Scholar Userguide Migration

docs/userguides/scholar/accounts.md

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+---
+tags:
+  - Scholar
+authors:
+  - jin456
+  - remender
+resource: scholar
+host: scholar.rcac.purdue.edu
+search:
+  boost: 2
+---
+
+{% set host = "scholar.rcac.purdue.edu" %}
+{% set resource = "scholar" %}
+
+# Accounts on Scholar
+
+## Obtaining an Account
+
+All Purdue faculty may request access to Scholar for use in the classroom. Please use the [Accounts for Classes](https://www.rcac.purdue.edu/account/class/) tool to create accounts for your class. You will need to select the semester and CRN of the class. All students registered in that class will be added once the request is fulfilled. You may add additional instructors or TAs from the same tool.
+
+## Logging In
+
+There are several ways to login to Scholar:
+
+## Thinlinc Web Client
+
+One can login to the Gautschi front-end with a full desktop environment via the [Thinlinc web client](https://desktop.{{host}})
+
+## Gateway / OnDemand
+
+One can login to Gautschi's [Gateway](https://gateway.{{host}}) to manage files in your home/scratch/depot directories and start Slurm jobs for supported OnDemand applications.
+
+## SSH Keys
+{{ ssh_keys_snippet(resource) }}
+
+## SSH X11 Forwarding
+{{ ssh_x11_snippet(resource) }}
+
+## Thinlinc
+{{ thinlinc_snippet(resource) }}

docs/userguides/scholar/compile.md

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+---
+tags:
+  - Scholar
+authors:
+  - jin456
+  - remender
+resource: scholar
+host: scholar.rcac.purdue.edu
+search:
+  boost: 2
+---
+
+# Compiling Source codes on Scholar
+
+- [Compiling GPU Programs](compile/compile_gpu.md)
+- [Compiling Hybrid Programs](compile/compile_hybrid.md)
+- [Compiling Serial Programs](compile/compile_serial.md)
+- [Compiling MPI Programs](compile/compile_mpi.md)
+- [Compiling OpenMP Programs](compile/compile_openmp.md)

docs/userguides/scholar/compile/compile_gpu.md

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+---
+tags:
+  - Scholar
+authors:
+  - jin456
+  - remender
+resource: scholar
+host: scholar.rcac.purdue.edu
+search:
+  boost: 2
+---
+
+{% set resource = "scholar" %}
+
+{{ compile_gpu_snippet(resource) }}
+
+[**Back to the Compiling Programs section**](../compile.md)

docs/userguides/scholar/compile/compile_hybrid.md

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+---
+tags:
+  - Scholar
+authors:
+  - jin456
+  - remender
+resource: scholar
+host: scholar.rcac.purdue.edu
+search:
+  boost: 2
+---
+
+--8<-- "docs/snippets/compile_hybrid.md"
+
+[**Back to the Compiling Programs section**](../compile.md)

docs/userguides/scholar/compile/compile_mpi.md

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+---
+tags:
+  - Scholar
+authors:
+  - jin456
+  - remender
+resource: scholar
+host: scholar.rcac.purdue.edu
+search:
+  boost: 2
+---
+
+--8<-- "docs/snippets/compile_mpi.md"
+
+[**Back to the Compiling Programs section**](../compile.md)

docs/userguides/scholar/compile/compile_openmp.md

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+---
+tags:
+  - Scholar
+authors:
+  - jin456
+  - remender
+resource: scholar
+host: scholar.rcac.purdue.edu
+search:
+  boost: 2
+---
+
+--8<-- "docs/snippets/compile_openmp.md"
+
+[**Back to the Compiling Programs section**](../compile.md)

docs/userguides/scholar/compile/compile_serial.md

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+---
+tags:
+  - Scholar
+authors:
+  - jin456
+  - remender
+resource: scholar
+host: scholar.rcac.purdue.edu
+search:
+  boost: 2
+---
+
+--8<-- "docs/snippets/compile_serial.md"
+
+[**Back to the Compiling Programs section**](../compile.md)

docs/userguides/scholar/faqs.md

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+---
+tags:
+  - Scholar
+authors:
+  - jin456
+  - remender
+resource: scholar
+host: scholar.rcac.purdue.edu
+search:
+  boost: 2
+---
+
+# Frequently Asked Questions on Scholar
+
+Some common questions, errors, and problems are categorized below. You can also use the search box above to search the user guide for any issues you are seeing. 
+
+## About Scholar
+
+### Can you remove me from the Scholar mailing list?
+Your subscription to the Scholar mailing list is tied to your access on Scholar. The only way to remove you from the Scholar mailing list is to remove your Scholar access.
+
+### Do I need to do anything to my firewall to access Scholar?
+No firewall changes are needed to access Scholar. However, to access data through Network Drives (i.e., CIFS, "Z: Drive"), you must be on a Purdue campus network or connected through [VPN](https://it.purdue.edu/services/vpn.php).
+
+### Does Scholar have the same home directory as other clusters?
+The Scholar `home` directory and its contents are exclusive to Scholar cluster front-end hosts and compute nodes. This `home` directory is not available on other RCAC machines but Scholar. There is no automatic copying or synchronization between `home` directories.
+
+At your discretion you can manually copy all or parts of your main research computing home to Scholar using one of the [suggested transfer methods in this section](./storage.md).
+
+## Applications
+
+### How should I launch common GUI applications on Scholar?
+Users who have access to **Scholar** can use **ThinLinc** to launch an interactive jobs. Refer to [this user guide section](./accounts.md/#thinlinc) to learn how to setup Thinlinc for Scholar.
+
+* In the upper left corner, the user can click on **Applications**, then **Cluster Software**, where multiple software options are listed with interactive SLURM jobs.
+
+    <figure style="text-align: center;">
+        ![Thinlinc Application](../../assets/images/userguides/gautschi/thinlinc-application1.png)
+        <figcaption>Thinlinc application menu</figcaption>
+    </figure>
+
+* The **GUI launcher** starts with a window that prompts the user to select the desired version of the software to launch and guides them through the job submission process.
+
+    <figure style="text-align: center;">
+        ![Thinlinc Application2](../../assets/images/userguides/gautschi/thinlinc-application2.png)
+        <figcaption>Thinlinc application selector</figcaption>
+    </figure>
+
+* The **GUI launcher** also makes it easy for users to view available accounts, the maximum wall times for each account, and the available computing resources with multiple help options at the bottom.
+
+    <figure style="text-align: center;">
+        ![Thinlinc Partition](../../assets/images/userguides/gautschi/thinlinc-partition.png)
+        <figcaption>Partition selection</figcaption>
+    </figure>
+
+* After choosing the partition, the user is prompted to provide the computing resource they need for their job to run while adjusting the memory for them automatically.
+
+    <figure style="text-align: center;">
+        ![Thinlinc Resource](../../assets/images/userguides/gautschi/thinlinc-resource_options.png)
+        <figcaption>Resource options for your job</figcaption>
+    </figure>
+
+* After requesting the resources the job will be submitted and waiting for slurm to allocate the computing resources.
+
+    <figure style="text-align: center;">
+        ![Thinlinc Application](../../assets/images/userguides/gautschi/thinlinc-jobsubmitted.png)
+        <figcaption>Interactive job has been submitted</figcaption>
+    </figure>
+
+### Close Firefox / Firefox is already running but not responding
+
+--8<-- "docs/snippets/firefox_lock.md"
+
+### Jupyter:  database is locked / can not load notebook format
+
+--8<-- "docs/snippets/jupyter_lock.md"

docs/userguides/scholar/gateway.md

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+---
+tags:
+  - Scholar
+authors:
+  - jin456
+  - remender
+resource: scholar
+host: scholar.rcac.purdue.edu
+search:
+  boost: 2
+---
+
+# Gateway (Open OnDemand)
+
+Scholar's Gateway is an [open-source HPC portal](http://openondemand.org/) developed by the [Ohio Supercomputing Center](https://www.osc.edu/). Open OnDemand allows one to interact with HPC resources through a web browser and easily manage files, submit jobs, and interact with graphical applications directly in a browser, all with no software to install. Scholar has an instance of OnDemand available that can be accessed via [gateway.{{host}}](https://gateway.{{host}}).
+
+## Logging In
+
+To log into Gateway:
+
+- Navigate to [gateway.{{host}}](https://gateway.{{host}})
+- Log in using your Career account username and Purdue Microsoft Authenticator app.
+- On the splash page you will see a quota usage report. If you are over 90% on any of your quotas a warning will be displayed. This information will update every 10-15 minutes while you are active on Gateway.
+
+## Apps
+
+There are a number of built-in apps in Gateway that can be accessed from the top menu bar. Below are links to documentation on each app.
+
+- [Interactive Apps](gateway/interactive_apps.md)
+- [Files](gateway/files.md)
+- [Jobs](gateway/jobs.md)
+- [Cluster Tools](gateway/cluster_tools.md)

docs/userguides/scholar/gateway/cluster_tools.md

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+---
+tags:
+  - Scholar
+authors:
+  - jin456
+  - remender
+resource: scholar
+host: scholar.rcac.purdue.edu
+search:
+  boost: 2
+---
+
+# Cluster Tools
+
+The Cluster Tools menu contains cluster utilities. At the moment, only a terminal app is provided. Additional apps may be developed and provided in the future.
+
+## Shell Access
+
+Launching the shell app will provide you with a web-based terminal session on the cluster front-end. This is equivalent to using a standalone SSH client to connect to ```{{ host }}``` where you are connected to one several front-ends. The normal acceptable [front-end use policy](https://www.rcac.purdue.edu/policies/frontenduse) applies to access through the web-app. X11 Forwarding is not supported. Use of one of the [interactive apps](interactive_apps.md) is recommended for graphical applications.
+
+[**Return to the Gateway / OnDemand section**](../gateway.md)

docs/userguides/scholar/gateway/files.md

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+---
+tags:
+  - Scholar
+authors:
+  - jin456
+  - remender
+resource: scholar
+host: scholar.rcac.purdue.edu
+search:
+  boost: 2
+---
+
+# Files
+
+The Files app will let you access your files in your [Home Directory](../storage/home_directory.md), [Scratch](../storage/scratch_space.md), and [Data Depot](https://www.rcac.purdue.edu/storage/depot) spaces. The app lets you manage create, manage, and delete files and directories from your web browser. Navigate by double clicking on folders in the file explorer or by using the file tree on the left.
+
+![file manager](../../../assets/images/userguides/files1.png)
+<figcaption>The browser-based file explorer. Navigate by double clicking on folders in the file explorer or by using the file tree on the left.</figcaption>
+
+On the top row, there are buttons to:
+
+- Go To: directly input a directory to navigate to
+- Open in Terminal: launches the Shell app and navigates you to the current directory in the terminal
+- New File: creates a new, empty file
+- New Dir: creates a new, empty directory
+- Upload: upload a file from your computer
+
+Note: File uploads from your browser are limited to 100 GB per file. Be mindful that uploads over a few gigabytes may be unreliable through your browser, especially from off-campus connections. For very large files or off-campus transfers alternative methods such as [Globus](../storage/globus.md) are highly recommended.
+
+The second row of buttons lets you perform typical file management operations. The Edit button will open files in a fully fledged browser based text editor - it features syntax highlighting and vim and Emacs key bindings.
+
+![Text Editor](../../../assets/images/userguides/files2.png)
+<figcaption>The browser-based text editor interface, shown here editing a Bash script, includes syntax highlighting, font-size adjustments, and various key bindings.</figcaption>
+
+[**Return to the Gateway / OnDemand section**](../gateway.md)