Commit 576e1443 authored by Michèle Huijberts's avatar Michèle Huijberts
parents 6d9ee8a0 e8d6f9c1
## Shark4FSW users information page.
On this page information can be found on the general usage of the LUMC central High Performance/Throughput cluster **Shark**.
On this page information can be found about the general usage of the LUMC central High Performance/Throughput cluster **Shark**.
[This page](https://git.lumc.nl/mwjhhuijberts/Shark4FSW) is a good starting point for using the Shark cluster for FSW users. It contains the general information about how to apply for an account on, and to connect to Shark. A general description of the available software can be found here and how to use it. Together with some '*Best Practices*'.
Please remember: *This page is a continuous work in progress.* Comments are welcome.
[This page](https://git.lumc.nl/mwjhhuijberts/Shark4FSW) is a starting point for using the Shark cluster for FSW users. It contains references to the corresponding Wiki and general information about how to apply for an account on, and to connect to Shark. A general description of the available software can be found here and how to use it. Together with some '*Best Practices*'.
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Support is given by:
**Michèle Huijberts**
......@@ -20,127 +19,44 @@ Support is given by:
For software-specific questions, please consult the colleagues at your own research group.
<p></p>
_ _ _
Apart from this page there is a more general (and more technical) Wiki page with information about Shark and the usage. This page can be found [here](https://git.lumc.nl/shark/SHARK/wikis/home).
This page uses several headings for different topics. You can (un)fold these topics by clicking on the headings. It is not adviced to read this page from top to bottom. You better click on the topics to find the information you need. Sometimes this implies that the needed information is in another topic.
To start working on Shark you need a so-called *LUMC Research account* [^LUMC_Research_Account]. Unfold the next topic to find more information about applying for that.
<details open>
<summary>Apply for an Account</summary>
<p>
Roadmap:
1. Gather the following information (if applicable):
- Your e-mailaddress from FSW (or student address).
- The purpose of using Shark (which software etc. is requested).
- The information about your 'normal' LUMC account.
- Which research group you want to join.
- The name of a new group, with the members.
See [ResearchGroups](ResearchGroups) for an overview of available research groups.
2. Send the information to <m.huijberts@lumc.nl>.
- The information will processed and you will get an invitation for attending the mandatory Shark introduction course given by Michel Villerius. For more information about the course see: [Shark Introduction Course](https://git.lumc.nl/shark/SHARK/wikis/Intro_course) and the [Shark Introduction Course schedule](https://git.lumc.nl/shark/SHARK/wikis/Intro_schedule_2017)
3. After attending the course you can start using Shark.
Best practices:
1. Get some basic Linux knowledge. See also next topic.
2. It is advised to get some understanding of the concepts of a computer cluster with a queue-ing system.
3. Maintaining the password.
- Change it every 3 months. (at least 8 characters with capitals )
- To see when your password expired use the command `AD-pwd-expiration.sh` on command-line of Shark.
4. Changing the password.
When your password is not expired you can change the password via:
- You can use the URL [Change LUMC Research Account Password](https://passwd.researchlumc.nl/RDWeb/Pages/en-US/password.aspx)
- type `passwd` on command-line of Shark and follow the instructions.
See also [Changepasswd](https://git.lumc.nl/shark/SHARK/wikis/ChangePasswd)
~~Request an account (what info needed?, call? mail address? single user of ook toegang tot groepen, zelf nw groep aanmaken?) Wat gebeurt er als je geen 0-aanstelling hebt bij LUMC? Studenten? verschil LUMCNET versus RESEARCHNET account, tijdig wachtwoord verlengen, handige tips misschien?
Do the course ... Frequency...~~
</p>
</details>
_ _ _
<details open>
<summary>Courses</summary>
Information about available courses.
</details>
_ _ _
<details open>
<summary>How to connect and start using Shark</summary>
The procedure to connect to Shark depends on your location and the computer you are using
In FSW building and wire connected to FSW outlet
Hier uitleggen hoe toegang to bring-your-own device network
In LUMC
Linkje naar andere pagina?
In FSW using wifi or elsewhere on the internet
via de jumpserver
<details open>
<summary>Windows</summary>
Here info for Windows users
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</details>
This page is meant for FSW users. There is also a more general (and more technical) Wiki page with information about Shark and the usage. This page can be found [here](https://git.lumc.nl/shark/SHARK/wikis/home).
<details open>
<summary>Mac</summary>
Here info for Mac users
Please remember: *This page is a continuous work in progress.* Due to changes in the hardware, software and network configurations, the information and structure of this page and the corresponding Wiki can change over time. Comments and remarks on errors and omission are welcome.
</details>
To start working on Shark you need a so-called **LUMC Research account**. Due to regulations Shark is not connected to the LUMC network, but on a separated network. Therefore you need another account as the 'normal' LUMC account (used for e-mail, workstation login etc.). If you do have a LUMC account, the username will be same as the LUMC Research Acoount.
<details open>
<summary>Linux</summary>
Here info for Linux users
</details>
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[Apply for an Account](https://git.lumc.nl/mwjhhuijberts/Shark4FSW/wikis/apply_for_an_account).
These are not the only ways to connect. You might use an alternative way. But
</details>
_ _ _
Which information do you need, and where to apply. More details on the process.
<details open>
<summary>Available Software</summary>
Here information about available software?
When you apply for an account the Shark Introduction Course is mandatory.
</details>
_ _ _
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[Shark Introduction Course](https://git.lumc.nl/mwjhhuijberts/Shark4FSW/wikis/shark_introduction_course).
Information about the Shark Introduction Course and other courses.
<details open>
<summary>How to use: `module load`, for a specific version</summary>
module load
Once you have an account and did the course you need login.
</details>
_ _ _
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[How to Connect](https://git.lumc.nl/mwjhhuijberts/Shark4FSW/wikis/how_to_connect).
Practical information about the LUMC Research account and how to connect to Shark from different networks on Windows, Mac and Linux. Information about the jumpserver and the password.
<details open>
<summary>(Extra) Software</summary>
Information about what to do when you need extra software?
Ater connecting to Shark, you want to start using software on a cluster.
</details>
_ _ _
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[Software](https://git.lumc.nl/mwjhhuijberts/Shark4FSW/wikis/software).
Information about the available software and how to use it with an cluster queue, together with how to apply new software or libaries. Information about the `module` tool, to use different versions of the same software.
<details open>
<summary>(Extra) Storage</summary>
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[Storage](https://git.lumc.nl/mwjhhuijberts/Shark4FSW/wikis/storage).
data moet opgeslagen worden op exports/fsw. Vraag: mag iedereen daar zomaar allemaal mappen aanhouden of willen jullie juist per persoon of groep mappen maken?
when a project is finished, data should be backupped to the J-drive and removed from the /exports/fsw folder.
Information about the storage. where to store your data on the cluster. And how to connect to the storage.
</details>
_ _ _
[^LUMC_Research_Account]: Due to regulations Shark is not connected to the LUMC network, but on a separated network. Therefore you need another account as the 'normal' LUMC account (used for e-mail, workstation login etc.). If you do have a LUMC account, the username will be same as the LUMC Research Acoount.
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