Cleaning

guides/index.rst

@@ -1,7 +1,7 @@
----
-toc: no
-title: Guides
-...
+
+
+Guides
+======
 
 * :doc:`User guides <user/index>`
 * :doc:`Application guides </applications/index>`

guides/user/account.rst

@@ -1,17 +1,18 @@
----
-title: Accounts and quotas
-...
+
+===================
+Accounts and quotas
+===================
 
 Getting started on the machine (account, quota, password)
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+=========================================================
 
 Before you start using Stallo, please read the :doc:`University of Tromsø's guidelines <guidelines>`.
 
 A general introduction to Notur can be found at
 `http://www.notur.no/quotas/rules/ <http://www.notur.no/quotas/rules/>`_
 
 How to get an account and a CPU quota on Stallo
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+===============================================
 
 To be able to work on Stallo you must have an account and you must have
 been granted CPU time on the system. There are two ways to achieve this:
@@ -38,7 +39,7 @@ Before you start using Stallo, please read the `University of
 Tromsø's guidelines <guidelines>`_.
 
 Information about how to log in on Stallo with ssh, and how to learn more about ssh.
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+====================================================================================
 
 An SSH client (Secure SHell) is the required tool to connect to
 Stallo. To learn more about this, check out the `Metasenter page on SSH 
@@ -47,13 +48,13 @@ Stallo. To learn more about this, check out the `Metasenter page on SSH
 .. FIXME: fix link to docs.notur.no 
 
 Obtain a new password
-~~~~~~~~~~~~~~~~~~~~~
+=====================
 
 When you have been granted an account on stallo.uit.no, your username and password is sent to you separat. 
 the username by email and the password by SMS.  The password you receive by SMS is temporally and only valid for 7 days.  
 
 The passwd command does not seem to work. My password is reset back to the old one after a while. Why is this happening?
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+------------------------------------------------------------------------------------------------------------------------
 
 The Stallo system is using a centralised database for user management.
 This will override the password changes done locally on Stallo.

guides/user/accounting.rst

@@ -1,9 +1,9 @@
----
-title: Accounting
-...
+
+Accounting
+==========
 
 CPU quota.
-~~~~~~~~~~
+----------
 
 To use the batch system you have to have a cpu quota, either local or
 natinoal. For every job you submit we check that you have sufficient
@@ -12,14 +12,14 @@ cpu-hours to run the job. The job will be submitted to queue, but will
 not start until you have enough cpu-hours to run it.
 
 Resource charging.
-~~~~~~~~~~~~~~~~~~
+------------------
 
 The accounting system charges for used processor equivalents (PE)
 times used walltime so if you ask for more than 2GB of memory per cpu
 you will get charged for more than the actual cpus you use.
 
 Processor equivalents.
-~~~~~~~~~~~~~~~~~~~~~~
+----------------------
 
 The best way to describe PE is maybe by example: Assume that you have a
 node with 8 cpu-cores and 16 GB memory (as most nodes on stallo are):
@@ -33,7 +33,7 @@ node with 8 cpu-cores and 16 GB memory (as most nodes on stallo are):
     if you ask for 16GB memory then PE=8 as you only can run one cpu per compute node.
 
 Inspecting your quota.
-~~~~~~~~~~~~~~~~~~~~~~
+----------------------
 
 You can use the cost command to check how much cpu-hours are left on
 your allocation:
@@ -60,7 +60,7 @@ Deposited:
     Allocated normal quota
 
 Inspecting historic use.
-~~~~~~~~~~~~~~~~~~~~~~~~
+------------------------
 
 You can view the accounting history of your projects using:
 
@@ -76,12 +76,12 @@ for more detail see:
 
 
 Job accounting.
-~~~~~~~~~~~~~~~~~~~~~~~~~
+---------------
 
 We charge for used resources, both cpu and memory.
 
 CPU quota.
-~~~~~~~~~~
+----------
 
 To use the batch system you have to have a cpu quota, either local or
 natinoal. For every job you submit we check that you have sufficient
@@ -90,14 +90,14 @@ cpu-hours to run the job. The job will be submitted to queue, but will
 not start until you have enough cpu-hours to run it.
 
 Resource charging.
-~~~~~~~~~~~~~~~~~~
+------------------
 
 The accounting system charges for used processor equivalents (PE)
 times used walltime so if you ask for more than 2GB of memory per cpu
 you will get charged for more than the actual cpus you use.
 
 Processor equivalents.
-~~~~~~~~~~~~~~~~~~~~~~
+----------------------
 
 The best way to describe PE is maybe by example: Assume that you have a
 node with 8 cpu-cores and 16 GB memory (as most nodes on stallo are):
@@ -111,14 +111,7 @@ node with 8 cpu-cores and 16 GB memory (as most nodes on stallo are):
     if you ask for 16GB memory then PE=8 as you only can run one cpu per compute node.
 
 Live status information
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-Live status information from Stallo
-
-Live status information
-~~~~~~~~~~~~~~~~~~~~~~~
-
-
+-----------------------
 
 From our monitoring tool Ganglia, you can watch live status information
 on Stallo:

guides/user/basics.rst

@@ -1,6 +1,7 @@
----
-title: Basic Information
-...
+
+
+Basic Information
+=================
 
 - Something about accounting, cpu quota on top of what is in the quick-start guide?
 

guides/user/firstjob.rst

@@ -1,12 +1,13 @@
----
-title: Example: First jobscript.
-...
+
+
+Example: First jobscript.
+=========================
 .. index:: first jobscript
 
 .. FIXME: inline job script example
 
 Setting up your first job-script.
-==========================================
+---------------------------------
 
 A job script is just a regular shell-script with some comments that are directives telling the batch system which resources this script needs when running.  
 
@@ -45,7 +46,7 @@ Here you see that your job is submitted with the queue with the job identity ``1
 
 
 Further reading.
-=====================
+----------------
 
 * :doc:`Batch system <./jobs>`.
 

guides/user/guidelines.rst

@@ -1,15 +1,12 @@
----
-title: Guidelines
-...
 
 Guidelines
-------------
+==========
 
 Guidelines for use of computer equipment at the University of Tromso
 
 
 Definitions
-~~~~~~~~~~~~~~~
+-----------
 
  Explanation of words and expressions used in these guidelines.
 
@@ -48,7 +45,7 @@ resources:
     equipment.
 
 Purpose
-~~~~~~~~~~~
+-------
 
  The purpose of these guidelines is to contribute towards the
 development of a computer environment in which the potential provided by
@@ -58,7 +55,7 @@ research and to disseminate knowledge about scientific methods and
 results.
 
 Application
-~~~~~~~~~~~~~~~
+-----------
 
  These guidelines apply to the use of the University's computer
 equipment and apply to all users who are granted access to the computer
@@ -68,7 +65,7 @@ The use of the computer equipment also requires that the user knows any
 possible supplementary regulations.
 
 Good Faith
-~~~~~~~~~~~~~~
+----------
 
  Never leave any doubt as to your identity and give your full name in
 addition to explaining your connection to the University. A user is
@@ -86,7 +83,7 @@ responsibility to ensure that copies of data owned or used by the
 University are secured on behalf of the University.
 
 Data Safety
-~~~~~~~~~~~~~~~
+-----------
 
  Users are obliged to take the necessity measures to prevent the loss of
 data etc. by taking back-up copies, careful storage of media, etc. This
@@ -103,7 +100,7 @@ the equipment to the closest superior or to the person who is
 responsible for data safety.
 
 Respect for Other Users Privacy
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+-------------------------------
 
  Users may not try to find out another persons password, etc., nor try
 to obtain unauthorized access to another persons data. This is true
@@ -122,7 +119,7 @@ definition in section 13 second section of the Administration Law,
 (forvaltningslovens section 13 annet ledd).
 
 Proper Use
-~~~~~~~~~~~~~~
+----------
 
  The computer equipment of the University may not be used to advance
 slander or discriminating remarks, nor to distribute pornography or
@@ -134,14 +131,14 @@ The computer equipment is to be used in accordance with the aims of the
 University. This excludes direct commercial use.
 
 Awareness of the Purposes for Use of Resources
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+----------------------------------------------
 
  The computer equipment of the University is to strengthen and support
 professional activity, administration, research and teaching. Users have
 a co-responsibility in making the best possible use of the resources.
 
 Rights
-~~~~~~~~~~
+------
 
  Data is usually linked to rights which make their use dependent on
 agreements with the holder of the rights. Users commit themselves to
@@ -150,7 +147,7 @@ makes data accessible. The copying of programs in violation of the
 rights of use and/or license agreement is not permitted.
 
 Liability
-~~~~~~~~~~~~~~
+---------
 
  Users themselves are responsible for the use of data which is made
 accessible via the computer equipment. The University disclaims all
@@ -162,7 +159,7 @@ responsible for damage or loss suffered by users as a consequence of
 insufficient protection of their own data.
 
 Surveillance
-~~~~~~~~~~~~~~~~~
+------------
 
  The systems manager has the right to seek access to the individual
 user's reserved areas on the equipment for the purpose of ensuring the
@@ -182,7 +179,7 @@ circumstances which could represent a violation of these guidelines may
 be reported to superior authorities.
 
 Sanctions
-~~~~~~~~~~~~~~
+---------
 
  Breach of these guidelines can lead to the user being denied access to
 the University's data services, in addition to which there are sanctions
@@ -196,7 +193,7 @@ University. Disciplinary measures against students are passed by the
 University Council, ref. section 47 of the University law.
 
 Complaints
-~~~~~~~~~~~~~~~
+----------
 
  Complaints about sanctions are to be directed to the person(s) who
 order sanctions. If the complaint is not complied with, it is sent on to

guides/user/helpdesk.rst

@@ -1,10 +1,11 @@
----
-title: Helpdesk
-...
+
+
+Helpdesk
+========
 
 
 Information regarding help-desk support
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+---------------------------------------
 
 How to get user support.
 
@@ -22,12 +23,12 @@ send an email to :doc:`support-uit@notur.no <mailto:support-uit@notur.no>`.
 From the web page you can also track your requests.
 
  Please remember to consult the :doc:`Stallo User Guide <.>` and the
-:doc:`FAQ <../faq>` for information that you are looking for.
+:ref:`faq` for information that you are looking for.
 
 
 
 About support requests
-~~~~~~~~~~~~~~~~~~~~~~
+----------------------
 
 * Requests will be handled as soon as possible by the support staff.
 * Please be as detailed as possible about your problem when submitting