Merge Pull Request #11582 from gsjaardema/Trilinos/SEACAS-snapshot-20…

…23-02-21

Automatically Merged using Trilinos Pull Request AutoTester
PR Title: Automatic snapshot commit from seacas at d4492cbf0f
PR Author: gsjaardema

packages/seacas/applications/conjoin/CJ_Variables.h

@@ -1,4 +1,4 @@
-// Copyright(C) 1999-2020, 2022 National Technology & Engineering Solutions
+// Copyright(C) 1999-2020, 2022, 2023 National Technology & Engineering Solutions
 // of Sandia, LLC (NTESS).  Under the terms of Contract DE-NA0003525 with
 // NTESS, the U.S. Government retains certain rights in this software.
 //
@@ -19,7 +19,7 @@ namespace Excn {
   struct Variables
   {
     explicit Variables(ObjectType otype, bool arg_add_status = false)
-        : objectType(otype), outputCount(0), addStatus(arg_add_status)
+        : objectType(otype), addStatus(arg_add_status)
     {
       SMART_ASSERT(otype == ObjectType::EBLK || otype == ObjectType::NSET ||
                    otype == ObjectType::SSET || otype == ObjectType::NODE ||
@@ -63,7 +63,7 @@ namespace Excn {
     bool add_status() const { return addStatus; }
 
     ObjectType  objectType;
-    int         outputCount;
+    int         outputCount{0};
     bool        addStatus;
     IntVector   index_{};
     std::string type_{};

packages/seacas/applications/conjoin/Conjoin.C

@@ -1,4 +1,4 @@
-// Copyright(C) 1999-2022 National Technology & Engineering Solutions
+// Copyright(C) 1999-2023 National Technology & Engineering Solutions
 // of Sandia, LLC (NTESS).  Under the terms of Contract DE-NA0003525 with
 // NTESS, the U.S. Government retains certain rights in this software.
 //
@@ -44,6 +44,14 @@
 #error "Requires exodusII version 4.68 or later"
 #endif
 
+#include "CJ_ExodusEntity.h"
+#include "CJ_ExodusFile.h"
+#include "CJ_Internals.h"
+#include "CJ_ObjectType.h"
+#include "CJ_SystemInterface.h"
+#include "CJ_Variables.h"
+#include "CJ_Version.h"
+
 namespace {
   template <typename T> void clear(std::vector<T> &vec)
   {
@@ -111,14 +119,6 @@ struct NodeInfo
 using GlobalMap = std::vector<NodeInfo>;
 using GMapIter  = GlobalMap::iterator;
 
-#include "CJ_ExodusEntity.h"
-#include "CJ_ExodusFile.h"
-#include "CJ_Internals.h"
-#include "CJ_ObjectType.h"
-#include "CJ_SystemInterface.h"
-#include "CJ_Variables.h"
-#include "CJ_Version.h"
-
 extern double seacas_timer();
 
 namespace {

packages/seacas/applications/ejoin/EJoin.C

@@ -1,4 +1,4 @@
-// Copyright(C) 1999-2022 National Technology & Engineering Solutions
+// Copyright(C) 1999-2023 National Technology & Engineering Solutions
 // of Sandia, LLC (NTESS).  Under the terms of Contract DE-NA0003525 with
 // NTESS, the U.S. Government retains certain rights in this software.
 //
@@ -257,6 +257,11 @@ int main(int argc, char *argv[])
     add_to_log(argv[0], time);
 
 #ifdef SEACAS_HAVE_MPI
+    MPI_Comm parent_comm;
+    MPI_Comm_get_parent(&parent_comm);
+    if (parent_comm != MPI_COMM_NULL) {
+      MPI_Barrier(parent_comm);
+    }
     MPI_Finalize();
 #endif
 

packages/seacas/applications/epu/epu.C

@@ -115,7 +115,7 @@ namespace {
     }
   }
 
-  void exodus_error(int lineno)
+  [[noreturn]] void exodus_error(int lineno)
   {
     std::ostringstream errmsg;
     fmt::print(errmsg,
@@ -3895,6 +3895,7 @@ namespace {
           size_t maximum_nodes = edgeblocks[p][b].entity_count();
           maximum_nodes *= edgeblocks[p][b].nodesPerEdge;
           std::vector<INT> local_linkage(maximum_nodes);
+          SMART_ASSERT(block_linkage != nullptr);
 
           ex_entity_id bid = edgeblocks[p][b].id;
           error = ex_get_conn(id, EX_EDGE_BLOCK, bid, local_linkage.data(), nullptr, nullptr);
@@ -4271,6 +4272,7 @@ namespace {
           size_t maximum_nodes = faceblocks[p][b].entity_count();
           maximum_nodes *= faceblocks[p][b].nodesPerFace;
           std::vector<INT> local_linkage(maximum_nodes);
+          SMART_ASSERT(block_linkage != nullptr);
 
           ex_entity_id bid = faceblocks[p][b].id;
           error = ex_get_conn(id, EX_FACE_BLOCK, bid, local_linkage.data(), nullptr, nullptr);

packages/seacas/applications/exo_format/exo_format.c

@@ -1,5 +1,5 @@
 /*
- * Copyright(C) 1999-2021 National Technology & Engineering Solutions
+ * Copyright(C) 1999-2021, 2023 National Technology & Engineering Solutions
  * of Sandia, LLC (NTESS).  Under the terms of Contract DE-NA0003525 with
  * NTESS, the U.S. Government retains certain rights in this software.
  *
@@ -55,7 +55,6 @@ int main(int argc, char *argv[])
   int   int64_status    = 0;
   int   max_name_length = 0;
   int   fn_idx          = 1;
-  char  cversion[9];
 
   CPU_word_size = 0; /* float or double */
   IO_word_size  = 0; /* use what is stored in file */
@@ -210,7 +209,8 @@ int main(int argc, char *argv[])
   }
 
   version += 0.00005F;
-  sprintf(cversion, "%4.2f", version);
+  char cversion[9];
+  snprintf(cversion, 9, "%4.2f", version);
 
   k = strlen(cversion);
   for (j = 0; j < k; j++) {

packages/seacas/applications/exodiff/ED_SystemInterface.C

@@ -24,7 +24,7 @@
 #include <SL_tokenize.h>
 
 namespace {
-  void Parse_Die(const char *line)
+  [[noreturn]] void Parse_Die(const char *line)
   {
     std::string sline = line;
     chop_whitespace(sline);

packages/seacas/applications/exodiff/exodiff.C

@@ -1,4 +1,4 @@
-// Copyright(C) 1999-2022 National Technology & Engineering Solutions
+// Copyright(C) 1999-2023 National Technology & Engineering Solutions
 // of Sandia, LLC (NTESS).  Under the terms of Contract DE-NA0003525 with
 // NTESS, the U.S. Government retains certain rights in this software.
 //
@@ -1506,7 +1506,7 @@ bool diff_globals(ExoII_Read<INT> &file1, ExoII_Read<INT> &file2, int step1, con
       const std::string &name = (interFace.glob_var_names)[out_idx];
       int idx1 = find_string(file1.Global_Var_Names(), name, interFace.nocase_var_names);
       int idx2 = find_string(file2.Global_Var_Names(), name, interFace.nocase_var_names);
-      if (idx1 < 0 || idx2 < 0 || vals2 == nullptr) {
+      if (idx1 < 0 || idx2 < 0) {
         Error(fmt::format("Unable to find global variable named '{}' on database.\n", name));
       }
       gvals[out_idx] = FileDiff(vals1[idx1], vals2[idx2], interFace.output_type);
@@ -1792,7 +1792,9 @@ bool diff_element(ExoII_Read<INT> &file1, ExoII_Read<INT> &file2, int step1, con
 
         if (el_flag >= 0) {
           if (elmt_map.empty()) {
-            v2 = vals2[e];
+            if (vals2 != nullptr) {
+              v2 = vals2[e];
+            }
           }
           else {
             // With mapping, map global index from file 1 to global index
@@ -1844,7 +1846,7 @@ bool diff_element(ExoII_Read<INT> &file1, ExoII_Read<INT> &file2, int step1, con
       }
 
       eblock1->Free_Results();
-      if (elmt_map.empty()) {
+      if (elmt_map.empty() && eblock2 != nullptr) {
         eblock2->Free_Results();
       }
 
@@ -1967,9 +1969,9 @@ bool diff_nodeset(ExoII_Read<INT> &file1, ExoII_Read<INT> &file2, int step1, con
       if (!interFace.quiet_flag) {
         Node_Set<INT> *nset = file1.Get_Node_Set_by_Id(max_diff.blk);
         std::string    buf  = fmt::format(
-                "   {:<{}} {} diff: {:14.7e} ~ {:14.7e} ={:12.5e} (set {}, node {})", name,
-                name_length(), interFace.ns_var[e_idx].abrstr(), max_diff.val1, max_diff.val2,
-                max_diff.diff, max_diff.blk, id_map[nset->Node_Id(max_diff.id) - 1]);
+            "   {:<{}} {} diff: {:14.7e} ~ {:14.7e} ={:12.5e} (set {}, node {})", name,
+            name_length(), interFace.ns_var[e_idx].abrstr(), max_diff.val1, max_diff.val2,
+            max_diff.diff, max_diff.blk, id_map[nset->Node_Id(max_diff.id) - 1]);
         DIFF_OUT(buf);
       }
       else {
@@ -2077,10 +2079,10 @@ bool diff_sideset(ExoII_Read<INT> &file1, ExoII_Read<INT> &file2, int step1, con
       if (!interFace.quiet_flag) {
         Side_Set<INT> *sset = file1.Get_Side_Set_by_Id(max_diff.blk);
         std::string    buf  = fmt::format(
-                "   {:<{}} {} diff: {:14.7e} ~ {:14.7e} ={:12.5e} (set {}, side {}.{})", name,
-                name_length(), interFace.ss_var[e_idx].abrstr(), max_diff.val1, max_diff.val2,
-                max_diff.diff, max_diff.blk, id_map[sset->Side_Id(max_diff.id).first - 1],
-                (int)sset->Side_Id(max_diff.id).second);
+            "   {:<{}} {} diff: {:14.7e} ~ {:14.7e} ={:12.5e} (set {}, side {}.{})", name,
+            name_length(), interFace.ss_var[e_idx].abrstr(), max_diff.val1, max_diff.val2,
+            max_diff.diff, max_diff.blk, id_map[sset->Side_Id(max_diff.id).first - 1],
+            (int)sset->Side_Id(max_diff.id).second);
         DIFF_OUT(buf);
       }
       else {
@@ -2331,9 +2333,9 @@ bool diff_edgeblock(ExoII_Read<INT> &file1, ExoII_Read<INT> &file2, int step1, c
       if (!interFace.quiet_flag) {
         Edge_Block<INT> *eblock = file1.Get_Edge_Block_by_Id(max_diff.blk);
         std::string      buf    = fmt::format(
-                    "   {:<{}} {} diff: {:14.7e} ~ {:14.7e} ={:12.5e} (edge block {}, edge {})", name,
-                    name_length(), interFace.eb_var[e_idx].abrstr(), max_diff.val1, max_diff.val2,
-                    max_diff.diff, max_diff.blk, eblock->Edge_Index(max_diff.id) + 1);
+            "   {:<{}} {} diff: {:14.7e} ~ {:14.7e} ={:12.5e} (edge block {}, edge {})", name,
+            name_length(), interFace.eb_var[e_idx].abrstr(), max_diff.val1, max_diff.val2,
+            max_diff.diff, max_diff.blk, eblock->Edge_Index(max_diff.id) + 1);
         DIFF_OUT(buf);
       }
       else {

packages/seacas/applications/exodiff/util.h

@@ -1,5 +1,5 @@
 /*
- * Copyright(C) 1999-2022 National Technology & Engineering Solutions
+ * Copyright(C) 1999-2023 National Technology & Engineering Solutions
  * of Sandia, LLC (NTESS).  Under the terms of Contract DE-NA0003525 with
  * NTESS, the U.S. Government retains certain rights in this software.
  *
@@ -14,9 +14,9 @@ int    name_length();
 char **get_name_array(int size, int length);
 void   free_name_array(char **names, int size);
 
-void Error(const std::string &x);
-void Error(std::ostringstream &buf);
-void Warning(const std::string &x);
-void ERR_OUT(std::ostringstream &buf);
+[[noreturn]] void Error(const std::string &x);
+[[noreturn]] void Error(std::ostringstream &buf);
+void              Warning(const std::string &x);
+void              ERR_OUT(std::ostringstream &buf);
 void DIFF_OUT(std::ostringstream &buf, fmt::detail::color_type color = fmt::color::red);
 void DIFF_OUT(const std::string &buf, fmt::detail::color_type color = fmt::color::red);

packages/seacas/applications/exotec2/tec.c

@@ -1,5 +1,5 @@
 /*
- * Copyright(C) 1999-2022 National Technology & Engineering Solutions
+ * Copyright(C) 1999-2023 National Technology & Engineering Solutions
  * of Sandia, LLC (NTESS).  Under the terms of Contract DE-NA0003525 with
  * NTESS, the U.S. Government retains certain rights in this software.
  *
@@ -425,17 +425,17 @@ void teczone(int nblk, int nnode, int elem_id, char *elem_type, int node_per_ele
          inode);
   char zname[80];
   char eltype[16];
-  sprintf(zname, "Zone %s_%d", elem_type, elem_id);
+  snprintf(zname, 80, "Zone %s_%d", elem_type, elem_id);
 
   if (ndim == 3 && (node_per_elem == 8 || (node_per_elem == 4 && ifac == 2) ||
                     (node_per_elem == 2 && ifac == 4)))
-    sprintf(eltype, "BRICK");
+    snprintf(eltype, 16, "BRICK");
   else if (ndim == 3 && node_per_elem == 4)
-    sprintf(eltype, "TETRAHEDRON");
+    snprintf(eltype, 16, "TETRAHEDRON");
   else if (ndim == 2 && (node_per_elem == 4 || (node_per_elem == 2 && ifac == 2)))
-    sprintf(eltype, "QUADRILATERAL");
+    snprintf(eltype, 16, "QUADRILATERAL");
   else if (ndim == 2 && node_per_elem == 3)
-    sprintf(eltype, "TRIANGLE");
+    snprintf(eltype, 16, "TRIANGLE");
   else {
     printf("\nBad element type found in teczone\n");
     printf("   Dimensions = %d\n", ndim);

packages/seacas/applications/nem_slice/elb_loadbal.C

@@ -1,5 +1,5 @@
 /*
- * Copyright(C) 1999-2021 National Technology & Engineering Solutions
+ * Copyright(C) 1999-2021, 2023 National Technology & Engineering Solutions
  * of Sandia, LLC (NTESS).  Under the terms of Contract DE-NA0003525 with
  * NTESS, the U.S. Government retains certain rights in this software.
  *
@@ -149,7 +149,6 @@ int generate_loadbal(Machine_Description *machine, Problem_Description *problem,
   int              tmp_lev;
   int             *tmp_v2p = nullptr;
 
-  float             *x_ptr = nullptr, *y_ptr = nullptr, *z_ptr = nullptr;
   float             *x_node_ptr = nullptr, *y_node_ptr = nullptr, *z_node_ptr = nullptr;
   std::vector<float> x_elem_ptr, y_elem_ptr, z_elem_ptr;
   float             *tmp_x = nullptr, *tmp_y = nullptr, *tmp_z = nullptr;
@@ -216,16 +215,15 @@ int generate_loadbal(Machine_Description *machine, Problem_Description *problem,
       y_node_ptr = (float *)calloc(mesh->num_nodes, sizeof(float));
       z_node_ptr = (float *)calloc(mesh->num_nodes, sizeof(float));
       break;
+
+    default: Gen_Error(0, "FATAL: Invalid mesh dimension.  Must be 1, 2, or 3."); return 0;
     }
   }
-  else {
-    x_node_ptr = y_node_ptr = z_node_ptr = nullptr;
-  }
 
   /* now set the pointers that are being sent to Chaco */
-  x_ptr = x_node_ptr;
-  y_ptr = y_node_ptr;
-  z_ptr = z_node_ptr;
+  float *x_ptr = x_node_ptr;
+  float *y_ptr = y_node_ptr;
+  float *z_ptr = z_node_ptr;
 
   /*
    * For an elemental decomposition using inertial, ZPINCH, BRICK
@@ -634,7 +632,8 @@ int generate_loadbal(Machine_Description *machine, Problem_Description *problem,
         tmp_z   = z_ptr;
         tmp_v2p = lb->vertex2proc;
 
-        for (int cnt = 0; cnt < machine->num_dims; cnt++) {
+        int upper = machine->num_dims > 3 ? 3 : machine->num_dims;
+        for (int cnt = 0; cnt < upper; cnt++) {
           tmpdim[cnt] = machine->dim[cnt];
         }
         if (machine->type == MESH) {

packages/seacas/applications/nem_slice/fix_column_partitions.C

@@ -1,5 +1,5 @@
 /*
- * Copyright(C) 1999-2021 National Technology & Engineering Solutions
+ * Copyright(C) 1999-2021, 2023 National Technology & Engineering Solutions
  * of Sandia, LLC (NTESS).  Under the terms of Contract DE-NA0003525 with
  * NTESS, the U.S. Government retains certain rights in this software.
  *
@@ -39,16 +39,16 @@ namespace {
 
     // Get nodes of this side (face) of the element
 
-    int nsnodes = is_hex(etype) ? 4 : 3;
-    INT side_nodes[9]; // SHELL9 has 9 nodes on a face.
+    int nsnodes       = is_hex(etype) ? 4 : 3;
+    INT side_nodes[9] = {0}; // SHELL9 has 9 nodes on a face.
 
     INT *elnodes = mesh->connect[cur_elem];
     ss_to_node_list(etype, elnodes, side_id, side_nodes);
 
     // How would these side's nodes be if they were viewed from the
     // adjacent element
 
-    INT side_nodes_flipped[9]; // Realistically: 4, max possible: 9
+    INT side_nodes_flipped[9] = {0}; // Realistically: 4, max possible: 9
     get_ss_mirror(etype, side_nodes, side_id, side_nodes_flipped);
 
     for (int i = 0; i < nadj; i++) {
@@ -139,7 +139,8 @@ int fix_column_partitions(LB_Description<INT> *lb, Mesh_Description<INT> const *
 
     int count = 0;
     for (int j = 0; j < nelfaces; j++) {
-      INT fnodes[9]; // Should only need 4, but ss_to_node_list can potentially access 9 (SHELL9).
+      INT fnodes[9] = {
+          0}; // Should only need 4, but ss_to_node_list can potentially access 9 (SHELL9).
 
       int nfn = 4;
       if (is_wedge(etype)) {
@@ -155,7 +156,7 @@ int fix_column_partitions(LB_Description<INT> *lb, Mesh_Description<INT> const *
       ss_to_node_list(etype, mesh->connect[i], j + 1, fnodes);
 
       // Translate global IDs of side nodes to local IDs in element
-      int fnodes_loc[9];
+      int fnodes_loc[9] = {0};
       for (int k = 0; k < nfn; k++) {
         bool found = false;
         for (int k2 = 0; k2 < nelnodes; k2++) {

packages/seacas/applications/slice/Slice.C

@@ -1718,7 +1718,12 @@ namespace {
 
     size_t proc_count = proc_region.size();
 
-    size_t                        node_count = region.get_property("node_count").get_int();
+    size_t node_count = region.get_property("node_count").get_int();
+    if (node_count == 0) {
+      // Should never happen, but makes static analyzers happy...
+      return;
+    }
+
     std::vector<std::vector<int>> proc_node(node_count);
 
     // Assume that the majority of nodes will be on 2 or less

packages/seacas/libraries/aprepro_lib/CMakeLists.txt

@@ -41,7 +41,7 @@ SET(SOURCES
  apr_units.cc
  apr_tokenize.cc
  apr_scanner.cc
- apr_getline_int.c
+ apr_getline.cc
  ${BISON_LIB_SOURCE}
  apr_exodus.cc
  apr_array.cc