View source for Tutorial Video Overviews

Learning to use PHASTA involves a lot of non-trivial steps, each that have a significant learning curve.  Videos are a natural way to learn but we have accumulated a lot of them and this makes it daunting to start.  The purpose of this page is to organize and index that knowledge and make it more enabling to self-paced learning.

Here are notes going over the contents of the [https://fluid.colorado.edu/tutorials/ different tutorial videos] with the goal of helping others find tutorial videos of use to them.

See [[#Meta|Meta]] for details on adding new entries.

== Video Table ==
{| class="wikitable"
! Video Name
! Date
! Software Used
! Description
! More Notes
! Misc. Tags
|-
| [https://fluid.colorado.edu/tutorials/tutorialVideos/CompressibleSimModeler.mp4	CompressibleSimModeler.mov	]
| 2021-06-15
| SimModeler
| Setting up a mesh and attributes for a compressible case within SimModeler. Explanation of 2D boundary layers, Extrusion Mesh, Mesh refinement, and attributes for compressible cases. 
| 
|-
|-
| [https://fluid.colorado.edu/tutorials/tutorialVideos/BlancoBuidingPHASTA.mov	BlancoBuidingPHASTA.mov	]
| 2020-05-19
| git, CMAKE, viznodes
| Build PHASTA on the viznodes with a particular branch/ debug errors extracted from compiler output
| 
|-
|-
| [https://fluid.colorado.edu/tutorials/tutorialVideos/CloneFromGithubAndBranch.mov	CloneFromGithubAndBranch.mov	]
| 2020-05-19
| git
| Create a clone of PHASTA git repo. Navigate to the branch of interest
| 
|-
|-
| [https://fluid.colorado.edu/tutorials/tutorialVideos/JamesW_pt2.mov	JamesW_pt2.mov	]
| 2020-02-11
| Chef, Globus, ALCF Theta, PHASTA
| Transfer partitioned mesh via globus to Theta, build and run a partitioning of/with chef on Theta, build and submit PHASTA simulation on Theta.
| 
|-
|-
| [https://fluid.colorado.edu/tutorials/tutorialVideos/JamesW_pt1.mov	JamesW_pt1.mov	]
| 2020-02-11
| Chef, Interpolation, ALCF Cooley
| Create a fine mesh via MATLAB, interpolate the solution from an existing simulation to the initial condition of the fine mesh via chef partitioning on Cooley
| 
|-
|-
| [https://fluid.colorado.edu/tutorials/tutorialVideos/PHASTA_workflow_RB.mkv	PHASTA_workflow_RB.mkv	]
| 2020-01-23
| SimModeler, Chef, PHASTA, Paraview
| Model via SimModeler, Partition via Chef, Run PHASTA, visualize results via Paraview
| 
|-
| [https://fluid.colorado.edu/tutorials/tutorialVideos/VNC_tutorialLonger.mov	VNC_tutorialLonger.mov	]
| 2019-12-09
| VNC, viznode
| login to viznodes/ close existing sessions
| 
|-
|-
| [https://fluid.colorado.edu/tutorials/tutorialVideos/VNC_tutorial.mov	VNC_tutorial.mov	]
| 2019-12-09
| VNC, viznode
| login to viznodes
| 
|-
|-
| [https://fluid.colorado.edu/tutorials/tutorialVideos/MeldChangesAcrossBranches.mov	MeldChangesAcrossBranches.mov	]
| 2020-05-19
| git, viznode
| Meld changes across git branches
| 
|-
|-
| [https://fluid.colorado.edu/tutorials/tutorialVideos/Mesh-Partition-Run_MatlabGeneratedMesh_RB.mkv	Mesh-Partition-Run_MatlabGeneratedMesh_RB.mkv	]
| 2019-11-19
| viznode, ALCF, MATLAB mesh, Chef, running PHASTA, SST model run, MATLAB post process
| Create a mesh via MATLAB, partition mesh via Chef viznode, partition mesh via Chef ALCF, Run RANS/IDDES turbulence models, Accumulate and visualize Spanwise averages via MATLAB. 
| 
|-
|-
| [https://fluid.colorado.edu/tutorials/tutorialVideos/RajDemoPrepSolvePost.mov RajDemoPrepSolvePost.mov]
| 2019-05-13
| viznode, convert, Chef, running PHASTA, Paraview
| Partition a mesh via chef, Run a simulation via PHASTA, Post-process via Paraview
| 
|-
| [https://fluid.colorado.edu/tutorials/tutorialVideos/PrepSolvePostBLandC.mp4 PrepSolvePostBLandC.mp4]
| 2020-04-15
| SimModeler, vglconnect
| Partition a mesh via chef, Run a simulation via PHASTA, Post-process via Paraview
| viznode, running PHASTA, Post proccessing
| [[Tutorial_Video_Overviews#PrepSolvePostBLandC.mp4|Jump to notes below.]]
|-
|-
| [https://fluid.colorado.edu/tutorials/tutorialVideos/RajDemo.mov Raj_demo.mov]
| 2019-05-12
| SimModeler, vglconnect
|
* Overview of using portal1/viznodes, how/when to use vglconnect etc (first ~10 minutes)
* Use of SimModeler for creating unstructured mesh of a windtunnel
| N/A
| viznode, meshing
|-
| [https://fluid.colorado.edu/tutorials/tutorialVideos/MatLabMeshAndConvert.mov MatLabMeshAndConvert.mov]
| 2019-09-09
| Matlab, StructMesh_Channel.m, runMatchedNodeElmReader.sh
| 
* Using Riccardo's Matlab script (StructMesh_Channel.m) to create structured mesh for LES_DNS simulation
* Converting that mesh for use with Chef using runMatchedNodeElmReader.sh
| [[#MatLabMeshAndConvert.mov|Jump to Notes Below]]
| Channel, Bump, meshing
|-
| [https://fluid.colorado.edu/tutorials/tutorialVideos/SpanWiseAveragingPostProcessing.mov SpanWiseAveragingPostProcessing.mov]
| 2020-02-11
| Matlab, Spanwise averaging Matlab scripts, PHASTA
| 
* Viewing required settings for PHASTA to create spanwise averaged statistic files
* Using Riccardo's Matlab script to take those files and plot them
| N/A
| post-processing 
|-
| [https://fluid.colorado.edu/tutorials/vtkpytoolsVideos/ barfiletoolsTutorials (1-3) ]
| 2021-03-23
| Python, [[VTKpytools]], [[Barfiletools]]
| 
* Overview of using the [[Barfiletools]] module for post-processing spanwise averaged results
* Goes over the three steps described in [[Barfiletools]]
| N/A
| post-processing
|}

== Video Notes ==
=== BlancoBuidingPHASTA.mov ===
==== Time Stamps ====
{| class="wikitable"
! Time
! Notes
|-
| 0:00
| preliminaries: Committing the code that is to be built to the git repo.
|-
|-
| 3:30
| Constructing build directory/enviornment variables on viz nodes
|-
|-
| 5:50
| build PHASTA executable/debug to be able to compute element size
|-
|}
==== Notes ====
After 5:50 of this video is a debugging exercise to get the code to compile on the viznodes. 
=== CloneFromGithubAndBranch.mov ===
==== Time Stamps ====
{| class="wikitable"
! Time
! Notes
|-
| 0:00
| Find the clone link via github online
|-
|-
| 2:00
| Perform clone on viznodes
|-
|-
| 3:00
| Navigate to branch of PHASTA on git
|-
|}
=== JamesW_pt2.mov ===
==== Time Stamps ====
{| class="wikitable"
! Time
! Notes
|-
| 0:00
| Partition case further for Cooley run
|-
|-
| 25:00
| On Cooley node with Chef.
|-
|-
| 30:00
| Further Partitioning
|-
|-
| 49:00
| Setting up globus data transfer
|-
|-
| 49:00
| Globus data transfer
|-
|-
| 1:00:00
| Theta partition
|-
|-
| 1:00:00
| ALCF Theta partition/Build Chef on Theta
|-
|-
| 1:40:00
| ALCF Theta build PHASTA on Theta
|-
|-
| 2:04:00
| ALCF Theta run Chef
|-
|}

=== JamesW_pt1.mov ===
==== Time Stamps ====
{| class="wikitable"
! Time
! Notes
|-
| 0:00
| Flat Plate Meshing with Tetrahedron
|-
|-
| 17:00
| Cooley Interpolation of one Solution to another for IC
|-
|-
| 24:00
| Interpolation Code overview
|-
|-
| 36:00
| Run Chef on Cooley to partition MATLAB generate mesh
|-
|}
==== Notes ====
The last half of this video is debugging on Cooley for Chef 

===PHASTA_workflow_RB.mkv===
==== Time Stamps ====
{| class="wikitable"
! Time
! Notes
|-
| 0:00
| On the a terminal: connecting to worknodes
|-
|-
| 1:20
| Problem Definition setup: create Model via SimModeler
|-
|-
| 27:00
| Convert SimModeler Mesh to simmetrix Mesh/Partition Problem via Chef
|-
|-
| 41:00
| Run PHASTA with partitioned mesh
|-
|-
| 53:30
| Visualization via Paraview
|-
|}
===VNC_tutorialLonger.mov ===
==== Time Stamps ====
{| class="wikitable"
! Time
! Notes
|-
| 0:00
| Advanced workspace: VNC settings screen size
|-
|-
| 1:30
| Advanced workspace: cmd on toolbar/worknodes description
|-
|-
| 3:35
| Advanced workspace: top
|-
|-
| 6:10
| Creating new session
|-
|-
| 12:50
| Advanced workspace: Connecting to a co-worker's session
|-
|-
| 15:53
| Advanced workspace: find and cleaning up a many sessions
|-
|-
| 18:00
| Discussions
|-
|}
===VNC_tutorial.mov ===
==== Time Stamps ====
{| class="wikitable"
! Time
! Notes
|-
| 0:00
| Description of end goal of user interface/ ssh demo/ port setup
|-
| 7:15
| Tunnel to created port number,portal1
|-
| 8:00
| closeout/ connect back
|-
|}
===MeldChangesAcrossBranches.mov ===
==== Time Stamps ====
{| class="wikitable"
! Time
! Notes
|-
| 0:00
| Initial description of git meld proccess
|-
| 3:00
| Meld of the two file trees in phSolver/common
|-
| 11:00
| Meld of the two file trees in phSolver/incompressible
|-

|}
===Mesh-Partition-Run_MatlabGeneratedMesh_RB.mkv ===
==== Time Stamps ====
{| class="wikitable"
! Time
! Notes
|-
| 0:00
| Create a mesh via MATLAB tool
|-
| 5:00
| Convert MATLAB mesh to SCOREC Mesh
|- 
| 7:50
| Chef partitioning/<>.spj Attribute file 
|- 
| 10:00
| Run RANS/ STGInflow.dat file description
|- 
| 12:20
| Spanwise averaging control/output
|- 
| 16:40
| MATLAB post-proccessing
|-
| 19:50 
| DEPRECIATED: ALCF CETUS Partitioning Chef
|-
| 23:20
| DEPRECIATED: Run on ALCF CETUS
|-
| 28:00
| Post-proccess IDDES data via MATLAB
|-
| 33:20
| 2-D Mesh creation/Accumulate Time average
|
|}

==== Notes ====
Partition a mesh via chef, Run a simulation via PHASTA, Post-process via Paraview 
=== RajDemoPrepSolvePost.mov ===

==== Time Stamps ====
{| class="wikitable"
! Time
! Notes
|-
| 2:14
| Convert a mesh from SimModeler
|-
| 8:00
| Partition via Chef 
|- 
| 18:40 
| Setup Run directory
|- 
| 22:40
| Execute PHASTA
|- 
| 32:20
| Setup/Overview Paraview 
|- 
| 37:00
| Post processing/ visualization of solution via Paraview
|-
|}

==== Notes ====
Partition a mesh via chef, Run a simulation via PHASTA, Post-process via Paraview 

=== PrepSolvePostBLandC.mp4 ===

==== Time Stamps ====
{| class="wikitable"
! Time
! Notes
|-
| 0:00
| Intro/ environment setup
|-
| 5:00
| Construct Partitioning directory with model files
|- 
| 7:10
| Create sub directory and convert Model
|- 
| 9:40
| Partition method after conversion step
|- 
| 13:10
| PHASTA Run directory setup
|- 
| 16:30
| Running PHASTA
|-
| 20:20
| Post processing/ visualization of solution via Paraview
|}

==== Notes ====
Partition a mesh via chef, Run a simulation via PHASTA, Post-process via Paraview 

=== MatLabMeshAndConvert.mov ===

==== Time Stamps ====
{| class="wikitable"
! Time
! Notes
|-
| 0:00
| Begin reviewing code of the Matlab scripts
|-
| 10:30
| Run Example Script
|- 
| 12:45
| Observing the files generated by Matlab
|- 
| 13:40
| Discussion of using <code>matchedNodeElmReader</code>
|- 
| 14:50
| Running of <code>runMatchedNodeElmReader.sh</code> script
|- 
| 16:10
| Viewing mesh in Paraview
|}

==== Notes ====
Create structured meshes using Matlab script created by Riccardo and other tools, such as the matched node element reader utility. 
Matlab script defines the "values" of the mesh to be generated, while <code>matchedNodeElmReader</code> actually generates the mesh files themselves.

Note that <code>matchedNodeElmReader</code> may also be referred to/named as <code>streamMds</code>.

Result of Matlab script is 5 different files:
{| class="wikitable"
| <code>*.crd</code>
| Coordinates of each vertex
|-
| <code>*.class</code>
| Classification with respect to the geometrical model (a box in this case)
|-
| <code>*.cnn</code>
| Connectivity of each element
|-
| <code>*.fathers2D</code>
| 2D grid of the fathers, Used in spanwise averaging
|-
| <code>*.match</code>
| "vertex matching flag" for periodic boundary conditions
|}

<code>matchedNodeElmReader</code> then takes these files as input and generates two directories: <code>outMesh</code> and <code>rendered</code>.
The <code>rendered</code> is a way to view the mesh in Paraview.

The code is run with:
 mpirun -np 1 matchedNodeElmReader *.cnn *.crd *.match *.class *.fathers2D output_model.dmg outputMeshDir/

where in the tutorial <code>matchedNodeElmReader</code> is located at <code>/users/rbalin/matchedReader/build-addNfathDebug/test/matchedNodeElnReader</code>.
The mesh files (SCOREC Mesh, <code>*.smb</code>) are then placed inside the output mesh directory.
A usage message can be shown by running the executable without any arguments.

This command can also be run with multiple MPI processes. Note that this process does "preliminary" partitioning, so the number of mpi processes used is the number of <code>*.smd</code>. The nodes are stored in z, y, x major order (which is generally spanwise, wall-normal, streamwise order), so Riccardo recommends that the number of mpi processes be evenly divisible by the number of streamwise nodes such that these partitions are not divided unevenly.

Once this is done, the <code>*.smb</code> and <code>*.dmg</code> files are fed to Chef for further partitioning and processing.

== Meta ==

==== Editing the Wiki Page ====
Just login to the wiki (click the login button at the top right of the page) and click the edit tab at the top of the page. Login information will be the same as your ''original'' login for jumpgate (the wiki password is not updated with your jumpgate password if you changed it)

==== Filling in New Entries ====

{| class="wikitable"
! Video Name
! Date
! Software Used
! Description
! Misc. Tags
|-
| Should be the exact name of the video file and should have a link to the actual video.
| ISO format (YYYY-MM-DD)
| List of software used, including relevant scripts
| Short description of what was done in the video
| Place for random key words that don't fit in other categories (ie. used for using the browsers search function)
|}