Error in Create data file for simulation

[Pratik Mitra]

Dear Community,

I am experiencing an issue in Creating a data file for the simulation.
Error as follows:

Code: Select all

LINE 0000: mesh_and_adjncy_vtu mesh-complete/mesh-complete.mesh.vtu


ERROR: In ./IO/XMLParser/vtkXMLParser.cxx, line 389
vtkXMLDataParser (0x616cbea6f930): Error parsing XML in stream at line 22, column 1, byte index 1456: not well-formed (invalid token)

ERROR: In ./IO/XML/vtkXMLReader.cxx, line 467
vtkXMLUnstructuredGridReader (0x616cbea66020): Error parsing input file.  ReadXMLInformation aborting.

ERROR: In ./Common/ExecutionModel/vtkExecutive.cxx, line 781
vtkCompositeDataPipeline (0x616cbea66eb0): Algorithm vtkXMLUnstructuredGridReader(0x616cbea66020) returned failure for request: vtkInformation (0x616cbea6d650)
  Debug: Off
  Modified Time: 83
  Reference Count: 1
  Registered Events: (none)
  Request: REQUEST_INFORMATION
  ALGORITHM_AFTER_FORWARD: 1
  FORWARD_DIRECTION: 0



ERROR:  Must specify number of nodes before you read them in!
ERROR:  command could not be processed.

Need some guidance regarding this issue.
I am running this on a local Ubuntu workstation.
I am trying to compile a case from the SimVascular Repository name "0042_H_ABAO_AAA".

Followed this command:
Downloaded and Installed svSolver and SimVascular.

Code: Select all

sudo apt-get install gfortran
sudo apt-get install openmpi-bin

mkdir $HOME/vtk
cd $HOME/vtk
wget https://www.vtk.org/files/release/8.2/VTK-8.2.0.tar.gz
tar xvf VTK-8.2.0.tar.gz 
mkdir build
cd build
cmake -DBUILD_SHARED_LIBS:BOOL=OFF \
      -DCMAKE_BUILD_TYPE:STRING=RELEASE \
      -DBUILD_EXAMPLES=OFF \
      -DBUILD_TESTING=OFF \
      -DVTK_USE_SYSTEM_EXPAT:BOOL=ON \
      -DVTK_USE_SYSTEM_ZLIB:BOOL=ON \
      -DVTK_LEGACY_REMOVE=ON \
      -DVTK_Group_Rendering=OFF \
      -DVTK_Group_StandAlone=OFF \
      -DVTK_RENDERING_BACKEND=None \
      -DVTK_WRAP_PYTHON=OFF \
      -DModule_vtkChartsCore=ON \
      -DModule_vtkCommonCore=ON \
      -DModule_vtkCommonDataModel=ON \
      -DModule_vtkCommonExecutionModel=ON \
      -DModule_vtkFiltersCore=ON \
      -DModule_vtkFiltersFlowPaths=ON \
      -DModule_vtkFiltersModeling=ON \
      -DModule_vtkIOLegacy=ON \
      -DModule_vtkIOXML=ON \
      -DVTK_GROUP_ENABLE_Views=NO \
      -DVTK_GROUP_ENABLE_Web=NO \
      -DVTK_GROUP_ENABLE_Imaging=NO \
      -DVTK_GROUP_ENABLE_Qt=DONT_WANT \
      -DVTK_GROUP_ENABLE_Rendering=DONT_WANT \
      -DCMAKE_INSTALL_PREFIX=/$HOME/vtk/install \
      ../VTK-8.2.0
make
make install

Kindly guide me in this.

Regards,
Pratik.

[David Parker]

Hi Pratik,

The 0042_H_ABAO_AAA VMR data set does not have the format expected by SV, we will correct the files.

The Python script here https://github.com/ktbolt/cardiovascula ... p-to-32.py can be used to convert the offending Int64 cell data arrays.

Cheers,
Dave

[Pratik Mitra]

Hi Dave,

Thank you for your reply. Now, I can execute that code.

Regards,
Pratik.

[David Parker]

Hi Pratik,

We have corrected the formatting of 0042_H_ABAO_AAA and a few other files in the VMR.

Cheers,
Dave

[Manideep Roy]

Hii Pratik and Dave,

I previously performed simulations using SimVascular (svsolver) and it worked successfully.

After installing SimVascular on a separate workstation, I am facing this same issue while creating data files for 3D simulation. I am running simulation for my own model (not from Vascular Model Repository).

Kindly guide me on how to resolve this issue.

Thanking You
Manideep

[David Parker]

Hi Manideep,

You need to describe what error you are seeing.

Errors creating solver input data files is typically caused by missing software: Fortran compilers, MPI, etc.

Cheers,
Dave

[Manideep Roy]

Hii Dave,

I have installed the gfortran, openmpi and vtk using the following commands:

sudo apt-get install gfortran
sudo apt-get install openmpi-bin

mkdir $HOME/vtk
cd $HOME/vtk
wget https://www.vtk.org/files/release/8.2/VTK-8.2.0.tar.gz
tar xvf VTK-8.2.0.tar.gz
mkdir build
cd build
cmake -DBUILD_SHARED_LIBS:BOOL=OFF \
-DCMAKE_BUILD_TYPE:STRING=RELEASE \
-DBUILD_EXAMPLES=OFF \
-DBUILD_TESTING=OFF \
-DVTK_USE_SYSTEM_EXPAT:BOOL=ON \
-DVTK_USE_SYSTEM_ZLIB:BOOL=ON \
-DVTK_LEGACY_REMOVE=ON \
-DVTK_Group_Rendering=OFF \
-DVTK_Group_StandAlone=OFF \
-DVTK_RENDERING_BACKEND=None \
-DVTK_WRAP_PYTHON=OFF \
-DModule_vtkChartsCore=ON \
-DModule_vtkCommonCore=ON \
-DModule_vtkCommonDataModel=ON \
-DModule_vtkCommonExecutionModel=ON \
-DModule_vtkFiltersCore=ON \
-DModule_vtkFiltersFlowPaths=ON \
-DModule_vtkFiltersModeling=ON \
-DModule_vtkIOLegacy=ON \
-DModule_vtkIOXML=ON \
-DVTK_GROUP_ENABLE_Views=NO \
-DVTK_GROUP_ENABLE_Web=NO \
-DVTK_GROUP_ENABLE_Imaging=NO \
-DVTK_GROUP_ENABLE_Qt=DONT_WANT \
-DVTK_GROUP_ENABLE_Rendering=DONT_WANT \
-DCMAKE_INSTALL_PREFIX=/$HOME/vtk/install \
../VTK-8.2.0
make
make install



But I am getting the following error:



LINE 0000: mesh_and_adjncy_vtu mesh-complete/mesh-complete.mesh.vtu


ERROR: In ./IO/XMLParser/vtkXMLParser.cxx, line 389
vtkXMLDataParser (0x616cbea6f930): Error parsing XML in stream at line 22, column 1, byte index 1456: not well-formed (invalid token)

ERROR: In ./IO/XML/vtkXMLReader.cxx, line 467
vtkXMLUnstructuredGridReader (0x616cbea66020): Error parsing input file. ReadXMLInformation aborting.

ERROR: In ./Common/ExecutionModel/vtkExecutive.cxx, line 781
vtkCompositeDataPipeline (0x616cbea66eb0): Algorithm vtkXMLUnstructuredGridReader(0x616cbea66020) returned failure for request: vtkInformation (0x616cbea6d650)
Debug: Off
Modified Time: 83
Reference Count: 1
Registered Events: (none)
Request: REQUEST_INFORMATION
ALGORITHM_AFTER_FORWARD: 1
FORWARD_DIRECTION: 0



ERROR: Must specify number of nodes before you read them in!
ERROR: command could not be processed.



It will be really helpful if you can guide me on resolving this issue.



Thanking You
Manideep

[David Parker]

HI Manideep,

You don't need to build VTK for svSolver, it is included with the installer.

The solver data files (probably a VTP file) does not have the format expected by SV or perhaps the file can't be found or is corrupted.

Cheers,
Dave

[Manideep Roy]

Hi Dave,

I am still getting the following error message wile creating data files for 3D simulation. I am facing this issue for my own models and also for models downloaded from Vascular Model Repository.

However, these models are working fine in other computers and workstation and I am not getting this error message. So kindly guide me in resolving this issue.

Thanking You
Manideep Roy


Error message:

LINE 0000: mesh_and_adjncy_vtu mesh-complete/mesh-complete.mesh.vtu


ERROR: In ./IO/XMLParser/vtkXMLParser.cxx, line 389
vtkXMLDataParser (0x5a13380f4990): Error parsing XML in stream at line 22, column 0, byte index 1455: not well-formed (invalid token)

ERROR: In ./IO/XML/vtkXMLReader.cxx, line 467
vtkXMLUnstructuredGridReader (0x5a13380eb140): Error parsing input file. ReadXMLInformation aborting.

ERROR: In ./Common/ExecutionModel/vtkExecutive.cxx, line 781
vtkCompositeDataPipeline (0x5a13380ebfd0): Algorithm vtkXMLUnstructuredGridReader(0x5a13380eb140) returned failure for request: vtkInformation (0x5a13380f26b0)
Debug: Off
Modified Time: 83
Reference Count: 1
Registered Events: (none)
Request: REQUEST_INFORMATION
FORWARD_DIRECTION: 0
ALGORITHM_AFTER_FORWARD: 1



ERROR: Must specify number of nodes before you read them in!
ERROR: command could not be processed.

[David Parker]

Hi Manideep,

Please upload your SV files someplace I can download them and I'll have a look.

Cheers,
Dave