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60 changes: 18 additions & 42 deletions docs/getting_started/faq.md
Original file line number Diff line number Diff line change
Expand Up @@ -46,10 +46,18 @@ Duo offers a variety of methods to log into your account. Depending on what you
2. Enter your identikey password when prompted.
3. Wait for a push to your phone.

![](./faq_images/duo_app2.png) ![](./faq_images/duo_app1.png)
`````{image} ./faq_images/duo_app2.png
:alt: The DUO app's home screen showing a pending login request for a CU Boulder managed DUO account.
:align: center
`````

`````{image} ./faq_images/duo_app1.png
:alt: A Duo Security login request showing the username, location and time details, and options to approve or deny the request.
:align: center
`````

```{note}
Duo push is tied to your device so [you will need to add or remove your device if you get a new phone.](#as-a-cu-boulder-user-how-can-i-manage-my-duo-devices)
Duo push is tied to your device so [you will need to add or remove your device if you get a new phone.](#as-a-cu-boulder-user-how-do-i-manage-my-duo-account)

There is also an option to generate a temporary passcode from within the Duo app. This passcode can be used to log into <https://duo.colorado.edu>.
```
Expand Down Expand Up @@ -93,53 +101,21 @@ This documentation is for customers who have [registered a Yubikey with CU Bould

::::::

### I have a new phone. As a CU Boulder user, how do I move my Duo onto it?
::::{dropdown} Show
:icon: note

You can add a new device to your duo account by visiting <a href="https://duo.colorado.edu">https://duo.colorado.edu</a>.
After a CU authorization page you will be directed to a Duo authentication page. **Ignore the Duo Push prompt and instead click "Add a new device":**

![](faq_images/duo_new_device1.png)

Duo will then try to authenticate your account by push notification to verify your identity. Cancel this push notification...

![](faq_images/duo_new_device2.png)

...and click on "Enter a Passcode", or "Call Me".
- If you select "Call Me" the simply receive the call and press 1.
- If you select "Enter a Passcode" then click "Text me new codes" and you will be sent a list of one time passwords. Type in any one of the codes and you will be authenticated.

Once you have verified your identity, follow the instructions provided by Duo to add your device.

If you cannot authenticate your account (e.g. do not have your old device), we suggest reviewing the [Duo FAQ page](https://oit.colorado.edu/services/identity-access-management/multi-factor-remote-access/faq) or contacting <oithelp@colorado.edu>.

::::

### As a CU Boulder user, how can I manage my Duo devices?
### As a CU Boulder user, how do I manage my DUO account?
::::{dropdown} Show
:icon: note

Users can manage their own Duo devices by visiting <https://duo.colorado.edu>. This enables users to add or remove activated devices at their discretion.

After a CU authorization page, you will be directed to a Duo authentication page. Do not respond to the Push notification and instead click the "Settings" button:
**Not sure how to setup your DUO account?**

![](./faq_images/duo-management1edit.png)
Then we recommend checking OIT's [Guide for DUO MFA](https://oit.colorado.edu/services/identity-access-management/duo-multi-factor-authentication).

This will bring up a menu that provides several options on device management and general help.
**Need to add a new device or manage existing DUO devices?**

Clicking "Add a new device" will allow you to add a new smart phone, tablet, or land-line. Simply select the option you wish to add and follow the steps provided by Duo to complete setting up your new device.
Then we recommend checking OIT's [Guide for Managing DUO Devices](https://oit.colorado.edu/tutorial/duo-multi-factor-authentication-manage-devices)

Selecting "My Settings & Devices" provides a more detailed list of all devices you have registered. From here you can also add a new device, set your default device, and change your default authentication method when you attempt to log in.
::::

### None of the FAQs for Duo resolved my issue, how do I proceed as a CU Boulder user?
::::{dropdown} Show
:icon: note
**Running into issues with using DUO MFA?**

If none of the above resolved the issues you were experiencing, then your Duo account may have expired. The university purges Duo accounts after six months of non-use. You can
re-enroll by visiting <https://duo.colorado.edu>. If that did not resolve your issue, then we suggest contacting the University helpdesk at <oithelp@colorado.edu> or calling
303-735-4357.
Then we recommend checking OIT's [DUO Troubleshooting Guide](https://oit.colorado.edu/services/identity-access-management/multi-factor-remote-access/faq)
::::

## Microsoft Multi-Factor Authentication
Expand Down Expand Up @@ -294,7 +270,7 @@ There are a couple ways you can check your FairShare priority:
```
The `sshare` command will print out a table of information regarding your usage and priority on all allocations. The `-U` flag will specify the current user and the `-l` flag will print out more details in the table. The field we are looking for is the _LevelFS_. The LevelFS holds a number from 0 to infinity that describes the fair share of an association in relation to its other siblings in an account. Over-serviced accounts will have a LevelFS between 0 and 1. Under-serviced accounts will have a LevelFS greater than 1. Accounts that haven't run any jobs will have a LevelFS of infinity (inf).

For more information on fair share the `sshare` command, [take a look at Slurm's documentation on fair share](https://slurm.schedmd.com/fair_tree.html) Or [check out the Slurm reference page on sshare](https://slurm.schedmd.com/sshare.html)
For more information on fair share the `sshare` command, [take a look at Slurm's documentation on fair share](https://slurm.schedmd.com/fair_tree.html) or [check out the Slurm reference page on sshare](https://slurm.schedmd.com/sshare.html)
::::

### Why is my job pending with reason `ReqNodeNotAvail`?
Expand Down
5 changes: 4 additions & 1 deletion docs/open_ondemand/files_app.md
Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,7 @@ The **Files** application allows users to easily make modifications to directori
```{eval-rst}
.. figure:: ./OnDemand/files_app_main_drop_down.png
:align: center
:alt: A screenshot of Open OnDemand's file browser with the "Files" dropdown expanded to list a user's home directory, scratch directory, projects directory, and PetaLibrary. Instructions for navigating the file browser are provided under the "Files application" header.
```

```{important}
Expand All @@ -24,11 +25,13 @@ From the picture provided above, one can see that there are several convenient f
```{eval-rst}
.. figure:: ./OnDemand/files_app_copy_move.png
:align: center
:alt: A closeup screenshot of the file browser's Copy or Move window. Instructions for using the Copy or Move window are provided under the "Files application features" header.
```
- Renaming, downloading, and deleting files or directories can be done from the drop-down menu next to the data. Additionally, one can view and edit files using this drop-down menu. The menu can be found by selecting the three vertical dots next to the data (pictured below).
- `Actions Dropdown` - Renaming, downloading, and deleting files or directories can be done from the drop-down menu next to the data. Additionally, one can view and edit files using this drop-down menu. The menu can be found by selecting the three vertical dots next to the data (pictured below).
```{eval-rst}
.. figure:: ./OnDemand/files_app_view_edit.png
:align: center
:alt: A screenshot of the actions dropdown which lists the options for potential file modifications as View, Edit, Rename, Download, and Delete.
```

```{note}
Expand Down
38 changes: 38 additions & 0 deletions docs/open_ondemand/jobs_app.md
Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,7 @@
The **Jobs** application within Open OnDemand is the perfect tool for individuals who would prefer to use a graphical user interface (GUI) to submit and monitor jobs. Users have the ability to interact with both the [Alpine](../clusters/alpine/index.md) and [Blanca](../clusters/blanca/blanca.md) clusters with a few simple clicks. To access either of these tools, select the **Jobs** tab (pictured below). This provides the user with two options **Active Jobs** and **Job Composer**. Details for both of these options are provided in the subsections that follow.
```{eval-rst}
.. figure:: ./OnDemand/jobs_tab.png
:alt: A screenshot of Open OnDemand's menu bar, showing the dropdown menu for "Jobs" which lists options for "Active Jobs" and "Job Composer"
:align: center
```

Expand All @@ -11,6 +12,7 @@ The **Jobs** application within Open OnDemand is the perfect tool for individual
The **Active Jobs** tool allows users to view any of their active jobs (or all jobs) for a specific cluster (or all clusters). A user can view jobs running on [Alpine](../clusters/alpine/index.md), [Blanca](../clusters/blanca/blanca.md), or Core (the cluster that [Core Desktop](./core_desktop.md) and the [MATLAB GUI](./matlab.md) run on) clusters. Additionally, users can cancel their jobs using this tool. To view currently running jobs, first select the **Active Jobs** tool, this will bring you to the interface pictured below. On the right-hand side, you will see a drop-down button that allows you to view all jobs on the specified cluster (determined by the furthest right button) or only your jobs. To cancel a running job, navigate to the job you would like to cancel and select the red delete button.
```{eval-rst}
.. figure:: ./OnDemand/active_jobs_interface.png
:alt: A screenshot showing Open OnDemands Active Jobs dashboard which lists a set of example active jobs. The screenshot highlights the ability to cancel jobs and change the cluster, both of which are explained under the "Active Jobs" heading.
:align: center
```

Expand All @@ -19,9 +21,45 @@ The **Active Jobs** tool allows users to view any of their active jobs (or all j
Although interactive jobs can be extremely helpful, it is often the case that a user would rather submit their job to a cluster where it can run whenever the resources are available. This is accomplished through [Batch Jobs and Job Scripting](../running-jobs/batch-jobs.md). To provide a simple interface for creating batch jobs and jobs scripting, we include the **Job Composer** tool. This tool allows users to modify and create job scripts, schedule jobs, and manage these jobs all in one central location. To create a job, navigate to the **Job Composer** tool and select **New Job**. When first getting started, it is easiest to select **From Default Template**, which will construct a template job with a default name and submit script (job script). Once a new job has been selected, a user can modify the job to their liking by navigating the provided interface. Below we provide a graphic that highlights some of the key features users may be interested in.
```{eval-rst}
.. figure:: ./OnDemand/job_composer_nav.png
:alt: A screen shot of the Open OnDemand Job Composer dashboard, which includes annotated notes for accessing the user interfaces different buttons and an example job script. Descriptions of each button and the screenshot's example code can be found under the "Job Composer Interface Description" heading.
:align: center
```

### Job Composer Interface Description
The Job Composer's interface includes the following key buttons for interacting with job batch scripts:

* Job Options : Click to modify a job's name, account, or cluster
* Submit : Click to submit the selected batch job(s)
* Stop : Click to cancel the selected batch job(s)
* Delete : Click to delete batch job script and its containing directory

The Job Detail's pane (on the right side of the display) will display the job's settings and basic information. An example job's information is provided below.

```
Job Name:
My First Job
Submit to:
Alpine
Account:
Not specified
Script location:
/projects/breyes@xsede.org/ondemand/projects/default/1
Script name:
main_job.sh
Folder Contents:
main_job.sh
```
The Submit Script pane, located beneath Job Details, includes the batch job's script. A starter scripted is provided and can be edited by clicking the "Open Editor" button.
```
#!/bin/bash
#SBATCH --time=00:01:00
#SBATCH --partition=amilan
#SBATCH --qos=normal
#SBATCH --output=sample-%j.out
echo "Hello World"
```


```{important}
Be sure to select the appropriate cluster when creating a job. Additionally, caution should be taken when selecting the delete button. The delete button will remove the entire directory created for the job. In the example provided above, this means that `/projects/breyes@xsede.org/ondemand/projects/default/1` would be completely deleted.
```
Expand Down
1 change: 1 addition & 0 deletions docs/open_ondemand/terminal_app.md
Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,7 @@ Individuals who are comfortable with the Linux command line may be interested in

```{eval-rst}
.. figure:: ./OnDemand/cluster_terminal_app.png
:alt: A screenshot that shows on the left the "Alpine Shell Access" option selected from the Cluster's dropdown menu in Open OnDemand. On the right is a screenshot of an active terminal session, where the terminal commands "module list" and "ls" have been entered.
:align: center
```

Expand Down
12 changes: 10 additions & 2 deletions docs/open_ondemand/vs_code-server.md
Original file line number Diff line number Diff line change
Expand Up @@ -4,17 +4,19 @@

```{eval-rst}
.. figure:: ./OnDemand/vs_code_server_gui.png
:alt: A screenshot of VS Code's GUI interface, showing a Hello World python program in the code editor. At the bottom of the screen is an active terminal showing the output of the program, a message of "Hello World!".
:align: center
```

## Launching a VS Code-Server

1. Navigate to either the __Interactive Apps__ or __My Interactive Sessions__ tab and select **VS Code-Server**.
1. In Open OnDemand, Navigate to either the __Interactive Apps__ or __My Interactive Sessions__ tab and select **VS Code-Server**.

2. Select the VS Code-Server version you would like to launch the application with.

```{eval-rst}
.. figure:: ./OnDemand/vs_code_server_config.png
:alt: A screenshot for Open OnDemand's VS Code configuration settings that shows the "Code-Server version" set to 4.16.1 via a dropdown menu.
:align: center
```

Expand All @@ -24,6 +26,7 @@

```{eval-rst}
.. figure:: ./OnDemand/vs_code_server_launch.png
:alt: A screenshot of Open OnDemand's interactive application launcher which is configured for the VS Code-Server application. The launcher shows information on the host, creation date, time remaining for the interactive app, the Session ID, and includes buttons labeled "Connect to VS Code" and "Delete".
:align: center
:scale: 50%
```
Expand All @@ -45,7 +48,12 @@ When attempting to install an extension, we suggest the following methods (liste
2. Use the provided search bar to search for the application you want.
3. Select the application and then click the `Install` button.

![](OnDemand/vs_code_marketplace_install.png)
```{eval-rst}
.. figure:: ./OnDemand/vs_code_marketplace_install.png
:alt: A screenshot of VS Code's Extension Marketplace showing an active search "Jupyter" and a listing of three different Jupyter extensions.
:align: center
:scale: 50%
```

- Install the application by dragging the downloaded file into the **extensions column** (for visual representation, please see above video).
1. Navigate to the [VS Code Marketplace](https://marketplace.visualstudio.com/vscode) in your browser.
Expand Down
6 changes: 2 additions & 4 deletions docs/running-jobs/error-status-codes.md
Original file line number Diff line number Diff line change
Expand Up @@ -25,8 +25,7 @@ may encounter when using squeue to check on your jobs.
| STOPPED | `ST` | A running job has been stopped with its cores retained. |

```{seealso}
A full list of these Job State codes can be found in [Slurm’s
documentation.](https://slurm.schedmd.com/squeue.html#lbAG)
A full list of these Job State codes can be found in [Slurm’s Job State Codes](https://slurm.schedmd.com/squeue.html#lbAG) documentation.
```

### Job Reason Codes
Expand All @@ -49,8 +48,7 @@ documentation.](https://slurm.schedmd.com/squeue.html#lbAG)
| `AssociationNodeLimit` | All nodes assigned to your job’s specified association are in use; the job will run eventually. |

```{seealso}
A full list of these Job Reason Codes can be found [in Slurm’s
documentation.](https://slurm.schedmd.com/squeue.html#lbAF)
A full list of these Job Reason Codes can be found in [Slurm’s Job Reason Codes](https://slurm.schedmd.com/squeue.html#lbAF) documentation.
```

## Alpine Job Submission Error Codes
Expand Down
20 changes: 15 additions & 5 deletions docs/running-jobs/interactive-jobs.md
Original file line number Diff line number Diff line change
Expand Up @@ -15,7 +15,7 @@ sinteractive --partition=acpu --time=00:10:00 --ntasks=1 --nodes=1 --qos=cpu-nor
This will run an interactive job to the Slurm queue that will start a terminal session that will run on one core of one node on the `acpu` partition for ten minutes. Once the session has started you can run any application or script you may need from the command line. For example, if you load the Python module using `module load python` and then type `python`, you will open an interactive python shell on a compute node (rather than the login nodes, which is forbidden). When you are finished with your interactive job, you can end the session by typing `exit`. If you do not end your session, the interactive job will run for the full time requested, which will use up part of your allocation.

```{seealso}
Check out this [page](job-resources.md) for a list of Slurm directives that can be used with interactive jobs.
Check out the [Slurm Flags, Partitions, and QoS](job-resources.md) page for a list of Slurm directives that can be used with interactive jobs.
```

## Interactive GUI Applications
Expand All @@ -36,11 +36,17 @@ this. [Download Xming here](http://www.straightrunning.com/XmingNotes/).

Download and install the [PuTTY application](https://www.chiark.greenend.org.uk/~sgtatham/putty/latest.html) here if you have not done so already.

![](./interactive_jobs_images/putty-1.png)
```{image} ./interactive_jobs_images/putty-1.png
:alt: A screenshot of the Putty application, with the SSH tab highlighted. Instructions for using Putty are provided under the "Windows setup" header.
:align: center
```

Expand the SSH tab on the left side of the application and click X11.

![](./interactive_jobs_images/putty-2.png)
```{image} ./interactive_jobs_images/putty-2.png
:alt: A screenshot of the Putty application, with the X11 tab and X11 configurations highlighted. Instructions for configuring X11 in Putty are provided under the "Windows setup" header.
:align: center
```

In the X11 Menu check the "Enable X11 Forwarding" checkbox and type "localhost:0" in the X display location field. Clicking "Open" will open a terminal window where you can login.
````
Expand All @@ -49,7 +55,7 @@ In the X11 Menu check the "Enable X11 Forwarding" checkbox and type "localhost:0
:sync: interactive-windows-command-prompt

```{seealso}
This tutorial assumes that you are already set up with OpenSSH for Windows. Here is a [guide](https://learn.microsoft.com/en-us/windows-server/administration/openssh/openssh_install_firstuse?tabs=gui) for setting up OpenSSH for Windows. Note that OpenSSH Server does not have to be running for you to proceed.
This tutorial assumes that you are already set up with OpenSSH for Windows. Here is a [guide for setting up OpenSSH for Windows](https://learn.microsoft.com/en-us/windows-server/administration/openssh/openssh_install_firstuse?tabs=gui). Note that OpenSSH Server does not have to be running for you to proceed.
```

You can deploy Xming by running the Xlaunch application (or opening the Xlaunch shortcut on your desktop). When prompted to select display settings, select 'Multiple windows' and set the Display number to 0. From there, use the default selections until Xlaunch is finished.
Expand Down Expand Up @@ -116,7 +122,11 @@ matlab
```
This will start MATLAB on the allocated compute node and display the interface on your local machine via X11 forwarding. The MATLAB window should appear shortly after the command is executed. See the example image below for reference.

![](./interactive_jobs_images/matlab_GUI.png)
```{image} ./interactive_jobs_images/matlab_GUI.png
:alt: A screenshot showing a MATLAB GUI being launched for an interactive terminal session. Instructions for launching MATLAB can be found under the "Running GUI Applications" header.
:align: center
```




Expand Down
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