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# System prepended metadata

title: HPC User manual port - notes

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# HPC User manual port - notes

[Port](https://users.ugent.be/~kehoste/vsc_user_docs_mkdocs_inuits/build/HPC)
[Port Readme](https://users.ugent.be/~kehoste/vsc_user_docs_mkdocs_inuits/README.md)

Am I correct to assume that anything that's not in the table of contents on the left, is not to be reviewed? There's many things available in the search function.

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You seem locked to 1 site & OS, with options to change between HPC and Linux.

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Did something happen to chapter numbers? I thought we needed those because we can't link to sections - mostly because of the OS restriction. It's already possible to link to a specific pdf.
Idea: Is it going to be possible to link to a section (without OS being in the link), where a user can then click their OS and still get to the section I linked?

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Here: https://users.ugent.be/~kehoste/vsc_user_docs_mkdocs_inuits/build/HPC/Gent/MacOS/intro-HPC/ch_introduction/#what-is-the-ugent-hpc
> The UGent-HPC relies on parallel-processing technology to offer **University of Gent**researchers an extremely fast solution for all their data processing needs.

Wrong rendering (including lack of a space)
Original:
> The UGent-HPC relies on parallel-processing technology to offer **UGent** researchers an extremely fast solution for all their data processing needs.

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I'm a fan of the tips when hovering certain words, but seeing HPC being underlined each time is a bit jarring

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off-topic, but this section is really weirdly written:
> The UGent-HPC currently consists of:
>
> a set of different compute clusters. For an up to date list of all clusters and their hardware, see https://vscdocumentation.readthedocs.io/en/latest/gent/tier2_hardware.html.
>
> **Job management** and **job scheduling** are performed by Slurm with a Torque frontend. We advise users to adhere to Torque commands mentioned in this document.

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These are 3 terms that are specialised enough to explain, but only 1 has the hover tip?
> ![](https://i.imgur.com/66bdP2X.png)

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Under "Sequential programs":
> It does not become faster by just throwing **in** more cores at it
Original:
> It does not become faster by just throwing more cores at it

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The recurring "UGent-HPC" becomes jarring, example:
> Additional software can be installed "on demand". Please contact the UGent-HPC staff to see whether the UGent-HPC can handle your specific requirements.

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Not a problem with this port, but some parts are outdated
> All nodes in the UGent-HPC cluster run under CentOS Linux release 7.8.2003 (Core), which is a specific version of RedHat Enterprise Linux. This means that all programs (executables) should be compiled for CentOS Linux release 7.8.2003 (Core).

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Nitpicking, but this list should really be i, ii, iii instead of a, b, c. The latter doesn't really imply a sequence to me
> ![](https://i.imgur.com/qL3kviO.png)

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[What is the next step?](https://users.ugent.be/~kehoste/vsc_user_docs_mkdocs_inuits/build/HPC/Gent/MacOS/intro-HPC/ch_introduction/#what-is-the-next-step)
This comes from "chapters **5** to **13**" but doesn't really work like this for me
> explore chapters [Running interactive jobs]() to [Fine-tuning Job Specifications]() which will help you [...]

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What are the "#" for? They put the URL with relevant section in the URL bar but don't copy to clipboard, maybe that might be more useful?

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[Getting ready to request an account](https://users.ugent.be/~kehoste/vsc_user_docs_mkdocs_inuits/build/HPC/Gent/MacOS/intro-HPC/ch_account/#getting-ready-to-request-an-account)
University Association (GUHA) <-> AUGent

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Pretty weird usage of UGent-HPC when explaining how public-key auth works - this is not specific to supercomputers, let alone the one from UGent.
> the public key is stored on the UGent-HPC.

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Problem in original manual (MacOS), chapter 2.1.2
> OpenSSH is a FREE implementation of the SSH connectivity protocol. **MacOS** comes with its own implementation of OpenSSH, so **you don't need to install any third-party software** to use it. Just open a terminal window and jump in!
> 
> On all popular **Linux** distributions, the OpenSSH software is readily available, and **most often installed by default**. You can check whether the OpenSSH software is installed by opening a terminal and typing: [...]

No version checking should be necessary on MacOS

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Bold text in the code block would be nice
Original:
> ![](https://i.imgur.com/zU5euo9.png)

Port:
> ![](https://i.imgur.com/9ipZFis.png)

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Off topic:
> Without your key pair, you won't be able to apply for a personal VSC account.
What about users who only expect to be using the web portal and its shell?

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Quotes are wrong
Original:
> ![](https://i.imgur.com/HJ5hyw4.png)

Port:
> ![](https://i.imgur.com/ShDKBfS.png)

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Different newlines?
Original:
> ![](https://i.imgur.com/PSohLlB.png)

Port:
> ![](https://i.imgur.com/ANRm41y.png)

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[Using an ssh agent](https://users.ugent.be/~kehoste/vsc_user_docs_mkdocs_inuits/build/HPC/Gent/Windows/intro-HPC/ch_account/#using-an-ssh-agent-optional)

Original
> The SSH agent will know which SSH key
should be used and you do not have to type the SSH passwords each time, this task is done by
> **Pageant** agent automatically.

Port
> The SSH agent will know which SSH key should be used and you do not have to type the SSH passwords each time, this task is done by agent automatically.

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[Applying for the account](https://users.ugent.be/~kehoste/vsc_user_docs_mkdocs_inuits/build/HPC/Gent/Windows/intro-HPC/ch_account/#applying-for-the-account)
![](https://i.imgur.com/9sfNKuz.png)

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[connection restrictions](https://users.ugent.be/~kehoste/vsc_user_docs_mkdocs_inuits/build/HPC/Gent/MacOS/intro-HPC/ch_connecting/#connection-restrictions)
> Use an VPN connection to connect to **University of Gent the network** (recommended). See https://helpdesk.ugent.be/vpn/en/ for more information.
this is not right

Original:
> Use an VPN connection to connect to the UGent network (recommended) [...]

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[connection restrictions](https://users.ugent.be/~kehoste/vsc_user_docs_mkdocs_inuits/build/HPC/Gent/MacOS/intro-HPC/ch_connecting/#connection-restrictions)
this should be a mailto link
> ![](https://i.imgur.com/QZWZ2jz.png)

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## Breaking the website with the search function:
Let's go to [MacOS - introduction to hpc](https://users.ugent.be/~kehoste/vsc_user_docs_mkdocs_inuits/build/HPC/Gent/MacOS/intro-HPC/ch_introduction/)
and search for "MacOS"
![](https://i.imgur.com/fXJX6mN.png)
Click the result
We're now at the landing page:
![](https://i.imgur.com/67Ubjro.png)
But on this URL: [https://users.ugent.be/~kehoste/vsc_user_docs_mkdocs_inuits/build/HPC/Gent/**MacOS**/index_os/?h=macos](https://users.ugent.be/~kehoste/vsc_user_docs_mkdocs_inuits/build/HPC/Gent/**MacOS**/index_os/?h=macos)

Let's click Windows:
![](https://i.imgur.com/Ls2npLQ.png)
URL behind the 404: [https://users.ugent.be/~kehoste/vsc_user_docs_mkdocs_inuits/build/HPC/Gent/**MacOS**/index_os/**Windows**/intro-HPC/ch_introduction.md](https://users.ugent.be/~kehoste/vsc_user_docs_mkdocs_inuits/build/HPC/Gent/**MacOS**/index_os/**Windows**/intro-HPC/ch_introduction.md)

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Operating system is 2 words

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[first time connection](https://users.ugent.be/~kehoste/vsc_user_docs_mkdocs_inuits/build/HPC/Gent/Linux/intro-HPC/ch_connecting/#first-time-connection-to-the-hpc-infrastructure)

> Open up a terminal and enter the following command to connect to the UGent-HPC.


```
$ ssh vsc20167@login.hpc.ugent.be
```
> Here, user vsc20167 wants to make a connection to the "**Leibniz**" cluster at University of Gent via the login node "login.hpc.ugent.be", so replace vsc20167 with your own VSC id in the above command.

UAntwerpen has invaded the document
Original says "hpcugent" cluster, which isn't as wrong but not much more informative

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Many times, the original doc has "see section [x]()"
The port should have "see [Explaning x]()" and not "see section [Explaining x]()"
example:
> Please check *section* [Warning message when first connecting to new host-first-connecting-to-new-host)]() on how to do this.

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[first time connection](https://users.ugent.be/~kehoste/vsc_user_docs_mkdocs_inuits/build/HPC/Gent/Linux/intro-HPC/ch_connecting/#first-time-connection-to-the-hpc-infrastructure)
> replace **vsc20167** with your own VSC id
> 
Im assuming this is UAntwerpen as well, original doc says vsc40000

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[first time connection](https://users.ugent.be/~kehoste/vsc_user_docs_mkdocs_inuits/build/HPC/Gent/Linux/intro-HPC/ch_connecting/#first-time-connection-to-the-hpc-infrastructure)
> You can now explore the content of this directory with the "ls --l" (**l**ists **l**ong) and the "cd" (change **irectory**) commands:

Notice the missing **d**

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[first time connection](https://users.ugent.be/~kehoste/vsc_user_docs_mkdocs_inuits/build/HPC/Gent/Linux/intro-HPC/ch_connecting/#first-time-connection-to-the-hpc-infrastructure)
> The first action is to copy the contents of the UGent-HPC examples directory to your home directory, so that you have your own personal copy and that you can start using the examples. The "-r" option of the copy command will also copy the contents of the sub-directories "recursively".
```
$ cp --r /apps/gent/tutorials/Intro-HPC/examples ~/
```

This says **`--r`** instead of `-r`

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https://users.ugent.be/~kehoste/vsc_user_docs_mkdocs_inuits/build/HPC/Gent/Linux/intro-HPC/ch_connecting/#connect
This doesn't render very clearly
![](https://i.imgur.com/kXRsPvy.png)

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(Windows only)
https://users.ugent.be/~kehoste/vsc_user_docs_mkdocs_inuits/build/HPC/Gent/Windows/intro-HPC/ch_connecting/#open-a-terminal
6. Now go back to **\\**, and fill in **"Leibniz"** in the Saved Sessions field and press Save to store the session information.

"\\" should be "\<Session\>"
"Leibniz" should be "hpcugent"

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(Windows only)
https://users.ugent.be/~kehoste/vsc_user_docs_mkdocs_inuits/build/HPC/Gent/Windows/intro-HPC/ch_connecting/#open-a-terminal
output of hostname is completely different (so is user but that doesn't matter as much I guess)
> ![](https://i.imgur.com/GRZr56E.png)
![](https://i.imgur.com/CWeU6Fv.png)

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(Windows only)
https://users.ugent.be/~kehoste/vsc_user_docs_mkdocs_inuits/build/HPC/Gent/Windows/intro-HPC/ch_connecting/#open-a-terminal
![](https://i.imgur.com/Um3gVtn.png)
Leibniz spilling again

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Chapter 3.3.3 (cyberduck) missing from mac guide and instead is visible in the Linux guide

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https://users.ugent.be/~kehoste/vsc_user_docs_mkdocs_inuits/build/HPC/Gent/Windows/intro-HPC/ch_connecting/#winscp
the windows manual contains host keys to verrify the connection, but they're old since rhel8 migration

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https://users.ugent.be/~kehoste/vsc_user_docs_mkdocs_inuits/build/HPC/Gent/Windows/intro-HPC/ch_connecting/#winscp
image missing
> ![](https://i.imgur.com/hZngp9f.png)

vs

> ![](https://i.imgur.com/SqjYVbW.png)

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searching for "winscp" in linux guide doesn't show any results. is this intended/wanted?





