SEACAS: July 2020 snapshot

Automatic snapshot commit from seacas at f3409ff

Origin repo remote tracking branch: 'origin/master'
Origin repo remote repo URL: 'origin = https://github.com/gsjaardema/seacas'

At commit:

commit f3409ffe20368526ef41851b0eeb51e7ab569079
Author:  Greg Sjaardema <gsjaardema@gmail.com>
Date:    Mon Jul 27 11:19:27 2020 -0600
Summary: APREPRO: Fix exit status for -F/-f options

* Aprepro: set exit status if using -F/-f option
* Use MPI_COMM_SELF with heartbeat files
* Better "compose" output filtering (performance improvement)
* EPU: In subcycle mode, don't map ids
* Slice: fix historgram output
* IOSS: rename member variable (prepend m_)
* IOSS:: sort test -- keep original vector for each test

packages/seacas/applications/aprepro/aprepro.C

@@ -17,6 +17,8 @@ int main(int argc, char *argv[])
 
   bool quiet = false;
 
+  int exit_status = EXIT_SUCCESS;
+
   // Parse all options...
   for (int ai = 1; ai < argc; ++ai) {
     std::string arg = argv[ai];
@@ -66,6 +68,14 @@ int main(int argc, char *argv[])
     aprepro.ap_options.interactive = true;
     try {
       aprepro.parse_stream(std::cin, "standard input");
+
+      if (aprepro.ap_options.errors_fatal && aprepro.get_error_count() > 0) {
+        exit_status = EXIT_FAILURE;
+      }
+      if ((aprepro.ap_options.errors_and_warnings_fatal) &&
+          (aprepro.get_error_count() + aprepro.get_warning_count() > 0)) {
+        exit_status = EXIT_FAILURE;
+      }
     }
     catch (std::exception &e) {
       std::cerr << "Aprepro terminated due to exception: " << e.what() << '\n';
@@ -116,6 +126,7 @@ int main(int argc, char *argv[])
         }
       }
       else {
+        exit_status = EXIT_FAILURE;
         std::cerr << "There were " << aprepro.get_error_count() << " errors and "
                   << aprepro.get_warning_count() << " warnings."
                   << "\n";
@@ -142,4 +153,5 @@ int main(int argc, char *argv[])
   if (aprepro.ap_options.debugging || aprepro.ap_options.dumpvars) {
     aprepro.dumpsym("variable", false);
   }
+  return exit_status;
 }

packages/seacas/applications/epu/EP_Version.h

@@ -10,8 +10,8 @@
 
 static char const *qainfo[] = {
     "epu --  E Pluribus Unum",
-    "2020/04/20",
-    "4.31",
+    "2020/06/17",
+    "4.32",
 };
 
 #endif // SEACAS_Version_h

packages/seacas/applications/epu/epu.C

@@ -723,9 +723,13 @@ int epu(SystemInterface &interFace, int start_part, int part_count, int cycle, T
     // must check for zero length blocks
     get_element_blocks(part_count, local_mesh, global, blocks, glob_blocks);
 
+    bool map_element_ids = interFace.map_element_ids();
+    if (interFace.subcycle() >= 0) {
+      map_element_ids = false;
+    }
     std::vector<INT> global_element_map(global.elementCount);
     build_reverse_element_map(local_element_to_global, local_mesh, blocks, glob_blocks, &global,
-                              part_count, global_element_map, interFace.map_element_ids());
+                              part_count, global_element_map, map_element_ids);
 
     //
     //    NOTE:  Node set/side set information can be different for each processor
@@ -1765,8 +1769,7 @@ namespace {
     for (int b = 0; b < global_num_blocks; b++) {
 
       if (debug_level & 4) {
-        fmt::print(stderr,
-                   "\nOutput element block info for...\n"
+        fmt::print("\nOutput element block info for...\n"
                    "Block {}, Id = {}, Name = '{}', Elements = {:12n}, Nodes/element = {}, "
                    "Attributes = {}\n"
                    "B{}:\t",

packages/seacas/applications/slice/SL_Version.h

@@ -1,15 +1,15 @@
 // Copyright(C) 1999-2020 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.
-// 
+//
 // See packages/seacas/LICENSE for details
 #ifndef SEACAS_Version_h
 #define SEACAS_Version_h
 
 static char const *qainfo[] = {
     "slice",
-    "2020/04/21",
-    "0.9.93",
+    "2020/06/10",
+    "0.9.94",
 };
 
 #endif // SEACAS_Version_h

packages/seacas/applications/slice/Slice.C

@@ -1409,7 +1409,7 @@ namespace {
     }
     // Output histogram..
     fmt::print(stderr, "Processor count per node histogram:\n");
-    for (size_t i = 0; i < proc_histo.size(); i++) {
+    for (size_t i = 1; i < proc_histo.size(); i++) {
       if (proc_histo[i] > 0) {
         fmt::print(stderr, "\tNodes on {:2n} processors = {:12n}\t({:2})%\n", i, proc_histo[i],
                    (proc_histo[i] * 100 + node_count / 2) / node_count);

packages/seacas/libraries/aprepro_lib/apr_aprepro.cc

@@ -24,7 +24,7 @@
 
 namespace {
   const unsigned int HASHSIZE       = 5939;
-  const char *       version_string = "5.16 (2020/06/09)";
+  const char *       version_string = "5.17 (2020/07/27)";
 
   void output_copyright();
 

packages/seacas/libraries/ioss/src/Ioss_CodeTypes.h

@@ -58,6 +58,9 @@ inline const std::string IOSS_SYM_TENSOR() { return std::string("sym_tensor_33")
     (void)(x);                                                                                     \
   } while (0)
 
+#ifndef MPI_COMM_SELF
+#define MPI_COMM_SELF 0
+#endif
 #ifndef MPI_COMM_WORLD
 #define MPI_COMM_WORLD 0
 using MPI_Comm       = int;

packages/seacas/libraries/ioss/src/Ioss_DatabaseIO.C

@@ -74,8 +74,8 @@ namespace {
     if (max_hash != min_hash) {
       const std::string &ge_name = ge->name();
       fmt::print(Ioss::WARNING(),
-                 "Parallel inconsistency detected for {} field '{}' on entity '{}'\n",
-                 in_out == 0 ? "writing" : "reading", field_name, ge_name);
+                 "[{}] Parallel inconsistency detected for {} field '{}' on entity '{}'. (Hash: {} {} {})\n",
+                 in_out == 0 ? "writing" : "reading", util.parallel_rank(), field_name, ge_name, hash_code, min_hash, max_hash);
       return false;
     }
     return true;
@@ -131,7 +131,9 @@ namespace {
 namespace Ioss {
   DatabaseIO::DatabaseIO(Region *region, std::string filename, DatabaseUsage db_usage,
                          MPI_Comm communicator, const PropertyManager &props)
-      : properties(props), DBFilename(std::move(filename)), dbUsage(db_usage), util_(communicator),
+      : properties(props), DBFilename(std::move(filename)), dbUsage(db_usage),
+        util_(db_usage == WRITE_HISTORY || db_usage == WRITE_HEARTBEAT ? MPI_COMM_SELF
+                                                                       : communicator),
         region_(region), isInput(is_input_event(db_usage)),
         singleProcOnly(db_usage == WRITE_HISTORY || db_usage == WRITE_HEARTBEAT ||
                        SerializeIO::isEnabled())

packages/seacas/libraries/ioss/src/exodus/Ioex_BaseDatabaseIO.C

@@ -216,7 +216,7 @@ namespace Ioex {
 
   void BaseDatabaseIO::set_int_byte_size_api(Ioss::DataSize size) const
   {
-    if (exodusFilePtr > 0) {
+    if (m_exodusFilePtr > 0) {
       int old_status = ex_int64_status(get_file_pointer());
       if (size == 8) {
         ex_set_int64_status(get_file_pointer(), EX_ALL_INT64_API | old_status);
@@ -226,7 +226,7 @@ namespace Ioex {
         if ((old_status & EX_ALL_INT64_API) != 0) {
           old_status &= ~EX_ALL_INT64_API;
           assert(!(old_status & EX_ALL_INT64_API));
-          ex_set_int64_status(exodusFilePtr, old_status);
+          ex_set_int64_status(m_exodusFilePtr, old_status);
         }
       }
     }
@@ -276,7 +276,7 @@ namespace Ioex {
   {
     // Returns the file_pointer used to access the file on disk.
     // Checks that the file is open and if not, opens it first.
-    if (exodusFilePtr < 0) {
+    if (m_exodusFilePtr < 0) {
       bool write_message  = true;
       bool abort_if_error = true;
       if (is_input()) {
@@ -288,24 +288,24 @@ namespace Ioex {
       }
 
       if (!m_groupName.empty()) {
-        ex_get_group_id(exodusFilePtr, m_groupName.c_str(), &exodusFilePtr);
+        ex_get_group_id(m_exodusFilePtr, m_groupName.c_str(), &m_exodusFilePtr);
       }
     }
-    assert(exodusFilePtr >= 0);
+    assert(m_exodusFilePtr >= 0);
     fileExists = true;
-    return exodusFilePtr;
+    return m_exodusFilePtr;
   }
 
   int BaseDatabaseIO::free_file_pointer() const
   {
-    if (exodusFilePtr != -1) {
+    if (m_exodusFilePtr != -1) {
       bool do_timer = false;
       if (isParallel) {
         Ioss::Utils::check_set_bool_property(properties, "IOSS_TIME_FILE_OPEN_CLOSE", do_timer);
       }
       double t_begin = (do_timer ? Ioss::Utils::timer() : 0);
 
-      ex_close(exodusFilePtr);
+      ex_close(m_exodusFilePtr);
       closeDW();
       if (do_timer && isParallel) {
         double t_end    = Ioss::Utils::timer();
@@ -315,9 +315,9 @@ namespace Ioex {
         }
       }
     }
-    exodusFilePtr = -1;
+    m_exodusFilePtr = -1;
 
-    return exodusFilePtr;
+    return m_exodusFilePtr;
   }
 
   bool BaseDatabaseIO::ok__(bool write_message, std::string *error_msg, int *bad_count) const
@@ -349,35 +349,35 @@ namespace Ioex {
       bool overwrite = false;
       is_ok = handle_output_file(write_message, error_msg, bad_count, overwrite, abort_if_error);
       // Close all open files...
-      if (exodusFilePtr >= 0) {
-        ex_close(exodusFilePtr);
-        exodusFilePtr = -1;
+      if (m_exodusFilePtr >= 0) {
+        ex_close(m_exodusFilePtr);
+        m_exodusFilePtr = -1;
       }
     }
     return is_ok;
   }
 
   void BaseDatabaseIO::finalize_file_open() const
   {
-    assert(exodusFilePtr >= 0);
+    assert(m_exodusFilePtr >= 0);
     // Check byte-size of integers stored on the database...
-    if ((ex_int64_status(exodusFilePtr) & EX_ALL_INT64_DB) != 0) {
+    if ((ex_int64_status(m_exodusFilePtr) & EX_ALL_INT64_DB) != 0) {
       if (myProcessor == 0) {
         fmt::print(Ioss::OUTPUT(),
                    "IOSS: Input database contains 8-byte integers. Setting Ioss to use "
                    "8-byte integers.\n");
       }
-      ex_set_int64_status(exodusFilePtr, EX_ALL_INT64_API);
+      ex_set_int64_status(m_exodusFilePtr, EX_ALL_INT64_API);
       set_int_byte_size_api(Ioss::USE_INT64_API);
     }
 
     // Check for maximum name length used on the input file.
-    int max_name_length = ex_inquire_int(exodusFilePtr, EX_INQ_DB_MAX_USED_NAME_LENGTH);
+    int max_name_length = ex_inquire_int(m_exodusFilePtr, EX_INQ_DB_MAX_USED_NAME_LENGTH);
     if (max_name_length > maximumNameLength) {
       maximumNameLength = max_name_length;
     }
 
-    ex_set_max_name_length(exodusFilePtr, maximumNameLength);
+    ex_set_max_name_length(m_exodusFilePtr, maximumNameLength);
   }
 
   bool BaseDatabaseIO::open_group__(const std::string &group_name)
@@ -388,9 +388,9 @@ namespace Ioex {
     int exoid = get_file_pointer();
 
     m_groupName = group_name;
-    ex_get_group_id(exoid, m_groupName.c_str(), &exodusFilePtr);
+    ex_get_group_id(exoid, m_groupName.c_str(), &m_exodusFilePtr);
 
-    if (exodusFilePtr < 0) {
+    if (m_exodusFilePtr < 0) {
       std::ostringstream errmsg;
       fmt::print(errmsg, "ERROR: Could not open group named '{}' in file '{}'.\n", m_groupName,
                  get_filename());
@@ -427,7 +427,7 @@ namespace Ioex {
         IOSS_ERROR(errmsg);
       }
       else {
-        exodusFilePtr = exoid;
+        m_exodusFilePtr = exoid;
         success       = true;
       }
     }
@@ -630,7 +630,7 @@ namespace Ioex {
 
     if (nblob > 0) {
       std::vector<ex_blob> blobs(nblob);
-      int max_name_length = ex_inquire_int(exodusFilePtr, EX_INQ_DB_MAX_USED_NAME_LENGTH);
+      int max_name_length = ex_inquire_int(m_exodusFilePtr, EX_INQ_DB_MAX_USED_NAME_LENGTH);
       for (auto &bl : blobs) {
         bl.name = new char[max_name_length + 1];
       }
@@ -2380,13 +2380,15 @@ namespace Ioex {
       }
       m_groupCount[EX_ELEM_BLOCK] = element_blocks.size();
 
-      // Set "global_entity_count" property on all blocks.
-      // Used to skip output on "globally" empty blocks.
-      Ioss::Int64Vector global_counts(element_counts.size());
-      util().global_count(element_counts, global_counts);
-      size_t idx = 0;
-      for (auto &element_block : element_blocks) {
-        element_block->property_add(Ioss::Property("global_entity_count", global_counts[idx++]));
+      if (isParallel) {
+	// Set "global_entity_count" property on all blocks.
+	// Used to skip output on "globally" empty blocks.
+	Ioss::Int64Vector global_counts(element_counts.size());
+	util().global_count(element_counts, global_counts);
+	size_t idx = 0;
+	for (auto &element_block : element_blocks) {
+	  element_block->property_add(Ioss::Property("global_entity_count", global_counts[idx++]));
+	}
       }
     }
 

packages/seacas/libraries/ioss/src/exodus/Ioex_BaseDatabaseIO.h

@@ -265,7 +265,10 @@ namespace Ioex {
 
     // Private member data...
   protected:
-    mutable int         exodusFilePtr{-1};
+    mutable int         m_exodusFilePtr{-1};
+    // If using links to file-per-state, the file pointer for "base" file.
+    mutable int         m_exodusBasePtr{-1}; 
+
     mutable std::string m_groupName;
 
     mutable EntityIdSet ids_;