Merge pull request #29 from mathiasbockwoldt/moreerrors

Remove even more errors that I did not see in first round due to caching

account/account.rst

@@ -10,23 +10,23 @@ Before you start using Stallo, please read the UiT The Arctic University of Norw
 
 A general introduction to Notur can be found at
 `https://www.notur.no/use-notur-resources <https://www.notur.no/use-notur-resources>`_
-                                  
+
 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:
 
 Research Council Quota
-------------------------
+----------------------
 
 National users (including users from UiT) may apply for an account and
 a CPU quota from the Research Councils share of Stallo. If you want to
-apply for such a quota please use this `National quota form.  
+apply for such a quota please use this `National quota form.
 <https://www.metacenter.no/mas/application/project/>`_
 
 UiT Quota
------------
+---------
 
 “Local users” (i.e. users from UiT and users affiliated with UiT in some way) can apply for an account and
 a quota from UiT’s share of Stallo. If you wan to apply for such a quota follow the instructions here:

account/login.rst

@@ -36,21 +36,24 @@ Log in with an ssh-key
 
 SSH clients for Windows and Mac
 -------------------------------
+
 At the `OpenSSH page <http://www.openssh.com>`_ you will find several *SSH* alternatives for both Windows and Mac.
 
 Please note that Mac OS X comes with its own implementation of *OpenSSH*, so you don't need to install any third-party software to take advantage of the extra security *SSH* offers. Just open a terminal window and jump in.
 
 
 Learning more about SSH
 -----------------------
+
 To learn more about using SSH, please also consult the `OpenSSH page <http://www.openssh.com>`_ page and take a look at the manual page on your system (*man ssh*).
 
 
 
 Obtain a new password
 =====================
+
 When you have been granted an account on stallo.uit.no, your username and password is sent to you separately.
-The username by email and the password by SMS. The password you receive by SMS is temporally and only valid for 7 days. 
+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?
@@ -98,16 +101,16 @@ Below is an example on how you can do this:
 
 ::
 
-    1) Log in on Stallo with display forwarding.  
+    1) Log in on Stallo with display forwarding.
+
+       $ ssh -Y stallo.uit.no
 
-       $ ssh -Y stallo.uit.no                       
-    
     2) Reserve and log in on a compute node with display forwarding.
        (start an interactive job.)
 
        $ srun srun -N 1 -t 1:0:0 --pty bash -i
-    
-    3) Open a new terminal window, type squeue -j <jobid> (it shows you which node(s) was allocated 
+
+    3) Open a new terminal window, type squeue -j <jobid> (it shows you which node(s) was allocated
        to that specific job). Then ssh -Y <nodename> to that node and start your preferred gui.
 
 
@@ -116,15 +119,15 @@ Graphical logon to Stallo
 
 If you want to run applications with graphical user interfaces we recommend you to use the
 `remote desktop service <http://stallo-gui.uit.no/vnc/>`_
-on Stallo. 
+on Stallo.
 
 If you have a new account and you have never logged in on Stallo before, first log in with a classical ssh connection (see above). Afterwards you can use the graphical logon. Otherwise it can happen that your /home will not be created and you will get an error message of the type: "Could not chdir to home directory /home/your_user_name: No such file or directory"
 
 **Important:**
- 
-If you are connecting from outside the networks of UNINETT and partners you need to log into 
+
+If you are connecting from outside the networks of UNINETT and partners you need to log into
 stallo-gui.uit.no with ssh to verify that you have a valid username and password on the Stallo system.
-After a successful login the service will automatically allow you to connect from the ip-address 
-your client currently has. The connection will be open for at least 5 minutes after you log in. 
-There is no need to keep the ssh-connection open after you have connected to the remote desktop, 
+After a successful login the service will automatically allow you to connect from the ip-address
+your client currently has. The connection will be open for at least 5 minutes after you log in.
+There is no need to keep the ssh-connection open after you have connected to the remote desktop,
 in fact you will be automatically logged off after 5 seconds.

account/uitquota.rst

@@ -23,6 +23,4 @@ To get a local account on Stallo, you need to provide us with:
 
 **If you are a student, PhD or post-doc,** you need to also provide us with the name of your advisor and name of the project you are to be a member of.
 
-
 Compile this list in a proper manner and send to support-uit@notur.no.
-

applications/chemistry/Gaussian/GaussView.rst

@@ -1,9 +1,11 @@
+.. _gaussview:
+
 ======================
 GaussView for Gaussian
 ======================
 
-Gaussview is a visualization program that can be used to open Gaussian output files and checkpoint files (.chk) to display structures, molecular orbitals, normal modes, etc. You can also set up jobs and submit them directly. 
- 
+Gaussview is a visualization program that can be used to open Gaussian output files and checkpoint files (.chk) to display structures, molecular orbitals, normal modes, etc. You can also set up jobs and submit them directly.
+
 
 GaussView on Stallo
 --------------------
@@ -17,4 +19,4 @@ More information about GaussView:
 ---------------------------------
 * General info about the program: http://www.gaussian.com/g_prod/gv5.htm
 * Online reference: http://www.gaussian.com/g_tech/gv5ref/gv5ref_toc.htm
- 
+

applications/chemistry/Gaussian/advanced.rst

@@ -1,4 +1,4 @@
-.. _g09:
+.. _gaussian09:
 
 ===========
 Gaussian 09
@@ -21,11 +21,8 @@ http://www.gaussian.com/g_tech/g_ur/g09help.htm.
 
 Please do read these sections carefully.
 
-**Information related to inputs and output:**
 
-* For information about Gaussian input: :ref:`gaussian_input`
-* For input-example to download: :ref:`gaussian_water_input`
-* For information on Gaussview for Gaussian: :ref:`gaussview`
+For information on Gaussview for Gaussian: :ref:`gaussview`
 
 
 Gaussian 09 on Stallo
@@ -41,14 +38,6 @@ Currently, both the minor revision b.01 and c.01 are available on Stallo, the de
 
 If you download a run script (see below), this will be taken care of by the script (though you have to change to your preferred flavor of the Gaussian 09 code). Two run scripts are available (for running in serial and parallel, respectively). Download one of the scripts to your home/$USER/bin and use it as described.
 
-Scriptfile-examples
--------------------
-
-- :ref:`gaussian_serial_run`
-- :ref:`gaussian_para_run`
-
-(These scripts are also available on Stallo under /global/apps/gaussian/usage).
-
 
 Job submission guidelines
 --------------------------
@@ -87,7 +76,7 @@ Best practice for running Gaussian 09 jobs
 -------------------------------------------
 
 - For geometry optimizations using DFT methods, we recommends using hybrid functionals. For pure functionals (no HF exchange) - unless you have tested it and know it works - we recommend to run Gaussian 09 only on not more than 3 nodes, using 14-16 cores/node. For hybrid functionals we have seen decent scaling up to 8 nodes using 16 cores/node for minor revision c.01. On old Stallo - we saw time gain up to 12 nodes, using 7 cores/node with c.01 and up to 8 nodes with b.01.
-- If your molecule is >60 atoms, Gaussian uses FMM by default (which is not parallelized), so do not run parallel in this case, unless you turn off FMM (NoFMM keyword). FMM is enabled for non-symmetric molecules with 60 atoms or more. For molecules with high symmetry this limit is 240 atoms for hybrid DFT and 360 atoms for pure DFT. (The text below is copied from http://www.gaussian.com/g_tech/g_ur/m_linda.htm)::
+- If your molecule is >60 atoms, Gaussian uses FMM by default (which is not parallelized), so do not run parallel in this case, unless you turn off FMM (NoFMM keyword). FMM is enabled for non-symmetric molecules with 60 atoms or more. For molecules with high symmetry this limit is 240 atoms for hybrid DFT and 360 atoms for pure DFT. (The text below is copied from http://www.gaussian.com/g_tech/g_ur/m_linda.htm):
 
 HF, CIS=Direct, and DFT calculations on molecules are Linda parallel, including energies, optimizations and frequencies. TDDFT energies and gradients and MP2 energies and gradients are also Linda parallel. Portions of MP2 frequency and CCSD calculations are Linda parallel, but others are only SMP-parallel, so they see some speedup from using a few nodes but no further improvement from larger numbers of nodes.
 

applications/chemistry/Gaussian/gaussian_on_stallo.rst

@@ -4,24 +4,24 @@
 About the Gaussian install on Stallo
 =====================================
 
-This page contains info about special features related to 
+This page contains info about special features related to
 the Gaussian install made on Stallo, but also generall issues
 vaguely documented elsewhere.
 
 Gaussian on Stallo:
 -------------------
 
-First note is that the Gaussian install on Stallo is the Linda parallel version, so it 
-scales somewhat initially. On top of this, Gaussian on Stallo is installed with a little trick, where the executables are intercepted before launced, and an 
-alternative socket library is loaded. This enables the possibility of running Gaussian natively on the infiniband 
+First note is that the Gaussian install on Stallo is the Linda parallel version, so it
+scales somewhat initially. On top of this, Gaussian on Stallo is installed with a little trick, where the executables are intercepted before launced, and an
+alternative socket library is loaded. This enables the possibility of running Gaussian natively on the infiniband
 network giving us two advantages:
 
 * The parallel faction of gaussian executables scales a lot "longer" (to more cores).
-* The shared memory performance is significantly enhanced (small scale performance). 
+* The shared memory performance is significantly enhanced (small scale performance).
 
-But since we do this trick, we are greatly depending on altering the specific nodal adress into the 
-input file: To run gaussian in parallel requires the additional keywords %LindaWorkers and %NProcshared 
-in the Link 0 part of the input file. This is taken care of by a wrapper, and is commented in jobscript example file. 
+But since we do this trick, we are greatly depending on altering the specific nodal adress into the
+input file: To run gaussian in parallel requires the additional keywords %LindaWorkers and %NProcshared
+in the Link 0 part of the input file. This is taken care of by a wrapper, and is commented in jobscript example file.
 Please do use this script or similar when submitting jobs; it will benefit all of us.
 
 We have also taken care of the rsh/ssh setup in our installation procedure, to avoid .tsnet.config dependency for users.
@@ -37,22 +37,22 @@ f cores to mirror the need. This also means that you allways should ask for full
 The %mem allocation of memory in the Gaussian input file means two things:
 
 * In general it means memory/node – for share between nprocshared, and aditional to the memory allocated pr. process. This is also documented by Gaussian.
-* For the mother superior (mother process/node) it also represents the network buffer allocated by Linda. So basically G09 takes a part and Linda takes a part the same 
-  size – thus you should never ask for more than half of the physical memory on the nodes, unless they have swap space available - which you never should assume. 
-  Basically, the general %mem limit will allways be half of the physical memory pool given in MB instead of GB - 16000MB instead of 16GB since this leaves a small part for the system. 
+* For the mother superior (mother process/node) it also represents the network buffer allocated by Linda. So basically G09 takes a part and Linda takes a part the same
+  size – thus you should never ask for more than half of the physical memory on the nodes, unless they have swap space available - which you never should assume.
+  Basically, the general %mem limit will allways be half of the physical memory pool given in MB instead of GB - 16000MB instead of 16GB since this leaves a small part for the system.
 
-For core-count, node-count and amounts of memory on Stallo, see :ref: about_stallo_ 
+For core-count, node-count and amounts of memory on Stallo, see :ref:`about_stallo`
 
 
 Scalability and parallel performance of Gaussian on Stallo:
 ------------------------------------------------------------
 
-Due to the nifty trick mentioned above, we have a somewhat more generous policy when it comes to 
+Due to the nifty trick mentioned above, we have a somewhat more generous policy when it comes to
 allocating cores/nodes to Gaussian jobs:
 
 #. We do advice people to use up to 16 nodes, at least 12 full nodes, with the current install on Stallo. We have proved acceptale scaling of the current
    Gaussian install beyond 16 nodes with 16 cores on each. So in essence; at least up to 16 nodes. Enjoy.
-#. Linda networking overhead seems to hit hard around this amount of cores; causing us to be somewhat reluctant to advice going to more than this. On the 
-   other hand, this will give you a maximum of 320 cores with the most recent hardware available on Stallo. 
+#. Linda networking overhead seems to hit hard around this amount of cores; causing us to be somewhat reluctant to advice going to more than this. On the
+   other hand, this will give you a maximum of 320 cores with the most recent hardware available on Stallo.
 
 We have been looking into issues related to this, and expect this situation to change when the new Gaussian Major release comes out late 2016/ early 2017.

applications/physics/COMSOL/COMSOL.rst

@@ -1,49 +1,49 @@
 .. _COMSOL:
 
-===========================================
+======================================
 The COMSOL Multiphysics software suite
-===========================================
+======================================
 
 Information regarding the computational physics program system COMSOL
 
 General Information:
-=====================
+====================
 
 Description:
----------------
+------------
 
 COMSOL Multiphysics® is a general-purpose software platform, based on advanced numerical methods, for modeling and simulating physics-based problems. It is highly visual, based on graphical interfaces - so users are adviced to use either the client installation on their client machine or the remote graphics solution on Stallo.
 
 Online info from vendor:
---------------------------
+------------------------
 
-* Homepage: http://www.comsol.com 
+* Homepage: http://www.comsol.com
 * Documentation/support: https://www.comsol.com/support
 
 
 License information:
-----------------------
+--------------------
 
 The license of COMSOL is commercial/proprietary.
 
 The installation of COMSOL on Stallo is for UiT users only. If you need/want access to COMSOL, you need to contact UiT support.
 
 
 Citation
-----------
+--------
 
 When publishing results obtained with the referred software referred, please do check the developers web page in order to find the correct citat\
 ion(s).
 
 
 Additional online info about COMSOL on Stallo:
-=================================================
+==============================================
 
 Usage
-------
+-----
 
 
-COMSOL is a rather memory intensive code, so we would generally advice users to either run their jobs on the highmem-nodes (with 8GB/core of memory) or less than full nodes on the slim nodes. 
+COMSOL is a rather memory intensive code, so we would generally advice users to either run their jobs on the highmem-nodes (with 8GB/core of memory) or less than full nodes on the slim nodes.
 
 Use
 
@@ -57,7 +57,7 @@ to see which versions of COMSOL are available. Use
 
  $ module load COMSOL/<version> # i.e 5.3-intel-2016a
 
-to get access to any given version of COMSOL.  
+to get access to any given version of COMSOL.
 
 The license of comsol is installed as a floating network license type, meaning that there is a server checking out license tokens upon request.
 If you want to know whether there are available license tokens or not, load the module as above. Then type
@@ -67,7 +67,7 @@ If you want to know whether there are available license tokens or not, load the
     $ lmstat -c $LMCOMSOL_LICENSE_FILE -a
 
 The first time you run an COMSOL job on Stallo?
-----------------------------------
+-----------------------------------------------
 
 Get the information you need here:
 
@@ -78,7 +78,7 @@ Get the information you need here:
  firsttime_comsol.rst
 
 
-Here we hold information for how to run on Stallo for the first time, and for using SLURM for the first time. 
+Here we hold information for how to run on Stallo for the first time, and for using SLURM for the first time.
 
 
 Happy calculations!

applications/physics/COMSOL/firsttime_comsol.rst

@@ -1,25 +1,22 @@
 .. _first_time_comsol:
 
-===================================
+=================================
 First time you run an COMSOL job?
-===================================
+=================================
 
-This page contains info aimed at first time 
-users of COMSOL on Stallo, but may also be usefull to 
-more experienced users. Please look carefully through the 
-provided examples. Also note that the job-script example is rather richly 
+This page contains info aimed at first time
+users of COMSOL on Stallo, but may also be usefull to
+more experienced users. Please look carefully through the
+provided examples. Also note that the job-script example is rather richly
 commented to provide additional and relevant info.
 
-If you want to run this testjob, download the copies of the scripts and put them 
+If you want to run this testjob, download the copies of the scripts and put them
 into your test job folder (which I assume you have created in advance).
 
 COMSOL input example:
---------------------
+---------------------
 
-.. include:: ../files/comsol_smalltest.mph
-   :literal:
-
-This file can also be downloaded here: :download:`Small test for COMSOL <../files/comsol_smalltest.mph>`.
+The file used in this example can also downloaded here: :download:`Small test for COMSOL <../files/comsol_smalltest.mph>`.
 
 Place this file in a job folder of choice, say COMSOLFIRSTJOB in your home directory on Stallo.
 

development/environment.rst

@@ -14,4 +14,4 @@ implementations are supported. By using the default compiler and MPI library,
 these problems can be avoided. In the future, we aim to automate the process so
 that all possible (valid) permutations are allowed.
 
-Read the :ref:`applications` section for an introduction on how to use modules.
+Read the :ref:`module_scheme` section for an introduction on how to use modules.