Cleaning files

applications/applications.rst

@@ -1,23 +1,23 @@
----
-toc: no
-title: Applications
-...
+.. _applications:
+
+Applications
+============
 
 Overview over SW installed on Stallo
 --------------------------------------
 
 For a complete list of applications see the :doc:`software page <software>`.
 
 Missing / new SW?
-...................
+-----------------
 
 If there is any SW missing on this list that you would like to have
 installed on Stallo, or you need help to install your own SW, please
 feel free to contact the support personal about this:
 :doc:`support-uit@notur.no <support-uit@notur.no>`
 
 Changes in application software
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+-------------------------------
 
 New and updated software will be announced on `UiT
 News <http://docs.notur.no/uit/uit-news>`_.
@@ -33,7 +33,7 @@ List all version of a specific software::
     module avail software-name
 
 Modules
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+-------
 
 Software installations on the clusters span many applications, and many
 different version numbers of the same application. It is not possible
@@ -44,7 +44,7 @@ specific session, there is a system for loading and unloading 'modules'
 which activate and deactivate the relevant parts of your user session.
 
 The modules command
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+-------------------
 
 An introduction to the Modules Command; a way to navigate between
 various settings, libraries and SW versions
@@ -63,7 +63,7 @@ page about link about Modules
 
 
 Which modules are loaded?
-~~~~~~~~~~~~~~~~~~~~~~~~~
+-------------------------
 
 To see the modules currently active in your session, use the
 command  
@@ -75,7 +75,7 @@ command
 
 
 Which modules are available?
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+----------------------------
 
 In order to see a complete list of available modules, issue the
 command 
@@ -93,7 +93,7 @@ pattern:
 *  (default) if default version
 
 How are modules loaded?
-~~~~~~~~~~~~~~~~~~~~~~~
+-----------------------
 
 In order to enable to make available, for instance, the netcdf library,
 issue the command  
@@ -114,7 +114,7 @@ just include the version:
 
 
 How are modules unloaded?
-~~~~~~~~~~~~~~~~~~~~~~~~~
+-------------------------
 
 Keeping with the above example, use the following command to unload the
 GLView module again:  
@@ -124,7 +124,7 @@ GLView module again:
     module unload netcdf
 
 Which version of a module is the default?
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+-----------------------------------------
 
 In order to see, for instance, which version of netcdf is loaded by the
 module, use:
@@ -138,7 +138,7 @@ This will show the version and path of the module.
 
 
 How do I switch to a different version of a module?
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+---------------------------------------------------
 
 Switching to another version is similar to loading a specific version.
 As an example, if you want to switch from the default (current) Intel
@@ -149,7 +149,7 @@ compilers version to version 8.0, type
     module switch intelcomp intelcomp/8.0
 
 How do I switch to a different version of a module?
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+---------------------------------------------------
 
 Say you want to switch from the intel compilers  version 11.1 to, e.g.
 version 11.0, use  

applications/index.rst

@@ -1,7 +1,4 @@
----
-toc: no
-title: Applications
-...
+.. _chem_prog_packages:
 
 Chemistry program packages 
 -----------------------------

applications/software.rst

@@ -1,10 +1,7 @@
----
-toc: no
-title: Applications
-...
+.. _sw_list:
 
-By category
-~~~~~~~~~~~~~~
+Applications by category
+========================
 
 * `Development packages <http://hpc.uit.no/software/development.html>`_
 * `Full package list <http://hpc.uit.no/software>`_

first_login_and_job.rst

@@ -1,9 +1,10 @@
----
-title: Logging in and running your first job (on Stallo).
-...
+.. _first_job:
+
+Logging in and running your first job (on Stallo).
+==================================================
 
 Install an ssh client.
-============================
+----------------------
 
 Linux and Mac users should already have an ssh client installed.  Windows users can use 
 `Putty <http://www.chiark.greenend.org.uk/~sgtatham/putty/download.html>`_.  
@@ -12,7 +13,7 @@ Linux and Mac users should already have an ssh client installed.  Windows users
 `Putty ssh intor on google <http://lmgtfy.com/?q=putty+ssh+intro>`_.
 
 Logging in.
-============================
+-----------
 
 First you connect from your computer with ssh.  Lets assume your username is marve::
 

getting_started.rst

@@ -1,11 +1,13 @@
----
-title: Getting started.
-...
-
 .. contents:: Table of contents.
 
 .. index:: getting started, quickstart guide
 
+.. _getting_started:
+
+===============
+Getting started
+===============
+
 The really quick and dirty startup guide for the pathologically impatient
 ================================================================================================