svMultiphysics docker container crashes for test case

[amscosta]

Hello guys,
Great job in doing the docker image.
Unfortunatelly, when I try to follow the guidelines in the github page, the following happens :

c0274@50u24:~$ docker run -it -v ~/svMultiPhysics/tests/cases/fluid/pipe_RCR_3d:/case simvascular/solver
root@a4c150b8dd9f:/# cd /case
root@a4c150b8dd9f:/case# mpirun -n 4 /build-trilinos/svMultiPhysics-build/bin/svmultiphysics solver.xml
2025-03-13 14:02:34.845 ( 0.046s) [ 7F577623F900] vtkXMLParser.cxx:364 ERR| vtkXMLDataParser (0x564c61bedff0): Error parsing XML in stream at line 1, column 0, byte index 0: syntax error
2025-03-13 14:02:34.845 ( 0.046s) [ 7F577623F900] vtkXMLReader.cxx:510 ERR| vtkXMLUnstructuredGridReader (0x564c61c49a60): Error parsing input file. ReadXMLInformation aborting.
2025-03-13 14:02:34.845 ( 0.046s) [ 7F577623F900] vtkExecutive.cxx:729 ERR| vtkCompositeDataPipeline (0x564c61c4a1c0): Algorithm vtkXMLUnstructuredGridReader (0x564c61c49a60) returned failure for request: vtkInformation (0x564c61c54ae0)
Debug: Off
Modified Time: 93
Reference Count: 1
Registered Events: (none)
Request: REQUEST_INFORMATION
ALGORITHM_AFTER_FORWARD: 1
FORWARD_DIRECTION: 0

terminate called after throwing an instance of 'std::runtime_error'
what(): Failed reading the VTK file 'mesh/mesh-complete.mesh.vtu'.
[a4c150b8dd9f:00015] *** Process received signal ***
[a4c150b8dd9f:00015] Signal: Aborted (6)
[a4c150b8dd9f:00015] Signal code: (-6)
[a4c150b8dd9f:00015] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x42520)[0x7f577697f520]
[a4c150b8dd9f:00015] [ 1] /lib/x86_64-linux-gnu/libc.so.6(pthread_kill+0x12c)[0x7f57769d39fc]
[a4c150b8dd9f:00015] [ 2] /lib/x86_64-linux-gnu/libc.so.6(raise+0x16)[0x7f577697f476]
[a4c150b8dd9f:00015] [ 3] /lib/x86_64-linux-gnu/libc.so.6(abort+0xd3)[0x7f57769657f3]
[a4c150b8dd9f:00015] [ 4] /lib/x86_64-linux-gnu/libstdc++.so.6(+0xa2b9e)[0x7f5776c2ab9e]
[a4c150b8dd9f:00015] [ 5] /lib/x86_64-linux-gnu/libstdc++.so.6(+0xae20c)[0x7f5776c3620c]
[a4c150b8dd9f:00015] [ 6] /lib/x86_64-linux-gnu/libstdc++.so.6(+0xae277)[0x7f5776c36277]
[a4c150b8dd9f:00015] [ 7] /lib/x86_64-linux-gnu/libstdc++.so.6(+0xae4d8)[0x7f5776c364d8]
[a4c150b8dd9f:00015] [ 8] /build-trilinos/svMultiPhysics-build/bin/svmultiphysics(+0x417cc7)[0x564c5f7cfcc7]
[a4c150b8dd9f:00015] [ 9] /build-trilinos/svMultiPhysics-build/bin/svmultiphysics(_ZN7vtk_xml8read_vtuERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEER7mshType+0x10b)[0x564c5fa37f2b]
[a4c150b8dd9f:00015] [10] /build-trilinos/svMultiPhysics-build/bin/svmultiphysics(_ZN8load_msh7read_svEP10SimulationR7mshTypePK14MeshParameters+0xc2)[0x564c5f9a38d2]
[a4c150b8dd9f:00015] [11] /build-trilinos/svMultiPhysics-build/bin/svmultiphysics(_ZN11read_msh_ns8read_mshEP10Simulation+0x31d)[0x564c5f9dc1bd]
[a4c150b8dd9f:00015] [12] /build-trilinos/svMultiPhysics-build/bin/svmultiphysics(_ZN13read_files_ns10read_filesEP10SimulationRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE+0x48)[0x564c5f9cf558]
[a4c150b8dd9f:00015] [13] /build-trilinos/svMultiPhysics-build/bin/svmultiphysics(main+0x2e5)[0x564c5f84f3f5]
[a4c150b8dd9f:00015] [14] /lib/x86_64-linux-gnu/libc.so.6(+0x29d90)[0x7f5776966d90]
[a4c150b8dd9f:00015] [15] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x80)[0x7f5776966e40]
[a4c150b8dd9f:00015] [16] /build-trilinos/svMultiPhysics-build/bin/svmultiphysics(_start+0x25)[0x564c5f877275]
[a4c150b8dd9f:00015] *** End of error message ***

prterun noticed that process rank 0 with PID 15 on node a4c150b8dd9f exited on
signal 6 (Aborted).

I am using WSL2 (Window 11) .

[dcodoni]

Hello,
The error you are facing looks like an xml parser error while reading the file 'mesh/mesh-complete.mesh.vtu'.
I was getting a similar error as yours when I tried to run the solver:latest container on my mac, but docker gave me a warning that my paltform (arm64) was different from the platform that built the container. I decided to build the container on my mac and I ran the same case and it is working fine.
When you pulled the container form dockerhub (docker pull simvascular/solver:latest) did you receive any warnings? Also, when you used 'docker run' did docker give you any warnings?

Best,
David

[amscosta]

Hi David
Apparently the mesh file exist in the running container

root@0293e0cc4d85:/case# ls
README.md lumen_inlet.fcs lumen_inlet.flow mesh result_002.vtu solver.xml
root@0293e0cc4d85:/case# cd mesh
root@0293e0cc4d85:/case/mesh# ls
mesh-complete.mesh.vtu mesh-surfaces

[dcodoni]

when you pulled the container from dockerhub, did you receive any warnings?

[dcodoni]

Another thing I would like to check is if you installed/activated git-lfs after downloading svMultiPhyisics:

• sudo apt-get install git-lfs
• git lfs install

[amscosta]

Now works. Many thanks.

c0274@50u24:$ sudo apt-get install git-lfs
...
c0274@50u24:$ git lfs install
Git LFS initialized.
...
c0274@50u24:$ git clone https://github.com/SimVascular/svMultiPhysics.git
Cloning into 'svMultiPhysics'...
remote: Enumerating objects: 9836, done.
remote: Counting objects: 100% (2680/2680), done.
remote: Compressing objects: 100% (633/633), done.
remote: Total 9836 (delta 2330), reused 2047 (delta 2047), pack-reused 7156 (from 2)
Receiving objects: 100% (9836/9836), 10.99 MiB | 7.71 MiB/s, done.
Resolving deltas: 100% (6818/6818), done.
Filtering content: 100% (617/617), 209.51 MiB | 10.73 MiB/s, done.
...
c0274@50u24:$ docker pull simvascular/solver:latest
latest: Pulling from simvascular/solver
Digest: sha256:153830da0dd199372d42ddfe02b1388bee21a26393686f354d58b2d28ca6d3ad
Status: Image is up to date for simvascular/solver:latest
docker.io/simvascular/solver:latest
...
c0274@50u24:~$ docker run -it -v ~/svMultiPhysics/tests/cases/fluid/pipe_RCR_3d:/caso simvascular/solver:latest
root@f40989b9f021:/# cd caso
root@f40989b9f021:/caso# ls
README.md lumen_inlet.fcs lumen_inlet.flow mesh result_002.vtu solver.xml
root@f40989b9f021:/caso# mpirun -n 4 /build-trilinos/svMultiPhysics-build/bin/svmultiphysics solver.xml

Eq N-i T dB Ri/R1 Ri/R0 R/Ri lsIt dB %t

NS 1-1 5.900e-02 [0 1.000e+00 1.000e+00 2.205e-04] [5 -18 69]
NS 1-2 1.010e-01 [-57 1.390e-03 1.390e-03 3.832e-04] [3 -19 57]
NS 1-3 1.490e-01 [-122 7.345e-07 7.345e-07 8.591e-04] [3 -17 63]
NS 1-4 1.960e-01 [-183 6.832e-10 6.832e-10 1.370e-04] [4 -21 64]
NS 1-5 2.400e-01 [-249 3.329e-13 3.329e-13 6.050e-04] [3 -16 55]
NS 2-1 2.760e-01 [0 1.000e+00 2.856e+01 8.914e-04] [2 -18 53]
NS 2-2 3.200e-01 [-60 9.113e-04 2.603e-02 8.651e-04] [3 -20 59]
NS 2-3 3.660e-01 [-120 9.460e-07 2.702e-05 7.081e-04] [3 -19 61]
NS 2-4 4.130e-01 [-182 7.582e-10 2.166e-08 1.360e-04] [4 -20 62]
NS 2-5s 4.600e-01 [-249 3.277e-13 9.361e-12 5.212e-04] [3 -16 53]
root@f40989b9f021:/caso#