Merge pull request #38 from flindersuni/feature/typos

Typo & clarity Updates
flindersuni · Apr 20, 2022 · 0ab111e · 0ab111e
2 parents a67bc7f + dd3487e
commit 0ab111e
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diff --git a/.gitignore b/.gitignore
@@ -6,4 +6,5 @@ docs/source/_build
 
 # Files used by Visual Code
 .vscode/settings.json
-*.code-workspace
+*.code-workspace
+.venv
diff --git a/docs/requirements.txt b/docs/requirements.txt
@@ -9,4 +9,6 @@ commonmark==0.9.1
 recommonmark==0.5.0 
 sphinx<2 
 sphinx-rtd-theme<0.5 
-readthedocs-sphinx-ext<1.1
+readthedocs-sphinx-ext<1.1
+MarkupSafe=<2.0.1 
+jinja<3.0.0
diff --git a/docs/source/FAQ/faq.rst b/docs/source/FAQ/faq.rst
@@ -7,7 +7,7 @@ Below are some of the common steps that the team has been asked to resolve more
 Host Not Found 
 ===============
 
-When attemtping to connect to the HPC, you receive a message that says 'Could not find deepthought.flinders.edu.au'. 
+When attempting to connect to the HPC, you receive a message that says 'Could not find deepthought.flinders.edu.au'. 
 
 1. If you are on campus, contact ServiceDesk via ServiceOne or Phone.
 2. If you are off campus or working remotely, connect to the VPN and retry.
@@ -74,7 +74,7 @@ Only thing you will need to decide is 'where you want to store my environment' y
 To get you up and running (anywhere it says FAN, please substitute yours):
 
 * module load miniconda/3.0
-* conda create -p /home/FAN/isoseq3 python=3.7
+* conda create -p /home/FAN/isoseq3 python=3.9
 * source activate /home/FAN/isoseq3
 * You may get a warning saying 'your shell is not setup to use conda/anaconda correctly' - let it do its auto-configuration. Then Issue
 

diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -18,7 +18,7 @@
 # -- Project information -----------------------------------------------------
 
 project = 'DeepThought HPC'
-copyright = '2021, Flinders University'
+copyright = '2022, Flinders University'
 author = 'Flinders University'
 
 # -- General configuration ---------------------------------------------------

diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -6,8 +6,8 @@ The new Flinders University HPC is called DeepThought. This new HPC comprises of
 .. _BeeGFS Section of Storage & Usage Guidelines: storage/storageusage.html
 
 .. attention:: 
-    The new BeeGFS Parallel Filesystem mounted at /cluster has just been deployed. For instructions on the restrictions and how to
-    take advantage of the performance increase this filesystem brings, please read the `BeeGFS Section of Storage & Usage Guidelines`_.
+    The new BeeGFS Parallel Filesystem mounted at /cluster has just been deployed, but is *not yet ready for usage*. It will appear in any disk 
+    usage listings on the HPC. For further information and to prepare for when this filesystem is fully released, please read the `BeeGFS Section of Storage & Usage Guidelines`_.
 
 .. attention::
     This documentation is under active development, meaning that it can

diff --git a/docs/source/software/ansys.rst b/docs/source/software/ansys.rst
@@ -23,29 +23,31 @@ To run a job with ANSYS on the HPC you will need the following:
     - An ANSYS Script file 
     - Any reference file(s) (eg, a .db file)
 
-Ensure that the paths to anything in the script file reflect where it lives on the HPC, not your local machine. Below are some exmaple command-line examples to get you started. 
+Ensure that the paths to anything in the script file reflect where it lives on the HPC, not your local machine. When running with the ``-dis`` option, you must 
+use a distributed filesystem like /scratch (or /cluster, when available) as all nodes will need to the the files, and /local is *not* visible between individual nodes. 
+Below are some example command-line examples to get you started. 
 
-Replace all <OPTIONS> to suit your requirements. 
+Replace all <OPTIONS> to suit your requirements. You can omit the > PATH_TO_OUTPUT_FILE, and SLURM will capture the ANSYS output and write it to your ``#SBATCH --output=/path/to/file.out``. 
 
 1. Shared-Memory Parallel (Single-Node)
 
 
-``ansys212 -smp -np $SLURM_NTASKS -db <DB File Memory Allocation> -m <SLURM Memory Allocation> -b -s < PATH_TO_SCRIPT_FILE > PATH_TO_OUTPUT_FILE``
+``ansys212 -smp -np $SLURM_NTASKS -b -s < PATH_TO_SCRIPT_FILE > PATH_TO_OUTPUT_FILE``
 
 2. Distributed Mode (Multi-Node) 
 
 
-``ansys212 -dis -np $SLURM_NTASKS -db <DB FILE Memory Allocation> -m <SLURM Memory Allocation> -b -s < PATH_TO_SCRIPT_FILE > PATH_TO_OUTPUT_FILE``
+``ansys212 -dis -np $SLURM_NTASKS -b -s < PATH_TO_SCRIPT_FILE > PATH_TO_OUTPUT_FILE``
 
 3. Hybrid Distributed Mode (Multi-Node Shared-Memory Parallel)
 
 
-``ansys212 -dis -np $SLURM_NTASKS -nt $SLURM_CPUS_PER_TASK -db <DB FILE Memory Allocation> -m <SLURM Memory Allocation> -b -s < PATH_TO_SCRIPT_FILE > PATH_TO_OUTPUT_FILE``
+``ansys212 -dis -np $SLURM_NTASKS -nt $SLURM_CPUS_PER_TASK <SLURM Memory Allocation> -b -s < PATH_TO_SCRIPT_FILE > PATH_TO_OUTPUT_FILE``
 
 4. GPU Hybrid Distributed Mode (Multi-Node Shared-Memory Parallel with GPU Acceleration)
 
 
-``ansys212 -dis -np $SLURM_NTASKS -nt $SLURM_CPUS_PER_TASK -acc nvidia -na <GPU_COUNT> -db <DB FILE Memory Allocation> -m <SLURM Memory Allocation> -b -s < PATH_TO_SCRIPT_FILE > PATH_TO_OUTPUT_FILE`` 
+``ansys212 -dis -np $SLURM_NTASKS -nt $SLURM_CPUS_PER_TASK -acc nvidia -na <GPU_COUNT_PER_NODE> -b -s < PATH_TO_SCRIPT_FILE > PATH_TO_OUTPUT_FILE`` 
 
 +++++++++++++++++++++++
 ANSYS CLI Quick List

diff --git a/docs/source/software/delft3d.rst b/docs/source/software/delft3d.rst
@@ -18,7 +18,7 @@ Delft3D is Open Source Software and facilitates the hydrodynamic (Delft3D-FLOW m
 
 
 ================================
-Known Issues
+Delft3D Known Issues
 ================================
 
 Delft3D does **not** currently support Multi-Node Execution.  The binary swan_mpi.exe will *not work and immediately crash with errors*.

diff --git a/docs/source/software/jupyter.rst b/docs/source/software/jupyter.rst
@@ -1,10 +1,10 @@
 ------------
 Jupyter Hub
 ------------
-==============
-Jupyter Status
-==============
-Released and accessible to all HPC USers at the correct URLs. 
+====================
+Jupyter Hub Status
+====================
+Released and accessible to all HPC Users at the correct URLs. 
 
 .. _Jupyter Enterprise Gateway: https://jupyter.org/hub
 .. _Jupyter URL: https://deepweb.flinders.edu.au/jupyter
@@ -20,7 +20,7 @@ If you have access to the HPC, you automatically have access to the Jupyter Lab.
 via the following `Jupyter URL`_ or manually via https://deepweb.flinders.edu.au/jupyter. Your credentials are the
 the same as the HPC, your FAN and password.
 
-If you are a student with access to the HPC, the above URLs may work - the URL http://deepteachweb.flinders.edu.au/jupyter is guaranteed to work correctly. 
+If you are a *student* with access to the HPC, the above URLs may work - the URL http://deepteachweb.flinders.edu.au/jupyter is guaranteed to work correctly. 
 
 
 ========================================

diff --git a/docs/source/storage/storageusage.rst b/docs/source/storage/storageusage.rst
@@ -20,19 +20,19 @@ Storage Accessibility Overview
 ################################
 As general guide, the following table presents the overall storage for the HPC.
 
-+-----------------------+--------------------------+------------------+
-| Filesystem Location   | Accessible From          | Capacity         |
-+=======================+==========================+==================+
-| /scratch              | All Nodes                | ~250TB           |
-+-----------------------+--------------------------+------------------+
-| /cluster              | All Nodes                | ~45TB            |
-+-----------------------+--------------------------+------------------+
-| /home                 | All Nodes                | ~12TB            |
-+-----------------------+--------------------------+------------------+
-| /local                | Individual Compute Nodes | ~400GB or ~1.5TB |
-+-----------------------+--------------------------+------------------+
-| /RDrive/\<Share Name> | Head Nodes               | Share Dependant  |
-+-----------------------+--------------------------+------------------+
++-----------------------+--------------------------+-------------------------+
+| Filesystem Location   | Accessible From          | Capacity                |
++=======================+==========================+=========================+
+| /scratch              | All Nodes                | ~250TB                  |
++-----------------------+--------------------------+-------------------------+
+| /cluster              | All Nodes                | ~41TB                   |
++-----------------------+--------------------------+-------------------------+
+| /home                 | All Nodes                | ~12TB                   |
++-----------------------+--------------------------+-------------------------+
+| /local                | Individual Compute Nodes | ~1TB (400GB on Node019) |
++-----------------------+--------------------------+-------------------------+
+| /RDrive/\<Share Name> | Head Nodes               | Share Dependant         |
++-----------------------+--------------------------+-------------------------+
 
 .. warning:: The HPC is classed as **volatile** storage. Your research data and dataset that you wanted backed up MUST be moved to /RDrive.
 
@@ -67,7 +67,16 @@ The directories tyou can write to in /cluster are controller by SLURM.  When you
 creates directories for you to use on this filesystem. See the environment variables sections of the SLURM guide for more information. 
 
 Once you job completes, is cancelled, or errors out, SLURM removes then entire directory of your job. That means, *if you do not move your data from the /cluster 
-filesystem, you will lose all of it*. This is by design, and the HPC Team cannot recover any data lost this way.
+filesystem, you will lose all of it*. This is by design, and the HPC Team cannot recover any data lost this way. 
+
+Each college is also limited to a **hard limit** on storage that mirrors their HPC SLURM allocation. This is currently
+
+1. 45% CSE, ~18TB 
+2. 45% CMPH, ~18TB 
+3. 10% Other, ~5TB 
+
+When this quota is exeeded, no more files can be written, so be mindful of your and others usage. The HPC Team is activly monitoring and 
+improving the quota system and the above may change without warning. 
 
 
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^

diff --git a/docs/source/system/deepthoughspecifications.md b/docs/source/system/deepthoughspecifications.md
@@ -16,7 +16,9 @@ The SLURM Scheduler as the notion of 'Job Queue' or 'Partitions'.  These manage
 
 Scratch: ~240TB of scratch disk, mounted on all nodes
 
-Per node /local: ~400GB to 3.2TB, depending on node layout
+Cluster: 41TB of High-Speed Paralllel Fileystem Storage, mounted on all nodes
+
+Per node /local: ~400GB to 1TB, depending on node layout
 
 ## Node Breakdown
 
@@ -36,7 +38,7 @@ There are 17 General Purpose nodes, each with:
 
 ### GPU Nodes
 
-There are 3 dedicated GPU nodes. They comprise of 2 'Standard' and One 'Light' Node:
+There are 3 dedicated GPU nodes. They comprise of two 'Standard' and One 'Light' Node:
 
 #### Standard GPU Nodes
 - CPU: