EXODUS: Prototype to see if can speed up field metadata output

packages/seacas/libraries/exodus/include/exodusII.h

@@ -1045,6 +1045,8 @@ EXODUS_EXPORT int ex_get_blob(int exoid, struct ex_blob *blob);
 EXODUS_EXPORT int ex_put_blobs(int exoid, size_t count, const struct ex_blob *blobs);
 EXODUS_EXPORT int ex_get_blobs(int exoid, struct ex_blob *blobs);
 
+EXODUS_EXPORT int ex_put_multi_field_metadata(int exoid, const ex_field *field,
+                                              const int field_count);
 EXODUS_EXPORT int ex_put_field_metadata(int exoid, const ex_field field);
 EXODUS_EXPORT int ex_put_field_suffices(int exoid, const ex_field field, const char *suffices);
 EXODUS_EXPORT int ex_get_field_metadata(int exoid, ex_field *field);

packages/seacas/libraries/exodus/include/exodusII_int.h

@@ -686,28 +686,31 @@ typedef enum exi_element_type exi_element_type;
 struct exi_file_item
 {
   int          file_id;
-  nc_type      netcdf_type_code;
+  nc_type      netcdf_type_code; /**< NC_FLOAT or NC_DOUBLE */
   int          int64_status;
   int          maximum_name_length;
   int          time_varid; /* Store to avoid lookup each timestep */
   unsigned int assembly_count;
   unsigned int blob_count;
+  unsigned int compression_level;        /**< 0 (disabled) to 9 (maximum) compression level for
+                                            gzip, 4..32 and even for szip; NetCDF-4 only */
+  unsigned int persist_define_mode : 10; /**< Stay in define mode until exi_persist_leavedef is
+                                            called. Set by exi_persist_redef... */
   unsigned int
-      compression_algorithm : 2;      /**< GZIP/ZLIB, SZIP, more may be supported by NetCDF soon */
-  unsigned int compression_level : 6; /**< 0 (disabled) to 9 (maximum) compression level for
-                                         gzip, 4..32 and even for szip; NetCDF-4 only */
+      compression_algorithm : 4; /**< GZIP/ZLIB, SZIP, more may be supported by NetCDF soon */
+  unsigned int shuffle : 1;      /**< 1 true, 0 false */
   unsigned int user_compute_wordsize : 1; /**< 0 for 4 byte or 1 for 8 byte reals */
-  unsigned int shuffle : 1;               /**< 1 true, 0 false */
   unsigned int
       file_type : 2; /**< 0 - classic, 1 -- 64 bit classic, 2 --NetCDF4,  3 --NetCDF4 classic */
-  unsigned int          is_write : 1;    /**< for output or append */
-  unsigned int          is_parallel : 1; /**< 1 true, 0 false */
-  unsigned int          is_hdf5 : 1;     /**< 1 true, 0 false */
-  unsigned int          is_pnetcdf : 1;  /**< 1 true, 0 false */
-  unsigned int          has_nodes : 1;   /**< for input only at this time */
-  unsigned int          has_edges : 1;   /**< for input only at this time */
-  unsigned int          has_faces : 1;   /**< for input only at this time */
-  unsigned int          has_elems : 1;   /**< for input only at this time */
+  unsigned int          is_write : 1;       /**< for output or append */
+  unsigned int          is_parallel : 1;    /**< 1 true, 0 false */
+  unsigned int          is_hdf5 : 1;        /**< 1 true, 0 false */
+  unsigned int          is_pnetcdf : 1;     /**< 1 true, 0 false */
+  unsigned int          has_nodes : 1;      /**< for input only at this time */
+  unsigned int          has_edges : 1;      /**< for input only at this time */
+  unsigned int          has_faces : 1;      /**< for input only at this time */
+  unsigned int          has_elems : 1;      /**< for input only at this time */
+  unsigned int          in_define_mode : 1; /**< Is the file in nc define mode... */
   struct exi_file_item *next;
 };
 
@@ -797,8 +800,8 @@ extern struct exi_obj_stats *exoII_fam;
 extern struct exi_obj_stats *exoII_nm;
 
 EXODUS_EXPORT struct exi_file_item *exi_find_file_item(int exoid);
-struct exi_file_item *exi_add_file_item(int exoid);
-struct exi_obj_stats *exi_get_stat_ptr(int exoid, struct exi_obj_stats **obj_ptr);
+struct exi_file_item               *exi_add_file_item(int exoid);
+struct exi_obj_stats               *exi_get_stat_ptr(int exoid, struct exi_obj_stats **obj_ptr);
 
 EXODUS_EXPORT void exi_rm_stat_ptr(int exoid, struct exi_obj_stats **obj_ptr);
 
@@ -854,9 +857,14 @@ EXODUS_EXPORT int  exi_put_names(int exoid, int varid, size_t num_entity, char *
                                  ex_entity_type obj_type, const char *subtype, const char *routine);
 EXODUS_EXPORT void exi_trim(char *name);
 EXODUS_EXPORT void exi_update_max_name_length(int exoid, int length);
+EXODUS_EXPORT int  exi_redef(int exoid, const char *call_func);
+EXODUS_EXPORT int  exi_persist_redef(int exoid, const char *call_func);
 EXODUS_EXPORT int  exi_leavedef(int         exoid,    /* NemesisI file ID         */
                                 const char *call_rout /* Name of calling function */
  );
+EXODUS_EXPORT int  exi_persist_leavedef(int         exoid,    /* NemesisI file ID         */
+                                        const char *call_rout /* Name of calling function */
+ );
 
 EXODUS_EXPORT int exi_check_version(int run_version);
 EXODUS_EXPORT int exi_handle_mode(unsigned int my_mode, int is_parallel, int run_version);

packages/seacas/libraries/exodus/src/ex__put_homogenous_block_params.c

@@ -118,7 +118,7 @@ int exi_put_homogenous_block_params(int exoid, size_t block_count, const struct
 
   /* ======================================================================== */
   /* put netcdf file into define mode  */
-  if ((status = nc_redef(exoid)) != NC_NOERR) {
+  if ((status = exi_redef(exoid, __func__)) != NC_NOERR) {
     snprintf(errmsg, MAX_ERR_LENGTH, "ERROR: failed to place file id %d into define mode", exoid);
     ex_err_fn(exoid, __func__, errmsg, status);
     return (EX_FATAL);

packages/seacas/libraries/exodus/src/ex_add_attr.c

@@ -123,7 +123,7 @@ int ex_add_attr(int exoid, ex_entity_type obj_type, ex_entity_id obj_id, int64_t
 
   /* element attribute array */
   /* put netcdf file into define mode  */
-  if ((status = nc_redef(exoid)) != NC_NOERR) {
+  if ((status = exi_redef(exoid, __func__)) != NC_NOERR) {
     snprintf(errmsg, MAX_ERR_LENGTH, "ERROR: failed to place file id %d into define mode", exoid);
     ex_err_fn(exoid, __func__, errmsg, status);
     EX_FUNC_LEAVE(EX_FATAL);

packages/seacas/libraries/exodus/src/ex_close.c

@@ -1,5 +1,5 @@
 /*
- * Copyright(C) 1999-2020, 2022, 2023 National Technology & Engineering Solutions
+ * Copyright(C) 1999-2020, 2022, 2023, 2024 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.
  *
@@ -57,6 +57,11 @@ int ex_close(int exoid)
     EX_FUNC_LEAVE(EX_FATAL);
   }
 
+#ifndef NDEBUG
+  struct exi_file_item *file = exi_find_file_item(exoid);
+  assert(!file->in_define_mode && file->persist_define_mode == 0);
+#endif
+
   /*
    * NOTE: If using netcdf-4, exoid must refer to the root group.
    * Need to determine whether there are any groups and if so,

packages/seacas/libraries/exodus/src/ex_conv.c

@@ -249,6 +249,8 @@ int exi_conv_init(int exoid, int *comp_wordsize, int *io_wordsize, int file_word
   new_file->has_edges             = 1;
   new_file->has_faces             = 1;
   new_file->has_elems             = 1;
+  new_file->in_define_mode        = 0;
+  new_file->persist_define_mode   = 0;
   new_file->is_write              = is_write;
 
   new_file->next = file_list;

packages/seacas/libraries/exodus/src/ex_copy.c

@@ -1,5 +1,5 @@
 /*
- * Copyright(C) 1999-2023 National Technology & Engineering Solutions
+ * Copyright(C) 1999-2024 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.
  *
@@ -108,7 +108,7 @@ static int ex_copy_internal(int in_exoid, int out_exoid, int mesh_only)
   }
 
   /* put output file into define mode */
-  EXCHECK(nc_redef(out_exoid));
+  EXCHECK(exi_redef(out_exoid, __func__));
 
   /* copy global attributes */
   EXCHECK(cpy_global_att(in_exoid, out_exoid));

packages/seacas/libraries/exodus/src/ex_create_group.c

@@ -1,5 +1,5 @@
 /*
- * Copyright(C) 1999-2020, 2022 National Technology & Engineering Solutions
+ * Copyright(C) 1999-2020, 2022, 2024 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.
  *
@@ -26,7 +26,7 @@ int ex_create_group(int parent_id, const char *group_name)
     EX_FUNC_LEAVE(EX_FATAL);
   }
 
-  if ((status = nc_redef(parent_id)) != NC_NOERR) {
+  if ((status = exi_redef(parent_id, __func__)) != NC_NOERR) {
     snprintf(errmsg, MAX_ERR_LENGTH, "ERROR: failed to put file id %d into define mode", parent_id);
     ex_err_fn(exoid, __func__, errmsg, status);
     EX_FUNC_LEAVE(EX_FATAL);

packages/seacas/libraries/exodus/src/ex_get_field_metadata.c

@@ -122,11 +122,11 @@ int ex_get_field_metadata(int exoid, ex_field *field)
   EX_FUNC_ENTER();
 
   int varid;
-  int att_count = exi_get_attribute_count(exoid, field->entity_type, field->entity_id, &varid);
+  int att_count = exi_get_attribute_count(exoid, field[0].entity_type, field[0].entity_id, &varid);
   if (att_count < 0) {
     char errmsg[MAX_ERR_LENGTH];
     snprintf(errmsg, MAX_ERR_LENGTH, "ERROR: Negative attribute count (%d) on %s with id %" PRId64,
-             att_count, ex_name_of_object(field->entity_type), field->entity_id);
+             att_count, ex_name_of_object(field[0].entity_type), field[0].entity_id);
     ex_err_fn(exoid, __func__, errmsg, EX_INTERNAL);
     EX_FUNC_LEAVE(EX_FATAL);
   }
@@ -140,7 +140,7 @@ int ex_get_field_metadata(int exoid, ex_field *field)
       char errmsg[MAX_ERR_LENGTH];
       snprintf(errmsg, MAX_ERR_LENGTH,
                "ERROR: failed to get attribute named %s on %s with id %" PRId64, attr_name,
-               ex_name_of_object(field->entity_type), field->entity_id);
+               ex_name_of_object(field[0].entity_type), field[0].entity_id);
       ex_err_fn(exoid, __func__, errmsg, status);
       EX_FUNC_LEAVE(EX_FATAL);
     }
@@ -165,6 +165,10 @@ int ex_get_field_metadata(int exoid, ex_field *field)
       if (found == -1) {
         which = count;
         strcpy(field[count].name, fld_name);
+	/* Set default separator type... */
+	field[count].component_separator[0] = '_';
+	field[count].component_separator[1] = '\0';
+
         count++;
       }
 
@@ -174,7 +178,7 @@ int ex_get_field_metadata(int exoid, ex_field *field)
         char errmsg[MAX_ERR_LENGTH];
         snprintf(errmsg, MAX_ERR_LENGTH,
                  "ERROR: failed to get parameters for attribute named %s on %s with id %" PRId64,
-                 attr_name, ex_name_of_object(field->entity_type), field->entity_id);
+                 attr_name, ex_name_of_object(field[0].entity_type), field[0].entity_id);
         ex_err_fn(exoid, __func__, errmsg, status);
         EX_FUNC_LEAVE(EX_FATAL);
       }
@@ -205,7 +209,7 @@ int ex_get_field_metadata(int exoid, ex_field *field)
         snprintf(
             errmsg, MAX_ERR_LENGTH,
             "ERROR: Invalid field metadata attribute type %s on field %s on %s with id %" PRId64,
-            fld_type, fld_name, ex_name_of_object(field->entity_type), field->entity_id);
+            fld_type, fld_name, ex_name_of_object(field[0].entity_type), field[0].entity_id);
         ex_err_fn(exoid, __func__, errmsg, status);
         EX_FUNC_LEAVE(EX_FATAL);
       }
@@ -214,7 +218,7 @@ int ex_get_field_metadata(int exoid, ex_field *field)
         snprintf(errmsg, MAX_ERR_LENGTH,
                  "ERROR: failed to read field metadata attribute type %s on field %s on %s with id "
                  "%" PRId64,
-                 fld_type, fld_name, ex_name_of_object(field->entity_type), field->entity_id);
+                 fld_type, fld_name, ex_name_of_object(field[0].entity_type), field[0].entity_id);
         ex_err_fn(exoid, __func__, errmsg, status);
         EX_FUNC_LEAVE(EX_FATAL);
       }

packages/seacas/libraries/exodus/src/ex_open.c

@@ -298,7 +298,7 @@ int ex_open_int(const char *path, int mode, int *comp_ws, int *io_ws, float *ver
     int    dim_str_name = 0;
     int    stat_dim     = nc_inq_dimid(exoid, DIM_STR_NAME, &dim_str_name);
     if (stat_att != NC_NOERR || stat_dim != NC_NOERR) {
-      if ((status = nc_redef(exoid)) != NC_NOERR) {
+      if ((status = exi_redef(exoid, __func__)) != NC_NOERR) {
         snprintf(errmsg, MAX_ERR_LENGTH,
                  "ERROR: failed to place file id %d named %s into define mode", exoid, canon_path);
         ex_err_fn(exoid, __func__, errmsg, status);

packages/seacas/libraries/exodus/src/ex_open_par.c

@@ -313,7 +313,7 @@ int ex_open_par_int(const char *path, int mode, int *comp_ws, int *io_ws, float
   if (mode & EX_WRITE) { /* Appending */
     /* turn off automatic filling of netCDF variables */
     if (is_pnetcdf) {
-      if ((status = nc_redef(exoid)) != NC_NOERR) {
+      if ((status = exi_redef(exoid, __func__)) != NC_NOERR) {
         snprintf(errmsg, MAX_ERR_LENGTH, "ERROR: failed to put file id %d into define mode", exoid);
         ex_err_fn(exoid, __func__, errmsg, status);
         free(canon_path);
@@ -335,7 +335,7 @@ int ex_open_par_int(const char *path, int mode, int *comp_ws, int *io_ws, float
     int     stat_dim = nc_inq_dimid(exoid, DIM_STR_NAME, &dim_str_name);
     if (stat_att != NC_NOERR || stat_dim != NC_NOERR) {
       if (!in_redef) {
-        if ((status = nc_redef(exoid)) != NC_NOERR) {
+        if ((status = exi_redef(exoid, __func__)) != NC_NOERR) {
           snprintf(errmsg, MAX_ERR_LENGTH, "ERROR: failed to put file id %d into define mode",
                    exoid);
           ex_err_fn(exoid, __func__, errmsg, status);

packages/seacas/libraries/exodus/src/ex_put_all_var_param_ext.c

@@ -144,7 +144,7 @@ int ex_put_all_var_param_ext(int exoid, const ex_var_params *vp)
                     EX_ELEM_SET, VAR_ELS_STAT, elset_stat);
 
   /* put file into define mode  */
-  if ((status = nc_redef(exoid)) != NC_NOERR) {
+  if ((status = exi_redef(exoid, __func__)) != NC_NOERR) {
     snprintf(errmsg, MAX_ERR_LENGTH, "ERROR: failed to put file id %d into define mode", exoid);
     ex_err_fn(exoid, __func__, errmsg, status);
     goto error_ret;

packages/seacas/libraries/exodus/src/ex_put_assemblies.c

@@ -45,7 +45,7 @@ int ex_put_assemblies(int exoid, size_t count, const struct ex_assembly *assembl
       /* Assembly has not already been defined */
       /* put netcdf file into define mode  */
       if (!in_define) {
-        if ((status = nc_redef(exoid)) != NC_NOERR) {
+        if ((status = exi_redef(exoid, __func__)) != NC_NOERR) {
           snprintf(errmsg, MAX_ERR_LENGTH, "ERROR: failed to put file id %d into define mode",
                    exoid);
           ex_err_fn(exoid, __func__, errmsg, status);

packages/seacas/libraries/exodus/src/ex_put_attr_param.c

@@ -149,7 +149,7 @@ int ex_put_attr_param(int exoid, ex_entity_type obj_type, ex_entity_id obj_id, i
   }
 
   /* put netcdf file into define mode  */
-  if ((status = nc_redef(exoid)) != NC_NOERR) {
+  if ((status = exi_redef(exoid, __func__)) != NC_NOERR) {
     snprintf(errmsg, MAX_ERR_LENGTH, "ERROR: failed to place file id %d into define mode", exoid);
     ex_err_fn(exoid, __func__, errmsg, status);
     EX_FUNC_LEAVE(EX_FATAL);

packages/seacas/libraries/exodus/src/ex_put_attribute.c

@@ -38,7 +38,7 @@ int ex_put_double_attribute(int exoid, ex_entity_type obj_type, ex_entity_id id,
   }
 
   /* put netcdf file into define mode  */
-  if ((status = nc_redef(exoid)) != NC_NOERR) {
+  if ((status = exi_redef(exoid, __func__)) != NC_NOERR) {
     snprintf(errmsg, MAX_ERR_LENGTH, "ERROR: failed to put file id %d into define mode", exoid);
     ex_err_fn(exoid, __func__, errmsg, status);
     EX_FUNC_LEAVE(EX_FATAL);
@@ -84,7 +84,7 @@ int ex_put_integer_attribute(int exoid, ex_entity_type obj_type, ex_entity_id id
   }
 
   /* put netcdf file into define mode  */
-  if ((status = nc_redef(exoid)) != NC_NOERR) {
+  if ((status = exi_redef(exoid, __func__)) != NC_NOERR) {
     snprintf(errmsg, MAX_ERR_LENGTH, "ERROR: failed to put file id %d into define mode", exoid);
     ex_err_fn(exoid, __func__, errmsg, status);
     EX_FUNC_LEAVE(EX_FATAL);
@@ -137,7 +137,7 @@ int ex_put_text_attribute(int exoid, ex_entity_type obj_type, ex_entity_id id, c
   }
 
   /* put netcdf file into define mode  */
-  if ((status = nc_redef(exoid)) != NC_NOERR) {
+  if ((status = exi_redef(exoid, __func__)) != NC_NOERR) {
     snprintf(errmsg, MAX_ERR_LENGTH, "ERROR: failed to put file id %d into define mode", exoid);
     ex_err_fn(exoid, __func__, errmsg, status);
     EX_FUNC_LEAVE(EX_FATAL);

packages/seacas/libraries/exodus/src/ex_put_blobs.c

@@ -29,7 +29,7 @@ int ex_put_blobs(int exoid, size_t count, const struct ex_blob *blobs)
 
   int *entlst_id = (int *)calloc(count, sizeof(int));
 
-  if ((status = nc_redef(exoid)) != NC_NOERR) {
+  if ((status = exi_redef(exoid, __func__)) != NC_NOERR) {
     snprintf(errmsg, MAX_ERR_LENGTH, "ERROR: failed to put file id %d into define mode", exoid);
     ex_err_fn(exoid, __func__, errmsg, status);
     free(entlst_id);

packages/seacas/libraries/exodus/src/ex_put_block_params.c

@@ -253,7 +253,7 @@ int ex_put_block_params(int exoid, size_t block_count, const struct ex_block *bl
   }
 
   /* put netcdf file into define mode  */
-  if ((status = nc_redef(exoid)) != NC_NOERR) {
+  if ((status = exi_redef(exoid, __func__)) != NC_NOERR) {
     snprintf(errmsg, MAX_ERR_LENGTH, "ERROR: failed to place file id %d into define mode", exoid);
     ex_err_fn(exoid, __func__, errmsg, status);
     free(blocks_to_define);

packages/seacas/libraries/exodus/src/ex_put_cmap_params.c

@@ -87,7 +87,7 @@ int ex_put_cmap_params(int exoid, const void_int *node_cmap_ids,
 
   /* Put NetCDF file into define mode */
   int status;
-  if ((status = nc_redef(exoid)) != NC_NOERR) {
+  if ((status = exi_redef(exoid, __func__)) != NC_NOERR) {
     snprintf(errmsg, MAX_ERR_LENGTH, "ERROR: failed to file ID %d into define mode", exoid);
     ex_err_fn(exoid, __func__, errmsg, status);
     EX_FUNC_LEAVE(EX_FATAL);

packages/seacas/libraries/exodus/src/ex_put_cmap_params_cc.c

@@ -215,7 +215,7 @@ file ID %d",
   } /* "if (num_e_comm_maps >0)" */
 
   /* Put NetCDF file into define mode */
-  if ((status = nc_redef(exoid)) != NC_NOERR) {
+  if ((status = exi_redef(exoid, __func__)) != NC_NOERR) {
     snprintf(errmsg, MAX_ERR_LENGTH, "ERROR: failed to put file ID %d into define mode", exoid);
     ex_err_fn(exoid, __func__, errmsg, status);
     EX_FUNC_LEAVE(EX_FATAL);

packages/seacas/libraries/exodus/src/ex_put_concat_all_blocks.c

@@ -205,7 +205,7 @@ int ex_put_concat_all_blocks(int exoid, const ex_block_params *param)
     EX_FUNC_LEAVE(EX_NOERR);
   }
   /* put netcdf file into define mode  */
-  if ((status = nc_redef(exoid)) != NC_NOERR) {
+  if ((status = exi_redef(exoid, __func__)) != NC_NOERR) {
     snprintf(errmsg, MAX_ERR_LENGTH, "ERROR: failed to place file id %d into define mode", exoid);
     ex_err_fn(exoid, __func__, errmsg, status);
     EX_FUNC_LEAVE(EX_FATAL);

packages/seacas/libraries/exodus/src/ex_put_concat_elem_block.c

@@ -144,7 +144,7 @@ int ex_put_concat_elem_block(int exoid, const void_int *elem_blk_id, char *const
   }
 
   /* put netcdf file into define mode  */
-  if ((status = nc_redef(exoid)) != NC_NOERR) {
+  if ((status = exi_redef(exoid, __func__)) != NC_NOERR) {
     snprintf(errmsg, MAX_ERR_LENGTH, "ERROR: failed to place file id %d into define mode", exoid);
     ex_err_fn(exoid, __func__, errmsg, status);
     free(eb_array);

packages/seacas/libraries/exodus/src/ex_put_concat_sets.c

@@ -171,7 +171,7 @@ int ex_put_concat_sets(int exoid, ex_entity_type set_type, const struct ex_set_s
   }
 
   /* put netcdf file into define mode  */
-  if ((status = nc_redef(exoid)) != NC_NOERR) {
+  if ((status = exi_redef(exoid, __func__)) != NC_NOERR) {
     snprintf(errmsg, MAX_ERR_LENGTH, "ERROR: failed to put file id %d into define mode", exoid);
     ex_err_fn(exoid, __func__, errmsg, status);
     free(set_stat);

packages/seacas/libraries/exodus/src/ex_put_coordinate_frames.c

@@ -57,7 +57,7 @@ int ex_put_coordinate_frames(int exoid, int nframes, const void_int *cf_ids,
   /* make the definitions */
   /* go into define mode. define num_frames, num_frames9 */
   int status;
-  if ((status = nc_redef(exoid)) != NC_NOERR) {
+  if ((status = exi_redef(exoid, __func__)) != NC_NOERR) {
     snprintf(errmsg, MAX_ERR_LENGTH, "ERROR: failed to place file id %d into define mode", exoid);
     ex_err_fn(exoid, __func__, errmsg, status);
     EX_FUNC_LEAVE(EX_FATAL);