Merged in iulian07/clang_osx_warnings (pull request #262)

Several warning fixes for OSX/Clang

config/compiler.m4

@@ -192,6 +192,9 @@ if (test "x$enable_debug" != "xno"); then # debug flags
 # GNU
 EXTRA_GNU_CXXFLAGS="-Wall -Wno-long-long -pipe -pedantic -Wshadow -Wunused-parameter -Wpointer-arith -Wformat -Wformat-security -Wextra -Wno-variadic-macros -Wno-unknown-pragmas"
 EXTRA_GNU_FCFLAGS="-pipe -pedantic -ffree-line-length-0"
+# CLANG
+EXTRA_CLANG_CXXFLAGS="$EXTRA_GNU_CXXFLAGS"
+EXTRA_CLANG_FCFLAGS="$EXTRA_GNU_FCFLAGS"
 # Intel
 EXTRA_INTEL_CXXFLAGS="-pipe -C"
 EXTRA_INTEL_FCFLAGS="-C"
@@ -205,8 +208,11 @@ fi
 
 if (test "x$enable_cxx_optimize" != "xno"); then  # optimization flags
 #GNU
-EXTRA_GNU_CXXFLAGS="$EXTRA_GNU_CXXFLAGS -finline-functions"
+EXTRA_GNU_CXXFLAGS="$EXTRA_GNU_CXXFLAGS -fprefetch-loop-arrays -finline-functions -march=native"
 EXTRA_GNU_FCFLAGS="$EXTRA_GNU_FCFLAGS -ffree-line-length-0 -finline-functions"
+#CLANG
+EXTRA_CLANG_CXXFLAGS="$EXTRA_CLANG_CXXFLAGS -march=native"
+EXTRA_CLANG_FCFLAGS="$EXTRA_CLANG_FCFLAGS -ffree-line-length-0 -finline-functions"
 # Intel
 EXTRA_INTEL_CXXFLAGS="$EXTRA_INTEL_CXXFLAGS -xHost -ip -no-prec-div" # -fast
 EXTRA_INTEL_FCFLAGS="$EXTRA_INTEL_FCFLAGS -xHost -ip -no-prec-div" # -fast
@@ -755,7 +761,7 @@ case "$cxx_compiler:$host_cpu" in
     FATHOM_CXX_SPECIAL="$EXTRA_PGI_CXXFLAGS"
     ;;
   Clang:*)
-    FATHOM_CXX_SPECIAL="$EXTRA_GNU_CXXFLAGS"
+    FATHOM_CXX_SPECIAL="$EXTRA_CLANG_CXXFLAGS"
     FATHOM_CXX_32BIT=-m32
     FATHOM_CXX_64BIT=-m64
     ;;
@@ -934,8 +940,8 @@ case "$cc_compiler:$host_cpu" in
     FATHOM_F77_SPECIAL="$EXTRA_PGI_FCFLAGS"
     ;;
   Clang:*)
-    FATHOM_CC_SPECIAL="$EXTRA_GNU_CXXFLAGS"
-    FATHOM_FC_SPECIAL="$EXTRA_GNU_FCFLAGS"
+    FATHOM_CC_SPECIAL="$EXTRA_CLANG_CXXFLAGS"
+    FATHOM_FC_SPECIAL="$EXTRA_CLANG_FCFLAGS"
     FATHOM_F77_SPECIAL="$FATHOM_FC_SPECIAL"
     FATHOM_CC_32BIT=-m32
     FATHOM_CC_64BIT=-m64

itaps/imesh/MOAB_iMeshP_unit_tests.cpp

@@ -2354,7 +2354,7 @@ int test_entity_copies( iMesh_Instance imesh, iMeshP_PartitionHandle prtn, const
     
       // add all vertices to local_data
     for (size_t j = 0; j < verts.size(); ++j) {
-      int tag;
+      int tag=0;
       ierr = vertex_tag( imesh, verts[j], tag );
       if (ierr)
         break;

itaps/imesh/iMesh_MOAB.cpp

@@ -2406,7 +2406,7 @@ extern "C" {
     EntityHandle set1 = ENTITY_HANDLE(entity_set_1),
       set2 = ENTITY_HANDLE(entity_set_2);
 
-    int isList1, isList2;
+    int isList1=0, isList2=0;
     iMesh_isList(instance, entity_set_1, &isList1, err);
     if (*err != iBase_SUCCESS) return;
     iMesh_isList(instance, entity_set_2, &isList2, err);
@@ -2455,7 +2455,7 @@ extern "C" {
     EntityHandle set1 = ENTITY_HANDLE(entity_set_1),
       set2 = ENTITY_HANDLE(entity_set_2);
 
-    int isList1, isList2;
+    int isList1=0, isList2=0;
     iMesh_isList(instance, entity_set_1, &isList1, err);
     if (*err != iBase_SUCCESS) return;
     iMesh_isList(instance, entity_set_2, &isList2, err);
@@ -2561,7 +2561,7 @@ extern "C" {
     EntityHandle set1 = ENTITY_HANDLE(entity_set_1),
       set2 = ENTITY_HANDLE(entity_set_2);
 
-    int isList1, isList2;
+    int isList1=0, isList2=0;
     iMesh_isList(instance, entity_set_1, &isList1, err);
     if (*err != iBase_SUCCESS) return;
     iMesh_isList(instance, entity_set_2, &isList2, err);

itaps/irel/test_entset.cpp

@@ -34,7 +34,7 @@ typedef void* iRel_EntityHandle;
 */
 void handle_error_code(const int result,
                        int *number_failed,
-                       int *number_not_implemented,
+                       int * /*number_not_implemented*/,
                        int *number_successful)
 {
   if (result) {

src/Core.cpp

@@ -359,7 +359,7 @@ ErrorCode Core::query_interface_type( const std::type_info& type, void*& ptr )
   }
   else if (type == typeid(WriteUtilIface)) {
     if(!mMBWriteUtil)
-      mMBWriteUtil = new WriteUtil(this, mError);
+      mMBWriteUtil = new WriteUtil(this);
     ptr = static_cast<WriteUtilIface*>(mMBWriteUtil);
   }
   else if (type == typeid(ReaderWriterSet)) {

src/DenseTag.cpp

@@ -104,7 +104,10 @@ ErrorCode DenseTag::get_array(const SequenceManager* seqman,
                               const unsigned char* const& ptr,
                               size_t& count) const
 {
-  return get_array(seqman, NULL, h, ptr, count);
+  //  cast away the const-ness; do we really want to do this?
+  // probably we are not calling this anywhere;
+  // clang compiler found this
+  return get_array(seqman, NULL, h, const_cast<unsigned char *> ( ptr ), count);
 }
 
 ErrorCode DenseTag::get_array(const SequenceManager* seqman,
@@ -140,7 +143,9 @@ ErrorCode DenseTag::get_array(const SequenceManager* seqman,
 ErrorCode DenseTag::get_array(const EntitySequence* seq,
                               const unsigned char* const & ptr) const
 {
-  return get_array(seq, ptr);
+  // cast away the constness; otherwise it would be infinite recursion
+  // probably we are not calling this anywhere
+  return get_array(seq, const_cast<unsigned char *> ( ptr ));
 }
 
 ErrorCode DenseTag::get_array(const EntitySequence* seq,

src/LocalDiscretization/LinearTet.cpp

@@ -104,7 +104,7 @@ namespace moab
 
         // find best initial guess to improve convergence
       CartVect tmp_params[] = {CartVect(-1,-1,-1), CartVect(1,-1,-1), CartVect(-1,1,-1), CartVect(-1,-1,1)};
-      double resl = HUGE;
+      double resl = std::numeric_limits<double>::max();
       CartVect new_pos, tmp_pos;
       ErrorCode rval;
       for (unsigned int i = 0; i < 4; i++) {

src/LocalDiscretization/LinearTri.cpp

@@ -101,7 +101,7 @@ namespace moab
 
         // find best initial guess to improve convergence
       CartVect tmp_params[] = {CartVect(-1,-1,-1), CartVect(1,-1,-1), CartVect(-1,1,-1)};
-      double resl = HUGE;
+      double resl = std::numeric_limits<double>::max();
       CartVect new_pos, tmp_pos;
       ErrorCode rval;
       for (unsigned int i = 0; i < 3; i++) {

src/MetisPartitioner.cpp

@@ -36,17 +36,14 @@ using namespace moab;
 
 const bool debug = false;
 
-MetisPartitioner::MetisPartitioner( Interface *impl, 
-                                    const bool use_coords,
-                                    int argc, 
-                                    char **argv) 
-                                  : PartitionerBase<idx_t>(impl,use_coords), 
-                                    argcArg(argc), 
-                                    argvArg(argv)
+MetisPartitioner::MetisPartitioner( Interface *impl,
+                                    const bool use_coords)
+                                  : PartitionerBase<idx_t>(impl,use_coords)
+
 {
 }
 
-MetisPartitioner::~MetisPartitioner() 
+MetisPartitioner::~MetisPartitioner()
 {
 }
 
@@ -63,7 +60,7 @@ ErrorCode MetisPartitioner::partition_mesh(const idx_t nparts,
 #ifdef MOAB_HAVE_MPI
     // should only be called in serial
   if (mbpc->proc_config().proc_size() != 1) {
-    std::cout << "MetisPartitioner::partition_mesh_and_geometry must be called in serial." 
+    std::cout << "MetisPartitioner::partition_mesh_and_geometry must be called in serial."
               << std::endl;
     return MB_FAILURE;
   }
@@ -76,7 +73,7 @@ ErrorCode MetisPartitioner::partition_mesh(const idx_t nparts,
               << std::endl;
     return MB_FAILURE;
   }
-  
+
   std::vector<double> pts; // x[0], y[0], z[0], ... from MOAB
   std::vector<idx_t> ids; // poidx_t ids from MOAB
   std::vector<idx_t> adjs, parts;
@@ -85,17 +82,17 @@ ErrorCode MetisPartitioner::partition_mesh(const idx_t nparts,
   // Get a mesh from MOAB and diide it across processors.
 
   clock_t t = clock();
-  
+
   ErrorCode result;
   if (!partition_tagged_sets && !partition_tagged_ents)
   {
     result = assemble_graph(part_dim, pts, ids, adjs, length, elems);MB_CHK_ERR(result);
   }
-  else if (partition_tagged_sets) 
+  else if (partition_tagged_sets)
   {
     result = assemble_taggedsets_graph(part_dim, pts, ids, adjs, length, elems, &(*aggregating_tag));MB_CHK_ERR(result);
   }
-  else if (partition_tagged_ents) 
+  else if (partition_tagged_ents)
   {
     result = assemble_taggedents_graph(part_dim, pts, ids, adjs, length, elems, &(*aggregating_tag));MB_CHK_ERR(result);
   }
@@ -109,7 +106,7 @@ ErrorCode MetisPartitioner::partition_mesh(const idx_t nparts,
     t = clock();
   }
 
-  std::cout << "Computing partition using " << method 
+  std::cout << "Computing partition using " << method
             <<" method for " << nparts << " processors..." << std::endl;
 
   idx_t nelems = length.size()-1;
@@ -124,14 +121,14 @@ ErrorCode MetisPartitioner::partition_mesh(const idx_t nparts,
   {
     idx_t options[METIS_NOPTIONS];
     METIS_SetDefaultOptions(options);
-    options[METIS_OPTION_CONTIG] = 1;  
+    options[METIS_OPTION_CONTIG] = 1;
     metis_RESULT = METIS_PartGraphKway(&nelems, &nconstraidx_ts, &length[0], &adjs[0], NULL, NULL, NULL, &nOfPartitions, NULL, NULL, options, &edgeCut, assign_parts);
   }
   else if (strcmp(method, "ML_RB") == 0)
   {
     idx_t options[METIS_NOPTIONS];
     METIS_SetDefaultOptions(options);
-    options[METIS_OPTION_OBJTYPE] = METIS_OBJTYPE_CUT; // CUT 
+    options[METIS_OPTION_OBJTYPE] = METIS_OBJTYPE_CUT; // CUT
     options[METIS_OPTION_IPTYPE] = METIS_IPTYPE_GROW; // GROW or RANDOM
     options[METIS_OPTION_CTYPE] = METIS_CTYPE_RM; // RM or SHEM
     options[METIS_OPTION_RTYPE] = METIS_RTYPE_FM; // FM
@@ -157,7 +154,7 @@ ErrorCode MetisPartitioner::partition_mesh(const idx_t nparts,
 
   if (metis_RESULT != METIS_OK)
     return MB_FAILURE;
-  
+
   // take results & write onto MOAB partition sets
   std::cout << "Saving partition information to MOAB..." << std::endl;
   {
@@ -184,21 +181,21 @@ ErrorCode MetisPartitioner::partition_mesh(const idx_t nparts,
 ErrorCode MetisPartitioner::assemble_taggedents_graph(const int dimension,
                                                           std::vector<double> &coords,
                                                           std::vector<idx_t> &moab_ids,
-                                                          std::vector<idx_t> &adjacencies, 
+                                                          std::vector<idx_t> &adjacencies,
                                                           std::vector<idx_t> &length,
                                                           Range &elems,
-					                  const char *aggregating_tag)
+                                                          const char *aggregating_tag)
 {
   Tag partSetTag;
   ErrorCode result = mbImpl->tag_get_handle(aggregating_tag, 1, MB_TYPE_INTEGER, partSetTag);
   if (MB_SUCCESS != result) return result;
- 
+
   Range allSubElems;
   result = mbImpl->get_entities_by_dimension(0, dimension, allSubElems);
   if (MB_SUCCESS != result || allSubElems.empty()) return result;
   idx_t partSet;
   std::map<idx_t, Range> aggloElems;
-  for (Range::iterator rit = allSubElems.begin(); rit != allSubElems.end(); rit++) 
+  for (Range::iterator rit = allSubElems.begin(); rit != allSubElems.end(); rit++)
   {
     EntityHandle entity = *rit;
     result = mbImpl->tag_get_data(partSetTag,&entity,1,&partSet);
@@ -212,26 +209,26 @@ ErrorCode MetisPartitioner::assemble_taggedents_graph(const int dimension,
   if (type == MB_TAG_DENSE)
   {
     // clear tag on ents and sets
-    result = mbImpl->tag_delete(partSetTag); 
+    result = mbImpl->tag_delete(partSetTag);
     if (MB_SUCCESS != result) return result;
   }
   if (type == MB_TAG_SPARSE)
   {
     // clear tag on ents
-    result = mbImpl->tag_delete_data(partSetTag, allSubElems); 
+    result = mbImpl->tag_delete_data(partSetTag, allSubElems);
     if (MB_SUCCESS != result) return result;
     // clear tag on sets
     result = mbImpl->get_entities_by_type_and_tag(0 , MBENTITYSET, &partSetTag, 0, 1, elems);
     if (MB_SUCCESS != result) return result;
-    result = mbImpl->tag_delete_data(partSetTag, elems); 
+    result = mbImpl->tag_delete_data(partSetTag, elems);
     if (MB_SUCCESS != result) return result;
     elems.clear();
   }
   result = mbImpl->tag_get_handle("PARALLEL_PARTITION", 1, MB_TYPE_INTEGER,
-                                  partSetTag, MB_TAG_SPARSE|MB_TAG_CREAT); 
+                                  partSetTag, MB_TAG_SPARSE|MB_TAG_CREAT);
   if (MB_SUCCESS != result) return result;
-  
-  for (std::map<idx_t, Range>::iterator mit = aggloElems.begin(); mit != aggloElems.end(); mit++) 
+
+  for (std::map<idx_t, Range>::iterator mit = aggloElems.begin(); mit != aggloElems.end(); mit++)
   {
     EntityHandle new_set;
     result = mbImpl->create_meshset(MESHSET_SET, new_set);
@@ -249,16 +246,16 @@ ErrorCode MetisPartitioner::assemble_taggedents_graph(const int dimension,
 ErrorCode MetisPartitioner::assemble_taggedsets_graph(const int dimension,
                                                           std::vector<double> &coords,
                                                           std::vector<idx_t> &moab_ids,
-                                                          std::vector<idx_t> &adjacencies, 
+                                                          std::vector<idx_t> &adjacencies,
                                                           std::vector<idx_t> &length,
                                                           Range &elems,
-					                  const char *aggregating_tag)
+                                                          const char *aggregating_tag)
 {
   length.push_back(0);
     // assemble a graph with vertices equal to elements of specified dimension, edges
     // signified by list of other elements to which an element is connected
 
-  // get the tagged elements 
+  // get the tagged elements
   Tag partSetTag;
   ErrorCode result = mbImpl->tag_get_handle(aggregating_tag, 1, MB_TYPE_INTEGER, partSetTag);MB_CHK_ERR(result);
   //ErrorCode result = mbImpl->tag_get_handle("PARALLEL_PARTITION_SET", 1, MB_TYPE_INTEGER, partSetTag);MB_CHK_ERR(result);
@@ -266,11 +263,11 @@ ErrorCode MetisPartitioner::assemble_taggedsets_graph(const int dimension,
   result = mbImpl->get_entities_by_type_and_tag(0 , MBENTITYSET, &partSetTag, 0, 1, elems);
   if (MB_SUCCESS != result || elems.empty()) return result;
 
-  //assign globla ids to elem sets based on aggregating_tag data 
+  //assign globla ids to elem sets based on aggregating_tag data
   Tag gid_tag;
   idx_t zero1 = -1;
   result = mbImpl->tag_get_handle("GLOBAL_ID_AGGLO", 1, MB_TYPE_INTEGER, gid_tag, MB_TAG_SPARSE|MB_TAG_CREAT, &zero1);MB_CHK_ERR(result);
-  for (Range::iterator rit = elems.begin(); rit != elems.end(); rit++) 
+  for (Range::iterator rit = elems.begin(); rit != elems.end(); rit++)
   {
     idx_t partSet;
     result = mbImpl->tag_get_data(partSetTag,&(*rit),1,&partSet);MB_CHK_ERR(result);
@@ -287,15 +284,15 @@ ErrorCode MetisPartitioner::assemble_taggedsets_graph(const int dimension,
   {
     result = mbImpl->tag_delete_data(partSetTag, elems);MB_CHK_ERR(result);
   }
-  
+
   // assemble the graph, using Skinner to get d-1 dimensional neighbors and then idx_tersecting to get adjacencies
   std::vector<Range> skin_subFaces(elems.size());
   unsigned int i = 0;
-  for (Range::iterator rit = elems.begin(); rit != elems.end(); rit++) 
+  for (Range::iterator rit = elems.begin(); rit != elems.end(); rit++)
   {
     Range part_ents;
     result = mbImpl->get_entities_by_handle(*rit, part_ents, false);
-    if (mbImpl->dimension_from_handle(*part_ents.rbegin()) != mbImpl->dimension_from_handle(*part_ents.begin())) 
+    if (mbImpl->dimension_from_handle(*part_ents.rbegin()) != mbImpl->dimension_from_handle(*part_ents.begin()))
     {
       Range::iterator lower = part_ents.lower_bound(CN::TypeDimensionMap[0].first),
       upper = part_ents.upper_bound(CN::TypeDimensionMap[dimension-1].second);
@@ -320,20 +317,20 @@ ErrorCode MetisPartitioner::assemble_taggedsets_graph(const int dimension,
       {
         Range subFaces = intersect(skin_subFaces[k],skin_subFaces[t]);
         if (subFaces.size() > 0)
-  	      adjs.push_back(elems[t]);
+              adjs.push_back(elems[t]);
       }
     }
-    if (!adjs.empty()) 
+    if (!adjs.empty())
     {
       neighbors.resize(adjs.size());
-      result = mbImpl->tag_get_data(gid_tag, &adjs[0], adjs.size(), &neighbors[0]);MB_CHK_ERR(result); 
+      result = mbImpl->tag_get_data(gid_tag, &adjs[0], adjs.size(), &neighbors[0]);MB_CHK_ERR(result);
     }
       // copy those idx_to adjacencies vector
     length.push_back(length.back()+(idx_t)adjs.size());
     std::copy(neighbors.begin(), neighbors.end(), std::back_inserter(adjacencies));
       // get the graph vertex id for this element
     const EntityHandle& setk = elems[k];
-    result = mbImpl->tag_get_data(gid_tag, &setk, 1, &moab_id); 
+    result = mbImpl->tag_get_data(gid_tag, &setk, 1, &moab_id);
     moab_ids.push_back(moab_id);
       // get average position of vertices
     Range part_ents;
@@ -371,9 +368,9 @@ ErrorCode MetisPartitioner::assemble_taggedsets_graph(const int dimension,
 ErrorCode MetisPartitioner::assemble_graph(const int dimension,
                                                std::vector<double> &coords,
                                                std::vector<idx_t> &moab_ids,
-                                               std::vector<idx_t> &adjacencies, 
+                                               std::vector<idx_t> &adjacencies,
                                                std::vector<idx_t> &length,
-                                               Range &elems) 
+                                               Range &elems)
 {
   length.push_back(0);
     // assemble a graph with vertices equal to elements of specified dimension, edges
@@ -382,10 +379,10 @@ ErrorCode MetisPartitioner::assemble_graph(const int dimension,
     // get the elements of that dimension
   ErrorCode result = mbImpl->get_entities_by_dimension(0, dimension, elems);
   if (MB_SUCCESS != result || elems.empty()) return result;
-  
+
 #ifdef MOAB_HAVE_MPI
     // assign global ids
-  result = mbpc->assign_global_ids(0, dimension, 0); 
+  result = mbpc->assign_global_ids(0, dimension, 0);
 #endif
 
     // now assemble the graph, calling MeshTopoUtil to get bridge adjacencies through d-1 dimensional
@@ -398,19 +395,19 @@ ErrorCode MetisPartitioner::assemble_graph(const int dimension,
 
   double avg_position[3];
   int moab_id;
-  
+
     // get the global id tag hanlde