Add build options for LTO and address sanitization (OpenFUSIONToolkit#328)

- Enable link-time optimization by default for Release builds
- Update `build_libs.py` to support setting new build options
- Remove Fortran flag specification from build_libs (already done in CMakeLists.txt)
- Update `cd_combined.yaml` and `container_cd.yaml` to only run on non-draft PRs
- Update exception handling in build_libs.py downloads

Author: hansec

.github/workflows/cd_combined.yaml

@@ -6,6 +6,11 @@ on:
       - main
       - pypi_release
   pull_request:
+    types:
+      - opened
+      - synchronize
+      - reopened
+      - ready_for_review
     paths:
       - .github/workflows/cd_combined.yaml
       - src/utilities/build_libs.py
@@ -18,7 +23,7 @@ concurrency:
 
 jobs:
   linux-build:
-    if: github.repository == 'OpenFUSIONToolkit/OpenFUSIONToolkit'
+    if: (github.event_name != 'pull_request' || github.event.pull_request.draft == false) && github.repository == 'OpenFUSIONToolkit/OpenFUSIONToolkit'
     name: ${{ format('Linux CD ({0})', matrix.config.name) }}
     runs-on: ${{ matrix.config.os }}
     container: ${{ matrix.config.image }}
@@ -144,7 +149,7 @@ jobs:
         retention-days: 2
 
   macos-build:
-    if: github.repository == 'OpenFUSIONToolkit/OpenFUSIONToolkit'
+    if: (github.event_name != 'pull_request' || github.event.pull_request.draft == false) && github.repository == 'OpenFUSIONToolkit/OpenFUSIONToolkit'
     name: ${{ format('macOS CD ({0})', matrix.config.name) }}
     runs-on: ${{ matrix.config.os }}
     timeout-minutes: 45

.github/workflows/ci_build.yaml

@@ -50,8 +50,8 @@ jobs:
             os: ubuntu-24.04,
             cc: "icx", cxx: "icx", fc: "ifx",
             python: "python3",
-            build_flags: "--nthread=4 --use_mkl --mkl_root=$MKLROOT",
-            mpi_build_flags: "--nthread=4 --use_mkl --mkl_root=$MKLROOT",
+            build_flags: "--nthread=4 --use_mkl --mkl_root=$MKLROOT --oft_use_lto=0",
+            mpi_build_flags: "--nthread=4 --use_mkl --mkl_root=$MKLROOT --oft_use_lto=0",
             oneapi_ver: "-2025.2"
           }
         - {
@@ -110,7 +110,7 @@ jobs:
               os: ubuntu-22.04,
               cc: "gcc-12", cxx: "g++-12", fc: "gfortran-12",
               python: "python3",
-              mpi_build_flags: "--nthread=2 --oblas_dynamic_arch --build_petsc=1 --petsc_version=3.23 --petsc_openmp=1 --build_cmake=1"
+              mpi_build_flags: "--nthread=2 --oblas_dynamic_arch --build_petsc=1 --petsc_version=3.23 --petsc_openmp=1 --build_cmake=1 --oft_use_lto=0"
             }
 
     steps:

.github/workflows/container_cd.yaml

@@ -5,6 +5,11 @@ on:
     branches:
       - container_release
   pull_request:
+    types:
+      - opened
+      - synchronize
+      - reopened
+      - ready_for_review
     paths:
       - .github/workflows/container_cd.yaml
       - src/utilities/build_libs.py
@@ -19,7 +24,7 @@ env:
 
 jobs:
   prepare-version:
-    if: github.repository == 'OpenFUSIONToolkit/OpenFUSIONToolkit'
+    if: (github.event_name != 'pull_request' || github.event.pull_request.draft == false) && github.repository == 'OpenFUSIONToolkit/OpenFUSIONToolkit'
     runs-on: ubuntu-latest
     outputs:
       version_tag: ${{ steps.version.outputs.version_tag }}
@@ -62,7 +67,7 @@ jobs:
     steps:
       - name: Checkout repository
         uses: actions/checkout@v5
-      
+
       - name: Get build architecture
         run: echo "ARCH_SUFFIX=$(dpkg --print-architecture)" >> "$GITHUB_ENV"
 

.github/workflows/cov_build.yaml

@@ -7,15 +7,20 @@ on:
       - cov_debug
   pull_request:
     types:
+      - opened
+      - synchronize
+      - reopened
       - ready_for_review
+    paths:
+      - .github/workflows/cov_build.yaml
 
 concurrency:
   group: cov-${{ github.ref }}
   cancel-in-progress: ${{ contains(github.ref, 'pull/')}}
 
 jobs:
   build:
-    if: github.repository == 'OpenFUSIONToolkit/OpenFUSIONToolkit'
+    if: (github.event_name != 'pull_request' || github.event.pull_request.draft == false) && github.repository == 'OpenFUSIONToolkit/OpenFUSIONToolkit'
     name: Code coverage
     runs-on: ubuntu-22.04
     env:
@@ -89,22 +94,22 @@ jobs:
       run: |
         source ${{ github.workspace }}/oft_venv/bin/activate
         make test
-    
+
     - name: Fixup cache
       shell: bash
       working-directory: builds
       run: |
         rm -rf build
         rm -rf petsc*
-    
+
     - name: Generate coverage report (GCOV)
       shell: bash
       working-directory: builds/build_release
       run: |
         lcov -c --directory . --output-file main_coverage.info --gcov-tool $GCOV
         lcov --ignore-errors unused -r main_coverage.info -o cleaned_coverage.txt '/opt/*' '/usr/*'
         lcov -l cleaned_coverage.txt
-    
+
     - name: Generate coverage report (Python)
       shell: bash
       working-directory: builds/build_release/tests
@@ -113,7 +118,7 @@ jobs:
         coverage combine . grid lin_alg fem physics
         coverage report
         coverage xml
-    
+
     - name: Upload coverage report to Codecov
       uses: codecov/codecov-action@v6
       with:

src/CMakeLists.txt

@@ -15,7 +15,10 @@ option(OFT_USE_MPI "Build with MPI support?" OFF)
 option(OFT_MPI_HEADER "Use MPI header interface instead of F08?" OFF)
 option(OFT_HDF5_HL "Search for and link with HDF5 HL interface?" OFF)
 option(OFT_USE_OpenMP "Build with OpenMP support?" ON)
+option(OFT_USE_LTO "Build with link time optimization (Release builds only)?" ON)
 option(OFT_DEBUG_STACK "Build with internal debugging stack?" OFF)
+option(OFT_DEBUG_CHECK "Build with compiler runtime debug checks (Debug builds only)?" ON)
+option(OFT_DEBUG_SANITIZER "Build with address sanitization checks (Debug builds only)?" OFF)
 option(OFT_PROFILING "Build with internal profiling enabled?" OFF)
 option(OFT_BUILD_PYTHON "Build Python wrappers?" ON)
 option(OFT_BUILD_DOCS "Build documentation?" OFF)
@@ -111,6 +114,14 @@ endif()
 enable_language( C )
 enable_language( CXX )
 enable_language( Fortran )
+# Flag checks
+if(OFT_DEBUG_SANITIZER AND APPLE)
+  message( FATAL_ERROR "Memory sanitization not supported on macOS" )
+endif()
+if(OFT_DEBUG_CHECK AND OFT_DEBUG_SANITIZER)
+  message( FATAL_ERROR "Cannot enable both compiler checks and address sanitization together" )
+endif()
+# Set flags based on compiler
 if ("${CMAKE_Fortran_COMPILER_ID}" MATCHES "Intel")
   if (NOT ("${CMAKE_C_COMPILER_ID}" MATCHES "Intel"))
     message( FATAL_ERROR "Fortran and C compilers must be from the same vendor" )
@@ -127,16 +138,30 @@ if ("${CMAKE_Fortran_COMPILER_ID}" MATCHES "Intel")
   set( CMAKE_C_FLAGS_RELEASE "" )
   set( CMAKE_CXX_FLAGS_RELEASE ${CMAKE_C_FLAGS_RELEASE} )
   set( CMAKE_Fortran_FLAGS_RELEASE ${CMAKE_C_FLAGS_RELEASE} )
-  if(NOT OFT_PACKAGE_BUILD)
-    if( "${CMAKE_CXX_COMPILER_ID}" MATCHES "IntelLLVM" )
-      set( CMAKE_Fortran_FLAGS_DEBUG "${CMAKE_Fortran_FLAGS_DEBUG} -check bounds,contiguous,pointers,shape,stack" )
-    else()
-      set( CMAKE_Fortran_FLAGS_DEBUG "${CMAKE_Fortran_FLAGS_DEBUG} -check bounds,pointers,shape,uninit" )
+  if( "${CMAKE_CXX_COMPILER_ID}" MATCHES "IntelLLVM" )
+    if(NOT OFT_PACKAGE_BUILD)
+      if(OFT_DEBUG_CHECK)
+        set( CMAKE_Fortran_FLAGS_DEBUG "${CMAKE_Fortran_FLAGS_DEBUG} -check bounds,contiguous,pointers,shape,stack" )
+      elseif(OFT_DEBUG_SANITIZER)
+        set( CMAKE_Fortran_FLAGS_DEBUG "${CMAKE_Fortran_FLAGS_DEBUG} -fsanitize=address" )
+      endif()
+    endif()
+  else()
+    if(NOT OFT_PACKAGE_BUILD)
+      if(OFT_DEBUG_CHECK)
+        set( CMAKE_Fortran_FLAGS_DEBUG "${CMAKE_Fortran_FLAGS_DEBUG} -check bounds,pointers,shape,uninit" )
+      elseif(OFT_DEBUG_SANITIZER)
+        message( FATAL_ERROR "Address sanitization not supported with classic intel compilers" )
+      endif()
     endif()
   endif()
   # Needed for new oneAPI Intel compilers
   if( "${CMAKE_CXX_COMPILER_ID}" MATCHES "IntelLLVM" )
     set( EXT_LIBS "-lstdc++" )
+    if( OFT_USE_LTO )
+      set( CMAKE_EXE_LINKER_FLAGS_RELEASE "${CMAKE_EXE_LINKER_FLAGS_RELEASE} -fuse-ld=lld")
+      set( CMAKE_SHARED_LINKER_FLAGS_RELEASE "${CMAKE_SHARED_LINKER_FLAGS_RELEASE} -fuse-ld=lld")
+    endif()
   endif()
 elseif("${CMAKE_Fortran_COMPILER_ID}" MATCHES "GNU")
   if (NOT ("${CMAKE_C_COMPILER_ID}" MATCHES "GNU"))
@@ -146,14 +171,14 @@ elseif("${CMAKE_Fortran_COMPILER_ID}" MATCHES "GNU")
     message( FATAL_ERROR "Fortran and C++ compilers must be from the same vendor" )
   endif()
   if(OFT_COVERAGE)
-    set( CMAKE_C_FLAGS_DEBUG "-Og --coverage -fprofile-update=atomic -g -Wuninitialized" ) # -fprofile-arcs -ftest-coverage
+    set( CMAKE_C_FLAGS_DEBUG "-g -Og -fno-omit-frame-pointer -Wuninitialized --coverage -fprofile-update=atomic" ) # -fprofile-arcs -ftest-coverage
     set( CMAKE_C_FLAGS_RELEASE ${CMAKE_C_FLAGS_DEBUG} )
     add_definitions( -DOFT_COVERAGE )
     set(CMAKE_C_OUTPUT_EXTENSION_REPLACE ON)
     set(CMAKE_CXX_OUTPUT_EXTENSION_REPLACE ON)
     set(CMAKE_Fortran_OUTPUT_EXTENSION_REPLACE ON)
   else()
-    set( CMAKE_C_FLAGS_DEBUG "-g -O0 -Wuninitialized" )
+    set( CMAKE_C_FLAGS_DEBUG "-g -Og -fno-omit-frame-pointer -Wuninitialized" )
     set( CMAKE_C_FLAGS_RELEASE "-O2" )
   endif()
   # Disable executable stack (default)
@@ -169,13 +194,32 @@ elseif("${CMAKE_Fortran_COMPILER_ID}" MATCHES "GNU")
   set( CMAKE_Fortran_FLAGS_DEBUG "${CMAKE_C_FLAGS_DEBUG} -Werror=line-truncation -Wconversion" )
   set( CMAKE_Fortran_FLAGS_RELEASE "${CMAKE_C_FLAGS_RELEASE} -Werror=line-truncation -Wconversion" )
   if(NOT OFT_PACKAGE_BUILD)
-    set( CMAKE_Fortran_FLAGS_DEBUG "${CMAKE_Fortran_FLAGS_DEBUG} -fcheck=all" )
+    if(OFT_DEBUG_CHECK)
+      set( CMAKE_Fortran_FLAGS_DEBUG "${CMAKE_Fortran_FLAGS_DEBUG} -fcheck=all" )
+    elseif(OFT_DEBUG_SANITIZER)
+      set( CMAKE_Fortran_FLAGS_DEBUG "${CMAKE_Fortran_FLAGS_DEBUG} -fsanitize=address" )
+    endif()
   endif()
   set( CMAKE_Fortran_FLAGS "-ffree-line-length-none ${CMAKE_Fortran_FLAGS}" )
   if(CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 10)
     set( CMAKE_Fortran_FLAGS "-fallow-argument-mismatch ${CMAKE_Fortran_FLAGS}" )
   endif()
 endif()
+# Enable IPO for release builds (not including coverage)
+if(OFT_USE_LTO)
+  if(CMAKE_BUILD_TYPE STREQUAL "Release" AND NOT OFT_COVERAGE)
+    include(CheckIPOSupported)
+    check_ipo_supported(RESULT ipo_supported)
+    if(ipo_supported)
+      set(CMAKE_INTERPROCEDURAL_OPTIMIZATION_RELEASE ON)
+      message( STATUS "Using Link-Time Optimization" )
+    else()
+      message( FATAL_ERROR "Link-Time Optimization is not supported on this platform" )
+    endif()
+  else()
+    message( WARNING "Link-Time Optimization only supported for Release builds, skipping" )
+  endif()
+endif()
 # Internal profiling
 if( OFT_PROFILING )
   add_definitions( -DOFT_STACK -DOFT_PROFILE )

src/base/oft_io.F90

@@ -434,8 +434,10 @@ subroutine xdmf_clear_timesteps(self,clear_static)
 END DO
 self%n_ts=0
 IF(istart==0)THEN
-  hdf5_path=TRIM(self%group_name)//"/"//TRIM(self%grid_names(j))
-  CALL hdf5_create_group(TRIM(self%file_path),TRIM(hdf5_path)//"/"//hdf5_ts_str(0))
+  DO j=1,self%n_grids
+    hdf5_path=TRIM(self%group_name)//"/"//TRIM(self%grid_names(j))
+    CALL hdf5_create_group(TRIM(self%file_path),TRIM(hdf5_path)//"/"//hdf5_ts_str(0))
+  END DO
 END IF
 if(oft_debug_print(2))THEN
   file_sizes = hdf5_file_size(TRIM(self%file_path))

src/ext_libs/CMakeLists.txt

@@ -11,6 +11,8 @@ add_library( oftext
   bvls.f90
   ${QUADPACK_OBJS}
 )
+# Always turn off IPO to avoid DLSODE common block issue
+set_property(TARGET oftext PROPERTY INTERPROCEDURAL_OPTIMIZATION_RELEASE OFF)
 
 # Local copy of triangle
 if( OFT_BUILD_PYTHON )
@@ -26,4 +28,4 @@ if( OFT_BUILD_PYTHON )
     DESTINATION bin
     COMPONENT app
   )
-endif()
+endif()

src/grid/mesh_native.F90

@@ -591,6 +591,7 @@ subroutine native_reflect(self,tol)
 integer(i4), allocatable :: newindex(:),hoindex(:),regtmp(:),ltemp(:,:)
 real(r8), allocatable :: rtemp(:,:),rlftemp(:,:),rctemp(:,:)
 DEBUG_STACK_PUSH
+ref_index=-1
 SELECT TYPE(self)
 CLASS IS(oft_bmesh)
   IF(self%dim==2)THEN
@@ -603,6 +604,8 @@ subroutine native_reflect(self,tol)
 CLASS IS(oft_mesh)
   ref_index=3
   IF(oft_debug_print(1))write(*,'(2A)')oft_indent,'Reflecting 3D volume mesh -> z'
+CLASS DEFAULT
+  CALL oft_abort('Unknown mesh type','native_reflect',__FILE__)
 END SELECT
 CALL oft_increase_indent
 !---Reflect points that are not on reflection plane

src/grid/mesh_type.F90

@@ -989,6 +989,7 @@ subroutine mesh_findcell(self,cell,pt,fout)
 if((cell<=0).OR.(cell>self%nc))then
   !---Find closest point in mesh
   d2min=1.d99
+  next=1
   do i=1,self%np
     d2=SUM((pt-self%r(:,i))**2)
     if(d2<d2min)then

src/utilities/build_libs.py

@@ -17,7 +17,7 @@
 import hashlib
 import http.client
 import urllib.request
-from urllib.error import URLError
+import urllib.error
 
 
 def error_exit(error_str, extra_info=None, exception=None):
@@ -336,8 +336,6 @@ def detect_compiler_target(compiler):
     config_dict['CC_VENDOR'] = cc_vendor
     config_dict['CC_VERSION'] = cc_version
     if cc_vendor == 'gnu':
-        if int(config_dict['CC_VERSION'].split(".")[0]) > 9:
-            config_dict['BASE_FFLAGS'] = "-fallow-argument-mismatch"
         config_dict['OMP_FLAGS'] = "-fopenmp"
         config_dict['DEBUG_FLAGS'] = "-g"
         config_dict['CHK_FLAGS'] = "-O0 -fcheck=all"
@@ -376,7 +374,8 @@ def detect_compiler_target(compiler):
 
 def build_cmake_script(mydict,build_debug=False,use_openmp=False,build_python=False,build_tests=False,
                        build_examples=False,build_docs=False,build_coverage=False,package_build=False,
-                       package_release=False,enable_debug_stack=False,enable_profiling=False):
+                       package_release=False,enable_debug_stack=False,enable_profiling=False,
+                       use_lto=True,debug_check_flags=True,debug_asanitizer=False):
     def bool_to_string(val):
         if val:
             return "TRUE"
@@ -401,10 +400,13 @@ def bool_to_string(val):
         "-DOFT_BUILD_PYTHON:BOOL={0}".format(bool_to_string(build_python)),
         "-DOFT_BUILD_DOCS:BOOL={0}".format(bool_to_string(build_docs)),
         "-DOFT_USE_OpenMP:BOOL={0}".format(bool_to_string(use_openmp)),
+        "-DOFT_USE_LTO:BOOL={0}".format(bool_to_string(use_lto)),
         "-DOFT_PACKAGE_BUILD:BOOL={0}".format(bool_to_string(package_build)),
         "-DOFT_PACKAGE_NIGHTLY:BOOL={0}".format(bool_to_string(not package_release)),
         "-DOFT_COVERAGE:BOOL={0}".format(bool_to_string(build_coverage)),
         "-DOFT_DEBUG_STACK:BOOL={0}".format(bool_to_string(enable_debug_stack)),
+        "-DOFT_DEBUG_CHECK:BOOL={0}".format(bool_to_string(debug_check_flags)),
+        "-DOFT_DEBUG_SANITIZER:BOOL={0}".format(bool_to_string(debug_asanitizer)),
         "-DOFT_PROFILING:BOOL={0}".format(bool_to_string(enable_profiling)),
         "-DOFT_THINCURR_LEGACY:BOOL=FALSE",
         "-DCMAKE_C_COMPILER:FILEPATH={CC}",
@@ -639,10 +641,11 @@ def fetch(self, force=False, nretry=2):
             for i in range(nretry+1):
                 try:
                     fetch_file(self.url, self.file)
-                except http.client.HTTPException:
+                except (urllib.error.URLError, http.client.HTTPException, OSError) as e:
                     if i == nretry:
                         raise
                     else:
+                        print(repr(e))
                         print('Warning: Retrying download ({0}/{1})'.format(i+1,nretry+1))
                         continue
                 break
@@ -660,10 +663,11 @@ def fetch(self, force=False, nretry=2):
                 for i in range(nretry+1):
                     try:
                         fetch_file(url, tmp_file)
-                    except http.client.HTTPException:
+                    except (urllib.error.URLError, http.client.HTTPException, OSError) as e:
                         if i == nretry:
                             raise
                         else:
+                            print(repr(e))
                             print('Warning: Retrying download ({0}/{1})'.format(i+1,nretry+1))
                             continue
                     break
@@ -2150,6 +2154,7 @@ def setup_build(self):
 group.add_argument("--oft_build_debug", default=0, type=int, choices=(0,1), help="Build debug version of OFT? (default: 0)")
 group.add_argument("--oft_build_python", default=1, type=int, choices=(0,1), help="Build OFT Python libraries? (default: 1)")
 group.add_argument("--oft_use_openmp", default=1, type=int, choices=(0,1), help="Build OFT with OpenMP support? (default: 1)")
+group.add_argument("--oft_use_lto", default=1, type=int, choices=(0,1), help="Build OFT with Link-Time Optimization? (default: 1)")
 group.add_argument("--oft_build_tests", default=0, type=int, choices=(0,1), help="Build OFT tests? (default: 0)")
 group.add_argument("--oft_py_kernel", default="python3", type=str, help="Name of Jupyter kernel for testing Python examples (default: python3)")
 group.add_argument("--oft_build_examples", default=0, type=int, choices=(0,1), help="Build OFT examples? (default: 0)")
@@ -2158,6 +2163,8 @@ def setup_build(self):
 group.add_argument("--oft_package_python", default=1, type=int, choices=(0,1), help="Setup for build of PYPI wheels when packaging?")
 group.add_argument("--oft_package_release", action="store_true", default=False, help="Perform a release package of OFT?")
 group.add_argument("--oft_build_coverage", action="store_true", default=False, help="Build OFT with code coverage flags?")
+group.add_argument("--oft_debug_checks", default=1, type=int, choices=(0,1), help="Build OFT with compiler runtime checks (requires Debug build)? (default: 1)")
+group.add_argument("--oft_debug_asanitizer", default=0, type=int, choices=(0,1), help="Build OFT with address sanitizer checks (requires Debug build)? (default: 0)")
 group.add_argument("--oft_debug_stack", action="store_true", default=False, help="Enable internal debug stack?")
 group.add_argument("--oft_profiling", action="store_true", default=False, help="Enable internal profiling?")
 #
@@ -2373,4 +2380,7 @@ def setup_build(self):
         package_release=options.oft_package_release,
         enable_debug_stack=options.oft_debug_stack,
         enable_profiling=options.oft_profiling,
+        use_lto=(options.oft_use_lto==1),
+        debug_check_flags=(options.oft_debug_checks==1),
+        debug_asanitizer=(options.oft_debug_asanitizer==1)
     )