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 different tutorial videos with the goal of helping others find tutorial videos of use to them.

See Meta for details on adding new entries.

Video Table

Video Name	Date	Software Used	Description	More Notes	Misc. Tags
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.
BlancoBuidingPHASTA.mov	2020-05-19	git, CMAKE, viznodes	Build PHASTA on the viznodes with a particular branch/ debug errors extracted from compiler output
CloneFromGithubAndBranch.mov	2020-05-19	git	Create a clone of PHASTA git repo. Navigate to the branch of interest
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.
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
PHASTA_workflow_RB.mkv	2020-01-23	SimModeler, Chef, PHASTA, Paraview	Model via SimModeler, Partition via Chef, Run PHASTA, visualize results via Paraview
VNC_tutorialLonger.mov	2019-12-09	VNC, viznode	login to viznodes/ close existing sessions
VNC_tutorial.mov	2019-12-09	VNC, viznode	login to viznodes
MeldChangesAcrossBranches.mov	2020-05-19	git, viznode	Meld changes across git branches
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.
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
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	Jump to notes below.
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
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	Jump to Notes Below	Channel, Bump, meshing
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
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

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

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

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

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

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

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

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

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

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

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

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

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 matchedNodeElmReader
14:50	Running of runMatchedNodeElmReader.sh 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 matchedNodeElmReader actually generates the mesh files themselves.

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

Result of Matlab script is 5 different files:

*.crd	Coordinates of each vertex
*.class	Classification with respect to the geometrical model (a box in this case)
*.cnn	Connectivity of each element
*.fathers2D	2D grid of the fathers, Used in spanwise averaging
*.match	"vertex matching flag" for periodic boundary conditions

matchedNodeElmReader then takes these files as input and generates two directories: outMesh and rendered. The rendered 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 matchedNodeElmReader is located at /users/rbalin/matchedReader/build-addNfathDebug/test/matchedNodeElnReader. The mesh files (SCOREC Mesh, *.smb) 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 *.smd. 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 *.smb and *.dmg files are fed to Chef for further partitioning and processing.

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