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Docsify
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76 changes: 39 additions & 37 deletions README.md
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## Gravity Documentation
[上海交通大学天文系Gravity集群文档](https://gravity-doc.github.io)

This is the documentation for the **Gravity Cluster** of [Department of Astronomy](http://astro.sjtu.edu.cn/en/) at [Shanghai Jiao Tong University (SJTU)](https://www.sjtu.edu.cn/).

### Welcome to contribute
This doc is hosted on [Github](https://github.com/gravity-doc/gravity-doc.github.io). Feel free to submit a pull request.

Your name will be honoured in the [contributor list](https://github.com/gravity-doc/gravity-doc.github.io/graphs/contributors) once your contributions are merged.

**中文内容也欢迎!🥳**


### Contact

You can contact us via

- [[email protected]](mailto:[email protected])
- **WeChat group**

if you need

1. create an **account** 🙋‍♂️🙋‍♀️
2. change **password** 🔐
3. **extend time** of your job ⌛
4. other problems ❔

### Acknowledging the Gravity Cluster

We would appreciate it if all publications that include results generated using **Gravity** cluster include a short statement in the Acknowledgment section. For example:

若您在论文中使用了Gravity得到的结果,希望您能够在致谢中提到**Gravity**。例如:

- **本工作的计算使用了上海交通大学天文系Gravity高性能计算集群**
- **This work made use of the Gravity Supercomputer at the Department of Astronomy, Shanghai Jiao Tong University.**

<img src="./docs/images/logo_DOA_large.png" height = "80" div align=right />
## Gravity Documentation

[上海交通大学天文系Gravity集群文档](https://gravity-doc.github.io)

This is the documentation for the **Gravity Cluster** of [Department of Astronomy](http://astro.sjtu.edu.cn/en/) at [Shanghai Jiao Tong University (SJTU)](https://www.sjtu.edu.cn/).

### Welcome to contribute

This doc is hosted on [Github](https://github.com/gravity-doc/gravity-doc.github.io). Feel free to submit a pull request.

Your name will be honoured in the [contributor list](https://github.com/gravity-doc/gravity-doc.github.io/graphs/contributors) once your contributions are merged.

**中文内容也欢迎!🥳**


### Contact

You can contact us via

- [[email protected]](mailto:[email protected])
- **WeChat group**

if you need

1. create an **account** 🙋‍♂️🙋‍♀️
2. change **password** 🔐
3. **extend time** of your job ⌛
4. other problems ❔

### Acknowledging the Gravity Cluster

We would appreciate it if all publications that include results generated using **Gravity** cluster include a short statement in the Acknowledgment section. For example:

若您在论文中使用了Gravity得到的结果,希望您能够在致谢中提到**Gravity**。例如:

- **本工作的计算使用了上海交通大学天文系Gravity高性能计算集群**
- **This work made use of the Gravity Supercomputer at the Department of Astronomy, Shanghai Jiao Tong University.**

![logo_DOA_large.png](./docs/images/logo_DOA_large.png)
39 changes: 16 additions & 23 deletions admin/websample.md
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---
sort: 10086
---

# Samples for web



## 主题和主题使用说明

[Theme](https://rundocs.io)

## examples for 各种框框

```note
### This is a note
Markdown is supported, Text can be **bold**, _italic_, or ~~strikethrough~~. [Links](https://github.com) should be blue with no underlines
`inline code`
> [!NOTE]
> ### This is a note
> Markdown is supported, Text can be **bold**, _italic_, or ~~strikethrough~~. [Links](https://github.com) should be blue with no underlines
> `inline code`
> [`inline code inside link`](#)
>
[`inline code inside link`](#)
```
> [!TIP]
> It's bigger than a bread box.
>
```tip
It's bigger than a bread box.
```
> [!WARNING]
> Strong prose may provoke extreme mental exertion. Reader discretion is strongly advised.
>
```warning
Strong prose may provoke extreme mental exertion. Reader discretion is strongly advised.
```

```danger
Mad scientist at work!
```
> [!ATTENTION]
> Mad scientist at work!
>
## 代码

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69 changes: 69 additions & 0 deletions convert_to_docsify.sh
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#!/bin/bash
################### convert_to_docsify.sh ###################
# This script is used to convert the original markdown files
# to docsify markdown files.
#############################################################
set -e

# Check if the script is running inside a Git repository
if ! git rev-parse --is-inside-work-tree >/dev/null 2>&1; then
echo "This script must be run inside a Git repository!!!"
exit 1
fi

# switch to docsify branch
git checkout docsify
# undo any changes
git checkout .
# pull latest changes
git pull

source_file="docs/index.md"
target_file="docs/README.md"

# Check if source file exists
if [ ! -f "$source_file" ]; then
echo "source file $source_file does not exist"
else
# Rename file
mv "$source_file" "$target_file"
fi

# Function to process markdown files
process_markdown() {
echo "Processing $1"
# Remove part of "--- ... ---"
sed -i '/^---[[:space:]]*$/,/^---[[:space:]]*$/d' "$1"

# Convert HTML image to markdown image
sed -i 's|<img src="\(.*\)/\([^"/]*\)"[^>]*>|![\2](\1/\2)|g' "$1"

# Convert danger, warning, note, and tip blocks
sed -i -E -e '/^```(danger|warning|note|tip)[[:space:]]*$/,/^```[[:space:]]*$/ {
/^```(danger|warning|note|tip)[[:space:]]*$/! {
s/^[>-][[:space:]]*//
s/^[[:digit:]]+\.*//
/^[[:space:]]*$/d
}
s/^```(danger|warning)[[:space:]]*$/!> \*\*Important\*\*⚠️/
s/^```(note|tip)[[:space:]]*$/?> \*\*Tip\*\*💡/
s/```[[:space:]]*$//
t
}' "$1"
}

export -f process_markdown

# Process markdown files using find and process_markdown function
find . -type f -name "*.md" -exec bash -c 'process_markdown "$0"' {} \;

# Build Docker image of docsify
if [ -d "docs" ] && [ "$(id -u)" = "0" ]; then
cd docs
docker build -f Dockerfile -t docsify/demo .
docker restart docsify
else
echo "docs directory does not exist or you are not root"
fi

echo "Done"
6 changes: 1 addition & 5 deletions docs/About.md
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---
sort: 2
title: System Specs
---
# Hardware
<img src="./images/hardware.jpg" width = "300" height = "500" div align=center />
![hardware.jpg](./images/hardware.jpg)

### Login nodes

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16 changes: 6 additions & 10 deletions docs/Advanced/Gitlab.md
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---
sort: 6
title: Gitlab
---

```note
There is a *self-hosted* **Gitlab** instance at **Gravity**: [https://git.gravity.sjtu.edu.cn](https://git.gravity.sjtu.edu.cn)
```
> [!NOTE]
> There is a *self-hosted* **Gitlab** instance at **Gravity**: [https://git.gravity.sjtu.edu.cn](https://git.gravity.sjtu.edu.cn)
>
## Login

[Open Gitlab on browser](https://git.gravity.sjtu.edu.cn/), there are **two ways** to login:

1. Your *Gravity* username and password
<img src="../images/Advanced/gitlab-passwd-login.png" height = "200" div align=center />
![gitlab-passwd-login.png](../images/Advanced/gitlab-passwd-login.png)
2. Use *Authelia* authorization at bottom of login page
<img src="../images/Advanced/gitlab-authelia-login.png" height = "200" div align=center />
<img src="../images/Advanced/gitlab-authelia-confirm.png" height = "200" div align=center />
![gitlab-authelia-login.png](../images/Advanced/gitlab-authelia-login.png)
![gitlab-authelia-confirm.png](../images/Advanced/gitlab-authelia-confirm.png)


## SSH Access
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12 changes: 4 additions & 8 deletions docs/Advanced/Globus.md
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---
sort: 5
title: Globus
---

# Globus
[Globus](https://www.globus.org) is quite popular to transfer large scientific data.
Expand All @@ -27,15 +23,15 @@ Here we provide the routine to install Globus personal version. You can also ch
./globusconnectpersonal -setup
```

<img src="../images/Advanced/globus-setup1.png" width = "600" div align=center />
![globus-setup1.png](../images/Advanced/globus-setup1.png)

A long link will be provided. Copy and open the above link in your browser. After sign in your globus account, an authorization code will be provided.

<img src="../images/Advanced/globus-setup2.png" width = "600" div align=center />
![globus-setup2.png](../images/Advanced/globus-setup2.png)

Input this code in your terminal, type the name for this Endpoint (Gravity2 in the above case) and finish the setup.

<img src="../images/Advanced/globus-setup3.png" width = "600" div align=center />
![globus-setup3.png](../images/Advanced/globus-setup3.png)

5. Run Globus personal without GUI.
```bash
Expand All @@ -44,7 +40,7 @@ Here we provide the routine to install Globus personal version. You can also ch

Check whether the Endpoint is correctly appeared in your Globus Endpoint Collections.

<img src="../images/Advanced/globus-setup4.png" width = "600" div align=center />
![globus-setup4.png](../images/Advanced/globus-setup4.png)

6. Stop Globus personal.
Please close your Globus personal when your transfer task is end, for safety and resources saving reason.
Expand Down
3 changes: 0 additions & 3 deletions docs/Advanced/README.md
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---
sort: 2
---

# Advanced

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41 changes: 18 additions & 23 deletions docs/Advanced/VNC.md
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---
sort: 2
title: VNC
---

```note
Considering security, *Gravity* closes ports except **22, 80, 443**.
Therefore, you need **ssh tunnel** to connect other service.
```

```tip
VNC is a fast tool to connect to a graphical desktop on the server.
You should add **5900** to your port. That is the **real** port. For example:
`vncserver :66`
Then, the real port VNC uses is **`66 + 5900 = 5966`**
When you use *SSH tunnel*, please connect to the real port, otherwise you will fail🤣
```
> [!NOTE]
> Considering security, *Gravity* closes ports except **22, 80, 443**.
> Therefore, you need **ssh tunnel** to connect other service.
>
> [!TIP]
> VNC is a fast tool to connect to a graphical desktop on the server.
> You should add **5900** to your port. That is the **real** port. For example:
> `vncserver :66`
> Then, the real port VNC uses is **`66 + 5900 = 5966`**
> When you use *SSH tunnel*, please connect to the real port, otherwise you will fail🤣
>
## Getting started

Expand All @@ -35,11 +31,10 @@ Take a note of the port number (37 in this case). You will need to connect to th

请记住这里显示的端口号(图中是37)。

```tip
You will be prompted to setup a password the first time you do this. This will be the password you use to connect to vnc. This password is separate from the ssh password.
第一次开启vnc时在输入命令后会先让你设置密码,之后再使用或者开启新的端口都会使用默认密码.
```
> [!TIP]
> You will be prompted to setup a password the first time you do this. This will be the password you use to connect to vnc. This password is separate from the ssh password.
> 第一次开启vnc时在输入命令后会先让你设置密码,之后再使用或者开启新的端口都会使用默认密码.
>
- checking for running servers

Expand Down Expand Up @@ -77,11 +72,11 @@ You will need to use a vnc client to connect to your server. On Linux, you can u

In Remmina, select "new connection". In protocol, select VNC. In the Basic tab, fill in the server address and vncserver port, your username and vnc password.

<img src="../images/Advanced/VNC_1.png" width=400/>
![VNC_1.png](../images/Advanced/VNC_1.png)

For security reasons, you can only connect to vnc through ssh-tunnel. This can be done in the "SSH Tunnel" tab. Select "Enable SSH tunnel", input your username, and select Public key authentication.

<img src="../images/Advanced/VNC_2.png" width=400/>
![VNC_2.png](../images/Advanced/VNC_2.png)

你可以使用喜欢的vnc客户端连到前面建立的vncserver。在客户端中输入服务器地址和vncserver端口号。由于安全原因,还需要选择打开ssh-tunnel选项。

Expand Down
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