PHASTA Wiki - User contributions [en]

ParaView/Tricks

2018-11-10T22:17:41Z

2017-04-26T17:18:15Z

Skinnerr: /* Acquiring Source Code */

== Acquiring Source Code ==

RPI maintains SCOREC Core, a set of C/C++ libraries for unstructured meshing and simulation pre-processing. The code base lives on a github page at https://github.com/SCOREC/core. To clone the source code, navigate to the desired directory and run
git clone https://github.com/SCOREC/core

General build instructions can be found at
https://github.com/SCOREC/core/wiki/General-Build-instructions

== Building on Viz Nodes ==

As of 2017-04-26, SCOREC-core lives in
/projects/tools/SCOREC-core/build-viz003

It was built using
soft add +openmpi-gnu-2.1.0-gnu49-thread
soft add +simmodsuite-11.0-170405dev
(no soft add for gcc, meaning the default gcc 4.9.2 is used)

If you want to build you own, do the following.
# go to where you have checked out SCOREC/core (or check it out yourself) and sit in the directory above it
# soft add necessary dependencies (see above)
# cp ~kjansen/compilation
# mkdir build (or whatever descriptive name you like)
# cd build
# . ../compilation/env_ucb_gnu_dev17_rhel7
# ../compilation/doConfigure-dev17-rhel7 (this step has OS version dependencies)
# make -j

=== Note ===
In general, you have to rebuild the partitionwrapper to match the mpi version. Ben did that for openmpi210 for rhel7. This is a fairly easy process ( e.g., cp -r /usr/local/simmetrix/simmodsuite/11.0-170405dev/code/PartitionWrapper tmpdir; cd tmpdir; make -f Makefile.custom PARALLEL=omp210 CC=mpicc CXX=mpicxx -j 8;) but the tricky bit is that you have to copy this wrapper to a place that the SCOREC cmake tools for tools will “find” it. For now, on viz003, Ben has copied it to the location of the rest of the Simmetrix libraries and named it with an openmpi210 extension which I made match in ../compilation/doConfigure-dev17-rhel7 line 15. This works fine when you have been the person who copied or setup the libraries but less great if not.

== Building on Summit ==

Building SCOREC Core

2017-04-26T17:17:43Z

Skinnerr: /* Building on Viz Nodes */

== Acquiring Source Code ==

RPI maintains SCOREC Core, a set of C/C++ libraries for unstructured meshing and simulation pre-processing. The code base lives on a github page at https://github.com/SCOREC/core. To clone the source code, navigate to the desired directory and run
git clone https://github.com/SCOREC/core

== Building on Viz Nodes ==

As of 2017-04-26, SCOREC-core lives in
/projects/tools/SCOREC-core/build-viz003

It was built using
soft add +openmpi-gnu-2.1.0-gnu49-thread
soft add +simmodsuite-11.0-170405dev
(no soft add for gcc, meaning the default gcc 4.9.2 is used)

If you want to build you own, do the following.
# go to where you have checked out SCOREC/core (or check it out yourself) and sit in the directory above it
# soft add necessary dependencies (see above)
# cp ~kjansen/compilation
# mkdir build (or whatever descriptive name you like)
# cd build
# . ../compilation/env_ucb_gnu_dev17_rhel7
# ../compilation/doConfigure-dev17-rhel7 (this step has OS version dependencies)
# make -j

=== Note ===
In general, you have to rebuild the partitionwrapper to match the mpi version. Ben did that for openmpi210 for rhel7. This is a fairly easy process ( e.g., cp -r /usr/local/simmetrix/simmodsuite/11.0-170405dev/code/PartitionWrapper tmpdir; cd tmpdir; make -f Makefile.custom PARALLEL=omp210 CC=mpicc CXX=mpicxx -j 8;) but the tricky bit is that you have to copy this wrapper to a place that the SCOREC cmake tools for tools will “find” it. For now, on viz003, Ben has copied it to the location of the rest of the Simmetrix libraries and named it with an openmpi210 extension which I made match in ../compilation/doConfigure-dev17-rhel7 line 15. This works fine when you have been the person who copied or setup the libraries but less great if not.

== Building on Summit ==

Building SCOREC core

2017-04-25T17:58:21Z

Skinnerr: Skinnerr moved page Building SCOREC core to Building SCOREC Core: captialization

#REDIRECT [[Building SCOREC Core]]

Building SCOREC Core

2017-04-25T17:58:21Z

Skinnerr: Skinnerr moved page Building SCOREC core to Building SCOREC Core: captialization

Building SCOREC Core

2017-04-25T17:57:32Z

Skinnerr: initial draft of page

SimModeler

2017-03-10T20:31:17Z

Skinnerr: /* Boundary conditions */

[[Category:Software]]

SimModeler is a model creation program from Simmetrix. It takes the mesh and geometric model and creates the input files for PHASTA.

== Running ==
To run SimModeler, first connect via VNC, then use vglconnect to connect to one of the compute machines:

vglconnect -s viz001

Add the desired version of SimModeler to your environment (the below example will get the "default" version):

soft add +simmodeler

and lunch the GUI:

vglrun simmodeler

== Converting old files ==
This is a guide for converting old files (parasolid and .spj) to the new format (.smd).

After connecting to one of the compute machines, add the suite of tools for SimModeler to your environment:

soft add +simmodsuite

From your case, make a new directory and copy your parasolid (.x_t or .xmt_txt), and .spj file into it. Rename the parasolid file to geom.xmt_txt and the .spj file to geom.spj, if they aren't already named that way. Then from the directory just created (now holds geom.xmt_txt and geom.spj) run:

/users/matthb2/simmodelerconvert/testConvert

Your directory now contains two new files: model.smd and model.x_t

== Creating new files ==

Loading in geometry is about as intuitive as is possibly can be. Go to File -> Import Geometry, browse to the appropriate model, and select Open. Once open, it is possible to both mesh the model and to create boundary conditions for it. Because BLMesher is presently the primary meshing tool, it is only necessary to use SimModeler to create boundary conditions. Go to Analysis -> Select Solver, and select phasta. After selecting phasta, the Analysis Attributes option under Analysis becomes valid. Clicking it brings up the corresponding window. From this new window, it is possible to apply boundary conditions and initial conditions by clicking the small button next to the drop down menu [add picture]. Note you must also double click on "problem definition" which will allow you to name the case. Later post processing expects the name "geom" so always name it so.

== Boundary conditions ==

Commonly boundary conditions include:

*comp3 - Specifies a 3D velocity vector
*comp1 - Specifies a 3D vector in which the velocity is constrained. Velocity normal to this vector is not directly affected. This is useful for creating slip walls and mimicking free stream regions.
*temperature - Sets the temperature of the wall. This is only needed for compressible cases.
*scalar_1 - Sets the scalar_1 / eddy viscosity to apply at a wall. For the Spalart Allmaras models, scalar_1 should be zero at physical walls where a boundary layer develops and 3 to 5 times the molecular viscosity at free stream boundaries (http://turbmodels.larc.nasa.gov/spalart.html)
*surf ID - Associates a number with one or more faces. This can then be read by Phasta and used to apply more complicated boundary conditions in software.
*natural pressure - Apply a mean pressure over a surface. The pressure at any particular point is still allowed to vary (someone verify).
*traction vector - ??. The zero vector is typically applied at outlet.
*heat flux - Specifies the rate at which heat is injected / removed (not sure which one) into / from the fluid domain. The value is almost always set to zero to create a perfectly insulated boundary.
*scalar_1 flux - set the flux of scalar_1 / eddy viscosity into / out of the domain (not sure which one). This is typically only used at outlets where high values of eddy viscosity have been convected downstream of turbulent walls. The value is almost always set to zero.
*turbulence wall - Indicates that a surface is to be included in the calculation of d2wall files (verify) which are then used by the Spalart Allmaras turbulence model to generate more physical turbulent kinetic energy production / dissipation budgets.

=== Incompressible ===

Common BCs used for an incompressible case with the S-A turbulence model

*Initial conditions
**initial velocity (nonzero, typically small)
**initial scalar_1 (3-5 times free-stream molecular viscosity)
*Inflow
**Comp 3
**scalar_1 (also 3-5 times free-stream molecular viscosity)
*Outflow
**natural pressure (zero)
**scalar_1 flux (zero)
**traction vector (zero vector)
*Solid physical walls
**Comp 3 (zero vector)
**scalar_1 (zero)
**turbulence wall (value unimportant; use zero)
*Impermeable slip walls
**Comp 1 (zero in wall-normal direction)
**scalar_1 flux (zero)
**traction vector (zero vector)

=== Compressible ===

Common BCs used for a compressible case with the S-A turbulence model

*Initial conditions
**initial velocity (nonzero, typically small)
**initial scalar_1 (3-5 times free-stream molecular viscosity)
**initial pressure
**initial temperature

*Inflow
**Comp 3
**scalar_1 (also 3-5 times free-stream molecular viscosity)
**temperature

*Outflow
**(?) pressure or natural pressure (zero)
**scalar_1 flux (zero)
**traction vector (zero vector)
**heat flux (zero)

*Solid physical walls
**Comp 3 (zero vector)
**scalar_1 (zero)
**turbulence wall (value unimportant; use zero)
**temperature or heat flux

2015-06-05T18:58:32Z

Skinnerr:

== Introduction ==

Git is a distributed revision control system (VCS), designed to work well with highly non-linear workflows. It was initially conceived to support development of the Linux kernel, and has since become the most widely-used VCS for software development.

This page is essentially a cheat-sheet for git commands frequently used by our group.

== Basic Git ==

Basic information to get started with Git can be found at http://rogerdudler.github.io/git-guide/.

; Git repository (repo)
: Is a directory that contains files of the current branch and a hidden <code>.git</code> directory
: Contains an '''Index''' in <code>.git</code> that acts as a staging area for all your branches
: Contains a '''HEAD''' in <code>.git</code> that points to the last commit you made
: Your PHASTA repository should always be at <code>~/git-phasta/phasta</code>

; Create a new repository
: <code>git init</code>

; Checkout a repository
: <code>git clone /path/to/repo</code>
: <code>git clone user@host:/path/to/repo</code>

; Add files to be tracked in the git index
: <code>git add <filename1> <filename2> ...</code>
: <code>git add *</code>
: <code>git add -u</code> (all files updated since last commit)

; Commit changes to HEAD
: <code>git commit -m "my_username: my comments about this commit"</code>

; Push changes to remote repo
: <code>git push origin master</code> (pushes the <code>master</code> branch to the original/main repo)

; Connect to a remote server
: <code>git remote add origin <server></code> (connects <code><server></code> to your main, or <code>origin</code> repository)
: <code>git remote add myrepo <server></code> (connects <code><server></code> to a named branch called <code>mybranch</code>)
: Note: <code><server></code> could be <code>user@host:/path/to/repo</code>

; Create and delete branch
: <code>git checkout -b branch_name</code> (creates and checkout branch)
: <code>git checkout master</code> (checkout master branch)
: <code>git branch -d branch_name</code> (delete branch we just created)

; Push branch to a remote
: <code>git push origin branch</code> (pushes from your main <code>origin</code> repo)

; Update and merge
: <code>git pull</code> (so all branches are up-to-date for the merge)
: <code>git merge origin/master</code> (merges current branch with <code>origin</code>'s <code>master</code> branch)
: If a merge has conflicts, you need to edit the conflict files provided by Git, and then mark them as merged with <code>git add</code>

; Compare code in different branches
: <code>git diff <branch_a> <branch_b></code>

; View history of commits
: <code>git log</code>
: <code>git log --author=foo</code>
: <code>git log --pretty=oneline</code> (show each commit as one line)
: <code>git log --graph --oneline --decorate --all</code> (ASCII tree of branches, commits, merges)
: <code>git log --name-status</code> (show which files changed in each commit)
: <code>git log --help</code> (more information)

== Advanced Git ==

== Git Prompt Statement (PS1) ==

# Acquire <code>git-prompt.sh</code> from https://github.com/git/git/blob/master/contrib/completion/git-prompt.sh, and save it somewhere like <code>~/.git-prompt.sh</code>
# Edit your <code>~/.bashrc</code> to say <code>source ~/.git-prompt.sh</code> before the lines that set your <code>PS1</code>
# Modify your <code>PS1</code> string to include <code>$(__git_ps1 "(%s)")</code> where you want the current branch to appear in your prompt

2015-03-06T20:32:54Z

Skinnerr: /* Windows */

VNC is a tool which projects a GUI session over the network. If may be useful if you want to use GUI tools remotely when X forwarding performs poorly.

'''Warning: This is still being tested and should NOT be considered stable (portal0 may be rebooted without warning)'''
'''Warning: The vnc password is transmitted in clear text over the network and should not be considered secure'''

Portal0 is designated to host VNC sessions.

You can start a session as follows:

ssh jumpgate-phasta.colorado.edu
ssh portal0
source /etc/profile
start_vnc.sh

And follow the directions

(You may want to remember your password and port number so that you can reuse your session)

When you are done, end your session by
source /etc/profile
stop_vnc.sh

== OpenGL ==

Portal0 is equipped with a VirtualGL install which will allow you to use OpenGL programs (which do not use pthreads)

Simply wrap your OpenGL program with the "vglrun" command
vlgrun glxgears

If you have access to another VirtualGL server you can connect to it first (Portal0 doesn't have a particularly fast graphics processor)
vglconnect server
vglrun glxgears

Note that VGL uses a number of threads. If you have trouble with vglrun crashing with a message about Thread::Start() make sure you haven't set your stack size too large (remove any ulimit -s or ulimit -n calls from your shell start scripts)

== Clients ==

Portal0 uses TurboVNC from the VirtualGL project, available from http://www.virtualgl.org/Downloads/TurboVNC

Other VNC viewers will also work, such as TightVNC and RealVNC

== Changing the VNC Password ==

/opt/tigervnc/bin/vncpasswd

== View Only Mode ==

To share your desktop with another user in view only mode set a view only password
by running
vncpasswd

Have the other user connect in the same way you would but have them set their viewer to be in view only mode and use your view only password. Typically this is done as follows:
vncviewer -viewonly

== Windows ==
The PuTTY SSH client can handle ssh tunneling on Windows based machines. You can download it here: http://www.chiark.greenend.org.uk/~sgtatham/putty/

When you open putty, enter jumpgate-phasta.colorado.edu as in the Host Name box. Then click the + button next to SSH on the left pane (to expand the SSH tree node). Choose the Tunnels page. The start_vnc.sh script should tell you to run "ssh -L????:portal0:???? jumpgate-phasta.colorado.edu" on your machine. Enter the number between the -L and the first colon in the "Source port" box. Enter the rest in the Destination box (starting with portal0) and '''click the add button'''. Then click "Open" and login as normal. You will then be able to use a vncviewer as instructed by the script.

Example:

The script says:
ssh -L5905:portal0:5900 jumpgate-phasta.colorado.edu
enter 5905 in the Source port box
enter portal0:5900 in the destination box.

Try using this viewer utility
http://www.tightvnc.com/download/1.3.10/tightvnc-1.3.10_x86_viewer.zip

'''Connecting to your VNC with PuTTY'''

Once we SSH to jumpgate (on the default SSH port 22), our main desktop on portal0 can be accessed via a VNC session as follows.

# The VNC server should already be running on portal0 using port 59xx.
## To check the port, on portal0 run <code>/opt/vnc_script/findsession.sh</code>
## To confirm the VNC server is running (and see port), run <code>ps aux | grep vnc</code>
# Open PuTTY on your local machine.
# Under "Session", SSH to <code>x@jumpgate-phasta.colorado.edu:22</code>, where <code>x</code> is your username on jumpgate, and <code>22</code> is the standard SSH port.
# Under "Session">"SSH">"Tunnels", select source port <code>59xx</code> and destination port <code>portal0:59xx</code>, where <code>xx</code> is the two-digit number of your VNC session. Select destination <code>local</code> and click "Add". We select <code>local</code> because we have a service (VNC Server) running on a machine (portal0) that can be reached from the remote machine (jumpgate), and we want to access it directly from the <code>local</code> machine.
# Confirm the dialog by clicking "Open", thus establishing an SSH connection between localhost and jumpgate, and tunneling localhost:59xx to portal0:59xx via this connection.
# Open RealVNC, and connect to <code>localhost:xx</code>, which is shorthand for <code>localhost:59xx</code>. VNC ports are enumerated starting with <code>5901</code>, so any two digit port <code>xx</code> is assumed to be port <code>59xx</code>.
# You should now have access to your desktop on portal0.

== Web Based Viewer ==

If you can't or don't want to install a VNC viewer you can use a Java based one. You will need a JVM and a Java browser plugin. You will also need the port that the start_vnc script assigned you to be free on your local computer

Forward your session through jumpgate as before before, adding a second port, 580n. For example, if the script tells you to

ssh -L5905:portal0:5902 jumpgate-phasta.colorado.edu you should
ssh -L5902:portal0:5902 -L5802:portal0:5802 jumpgate-phasta.colorado.edu
Then point your browser to http://localhost:5802 and log in with the password specified by the script when prompted. (Replace 2 with the value specified by the script)

== Changing the Size (Resolution) of an Existing Session ==

You can usually use the "xrandr" tool to change the resolution of a running vnc session. First you'll need to know your session's display number (this should be the last digit or two of the port number). For example, if your VNC session is running on port 5902, then your screen number should be :2. For this example, we'll use screen 2.

Once you know your screen number, you can see the list of supported modes as follows:
xrandr -display :2

Once you pick the one you want (generally the same size or smaller than the native resolution of your client), you can choose it by running a command like
xrandr -s 1400x1050 -display :2

(this example will set the resolution to 1400 pixels by 1050 pixels)

You'll probably be disconnected at this point, but when you reconnect your screen size should be changed (hopefully without crashing your running programs).

== Finding an Existing Session ==
SSH to portal0 and then run:
/opt/vnc_script/findsession.sh

Which will return the shortened port number of each of your currently running sessions.

== Troubleshooting ==

If you have used vncserver (It doesn't matter which version) on a SCOREC machine before, you will need to clear your vnc settings for the script to work. You can do this by running rm -rf ~/.vnc

stop_vnc.sh may display some errors; this is normal.

If you have trouble deleting ~/.vnc send an email to Benjamin.A.Matthews@colorado.edu

If any of these commands fail, you may need to source /etc/profile to get the necessary environment variables (this should be fixed soon)

VirtualGL has trouble with some threaded programs. If your OpenGL program exhibits segmentation faults or other issues, this could be the problem. Check back for the solution later.

If the given password is rejected you can run stop_vnc.sh and restart to get a new one. Occasionally the random password generator may generate passwords which VNC doesn't like.

If VirtualGL complains about not being able to get a 24bit FB config either vglconnect to another VirtualGL enabled server or complain to Benjamin.A.Matthews@Colorado.edu

If your VNC connection is very slow, you might want to try changing the compression and encoding options. See your vncviewer's documentation or try this
vncviewer -encodings tight -quality 6 -compresslevel 6
If you have trouble with text distortion try adding
-nojpeg

If you're running OSX and see an error about Zlib, try changing your compression settings (maximum quality usually works) or use a different client. RealVNC and certain versions of ChickenOfTheVNC both exhibit this issue. The latest build of TigerVNC should work reliably, as does the Java based TightVNC client.