Corrected and updated several links.

Author: klust

docs/2022-CSC_and_LO/1_Intro/1_01_what_is_easybuild.md

@@ -4,14 +4,14 @@
 
 <p align="center"><img src="../../../img/easybuild_logo_alpha.png" alt="EasyBuild logo" width="300px"/></p>
 
-**[EasyBuild](http://easybuild.io)** is a **software build and installation framework**
+**[EasyBuild](https://easybuild.io)** is a **software build and installation framework**
 that manages (scientific) software in an efficient way, without compromising on performance.
 Easybuild is especially tailored towards [**High Performance Computing (HPC)**](https://en.wikipedia.org/wiki/Supercomputer) systems,
 and provides a **command-line interface** to facilitate the installation and management of a scientific software stack.
 
 ---
 
-<a href="http://geek-and-poke.com/geekandpoke/2010/5/14/how-to-become-invaluable.html">
+<a href="https://geek-and-poke.com/geekandpoke/2010/5/14/how-to-become-invaluable.html">
 <img src="../../../img/geek-and-poke-invaluable.png" style="float:right" width="45%"/>
 </a>
 
@@ -68,7 +68,7 @@ as it is performed.
 
 EasyBuild supports using a **custom module naming scheme**, allows for
 *hierarchical* module naming schemes, and **integrates with various other tools** ranging from  resource managers ([Slurm](https://slurm.schedmd.com) and [GC3Pie](https://github.com/gc3pie/gc3pie)),
-container tools ([Singularity](https://github.com/hpcng/singularity) and [Docker](https://www.docker.com)),
+container tools ([Singularity](https://github.com/apptainer/singularity) and [Docker](https://www.docker.com)),
 packaging tools ([FPM](https://fpm.readthedocs.io)), and so on.
 
 ---
@@ -127,7 +127,7 @@ and to [**contribute back**](https://docs.easybuild.io/en/latest/Contributing.ht
 by opening pull requests to the [GitHub repositories](https://github.com/easybuilders) or the [documentation](https://docs.easybuild.io).
 
 The EasyBuild community also provides packages for two standard toolchains, called the 
-[**common toolchains**](https://easybuild.readthedocs.io/en/latest/Common-toolchains.html). 
+[**common toolchains**](https://docs.easybuild.io/en/latest/Common-toolchains.html). 
 The so-called ``foss`` is based on free and open software (GNU compilers, FlexiBlas with OpenBLAS backend, LaPACK, FFTW and Open MPI)
 while the ``intel`` toolchain uses the full stack of Intel compilers, libraries and MPI. Currently these toolchains
 cannot be supported on LUMI though as getting Open MPI to run on LUMI is challenging and as the Intel libraries and
@@ -137,7 +137,7 @@ Focusing the efforts on those two popular common toolchains makes it possible to
 collected in the [central repository](https://github.com/easybuilders/easybuild-easyconfigs).
 They can still serve as a basis to develop build recipes for the HPE Cray Programming Environment.
 
-Last but not least, EasyBuild provides various [**GitHub integration features**](https://easybuild.readthedocs.io/en/latest/Integration_with_GitHub.html)
+Last but not least, EasyBuild provides various [**GitHub integration features**](https://docs.easybuild.io/en/latest/Integration_with_GitHub.html)
 that greatly facilitate the contribution process: opening, updating, and testing pull requests,
 reviewing incoming contributions, and much more can all be done directly from the EasyBuild
 command line. This not only saves time, effort, brain cycles, and mouse clicks for contributors,
@@ -225,12 +225,12 @@ sites leverage it, and integrate it with other tools like [Jenkins](https://www.
 
 HPC sites, consortia, and companies that use EasyBuild include (but are not limited to):
 
-<a href="https://vscentrum.be"><img src="../../../img/vsc_logo.png" alt="VSC logo" width="40%"></a>
+<a href="https://www.vscentrum.be"><img src="../../../img/vsc_logo.png" alt="VSC logo" width="40%"></a>
 <a href="https://www.fz-juelich.de/ias/jsc"><img src="../../../img/jsc_logo.png" alt="JSC logo" width="28%"></a>
 <a href="https://hpcnow.com/"><img src="../../../img/hpcnow_logo.png" alt="HPCNow! logo" width="25%"></a>
 <a href="https://www.fredhutch.org/"><img src="../../../img/fredhutch_logo.png" alt="Fred Hutch logo" width="22%"></a>
 <a href="https://www.viennabiocenter.org/"><img src="../../../img/vienna_biocenter_logo.png" alt="Vienna BioCenter logo" width="23%"></a>
-<a href="http://www.ceci-hpc.be/"><img src="../../../img/ceci_logo.png" alt="CÉCI logo" width="18%"></a>
+<a href="https://www.ceci-hpc.be/"><img src="../../../img/ceci_logo.png" alt="CÉCI logo" width="18%"></a>
 <a href="https://www.computecanada.ca/home/"><img src="../../../img/computecanada_logo.png" alt="Compute Canada logo" width="32%"></a>
 <a href="https://www.uio.no/english/services/it/research/hpc/"><img src="../../../img/uio_logo.png" alt="UiO logo" width="25%"></a>
 <a href="https://intranet.birmingham.ac.uk/bear"><img src="../../../img/bear_logo.png" alt="BEAR logo" width="20%"></a>
@@ -242,7 +242,7 @@ HPC sites, consortia, and companies that use EasyBuild include (but are not limi
 <a href="https://dashboard.hpc.unimelb.edu.au/"><img src="../../../img/univ_melbourne_logo.png" alt="University of Melbourne logo" width="16%"></a>
 <a href="https://hpc.uni.lu/"><img src="../../../img/unilu_logo.png" alt="University of Luxembourg logo" width="18%"></a>
 <a href="https://www.epcc.ed.ac.uk/"><img src="../../../img/epcc_logo.png" alt="EPCC logo" width="21%"></a>
-<a href="http://hpcf.cyi.ac.cy/"><img src="../../../img/cyi_logo.png" alt="Cyprus Institute logo" width="26%"></a>
+<a href="https://hpcf.cyi.ac.cy/"><img src="../../../img/cyi_logo.png" alt="Cyprus Institute logo" width="26%"></a>
 <a href="https://scicore.unibas.ch/"><img src="../../../img/basel_logo.png" alt="University of Basel logo" width="26%"></a>
 <a href="https://techcommunity.microsoft.com/t5/azure-global/running-long-hpc-jobs-on-azure-with-checkpointing-using-lammps/ba-p/1335148"><img src="../../../img/microsoft_logo.png" alt="Microsoft logo" width="23%"></a>
 

docs/2022-CSC_and_LO/1_Intro/1_02_Lmod.md

@@ -78,7 +78,7 @@ to a hierarchy with 3 levels:
     Here is a simple example of such a 3-level module hierarchy
     (that almost could have been generated by EasyBuild):
 
-    <div align="center"><img src="../../img/hmns.png" width="60%"/></div>
+    <div align="center"><img src="../../../img/hmns.png" width="60%"/></div>
 
     In this example the ``Core`` level only includes a single module `GCC/9.3.0`,
     while  the ``Compiler`` level includes two modules: `OpenMPI/4.0.3` and `MPICH/3.3.2`.
@@ -268,7 +268,7 @@ is included in the module files to improve discoverability of software.
 
 !!! Note "Documentation in the LUMI documentation"
     Extensive information on search commands with examples of how to use them on LUMI can be found
-    in the [LUMI documentation]([https://)](https://docs.lumi-supercomputer.eu/), in
+    in the [LUMI documentation](https://docs.lumi-supercomputer.eu/), in
     [the computing section, "Module environment page", "Finding modules" section](https://docs.lumi-supercomputer.eu/computing/Lmod_modules/#finding-modules).
 
 

docs/2022-CSC_and_LO/1_Intro/1_03_CPE.md

@@ -122,7 +122,8 @@ LUMI environment and the integration with the Cray environment still seems to be
 The Cray PE also provides a programming environment module to enable
 the Intel® oneAPI compiler and tools. 
 
-The documentation is available in the [Intel® oneAPI Programming Guide](https://software.intel.com/content/www/us/en/develop/documentation/oneapi-programming-guide/top/oneapi-development-environment-setup.html)
+The documentation is available in the 
+[Intel® oneAPI Programming Guide](https://www.intel.com/content/www/us/en/develop/documentation/oneapi-programming-guide/top/oneapi-development-environment-setup.html)
 
 Cray provides a bundled package of support libraries to install into the Cray PE to enable the Intel compiler, allowing
 utilities such as debuggers and performance tools to work with it. 
@@ -166,7 +167,7 @@ The CSML collection contains the following Scientific Libraries:
 
 * Manpages: `intro_mpi`
 
-* Website: [http://www.mpi-forum.org](http://www.mpi-forum.org)
+* Website: [http://www.mpi-forum.org](https://www.mpi-forum.org)
 
 MPI is a widely used parallel programming model that establishes a practical, portable, efficient, 
 and flexible standard for passing messages between ranks in parallel processes. 

docs/2022-CSC_and_LO/1_Intro/1_05_terminology.md

@@ -85,8 +85,11 @@ The `foss` toolchain consists of all open source components (hence the name:
 In recent versions (since 2021a), [FlexiBLAS](https://www.mpi-magdeburg.mpg.de/projects/flexiblas)
 is used as the BLAS library, with OpenBLAS and LAPACK as the backend.
 
-The `intel` toolchain consists of the [Intel C, C++ and Fortran compilers](https://software.intel.com/content/www/us/en/develop/tools/compilers.html) (on top of a `GCC` version
-controlled through EasyBuild) alongside the [Intel MPI](https://software.intel.com/content/www/us/en/develop/tools/mpi-library.html) and [Intel MKL](https://software.intel.com/content/www/us/en/develop/tools/math-kernel-library.html) libraries.
+The `intel` toolchain consists of the 
+[Intel C, C++ and Fortran compilers](https://www.intel.com/content/www/us/en/developer/tools/oneapi/dpc-compiler.html) 
+(on top of a `GCC` version controlled through EasyBuild) alongside the 
+[Intel MPI](https://www.intel.com/content/www/us/en/developer/tools/oneapi/mpi-library.html) and 
+[Intel MKL](https://www.intel.com/content/www/us/en/developer/tools/oneapi/onemkl.html) libraries.
 
 Roughly every 6 months, a new version of these common toolchains is agreed upon
 in the EasyBuild community, after extensive testing.

docs/2022-CSC_and_LO/1_Intro/1_06_installation.md

@@ -85,11 +85,11 @@ If you see output that starts with a line like "`VERSION=3.2.10`" or "`Modules R
 you have the original Tcl-based environment modules tool installed, either in its original
 C-based imnplementation (``VERSION=3.2.10``) or the new Tcl-based implementation developed at CEA
 (``Modules Release 4.5.0``)
-and <a href="https://easybuild.readthedocs.io/en/latest/Configuration.html#modules-tool-modules-tool">*EasyBuild will need to be configured to use it after installation*</a>.
+and <a href="https://docs.easybuild.io/en/latest/Configuration.html#modules-tool-modules-tool">*EasyBuild will need to be configured to use it after installation*</a>.
 
 If the `module` function is not defined either you do not have a modules tool installed
 or your environment is not properly set up to use it. In this case,
-please refer to the EasyBuild documentation <a href="https://easybuild.readthedocs.io/en/latest/Installation.html#required-modules-tool">here</a> for more information.
+please refer to the EasyBuild documentation <a href="https://docs.easybuild.io/en/latest/Installation.html#required-modules-tool">here</a> for more information.
 
 HPE Cray supports both the old-style Environments Modules (based on version 3.2.10) and Lmod. On LUMI,
 we use Lmod as the default module system for users, and EasyBuild is configured to use that one.
@@ -466,7 +466,7 @@ eb --show-config
 ```
 
 This should tell you that EasyBuild (ab)uses `$HOME/.local/easybuild` as a default location.
-More on configuring EasyBuild in the [next part of the tutorial](configuration).
+More on configuring EasyBuild in the [next part of the tutorial](../1_07_configuration).
 
 #### System information
 

docs/2022-CSC_and_LO/1_Intro/1_07_configuration.md

@@ -186,7 +186,7 @@ archive, the location of which is specified by the `repositorypath` configuratio
 
 By default the specified path is assumed to be a regular directory, but using a Git repository
 as easyconfigs archive is also supported (for more details, see 
-[the EasyBuild documentation](https://easybuild.readthedocs.io/en/latest/Configuration.html#easyconfigs-repository-repository-repositorypath)).
+[the EasyBuild documentation](https://docs.easybuild.io/en/latest/Configuration.html#easyconfigs-repository-repository-repositorypath)).
 
 
 ---
@@ -204,7 +204,7 @@ are using a different modules tool; see the output of `eb --avail-modules-tools`
 modules tools.
 Note that for anything other than Lmod, you *must* make
 sure that the actual modules tool binary command is available through `$PATH` (more information
-on this [in the EasyBuild documentation](https://easybuild.readthedocs.io/en/latest/Configuration.html#modules-tool-modules-tool)).
+on this [in the EasyBuild documentation](https://docs.easybuild.io/en/latest/Configuration.html#modules-tool-modules-tool)).
 
 If you prefer that EasyBuild generates module files in [Tcl](https://tcl.tk/) syntax, you can instruct
 it to do so via the `module-syntax` configuration setting. Note that this is *required* if you are using
@@ -246,7 +246,7 @@ software.***
     There are ways around this however, which are outside of the scope of this tutorial.
 
     For more information, 
-    [see the EasyBuild documentation](https://easybuild.readthedocs.io/en/latest/Using_the_EasyBuild_command_line.html#controlling-robot-search-path).
+    [see the EasyBuild documentation](https://docs.easybuild.io/en/latest/Using_the_EasyBuild_command_line.html#controlling-robot-search-path).
 
     *On LUMI the included easyconfig files cannot be used without changes as they are for the
     common toolchains which are currently not supported in the LUMI software stacks.*  
@@ -280,7 +280,7 @@ The default `EasyBuildMNS` module naming scheme roughly corresponds to the filen
 and consists of the software name followed by a combination of the software version, toolchain and
 an optional label (which corresponds to the value of the `versionsuffix` easyconfig parameter):
 `<name>/<version><-toolchain><versionsuffix>`. Just like with [names of easyconfig
-files](1_05_terminology#easyconfig-files), the `<-toolchain>` part is omitted when the `system` toolchain is used,
+files](../1_05_terminology#easyconfig-files), the `<-toolchain>` part is omitted when the `system` toolchain is used,
 and the `<versionsuffix>` value is empty by default.
 
 !!! Note "Module naming scheme on LUMI"
@@ -366,9 +366,9 @@ across different software installations. They define *configuration settings*,
 such as the location where software should be installed, or the syntax that should
 be used when generating module files.
 
-An [easyconfig file](1_05_terminology#easyconfig-files) (`*.eb`) on the other hand *specifies the details for one particular software installation*.
+An [easyconfig file](../1_05_terminology#easyconfig-files) (`*.eb`) on the other hand *specifies the details for one particular software installation*.
 It does this by defining a set of *easyconfig parameters*, which tell EasyBuild the name and version
-of the software to install, which [toolchain](1_05_terminology#toolchains) and [easyblock](1_05_terminology#easyblocks) to use, etc.
+of the software to install, which [toolchain](../1_05_terminology#toolchains) and [easyblock](../1_05_terminology#easyblocks) to use, etc.
 
 For each software installation performed by EasyBuild, there is a corresponding easyconfig file.
 There typically are only a handful of configuration files used however, for example a system-level

docs/2022-CSC_and_LO/1_Intro/1_08_basic_usage.md

@@ -189,7 +189,7 @@ operations involving lots of (small) files can be slow.
 
 For the easyconfig files included with an EasyBuild release, a search index is readily provided.
 For other directories, you can create a search index using `eb --create-index <path>`.
-[See the EasyBuild documentation for more information](https://easybuild.readthedocs.io/en/latest/Easyconfigs_index.html).
+[See the EasyBuild documentation for more information](https://docs.easybuild.io/en/latest/Easyconfigs_index.html).
 
 ---
 
@@ -307,7 +307,7 @@ are already installed, and which ones are still missing.
 This can be helpful to ensure that your EasyBuild configuration is set up correctly,
 and to prevent from accidentally installing an entirely new software stack from scratch
 in an unintended location (like `$HOME/.local/easybuild`, the
-[default installation path](../configuration/#install-path)).
+[default installation path](../1_07_configuration/#install-path)).
 
 ---
 

docs/2022-CSC_and_LO/2_Using/2_01_troubleshooting.md

@@ -28,7 +28,8 @@ Things that could go wrong during an installation include:
 * required dependencies that are not specified in the easyconfig file;
 * failing shell commands;
 * running out of available memory or disk space;
-* a segmentation fault caused by a flipped bit triggered by a cosmic ray ([really, it happens!](https://blogs.oracle.com/linux/attack-of-the-cosmic-rays-v2));
+* a segmentation fault caused by a flipped bit triggered by a cosmic ray 
+  ([really, it happens!](https://blogs.oracle.com/linux/post/attack-of-the-cosmic-rays));
 
 Unfortunately this is not an exhaustive list, there are plenty of other
 potential problems that could result in a failing installation...
@@ -219,7 +220,7 @@ Let's work our way through a less smooth software installation,
 using the easyconfig file that is provided below.
 
 Don't worry if most of this is still unclear to you, we'll get
-to writing easyconfig files from scratch [later in this tutorial](2_02_creating_easyconfig_files).
+to writing easyconfig files from scratch [later in this tutorial](../2_02_creating_easyconfig_files).
 
 ```python
 easyblock = 'MakeCp'

docs/2022-CSC_and_LO/2_Using/2_02_creating_easyconfig_files.md

@@ -58,15 +58,15 @@ Reasons to consider implementing a software-specific easyblock rather than using
     bootstrapping with the system compiler and then re-installing with itself.* 
 
 For implementing easyblocks we refer to the 
-["Implementing easyblocks" section of this tutorial](2_03_implementing_easyblocks)
+["Implementing easyblocks" section of this tutorial](../2_04_implementing_easyblocks)
 and the [EasyBuild documentation](https://docs.easybuild.io/en/latest/Implementing-easyblocks.html).
 
 ## Writing easyconfig files
 
 Writing an easyconfig file boils down to defining a set of easyconfig parameters in a text file,
 which we give a '`.eb`' extension by convention. The name of an easyconfig file doesn't matter
 when using it directly to install software, but it does matter when EasyBuild needs to find it
-to resolve a dependency for example (as we [discussed earlier](../1_08_basic_usage/#easyconfig-filenames)).
+to resolve a dependency for example (as we [discussed earlier](../../1_Intro/1_08_basic_usage/#easyconfig-filenames)).
 
 The syntax for easyconfig files is *Python syntax*: you are basically defining a bunch of Python variables
 that correspond to easyconfig parameters.
@@ -469,7 +469,7 @@ moduleclass = 'lib'
 ```
 
 This is done to categorize software, and it is used to group the generated module files into smaller sets 
-([remember what we saw when installing software earlier](../1_08_basic_usage/#using-installed-software)).
+([remember what we saw when installing software earlier](../../1_Intro/1_08_basic_usage/#using-installed-software)).
 
 This is currently not used on LUMI since we feel that (a) it is not easy to explain to users how they can
 then only make certain classes that are useful to them visible and more importantly (b) since it is not
@@ -590,9 +590,9 @@ In this simple case it doesn't, since we can leverage one of the available *gene
 But, which one?
 
 Build instructions are usually included in a `README` file, or in the documentation.
-In this case, there's indeed a minimal [`README`
-file](https://github.com/easybuilders/easybuild-tutorial/tree/main/docs/files/eb-tutorial-1.0.1/README) available,
-which tells us that we should use the `cmake` command to configure the installation, followed by `make` and `make install`.
+In this case, there's indeed a minimal 
+[`README` file](https://github.com/easybuilders/easybuild-tutorial/blob/main/docs/files/eb-tutorial-1.0.1/README) 
+available, which tells us that we should use the `cmake` command to configure the installation, followed by `make` and `make install`.
 
 [We briefly discussed](#easyblock) a generic easyblock that does exactly this: `CMakeMake`.