Path selection 3D visualization

[Surabhi Rathore]

Hi,

I am doing a practice on the available data. When, I was choosing the control points to generate path but its 3D visualization is very surprising. As the points in the other section is very tiny and in 3D it is very big cubic. May I know how to do the setting?

I am here attaching the screenshot.

Best,
Surabhi

[David Parker]

Hi Surabhi,

The size of the control point markers is set using the following steps

1) Right click on the path data node under SV Data Manager / Paths

2) Select the Point 3D Size menu item

Cheers,
Dave

[Surabhi Rathore]

Hi Dave,

Thanks for the information.
Now, I have some more questions regarding the svFSI solver. I installed the svFSI using the svFSI-linux-x64-2018.07.03.deb and CMake.

I have no experience with CMake.
I want to do the svFSI simulation for the "CylinderProject" using the command line.
Please give me the steps for doing the FSI simulation using the CMake.

Also, I am curious to know what difference it will make when we do the FSI simulation from SV GUI or CMake command line?
Or it will only be possible from the command line using the CMake only? As I read it from the guidelines.
I will look forward to your suggestion to do the simulation for FSI using the CMake.

Thank you very much.
Surabhi

[Surabhi Rathore]

Hi Dave,

Thank you very much for the information.
Now, I have some more questions regarding the svFSI solver. I installed the svFSI using the svFSI-linux-x64-2018.07.03.deb and CMake.

I have no experience with CMake.
I want to do the svFSI simulation for the "CylinderProject" using the command line.
Please give me the steps for doing the FSI simulation using the CMake.

Also, I am curious to know what difference it will make when we do the FSI simulation from SV GUI or CMake command line?
Or it will only be possible from the command line using the CMake only? As I read it from the guidelines.
I will look forward to your suggestion to do the simulation for FSI using the CMake. I am doing the simualtion on the PC not on the cluster.

Thank you very much.
Surabhi

[Surabhi Rathore]

Hi Dave,

I am having some more issues regarding the installation and running by utilizing the command line.

1.) I am trying to install svSolver in the home directory by using these lines:

$mkdir sv_Solver
$ cd sv_Solver
$ git clone https://github.com/SimVascular/svSolver
$ mkdir build
$ cd build
$ ccmake ../svSolver
$ make

In doing so, I am getting this error, please let me know why is it happening?

svSolver installing issue

Screenshot from 2019-12-09 11-57-01.png (410.7 KiB) Viewed 1150 times

2.) In similar lines, I installed the svFSI solver. Here, I am facing the issue regarding the FSI simulation for "cylinder_ALE_FSI" example.
I m using the command:

mpiexec -n 4 svfsi/build/svFSI-build/myfsi

svFSI running issue

Screenshot from 2019-12-09 15-35-22.png (164.83 KiB) Viewed 1150 times

Please give me your comments.

Thank you,
Surabhi

[David Parker]

Hi Surabhi,

You need to buildsvSolver with MPICH, not OpenMPI. Uninstall OpenMPI and install MPICH.

Install svFSI and building it using CMake are two different things.

When you install svFSI using the installer .deb file the executable is placed in /usr/local/sv/svFSI/2018-07-03/svfsi. You can then execute the solver using

Code: Select all

mpiexec -n 4 /usr/local/sv/svFSI/2018-07-03/svfsi SOLVER_INPUT_FILE.txt

When you build svFSI using CMake the executable is in the build directory, something like $HOME/svFSI/build/svFSI-build/mysvfsi. You can execute that using

Code: Select all

mpiexec -n 4 $HOME/svFSI/build/svFSI-build/mysvfsi SOLVER_INPUT_FILE.txt

Cheers,
Dave

[Surabhi Rathore]

Dear Dave,

Thank you very much for the reply. Here, I have some more questions which are in sequence.

1.) After removing the openmpi, I am still getting the similar error.

Same error

Screenshot from 2019-12-10 03-22-09.png (412.45 KiB) Viewed 1129 times

Here, I am adding the one more clip about the mpi in my system.

mpi formats

Screenshot from 2019-12-10 03-32-38.png (152.45 KiB) Viewed 1129 times

I have also uninstalled the paraview as you suggested in one of your forum linked as;
viewtopicPhpbb.php?f=188&t=10127&p=27941&start=0&view
But unsuccessful to build the svSolver using the command line.

2.) I also tried to build the svsolver and svFSI in Centos7 also but I failed. Here, I some different issues which you can see in the screenshot.

svSolver issue on Centos7

Screenshot from 2019-12-09 00-13-14.png (370.22 KiB) Viewed 1129 times

svFSI issue on centos7

Screenshot from 2019-12-09 00-11-39.png (233.47 KiB) Viewed 1129 times

for centos7, I have installed all the utilities from the link
[url]https:/github.com/SimVascualr.blob/master/External/Prep.2019-02/centos-7-prep.sh[/url]

3.) Other than this, I have some question to compute the all_results files in the form of .vtp and .vtu.

I computed the all_results file but they do not the results for the all variables (like, TAWSS, OSI and others). I only have the results for velocity, pressure, averaged WSS and time derivative. I used this command

/usr/local/sv/svsolver/2019-02-07/svpost -all -indir<job> -outdir<demo_converted_results> -start 0 -stop 200 -incr 10 -vtp all_results -vtp all_results

However, I want to compute the results for TAWSS, OSI also.

Please give me your suggestions.

Thank you,
surabhi

[David Parker]

Hi Surabhi,

The errors to undefined references like ompi_mpi mean that you are still building against OpenMPI. Be sure to remove all files from the build directory before you run the ccmake command.

Run the readlink command to make sure you are using MPICH

Code: Select all

$ readlink -f `which mpic++`
/usr/bin/mpicxx.mpich

Building on CentOS 7 will not work for svSolver because it depends on VTK externals. We are in the process of figuring out how to build on CentOS and will document it. Stay tuned!

Cheers,
Dave

[Surabhi Rathore]

Hi Dave,

Still, I am not able to build svSover but I am working on GUI for time being.
I have to do some simulation for the presentation.

Later, I will more thoughts on this and find the way to build the svSovler.
I will come to you when I will have questions.

Thank you very much
Surabhi

[David Parker]

Hi Surabhi,

Building on Virtual Box can be a bit tricky! If you tell me the version of Virtual Box are you using and what version of Ubuntu are you using for the virtual machine I will post the steps I use to build svSolver.

Cheers,
Dave