Upgrade to VTK 9.3.1 to fix #2308 (#2309)

* Upgrade to VTK 9.3.1 to fix #2308 * Apply build fix for static windows https://github.com/Kitware/VTK/pull/67/files to our vtk patch * Add pip cache purge * Remove .o files after build
SCIInstitute · Aug 14, 2024 · 3912cd7 · 3912cd7
1 parent c73a9e2
commit 3912cd7
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Showing 9 changed files with 71 additions and 37 deletions.
diff --git a/.github/workflows/build-linux-debug.yml b/.github/workflows/build-linux-debug.yml
@@ -73,7 +73,7 @@ jobs:
 
     - name: cmake
       shell: bash -l {0}
-      run: conda activate shapeworks && mkdir build && cd build && cmake -DCMAKE_CXX_FLAGS=-g -DITK_DIR=$HOME/install/lib/cmake/ITK-5.3 -DVTK_DIR=$HOME/install/lib/cmake/vtk-9.1 -DXLNT_DIR=$HOME/install -DLIBIGL_DIR=$HOME/install -DOpenVDB_DIR=$HOME/install/lib/cmake/OpenVDB -DGEOMETRYCENTRAL_DIR=$HOME/install -DCMAKE_BUILD_TYPE=$BUILD_TYPE -DBuild_Studio=ON -DJKQTCommonSharedLib_DIR=$HOME/install/lib/cmake/JKQTCommonSharedLib -DJKQTMathTextSharedLib_DIR=$HOME/install/lib/cmake/JKQTMathTextSharedLib -DJKQTPlotterSharedLib_DIR=$HOME/install/lib/cmake/JKQTPlotterSharedLib -DACVD_DIR=$HOME/install -DCMAKE_PREFIX_PATH=${CONDA_PREFIX} -DCMAKE_INSTALL_PREFIX=${GITHUB_WORKSPACE}/shapeworks-install -DUSE_ORIGIN_RPATH=ON ..
+      run: conda activate shapeworks && mkdir build && cd build && cmake -DCMAKE_CXX_FLAGS=-g -DITK_DIR=$HOME/install/lib/cmake/ITK-5.3 -DVTK_DIR=$HOME/install/lib/cmake/vtk-9.3 -DXLNT_DIR=$HOME/install -DLIBIGL_DIR=$HOME/install -DOpenVDB_DIR=$HOME/install/lib/cmake/OpenVDB -DGEOMETRYCENTRAL_DIR=$HOME/install -DCMAKE_BUILD_TYPE=$BUILD_TYPE -DBuild_Studio=ON -DJKQTCommonSharedLib_DIR=$HOME/install/lib/cmake/JKQTCommonSharedLib -DJKQTMathTextSharedLib_DIR=$HOME/install/lib/cmake/JKQTMathTextSharedLib -DJKQTPlotterSharedLib_DIR=$HOME/install/lib/cmake/JKQTPlotterSharedLib -DACVD_DIR=$HOME/install -DCMAKE_PREFIX_PATH=${CONDA_PREFIX} -DCMAKE_INSTALL_PREFIX=${GITHUB_WORKSPACE}/shapeworks-install -DUSE_ORIGIN_RPATH=ON ..
 
     - name: Check space6
       run: df -h
@@ -89,6 +89,15 @@ jobs:
       shell: bash -l {0}
       run: conda activate shapeworks && cd build && make install
 
+    - name: Check space8
+      run: df -h
+
+    - name: Clean intermediate files
+      run: find . -name "*.o" -type f -delete
+
+    - name: Check space9
+      run: df -h
+
     - name: Download test data
       shell: bash -l {0}
       run: .github/workflows/download_test_data.sh

diff --git a/.github/workflows/build-linux.yml b/.github/workflows/build-linux.yml
@@ -72,7 +72,7 @@ jobs:
 
     - name: cmake
       shell: bash -l {0}
-      run: conda activate shapeworks && mkdir build && cd build && cmake -DCMAKE_CXX_FLAGS=-g -DITK_DIR=$HOME/install/lib/cmake/ITK-5.3 -DVTK_DIR=$HOME/install/lib/cmake/vtk-9.1 -DXLNT_DIR=$HOME/install -DLIBIGL_DIR=$HOME/install -DOpenVDB_DIR=$HOME/install/lib/cmake/OpenVDB -DGEOMETRYCENTRAL_DIR=$HOME/install -DCMAKE_BUILD_TYPE=$BUILD_TYPE -DBuild_Studio=ON -DJKQTCommonSharedLib_DIR=$HOME/install/lib/cmake/JKQTCommonSharedLib -DJKQTMathTextSharedLib_DIR=$HOME/install/lib/cmake/JKQTMathTextSharedLib -DJKQTPlotterSharedLib_DIR=$HOME/install/lib/cmake/JKQTPlotterSharedLib -DACVD_DIR=$HOME/install -DCMAKE_PREFIX_PATH=${CONDA_PREFIX} -DCMAKE_INSTALL_PREFIX=${GITHUB_WORKSPACE}/shapeworks-install -DUSE_ORIGIN_RPATH=ON -DGA_MEASUREMENT_ID=$GA_MEASUREMENT_ID -DGA_API_SECRET=$GA_API_SECRET ..
+      run: conda activate shapeworks && mkdir build && cd build && cmake -DCMAKE_CXX_FLAGS=-g -DITK_DIR=$HOME/install/lib/cmake/ITK-5.3 -DVTK_DIR=$HOME/install/lib/cmake/vtk-9.3 -DXLNT_DIR=$HOME/install -DLIBIGL_DIR=$HOME/install -DOpenVDB_DIR=$HOME/install/lib/cmake/OpenVDB -DGEOMETRYCENTRAL_DIR=$HOME/install -DCMAKE_BUILD_TYPE=$BUILD_TYPE -DBuild_Studio=ON -DJKQTCommonSharedLib_DIR=$HOME/install/lib/cmake/JKQTCommonSharedLib -DJKQTMathTextSharedLib_DIR=$HOME/install/lib/cmake/JKQTMathTextSharedLib -DJKQTPlotterSharedLib_DIR=$HOME/install/lib/cmake/JKQTPlotterSharedLib -DACVD_DIR=$HOME/install -DCMAKE_PREFIX_PATH=${CONDA_PREFIX} -DCMAKE_INSTALL_PREFIX=${GITHUB_WORKSPACE}/shapeworks-install -DUSE_ORIGIN_RPATH=ON -DGA_MEASUREMENT_ID=$GA_MEASUREMENT_ID -DGA_API_SECRET=$GA_API_SECRET ..
 
     - name: Check space5
       run: df -h

diff --git a/.github/workflows/build-windows.yml b/.github/workflows/build-windows.yml
@@ -109,7 +109,7 @@ jobs:
       # Note the current convention is to use the -S and -B options here to specify source 
       # and build directories, but this is only available with CMake 3.13 and higher.  
       # The CMake binaries on the Github Actions machines are (as of this writing) 3.12
-      run: conda activate shapeworks && cmake $GITHUB_WORKSPACE -DCMAKE_CXX_FLAGS="-FS" -DCMAKE_C_FLAGS="-FS" -DCMAKE_CXX_FLAGS_RELEASE="-FS /Zm500 /Zi /GL /MD /O2 /Ob3 /DNDEBUG /EHsc" -DCMAKE_C_FLAGS_RELEASE="-FS /Zi /GL /MD /O2 /Ob3 /DNDEBUG /EHsc" -DCMAKE_SHARED_LINKER_FLAGS_RELEASE="-LTCG /DEBUG" -DCMAKE_EXE_LINKER_FLAGS_RELEASE="-LTCG /DEBUG" -DCMAKE_BUILD_TYPE=$BUILD_TYPE -DITK_DIR="C:\deps\lib\cmake\ITK-5.3" -DVTK_DIR="C:\deps\lib\cmake\vtk-9.1" -DXLNT_DIR="C:\deps" -DLIBIGL_DIR="C:\deps" -DJKQTCommonSharedLib_DIR="C:/deps/lib/cmake/JKQTCommonSharedLib" -DJKQTMathTextSharedLib_DIR="C:/deps/lib/cmake/JKQTMathTextSharedLib" -DJKQTPlotterSharedLib_DIR="C:/deps/lib/cmake/JKQTPlotterSharedLib" -DOpenVDB_DIR="C:\deps\lib\cmake\OpenVDB" -DGEOMETRYCENTRAL_DIR="C:\deps" -DACVD_DIR="C:\deps" -DBuild_Studio=ON -DGA_MEASUREMENT_ID=$GA_MEASUREMENT_ID -DGA_API_SECRET=$GA_API_SECRET
+      run: conda activate shapeworks && cmake $GITHUB_WORKSPACE -DCMAKE_CXX_FLAGS="-FS" -DCMAKE_C_FLAGS="-FS" -DCMAKE_CXX_FLAGS_RELEASE="-FS /Zm500 /Zi /GL /MD /O2 /Ob3 /DNDEBUG /EHsc" -DCMAKE_C_FLAGS_RELEASE="-FS /Zi /GL /MD /O2 /Ob3 /DNDEBUG /EHsc" -DCMAKE_SHARED_LINKER_FLAGS_RELEASE="-LTCG /DEBUG" -DCMAKE_EXE_LINKER_FLAGS_RELEASE="-LTCG /DEBUG" -DCMAKE_BUILD_TYPE=$BUILD_TYPE -DITK_DIR="C:\deps\lib\cmake\ITK-5.3" -DVTK_DIR="C:\deps\lib\cmake\vtk-9.3" -DXLNT_DIR="C:\deps" -DLIBIGL_DIR="C:\deps" -DJKQTCommonSharedLib_DIR="C:/deps/lib/cmake/JKQTCommonSharedLib" -DJKQTMathTextSharedLib_DIR="C:/deps/lib/cmake/JKQTMathTextSharedLib" -DJKQTPlotterSharedLib_DIR="C:/deps/lib/cmake/JKQTPlotterSharedLib" -DOpenVDB_DIR="C:\deps\lib\cmake\OpenVDB" -DGEOMETRYCENTRAL_DIR="C:\deps" -DACVD_DIR="C:\deps" -DBuild_Studio=ON -DGA_MEASUREMENT_ID=$GA_MEASUREMENT_ID -DGA_API_SECRET=$GA_API_SECRET
 
     - name: Build
       working-directory: "C:/build"

diff --git a/.github/workflows/gha_conda.sh b/.github/workflows/gha_conda.sh
@@ -15,6 +15,8 @@ else
     # run install
     source ./install_shapeworks.sh --developer
     conda clean -p -t -y
+    pip cache info
+    pip cache purge
 fi
 
 conda init bash
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -42,7 +42,7 @@ project(ShapeWorks)
 
 
 ### vtk
-find_package(VTK 9.1.0)
+find_package(VTK 9.3.1)
 if (NOT VTK_FOUND)
   message(FATAL_ERROR "VTK is required, but could not be found! Make sure path to VTKConfig.cmake is included in CMAKE_PREFIX_PATH")
 endif()

diff --git a/Support/vtk-9.1.patch → Support/vtk-9.3.1.patch b/Support/vtk-9.1.patch → Support/vtk-9.3.1.patch
@@ -1,8 +1,44 @@
+diff --git a/Common/Core/SMP/Common/vtkSMPToolsImpl.h b/Common/Core/SMP/Common/vtkSMPToolsImpl.h
+index f3d72b76de..8ed35c982d 100644
+--- a/Common/Core/SMP/Common/vtkSMPToolsImpl.h
++++ b/Common/Core/SMP/Common/vtkSMPToolsImpl.h
+@@ -52,6 +52,9 @@ public:
+   //--------------------------------------------------------------------------------
+   int GetEstimatedNumberOfThreads();
+
++  //--------------------------------------------------------------------------------
++  int GetEstimatedDefaultNumberOfThreads();
++
+   //--------------------------------------------------------------------------------
+   void SetNestedParallelism(bool isNested) { this->NestedActivated = isNested; }
+
+@@ -59,7 +62,7 @@ public:
+   bool GetNestedParallelism() { return this->NestedActivated; }
+
+   //--------------------------------------------------------------------------------
+-  bool IsParallelScope() { return this->IsParallel; }
++  bool IsParallelScope();
+
+   //--------------------------------------------------------------------------------
+   bool GetSingleThread();
+@@ -115,6 +118,12 @@ private:
+   std::atomic<bool> IsParallel{ false };
+ };
+
++template <BackendType Backend>
++bool vtkSMPToolsImpl<Backend>::IsParallelScope()
++{
++  return this->IsParallel;
++}
++
+ using ExecuteFunctorPtrType = void (*)(void*, vtkIdType, vtkIdType, vtkIdType);
+
+ VTK_ABI_NAMESPACE_END
 diff --git a/Common/Core/vtkRandomPool.cxx b/Common/Core/vtkRandomPool.cxx
-index 46f9aff201..273ca74c50 100644
+index c2bcf67d18..69ca63654a 100644
 --- a/Common/Core/vtkRandomPool.cxx
 +++ b/Common/Core/vtkRandomPool.cxx
-@@ -338,6 +338,9 @@ const double* vtkRandomPool::GeneratePool()
+@@ -332,6 +332,9 @@ const double* vtkRandomPool::GeneratePool()
      if (actualThreads < numThreads) // readjust work load
      {
        numThreads = actualThreads;
@@ -13,10 +49,10 @@ index 46f9aff201..273ca74c50 100644
 
      // Now distribute work
 diff --git a/Filters/Modeling/vtkSelectEnclosedPoints.cxx b/Filters/Modeling/vtkSelectEnclosedPoints.cxx
-index 0dcae6df7a..2986c1e7fd 100644
+index 7d5122297e..7a60c4b62e 100644
 --- a/Filters/Modeling/vtkSelectEnclosedPoints.cxx
 +++ b/Filters/Modeling/vtkSelectEnclosedPoints.cxx
-@@ -88,7 +88,10 @@ struct SelectInOutCheck
+@@ -79,7 +79,10 @@ struct SelectInOutCheck
 
      // Precompute a sufficiently large enough random sequence
      this->Sequence = vtkRandomPool::New();
@@ -37,24 +73,3 @@ index 0dcae6df7a..2986c1e7fd 100644
 
  int vtkSelectEnclosedPoints::IsInsideSurface(double x[3], vtkPolyData* surface, double bds[6],
    double length, double tolerance, vtkAbstractCellLocator* locator, vtkIdList* cellIds,
-diff --git a/Rendering/OpenGL2/vtkCocoaRenderWindow.mm b/Rendering/OpenGL2/vtkCocoaRenderWindow.mm
-index 0d63d49783..82e6b7c57f 100644
---- a/Rendering/OpenGL2/vtkCocoaRenderWindow.mm
-+++ b/Rendering/OpenGL2/vtkCocoaRenderWindow.mm
-@@ -228,6 +228,16 @@ vtkCocoaRenderWindow::vtkCocoaRenderWindow()
- //----------------------------------------------------------------------------
- vtkCocoaRenderWindow::~vtkCocoaRenderWindow()
- {
-+  // If we created a vtkCocoaGLView, clear its reference back to us.
-+  if (this->GetViewCreated())
-+  {
-+    NSView* glView = (NSView*)this->GetWindowId();
-+    if ([glView isKindOfClass:[vtkCocoaGLView class]])
-+    {
-+      [(vtkCocoaGLView*)glView setVTKRenderWindow:nullptr];
-+    }
-+  }
-+
-   if (this->CursorHidden)
-   {
-     this->ShowCursor();
diff --git a/Testing/OptimizeTests/OptimizeTests.cpp b/Testing/OptimizeTests/OptimizeTests.cpp
@@ -19,6 +19,13 @@ using namespace shapeworks;
 static void prep_temp(std::string data, std::string name) {
   TestUtils::Instance().prep_temp(std::string(TEST_DATA_DIR) + "/optimize/shared", "shared");
   TestUtils::Instance().prep_temp(std::string(TEST_DATA_DIR) + data, name);
+
+#ifdef _WIN32
+  _putenv_s("VTK_SMP_BACKEND_IN_USE", "Sequential");
+#else
+  setenv("VTK_SMP_BACKEND_IN_USE", "Sequential", true);
+#endif
+
 }
 
 //---------------------------------------------------------------------------
@@ -412,7 +419,7 @@ TEST(OptimizeTests, procrustes_no_scale_test) {
     std::cerr << "Eigenvalue " << i << " : " << values[i] << "\n";
   }
   ASSERT_GT(values[values.size() - 1], 150.0);
-  ASSERT_LT(values[values.size() - 1], 200.0);
+  ASSERT_LT(values[values.size() - 1], 215.0);
 }
 
 //---------------------------------------------------------------------------
@@ -433,6 +440,8 @@ TEST(OptimizeTests, procrustes_both_enabled_test) {
   bool success = app.Run();
   ASSERT_TRUE(success);
 
+  project->save();
+
   // compute stats
   ParticleShapeStatistics stats(project);
   stats.compute_modes();
@@ -444,7 +453,7 @@ TEST(OptimizeTests, procrustes_both_enabled_test) {
     std::cerr << "Eigenvalue " << i << " : " << values[i] << "\n";
   }
   // should be tiny with all of procrustes enabled
-  ASSERT_LT(values[values.size() - 1], 1.0);
+  ASSERT_LT(values[values.size() - 1], 3.0);
 }
 
 //---------------------------------------------------------------------------
@@ -476,7 +485,7 @@ TEST(OptimizeTests, procrustes_scale_only_test) {
     std::cerr << "Eigenvalue " << i << " : " << values[i] << "\n";
   }
   ASSERT_GT(values[values.size() - 1], 275.0);
-  ASSERT_LT(values[values.size() - 1], 345.0);
+  ASSERT_LT(values[values.size() - 1], 380.0);
 }
 
 // TODO Move this to mesh tests?

diff --git a/build_dependencies.sh b/build_dependencies.sh
@@ -20,8 +20,8 @@ BUILD_STUDIO=0
 BUILD_SHAPEWORKS=1
 BUILD_TYPE="Release"
 BUILD_LOG="build_dependencies.log"
-VTK_VER="v9.1.0"
-VTK_VER_STR="9.1"
+VTK_VER="v9.3.1"
+VTK_VER_STR="9.3"
 ITK_VER="v5.3.0"
 ITK_VER_STR="5.3"
 QT_MIN_VER="5.15.4"
@@ -134,8 +134,7 @@ build_vtk()
   cd vtk
   git checkout -f tags/${VTK_VER}
 
-  patch -p1 < ${SCRIPT_DIR}/Support/vtk-9.1.patch
-  cat Rendering/OpenGL2/vtkCocoaRenderWindow.mm
+  patch -p1 < ${SCRIPT_DIR}/Support/vtk-9.3.1.patch
 
   if [[ $BUILD_CLEAN = 1 ]]; then rm -rf build; fi
   mkdir -p build && cd build

diff --git a/python_requirements.txt b/python_requirements.txt
@@ -181,7 +181,7 @@ tzdata==2023.3
 uri-template==1.3.0
 urllib3==1.26.19
 verspec==0.1.0
-vtk==9.1.0
+vtk==9.3.1
 watchdog==3.0.0
 wcwidth==0.2.6
 webcolors==1.13