Error using svFSI on Ubuntu 18.04
- Hannah Cebull
- Posts: 13
- Joined: Thu Aug 24, 2017 11:45 am
Error using svFSI on Ubuntu 18.04
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
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
- Posts: 1677
- Joined: Tue Aug 23, 2005 2:43 pm
Re: Error using svFSI on Ubuntu 18.04
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
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
- Posts: 13
- Joined: Thu Aug 24, 2017 11:45 am
Re: Error using svFSI on Ubuntu 18.04
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
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
- Posts: 1677
- Joined: Tue Aug 23, 2005 2:43 pm
Re: Error using svFSI on Ubuntu 18.04
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
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
- Posts: 1677
- Joined: Tue Aug 23, 2005 2:43 pm
Re: Error using svFSI on Ubuntu 18.04
Hi Hannah,
I've added an svFSI installer for Ubuntu 18 on SimTK.
Cheers,
Dave
I've added an svFSI installer for Ubuntu 18 on SimTK.
Cheers,
Dave
- Hannah Cebull
- Posts: 13
- Joined: Thu Aug 24, 2017 11:45 am
Re: Error using svFSI on Ubuntu 18.04
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
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
- Posts: 19
- Joined: Fri Sep 20, 2019 7:20 am
Re: Error using svFSI on Ubuntu 18.04
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
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
- Posts: 1677
- Joined: Tue Aug 23, 2005 2:43 pm
Re: Error using svFSI on Ubuntu 18.04
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
If you want to run the solver using MPI and four processors then the command would be
The solver input file is created using the SimVascular svFSI tool.
Cheers,
Dave
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
Code: Select all
mpiexec -np 4 svFSI demo_fsi.txt
Cheers,
Dave
- Michela Garau
- Posts: 19
- Joined: Fri Sep 20, 2019 7:20 am
Re: Error using svFSI on Ubuntu 18.04
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
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
- Posts: 1677
- Joined: Tue Aug 23, 2005 2:43 pm
Re: Error using svFSI on Ubuntu 18.04
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
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