stk snapshot as of 10/27/2020

trilinos · Oct 28, 2020 · 1e9747d · 1e9747d
1 parent 59c79de
commit 1e9747d
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Showing 230 changed files with 11,774 additions and 5,291 deletions.
diff --git a/packages/stk/cmake/Dependencies.cmake b/packages/stk/cmake/Dependencies.cmake
@@ -1,11 +1,11 @@
 SET(SUBPACKAGES_DIRS_CLASSIFICATIONS_OPTREQS
-  Math            stk_math             PT  OPTIONAL
   Util            stk_util             PT  OPTIONAL
+  Math            stk_math             PT  OPTIONAL
   Simd            stk_simd             PT  OPTIONAL
+  NGP_TEST        stk_ngp_test         PT  OPTIONAL
   Topology        stk_topology         PT  OPTIONAL
   Mesh            stk_mesh             PT  OPTIONAL
   IO              stk_io               PT  OPTIONAL
-  NGP_TEST        stk_ngp_test         PT  OPTIONAL
   Unit_test_utils stk_unit_test_utils  PT  OPTIONAL
   Search          stk_search           PT  OPTIONAL
   SearchUtil      stk_search_util      PT  OPTIONAL

diff --git a/packages/stk/cmake/STK_Trilinos_config.h.in b/packages/stk/cmake/STK_Trilinos_config.h.in
@@ -56,12 +56,20 @@
 
 /* Non-typical "not" macro for optional dependence on SEACASAprepro_lib (See
  * STK #17354) */
+#ifndef NOT_HAVE_STK_SEACASAPREPRO_LIB
 #cmakedefine NOT_HAVE_STK_SEACASAPREPRO_LIB
+#endif
 
+#ifndef FORTRAN_NO_UNDERSCORE
 #cmakedefine FORTRAN_NO_UNDERSCORE
+#endif
 
+#ifndef FORTRAN_ONE_UNDERSCORE
 #cmakedefine FORTRAN_ONE_UNDERSCORE
+#endif
 
+#ifndef FORTRAN_TWO_UNDERSCORES
 #cmakedefine FORTRAN_TWO_UNDERSCORES
+#endif
 
 #define SIERRA_MIGRATION
diff --git a/packages/stk/stk_balance/Jamfile b/packages/stk/stk_balance/Jamfile
@@ -185,7 +185,7 @@ lib stk_balance_lib
     /sierra/stk_search//stk_search
     /sierra/stk_tools//stk_tools_lib
     /sierra/stk_util//stk_util_command_line
-    /sierra/stk_math//stk_math_headers
+    /sierra/stk_math//stk_math
   :
     <include>$(stk_balance-root-inc)/stk_balance
     [ ifuserbuild <file>$(stk_balance-root)/lib/libstk_balance_lib.a

diff --git a/packages/stk/stk_balance/stk_balance/CMakeLists.txt b/packages/stk/stk_balance/stk_balance/CMakeLists.txt
@@ -95,22 +95,19 @@ TRIBITS_ADD_LIBRARY(
   stk_balance_lib
   NOINSTALLHEADERS ${HEADERS} ${HEADERS_INTERNAL} ${HEADERS_SETUP} ${HEADERS_SEARCH_TOLERANCE} ${HEADERS_SEARCH_TOLERANCE_ALGS}
   SOURCES ${SOURCES} ${SOURCES_INTERNAL} ${SOURCES_SETUP} ${SOURCES_SEARCH_TOLERANCE_ALGS}
-  DEPLIBS
   )
 
 IF(TPL_ENABLE_Boost)
 
 TRIBITS_ADD_EXECUTABLE(
     stk_balance
     SOURCES ${SOURCES_MAIN}
-    DEPLIBS
     NOEXEPREFIX INSTALLABLE
     )
 
 TRIBITS_ADD_EXECUTABLE(
     stk_balance_m2n
     SOURCES ${SOURCES_M2N_MAIN}
-    DEPLIBS
     NOEXEPREFIX INSTALLABLE
     )
 

diff --git a/packages/stk/stk_balance/stk_balance/internal/NodeBalancer.cpp b/packages/stk/stk_balance/stk_balance/internal/NodeBalancer.cpp
@@ -5,6 +5,7 @@
 #include <stk_mesh/base/EntityKey.hpp>
 #include <stk_mesh/base/MetaData.hpp>
 #include <stk_mesh/base/Selector.hpp>
+#include <stk_mesh/base/GetEntities.hpp>
 #include <stk_topology/topology.hpp>
 #include <stk_util/environment/Env.hpp>
 #include <stk_util/parallel/ParallelReduce.hpp>
@@ -86,7 +87,7 @@ NodeBalancer::getGlobalLoadImbalance(double &loadFactor, int& numLocallyOwnedNod
 {
   stk::mesh::Selector localSelector = m_metaData.locally_owned_part();
   stk::mesh::EntityVector ownedNodes;
-  m_bulkData.get_entities(stk::topology::NODE_RANK, localSelector, ownedNodes);
+  stk::mesh::get_entities(m_bulkData, stk::topology::NODE_RANK, localSelector, ownedNodes);
 
   numLocallyOwnedNodes = ownedNodes.size();
   int maxLocallyOwned = 0;

diff --git a/packages/stk/stk_balance/stk_balance/internal/StkMeshAdapterForZoltan2.cpp b/packages/stk/stk_balance/stk_balance/internal/StkMeshAdapterForZoltan2.cpp
@@ -48,15 +48,15 @@ int StkMeshZoltanAdapter::getDimension() const
 void StkMeshZoltanAdapter::debuggingInfo(int proc_id, std::ofstream& out) const
 {
     int stride = 0;
-    const scalar_t** coords = new const scalar_t*[this->getDimension()]; // int *vect = new int[num];
+    const scalar_t** coords = new const scalar_t*[this->getDimension()];
 
     for(int coordim = 0; coordim < this->getDimension(); ++coordim)
     {
         this->getCoordinatesViewOf(getPrimaryEntityType(), coords[coordim], stride, coordim);
     }
 
     // vertex weights
-    const scalar_t** weights = new const scalar_t*[getNumWeightsPerOf(getPrimaryEntityType())]; // int *vect = new int[num];
+    const scalar_t** weights = new const scalar_t*[getNumWeightsPerOf(getPrimaryEntityType())];
     int weightstride = 0;
     for(int weightdim = 0; weightdim < getNumWeightsPerOf(getPrimaryEntityType()); ++weightdim)
     {
@@ -107,7 +107,6 @@ int StkMeshZoltanAdapter::getNumWeightsPerOf(Zoltan2::MeshEntityType etype) cons
     {
         numWeightsPerVertex = mGraph.get_num_field_criteria();
     }
-    //std::cerr << "Num weights per = " << numWeightsPerVertex << std::endl;
     return numWeightsPerVertex;
 }
 
@@ -122,7 +121,6 @@ void StkMeshZoltanAdapter::getWeightsViewOf(Zoltan2::MeshEntityType etype, const
             weights = mGraph.get_vertex_weights().data() + idx;
         }
     }
-    //std::cerr << "Weights = " << weights[0] << ", " << weights[1] << ", " << weights[2] << ", " << weights[3] << std::endl;
 }
 
 bool StkMeshZoltanAdapter::avail2ndAdjs(Zoltan2::MeshEntityType sourcetarget, Zoltan2::MeshEntityType through) const
@@ -165,7 +163,6 @@ int StkMeshZoltanAdapter::getNumWeightsPer2ndAdj(Zoltan2::MeshEntityType sourcet
     if(sourcetarget == Zoltan2::MESH_REGION && through == Zoltan2::MESH_FACE)
     {
         numWeightsPerEdge = 1;
-        // numWeightsPerEdge = mEdgeWeights.size();
     }
     return numWeightsPerEdge;
 }

diff --git a/packages/stk/stk_balance/stk_balance/internal/privateDeclarations.cpp b/packages/stk/stk_balance/stk_balance/internal/privateDeclarations.cpp
@@ -5,7 +5,6 @@
 #include <stk_balance/internal/StkGeometricMethodViaZoltan.hpp>
 #include <stk_balance/internal/MxNutils.hpp>
 #include <stk_balance/internal/StkBalanceUtils.hpp>
-#include <stk_balance/internal/SideGeometry.hpp>
 
 #include <stk_mesh/base/MetaData.hpp>
 #include <stk_mesh/base/SkinMesh.hpp>
@@ -25,6 +24,7 @@
 #include <stk_util/environment/WallTime.hpp>
 #include <stk_util/environment/LogWithTimeAndMemory.hpp>
 #include <stk_util/diag/StringUtil.hpp>
+#include <stk_math/SideGeometry.hpp>
 #include <zoltan.h>
 #include <Zoltan2_Version.hpp>
 #include <map>
@@ -306,7 +306,7 @@ struct SideInfo {
 };
 
 using SideInfoMap = std::map<stk::mesh::EntityId, std::vector<SideInfo>>;
-using SideGeometryPtr = std::unique_ptr<SideGeometry>;
+using SideGeometryPtr = std::unique_ptr<stk::math::SideGeometry>;
 
 bool is_line_side(const stk::topology::topology_t & t)
 {
@@ -321,22 +321,22 @@ bool is_point_side(const stk::topology::topology_t & t)
 SideGeometryPtr makeSideGeometry(const SideInfo & sideInfo)
 {
   if (stk::is_quad_side(sideInfo.sideTopology)) {
-    return SideGeometryPtr(new QuadGeometry(sideInfo.nodeCoordinates[0],
-                                              sideInfo.nodeCoordinates[1],
-                                              sideInfo.nodeCoordinates[2],
-                                              sideInfo.nodeCoordinates[3]));
+    return SideGeometryPtr(new stk::math::QuadGeometry(sideInfo.nodeCoordinates[0],
+                                                       sideInfo.nodeCoordinates[1],
+                                                       sideInfo.nodeCoordinates[2],
+                                                       sideInfo.nodeCoordinates[3]));
   }
   else if (stk::is_tri_side(sideInfo.sideTopology)) {
-    return SideGeometryPtr(new TriGeometry(sideInfo.nodeCoordinates[0],
-                                             sideInfo.nodeCoordinates[1],
-                                             sideInfo.nodeCoordinates[2]));
+    return SideGeometryPtr(new stk::math::TriGeometry(sideInfo.nodeCoordinates[0],
+                                                      sideInfo.nodeCoordinates[1],
+                                                      sideInfo.nodeCoordinates[2]));
   }
   else if (is_line_side(sideInfo.sideTopology)) {
-    return SideGeometryPtr(new LineGeometry(sideInfo.nodeCoordinates[0],
-                                            sideInfo.nodeCoordinates[1]));
+    return SideGeometryPtr(new stk::math::LineGeometry(sideInfo.nodeCoordinates[0],
+                                                       sideInfo.nodeCoordinates[1]));
   }
   else if (is_point_side(sideInfo.sideTopology)) {
-    return SideGeometryPtr(new PointGeometry(sideInfo.nodeCoordinates[0]));
+    return SideGeometryPtr(new stk::math::PointGeometry(sideInfo.nodeCoordinates[0]));
   }
   else {
     ThrowErrorMsg("Unsupported side topology: " << stk::topology(sideInfo.sideTopology).name());
@@ -780,7 +780,7 @@ void fill_decomp_using_geometric_method(const BalanceSettings& balanceSettings,
     if (balanceSettings.isMultiCriteriaRebalance())
         get_multicriteria_decomp_using_selectors_as_segregation(stkMeshBulkData, selectors, balanceSettings, numSubdomainsToCreate, decomp, localIds);
     else
-        for(const stk::mesh::Selector selector : selectors)
+        for(const stk::mesh::Selector& selector : selectors)
             get_multicriteria_decomp_using_selectors_as_segregation(stkMeshBulkData, std::vector<stk::mesh::Selector>{selector}, balanceSettings, numSubdomainsToCreate, decomp, localIds);
 
     logMessage(stkMeshBulkData.parallel(), "Finished decomposition solve");
@@ -973,7 +973,7 @@ void pack_new_spider_entity_owners(const stk::mesh::BulkData & bulk,
                                    stk::CommSparse & comm,
                                    const stk::mesh::EntityProcMap & newSpiderEntityOwners)
 {
-  for (const stk::mesh::EntityProc & entityNewOwner : newSpiderEntityOwners) {
+  for (const stk::mesh::EntityProcMap::value_type & entityNewOwner : newSpiderEntityOwners) {
     const int currentOwner = bulk.parallel_owner_rank(entityNewOwner.first);
     const stk::mesh::EntityKey entityKey = bulk.entity_key(entityNewOwner.first);
     comm.send_buffer(currentOwner).pack<stk::mesh::EntityKey>(entityKey);

diff --git a/packages/stk/stk_doc_tests/cmake/Dependencies.cmake b/packages/stk/stk_doc_tests/cmake/Dependencies.cmake
@@ -1,9 +1,8 @@
-SET(LIB_REQUIRED_DEP_PACKAGES Gtest)
-SET(LIB_OPTIONAL_DEP_PACKAGES STKTopology STKMath STKSimd STKUtil STKMesh STKIO)
-SET(TEST_OPTIONAL_DEP_PACKAGES STKUnit_test_utils)
-SET(TEST_REQUIRED_DEP_PACKAGES)
+SET(LIB_REQUIRED_DEP_PACKAGES)
+SET(LIB_OPTIONAL_DEP_PACKAGES)
+SET(TEST_OPTIONAL_DEP_PACKAGES STKTopology STKMath STKSimd STKMesh STKIO)
+SET(TEST_REQUIRED_DEP_PACKAGES Gtest STKUtil STKNGP_TEST STKUnit_test_utils)
 SET(LIB_REQUIRED_DEP_TPLS)
-SET(LIB_OPTIONAL_DEP_TPLS Boost)
+SET(LIB_OPTIONAL_DEP_TPLS)
 SET(TEST_REQUIRED_DEP_TPLS)
-SET(TEST_OPTIONAL_DEP_TPLS)
-SET(TEST_OPTIONAL_DEP_TPLS Boost)
+SET(TEST_OPTIONAL_DEP_TPLS Boost MPI)
diff --git a/packages/stk/stk_doc_tests/stk_balance/CMakeLists.txt b/packages/stk/stk_doc_tests/stk_balance/CMakeLists.txt
@@ -41,7 +41,6 @@ FILE(GLOB SOURCES *.cpp)
 TRIBITS_ADD_EXECUTABLE_AND_TEST(
     stk_balance_doc_tester
     SOURCES ${SOURCES}
-    TESTONLYLIBS stk_unit_main
     ARGS ""
     COMM serial mpi
     NUM_MPI_PROCS 1-4

diff --git a/packages/stk/stk_doc_tests/stk_balance/howToUseStkBalance.cpp b/packages/stk/stk_doc_tests/stk_balance/howToUseStkBalance.cpp
@@ -336,7 +336,7 @@ void put_elements_in_different_parts(stk::mesh::BulkData &bulk, stk::mesh::Part
 void verify_mesh_balanced_wrt_selectors(const stk::mesh::BulkData& bulk, const std::vector<stk::mesh::Selector> &selectors)
 {
     std::vector<size_t> counts;
-    for(const stk::mesh::Selector sel : selectors)
+    for(const stk::mesh::Selector & sel : selectors)
     {
         stk::mesh::EntityVector elements;
         size_t num_elements = stk::mesh::count_selected_entities(sel, bulk.buckets(stk::topology::ELEM_RANK));

diff --git a/packages/stk/stk_doc_tests/stk_io/CMakeLists.txt b/packages/stk/stk_doc_tests/stk_io/CMakeLists.txt
@@ -56,9 +56,9 @@ LIST(REMOVE_ITEM SOURCES "${CMAKE_CURRENT_SOURCE_DIR}/RenamedInputFields.cpp")
 TRIBITS_ADD_EXECUTABLE_AND_TEST(
     stk_io_doc_tests
     SOURCES ${SOURCES}
-    TESTONLYLIBS stk_unit_main
     ARGS ""
     COMM serial mpi
     NUM_MPI_PROCS 1
+    NOEXEPREFIX
     )