minor cleanup

s-sajid-ali · s-sajid-ali · commit 63f58aa4ad43 · 2025-10-15T16:05:43.000-04:00
modified:   docs/hpc/01_getting_started/03_walkthrough_request_hpc_account.mdx
	modified:   docs/hpc/01_getting_started/06_hpc_accounts_external_collaborators.md
	renamed:    docs/hpc/02_connecting_to_hpc/01_connecting_to_hpc.mdx -&gt; docs/hpc/02_connecting_to_hpc/01_connecting_to_hpc.md
	modified:   docs/hpc/03_storage/08_transferring_cloud_storage_data_with_rclone.md
	modified:   docs/hpc/08_ml_ai_hpc/03_run_hf_model.md
	modified:   docs/hpc/09_ood/01_ood_intro.md
	modified:   docs/hpc/09_ood/07_jupyter_with_conda_singularity.mdx
diff --git a/docs/hpc/01_getting_started/03_walkthrough_request_hpc_account.mdx b/docs/hpc/01_getting_started/03_walkthrough_request_hpc_account.mdx
@@ -4,7 +4,7 @@ import TabItem from '@theme/TabItem';
 # How to request an HPC account
 
 :::tip
-Make sure you don't already have an HPC account. You can check this by attempting to log in to the cluster, according to the instructions at [Connecting to the HPC Cluster](../02_connecting_to_hpc/01_connecting_to_hpc.mdx).
+Make sure you don't already have an HPC account. You can check this by attempting to log in to the cluster, according to the instructions at [Connecting to the HPC Cluster](../02_connecting_to_hpc/01_connecting_to_hpc.md).
 :::
 
 Login to the URL given below, using your NetID/password, to create or manage HPC Account Requests:
diff --git a/docs/hpc/01_getting_started/06_hpc_accounts_external_collaborators.md b/docs/hpc/01_getting_started/06_hpc_accounts_external_collaborators.md
@@ -13,7 +13,7 @@ External (non-NYU) collaborators can access, with proper sponsorship, the NYU HP
 :::note
 Once the sponsoring faculty approves the account request, the HPC account is created within one hour.
 :::
--   Once the HPC account is created, the external collaborator can access HPC resources as described in our documentation page [Connecting to the HPC Cluster](../02_connecting_to_hpc/01_connecting_to_hpc.mdx).
+-   Once the HPC account is created, the external collaborator can access HPC resources as described in our documentation page [Connecting to the HPC Cluster](../02_connecting_to_hpc/01_connecting_to_hpc.md).
 
 :::note
 As with all sponsored accounts, HPC accounts for external collaborators are valid for a period of 12 months, at which point a renewal process is required to continue access to the NYU HPC environment.  You can find information about renewing your account on our documentation page [Getting and Renewing an HPC Account](./02_getting_and_renewing_an_account.mdx).
diff --git a/docs/hpc/02_connecting_to_hpc/01_connecting_to_hpc.md b/docs/hpc/02_connecting_to_hpc/01_connecting_to_hpc.md
@@ -4,7 +4,7 @@
 This page gives an overview of connecting to the HPC cluster, for a tutorial on this topic, head to the [this section](../12_tutorial_intro_shell_hpc/02_connecting_to_hpc.mdx)! 
 :::
 
-There are several ways to interact with the Greene HPC cluster. Similar to other Linux clusters, the most common method of connection is via a Command Line Interface (CLI). A CLI is a program that allows you to create and delete files, run programs, and navigate through directories and files via a typed prompt. On Mac, the built-in CLI application is called Terminal. While Windows 11 machines support a Linux Subsystem, which allows for similar functionality, a popular tool used to connect to a Linux server is a free application called [PuTTY][putty link]. 
+There are several ways to interact with the Greene HPC cluster. Similar to other Linux clusters, the most common method of connection is via a Command Line Interface (CLI). A CLI is a program that allows you to create and delete files, run programs, and navigate through directories and files via a typed prompt. On Mac, the built-in CLI application is called Terminal. While Windows 11 machines support a Linux Subsystem, which allows for similar functionality, a popular tool used to connect to a Linux server is a free application called [MoabXterm](https://mobaxterm.mobatek.net/documentation.html) 
 
 :::tip
 If you'd prefer to access the HPC cluster via a web gateway instead, please refer to [the section describing Open OnDemand (OOD)](../09_ood/01_ood_intro.md).
@@ -100,14 +100,14 @@ ssh <Your NetID>@greene.hpc.nyu.edu
 #### Powershell
 You can access the ssh client via Powershell, either by installing [Windows Terminal](https://apps.microsoft.com/detail/9n0dx20hk701?hl=en-US&gl=US) or [Powershell](https://learn.microsoft.com/en-us/powershell/scripting/install/installing-powershell-on-windows) directly. With powershell, you would log into the HPC systems the same way as with a Linux terminal.
 
-### Windows WSL2
+#### Windows WSL2
 
 Alternatively, you can install WSL2, and then install Ubuntu or other Linux distribution (for example, from Microsoft Store). You will have a fully functional Ubuntu with terminal and can connect to cluster using instructions provided above for Linux/Mac users. Instructions on WSL installation can be found here: [https://docs.microsoft.com/en-us/windows/wsl/install-win10][wsl installation link]
 
 With [Windowns Terminal](https://apps.microsoft.com/detail/9n0dx20hk701?hl=en-US&gl=US), you can access both the Linux WSL2 shell and the Windows Powershell from the same application.
  
 :::tip
--   If you are using WSL 2 (Windows subsystem for Linux), you may not be able to access internet when Cisco AnyConnect VPN, installed from exe file, is activated. A potential solution: uninstall Cisco AnyConnect and install AnyConnect using Microsoft Store, and then setup new VPN connection using settings described on [IT webpage][install vpn on windows link].
+-   If you are using WSL 2 (Windows subsystem for Linux 2), you may not be able to access internet when Cisco AnyConnect VPN, installed from exe file, is activated. A potential solution: uninstall Cisco AnyConnect and install AnyConnect using Microsoft Store, and then setup new VPN connection using settings described on [IT webpage][install vpn on windows link].
 :::
 
 ## Additional Tips
diff --git a/docs/hpc/03_storage/08_transferring_cloud_storage_data_with_rclone.md b/docs/hpc/03_storage/08_transferring_cloud_storage_data_with_rclone.md
@@ -29,7 +29,7 @@ There are specific instruction on the [rclone web site](https://rclone.org/drive
 
 ### Step 1: Login to Greene:
 
-Follow [instructions](../02_connecting_to_hpc/01_connecting_to_hpc.mdx) to log into the Greene HPC cluster.
+Follow [instructions](../02_connecting_to_hpc/01_connecting_to_hpc.md) to log into the Greene HPC cluster.
 
 ### Step 2: Load the rclone module
 ```sh
diff --git a/docs/hpc/08_ml_ai_hpc/03_run_hf_model.md b/docs/hpc/08_ml_ai_hpc/03_run_hf_model.md
@@ -5,7 +5,7 @@ Here we provide an example of how one can run a Hugging Face Large-language mode
 ## Prepare environment
 ### Create project directory
 
-After [logging on to a Greene login node](../02_connecting_to_hpc/01_connecting_to_hpc.mdx), make a directory for this project:
+After [logging on to a Greene login node](../02_connecting_to_hpc/01_connecting_to_hpc.md), make a directory for this project:
 ```bash
 [NetID@log-1 ~]$ mkdir -p /scratch/NetID/llm_example
 [NetID@log-1 ~]$ cd /scratch/NetID/llm_example
diff --git a/docs/hpc/09_ood/01_ood_intro.md b/docs/hpc/09_ood/01_ood_intro.md
@@ -63,4 +63,4 @@ Just click on the `Session ID` link and a tab will open with the contents of the
 
 #### From terminal
 
-If your session is no longer visible from within OOD you may still be able to find your logs via the terminal.  Simply [log into Greene](../02_connecting_to_hpc/01_connecting_to_hpc.mdx) and `cd` to `/home/$USER/ondemand/data/sys/dashboard/batch_connect/sys/` and then `cd` into the directory for the app that you're interested in.  You should find the file `output.log` there.
+If your session is no longer visible from within OOD you may still be able to find your logs via the terminal.  Simply [log into Greene](../02_connecting_to_hpc/01_connecting_to_hpc.md) and `cd` to `/home/$USER/ondemand/data/sys/dashboard/batch_connect/sys/` and then `cd` into the directory for the app that you're interested in.  You should find the file `output.log` there.
diff --git a/docs/hpc/09_ood/07_jupyter_with_conda_singularity.mdx b/docs/hpc/09_ood/07_jupyter_with_conda_singularity.mdx
@@ -4,7 +4,7 @@
 This page describes how to use your Singularity with conda environment in OOD GUI at Greene. 
 
 ### Log Into Greene via the Terminal
-The following commands must be run from the terminal. Information on accessing via the terminal can be found at [Connecting to the HPC](../02_connecting_to_hpc/01_connecting_to_hpc.mdx) or you can log into OOD and select the `Clusters` tab at the top of the page and select `Greene Shell Access`.
+The following commands must be run from the terminal. Information on accessing via the terminal can be found at [Connecting to the HPC](../02_connecting_to_hpc/01_connecting_to_hpc.md) or you can log into OOD and select the `Clusters` tab at the top of the page and select `Greene Shell Access`.
 
 ### Preinstallation Warning
 :::warning

Original file line number	Diff line number	Diff line change
@@ -63,4 +63,4 @@ Just click on the `Session ID` link and a tab will open with the contents of the
`63`	`63`
`64`	`64`	`#### From terminal`
`65`	`65`
`66`		-If your session is no longer visible from within OOD you may still be able to find your logs via the terminal. Simply [log into Greene](../02_connecting_to_hpc/01_connecting_to_hpc.mdx) and `cd` to `/home/$USER/ondemand/data/sys/dashboard/batch_connect/sys/` and then `cd` into the directory for the app that you're interested in. You should find the file `output.log` there.
	`66`	+If your session is no longer visible from within OOD you may still be able to find your logs via the terminal. Simply [log into Greene](../02_connecting_to_hpc/01_connecting_to_hpc.md) and `cd` to `/home/$USER/ondemand/data/sys/dashboard/batch_connect/sys/` and then `cd` into the directory for the app that you're interested in. You should find the file `output.log` there.