Compilation error

[lilux618]

After running cmake .. when running make command I get compilation error like this :

System info: Linux version 5.4.0-120-generic (buildd@lcy02-amd64-037) (gcc version 7.5.0 (Ubuntu 7.5.0-3ubuntu118.04)) #13618.04.1-Ubuntu SMP Fri Jun 10 18:00:44 UTC 2022

[ktbolt]

@lilux618 The error indicates that there are no pre-built external libraries that match your computer's configuration. The externals are obtained from here http://simvascular.stanford.edu/downloads/public/simvascular/externals/2019.06/linux/

What OS are you running?

[lilux618]

I run ubantu22.04 within a container

[lilux618]

I just want to compile the svSolver, there are so many thirdparty packages in http://simvascular.stanford.edu/downloads/public/simvascular/externals/2019.06/linux/ , which ione should I install ?

[ktbolt]

No external packages have yet been created for Ubuntu 22. Externals are primarily used for the SimVascular application, svSolver just needs VTK from the externals.

You can build svSolver using VTK that has been locally installed (see Building using a locally installed version of VTK section in the svSolver README).

[lilux618]

I change the system to ubuntu 20.04, and download the packages in http://simvascular.stanford.edu/downloads/public/simvascular/externals/2019.06/linux/ , but the error still exist ,

It seems the vtk package from http://simvascular.stanford.edu/downloads/public/simvascular/externals/2019.06/linux/ is pre-build, where this folder should be located?

[ktbolt]

If you just want to build svSolver then first install VTK on your computer

sudo apt-get install libvtk7-dev

Then build using

cmake -DSV_USE_LOCAL_VTK=ON ..

[lilux618]

Thank you! The svsolver is installed now, I get four binary executables svpost svpre svsolver svsolver-nompi . However , when I run ./svsolver to simluate a case, it gives an error like this :

What's wrong with me ?

[ktbolt]

This appears to be a problem with using OpenMPI in a Docker container. It may be that ssh is not installed in your container. Note that it is better to use singularity for HPC applications.

[lilux618]

However , I run this solver just in one computer, and it can be used in windows system. Should I use openmpi instead of mpich ? By the way , can this solver run with openmp parallel ? I set OMP_NUM_THREADS=32 , but svsolver-nompi still run with one core .

[ktbolt]

I build svSolver with OpenMPI.

There is no support for OpenMP.