Merge pull request #70 from university-of-york/feature/newpages

fix errors
university-of-york · Oct 24, 2023 · 2d80133 · 2d80133
2 parents 5857142 + 3053508
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diff --git a/docs/source/__pycache__/replacements.cpython-38.pyc b/docs/source/__pycache__/replacements.cpython-38.pyc
diff --git a/docs/source/getting_started/backing_up.rst b/docs/source/getting_started/backing_up.rst
@@ -26,6 +26,12 @@ To move your data from Viking and to the Filestore ("Storage"), the address you
 
     sftp.york.ac.uk:/shared/storage/<filestore>
 
+
+.. tip::
+
+    Please speak to your department if you need access to your department's shared filestore.
+
+
 You can use ``PuTTY`` on Windows and the command line on Linux and MacOS with commands such as ``rsync``  and ``scp`` much like the examples on the :ref:`Data Management page <transfer_files_linux>`, examples below.
 
 .. code-block:: console

diff --git a/docs/source/getting_started/code_of_conduct.rst b/docs/source/getting_started/code_of_conduct.rst
@@ -23,7 +23,7 @@ Virtual desktop sessions don't close if you simply disconnect, this is to allow
 Backing up data
 ----------------
 
-The ``scratch`` folder, the main folder in your home directory where you store data, is not backed up. This is partyly due to the sheer size of the filesystem and so this means that backing up your data is every users responsibility. In the worst case scenario all data could be lost, therefore you should regularly :doc:`back up your data </getting_started/backing_up>`.
+The ``scratch`` folder, a large area in your home directory where you can store data, is **not backed up**. This is partly due to the sheer size of the filesystem and so this means that backing up your data is each users responsibility. In a worst case scenario all data could be lost, therefore you should regularly :doc:`back up your data </getting_started/backing_up>`. If you need any help with this, please get in touch with [email protected].
 
 
 Deleting Unneeded Files

diff --git a/docs/source/getting_started/data_management_and_user_quota.rst b/docs/source/getting_started/data_management_and_user_quota.rst
@@ -25,17 +25,22 @@ Where ``abc123`` will be replaced by your username. This home directory has a si
 
     /users/abc123/scratch
 
+.. FIXME: needs size
+
 This is a special high-performance filestore with a default size of **3TB** and **no limit** on the number of files. Because of this, you should run all your jobs on Viking from this directory rather than the home directory.
 
 .. tip::
     If you need more ``scratch`` storage space, please email us at [email protected], we are more than happy to accommodate large projects.
 
 
-Additionally, you also have access to the ``warm storage`` area, linked as ``FIXME: warm_storage`` which is **FIXME:??TB** and has no file limit. This is used for FIXME: What is it used for?
+.. FIXME: add size, and file duration
+
+Additionally you also have access to two more folders, ``localscratch`` and ``localtmp`` which points to some storage space on the current node you are logged into, on fast SSD drives. You can access these directories at:
 
 .. code-block:: console
 
-    /users/abc123/FIXME: warm
+    /users/abc123/localscratch
+    /users/abc123/localtmp
 
 Checking Your Quota
 -------------------
@@ -48,6 +53,8 @@ To check how much space you have left, run the following command:
 
 Which will produce the following result:
 
+.. FIXME: update this
+
 .. code-block:: console
 
     Scratch quota:
@@ -111,6 +118,11 @@ scp
 
 This is recommended for transferring a small number of files. This example will copy data from your device to your ``scratch`` directory on Viking
 
+.. hint::
+
+    The 'tilde' symbol ``~`` is shorthand for your home directory, e.g ``/users/abc123``
+
+
 .. code-block:: console
     :caption: for an individual file
 

diff --git a/docs/source/getting_started/quickstart.rst b/docs/source/getting_started/quickstart.rst
@@ -23,20 +23,25 @@ Find the Software You Need
 
 .. code-block:: console
 
-    $ module spider lang/Python
+    $ module spider Python
+
+
+.. FIXME: add example output
 
 
 Load a Module
 --------------
 
 .. code-block:: console
 
-    $ module load lang/Python/3.10.8-GCCcore-12.2.0
+    $ module load {MOD_PYTHON}
 
 
 .. hint::
 
-    The module name scheme on Viking is as follows: ``category`` / ``program_name`` / ``version`` - ``toolchain`` - ``toolchain_version``, where sometimes ``toolchain`` and ``toolchain_version`` not listed.
+.. FIXME: check this is correct
+
+    The module name scheme on Viking is as follows: ``program_name`` / ``version`` or sometimes - ``program_name`` / ``version`` / ``toolchain`` - ``toolchain_version``.
 
     To read more about the EasyBuild concept of *common toolchains*, please see the `EasyBuild docs <https://docs.easybuild.io/common-toolchains/>`_. In it's simplest sense, think of it as the compiler version the software was build with.
 
@@ -82,7 +87,7 @@ In your favorite text editor, create a jobscript for your job. Save it as someth
     module purge
 
     # Load modules #
-    module load lang/Python/3.10.8-GCCcore-12.2.0
+    module load {MOD_PYTHON}
 
     # Commands to run #
     echo My working directory is: `pwd`

diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -5,7 +5,7 @@ Welcome to the Viking Documentation!
 
 .. caution::
 
-   This project is under active development.
+   Please note, his project is under active development.
 
 .. list of all the pages which are hidden on this page but used to build the navbar
 

diff --git a/docs/source/replacements.py b/docs/source/replacements.py
@@ -20,24 +20,24 @@ def variableReplace(app, docname, source):
     "{SHEBANG}" : "#!/usr/bin/env bash",  # used in all the example jobscripts
 
     # modules and versions used in the various jobscript examples for easy updating & consistency
-    "{MOD_PYTHON}": "lang/Python/3.10.8-GCCcore-12.2.0",
-    "{MOD_COMPILER}": "compiler/GCC/12.2.0",
-    "{MOD_R}": "lang/R/4.2.1-foss-2022a",
-    "{MOD_AMBER_CPU}": "chem/Amber/22.3-foss-2022b-AmberTools-23.0",
-    "{MOD_AMBER_GPU}": "chem/Amber/16-foss-2018a-AmberTools-17-CUDA",
-    "{MOD_GAUSSIAN}": "chem/Gaussian/G16a03",
-    "{MOD_MATLAB}": "math/MATLAB/2022a",
-    "{MOD_MONGODB}": "tools/MongoDB/4.2.3",
-    "{MOD_VOXFE}": "bio/VOX-FE/2.0.1-foss-2017b",
-    "{MOD_RELION}": "bio/RELION/4.0.1-foss-2021a",
-    "{MOD_ALPHAFOLD_CPU}": "bio/AlphaFold/2.1.2-foss-2021a",
-    "{MOD_ALPHAFOLD_GPU}": "bio/AlphaFold/2.3.1-foss-2022a-CUDA-11.7.0",
+    "{MOD_PYTHON}": "Python/3.10.8-GCCcore-12.2.0",
+    "{MOD_COMPILER}": "GCC/12.2.0",
+    "{MOD_R}": "R/4.2.1-foss-2022a",
+    "{MOD_AMBER_CPU}": "Amber/22.3-foss-2022b-AmberTools-23.0",
+    "{MOD_AMBER_GPU}": "Amber/16-foss-2018a-AmberTools-17-CUDA",
+    "{MOD_GAUSSIAN}": "Gaussian/G16a03",
+    "{MOD_MATLAB}": "MATLAB/2022a",
+    "{MOD_MONGODB}": "MongoDB/4.2.3",
+    "{MOD_VOXFE}": "VOX-FE/2.0.1-foss-2017b",
+    "{MOD_RELION}": "RELION/4.0.1-foss-2021a",
+    "{MOD_ALPHAFOLD_CPU}": "AlphaFold/2.1.2-foss-2021a",
+    "{MOD_ALPHAFOLD_GPU}": "AlphaFold/2.3.1-foss-2022a-CUDA-11.7.0",
     "{ALPHAFOLD_DB_PATH}": "/mnt/bb/striped/alphafold_db/",
     "{APLHPFOLD_DB_DATE}": "20230518",
-    "{MOD_VASP}": "phys/VASP/5.4.4-intel-2019a",
-    "{MOD_TOOLCHAIN_FOSS}": "toolchain/foss/2022b",  # used in the AtChem2 example
-    "{MOD_CMAKE}": "devel/CMake/3.24.3-GCCcore-12.2.0",  # used in the AtChem2 example
-    "{MOD_APPTAINER}": "tools/Singularity/3.5.3",  # has own page
+    "{MOD_VASP}": "VASP/5.4.4-intel-2019a",
+    "{MOD_TOOLCHAIN_FOSS}": "foss/2022b",  # used in the AtChem2 example
+    "{MOD_CMAKE}": "CMake/3.24.3-GCCcore-12.2.0",  # used in the AtChem2 example
+    "{MOD_APPTAINER}": "Singularity/3.5.3",  # has own page
     "{NAME_APPTAINER}": "singularity",
     "{MOD_MINICONDA}": "lang/Miniconda3",
 

diff --git a/docs/source/using_viking/software_on_viking.rst b/docs/source/using_viking/software_on_viking.rst
@@ -20,7 +20,7 @@ For a quick overview of the available ``module`` sub-commands and options, try t
 
 .. tip::
 
-    The command ``ml`` is a handy front end for the ``module`` command. On Viking try typing ``ml --help`` to see how you can use it as shorthand for ``module load`` and other commands. We'll continue to use explicit commands like ``module load`` in this guide but know you can use ``ml`` a lot of the time instead. Try it out! 😎
+    The command ``ml`` is a handy front end for the ``module`` command. On Viking, try typing ``ml --help`` to see how you can use it as shorthand for ``module load`` and other commands. We'll continue to use explicit commands like ``module load`` in this guide but know you can use ``ml`` a lot of the time instead. Try it out! 😎
 
 
 Using the Module Command
@@ -41,7 +41,7 @@ Loading a Module
 
 .. code-block:: console
 
-    $ module load lang/Python/3.10.8-GCCcore-12.2.0
+    $ module load {MOD_PYTHON}
 
 
 .. attention::
@@ -62,7 +62,7 @@ Unloading a Module
 
 .. code-block:: console
 
-    $ module unload lang/Python/3.10.8-GCCcore-12.2.0
+    $ module unload {MOD_PYTHON}
 
 
 Purge All Modules