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Added more details in access and all new details on obtain #99

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18 changes: 18 additions & 0 deletions docs/services/on-prem/Pantarhei/RunningJobs/computenode.md
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---
sidebar_position: 1
title: "Accessing the Compute Nodes"
description: ""
tags:
- HPC
- On-Premises
- Slurm
- Pantarhei
---

Pantarhei employs the [Slurm Workload Manager](https://slurm.schedmd.com/documentation.html) for the purpose of job scheduling and management. Utilizing Slurm, a user initiates a request for resources and submits a job to a designated queue. Subsequently, the system undertakes the task of extracting jobs from the queues, assigning the requisite compute nodes, and executing the submitted tasks. Although users typically access the Slurm job scheduler by SSH-ing to a Pantarhei login node, it is imperative to emphasize that the recommended practice entails utilizing Slurm to submit work as a job, as opposed to executing computationally intensive tasks directly on a login node. Given that all users share the login nodes, running anything beyond minimal test jobs can adversely affect the collective ability of users to effectively utilize Pantarhei resources.

Pantarhei's framework is tailored to accommodate the moderate-scale computational and data requirements of the majority of CIROH users. Users with allocations possess the capability to submit tasks to a diverse array of queues, each featuring distinct job size and walltime constraints. Dedicated sets of queues are allocated for CPU, GPU, and FPGA nodes, with typically shorter walltime and smaller job size limits translating to expedited turnaround times. Several additional considerations regarding Pantarhei queues merit attention:

1. Pantarhei facilitates shared jobs, whereby multiple tasks can be executed on a single node. This approach enhances job throughput, maximizes overall system utilization, and fosters increased user accessibility to Pantarhei resources.
2. Pantarhei accommodates long-running jobs, with run times extendable up to seven days for tasks utilizing up to 6 full nodes.
3. The maximum permissible job size on Pantarhei is 240 cores. For tasks exceeding this threshold, users are advised to initiate a consulting ticket to engage in further discussion with Pantarhei support personnel.
19 changes: 19 additions & 0 deletions docs/services/on-prem/Pantarhei/RunningJobs/index.md
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---
sidebar_position: 4
title: "Running Jobs"
tags:
- HPC
- On-Premises
- Slurm
- Pantarhei
---

Proficient users acquainted with the Linux command line interface have the option to utilize standard job submission utilities for the purpose of managing and executing tasks on the computational nodes within the Pantarhei system.

------------------------------------------------

### Navigational Resources

import DocCardList from '@theme/DocCardList';

<DocCardList />
190 changes: 87 additions & 103 deletions docs/services/on-prem/Pantarhei/access.md
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---
sidebar_position: 2
sidebar_position: 3
title: "Accessing the System"
description: "Access of On-Premises Cluster Pantarhei"
tags:
Expand All @@ -13,120 +13,104 @@ Pantarhei curretly only supports the Secure Shell (SSH) mechanisms for logging i

### General overview

To connect to Pantarhei using SSH, you must follow three high-level steps:
To connect to Pantarhei using SSH, you must follow two high-level steps:
* [Connect to the University of Alabama (UA) Network](#connect-to-the-network)
* [Connect to the Secure Shell (SSH)](#connect-to-the-ssh)

:::info[Obtain Pantarhei Access]
In the case that access to the Pantarhei system is unavailable to you, please follow the instructions on [Obtaining an Account](/docs/services/on-prem/Pantarhei/obtain).
:::

### Connect to the Network

University of Alabama (UA) requires that you use the Virtual private network (VPN) to connect to the UA campus network in order to connect to the Pantarhei cluster.
University of Alabama (UA) requires users to use the Virtual private network (VPN) to connect to the UA campus network in order to connect to the Pantarhei cluster.

:::tip
To request credentials for VPN Access, please fill this form [CIROH Service Request Form](https://forms.office.com/Pages/DesignPageV2.aspx?subpage=design&token=eaeef2bd5f894e62ab350cafb3b5ea76&id=jnIAKtDwtECk6M5DPz-8p4IIpHdEnmhNgjOa9FjrwGtUME1GV1JXRFVSQzQxM1FFRUc4SDhCOFNONy4u)
:::
:::tip
For more information on setting up a VPN, please visit the [Office of Information Technology (OIT) website](https://oit.ua.edu/services/internet-networking/vpn/)
For more information on setting up a VPN, please visit the [Office of Information Technology (OIT) website](https://oit.ua.edu/services/internet-networking/vpn/).
:::

### Connect to the SSH

#### Mac and Linux:

Once you are connected to the VPN, follow these steps to access Pantarhei:

1. **Open a Terminal:** Find `Terminal` in your local machine and open it.
:::tip
In MacOS, use Spotlight search (**Command** + **Spacebar**) and type `Terminal` to open a new terminal window.
:::

2. **Connect via SSH:** In the terminal,
* Use the SSH command to connect to Pantarhei.
```Shell
ssh <USERNAME>@pantarhei.ua.edu
```
:::note
Replace `<USERNAME>` with your actual Pantarhei username.
:::
* Enter your Pantarhei password


#### Windows:
<table style={{'width':'100%'}}>
<tr>
<th colspan="2">Windows SSH Instruction </th>
</tr>
<tr>
<th>Programs</th>
<th>Instructions</th>
</tr>
<tr>
<td>MobaXterm</td>
<td>Open a local terminal and [follow above steps](#mac-and-linux)&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;</td>
</tr>
<tr>
<td>Git Bash</td>
<td>[Follow above steps](#mac-and-linux)</td>
</tr>
<tr>
<td>Windows 10 PowerShell</td>
<td>[Follow above steps](#mac-and-linux)</td>
</tr>
<tr>
<td>Windows 10 Subsystem for Linux</td>
<td>[Follow above steps](#mac-and-linux)</td>
</tr>
<tr>
<td>PuTTY</td>
<td>[Follow steps below](#putty)</td>
</tr>
</table>

#### PuTTY:
PuTTY, initially developed by Simon Tatham for the Windows operating system, serves as a client application for both SSH (Secure Shell) and telnet protocols. It is characterized by its open-source nature, providing access to its source code, and is maintained through collaborative efforts by a community of volunteers.

import Tabs from '@theme/Tabs';
import TabItem from '@theme/TabItem';

<Tabs groupId="current-os" queryString>
<TabItem value="mac" label="MacOS and Linux" default>
Once you are connected to the VPN, follow these steps to access Pantarhei:

1. **Open a Terminal:** Find `Terminal` in your local machine and open it.

:::tip
In MacOS, use Spotlight search (**Command** + **Spacebar**) and type `Terminal` to open a new terminal window.
:::

2. **Connect via SSH:** In the terminal,
* Use the SSH command to connect to Pantarhei.
```Shell
ssh <USERNAME>@pantarhei.ua.edu
```
:::note
Replace `<USERNAME>` with your actual Pantarhei username.
:::
* Enter your Pantarhei password
</TabItem>
<TabItem value="win" label="Windows">
<table style={{'width':'100%'}}>
<tr>
<th colspan="2">Windows SSH Instruction </th>
</tr>
<tr>
<th>Programs</th>
<th>Instructions</th>
</tr>
<tr>
<td>MobaXterm</td>
<td>Open a local terminal and [follow steps](/docs/services/on-prem/Pantarhei/access?current-os=mac#connect-to-the-ssh)&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;</td>
</tr>
<tr>
<td>Git Bash</td>
<td>[follow steps](/docs/services/on-prem/Pantarhei/access?current-os=mac#connect-to-the-ssh)</td>
</tr>
<tr>
<td>Windows 10 PowerShell</td>
<td>[follow steps](/docs/services/on-prem/Pantarhei/access?current-os=mac#connect-to-the-ssh)</td>
</tr>
<tr>
<td>Windows 10 Subsystem for Linux</td>
<td>[follow steps](/docs/services/on-prem/Pantarhei/access?current-os=mac#connect-to-the-ssh)</td>
</tr>
<tr>
<td>PuTTY</td>
<td>
[Follow steps below](/docs/services/on-prem/Pantarhei/access?current-os=win#putty)
</td>
</tr>
</table>

------------------------------------------------

#### PuTTY

PuTTY, initially developed by Simon Tatham for the Windows operating system, serves as a client application for both SSH (Secure Shell) and telnet protocols. It is characterized by its open-source nature, providing access to its source code, and is maintained through collaborative efforts by a community of volunteers.
:::tip
For more information on PuTTY, please visit the [PuTTY website](https://www.putty.org/)
:::

1. **Download PuTTY:** To download PuTTY, click [download page](https://www.chiark.greenend.org.uk/~sgtatham/putty/latest.html)
2. **Open PuTTY:** Open downloaded file `putty.exe`
<p align="center">
<img src="/img/putty/image.png" alt="putty" style={{'width':'50%', 'height':'50%'}}/>
</p>
3. **Host Name:** In the <mark>___Host Name (or IP address)___</mark> field enter the `pantarhei.ua.edu`
4. **Port:** In the <mark>___Port___</mark> field enter the `22`
5. **Open:** Click on the <mark>___Open___</mark> button. This will prompt a new login Secure Shell window.
6. **User Name:** In given new window, enter your Pantarhei <mark>___User Name___</mark>.
<p align="center">
<img src="/img/putty/frame08_1.webp" alt="putty"/>
</p>
7. **Password:** Enter your Pantarhei account <mark>___Password___</mark>.
<p align="center">
<img src="/img/putty/frame09_1.webp" alt="putty"/>
</p>

<!-- 3. **Submit a Job:** Start a job using either a GPU or CPU job file, depending on your requirements. Replace `THE_NAME_OF_THE_JOB_FILE` with your specific job file name.
```
sbatch THE_NAME_OF_THE_JOB_FILE
```

4. **Monitor Your Job:** To get a list of job IDs, use the following command:
```
squeue
```
To check the log file of a specific job, replace `JOBID` with your job's ID.
```
cat jupyter-notebook-JOBID.log
```

5. **Access Jupyter Notebook:** Open a new terminal tab, then copy and paste the SSH command from the top of the log file into the new terminal tab. Enter your password again when prompted.

6. **Open the Jupyter Notebook:** Return to the original terminal tab and locate the HTTP link at the end of the log file. Copy this link and paste it into a web browser to access the Jupyter Notebook interface.

7. **You are ready to go now!** Explore the Jupyter Notebook environment to conduct your research computations.

### Additional Notes:
- Ensure your Pantarhei username and the job file name are correct.
- If you encounter any issues, please contact CIROH's support team for assistance. -->
1. **Download PuTTY:** To download PuTTY, click [download page](https://www.chiark.greenend.org.uk/~sgtatham/putty/latest.html)
2. **Open PuTTY:** Open downloaded file `putty.exe`
<p align="center">
<img src="/img/putty/image.png" alt="putty" style={{'width':'50%', 'height':'50%'}}/>
</p>
3. **Host Name:** In the <mark>___Host Name (or IP address)___</mark> field enter the `pantarhei.ua.edu`
4. **Port:** In the <mark>___Port___</mark> field enter the `22`
5. **Open:** Click on the <mark>___Open___</mark> button. This will prompt a new login Secure Shell window.
6. **User Name:** In given new window, enter your Pantarhei <mark>___User Name___</mark>.
<p align="center">
<img src="/img/putty/frame08_1.webp" alt="putty"/>
</p>
7. **Password:** Enter your Pantarhei account <mark>___Password___</mark>.
<p align="center">
<img src="/img/putty/frame09_1.webp" alt="putty"/>
</p>
</TabItem>
</Tabs>

We hope this guide helps you efficiently utilize the Pantarhei HPC system for your research needs. Happy computing!
10 changes: 2 additions & 8 deletions docs/services/on-prem/Pantarhei/index.md
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Expand Up @@ -17,16 +17,10 @@ Use of this resource is governed by the University of Alabama Acceptable Use Pol
2. [Information Classification Policy](https://ua-public.policystat.com/policy/14809337/latest/)
3. [Information Protection Procedure](https://oit.ua.edu/internaldocs/20210205-UA%20Information%20Protection%20Procedures.pdf)


<!-- Pantarhei cluster has 8 nodes including 1 login node, 6 CPU nodes, 1 GPU node, 1 FPGA node, totally equipped with 296 Intel Xeon Scalable Processors, 2.8 TB memory, 32 TB local storage, 108 TB file system.
- CPU node: 2 Intel Xeon Gold 6148 Processors, 384 GB memory, 4 TB NVMe.
- GPU node: 4 NVIDIA Tesla V100 GPUs, 2 Intel Xeon Gold 6148 Processors, 384 GB memory, 3.2 TB NVMe.
- FPGA node: 1 Intel Arria 10 FPGA, 2 Intel Xeon Gold 6148 6148 Processors, 384 GB memory, 1.6 TB NVMe.
- Interconnect: all nodes are connected to a Mellanox InfiniBand switch with FDR 56 Gb/s networks. -->


------------------------------------------------

### Navigational Resources

import DocCardList from '@theme/DocCardList';

<DocCardList />
43 changes: 43 additions & 0 deletions docs/services/on-prem/Pantarhei/obtain.md
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---
sidebar_position: 2
title: "Obtaining an Account"
description: "Obtain an account on Pantarhei"
tags:
- HPC
- On-Premises
- Account
- Pantarhei
---

Pantarhei cluster is accessible to the research community of the Cooperative Institute for Research to Operations in Hydrology (CIROH).

### General overview

To obtain an account, users will need to follow these step:

1. Submit [On-premises Infrastructure Request Form](/docs/services/access#on-premises) and describe full project information and resouce requirements.

::::::warning
This GitHub issue must be submitted by Principal Investigator (PI) of the project.

:::info[Hint]
In the GitHub issue PI should mention following details:
1. PI's __Full Name__
2. PI's __Affiliated Institute__
3. PI's __Affiliated Email Address__
4. List of students who will need access, also please provide following details of each student
* __Full Name__ of student
* __GitHub User Name__ of student
* __Affiliated Email Address__ of student
:::
::::::
2. Submit On-premise Access Request form in [CIROH Service Request](https://forms.office.com/r/CQucJqqADx).
::::::tip
The administration of the Pantarhei cluster falls under the purview of the CIROH IT Computing group at the University of Alabama (UA). Consequently, individuals lacking UA credentials (*MyBama ID*, *VPN User Name*, and *CWID*) are obliged to complete the __`VPN Access Request`__ form, followed by the __`On-premise Access Request`__ form within [CIROH Service Request](https://forms.office.com/r/CQucJqqADx).

:::warning[Account Creation]
Creation of accounts on the Pantarhei system necessitates submission of individual forms by each respective user.

For instance, a Principal Investigator (PI) submits a GitHub issue pertaining to a project, and three students require access to the Pantarhei system for project-related work, three separate account creation forms must be duly submitted during this process.
:::
::::::
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