Merge 'trilinos/Trilinos:develop' (b7e9fc1) into 'tcad-charon/Trilino…

…s:develop' (d850978). * trilinos-develop: Automatic snapshot commit from seacas at 500c3cef0 Tpetra: Fixes for Distributor timings Tacho - fix external example for openmp and serial build Tpetra: Distributor timers now controlled by config-option, not code modification
tcad-charon · Mar 31, 2020 · a4157fa · a4157fa
2 parents d850978 + b7e9fc1
commit a4157fa
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Showing 35 changed files with 759 additions and 763 deletions.
diff --git a/packages/seacas/applications/nem_spread/el_exoII_io.C b/packages/seacas/applications/nem_spread/el_exoII_io.C
@@ -1,5 +1,5 @@
 /*
- * Copyright (C) 2009-2017 National Technology & Engineering Solutions of
+ * Copyright (C) 2009-2017, 2020 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.
  *
@@ -956,10 +956,10 @@ void NemSpread<T, INT>::read_coord(int exoid, int max_name_length)
    * output databases.
    */
   {
-    int sequential = 1;
+    bool sequential = true;
     for (size_t i = 0; i < globals.Num_Node; i++) {
       if ((size_t)global_node_ids[i] != i + 1) {
-        sequential = 0;
+        sequential = false;
         break;
       }
     }
@@ -974,12 +974,12 @@ void NemSpread<T, INT>::read_coord(int exoid, int max_name_length)
                    "       All global ids must be greater than 0. The map will be ignored.\n"
                    "---------------------------------------------------------------------\n",
                    i + 1, global_node_ids[i]);
-        sequential = 1; // Map is invalid, ignore it.
+        sequential = true; // Map is invalid, ignore it.
         break;
       }
     }
 
-    if (sequential == 0) {
+    if (!sequential) {
       for (int iproc = Proc_Info[4]; iproc < Proc_Info[4] + Proc_Info[5]; iproc++) {
 
         size_t itotal_nodes = globals.Num_Internal_Nodes[iproc] + globals.Num_Border_Nodes[iproc] +
@@ -1483,6 +1483,22 @@ template <typename T, typename INT> void NemSpread<T, INT>::read_elem_blk(int ex
         break;
       }
     }
+
+    // Check that map is valid 1 <= global_node_id[*]
+    // If not, output a warning and disable the map.
+    for (size_t i = 0; i < globals.Num_Elem; i++) {
+      if (global_ids[i] <= 0) {
+        fmt::print(stderr,
+                   "---------------------------------------------------------------------\n"
+                   "ERROR: Local element {:n} has a global id of {:n} which is invalid.\n"
+                   "       All global ids must be greater than 0. The map will be ignored.\n"
+                   "---------------------------------------------------------------------\n",
+                   i + 1, global_ids[i]);
+        sequential = true; // Map is invalid, ignore it.
+        break;
+      }
+    }
+
     if (!sequential) {
       for (int iproc = Proc_Info[4]; iproc < Proc_Info[4] + Proc_Info[5]; iproc++) {
 

diff --git a/packages/seacas/libraries/exodus/src/ex_get_var_time.c b/packages/seacas/libraries/exodus/src/ex_get_var_time.c
@@ -1,5 +1,5 @@
 /*
- * Copyright (c) 2005-2017 National Technology & Engineering Solutions
+ * Copyright (c) 2005-2017, 2020 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.
  *
@@ -158,7 +158,7 @@ int ex_get_var_time(int exoid, ex_entity_type var_type, int var_index, int64_t i
   }
 
   /* allocate space for stat array */
-  if (!(stat_vals = malloc(num_obj * sizeof(int)))) {
+  if (!(stat_vals = calloc(num_obj, sizeof(int)))) {
     snprintf(errmsg, MAX_ERR_LENGTH,
              "ERROR: failed to allocate memory for %s status array for file id %d",
              ex_name_of_object(var_type), exoid);

diff --git a/packages/seacas/libraries/exodus/src/ex_put_variable_names.c b/packages/seacas/libraries/exodus/src/ex_put_variable_names.c
@@ -1,5 +1,5 @@
 /*
- * Copyright (c) 2005-2017 National Technology & Engineering Solutions
+ * Copyright (c) 2005-2017, 2020 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.
  *
@@ -151,7 +151,8 @@ error = ex_put_variable_names (exoid, EX_NODAL, num_nod_vars, var_names);
 
 int ex_put_variable_names(int exoid, ex_entity_type obj_type, int num_vars, char *var_names[])
 {
-  int  varid, status;
+  int  varid  = 0;
+  int  status = 0;
   char errmsg[MAX_ERR_LENGTH];
 
   EX_FUNC_ENTER();

diff --git a/packages/seacas/libraries/exodus/src/herrin-552-str-1.out b/packages/seacas/libraries/exodus/src/herrin-552-str-1.out
diff --git a/packages/seacas/libraries/exodus/test/testwt-localization.C b/packages/seacas/libraries/exodus/test/testwt-localization.C
@@ -1,5 +1,5 @@
 /*
- * Copyright (c) 2005-2017 National Technology & Engineering Solutions
+ * Copyright (c) 2005-2017, 2020 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.
  *
@@ -44,12 +44,6 @@
 #include "exodusII.h"
 #include "exodusII_int.h"
 
-#if __cplusplus > 199711L
-#define TOPTR(x) x.data()
-#else
-#define TOPTR(x) (x.empty() ? nullptr : &x[0])
-#endif
-
 #define STRINGIFY(x) #x
 #define TOSTRING(x) STRINGIFY(x)
 #define EXCHECK(funcall)                                                                           \
@@ -165,7 +159,7 @@ int main()
     z[i + num_nodes / 2] = 1.0;
   }
 
-  EXCHECK(ex_put_coord(exoid, TOPTR(x), TOPTR(y), TOPTR(z)));
+  EXCHECK(ex_put_coord(exoid, x.data(), y.data(), z.data()));
 
   const char *coord_names[3];
   coord_names[0] = "xcoor";
@@ -200,7 +194,7 @@ int main()
   block_names[1] = "block_20";
   block_names[2] = "block_30";
 
-  EXCHECK(ex_put_block_params(exoid, num_elem_blk, TOPTR(blocks)));
+  EXCHECK(ex_put_block_params(exoid, num_elem_blk, blocks.data()));
 
   /* Write element block names */
   for (int i = 0; i < num_elem_blk; i++) {
@@ -288,14 +282,14 @@ int main()
     }
 
     EXCHECK(
-        ex_put_var(exoid, whole_time_step, EX_GLOBAL, 1, 1, num_glo_vars, TOPTR(glob_var_vals)));
+        ex_put_var(exoid, whole_time_step, EX_GLOBAL, 1, 1, num_glo_vars, glob_var_vals.data()));
 
     // write nodal variables
     for (int k = 1; k <= num_nod_vars; k++) {
       for (int j = 0; j < num_nodes; j++) {
         nodal_var_vals[j] = (double)k + ((double)(j + 1) * time_value);
       }
-      EXCHECK(ex_put_var(exoid, whole_time_step, EX_NODAL, k, 1, num_nodes, TOPTR(nodal_var_vals)));
+      EXCHECK(ex_put_var(exoid, whole_time_step, EX_NODAL, k, 1, num_nodes, nodal_var_vals.data()));
     }
 
     // write element variables
@@ -305,7 +299,7 @@ int main()
           elem_var_vals[m] = (double)(k + 1) + (double)(j + 2) + ((double)(m + 1) * time_value);
         }
         EXCHECK(ex_put_var(exoid, whole_time_step, EX_ELEM_BLOCK, k, blocks[j].id,
-                           blocks[j].num_entry, TOPTR(elem_var_vals)));
+                           blocks[j].num_entry, elem_var_vals.data()));
       }
     }
 

diff --git a/packages/seacas/libraries/exodus/test/testwt-results.c b/packages/seacas/libraries/exodus/test/testwt-results.c
@@ -1,5 +1,5 @@
 /*
- * Copyright (c) 2005-2017 National Technology & Engineering Solutions
+ * Copyright (c) 2005-2017, 2020 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.
  *
@@ -93,8 +93,8 @@ int main(int argc, char **argv)
   num_node_sets = 0;
   num_side_sets = 0;
 
-  error = ex_put_init(exoid, title, num_dim, num_nodes, num_elem, num_elem_blk, num_node_sets,
-                      num_side_sets);
+  ex_put_init(exoid, title, num_dim, num_nodes, num_elem, num_elem_blk, num_node_sets,
+              num_side_sets);
 
   /* write element block parameters */
   for (i = 0; i < 10; i++) {

diff --git a/packages/seacas/libraries/ioss/src/Ioss_DatabaseIO.C b/packages/seacas/libraries/ioss/src/Ioss_DatabaseIO.C
@@ -327,16 +327,16 @@ namespace Ioss {
       Ioss::FileInfo path{filename};
       Ioss::FileInfo bb_file{get_dwPath() + path.tailname()};
       if (bb_file.exists() && !bb_file.is_writable()) {
-	// already existing file which has been closed If we can't
+        // already existing file which has been closed If we can't
         // write to the file on the BB, then it is a file which is
         // being staged by datawarp system over to the permanent
         // filesystem.  Wait until staging has finished...  stage wait
         // returns 0 = success, -ENOENT or -errno
 #if defined SEACAS_HAVE_DATAWARP
 #if IOSS_DEBUG_OUTPUT
         if (myProcessor == 0) {
-	  fmt::print(stderr, "DW: dw_wait_file_stage({});\n", bb_file.filename());
-	}
+          fmt::print(stderr, "DW: dw_wait_file_stage({});\n", bb_file.filename());
+        }
 #endif
         int dwret = dw_wait_file_stage(bb_file.filename().c_str());
         if (dwret < 0) {
@@ -365,25 +365,25 @@ namespace Ioss {
     if (using_dw()) {
       if (!using_parallel_io() || (using_parallel_io() && myProcessor == 0)) {
 #if defined SEACAS_HAVE_DATAWARP
-	int complete=0, pending=0, deferred=0, failed=0;
-	dw_query_file_stage(get_dwname().c_str(), &complete, &pending, &deferred, &failed);
+        int complete = 0, pending = 0, deferred = 0, failed = 0;
+        dw_query_file_stage(get_dwname().c_str(), &complete, &pending, &deferred, &failed);
 #if IOSS_DEBUG_OUTPUT
         auto initial = std::chrono::high_resolution_clock::now();
-	fmt::print(stderr, "Query: {}, {}, {}, {}\n", complete, pending, deferred, failed);
+        fmt::print(stderr, "Query: {}, {}, {}, {}\n", complete, pending, deferred, failed);
 #endif
-	if (pending > 0) {
-	  int dwret = dw_wait_file_stage(get_dwname().c_str());
-	  if (dwret < 0) {
-	    std::ostringstream errmsg;
-	    fmt::print(errmsg, "ERROR: failed waiting for file stage `{}`: {}\n", get_dwname(),
-		       std::strerror(-dwret));
-	    IOSS_ERROR(errmsg);
-	  }
+        if (pending > 0) {
+          int dwret = dw_wait_file_stage(get_dwname().c_str());
+          if (dwret < 0) {
+            std::ostringstream errmsg;
+            fmt::print(errmsg, "ERROR: failed waiting for file stage `{}`: {}\n", get_dwname(),
+                       std::strerror(-dwret));
+            IOSS_ERROR(errmsg);
+          }
 #if IOSS_DEBUG_OUTPUT
-	  dw_query_file_stage(get_dwname().c_str(), &complete, &pending, &deferred, &failed);
-	  fmt::print(stderr, "Query: {}, {}, {}, {}\n", complete, pending, deferred, failed);
+          dw_query_file_stage(get_dwname().c_str(), &complete, &pending, &deferred, &failed);
+          fmt::print(stderr, "Query: {}, {}, {}, {}\n", complete, pending, deferred, failed);
 #endif
-	}
+        }
 
 #if IOSS_DEBUG_OUTPUT
         fmt::print(stderr, "\nDW: BEGIN dw_stage_file_out({}, {}, DW_STAGE_IMMEDIATE);\n",
@@ -393,7 +393,7 @@ namespace Ioss {
             dw_stage_file_out(get_dwname().c_str(), get_pfsname().c_str(), DW_STAGE_IMMEDIATE);
 
 #if IOSS_DEBUG_OUTPUT
-        auto time_now = std::chrono::high_resolution_clock::now();
+        auto                          time_now = std::chrono::high_resolution_clock::now();
         std::chrono::duration<double> diff     = time_now - initial;
         fmt::print(stderr, "\nDW: END dw_stage_file_out({})\n", diff.count());
 #endif
@@ -964,7 +964,7 @@ namespace Ioss {
         IOSS_ERROR(errmsg);
       }
 
-      result = MPI_Waitall(req_cnt, TOPTR(request), TOPTR(status));
+      result = MPI_Waitall(req_cnt, request.data(), status.data());
 
       if (result != MPI_SUCCESS) {
         fmt::print(stderr, "ERROR: MPI_Waitall error on processor {} in {}", util().parallel_rank(),
@@ -1026,7 +1026,7 @@ namespace Ioss {
       }
 
       std::vector<unsigned> out_data(element_blocks.size() * bits_size);
-      MPI_Allreduce((void *)TOPTR(data), TOPTR(out_data), static_cast<int>(data.size()),
+      MPI_Allreduce((void *)data.data(), out_data.data(), static_cast<int>(data.size()),
                     MPI_UNSIGNED, MPI_BOR, util().communicator());
 
       offset = 0;