Error using svFSI on Ubuntu 18.04

[Hannah Cebull]

Hello,

I'm trying to svFSI but I keep getting the error:

libmpi_mpifh.so.12: cannot open

I tried replacing the svFSI executable with the new one on GitHub, but it didn't seem to do anything. Do you have any suggestions for correcting this error?
For background, I just installed Ubuntu 18.04 on my laptop and am a brand new Linux user so it may be that I don't have certain packages installed, but I have tried to download all the basic ones the past few days.

Thanks,
Hannah

[David Parker]

Hi Hannah,

The svFSI executable from the SimTK installer is old and will not run on Ubuntu 18, it is looking for an MPI library that is no longer supported.

The latest svFSI source on GitHub is currently incompatible with the format of the solver input file produced by the SV svFSI Tool. We will be releasing a new svFSI and SV versions in a couple of weeks or so that fixes this problem.

Cheers,
Dave

[Hannah Cebull]

Hi David,

Thank you for your prompt reply. I'm working on a time-sensitive project, so I think I will just try to downgrade Ubuntu so that I can run svFSI. If I do this, what version of Ubuntu do you recommend? Will 16.04 work with this program? Just want to make sure before I begin re-installing the software.

Thanks so much for your help!

Best,
Hannah

[David Parker]

Hi Hannah,

I built an svFSI executable for Ubuntu 18 from the old svFSI code. I tested it and it seemed to work OK. You can download the executable from https://github.com/ktbolt/cardiovascula ... .ubuntu.18.

Cheers,
Dave

[David Parker]

Hi Hannah,

I've added an svFSI installer for Ubuntu 18 on SimTK.

Cheers,
Dave

[Hannah Cebull]

Hi Dave,

Thank you very much! The new version of svFSI now works on my version of Ubuntu. I really appreciate your help.

Best,
Hannah

[Michela Garau]

Hi David,
I am also trying to use svFSI on Ubuntu 18.04. I downloaded the svFSI.ubuntu.18 executable file as you indicated, but when I tried to run it, I got an error: "Configuration file name is required as an argument". Maybe should I place it in a particular folder? Are there other instructions I should follow?
Thanks for your help,

Michela

[David Parker]

Hi Michela,

I looked at the svFSI documentation and see that it does not describe how to run svFSI from the command line! You must give the solver input file on the command line. For example, if your solver input file is demo_fsi.txt then you would run the solver using the command

Code: Select all

svFSI demo_fsi.txt

If you want to run the solver using MPI and four processors then the command would be

Code: Select all

mpiexec -np 4 svFSI demo_fsi.txt

The solver input file is created using the SimVascular svFSI tool.

Cheers,
Dave

[Michela Garau]

Thank you David for your reply.

Unfortunately I still have the same error:

ERROR occurred, see below for more explanation
ERROR: Failed to project faces between <interface_solid> and <interface_fluid>. Try changing the tolerance of the closest-node-finding algorithm

thus it is not a problem linked with the Ubuntu version that I am using.
I already read the discussion in which the use of meshMixer is suggested, I will try to run it.
Anyway, about the "tolerance of the closest-node-finding algorithm ", how can I change it ?
Thank you

Michela

[David Parker]

Hi Michela,

I'm not sure what changing the tolerance of the closest-node-finding algorithm means. Maybe it refers to change the svFSI code.

I think the Failed to project faces error you are seeing is caused by the solid and fluid meshes not having the same node IDs at their interface. If you put the mesh someplace I can download it I'll have a look.

Cheers,
Dave