Presolver scriptfile error

[David Parker]

Hi Charlie,

The the error code

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"Fatal: Total Element Block Allocation Exceeded.
Use more processors for this problem or modify MAXBLK in the code."

means that the number of element blocks exceeds the maximum hard coded value, which is 5000. You can calculate the approximate number of elements per block using

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np = number of processors
number_of_elements = number of elements in the mesh
num_elem_per_block = 255 (hard coded in svSolver)
num_elem_per_node = number_of_elements / (np * num_elem_per_block) < 5000

Just increase the number of processors you are using to run the simulation.

Thanks for the detailed analysis of the meshing problems you are seeing! It will take me some time to go through it and investigate.

SV uses VMTK to generate a boundary layer mesh using a simple algorithm that is not that robust. I've seen boundary layer meshing create tangled elements for vessels joined at acute angles, like the one in your model (see image). There are GitHub Issues opened on some of the problems you are seeing (https://github.com/SimVascular/SimVascular/issues/411, https://github.com/SimVascular/SimVascular/issues/652).

I've not had time to look into meshing problems. But several users are having problems so I think I will allocate time to try to understand what is causing problems, your analysis will be very useful for this.

Cheers,
Dave

[Charlie Bright]

Hi Dave,

Perfect, thank you for explaining that. I'll be sure to check the numbers on my meshes in the future.

Not a problem, glad to help!
Thanks for taking a look at my files so quickly. I'll have a mess around with my model's geometry as a fix in the mean time.

All the best,
Charlie

[Charlie Bright]

Hi Dave,

I've recently been in contact with Simmetrix and obtained the license keys for using SimModSuite within SimVascular - hopefully that'll provide a good work around to these meshing problems.

Do you have any guidance/literature available on setting up SimVascular to work with it?

Thanks in advance,
Charlie

[David Parker]

Hi Charlie,

Using MeshSim within SimVascular requires a plugin that is private to the lab that includes our license files. I can build you an installer without the license files. You are running on Ubuntu?

The MeshSim plugin requires a Parasolid plugin that is private to the lab. I can build a custom installer for you that does not contain the Parasolid libraries. Do you have Parasolid libraries?

Cheers,
Dave

[Charlie Bright]

Hi Dave,

That would be perfect, thank you very much!
I primarily run the Windows variant on Windows 10, but I'd happily use the Ubuntu version (I currently run Ubuntu 18.04) if that suits better.

I don't believe I have the Parasolid libraries (unless they are included in another package like SOLIDWORKS that I have installed?).
Otherwise, would you know where I could get in contact with to obtain them, SIEMENS?

Thanks again,
Charlie

[David Parker]

Hi Charlie,

I'm not quite sure how to build the plugins on Windows (yet!) so for now I will build them for Ubuntu 18.

It's probably best to contact Siemens to get the libraries.

Cheers,
Dave

[Charlie Bright]

Hi Dave,

No problem, thank you I appreciate the help.
I should be granted access to Siemens' support portal tomorrow so I'll see what I can get.

Have a good day,
Charlie

[Charlie Bright]

Hi Dave,

Hope you're doing well.

I've been in contact with Siemens and think I'll have the libraries soon.
I was wondering how building the plugins are going?
Just to check as well, I'll be compiling SV on a CentOS cluster at my university this week. Will meshes generated via MeshSim on my local PC be read on the cluster without the plugin ok?

All the best,
Charlie

[David Parker]

Hi Charlie,

I will add an option to build the MeshSim and Parasolid plugins installers without including a license and libraries. I'll then create installers for Ubuntu 18.04, I'll try to get this done by next week.

The MeshSim plugin writes meshes in a VTK .vtu format file so there is no problem reading them form CentOS.

Cheers,
Dave

[Charlie Bright]

Hi Dave,

That's great thank you.
Cheers for the information.

Regards,
Charlie