Merge branch 'main' into cmesh-mpicomm

Author: sandro-elsweijer

CMakeLists.txt

@@ -91,6 +91,14 @@ if(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CONFIGURATION_TYPES)
     "Debug" "Release" "RelWithDebInfo")
 endif()
 
+if( CMAKE_BUILD_TYPE STREQUAL "Debug" )
+  # Option to generate code coverage target.
+  option( T8CODE_CODE_COVERAGE "Enable code coverage reporting" OFF)
+  if(T8CODE_CODE_COVERAGE)
+    include(./cmake/CodeCoverage.cmake)
+  endif()
+endif()
+
 set(CMAKE_MODULE_PATH "${PROJECT_SOURCE_DIR}/cmake" ${CMAKE_MODULE_PATH})
 
 if( T8CODE_BUILD_FORTRAN_INTERFACE )

benchmarks/t8_time_fractal.cxx

@@ -35,7 +35,7 @@
 #include <sc_options.h>
 
 /* Refine a tree with quadrilateral elements.
- * At every second adaptcall (level is even) remove the central elements 
+ * At every second adaptcall (level is even) remove the central elements
  * of the mesh or leave them untouched. Refine the remaining elements.
  *
  *  |x|x|x|x|       |x|x|x|x|
@@ -75,7 +75,7 @@ t8_adapt_menger_quad (t8_forest_t forest, [[maybe_unused]] t8_forest_t forest_fr
 }
 
 /* Refine a tree with triangular elements.
- * At every adaptcall remove the central element with child id 2 
+ * At every adaptcall remove the central element with child id 2
  * of the mesh or leave it untouched. Refine the remaining elements.
  */
 static int
@@ -102,7 +102,7 @@ t8_adapt_sierpinski_tri (t8_forest_t forest, [[maybe_unused]] t8_forest_t forest
 }
 
 /* Refine a tree with hexahedral elements.
- * At every second adaptcall (level is even) remove the central elements 
+ * At every second adaptcall (level is even) remove the central elements
  * of the mesh or leave them untouched. Refine the remaining elements.
  */
 static int
@@ -153,7 +153,7 @@ t8_adapt_menger_hex (t8_forest_t forest, [[maybe_unused]] t8_forest_t forest_fro
 }
 
 /* Refine a tree with tetrahedral elements.
- * At every adaptcall remove the elements with child id 2, 3, 5 and 6 
+ * At every adaptcall remove the elements with child id 2, 3, 5 and 6
  * of the mesh or leave it untouched. Refine the remaining elements.
  */
 static int
@@ -180,7 +180,7 @@ t8_adapt_sierpinski_tet (t8_forest_t forest, [[maybe_unused]] t8_forest_t forest
 }
 
 /* Refine a tree with prism elements.
- * At every adaptcall remove the elements with child id 2 and 6 
+ * At every adaptcall remove the elements with child id 2 and 6
  * of the mesh or leave it untouched. Refine the remaining elements.
  */
 static int
@@ -207,7 +207,7 @@ t8_adapt_sierpinski_prism (t8_forest_t forest, [[maybe_unused]] t8_forest_t fore
 }
 
 /* Refine a tree with pyramid elements.
- * At every adaptcall remove the elements with child id 1, 3, 5, 6 and 8 
+ * At every adaptcall remove the elements with child id 1, 3, 5, 6 and 8
  * of the mesh or leave it untouched. Refine the remaining elements.
  */
 static int
@@ -252,7 +252,7 @@ t8_adapt_coarse ([[maybe_unused]] t8_forest_t forest, [[maybe_unused]] t8_forest
  * \param [in] level_end     Final level of the fractal.
  * \param [in] iterative     1 if fractal is constructed iterative
  *                           0 if recursive
- * \param [in] remove        1 if elements that will not get refined will be 
+ * \param [in] remove        1 if elements that will not get refined will be
  *                           removed instead.
  * \param [in] trees         Number of trees the forest will contain.
  * \param [in] eclass        Element type for each tree.
@@ -267,12 +267,12 @@ t8_construct_fractal (int level_initial, int level_end, const int iterative, con
   T8_ASSERT (eclass == T8_ECLASS_QUAD || eclass == T8_ECLASS_TRIANGLE || eclass == T8_ECLASS_HEX
              || eclass == T8_ECLASS_TET || eclass == T8_ECLASS_PRISM || eclass == T8_ECLASS_PYRAMID);
 
-  /* Quadrilateral and hexahedron elements must have an even initial level 
+  /* Quadrilateral and hexahedron elements must have an even initial level
    * greater 0, such that the refinement pattern can be applied. */
   T8_ASSERT ((eclass == T8_ECLASS_QUAD || eclass == T8_ECLASS_HEX) && level_initial > 1 && 0 == level_initial % 2
              && 0 == level_end % 2);
 
-  /* Set up userdata to adapt forest. 
+  /* Set up userdata to adapt forest.
    * user_data[0] -> level_end
    * user_data[1] -> {0, -2} -> return for adapt callback */
   int user_data[2] = { level_end, (remove == 1) ? -2 : remove };
@@ -385,7 +385,7 @@ main (int argc, char **argv)
 
   if (sreturnA > BUFSIZ || sreturnB > BUFSIZ) {
     /* The usage string or help message was truncated */
-    /* Note: gcc >= 7.1 prints a warning if we 
+    /* Note: gcc >= 7.1 prints a warning if we
      * do not check the return value of snprintf. */
     t8_debugf ("Warning: Truncated usage string and help message to '%s' and '%s'\n", usage, help);
   }
@@ -439,7 +439,7 @@ main (int argc, char **argv)
   sc_options_add_int (opt, 'c', "coarse", &coarse, 0, "Number of times to coarse hole mesh.");
   sc_options_add_int (opt, 'r', "runs", &runs, 1,
                       "Number of times the fractal gets constructed. The default is 1.\n"
-                      "\t\t\t\t     Note, the runntime summs up.");
+                      "\t\t\t\t     Note, the runtime summs up.");
 
   int parsed = sc_options_parse (t8_get_package_id (), SC_LP_ERROR, opt, argc, argv);
   if (helpme) {

cmake/CodeCoverage.cmake

@@ -13,8 +13,8 @@
 # Adds compiler flags necessary to be able to collect coverage information.
 # 
 function(append_coverage_compiler_flags)
-  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -g --coverage" PARENT_SCOPE)
-  set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -g --coverage" PARENT_SCOPE)
+  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -g --coverage -O0" PARENT_SCOPE)
+  set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -g --coverage -O0" PARENT_SCOPE)
   set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} --coverage" PARENT_SCOPE)
   set(CMAKE_SHARED_LINKER_FLAGS "${CMAKE_SHARED_LINKER_FLAGS} --coverage" PARENT_SCOPE)
 endfunction() # append_coverage_compiler_flags
@@ -79,8 +79,6 @@ function(setup_target_for_coverage)
 
     # Generate HTML file using genhtml.
     COMMAND ${GENHTML_PATH} -o ${Coverage_NAME} ${Coverage_NAME}.info
-    # Show result in terminal.
-    COMMAND ${LCOV_PATH} --list ${Coverage_NAME}.info
 
     BYPRODUCTS
       ${Coverage_NAME}.base
@@ -95,9 +93,11 @@ function(setup_target_for_coverage)
 endfunction() # setup_target_for_coverage
 
 # Call functions defined above with customized arguments.
+# Attention: For some gcov versions, you have to add --ignore-errors mismatch to the LCOV_ARGS.
+# This seems to be a common gcov problem.
 append_coverage_compiler_flags()
 setup_target_for_coverage(
   NAME coverage
-  EXCLUDE "${CMAKE_SOURCE_DIR}/sc*"
-  LCOV_ARGS "--no-external"
+  EXCLUDE "${CMAKE_SOURCE_DIR}/sc*" "${CMAKE_SOURCE_DIR}/p4est*" "${CMAKE_SOURCE_DIR}/test*" "${CMAKE_SOURCE_DIR}/thirdparty*" "${CMAKE_SOURCE_DIR}/tutorials*" "${CMAKE_SOURCE_DIR}/example*" "${CMAKE_SOURCE_DIR}/benchmarks*"
+  LCOV_ARGS --no-external --ignore-errors gcov
 )

doc/author_lampert.txt

@@ -0,0 +1 @@
+I place my contributions to t8code under the FreeBSD license. Joshua Lampert (joshua.lampert@uni-hamburg.de)

src/CMakeLists.txt

@@ -41,12 +41,6 @@ if( CMAKE_BUILD_TYPE STREQUAL "RelWithDebInfo" )
 endif()
 
 if( CMAKE_BUILD_TYPE STREQUAL "Debug" )
-  # Option to generate code coverage target.
-  option( T8CODE_CODE_COVERAGE "Enable code coverage reporting" OFF)
-  if(T8CODE_CODE_COVERAGE)
-    include(CodeCoverage)
-  endif()
-
   set (T8_CXXFLAGS "${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_DEBUG}")
   set (T8_CFLAGS "${CMAKE_C_FLAGS} ${CMAKE_C_FLAGS_DEBUG}")
 

src/t8_cmesh/t8_cmesh_commit.cxx

@@ -534,7 +534,7 @@ t8_cmesh_commit_from_stash (t8_cmesh_t cmesh, sc_MPI_Comm comm)
 }
 
 /* TODO: set boundary face connections here.
- *       not trivial if replicated and not level 3 face_knowledg
+ *       not trivial if replicated and not level 3 face_knowledge
  *       Edit: boundary face is default. If no face-connection is added then
  *             we assume a boundary face.
  * TODO: Implement a debug check for mesh consistency between processes.

src/t8_cmesh/t8_cmesh_trees.cxx

@@ -214,7 +214,7 @@ t8_cmesh_trees_start_part (const t8_cmesh_trees_t trees, const int proc, const t
 }
 
 /**
- * 
+ *
  * Helper struct for sorting the number of ghost attributes by global id.
  * In order to sort them, we need the part ghost id to access the global id.
  * Thus, we store both the part id and the number of attributes.
@@ -262,7 +262,7 @@ t8_cmesh_allocate_ghost_num_atts_array (t8_locidx_t part_num_ghosts)
  * stored temporarily in the att_offset variable
  * we grow the part array by the needed amount of memory and set the
  * offsets appropriately */
-/* The workflow can be: call start_part, set tree and ghost classes maually, call
+/* The workflow can be: call start_part, set tree and ghost classes manually, call
  * init_attributes, call finish_part, successively call add_attributes
  * and also set all face neighbors (TODO: write function)*/
 void

src/t8_cmesh/t8_cmesh_vertex_connectivity/t8_cmesh_vertex_connectivity.cxx

@@ -60,7 +60,9 @@ t8_cmesh_get_global_vertices_of_tree (const t8_cmesh_t cmesh, const t8_locidx_t
 {
   T8_ASSERT (t8_cmesh_is_committed (cmesh));
   const auto global_vertices = cmesh->vertex_connectivity->get_global_vertices_of_tree (local_tree);
-  *num_vertices = global_vertices.size ();
+  if (num_vertices) {
+    *num_vertices = global_vertices.size ();
+  }
   return global_vertices.data ();
 }
 

src/t8_cmesh/t8_cmesh_vertex_connectivity/t8_cmesh_vertex_connectivity.h

@@ -66,7 +66,7 @@ t8_cmesh_get_num_local_vertices (const t8_cmesh_t cmesh);
 /** Get the global vertex indices of a tree in its local vertex order.
  * \param [in] cmesh A committed cmesh.
  * \param [in] local_tree A local tree in \a cmesh.
- * \param [out] num_vertices The number of vertices of \a local_tree
+ * \param [out] num_vertices The number of vertices of \a local_tree, if not null
  * \return The global vertices of \a local_tree
  */
 const t8_gloidx_t *

src/t8_cmesh_readmshfile.h

@@ -21,8 +21,8 @@
 */
 
 /** \file t8_cmesh_readmshfile.h
- * We define function here that serve to open a mesh file generated by
- * GMSH and consructing a cmesh from it.
+ * We define a function here that serves to open a mesh file generated by
+ * GMSH and constructing a cmesh from it.
  */
 
 #ifndef T8_CMESH_READMSHFILE_H