Parallelproj old OpenMP fix

.appveyor.yml

@@ -31,15 +31,30 @@ build_script:
   # find boost on Appveyor. Version depends on VM
   - for /D %%d in (C:\Libraries\boost_*) do set BOOST_ROOT=%%d
   - echo Using Boost %BOOST_ROOT%
+  # find miniconda
+  - for /D %%d in (C:\Miniconda*-x64) do set MINICONDA=%%d
+  - echo Using Miniconda %MINICONDA%
+  - "set PATH=%MINICONDA%;%MINICONDA%\\Scripts;%MINICONDA%\\Library\\bin;%PATH%"
+  # install parallelproj and Python stuff
+  - conda install -c conda-forge  -yq libparallelproj swig numpy pytest
+  - CALL conda.bat activate base
+  - python --version
   - mkdir build
   - mkdir install
   - cd build
-  - cmake.exe .. -DCMAKE_INSTALL_PREFIX="C:\projects\stir\install" -DCMAKE_BUILD_TYPE=%CONFIGURATION%  -DCMAKE_CONFIGURATION_TYPES=%CONFIGURATION% -DSTIR_OPENMP:BOOL=ON -DBUILD_DOCUMENTATION:BOOL=OFF
+  - cmake.exe .. -A x64 -DCMAKE_INSTALL_PREFIX="C:\projects\stir\install" -DCMAKE_BUILD_TYPE=%CONFIGURATION%  -DCMAKE_CONFIGURATION_TYPES=%CONFIGURATION% -DSTIR_OPENMP:BOOL=ON -DBUILD_DOCUMENTATION:BOOL=OFF -DBUILD_SWIG_PYTHON:BOOL=ON -DPython_EXECUTABLE="%MINICONDA%\\python.exe"
   - cmake.exe --build . --config %CONFIGURATION%
   - cmake.exe --build . --target install --config %CONFIGURATION%
+  - conda deactivate
 
 test_script:
   - cd C:\projects\stir\build
+  - CALL conda.bat activate base
+  - python --version
   - ctest --output-on-failure  -C %CONFIGURATION%
   - cd ..\recon_test_pack
   - run_tests --nointbp "C:\projects\stir\install\bin\"
+  - cd ..\src
+  - "set PYTHONPATH=C:\\projects\\stir\\install\\python"
+  - python -m pytest .
+  - conda deactivate

CMakeLists.txt

@@ -5,11 +5,11 @@
 # See STIR/LICENSE.txt for details
 
 # cmake file for building STIR. See the STIR User's Guide and http://www.cmake.org.
-cmake_minimum_required(VERSION 3.1.0)
-
-
-# avoid warning about WIN32 no longer defined in CYGWIN
-set(CMAKE_LEGACY_CYGWIN_WIN32 0) 
+if (CMAKE_HOST_WIN32)
+  cmake_minimum_required(VERSION 3.12.0)
+else()
+  cmake_minimum_required(VERSION 3.1.0)
+endif()
 
 # enable ccache https://ccache.samba.org/
 find_program(CCACHE_PROGRAM ccache)

documentation/release_5.2.htm

@@ -105,6 +105,7 @@ <h3>Deprecated functionality</h3>
 
 <h3>Build system and dependencies</h3>
 <ul>
+  <li>CMake 3.12 is now required on Windows. (It will be required on all platforms in the next version).</li>
   <li>We now use CMake's <a href=https://gitlab.kitware.com/cmake/community/-/wikis/doc/tutorials/Object-Library>OBJECT library feature</a> for the registries. This avoids re-compilation of the registries for every executable and therefore speeds-up building time. Use of STIR in an external project is not affected as long as the recommended practice was followed. This is now documented in the User's Guide.
     <br /><a href="https://github.com/UCL/STIR/pull/1141/">PR #1141</a>.
   </li>

src/recon_buildblock/Parallelproj_projector/ParallelprojHelper.cxx

@@ -79,6 +79,22 @@ detail::ParallelprojHelper::ParallelprojHelper(const ProjDataInfo& p_info, const
 #ifdef STIR_OPENMP
   // Using too many threads is counterproductive according to my timings, so I limited to 8 (not necessarily optimal!).
   const auto num_threads_to_use = std::min(8,get_max_num_threads());
+#  if _OPENMP >=201012
+#    define ATOMICWRITE _Pragma("omp atomic write") \
+
+#    define CRITICALSECTION
+#  else
+#    define ATOMICWRITE
+#    if defined(_MSC_VER) && (_MSC_VER < 1910)
+       // no _Pragma until VS 2017
+#      define CRITICALSECTION
+#    else
+#      define CRITICALSECTION _Pragma("omp critical(PARALLELPROJHELPER_INIT)")
+#    endif
+#  endif
+#else
+#  define ATOMICWRITE
+#  define CRITICALSECTION
 #endif
   for (int seg : segment_sequence)
     {
@@ -97,66 +113,37 @@ detail::ParallelprojHelper::ParallelprojHelper(const ProjDataInfo& p_info, const
                   bin.view_num() = view_num;
                   bin.tangential_pos_num() = tangential_pos_num;
                   // compute index for this bin (independent of multi-threading)
-                  std::size_t this_index = index + (bin.tangential_pos_num() - p_info.get_min_tangential_pos_num())*3;
+                  const std::size_t this_index = index + (bin.tangential_pos_num() - p_info.get_min_tangential_pos_num())*3;
                   LORInAxialAndNoArcCorrSinogramCoordinates<float> lor;
                   LORAs2Points<float> lor_points;
 
                   p_info.get_LOR(lor, bin);
                   if (lor.get_intersections_with_cylinder(lor_points, radius) == Succeeded::no)
-                    {  // memory is already allocated, so just passing in points that will produce nothing
-#ifdef STIR_OPENMP
-#pragma omp atomic write
-#endif
-                    xstart[this_index] = 0;
-#ifdef STIR_OPENMP
-#pragma omp atomic write
-#endif
-                    xend[this_index] = 0;
-#ifdef STIR_OPENMP
-#pragma omp atomic write
-#endif
-                    xstart[this_index+1] = 0;
-#ifdef STIR_OPENMP
-#pragma omp atomic write
-#endif
-                    xend[this_index+1] = 0;
-#ifdef STIR_OPENMP
-#pragma omp atomic write
-#endif
-                    xstart[this_index+2] = 0;
-#ifdef STIR_OPENMP
-#pragma omp atomic write
-#endif
-                    xend[this_index+2] = 0;
+                    {
+                      // memory is already allocated, so just passing in points that will produce nothing
+                      CRITICALSECTION
+                        {
+                          ATOMICWRITE xstart[this_index] = 0;
+                          ATOMICWRITE xend[this_index] = 0;
+                          ATOMICWRITE xstart[this_index+1] = 0;
+                          ATOMICWRITE xend[this_index+1] = 0;
+                          ATOMICWRITE xstart[this_index+2] = 0;
+                          ATOMICWRITE xend[this_index+2] = 0;
+                        }
                   }
                   else
                   {
-                    const CartesianCoordinate3D<float> p1 = lor_points.p1()*rescale;
-                    const CartesianCoordinate3D<float> p2 = lor_points.p2()*rescale;
-#ifdef STIR_OPENMP
-#pragma omp atomic write
-#endif
-                    xstart[this_index] = p1[1];
-#ifdef STIR_OPENMP
-#pragma omp atomic write
-#endif
-                    xend[this_index] = p2[1];
-#ifdef STIR_OPENMP
-#pragma omp atomic write
-#endif
-                    xstart[this_index+1] = p1[2];
-#ifdef STIR_OPENMP
-#pragma omp atomic write
-#endif
-                    xend[this_index+1] = p2[2];
-#ifdef STIR_OPENMP
-#pragma omp atomic write
-#endif
-                    xstart[this_index+2] = p1[3];
-#ifdef STIR_OPENMP
-#pragma omp atomic write
-#endif
-                    xend[this_index+2] = p2[3];
+                    const auto p1 = lor_points.p1()*rescale;
+                    const auto p2 = lor_points.p2()*rescale;
+                    CRITICALSECTION
+                      {
+                        ATOMICWRITE xstart[this_index] = p1[1];
+                        ATOMICWRITE xend[this_index] = p2[1];
+                        ATOMICWRITE xstart[this_index+1] = p1[2];
+                        ATOMICWRITE xend[this_index+1] = p2[2];
+                        ATOMICWRITE xstart[this_index+2] = p1[3];
+                        ATOMICWRITE xend[this_index+2] = p2[3];
+                      }
                   }
                 }
               index += p_info.get_num_tangential_poss()*3;

src/swig/CMakeLists.txt

@@ -1,5 +1,5 @@
 # Copyright 2012 Kris Thielemans
-# Copyright 2014, 2018, 2020, 2022 University College London
+# Copyright 2014, 2018, 2020, 2022, 2023 University College London
 # This file is part of STIR.
 #
 # SPDX-License-Identifier: Apache-2.0
@@ -151,6 +151,9 @@ if(BUILD_SWIG_PYTHON)
     SWIG_ADD_MODULE(stir python stir.i $<TARGET_OBJECTS:stir_registries>)
   else()
     SWIG_ADD_LIBRARY(stir LANGUAGE python TYPE MODULE SOURCES stir.i $<TARGET_OBJECTS:stir_registries>)
+    if("${CMAKE_CXX_COMPILER_ID}" MATCHES "MSVC")
+     set_property(TARGET ${SWIG_MODULE_stir_REAL_NAME} PROPERTY SWIG_GENERATED_COMPILE_OPTIONS /bigobj)
+   endif()
   endif()
   SWIG_WORKAROUND(${SWIG_MODULE_stir_REAL_NAME})
   SWIG_LINK_LIBRARIES(stir ${STIR_LIBRARIES} ${STIR_Python_dependency})
@@ -198,6 +201,9 @@ if (BUILD_SWIG_OCTAVE)
     SWIG_ADD_MODULE(stiroct octave stir.i $<TARGET_OBJECTS:stir_registries>)
   else()
     SWIG_ADD_LIBRARY(stiroct LANGUAGE octave TYPE MODULE SOURCES stir.i $<TARGET_OBJECTS:stir_registries>)
+    if("${CMAKE_CXX_COMPILER_ID}" MATCHES "MSVC")
+     set_property(TARGET ${SWIG_MODULE_stiroct_REAL_NAME} PROPERTY SWIG_GENERATED_COMPILE_OPTIONS /bigobj)
+   endif()
   endif()
   SET_TARGET_PROPERTIES(${SWIG_MODULE_stiroct_REAL_NAME} PROPERTIES SUFFIX ${OCTAVE_SUFFIX} PREFIX "${OCTAVE_PREFIX}")
   SWIG_WORKAROUND(${SWIG_MODULE_stiroct_REAL_NAME})
@@ -224,6 +230,9 @@ if (BUILD_SWIG_MATLAB)
     SWIG_ADD_MODULE(stirMATLAB matlab stir.i $<TARGET_OBJECTS:stir_registries>)
   else()
     SWIG_ADD_LIBRARY(stirMATLAB LANGUAGE matlab TYPE MODULE SOURCES stir.i $<TARGET_OBJECTS:stir_registries>)
+    if("${CMAKE_CXX_COMPILER_ID}" MATCHES "MSVC")
+     set_property(TARGET ${SWIG_MODULE_stirMATLAB_REAL_NAME} PROPERTY SWIG_GENERATED_COMPILE_OPTIONS /bigobj)
+   endif()
   endif()
   if (WIN32)
      set (Matlab_CXXLINKER_FLAGS "/EXPORT:mexFunction")