win10Session.png" width="450">
 
 Fill in the *Host Name (or IP address)* field with the IP address of you
 instance.  Choose a name to save the settings for your instance with and
 enter it in the *Saved Sessions* field.
 
-{{< figure src="/images/13599242.png" width="450" >}}
+<img src="/images/AnvilLinux-Win10SessionSaved.png" width="450">
 
 Click the *Save* button to save everything.
 
-{{< figure src="/images/13599246.png" width="450" >}}
+<img src="/images/AnvilLinux-Win10SessionSavedButton.png" width="450">
 
 Next, click *Open* to connect to your instance.
 
-{{< figure src="/images/13599248.png" width="450" >}}
+<img src="/images/AnvilLinux-Win10SessionOpen.png" width="450">
 
 Since this is the first time connecting to the instance, a warning box
-will appear.  Click *Yes* to continue and save the instance's key.  This
+will appear.  Click *Accept* to continue and save the instance's key.  This
 warning box will not appear on subsequent connections.
 
-{{< figure src="/images/13599251.png" >}}
+<img src="/images/AnvilLinux-Win10SessionSecurity.png">
 
 You should then see a terminal window prompting for a username.
 
-{{< figure src="/images/13599255.png" >}}
+<img src="/images/AnvilLinux-Win10Terminal.png">
 
 Depending on which Linux OS you're using for your instance, the
 username will be different.  See the 
-[Available Images]({{< relref "available_images" >}})
+[Available Images](../available_images/)
 page for a table with the username corresponding to each OS.  The
 example instance here is CentOS, so the username is `centos.`  Enter
 the appropriate username and hit Enter.  You should then be logged in.
 
-{{< figure src="/images/13599258.png" >}}
+<img src="/images/13599258.png">

content/anvil/connecting_to_linux_instances_using_x2go.md → docs/anvil/connecting_to_linux_instances_using_x2go.md

-+++
-title = "Connecting to Linux Instances using X2Go"
-description = "How to connect to Linux-based instances using X2Go (for images with Xfce)"
-+++
+---
+title: Connecting to Linux Instances using X2Go
+summary: "How to connect to Linux-based instances using X2Go (for images with Xfce)"
+---
 
 ### Install the X2Go Client
 
@@ -18,19 +18,19 @@ description = "How to connect to Linux-based instances using X2Go (for images wi
 ### Start an instance on Anvil with Xfce
 
 Start a new instance with any of the 
-[images that include Xfce]({{< relref "available_images" >}}).
+[images that include Xfce](../available_images/).
 
 Steps:
 
 1.  Under Compute... Instances... click the 'Launch Instance' button
 2.  Choose 'Boot from image', and select your desired image (here
     'CentOS 7.2 Xfce' is used)
-    {{< figure src="/images/16520061.png" width="550" >}}
+    <img src="/images/16520061.png" width="550">
 3.  On the 'Access and Security' tab, ensure the 'default' security
     group is checked. This will allow incoming SSH access.  
-    {{< figure src="/images/16520060.png" height="250" >}}
+    <img src="/images/16520060.png" height="250">
 4.  On the 'Networking' tab, add the 'Cluster Interface' network only
-    {{< figure src="/images/16520059.png" width="550" >}}
+    <img src="/images/16520059.png" width="550">
 5.  Launch the instance
 6.  On the instances page, note the IP Address of your new instance
 
@@ -39,25 +39,31 @@ Steps:
 Create a new session with the following settings:
 
 1.  Host: IP address of your instance
-2.  Login: centos
+2.  Login: Depends on the Linux version (For example: CentOS - `centos`, Alma - `almalinux`, Ubuntu - `ubuntu`, Fedora - `fedora`, etc.)  See the "Username to Connect" column on [this page](../available_images/) for a complete list.  Here `centos` is used.
 3.  RSA key: Configure with the id\_rsa key pair you used to create the
     instance
 4.  Session type: XFCE
 5.  Click 'OK' to save your new session
 
-{{< figure src="/images/16520057.png" width="550" >}}
+<img src="/images/16520057.png" width="550">
+
+We also recommend adjusting the settings as follows for better performance:
+
+1.  Under *Connection*, set "Connection speed" to "WAN" and "Compression Method" to `4k-png`.
+2.  Under *Media*, ensure that both "Enable sound support" and "Client side printing support" are both _unchecked_.
+3.  Shared folders can also impact performance.  Ensure that none are listed under _Shared folders_ by default unless they are needed.
 
 Open the connection:
 
 1.  Anvil instances are on a private network. To reach them with SSH,
     you'll need to connect to the 
-    [Anvil VPN]({{< relref "connecting_to_the_anvil_vpn" >}}).
+    [Anvil VPN](../connecting_to_the_anvil_vpn/).
 2.  Click on the session in X2Go Client to open it
 3.  The first time you connect, you'll be asked to confirm the SSH key
     of the remote server.
-    {{< figure src="/images/16520058.png" width="500" >}}
+    <img src="/images/16520058.png" width="500">
 4.  After a couple seconds, a desktop will open. Click 'Use default
     config' to get a standard Xfce Linux desktop.  
-    {{< figure src="/images/16520055.png" width="345" >}}
+    <img src="/images/16520055.png" width="345">
 5.  You're ready to use your Xfce Linux desktop
-    {{< figure src="/images/16520056.png" width="333" >}}
+    <img src="/images/16520056.png" width="333">

content/anvil/connecting_to_the_anvil_vpn.md → docs/anvil/connecting_to_the_anvil_vpn.md

-+++
-title = "Connecting to the Anvil VPN"
-description = "You must first connection to the Anvil VPN to access your instance."
-+++
+---
+title: Connecting to the Anvil VPN
+summary: "You must first connection to the Anvil VPN to access your instance."
+---
 
 Instances running in Anvil are assigned a private IP address starting
 with "10.71". You can connect to these private IP addresses from any HCC
@@ -14,33 +14,37 @@ connect to the Anvil VPN service.
 
 ### Installing software for your PC
 
-If you've connected to NU's VPN previously, you should already have the
-Cisco AnyConnect client installed.
+!!! note
+    The Cisco AnyConnect client is available at [this link](https://hcc.unl.edu/vpn/).
+
+
+_Please note you will be required to sign in using your HCC credentials in order to download the software._
+
+After signing in, download the package appropriate for your operating system and run the installer.
 
-- UNL/UNO/UNK: https://vpn.nebraska.edu
+!!! warning
+    When installing Cisco AnyConnect, please unselect all install options except the **Core & VPN** one.
+    Not doing this will cause frequent loss of network connectivity when using the Cisco AnyConnect client.
 
-To install the Cisco AnyConnect client, go to https://vpn.nebraska.edu and sign in with your NUID and associated password.
-You will be asked to authenticate with DUO for TrueYou. If you do not have DUO setup for TrueYou UNL ITS has [instructions](https://fireflyhelp.nebraska.edu/fireflyhelp/Duo/TrueYouDuo.html) provided on how to set it up.
-After login, you will be directed to a page where you can download the Cisco AnyConnect client.
 
-Otherwise, we recommend the [OpenConnect VPN client](http://openconnect.github.io/openconnect-gui).
+Alternatively, you may use the freely available [OpenConnect VPN client](http://openconnect.github.io/openconnect-gui).
 
 
 #### Connecting with the Cisco client
 
 Open the "Cisco AnyConnect Secure Mobility Client" and connect to **anvil-vpn.unl.edu**
 
-{{< figure src="/images/13042825.png" >}}
+<img src="/images/13042825.png">
 
 Login with your HCC username and password
 
-{{< figure src="/images/13042826.png" >}}
+<img src="/images/13042826.png">
 
-{{< figure src="/images/13042827.png" >}}
+<img src="/images/13042827.png">
 
 Login with Duo
 
-{{< figure src="/images/13042828.png" >}}
+<img src="/images/13042828.png">
 
 
 | Type...    | To...                                                                                    |

content/anvil/connecting_to_windows_instances.md → docs/anvil/connecting_to_windows_instances.md

-+++
-title = "Connecting to Windows Instances"
-description = "How to connect to Windows-based instances"
-+++
+---
+title: Connecting to Windows Instances
+summary: "How to connect to Windows-based instances"
+---
 
-{{% notice info %}}
+!!! note
     This guide assumes you associated your SSH Key Pair with the instance
-when it was created, and that you are connected to the [Anvil VPN]({{< relref "connecting_to_the_anvil_vpn" >}}).
-{{% /notice %}}
+    when it was created, and that you are connected to the [Anvil VPN](../connecting_to_the_anvil_vpn/).
+
 
 Access to Windows instances is provided via Remote Desktop (RDP).  When
 the Windows instance is created, the password is set randomly using your
 SSH Key Pair.  This password can be retrieved via the Dashboard web
 interface, and then is used to login via Remote Desktop. 
 
-{{% notice info %}}
-Due to the size of the image and other factors, it may take several
-minutes for a Windows instance to complete setup and be accessible. It
-is recommended to wait **15 minutes** after the *Status* field shows
-*Active* before trying to connect.
-{{% /notice %}}
-
 Once your instance is running, login to the Anvil web dashboard
 at https://anvil.unl.edu and click the *Instances* menu option on left-hand side.
 You should see an entry for your instance similar to the following:
 
-{{< figure src="/images/13042887.png" width="900" >}}
+<img src="/images/13042887.png" width="900">
 
 Click the down arrow next to *Create Snapshot* to open the drop-down
 menu and select *Retrieve Password*:
 
-{{< figure src="/images/13042846.png" height="400" >}}
+<img src="/images/13042846.png" height="400">
 
 This will open a new pop-up window where you will need to select
 your **private** SSH key file.  Click the *Choose File* button to open a
 file explorer window.  
 
-{{< figure src="/images/13042857.png" width="600">}}
+!!! warning 
+    Due to the size of the image and other factors, it may take several
+    minutes for a Windows instance to complete setup and be accessible. It
+    is recommended to wait **15-30 minutes** after the *Status* field shows
+    *Active* before trying to connect.
+
+<img src="/images/13042857.png" width="600">
 
 Navigate to your private key file and choose to open the file.  The
 large text box should now have the contents of your private key.  Click
 the *Decrypt Password* button: 
 
-{{< figure src="/images/13042860.png" width="600" >}}
+<img src="/images/13042860.png" width="600">
 
 The randomly generate password should appear in the *Password* field.
 
-{{< figure src="/images/13042862.png" width="600" >}}
+<img src="/images/13042862.png" width="600">
 
 Copy and paste this password into a convenient text editor.
 
@@ -54,38 +53,35 @@ will already have the Windows-provided client program installed. For
 Mac users, there is a free [Microsoft client](https://itunes.apple.com/us/app/microsoft-remote-desktop/id714464092?mt=8")
 in the app store.
 
-{{% notice info %}}
+!!! note
     Older Remote Desktop clients may have problems connecting to Windows 10
     instances due to changes in the security protocols for Remote Desktop.
     Be sure to use an up-to-date client program when connecting to Windows
     10 instances.
-{{% /notice %}}
+
 
 Determine the IP address of your instance by looking at the fourth
 column entry on the *Instances* page:
 
-{{< figure src="/images/13042890.png" width="900" >}}
+<img src="/images/13042890.png" width="900">
 
 Start your Remote Desktop client, enter the IP address in the name (or
 address) field, and click "Connect":
 
-{{< figure src="/images/13042879.png" >}}
+<img src="/images/Anvil-win10RDPClient.png">
 
-When prompted, enter **cloud-user** for the username if connecting to a
-Windows 7 instance; **.\\cloud-user** if connecting to a Windows 10
+When prompted, enter **.\\cloud-user** for the username when connecting to a Windows 10
 instance, and the previously recovered password.
 
-{{% notice info %}}
-For Windows 7, the username used to connect is always `cloud-user`
-
+!!! note
     For Windows 10, the username used to connect is always `.\cloud-user`
-{{% /notice %}}
+
 
 You may see a warning box about the certificate of the remote computer.
 To avoid this warning in the future, check the box that says "Don't ask
 me again for connections to this computer".
 
-{{< figure src="/images/13042885.png" height="400" >}}
+<img src="/images/Anvil-win10RDPCert.png" height="400">
 
 Click "Yes" to continue connecting.  The Remote Desktop session should
 then start and you will be connected to your instance.