Merge branch 'main' of https://github.com/UPPMAX/UPPMAX-documentation

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diff --git a/.wordlist.txt b/.wordlist.txt
@@ -873,4 +873,36 @@ ies
 ReadTheDocs
 Klemming
 Svanslös
-
+Bilderbeek
+bioinformaticians
+Busybox
+Eklund
+Filezilla
+gff
+gnuplot
+KRT
+nd
+oneliners
+SSD
+Söderberg
+Tilda
+vCPU
+VirtualBox
+virtualized
+xNVIDIA
+DNS
+lookups
+misconfiguration
+bootstrapotp
+Authy
+twofactor
+Lastpass
+softwares
+SOMETEXT
+otpauth
+totp
+dns
+whatismyip
+ifconfig
+LastPass
+SWAMID
diff --git a/docs/cluster_guides/bianca_login_node.md b/docs/cluster_guides/bianca_login_node.md
@@ -0,0 +1,11 @@
+---
+tags:
+  - Bianca
+  - login node
+  - login
+  - node
+---
+
+# Bianca login node
+
+There are running up to 7 login nodes on a physical Bianca-node.
diff --git a/docs/cluster_guides/cluster_speeds.md b/docs/cluster_guides/cluster_speeds.md
@@ -0,0 +1,79 @@
+---
+tags:
+  - UPPMAX
+  - cluster
+  - clusters
+  - speed
+  - fast
+  - slow
+---
+
+# Cluster speeds
+
+Sometimes you feel a cluster is slow.
+
+Below are some benchmark results, so you can compare with what you are
+experiencing.
+
+Please [contact support](../support.md) when you find out that your favorite
+cluster is slower than expected.
+
+???- question "What could cause such a slowdown?"
+
+
+    > When things are slow it is usually due to latency
+    > when many processes are accessing the same files
+    > and physical hard drives
+
+    Examples:
+
+    - 2024-12-06: Castor is still holding some file systems for Bianca
+      or a user that is running a lot of very short lived Perl jobs on Bianca,
+      that are running too hard on Castor.
+
+## Starting an interactive session with two cores for one hour
+
+In general:
+
+- It takes seconds if a free compute node is available
+- It takes minutes to start a new node
+
+Date and time  |Cluster|Command                                     |You waited for `x` seconds|Complete time (secs)
+---------------|-------|--------------------------------------------|--------------------------|--------------------
+2024-12-19 8:00|Bianca |`interactive -A sens2023036 -n 2 -t 1:00:00`|518 (8:38)                |548 (9:08)
+
+## Loading the `R_packages/4.3.1` module
+
+For [a benchmark to solve a ticket](https://github.com/UPPMAX/ticket_304069/blob/master/module_load.md#answers),
+the following command was run in multiple settings:
+
+```bash
+time module load R_packages/4.3.1
+```
+
+From the three resulting times, the 'Real' time is used.
+
+Here are some expected timings:
+
+Project    |Setting                     |Real loading time
+-----------|----------------------------|-----------------
+Rackham    |SSH                         |0m0.758s
+Bianca     |SSH                         |0m8.984s
+
+Here are some unexpected timings:
+
+Project    |Setting                     |Real loading time
+-----------|----------------------------|-----------------
+sens2023598|SSH                         |6m1.265s
+sens2023598|Website                     |6m20.234s
+sens2017625|SSH                         |6m4.584s
+sens2017625|Website, interactive session|7m41.433s
+sens2017625|SSH, interactive session    |7m13.111s
+
+
+## Loading the `RStudio/2023.12.1-402` module
+
+Project    |Setting                     |Real loading time
+-----------|----------------------------|-----------------
+Bianca     |Website                     |2m3.184s
+
diff --git a/docs/cluster_guides/gorilla.md b/docs/cluster_guides/gorilla.md
@@ -1,3 +1,4 @@
 # Gorilla
 
-Gorilla will be ceph
+Gorilla is a future storage system,
+using the ceph file system.
diff --git a/docs/cluster_guides/img/bianca_system_usage_20241218.png b/docs/cluster_guides/img/bianca_system_usage_20241218.png
diff --git a/docs/cluster_guides/img/cpu_usage_sens2017625.png b/docs/cluster_guides/img/cpu_usage_sens2017625.png
diff --git a/docs/cluster_guides/img/cpu_usage_sens2023036.png b/docs/cluster_guides/img/cpu_usage_sens2023036.png
diff --git a/docs/cluster_guides/pelle.md b/docs/cluster_guides/pelle.md
@@ -9,7 +9,6 @@ tags:
 
 ![Image of Pelle Svanslös, from https://www.comics.org/issue/105368/cover/4](./img/pelle.jpg)
 
-
 ???- question "Why such a bad image?"
 
     Copyright. This is one of the few images that shows Pelle Svanslös
@@ -24,17 +23,36 @@ by UPPMAX after [applying to a Pelle project](../getting_started/project_apply_p
 Non-Uppsala users of [Rackham](rackham.md) can move their data to
 Dardel, see [the Rackham to Dardel migration guide](../cluster_guides/dardel_migration.md).
 
+!!! warning "Status"
+
+    Pelle is in the process of being set up. Here is the current
+    status of Pelle.
+
+    The delivery of the new UPPMAX system, Pelle, faces continued delays. UPPMAX now has a plan for provisioning Rackham to Uppsala University researchers until Pelle is ready.
+
+    We have started to approve proposals submitted to the UPPMAX Local 2025 round. This will take a little time, but when your project is approved we ask you to examine the decision email closely and let us know if we’re missing any projects for data migration.
+
+    New projects with Pelle and Gorilla resources will not be able to use Pelle or Gorilla until the systems are operational. The projects will have those resources represented in SUPR anyway.
+
+    Approved projects will receive a Rackham allocation, in addition to the resources you asked for, which will let you log in and submit jobs to Rackham.
+
+    Access to storage directories on Crex belonging to UU-affiliated projects will not expire, so you will have continued access to data in UU-affiliated projects on Crex until Pelle is ready. Therefore, most approved projects will not receive a Crex allocation. If we can not identify existing storage allocations for you, then we will create a Crex allocation for your storage needs.
+
+    When Pelle is operational, we will move data from the NAISS projects you’ve mentioned in the proposals to the UPPMAX Local projects for you. Then, we will switch off Rackham and Crex and let you use Pelle and Gorilla.
+
+    The “UPPMAX for Education” service on Snowy will, for now, continue as normal. At some point, we will move the GPUs from Snowy to newer hardware. At the same time, we will add Rackham and/or Pelle allocations to projects and shut down Snowy. We will inform you before we do this.
+
 ## [How to apply to a Pelle project](../getting_started/project_apply_pelle.md)
 
 See [how to apply to a Pelle project](../getting_started/project_apply_pelle.md).
 
 ## Features of Pelle, compared to Rackham
 
 Although we from UPPMAX cannot say exactly how Pelle will look,
-we try to have Pelle be as similar to Rackham as possible.
+we try to have Pelle be as similar to [Rackham](rackham.md) as possible.
 
 ## Migration from Rackham to Pelle
 
 As both clusters are UPPMAX clusters,
-we will transfer your data from Rackham
+we will transfer your data from [Rackham](rackham.md)
 to Pelle. Users will have to [apply to a Pelle project](../getting_started/project_apply_pelle.md).
diff --git a/docs/cluster_guides/rackham_modules.md b/docs/cluster_guides/rackham_modules.md
@@ -8,7 +8,3 @@ do their work independently and undisturbed.
 
 Because this is the same for nearly all UPPMAX clusters,
 there is a general page on modules [here](modules.md)
-
-## Sidebar
-
-This is to see if a sidebar appears.
diff --git a/docs/getting_started/get_uppmax_2fa.md b/docs/getting_started/get_uppmax_2fa.md
@@ -7,18 +7,106 @@ tags:
 
 # Setting up two factor authentication for UPPMAX
 
+Two factor authentication (abbreviated to '2FA')
+increases the security of your UPPMAX account
+and is mandatory is multiple contexts.
+
+???- question "Why is this important?"
+
+    See [Why is 2FA important?](why_2fa.md)
+
+This page describes how to set this up.
+
+## Procedure
+
 ???- question "Prefer a video?"
 
     Watch [the YouTube video 'Get your UPPMAX 2FA'](https://youtu.be/eSn0kLkU5Dc)
 
-Follow the guide [Setting up two factor authentication for UPPMAX](https://www.uu.se/en/centre/uppmax/get-started/2-factor).
+### 1. Install a 2FA app
+
+Install an app to use for 2FA.
+
+???- question "Which app do you recommend?"
+
+    Any app that works for you.
+
+    Search for '2FA' or 'OTP' (short for
+    'one time password')..
+
+    Wikipedia maintains a list of 2FA apps
+    [here](https://en.wikipedia.org/wiki/Comparison_of_OTP_applications).
+
+### 2. Go to <https://suprintegration.uppmax.uu.se/bootstrapotp/>
+
+In your web browser, go to <https://suprintegration.uppmax.uu.se/bootstrapotp/>.
+
+???- question "How does this look like?"
+
+    Here is how <https://suprintegration.uppmax.uu.se/bootstrapotp/>
+    looks like:
+
+    ![https://suprintegration.uppmax.uu.se/bootstrapotp](./img/suprintegration_uppmax_uu_se_bootstrapotp.png)
+
+This will take you to the UU page to request a second factor for your UPPMAX account.
+
+### 3. Click on 'Continue'
+
+At this page, click on 'Continue' to be sent to a 'Login to SUPR' page.
+
+Click on 'Continue' to be sent to a 'Login to SUPR' page.
+
+### 4. Log in to SUPR
+
+At the 'Login to SUPR' page, log in, in any way that works for you.
+
+???- question "How does this look like?"
+
+    ![Login to SUPR page when requesting a 2FA](./img/supr_login_for_2fa.png)
+
+In case you are not logged in already, log in to SUPR.
+
+### 5. Press the button 'Prove My Identity to UPPMAX'
+
+Acknowledge to SUPR that they may tell UPPMAX who you are,
+by pressing the button "Prove My Identity to UPPMAX" on the page.
+
+### 6. Scan the QR-code with your 2FA app
+
+Scan the QR-code with your 2FA app.
+
+???- question "How does that look like?"
+
+    ![Getting an UPPMAX 2FA QR code](./img/get_uppmax_2fa_qr.png)
+
+More details [here](get_uppmax_2fa_qr.md).
+
+### 7. Enter the code on the webpage
+
+Your application will show you a code, enter this code on the same webpage.
+
+More details [here](get_uppmax_2fa_qr_code.md).
+
+### 8. See acknowledgement that the new two factor has been registered
+
+You should see an acknowledgement that the new two factor has been registered.
+
+???- question "How does that look like?"
+
+    ![The final page](./img/get_uppmax_2fa_qr_code.png)
+
+### 9. Wait for a confirmation email
 
 After this procedure, it takes around 15 minutes before you can use
 the 2FA to log in.
 
-![UPPMAX 2FA set up for a fictional UPPMAX user called `sven`](./img/uppmax_2fa.png)
+## FAQ
+
+???- question "How does the use of a 2FA app looks like?"
 
-> UPPMAX 2FA set up for a fictional UPPMAX user called `sven`
+    ![UPPMAX 2FA set up for a fictional UPPMAX user called `sven`](./img/uppmax_2fa.png)
+
+    > UPPMAX 2FA set up for a fictional UPPMAX user called `sven`
 
 ???- question "How do I know I used my new 2FA too early?"
 
@@ -31,6 +119,27 @@ the 2FA to log in.
 
     ![Authentication failed](./img/get_uppmax_2fa_authentication_failed_directly_after_new_2fa.png)
 
-## Link
+???- question "How long does it take before my 2FA is active?"
+
+    This is a matter of minutes.
+
+    It takes a little while before your newly registered factor is usable,
+    but this should be a matter of minutes, not days.
+
+???- question "Will I get an email when my 2FA is active?"
+
+    No.
+
+    There is no extra mail sent to let you know that the newly registered
+    factor is usable, just the confirmation mail that mentions
+    that it will be activated soon.
+
+
+## Troubleshooting
+
+Some of the common problems we've seen include
 
-- [Setting up two factor authentication for UPPMAX](https://www.uu.se/en/centre/uppmax/get-started/2-factor)
+- Not having an account at UPPMAX. This is required to get the second factor for your account.
+- Using a device having it's time set differently from our systems. There are services on the internet (e.g. <https://time.is/>) you can visit from the device you try to manage the code on that will show you if your device settings are problematic.
+- Noting the code given at first and trying to use it every time when asked for a code. The code to give will change every thirty second and you should give whatever code is shown at the time.
+- Expecting something else to be sent to you. You register the new second factor as part of the process. A confirmation mail is sent as well, but this is mostly to let you know in case your account details in SUPR have gone astray and someone else has registered a second factor for your account.
diff --git a/docs/getting_started/get_uppmax_2fa_qr.md b/docs/getting_started/get_uppmax_2fa_qr.md
@@ -0,0 +1,37 @@
+---
+tags:
+  - 2FA
+  - MFA
+  - UPPMAX
+  - QR
+---
+
+# Setting up the QR code for two factor authentication for UPPMAX
+
+Part of [setting up two factor authentication for UPPMAX](get_uppmax_2fa.md)
+is to get a QR code.
+
+![Getting an UPPMAX 2FA QR code](./img/get_uppmax_2fa_qr.png)
+
+You need to scan this QR code to add your account to your software.
+Most softwares call this "Add account" or similar
+and will offer an option to scan a QR code using the smartphone camera
+or select an area of the screen where the code is.
+
+Note that this must often be done from
+within the app for two factor authentication.
+
+If you see a string similar to
+
+```text
+otpauth://totp/username@UPPMAX?secret=SOMETEXT&issuer=UPPMAX
+```
+
+it didn't work and you probably need to do something different
+(such as starting the app and select scan from within).
+
+Once you've scanned the code, you are often allowed to change the name the
+software will use for the account before you add it.
+You can change the name if you want - changing the name does not affect the
+codes generated.
+Finish adding the account to the software.
diff --git a/docs/getting_started/get_uppmax_2fa_qr_code.md b/docs/getting_started/get_uppmax_2fa_qr_code.md
@@ -0,0 +1,25 @@
+---
+tags:
+  - 2FA
+  - MFA
+  - UPPMAX
+  - QR
+  - code
+---
+
+# Setting up the QR code for two factor authentication for UPPMAX
+
+Once you have the new account, you should get one time codes for it when you
+have it selected.
+To finish the registration at UPPMAX, you need to enter the code
+that is displayed in the field where it says "Code:" and submit.
+The codes will change over time, don't worry about this,
+you just need to use whatever code is current.
+
+Once you have entered and submitted the current code,
+you should see a final page:
+
+![The final page](./img/get_uppmax_2fa_qr_code.png)
+
+When you see that page, it will take a little while and the token will
+be activated (you should also receive an e-mail about the new token).
diff --git a/docs/getting_started/img/accounts.jpg b/docs/getting_started/img/accounts.jpg
diff --git a/docs/getting_started/img/find_inst.PNG b/docs/getting_started/img/find_inst.PNG
diff --git a/docs/getting_started/img/get_uppmax_2fa_qr.png b/docs/getting_started/img/get_uppmax_2fa_qr.png
diff --git a/docs/getting_started/img/get_uppmax_2fa_qr_code.png b/docs/getting_started/img/get_uppmax_2fa_qr_code.png
diff --git a/docs/getting_started/img/proj.PNG b/docs/getting_started/img/proj.PNG
diff --git a/docs/getting_started/img/proj_red.PNG b/docs/getting_started/img/proj_red.PNG
diff --git a/docs/getting_started/img/proj_request.PNG b/docs/getting_started/img/proj_request.PNG
diff --git a/docs/getting_started/img/reg_form.PNG b/docs/getting_started/img/reg_form.PNG
diff --git a/docs/getting_started/img/reg_new_person.PNG b/docs/getting_started/img/reg_new_person.PNG
diff --git a/docs/getting_started/img/request_account.jpg b/docs/getting_started/img/request_account.jpg
diff --git a/docs/getting_started/img/supr_login.PNG b/docs/getting_started/img/supr_login.PNG
diff --git a/docs/getting_started/img/supr_login_for_2fa.png b/docs/getting_started/img/supr_login_for_2fa.png
diff --git a/docs/getting_started/img/supr_request_2fa.png b/docs/getting_started/img/supr_request_2fa.png
diff --git a/docs/getting_started/img/suprintegration_uppmax_uu_se_bootstrapotp.png b/docs/getting_started/img/suprintegration_uppmax_uu_se_bootstrapotp.png
diff --git a/docs/getting_started/img/suprintegration_uppmax_uu_se_bootstrapotp_ubuntu.png b/docs/getting_started/img/suprintegration_uppmax_uu_se_bootstrapotp_ubuntu.png
diff --git a/docs/getting_started/img/usr_agree.PNG b/docs/getting_started/img/usr_agree.PNG