Merge branch 'radovan/404' into 'main'

fixes/workarounds for so many broken links See merge request documentation/public!929
UNINETTSigma2 · Jun 12, 2024 · f23ca1f · f23ca1f
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diff --git a/_static/fonts/README.md b/_static/fonts/README.md
@@ -1,3 +1,7 @@
+---
+orphan: true
+---
+
 Font designed by Łukasz Dziedzic and obtained from
 https://github.com/googlefonts/carlito and released under the [SIL Open Font
 License 1.1](https://github.com/googlefonts/carlito/blob/main/OFL.txt).
diff --git a/about_us.md b/about_us.md
@@ -28,7 +28,7 @@ please also see <https://www.sigma2.no>.
 
 We offer compute resources {ref}`betzy`, {ref}`fram`, and {ref}`saga`, storage
 resources {ref}`nird`, as well as the [NIRD
-Toolkit](https://www.sigma2.no/nird-toolkit) platform for pre- and
+Service Platform](https://www.sigma2.no/service/nird-service-platform) for pre- and
 post-processing analysis, data intensive processing, visualization, artificial
 intelligence, and machine learning.
 

diff --git a/code_development/guides/containers.md b/code_development/guides/containers.md
@@ -60,7 +60,7 @@ singularity version 3.6.4-1.el7
  - [Singularity Hub](https://singularity-hub.org/)
  - [RedHat](https://quay.io/)
  - [BioContainers](https://biocontainers.pro/)
- - [AMD](https://www.amd.com/en/technologies/infinity-hub)
+ - [AMD](https://www.amd.com/en/developer/resources/infinity-hub.html)
  - From software developers
 
 

diff --git a/code_development/performance/vtune.md b/code_development/performance/vtune.md
@@ -47,8 +47,8 @@ $ ml load VTune/2018_update3
 ```
 
 To gather information about a code's performance one needs to execute
-the code using the [`amplxe-cl`
-command](https://software.intel.com/en-us/vtune-amplifier-help-amplxe-cl-command-syntax). Depending
+the code using the `amplxe-cl`
+command. Depending
 on the needs, `amplxe-cl` can gather all sorts of performance statistics: FPU
 utilization, usage of vector (SIMD) AVX insturctions, instructions per
 clock, memory bandwidth, cache utilization, threading level, etc. For
@@ -60,7 +60,7 @@ $ amplxe-cl -collect hotspots ./your-program your-arguments
 ```
 
 For a complete list of analysis modes please consult the [VTune
-documentation](https://software.intel.com/content/www/us/en/develop/tools/vtune-profiler.html). A
+documentation](https://www.intel.com/content/www/us/en/developer/tools/oneapi/vtune-profiler.html). A
 useful set of performance metrics is gathered by the
 `hрc-performance` analysis, which can help to identify opportunities
 to optimize CPU, memory, and vectorization level:

diff --git a/computing/tuning-applications.md b/computing/tuning-applications.md
@@ -268,7 +268,7 @@ if you are unfamiliar with it.
 
 This case study does not go into depth on how to understand the
 advisor tool, this is far better covered in the Intel tools
-[documentation](https://software.intel.com/content/www/us/en/develop/documentation.html),
+[documentation](https://www.intel.com/content/www/us/en/resources-documentation/developer.html)
 where they also provide a nice selection of tutorials.
 
 

diff --git a/files_storage/nird_lmd.md b/files_storage/nird_lmd.md
@@ -16,9 +16,9 @@ publishing research data or searching digital databases and collections.
 NIRD is a high-performance storage system, capable of supporting AI and analytics workloads, offering simultaneous multi-protocol access to the same data.
 ```
 
-The next generation NIRD storage system is installed in [Lefdal Mine Datacenter](https://www.sigma2.no/data-centre-facility).
+The next generation NIRD storage system is installed in [Lefdal Mine Datacenter](https://www.sigma2.no/our-data-centre).
 The new NIRD is redesigned for the evolving needs of Norwegian researchers and has
-been procured through [the NIRD2020 project](https://www.sigma2.no/procurement-project-nird2020).
+been procured through [the NIRD2020 project](https://www.sigma2.no/procurement-project-nird-2020).
 
 
 NIRD provides storage resources with yearly capacity upgrades, data security

diff --git a/getting_started/applying_resources.md b/getting_started/applying_resources.md
@@ -9,7 +9,7 @@ Applications for computing and storage resources should be submitted through NRI
 Resources on the national e-infrastructure are granted on a period basis and
 the **allocation periods have deadlines**.
 
-Please check <https://www.sigma2.no/apply-e-infrastructure-resources#deadlines>
+Please check <https://www.sigma2.no/apply-e-infrastructure-resources>
 to find information about when the next allocation period starts and to not
 miss the next application deadline.
 ```

diff --git a/jobs/guides/running_mpi_jobs.md b/jobs/guides/running_mpi_jobs.md
@@ -136,10 +136,10 @@ mpirun /path/to/MySoftWare_exec
 
 In the above, `MySoftWare_exec` is subject to `mpirun`'s internal
 mapping and binding algorithms. Intel's `mpirun` uses it's own default
-binding settings, which can be modified either by [command line
-parameters](https://software.intel.com/en-us/node/589999), or by
-[environment
-variables](https://software.intel.com/content/www/us/en/develop/documentation/mpi-developer-reference-linux/top/environment-variable-reference/process-pinning/environment-variables-for-process-pinning.html).
+binding settings, which can be modified either by command line
+parameters, or using
+environment
+variables (see <https://www.intel.com/content/www/us/en/docs/mpi-library/developer-reference-linux/2021-12/overview.html>).
 Special care must be taken when running hybrid MPI-OpenMP cores. If
 this is your case, please refer to the documentation regarding
 [Interoperability between MPI and OpenMP](https://software.intel.com/content/www/us/en/develop/documentation/mpi-developer-reference-windows/top/environment-variable-reference/main-thread-pinning/interoperability-with-openmp-api.html).

diff --git a/jobs/parallel-calculations.md b/jobs/parallel-calculations.md
@@ -242,8 +242,7 @@ Transport layer PML (point-to-point message layer):
 Transport layer UCX:
 <https://www.openucx.org/ and https://github.com/openucx/ucx/wiki/UCX-environment-parameters>
 
-Collective optimisation library hcoll from Mellanox is also an option:
-<https://docs.mellanox.com/pages/viewpage.action?pageId=12006295>
+Collective optimisation library hcoll from Mellanox is also an option.
 
 Setting the different devices and transports can be done using environment variables:
 ```

diff --git a/services/easydmp-user-documentation-rfk.md b/services/easydmp-user-documentation-rfk.md
@@ -10,7 +10,6 @@ orphan: true
 - {ref}`Review and manage your plans  <Review-and-manage-your-plan-rfk>`
 - {ref}`Export your plan  <Management-Options-rfk>`
 - {ref}`Request support  <Request-Support-easydmp-rfk>`
-- {ref}`Example plan <Example-plan-rfk>`
 
 
 (access-easydmp-rfk)=
@@ -91,10 +90,3 @@ You can click on the ‘cog’ next to your plan title (see the above figure). C
 
 If you experience any problems, or you have any question, please contact  <[email protected]>.
 Your request will be handled within the next 24 hours during working days.
-
-
-
-(Example-plan-rfk)=
-## Example plan
-
-An example plan can be found [here](https://www.sigma2.no/sites/default/files/imce/Support/ExamplePlan.pdf).
diff --git a/software/application_guides/bioinfo/obitools.md b/software/application_guides/bioinfo/obitools.md
@@ -23,7 +23,7 @@ To use OBITools type
 ## License Information
 
 OBITools is available under the [CeCILL v2
-license](https://cecill.info/licences/Licence_CeCILL_V2-en.html)
+license](http://www.cecill.info/licences/Licence_CeCILL_V2-en.html).
 
 It is the user's responsibility to make sure they adhere to the license agreements.
 

diff --git a/software/application_guides/castep/castep.md b/software/application_guides/castep/castep.md
@@ -19,7 +19,9 @@ website](http://www.castep.org).
 (access)=
 ### License and access
 
-The CASTEP Developers' Group (CDG) and Cambridge Enterprise have announced a cost-free worldwide source code license to CASTEP and NMR CASTEP for academic use. Detailed information about this is given [here](http://www.castep.org/CASTEP/GettingCASTEP).
+The CASTEP Developers' Group (CDG) and Cambridge Enterprise have announced a
+cost-free worldwide source code license to CASTEP and NMR CASTEP for academic
+use.
 
 To get access to CASTEP, you need to follow the procedure described below. 
 
@@ -47,7 +49,7 @@ We will then have to manually verify this information with STFC UK/CASTEP before
 
 ### Citation
 
-For the recommended citation, please consult the [CASTEP referencing page](http://www.castep.org/CASTEP/ReferencingAndLogo).
+For the recommended citation, please consult the [CASTEP page](http://www.castep.org).
 
 ## CASTEP on NRIS machinery
 
@@ -87,7 +89,7 @@ and one called ethene.param with the contents
 
 Running **CASTEP** would produce an ethene.castep file (amongst others) within seconds for the running examples provided below. Towards the end of this file, there are final structure energy outputs printed, ```Final energy, E```; values here should be in the range of -378.015eV.
 
-A subset of the benchmark sets, the medium set [al3x3](http://www.castep.org/CASTEP/Al3x3) and [solid benzene](http://www.castep.org/CASTEP/SolidBenzene) together with the ethene-example used here has been added to the CASTEP home folder on both Fram and Saga. You get them into your working directory by typing
+A subset of the benchmark sets, the medium set al3x3 and solid benzene together with the ethene-example used here has been added to the CASTEP home folder on both Fram and Saga. You get them into your working directory by typing
 
 ```bash
 cp /cluster/software/CASTEP/benchmarks/* .

diff --git a/software/application_guides/ncview.md b/software/application_guides/ncview.md
@@ -2,7 +2,7 @@
 
 Ncview is a visual browser for NetCDF files.
 
-[More information here.](http://meteora.ucsd.edu/~pierce/ncview_home_page.html)
+[More information here.](https://cirrus.ucsd.edu/~pierce/software/ncview/index.html)
 
 ## Running Ncview
 

diff --git a/software/application_guides/paraview_web.md b/software/application_guides/paraview_web.md
@@ -17,7 +17,9 @@ Running ParaView through a container has a few advantages:
 
 In this guide, we are going to use containers provided on NVIDIA NGC, which is a hub for GPU-optimized software for deep learning, machine learning, and HPC: https://catalog.ngc.nvidia.com/orgs/nvidia-hpcvis/containers/paraview
 
-**NOTE**: We are going to use `$USERWORK` for space purposes. Please, remember that this folder is subject to automatic clean up: https://documentation.sigma2.no/files_storage/clusters.html#user-work-area . It might be necessary to download the container again at some point in the future (which will be available as long as Nvidia maintains it) but, DO NOT store important data under this directory.
+**NOTE**: We are going to use `$USERWORK` for space purposes. Please, remember that this folder is subject to automatic clean up
+(see also {ref}`storage-areas`).
+It might be necessary to download the container again at some point in the future (which will be available as long as Nvidia maintains it) but, DO NOT store important data under this directory.
 
 
 ## Pulling ParaView image
@@ -39,7 +41,7 @@ This will create a `.sif` file in the directory from where you pulled it (you ca
 
 **WARNING**: If you want to run a different ParaView version, you can do so by replacing the url after "docker://", copying the new one from here: https://catalog.ngc.nvidia.com/orgs/nvidia-hpcvis/containers/paraview/tags.
 
-However, if you do this, be careful to use the correct PATH for Paraview because for tags `egl-py3-5.9.0` and `egl-py3-5.8.0`, Paraview was installed in `/opt/paraview` whereas for tags `egl-py3-5.11.0`, `glx-5.6.0rc3` and `egl-5.6.0rc` it is installed in `/usr/local/paraview`, so modify the PATH in "[Apptainer exec command](https://documentation.sigma2.no/software/application_guides/paraview.html#running-the-container)" accordingly.
+However, if you do this, be careful to use the correct PATH for Paraview because for tags `egl-py3-5.9.0` and `egl-py3-5.8.0`, Paraview was installed in `/opt/paraview` whereas for tags `egl-py3-5.11.0`, `glx-5.6.0rc3` and `egl-5.6.0rc` it is installed in `/usr/local/paraview`, so modify the PATH in the `apptainer exec` command accordingly.
 
 
 ## Allocating resources for the project

diff --git a/software/userinstallsw/mathematica.md b/software/userinstallsw/mathematica.md
@@ -42,7 +42,7 @@ singularity run --bind path/mathematica-license.txt:/root/.WolframEngine/Licensi
 
 ## Your first mathematica job
 
-To create the job script we recommend using the [Slurm job script generator](https://open.pages.sigma2.no/job-script-generator/.https://open.pages.sigma2.no/job-script-generator/). The following is an example of a job script that runs a Mathematica script named `mathematica-script.wl` on Fram :
+To create the job script we recommend using the [Slurm job script generator](https://open.pages.sigma2.no/job-script-generator/). The following is an example of a job script that runs a Mathematica script named `mathematica-script.wl` on Fram :
 
 ```bash
 #!/bin/bash

diff --git a/training/events/2021-11-hpc-nird-toolkit-user-course.md b/training/events/2021-11-hpc-nird-toolkit-user-course.md
@@ -144,12 +144,12 @@ Break for 10 minutes
 - **Session Q&A: 12:50-13:00 Questions & Answers**
 
 
-### Day 3: 04-11-2021:  Containers on HPC and NIRD Toolkit
+### Day 3: 04-11-2021: Containers on HPC and NIRD Toolkit
 
 - **Get ready: 08:50-09:00 Connect to zoom meeting**
 
 - **Session 1: 09:00-10:20 Containers on HPC (part I)**
-    - [Course material](https://documentation.sigma2.no/software/containers.html)
+    - {ref}`Course material <running-containers>`
 
 Break for 10 minutes
 

diff --git a/training/events/2022-11-best-practices-on-NRIS-clusters.md b/training/events/2022-11-best-practices-on-NRIS-clusters.md
@@ -85,7 +85,7 @@ The course is free of charge and is organised by the NRIS partners UiB, UiO, UiT
 - 10:05-10:45 - [Software Installation - Python Packages Continues](https://documentation.sigma2.no/software/userinstallsw/python.html) (Sabry Razick & Jørn Dietze)
 - 10:45-11:00 - Break
 - 11:00-11:30 - [R packages](https://documentation.sigma2.no/software/userinstallsw/R.html) (Sabry Razick & Jørn Dietze)
-- 11:30-12:15 - [Singularity on HPC](https://documentation.sigma2.no/software/containers.html) (Sabry Razick & Jørn Dietze)
+- 11:30-12:15 - {ref}`Singularity on HPC <running-containers>` (Sabry Razick & Jørn Dietze)
 - 12:15-12:30 - Q&A 
 
 ## Code of Conduct