updating wrt modules

source/software/software_stack.rst

@@ -1,8 +1,19 @@
 .. _specific software documentation:
 
-Packages with additional documentation
+Using MATLAB and R
 ======================================
 
+Some programming languages have an extensive standard library, and
+additionally allow to install extra packages. For most languages, the
+user can install packages in his own home directory without system
+administrator intervention. Some documentation for doing this for
+:ref:`Perl <Perl packages>` and :ref:`Python <Python packages>` is 
+provided.
+
+MATLAB and R are two of such programming languages, where we would
+like to introduce some of their specific features.
+
+
 MATLAB (a package by `MathWorks`_)
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
@@ -21,12 +32,3 @@ R
    r_command_line_arguments_in_scripts
    r_integrating_c_functions
 
-Programming Languages
----------------------
-
-Some programming languages have an extensive standard library, but
-optionally allow to install extra packages. For most languages, the
-user can install packages in his own home directory without system
-administrator intervention. Some documentation for doing this for
-:ref:`Perl <Perl packages>` and :ref:`Python <Python packages>` is provided.
-

source/software/using_software.rst

@@ -4,27 +4,38 @@ Using software
 Software installation and maintenance on HPC infrastructure such as the
 VSC clusters poses a number of challenges not encountered on a
 workstation or a departmental cluster. For many libraries and programs,
-multiple versions have to installed and maintained as some users require
+multiple versions have to be installed and maintained as some users require
 specific versions of those. In turn, those libraries or executables sometimes
 rely on specific versions of other libraries, further complicating the
 matter.
 
 The way Linux finds the right executable for a command, and a program
 loads the right version of a library or a plug-in, is through so-called
 environment variables. These can, e.g., be set in your shell
-configuration files (e.g., ``.bashrc``), but this requires a certain
+configuration files (e.g., ``.bashrc``); however, this requires a certain
 level of expertise. Moreover, getting those variables right is tricky
 and requires knowledge of where all files are on the cluster. Having to
 manage all this by hand is clearly not an option.
 
 We deal with this on the VSC clusters in the following way.
 
-* First, we've defined the concept of a :ref:`toolchain <toolchains>`. They consist of a set of compilers, MPI library and basic libraries that work together well with each other, and then a number of applications and other libraries compiled with that set of tools and thus often dependent on those. We use tool chains based on the Intel and GNU compilers, and refresh them twice a year, leading to version numbers like 2021a, 2021b or 2022a for the first and second refresh of a given year. Some tools are installed outside a toolchain, e.g., additional versions requested by a small group of users for specific experiments, or tools that only depend on basic system libraries.
+* First, we've defined the concept of a :ref:`toolchain <toolchains>`. 
+  They consist of a set of compilers, MPI libraries and basic libraries 
+  that work together well with each other. Then come a number of applications 
+  and other libraries compiled with those set of tools, and hence depending
+  on them. We use toolchains based on the Intel and GNU compilers. New toolchains
+  which offer reasonable compute performance are regularly installed, leading to 
+  version numbers like 2021a, 2021b or 2022a (for the first and second halves of 
+  a given year). Some tools are installed outside a toolchain, e.g., additional 
+  versions requested by a small group of users for specific experiments, or tools 
+  that only depend on basic system libraries.
 
-* Second, we use the `module system <module_system>` to manage the environment variables and all dependencies and possible conflicts between various programs and libraries.
+* Second, we use the `module system <module_system>` to manage the environment 
+  variables and all dependencies and to prevent possible conflicts between various 
+  programs and libraries.
 
 
-!!!!!!!!HERE SHOULD COME A LINK TOTHE GENERATED PAGE WITH AVAILABLE SOFTWARE!!!!!!!!!
+!!!!!!!!HERE SHOULD COME A LINK TO THE GENERATED PAGE WITH AVAILABLE SOFTWARE!!!!!!!!!
 
 .. toctree::
    :maxdepth: 2