Merge branch 'remark' of gitlab.it4i.cz:it4i-admins/docs.it4i into remark

docs.it4i/salomon/software/intel-xeon-phi.md

 # Intel Xeon Phi
 
-\##A guide to Intel Xeon Phi usage
+## A guide to Intel Xeon Phi usage
 
 Intel Xeon Phi can be programmed in several modes. The default mode on Anselm is offload mode, but all modes described in this document are supported.
 
@@ -600,13 +600,13 @@ An example of basic MPI version of "hello-world" example in C language, that can
 Intel MPI for the Xeon Phi coprocessors offers different MPI programming models:
 
 !!! Note "Note"
-	**Host-only model** - all MPI ranks reside on the host. The coprocessors can be used by using offload pragmas. (Using MPI calls inside offloaded code is not supported.)
+    **Host-only model** - all MPI ranks reside on the host. The coprocessors can be used by using offload pragmas. (Using MPI calls inside offloaded code is not supported.)
 
     **Coprocessor-only model** - all MPI ranks reside only on the coprocessors.
 
     **Symmetric model** - the MPI ranks reside on both the host and the coprocessor. Most general MPI case.
 
-\###Host-only model
+### Host-only model
 
 In this case all environment variables are set by modules, so to execute the compiled MPI program on a single node, use:
 

docs.it4i/salomon/software/mpi/mpi4py-mpi-for-python.md

@@ -52,7 +52,7 @@ For example
     comm.Barrier()   # wait for everybody to synchronize
 ```
 
-\###Collective Communication with NumPy arrays
+### Collective Communication with NumPy arrays
 
 ```cpp
     from __future__ import division

docs.it4i/salomon/software/numerical-languages/matlab.md

@@ -245,7 +245,7 @@ This is an example of m-script using direct mode:
 
 ### Non-interactive Session and Licenses
 
-If you want to run batch jobs with Matlab, be sure to request appropriate license features with the PBS Pro scheduler, at least the " -l **feature**matlab\_\_MATLAB=1" for EDU variant of Matlab. More information about how to check the license features states and how to request them with PBS Pro, please [look here](../../../anselm-cluster-documentation/software/isv_licenses/).
+If you want to run batch jobs with Matlab, be sure to request appropriate license features with the PBS Pro scheduler, at least the `-l __feature__matlab__MATLAB=1` for EDU variant of Matlab. More information about how to check the license features states and how to request them with PBS Pro, please [look here](../../../anselm-cluster-documentation/software/isv_licenses/).
 
 The licensing feature of PBS is currently disabled.
 

docs.it4i/software/lmod.md

 # Lmod Environment
 
-Lmod as a modules tool, a modern alternative to the oudated & no longer actively maintained Tcl-based environment modules tool.
+Lmod is a modules tool, a modern alternative to the oudated & no longer actively maintained Tcl-based environment modules tool.
 
 Detailed documentation on Lmod is available at [here](http://lmod.readthedocs.io).
 
 ## Benefits
 
--   significantly more responsive module commands, in particular module avail (ml av)
--   easier to use interface
--   module files can be written in either Tcl or Lua syntax (and both types of modules can be mixed together)
+* significantly more responsive module commands, in particular module avail (ml av)
+* easier to use interface
+* module files can be written in either Tcl or Lua syntax (and both types of modules can be mixed together)
 
 ## Introduction
 
@@ -39,7 +39,7 @@ Currently Loaded Modules:
 ```
 
 !!! tip
-	for more details on sticky modules, see the section on [ml purge](#resetting-by-unloading-all-modules-ml-purge-module-purge)
+    for more details on sticky modules, see the section on [ml purge](#resetting-by-unloading-all-modules-ml-purge-module-purge)
 
 ## Searching for available modules: ml av (module avail) and ml spider
 
@@ -59,11 +59,11 @@ $ ml av
 
 In the current module naming scheme, each module name consists of two parts:
 
--   the part before the first /, corresponding to the software name; and
--   the remainder, corresponding to the software version, the compiler toolchain that was used to install the software, and a possible version suffix
+* the part before the first /, corresponding to the software name; and
+* the remainder, corresponding to the software version, the compiler toolchain that was used to install the software, and a possible version suffix
 
 !!! tip
-	The (D) indicates that this particular version of the module is the default, but we strongly recommend to not rely on this as the default can change at any point. Usuall, the default will point to the latest version available.
+    The (D) indicates that this particular version of the module is the default, but we strongly recommend to not rely on this as the default can change at any point. Usuall, the default will point to the latest version available.
 
 ## Searching for modules: ml spider
 
@@ -235,7 +235,7 @@ For example, once you have loaded one or more modules that were installed with t
 
 In addition, only **one single version** of each software package can be loaded at a particular time. For example, once you have the Python/3.5.2-intel-2017.00 module loaded, you can not load a different version of Python in the same session/job script; neither directly, nor indirectly as a dependency of another module you want to load.
 
-Unloading modules: ml -<modname(s)> (module unload <modname(s)>)
+Unloading modules: ml modname(s) (module unload modname(s))
 
 To revert the changes to the environment that were made by a particular module, you can use module unload or ml -<modname>.
 For example:

docs.it4i/software/orca.md

@@ -32,6 +32,7 @@ Currently Loaded Modulefiles:
 
 Create a file called orca_serial.inp that contains the following orca commands
 
+```cpp
     # My first ORCA calculation :-)
     #
     # Taken from the Orca manual
@@ -41,6 +42,7 @@ Create a file called orca_serial.inp that contains the following orca commands
       C 0 0 0
       O 0 0 1.13
     *
+```
 
 Create a Sun Grid Engine submission file called submit_serial.sh that looks like this