Add sctricter link check and fix most of the new errors

STYLEGUIDE.md

@@ -91,7 +91,7 @@
  - For a list of all supported languages see: http://pygments.org/docs/lexers/
  - Give commands, environment variables, command options, as well as partition 
    names between two backticks, i.e. \`srun\`, \`$LOCAL_SCRATCH\`, \`--gres\`, \`small\`
- - Refer to servicedesk via the docs contact page: as in `[contact ServiceDesk](/support/contact/)`  
+ - Refer to servicedesk via the docs contact page: as in `[contact ServiceDesk](/support/contact.md)`
       - Page has email, service times, phone, support request how-to
 
 ## Redirecting pages

csc-overrides/assets/snippets/rahtibeta_announcement.md

@@ -1,3 +1,3 @@
 !!! warning-label
 
-    *This version of Rahti is deprecated.* The projects need to be migrated from Rahti 1 platform to the new Rahti 2 production platform by June 2024. Please consult the [migration guide](/cloud/rahti/rahti-migration/) for more information.
+    *This version of Rahti is deprecated.* The projects need to be migrated from Rahti 1 platform to the new Rahti 2 production platform by June 2024. Please consult the [migration guide](/cloud/rahti/rahti-migration.md) for more information.

docs/accounts/fmi.md

@@ -51,6 +51,6 @@ Puhti FMI works similarly to the regular Puhti system, the main difference being
 3. the FMI compute nodes have simultaneous multithreading (SMT/hyper threading) enabled, thus most tools, such as `htop`,
    show 80 logical cpus instead of 40, `seff` CPU efficiency report is computed with 80 logical cpus, etc. The configuration
    and the usage is similar to Mahti, see
-   [Hybrid jobs with SMT](/computing/running/creating-job-scripts-mahti/#hybrid-batch-jobs-with-simultaneous-multithreading-smt).
+   [Hybrid jobs with SMT](../computing/running/creating-job-scripts-mahti.md#hybrid-batch-jobs-with-simultaneous-multithreading-smt).
 
 In addition to the regular CSC's user support, [servicedesk@csc.fi](mailto:servicedesk@csc.fi), FMI specific support is available in the internal wiki pages [FMI Puhti Guide](https://wiki.fmi.fi/display/VTUKI/FMI+Puhti+guide), and in the very active FMI's Slack channel 'fmi-computing'.

docs/accounts/how-to-increase-disk-quotas.md

@@ -2,7 +2,7 @@
 
 ## Increasing the storage capacity in Puhti and Mahti
 
-The quotas of the [scratch](../../computing/disk/#scratch-directory) and [projappl](../../computing/disk/#projappl-directory) directories of Puhti and Mahti servers can be
+The quotas of the [scratch](../computing/disk.md#scratch-directory) and [projappl](../computing/disk.md#projappl-directory) directories of Puhti and Mahti servers can be
 increased if needed.
 
 You can use MyCSC to manage these quotas.
@@ -37,3 +37,4 @@ i.e. 1 TB of data stored in Allas consumes 24 BU in a day and 8760 BU in a year.
 ## Increasing the storage capacity in IDA
 
 [About Monitoring and Adjusting Project Quota in IDA User Guide](https://www.fairdata.fi/en/user-guides/user-guide/#project-quota)
+

docs/accounts/how-to-manage-your-project.md

@@ -15,7 +15,7 @@ CSC Project needs to be extended yearly.
 
 Users are primarily responsible for [moving data](../data/moving/index.md) or deleting the project content themselves before the project is closed. 
 If you're unsure about your CSC Project's or Account's status, please log in [MyCSC](https://my.csc.fi) to extend your project or change your account password.
-If you want to close your Project, change your account email address or change the Project Manager, kindly [contact ServiceDesk](/support/contact/)
+If you want to close your Project, change your account email address or change the Project Manager, kindly [contact ServiceDesk](../support/contact.md)
 
 ## Project lifetime extension
 

docs/accounts/index.md

@@ -14,7 +14,7 @@ The Project Manager is typically a leader of a research team or other senior res
 *   **Billing Units** (BUs) are used to allocate resources to users' projects. You can apply for Billing Units in [MyCSC](https://my.csc.fi) portal and CSC grants BUs to projects. [Usage consumes billing units](billing.md) but **no actual payment** is required.
 However, the amount of billing units must always remain positive.
 
-*   **LUMI projects** used to manage access to LUMI and the resources provided by it. LUMI projects are restricted to LUMI environment only (LUMI-C, LUMI-G etc.). Finnish LUMI projects are fixed in time and resources, and the total resources must be defined already in the project application. Lumi projects are also used for [Helmi quantum computer](../computing/quantum-computing/helmi/helmi-from-lumi/). For further information please see [these instructions](https://www.lumi-supercomputer.eu/get-started-2021/users-in-finland/){:target="_blank"}. 
+*   **LUMI projects** used to manage access to LUMI and the resources provided by it. LUMI projects are restricted to LUMI environment only (LUMI-C, LUMI-G etc.). Finnish LUMI projects are fixed in time and resources, and the total resources must be defined already in the project application. Lumi projects are also used for [Helmi quantum computer](../computing/quantum-computing/helmi/helmi-from-lumi.md). For further information please see [these instructions](https://www.lumi-supercomputer.eu/get-started-2021/users-in-finland/){:target="_blank"}. 
 
 *   **My.csc.fi portal** MyCSC is the self-service CSC customer portal for research and education customers and end-users. MyCSC is also available for any other CSC customer or end-user, if they have CSC user accounts according to the CSCID policies.
 MyCSC portal offers users the functionality for registering CSC user accounts, creating computing or data projects, adding members to projects, and applying resources for projects. Users can also manage their projects and project lifecycles through MyCSC, and they can see the resources consumption and amount of stored data there.

docs/apps/ams.md

@@ -31,7 +31,7 @@ module load ams/2024.102
 ### Example batch scripts
 
 !!! warning "Note"
-    Particularly some property calculations can be very disk I/O intensive. Such jobs benefit from using the [fast local storage (NVMe)](../../computing/running/creating-job-scripts-puhti/#local-storage) on Puhti. Using local disk for such jobs will also reduce the load on the Lustre parallel file system.
+    Particularly some property calculations can be very disk I/O intensive. Such jobs benefit from using the [fast local storage (NVMe)](../computing/running/creating-job-scripts-puhti.md#local-storage) on Puhti. Using local disk for such jobs will also reduce the load on the Lustre parallel file system.
 
 
 === "Puhti"

docs/apps/gaussian.md

@@ -46,7 +46,7 @@ be found [here](http://gaussian.com/running/?tabid=3).
 
 Particularly some wave function-based electron correlation methods can
 be very disk I/O intensive. Such jobs benefit from using the fast
-[NMVE local disk](../../computing/running/creating-job-scripts-puhti/#local-storage)
+[NMVE local disk](../computing/running/creating-job-scripts-puhti.md#local-storage)
 on Puhti. Using local disk for such jobs will also reduce the overall load on the
 Lustre parallel file system.
 
@@ -111,7 +111,7 @@ well as use of local disk (nvme) significantly affects the performance:
 From these results we conclude that 80 GB seems to be the optimal memory allocation and
 that the use of local disk clearly improves the performance. The speedup when going from
 20 to 40 cores, and using local disk is 1.35, that is below the
-[recommended minimum of 1.5](../../accounts/how-to-access-mahti-large-partition/#scalability-testing).
+[recommended minimum of 1.5](../accounts/how-to-access-mahti-large-partition.md#scalability-testing).
 Hence, the most efficient resource usage would correspond to 20 cores, 80 GB of memory and local disk
 on Puhti. For this type of calculation Mahti isn't the optimal choice.
 

docs/apps/maestro.md

@@ -63,7 +63,7 @@ Maestro is available for all academic users in Finland: staff and students, for
 purposes. Please consult the [EULA](https://www.schrodinger.com/maestro-academic-eula)
 for the exact definition. Using Maestro means that you accept the EULA linked to above.
 The Maestro license consists of floating licenses and tokens. If licenses run out, contact
-us via [ServiceDesk](/support/contact/).
+us via [ServiceDesk](../support/contact.md).
 
 ## Usage
 
@@ -156,7 +156,7 @@ bash your_script_name.sh
     [the Puhti web interface remote desktop](../computing/webinterface/desktop.md), but
     the performance may be somewhat slow and submitted jobs may end up fizzled. Also,
     **no long/heavy tasks** should be done on the login nodes. Please consult the
-    [Usage policy](../../computing/usage-policy) page for more details.
+    [Usage policy](../computing/usage-policy.md) page for more details.
 
 !!! info "Note for Windows users"
     **Windows** users may need to edit the script created by the GUI a little.

docs/apps/molpro.md

@@ -45,7 +45,7 @@ rm -rf $MOLPRO_TMP
 ```
 
 !!! info "Note"
-    Particularly some of the wavefunction-based electron correlation methods can be very disk I/O intensive. Such jobs benefit from using the [fast local storage](../../computing/running/creating-job-scripts-puhti/#local-storage) on Puhti. Using local disk for such jobs will also reduce the load on the Lustre parallel file system.
+    Particularly some of the wavefunction-based electron correlation methods can be very disk I/O intensive. Such jobs benefit from using the [fast local storage](../computing/running/creating-job-scripts-puhti.md#local-storage) on Puhti. Using local disk for such jobs will also reduce the load on the Lustre parallel file system.
 
 ### Example batch script for Puhti using MPI parallelization and local disk (NVMe)
 

docs/apps/openfoam.md

@@ -101,7 +101,7 @@ The example scripts for separate batch runs for decomposition, solver and recons
 $WM_PROJECT_INST_DIR/batch_script_examples
 ```
 
-Please note that, on Mahti, decomposition and reconstruction must be done using the [interactive queue](../../computing/running/batch-job-partitions/).
+Please note that, on Mahti, decomposition and reconstruction must be done using the [interactive queue](../computing/running/batch-job-partitions.md).
 
 ## Support
 

docs/apps/python-data.md

@@ -68,7 +68,7 @@ data analytics and machine learning, for example:
 
 If you find that some package is missing, you can often install it
 yourself with `pip install --user`.  See [our Python
-documentation](python.md#installing-python-packages-to-existing-modules)
+documentation](../support/tutorials/python-usage-guide.md#installing-python-packages-to-existing-modules)
 for more information on how to install packages yourself.
 
 It is also possible to use [Python virtual

docs/apps/python.md

@@ -31,7 +31,7 @@ using different development environments and doing parallel processing
 with Python.
 
 It is generally recommended to use one of
-[pre-installed Python environments](python.md#pre-installed-python-environments)
+[pre-installed Python environments](./python.md#pre-installed-python-environments)
 for computing,
 since these already contain the essential libraries for most uses.
 If for some reason one wishes to use Python without loading an environment

docs/apps/r-env.md

@@ -5,7 +5,7 @@ tags:
 
 # r-env
 
-`r-env` is an [Apptainer container](../../computing/containers/run-existing/) including R and RStudio Server, and several other features to facilitate their use. 
+`r-env` is an [Apptainer container](../computing/containers/run-existing.md) including R and RStudio Server, and several other features to facilitate their use. 
 
 - R is an open-source language and environment for statistical computing and graphics. More information on R can be found on [the R Project website](https://www.r-project.org/about.html). Many useful [R manuals are also hosted on CRAN](https://cran.r-project.org/manuals.html).
 
@@ -60,8 +60,8 @@ Licensing information within the `r-env` container is available in the file `/us
 There are several ways to use the `r-env` module on Puhti:
 
 * Non-interactive batch jobs without limits on the reserved computing resources (other than those applying to Puhti in general). Use this option for analyses that take longer or require a lot of memory.
-* [Interactive jobs on a compute node](../../computing/running/interactive-usage/), using either the R console or RStudio Server. Use this option for preparing your code and for smaller analyses. Interactive jobs may use limited resources.
-* Interactively on the login node, using the R console. Use this option only for moving data, checking package availability and installing packages. Puhti login nodes are [not intended for heavy computing](../../computing/usage-policy#login-nodes). 
+* [Interactive jobs on a compute node](../computing/running/interactive-usage.md), using either the R console or RStudio Server. Use this option for preparing your code and for smaller analyses. Interactive jobs may use limited resources.
+* Interactively on the login node, using the R console. Use this option only for moving data, checking package availability and installing packages. Puhti login nodes are [not intended for heavy computing](../computing/usage-policy.md#login-nodes). 
 
 #### Interactive use on a compute node
 
@@ -628,7 +628,7 @@ It is possible to configure `r-env` to use NVIDIA NVBLAS, a drop-in BLAS replace
 
 Compared to CPU jobs, using NVBLAS may offer speed improvements without changes to the underlying R code. However, the benefits afforded are strongly analysis-specific. Additionally, NVBLAS jobs make sub-optimal use of reservations on the GPU partition, with only certain operations being routed to the GPU.
 
-Prior to running a NVBLAS job, consider the [Puhti GPU node usage policy](../../computing/usage-policy#gpu-nodes) and this checklist:
+Prior to running a NVBLAS job, consider the [Puhti GPU node usage policy](../computing/usage-policy.md#gpu-nodes) and this checklist:
 
 - Are BLAS3 routines the main bottleneck in your workflow? 
 - Are speed-ups possible through other means (e.g. rewriting your code)?

docs/apps/tmolex.md

@@ -33,7 +33,7 @@ academic (i.e. degree-granting) institutes.
 Go to [puhti.csc.fi](https://puhti.csc.fi/) using a web browser and login using
 your CSC/Haka user account.
 
-1. From there [launch a Desktop](../../computing/webinterface/desktop/#launching). 
+1. From there [launch a Desktop](../computing/webinterface/desktop.md#launching). 
 2. Open a `Terminal` and load the TURBOMOLE module `module load turbomole/7.8`.
 3. Start TmoleX with the command `TmoleX24`.
 4. Select `New Project` and define a suitable project in the `File Name` slot

docs/cloud/dbaas/security-guides.md

@@ -8,7 +8,7 @@ You can find out more about how to use firewalls in the [Firewall section](firew
 
 ## Authentication
 
-You can log in to the DBaaS service with many different authentication methods as long as you have a [CSC account](../../../accounts/how-to-create-new-user-account/) and belong to a project that has applied for DBaaS access.
+You can log in to the DBaaS service with many different authentication methods as long as you have a [CSC account](../../accounts/how-to-create-new-user-account.md) and belong to a project that has applied for DBaaS access.
 
 From the web interface, you can create application credentials if you like to automate your database management from another application.
 

docs/cloud/noppe/guide_for_teachers.md

@@ -11,7 +11,7 @@ Instead of a course you can also use Noppe for collaboration. The workflow is si
 
 ### 1. Become a workspace owner and create a workspace
 * Login to Noppe using your CSC account by choosing 'CSC Login' option after clicking 'Login'.
-  If you don't have a CSC account yet, [see the instructions on how to create new user account](../../../accounts/how-to-create-new-user-account/).
+  If you don't have a CSC account yet, [see the instructions on how to create new user account](../../accounts/how-to-create-new-user-account.md).
 * Open `Manage workspaces` from the left panel and create a new workspace.
     * Workspace type:
       * Fixed-time course with limited lifetime: Valid for limited months.

docs/cloud/pouta/application-credentials.md

@@ -1,6 +1,6 @@
 # Application credentials
 
-Application credentials allow you to interact with Pouta via the [OpenStack command-line tools](../command-line-tools) or directly via the API, by allowing you to create a **role specific** and **time limited** _TOKEN_ that can be revoked at any time. The most immediate advantage is that you no longer need to use or write your CSC password while using Pouta's API.
+Application credentials allow you to interact with Pouta via the [OpenStack command-line tools](command-line-tools.md) or directly via the API, by allowing you to create a **role specific** and **time limited** _TOKEN_ that can be revoked at any time. The most immediate advantage is that you no longer need to use or write your CSC password while using Pouta's API.
 
 * **Role specific** means that the credentials can be created with limited permissions. You can create credentials that are only allowed to get data of your project, but not modify it. You can also create credentials that can only modify a specific resource. It is also possible to create credentials that can do everything that you can.
 
@@ -51,7 +51,7 @@ file that you can source, a YAML file that can be used directly by the CLI, or a
     export OS_APPLICATION_CREDENTIAL_SECRET=xxxxxxxxxxxxxxxxxxx
     ```
 
-    If you source that file, you can use it together with with [OpenStack command-line tools](../command-line-tools).
+    If you source that file, you can use it together with with [OpenStack command-line tools](command-line-tools.md).
 
     You can also download the `cloud.yaml` file that will look like this:
 

docs/cloud/pouta/connecting-to-vm.md

@@ -1,6 +1,6 @@
 # Connecting to your virtual machine
 
-This article describes several ways to connect to a running virtual machine. In order to create a Virtual Machine, check out [Creating a virtual machine in Pouta](../launch-vm-from-web-gui/).
+This article describes several ways to connect to a running virtual machine. In order to create a Virtual Machine, check out [Creating a virtual machine in Pouta](launch-vm-from-web-gui.md).
 
 !!! info "Password access disabled"
 
@@ -94,7 +94,7 @@ By enabling agent forwarding, you enable the ssh agent running on the remote Vir
 
 ### Putty
 
-Open Putty, after following the instructions at [windows-putty](/cloud/pouta/launch-vm-from-web-gui/#windows-putty) you should have a saved session with the private key stored on it.
+Open Putty, after following the instructions at [windows-putty](./launch-vm-from-web-gui.md#windows-putty) you should have a saved session with the private key stored on it.
 
 * Load the saved session.
 

docs/cloud/pouta/images.md

@@ -15,7 +15,7 @@ images are not suitable. In this case, it is possible to create your
 own images and use them instead. However, there are some caveats 
 to consider when creating your own images that you would not
 need to consider when using the default images. For more information,,
-see [Advanced images](../adding-images)
+see [Advanced images](adding-images.md)
 
 ## The main features of the images provided by CSC
 
@@ -71,7 +71,7 @@ Ubuntu images, and their default username is `ubuntu` instead of `cloud-user`.
 
 ## Snowflake images
 These images you should probably not use without a really good
-reason. You might be better off [creating your own image](../adding-images)
+reason. You might be better off [creating your own image](adding-images.md)
 
 If there any images that you think we should add, do not hesitate to contact
 [Service Desk](mailto:servicedesk@csc.fi).

docs/cloud/pouta/index.md

@@ -76,5 +76,5 @@ Other useful links are:
 ## Self study and troubleshooting
 
 * [Pouta videos](tutorials/pouta-videos.md)
-* [Known problems and limitations](known-problems.md)
+* [Known problems and limitations](./known-problems.md)
 * [Pouta FAQ](../../support/faq/index.md#pouta)

docs/cloud/pouta/known-problems.md

@@ -35,5 +35,5 @@
 -   EC2 is presently not supported. EC2 credentials can, however, be
     used with the object storage.
 
-## [Pouta FAQ entries](../../../support/faq/#pouta)
+## [Pouta FAQ entries](../../support/faq/index.md#pouta)