Merge branch 'SCS5Software' into 'preview'

SCS5Software: Fix checks

See merge request zih/hpc-compendium/hpc-compendium!116

doc.zih.tu-dresden.de/docs/software/SCS5Software.md

@@ -13,23 +13,24 @@ Here are the major changes from the user's perspective:
 
 ## Host Keys
 
-Due to the new operating system, the host keys of the login nodes have
-also changed. If you have logged into tauruslogin6 before and still have
-the old one saved in your `known_hosts` file, just remove it and accept
-the new one after comparing its fingerprint with those listed under
-[Login](Login#tableLogin2).
+Due to the new operating system, the host keys of the login nodes have also changed. If you have
+logged into tauruslogin6 before and still have the old one saved in your `known_hosts` file, just
+remove it and accept the new one after comparing its fingerprint with those listed under
+[Login](../access/Login.md#ssh-access).
 
-## Using software modules
+## Using Software Modules
 
 Starting with SCS5, we only provide
-[Lmod](RuntimeEnvironment#Lmod:_An_Alternative_Module_Implementation) as
-the environment module tool of choice.
+[Lmod](../data_management/RuntimeEnvironment.md#lmod-an-alternative-module-implementation) as the
+environment module tool of choice.
 
 As usual, you can get a list of the available software modules via:
 
-    module available
-    # or short:
-    ml av
+```Bash
+module available
+# or short:
+ml av
+```
 
 There is a special module that is always loaded (sticky) called
 **modenv**. It determines the module environment you can see.
@@ -47,48 +48,45 @@ still work under SCS5. That's why those modenv versions are hidden.
 
 Example:
 
-    $ ml modenv/classic ansys/19.0
+```Bash
+$ ml modenv/classic ansys/19.0
 
-    The following have been reloaded with a version change:
-      1) modenv/scs5 => modenv/classic
+The following have been reloaded with a version change:
+  1) modenv/scs5 => modenv/classic
 
-    Module ansys/19.0 loaded.
+Module ansys/19.0 loaded.
+```
 
 **modenv/scs5** will be loaded by default and contains all the software
 that was built especially for SCS5.
 
 ### Which modules should I use?
 
-If possible, please use the modules from **modenv/scs5**. In case there
-is a certain software missing, you can write an email to
-<hpcsupport@zih.tu-dresden.de> and we will try to install the latest
-version of this particular software for you.
+If possible, please use the modules from **modenv/scs5**. In case there is a certain software
+missing, you can write an [email to hpcsupport](mailto:hpcsupport@zih.tu-dresden.de) and we will try
+to install the latest version of this particular software for you.
 
-However, if you still need *older* versions of some software, you have
-to resort to using the modules in the old module environment
-(**modenv/classic** most probably). We won't keep those around forever
-though, so in the long-term, it is advisable to migrate your workflow to
-up-to-date versions of the software used.
+However, if you still need *older* versions of some software, you have to resort to using the
+modules in the old module environment (**modenv/classic** most probably). We won't keep those around
+forever though, so in the long-term, it is advisable to migrate your workflow to up-to-date versions
+of the software used.
 
 ### Compilers, MPI-Libraries and Toolchains
 
-Since we are mainly using EasyBuild to install software now, we are
-following their toolchain schemes:
-<http://easybuild.readthedocs.io/en/latest/Common-toolchains.html>
+Since we are mainly using EasyBuild to install software now, we are following their
+[toolchain schemes](http://easybuild.readthedocs.io/en/latest/Common-toolchains.html).
 
-We mostly install software using the "intel" toolchain, because in most
-cases, the resulting code performs best on our Intel-based
-architectures. There are alternatives like GCC (foss), PGI or Clang/LLVM
-though.
+We mostly install software using the "intel" toolchain, because in most cases, the resulting code
+performs best on our Intel-based architectures. There are alternatives like GCC (foss), PGI or
+Clang/LLVM though.
 
-Generally speaking, the toolchains in this new environment are separated
-into more parts (modules) than you will be used to, coming from
-modenv/classic. A full toolchain, like "intel", "foss" or "iomkl"
-consists of several sub-modules making up the layers of
+Generally speaking, the toolchains in this new environment are separated into more parts (modules)
+than you will be used to, coming from modenv/classic. A full toolchain, like "intel", "foss" or
+"iomkl" consists of several sub-modules making up the layers of
 
--   compilers
--   MPI library
--   math library (providing BLAS/LAPACK/FFT routines etc.)
+- compilers
+- MPI library
+- math library (providing BLAS/LAPACK/FFT routines etc.)
 
 For instance, the "intel" toolchain has the following structure:
 
@@ -108,8 +106,8 @@ On the other hand, the "foss" toolchain looks like this:
 | mpi library    | OpenMPI             |
 | math libraries | OpenBLAS, FFTW      |
 
-If you want to combine the Intel compilers and MKL with OpenMPI, you'd
-have to use the "iomkl" toolchain:
+If you want to combine the Intel compilers and MKL with OpenMPI, you'd have to use the "iomkl"
+toolchain:
 
 |              |            |
 |--------------|------------|
@@ -118,40 +116,34 @@ have to use the "iomkl" toolchain:
 | mpi library  | OpenMPI    |
 | math library | imkl       |
 
-There are also subtoolchains that skip a layer or two, e.g. "iccifort"
-only consists of the respective compilers, same as "GCC". Then there is
-"iompi" that includes Intel compilers+OpenMPI but no math library, etc.
+There are also subtoolchains that skip a layer or two, e.g. "iccifort" only consists of the
+respective compilers, same as "GCC". Then there is "iompi" that includes Intel compilers+OpenMPI but
+no math library, etc.
 
 #### What is this "GCCcore" I keep seeing and how does it relate to "GCC"?
 
-GCCcore includes only the compilers/standard libraries of the GNU
-compiler collection but without "binutils". It is used as a dependency
-for many modules without getting in the way, e.g. the Intel compilers
-also rely on libstdc++ from GCC, but you don't want to load two compiler
-modules at the same time, so "intel" also depends on "GCCcore". You can
-think of it as more of a runtime dependency rather than a full-fledged
-compiler toolchain. If you want to compile your own code with the GNU
-compilers, you have to load the module: "**GCC"** instead, "GCCcore"
-won't be enough.
-
-There are [ongoing
-discussions](https://github.com/easybuilders/easybuild-easyconfigs/issues/6366)
-in the EasyBuild community to maybe change this in the future in order
-to avoid the potential confusion this GCCcore module brings with it.
+GCCcore includes only the compilers/standard libraries of the GNU compiler collection but without
+"binutils". It is used as a dependency for many modules without getting in the way, e.g. the Intel
+compilers also rely on libstdc++ from GCC, but you don't want to load two compiler modules at the
+same time, so "intel" also depends on "GCCcore". You can think of it as more of a runtime dependency
+rather than a full-fledged compiler toolchain. If you want to compile your own code with the GNU
+compilers, you have to load the module: "**GCC"** instead, "GCCcore" won't be enough.
+
+There are [ongoing discussions](https://github.com/easybuilders/easybuild-easyconfigs/issues/6366)
+in the EasyBuild community to maybe change this in the future in order to avoid the potential
+confusion this GCCcore module brings with it.
 
 #### I have been using "bullxmpi" so far, where can I find it?
 
-bullxmpi was more or less a rebranded OpenMPI 1.6 with some additions
-from Bull. It is not supported anymore and Bull has abandoned it in
-favor of a standard OpenMPI 2.0.2 build as their default in SCS5. You
-should migrate your code to our OpenMPI module or maybe even try Intel
-MPI instead.
+bullxmpi was more or less a rebranded OpenMPI 1.6 with some additions from Bull. It is not supported
+anymore and Bull has abandoned it in favor of a standard OpenMPI 2.0.2 build as their default in
+SCS5. You should migrate your code to our OpenMPI module or maybe even try Intel MPI instead.
 
 #### Where have the analysis tools from Intel Parallel Studio XE gone?
 
-Since "intel" is only a toolchain module now, it does not include the
-entire Parallel Studio anymore. Tools like the Intel Advisor, Inspector,
-Trace Analyzer or VTune Amplifier are available as separate modules now:
+Since "intel" is only a toolchain module now, it does not include the entire Parallel Studio
+anymore. Tools like the Intel Advisor, Inspector, Trace Analyzer or VTune Amplifier are available as
+separate modules now:
 
 | product               | module    |
 |:----------------------|:----------|