Documentation/release/dev/updated-seacas-2025-02-07.md

+## Update exodusII and Ioss to be based on SEACAS 2025-02-27
+
+Update `exodusII` and `Ioss` third party libraries to be based
+on [SEACAS 2025-02-27](https://github.com/sandialabs/seacas/releases/tag/v2025-02-27).

ThirdParty/exodusII/vtkexodusII/include/exodusII.h

 /*
- * Copyright(C) 1999-2024 National Technology & Engineering Solutions
+ * Copyright(C) 1999-2025 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.
  *
@@ -59,12 +59,12 @@
 #endif
 
 /* EXODUS version number */
-#define EXODUS_VERSION       "9.00"
+#define EXODUS_VERSION       "9.04"
 #define EXODUS_VERSION_MAJOR 9
-#define EXODUS_VERSION_MINOR 0
-#define EXODUS_RELEASE_DATE  "May 30, 2024"
+#define EXODUS_VERSION_MINOR 4
+#define EXODUS_RELEASE_DATE  "November 5, 2024"
 
-#define EX_API_VERS       9.00f
+#define EX_API_VERS       9.04f
 #define EX_API_VERS_NODOT (100 * EXODUS_VERSION_MAJOR + EXODUS_VERSION_MINOR)
 #define EX_VERS           EX_API_VERS
 
@@ -219,6 +219,7 @@ enum ex_inquiry {
   EX_INQ_NUM_ELEM_SET_VAR    = 69, /**< number of element set variables */
   EX_INQ_NUM_SIDE_SET_VAR    = 70, /**< number of sideset variables */
   EX_INQ_NUM_GLOBAL_VAR      = 71, /**< number of global variables */
+  EX_INQ_FILE_FORMAT         = 72, /**< netCDF file format */
   EX_INQ_INVALID             = -1
 };
 
@@ -246,9 +247,11 @@ NetCDF-4.?.? and later
 enum ex_option_type {
   EX_OPT_MAX_NAME_LENGTH =
       1, /**< Maximum length of names that will be returned/passed via api call. */
-  EX_OPT_COMPRESSION_TYPE,    /**<  Not currently used; default is gzip */
-  EX_OPT_COMPRESSION_LEVEL,   /**<  In the range [0..9]. A value of 0 indicates no compression */
+  EX_OPT_COMPRESSION_TYPE,    /**<  Default is gzip */
+  EX_OPT_COMPRESSION_LEVEL,   /**<  Range depends on compression type. */
   EX_OPT_COMPRESSION_SHUFFLE, /**<  1 if enabled, 0 if disabled */
+  EX_OPT_QUANTIZE_NSD,        /**< if > 0, Number of significant digits to retain in lossy quantize
+                                 compression */
   EX_OPT_INTEGER_SIZE_API, /**<  4 or 8 indicating byte size of integers used in api functions. */
   EX_OPT_INTEGER_SIZE_DB,  /**<  Query only, returns 4 or 8 indicating byte size of integers stored
                              on  the database. */
@@ -259,6 +262,8 @@ enum ex_compression_type {
   EX_COMPRESS_ZLIB = 1, /**< Use ZLIB-based compression (if available) */
   EX_COMPRESS_GZIP = 1, /**< Same as ZLIB, but typical alias used */
   EX_COMPRESS_SZIP,     /**< Use SZIP-based compression (if available) */
+  EX_COMPRESS_ZSTD,     /**< Use ZStandard compression (if available) */
+  EX_COMPRESS_BZ2,      /**< Use BZ2 / Bzip2 compression (if available) */
 };
 typedef enum ex_compression_type ex_compression_type;
 /** @}*/
@@ -345,13 +350,13 @@ typedef struct ex_basis
   /*
    clang-format off
    *
-   * subc_dim: dimension of the subcell associated with the specified DoF ordinal 
+   * subc_dim: dimension of the subcell associated with the specified DoF ordinal
    *      -- 0 node, 1 edge, 2 face, 3 volume [Range: 0..3]
    * subc_ordinal: ordinal of the subcell relative to its parent cell
-   *      -- 0..n for each ordinal with the same subc dim [Range: <= DoF ordinal] 
-   * subc_dof_ordinal: ordinal of the DoF relative to the subcell 
-   * subc_num_dof: cardinality of the DoF set associated with this subcell. 
-   * xi, eta, mu (ξ, η, ζ): Parametric coordinate location of the DoF 
+   *      -- 0..n for each ordinal with the same subc dim [Range: <= DoF ordinal]
+   * subc_dof_ordinal: ordinal of the DoF relative to the subcell
+   * subc_num_dof: cardinality of the DoF set associated with this subcell.
+   * xi, eta, mu (ξ, η, ζ): Parametric coordinate location of the DoF
    *      -- (Only first ndim values are valid)
    *
    clang-format on
@@ -971,7 +976,7 @@ EXODUS_EXPORT int ex_get_block(int exoid, ex_entity_type blk_type, ex_entity_id
 /*  Read Edge Face or Element Block Parameters */
 EXODUS_EXPORT int ex_get_block_param(int exoid, ex_block *block);
 
-EXODUS_EXPORT int ex_put_block_param(int exoid, const ex_block block);
+EXODUS_EXPORT int ex_put_block_param(int exoid, ex_block block);
 
 EXODUS_EXPORT int ex_get_block_params(int exoid, size_t block_count, struct ex_block **blocks);
 
@@ -1037,34 +1042,35 @@ EXODUS_EXPORT int ex_put_attr_names(int exoid, ex_entity_type blk_type, ex_entit
 EXODUS_EXPORT int ex_get_attr_names(int exoid, ex_entity_type obj_type, ex_entity_id obj_id,
                                     char **names);
 
-EXODUS_EXPORT int ex_put_assembly(int exoid, const struct ex_assembly assembly);
+EXODUS_EXPORT int ex_put_assembly(int exoid, struct ex_assembly assembly);
 EXODUS_EXPORT int ex_get_assembly(int exoid, struct ex_assembly *assembly);
 
 EXODUS_EXPORT int ex_put_assemblies(int exoid, size_t count, const struct ex_assembly *assemblies);
 EXODUS_EXPORT int ex_get_assemblies(int exoid, struct ex_assembly *assemblies);
 
-EXODUS_EXPORT int ex_put_blob(int exoid, const struct ex_blob blob);
+EXODUS_EXPORT int ex_put_blob(int exoid, struct ex_blob blob);
 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_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_put_multi_field_metadata(int exoid, const ex_field *field, int field_count);
+EXODUS_EXPORT int ex_put_field_metadata(int exoid, ex_field field);
+EXODUS_EXPORT int ex_put_field_suffices(int exoid, ex_field field, const char *suffices);
 EXODUS_EXPORT int ex_get_field_metadata(int exoid, ex_field *field);
 EXODUS_EXPORT int ex_get_field_metadata_count(int exoid, ex_entity_type obj_type, ex_entity_id id);
-EXODUS_EXPORT int ex_get_field_suffices(int exoid, const ex_field field, char *suffices);
+EXODUS_EXPORT int ex_get_field_suffices(int exoid, ex_field field, char *suffices);
 
 EXODUS_EXPORT int ex_get_basis_count(int exoid);
 EXODUS_EXPORT int ex_get_basis(int exoid, ex_basis **pbasis, int *num_basis);
-EXODUS_EXPORT int ex_put_basis(int exoid, const ex_basis basis);
+EXODUS_EXPORT int ex_put_basis(int exoid, ex_basis basis);
 
 EXODUS_EXPORT int ex_get_quadrature_count(int exoid);
 EXODUS_EXPORT int ex_get_quadrature(int exoid, ex_quadrature **pquad, int *num_quad);
-EXODUS_EXPORT int ex_put_quadrature(int exoid, const ex_quadrature quad);
+EXODUS_EXPORT int ex_put_quadrature(int exoid, ex_quadrature quad);
 
 /*  Write arbitrary integer, double, or text attributes on an entity */
-EXODUS_EXPORT int ex_put_attribute(int exoid, const ex_attribute attributes);
+EXODUS_EXPORT int ex_put_attribute(int exoid, ex_attribute attributes);
 EXODUS_EXPORT int ex_put_attributes(int exoid, size_t attr_count, const ex_attribute *attributes);
 
 EXODUS_EXPORT int ex_put_double_attribute(int exoid, ex_entity_type obj_type, ex_entity_id id,
@@ -1318,10 +1324,10 @@ EXODUS_EXPORT int ex_initialize_quadrature_struct(ex_quadrature *quad, size_t nu
 EXODUS_EXPORT const char *ex_component_field_name(ex_field *field,
                                                   int       component[EX_MAX_FIELD_NESTING]);
 EXODUS_EXPORT const char *ex_field_component_suffix(ex_field *field, int nest_level, int component);
-EXODUS_EXPORT int         ex_field_cardinality(const ex_field_type field_type);
-EXODUS_EXPORT const char *ex_field_type_name(const ex_field_type field_type);
+EXODUS_EXPORT int         ex_field_cardinality(ex_field_type field_type);
+EXODUS_EXPORT const char *ex_field_type_name(ex_field_type field_type);
 EXODUS_EXPORT ex_field_type ex_string_to_field_type_enum(const char *field_name);
-EXODUS_EXPORT const char   *ex_field_type_enum_to_string(const ex_field_type field_type);
+EXODUS_EXPORT const char   *ex_field_type_enum_to_string(ex_field_type field_type);
 
 /*! @} */
 
@@ -1958,6 +1964,8 @@ enum ex_error_return_code {
   EX_NULLENTITY    = -1006, /**< null entity found                        */
   EX_NOENTITY      = -1007, /**< no entities of that type on database    */
   EX_NOTFOUND      = -1008, /**< could not find requested variable on database */
+  EX_INTSIZEMISMATCH =
+      -1009, /**< integer sizes do not match on input/output databases in ex_copy  */
 
   EX_FATAL = -1, /**< fatal error flag def                     */
   EX_NOERR = 0,  /**< no error flag def                        */

ThirdParty/exodusII/vtkexodusII/include/exodusII_int.h

@@ -28,6 +28,18 @@
 #endif
 #endif
 
+#if NC_HAS_ZSTD == 1 || NC_HAS_BZ2
+#include "netcdf_filter.h"
+#endif
+
+#if !defined NC_FillValue
+#if defined _FillValue
+#define NC_FillValue _FillValue
+#else
+#define NC_FillValue "_FillValue"
+#endif
+#endif
+
 #if defined(_WIN32) && defined(_MSC_VER) && _MSC_VER < 1900
 #define PRId64 "I64d"
 #else
@@ -687,29 +699,35 @@ typedef enum exi_element_type exi_element_type;
 
 struct exi_file_item
 {
-  int          file_id;
-  nc_type      netcdf_type_code;
-  int          int64_status;
-  int          maximum_name_length;
-  int          time_varid; /* Store to avoid lookup each timestep */
+  int     file_id;
+  nc_type netcdf_type_code;
+  int     int64_status;
+  int     maximum_name_length;
+  int     time_varid;        /* Store to avoid lookup each timestep */
+  int     compression_level; /**< 0 (disabled) to 9 (maximum) compression level for
+                                gzip, 4..32 and even for szip; -131072..22 for zstd, NetCDF-4 only */
   unsigned int assembly_count;
   unsigned int blob_count;
+
+  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 quantize_nsd : 4; /**< 0 (disabled) to 15 (maximum) number of significant digits
+                                    retained for lossy quanitzation compression */
+  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;
 };
 
@@ -799,8 +817,8 @@ 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);
 
@@ -856,9 +874,14 @@ 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);

ThirdParty/exodusII/vtkexodusII/include/vtk_exodusII_mangle.h

@@ -4,7 +4,7 @@
 /**
  * Generated using:
  *
- * nm -g lib/libvtkexodusII-9.3.so |   grep -e ' [TDRSB] ' |\
+ * nm -g lib/libvtkexodusII-9.4.so |   grep -e ' [TDRSB] ' |\
  *   cut -d' ' -f3 | grep -v -e '^_init$' -e '^_fini$' -e '^_edata$' -e '^__bss_start$' -e 'vtkexodusII_' | \
  *   sort | sed -e 's/\(.*\)/#define \1 vtkexodusII_\1/' > /tmp/vtk_exodusII_mangle.h
  */
@@ -232,6 +232,8 @@
 #define ex_inquire_int vtkexodusII_ex_inquire_int
 #define ex_int64_status vtkexodusII_ex_int64_status
 #define ex_int_write_conn vtkexodusII_ex_int_write_conn
+#define exi_persist_leavedef vtkexodusII_exi_persist_leavedef
+#define exi_persist_redef vtkexodusII_exi_persist_redef
 #define exi_populate_header vtkexodusII_exi_populate_header
 #define exi_pthread_first_thread_init vtkexodusII_exi_pthread_first_thread_init
 #define exi_put_assembly_name vtkexodusII_exi_put_assembly_name
@@ -244,6 +246,7 @@
 #define exi_put_partial_nodal_var vtkexodusII_exi_put_partial_nodal_var
 #define exi_put_quad_attribute vtkexodusII_exi_put_quad_attribute
 #define exi_put_type_attribute vtkexodusII_exi_put_type_attribute
+#define exi_redef vtkexodusII_exi_redef
 #define exi_reset_error_status vtkexodusII_exi_reset_error_status
 #define exi_rm_file_item vtkexodusII_exi_rm_file_item
 #define exi_rm_stat_ptr vtkexodusII_exi_rm_stat_ptr
@@ -321,6 +324,7 @@
 #define ex_put_loadbal_param_cc vtkexodusII_ex_put_loadbal_param_cc
 #define ex_put_map vtkexodusII_ex_put_map
 #define ex_put_map_param vtkexodusII_ex_put_map_param
+#define ex_put_multi_field_metadata vtkexodusII_ex_put_multi_field_metadata
 #define ex_put_name vtkexodusII_ex_put_name
 #define ex_put_names vtkexodusII_ex_put_names
 #define ex_put_n_attr vtkexodusII_ex_put_n_attr

ThirdParty/exodusII/vtkexodusII/src/deprecated/ex_get_var_param.c

 /*
- * Copyright(C) 1999-2020 National Technology & Engineering Solutions
+ * Copyright(C) 1999-2020, 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.
  *
@@ -36,5 +36,5 @@ int ex_get_var_param(int exoid, const char *var_type, int *num_vars)
 {
   ex_entity_type obj_type;
   obj_type = ex_var_type_to_ex_entity_type(*var_type);
-  return (ex_get_variable_param(exoid, obj_type, num_vars));
+  return ex_get_variable_param(exoid, obj_type, num_vars);
 }

ThirdParty/exodusII/vtkexodusII/src/deprecated/ex_put_var_param.c

 /*
- * Copyright(C) 1999-2020 National Technology & Engineering Solutions
+ * Copyright(C) 1999-2020, 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.
  *
@@ -39,5 +39,5 @@ int ex_put_var_param(int exoid, const char *var_type, int num_vars)
 {
   ex_entity_type obj_type;
   obj_type = ex_var_type_to_ex_entity_type(*var_type);
-  return (ex_put_variable_param(exoid, obj_type, num_vars));
+  return ex_put_variable_param(exoid, obj_type, num_vars);
 }

ThirdParty/exodusII/vtkexodusII/src/ex__put_homogenous_block_params.c

 /*
- * 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.
  *
@@ -47,7 +47,7 @@ int exi_put_homogenous_block_params(int exoid, size_t block_count, const struct
              "ERROR: Bad block type (%d) specified for all blocks file id %d", blocks[0].type,
              exoid);
     ex_err_fn(exoid, __func__, errmsg, EX_BADPARAM);
-    return (EX_FATAL);
+    return EX_FATAL;
   }
 
   { /* Output ids for this block */
@@ -58,7 +58,7 @@ int exi_put_homogenous_block_params(int exoid, size_t block_count, const struct
                "array in file id %d",
                exoid);
       ex_err_fn(exoid, __func__, errmsg, EX_MEMFAIL);
-      return (EX_FATAL);
+      return EX_FATAL;
     }
 
     for (size_t i = 0; i < block_count; i++) {
@@ -70,7 +70,7 @@ int exi_put_homogenous_block_params(int exoid, size_t block_count, const struct
                ex_name_of_object(blocks[0].type), exoid);
       ex_err_fn(exoid, __func__, errmsg, status);
       free(ids);
-      return (EX_FATAL);
+      return EX_FATAL;
     }
 
     if ((status = nc_put_var_longlong(exoid, varid, ids)) != NC_NOERR) {
@@ -78,7 +78,7 @@ int exi_put_homogenous_block_params(int exoid, size_t block_count, const struct
                ex_name_of_object(blocks[0].type), exoid);
       ex_err_fn(exoid, __func__, errmsg, status);
       free(ids);
-      return (EX_FATAL);
+      return EX_FATAL;
     }
     free(ids);
   }
@@ -91,7 +91,7 @@ int exi_put_homogenous_block_params(int exoid, size_t block_count, const struct
                "array in file id %d",
                exoid);
       ex_err_fn(exoid, __func__, errmsg, EX_MEMFAIL);
-      return (EX_FATAL);
+      return EX_FATAL;
     }
 
     for (size_t i = 0; i < block_count; i++) {
@@ -103,7 +103,7 @@ int exi_put_homogenous_block_params(int exoid, size_t block_count, const struct
                ex_name_of_object(blocks[0].type), exoid);
       ex_err_fn(exoid, __func__, errmsg, status);
       free(stat);
-      return (EX_FATAL);
+      return EX_FATAL;
     }
 
     if ((status = nc_put_var_int(exoid, varid, stat)) != NC_NOERR) {
@@ -111,17 +111,17 @@ int exi_put_homogenous_block_params(int exoid, size_t block_count, const struct
                ex_name_of_object(blocks[0].type), exoid);
       ex_err_fn(exoid, __func__, errmsg, status);
       free(stat);
-      return (EX_FATAL);
+      return EX_FATAL;
     }
     free(stat);
   }
 
   /* ======================================================================== */
   /* 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);
+    return EX_FATAL;
   }
 
   /* inquire previously defined dimensions  */
@@ -348,7 +348,7 @@ int exi_put_homogenous_block_params(int exoid, size_t block_count, const struct
   if ((status = exi_leavedef(exoid, __func__)) != NC_NOERR) {
     snprintf(errmsg, MAX_ERR_LENGTH, "ERROR: failed to exit define mode in file id %d", exoid);
     ex_err_fn(exoid, __func__, errmsg, status);
-    return (EX_FATAL);
+    return EX_FATAL;
   }
 
   /* ======================================================================== */
@@ -357,7 +357,7 @@ int exi_put_homogenous_block_params(int exoid, size_t block_count, const struct
     case EX_EDGE_BLOCK: vblkids = VAR_ID_ED_BLK; break;
     case EX_FACE_BLOCK: vblkids = VAR_ID_FA_BLK; break;
     case EX_ELEM_BLOCK: vblkids = VAR_ID_EL_BLK; break;
-    default: return (EX_FATAL); /* should have been handled earlier; quiet compiler here */
+    default: return EX_FATAL; /* should have been handled earlier; quiet compiler here */
     }
 
     int att_name_varid = -1;
@@ -375,17 +375,17 @@ int exi_put_homogenous_block_params(int exoid, size_t block_count, const struct
       start[1] = 0;
       count[1] = strlen(text) + 1;
 
-      for (size_t j = 0; j < blocks[i].num_attribute; j++) {
+      for (int64_t j = 0; j < blocks[i].num_attribute; j++) {
         start[0] = j;
         nc_put_vara_text(exoid, att_name_varid, start, count, text);
       }
     }
   }
 
-  return (EX_NOERR);
+  return EX_NOERR;
 
 /* Fatal error: exit definition mode and return */
 error_ret:
   exi_leavedef(exoid, __func__);
-  return (EX_FATAL);
+  return EX_FATAL;
 }

ThirdParty/exodusII/vtkexodusII/src/ex__put_nodal_var_multi_time.c

 /*
- * Copyright(C) 1999-2020, 2023 National Technology & Engineering Solutions
+ * Copyright(C) 1999-2020, 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.
  *
@@ -88,7 +88,7 @@ int exi_put_nodal_var_time(int exoid, int nodal_var_index, int64_t num_nodes, in
     snprintf(errmsg, MAX_ERR_LENGTH, "Warning: could not find nodal variable %d in file id %d",
              nodal_var_index, exoid);
     ex_err_fn(exoid, __func__, errmsg, status);
-    return (EX_WARN);
+    return EX_WARN;
   }
   start[0] = --beg_time_step;
   start[1] = 0;
@@ -106,7 +106,7 @@ int exi_put_nodal_var_time(int exoid, int nodal_var_index, int64_t num_nodes, in
   if (status != NC_NOERR) {
     snprintf(errmsg, MAX_ERR_LENGTH, "ERROR: failed to store nodal variables in file id %d", exoid);
     ex_err_fn(exoid, __func__, errmsg, status);
-    return (EX_FATAL);
+    return EX_FATAL;
   }
-  return (EX_NOERR);
+  return EX_NOERR;
 }

ThirdParty/exodusII/vtkexodusII/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);

ThirdParty/exodusII/vtkexodusII/src/ex_close.c

 /*
- * 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,
@@ -66,16 +71,16 @@ int ex_close(int exoid)
   /*
    * Get exoid of root group
    */
-  exoid &= EX_FILE_ID_MASK;
 
   if ((status1 = nc_sync(exoid)) != NC_NOERR) {
     snprintf(errmsg, MAX_ERR_LENGTH, "ERROR: failed to update file id %d", exoid);
     ex_err_fn(exoid, __func__, errmsg, status1);
   }
 
-  if ((status2 = nc_close(exoid)) != NC_NOERR) {
-    snprintf(errmsg, MAX_ERR_LENGTH, "ERROR: failed to close file id %d", exoid);
-    ex_err_fn(exoid, __func__, errmsg, status2);
+  int root_id = exoid & EX_FILE_ID_MASK;
+  if ((status2 = nc_close(root_id)) != NC_NOERR) {
+    snprintf(errmsg, MAX_ERR_LENGTH, "ERROR: failed to close file id %d", root_id);
+    ex_err_fn(root_id, __func__, errmsg, status2);
   }
 
   /* Even if we have failures above due to nc_sync() or nc_close(), we still need to clean up our

ThirdParty/exodusII/vtkexodusII/src/ex_conv.c

@@ -37,7 +37,7 @@ struct exi_file_item *exi_find_file_item(int exoid)
     }
     ptr = ptr->next;
   }
-  return (ptr);
+  return ptr;
 }
 
 #define EX__MAX_PATHLEN 8192
@@ -80,7 +80,8 @@ int exi_check_valid_file_id(int exoid, const char *func)
   }
 #if !defined BUILT_IN_SIERRA
   else {
-    struct exi_file_item *file = exi_find_file_item(exoid);
+    int                   rootid = exoid & EX_FILE_ID_MASK;
+    struct exi_file_item *file   = exi_find_file_item(rootid);
 
     if (!file) {
       error = true;
@@ -93,13 +94,14 @@ int exi_check_valid_file_id(int exoid, const char *func)
     if (old_opt & EX_ABORT) {
       ex_opts(EX_VERBOSE | EX_ABORT);
     }
+    int  rootid = exoid & EX_FILE_ID_MASK;
     char errmsg[MAX_ERR_LENGTH];
     snprintf(errmsg, MAX_ERR_LENGTH,
              "ERROR: In \"%s\", the file id %d was not obtained via a call "
              "to \"ex_open\" or \"ex_create\".\n\t\tIt does not refer to a "
              "valid open exodus file.\n\t\tAborting to avoid file "
              "corruption or data loss or other potential problems.",
-             func, exoid);
+             func, rootid);
     ex_err(__func__, errmsg, EX_BADFILEID);
     ex_opts(old_opt);
     return EX_FATAL;
@@ -231,7 +233,7 @@ int exi_conv_init(int exoid, int *comp_wordsize, int *io_wordsize, int file_word
     EX_FUNC_LEAVE(EX_FATAL);
   }
 
-  new_file->file_id               = exoid;
+  new_file->file_id               = (unsigned)exoid & EX_FILE_ID_MASK;
   new_file->user_compute_wordsize = *comp_wordsize == 4 ? 0 : 1;
   new_file->int64_status          = int64_status;
   new_file->maximum_name_length   = exi_default_max_name_length;
@@ -240,6 +242,7 @@ int exi_conv_init(int exoid, int *comp_wordsize, int *io_wordsize, int file_word
   new_file->assembly_count        = 0;
   new_file->blob_count            = 0;
   new_file->compression_level     = 0;
+  new_file->quantize_nsd          = 0;
   new_file->shuffle               = 0;
   new_file->file_type             = filetype - 1;
   new_file->is_parallel           = is_parallel;
@@ -249,6 +252,8 @@ 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;
@@ -282,9 +287,11 @@ void exi_conv_exit(int exoid)
   struct exi_file_item *file = file_list;
   struct exi_file_item *prev = NULL;
 
+  int root_id = (unsigned)exoid & EX_FILE_ID_MASK;
+
   EX_FUNC_ENTER();
   while (file) {
-    if (file->file_id == exoid) {
+    if (file->file_id == root_id) {
       break;
     }
 
@@ -441,19 +448,76 @@ int ex_set_option(int exoid, ex_option_type option, int option_value)
           char errmsg[MAX_ERR_LENGTH];
           snprintf(errmsg, MAX_ERR_LENGTH,
                    "ERROR: invalid value %d for SZIP Compression.  Must be even and 4 <= value <= "
-                   "32. Ignoring.",
+                   "32. Setting value to 4.",
+                   value);
+          ex_err_fn(exoid, __func__, errmsg, EX_BADPARAM);
+          value = 4;
+        }
+      }
+      else if (file->compression_algorithm == EX_COMPRESS_ZSTD) {
+#if NC_HAS_ZSTD == 1
+        if (value < -131072 || value > 22) {
+          char errmsg[MAX_ERR_LENGTH];
+          snprintf(errmsg, MAX_ERR_LENGTH,
+                   "ERROR: invalid value %d for ZSTD Compression.  Must be between -131072 and 22. "
+                   "Setting value to 4",
                    value);
           ex_err_fn(exoid, __func__, errmsg, EX_BADPARAM);
-          EX_FUNC_LEAVE(EX_FATAL);
+          value = 4;
         }
+#else
+        char errmsg[MAX_ERR_LENGTH];
+        snprintf(
+            errmsg, MAX_ERR_LENGTH,
+            "ERROR: Zstandard compression is not supported in this version of netCDF library.");
+        ex_err_fn(exoid, __func__, errmsg, EX_BADPARAM);
+#endif
+      }
+      else if (file->compression_algorithm == EX_COMPRESS_BZ2) {
+#if NC_HAS_BZ2 == 1
+        if (value < 0 || value > 9) {
+          char errmsg[MAX_ERR_LENGTH];
+          snprintf(errmsg, MAX_ERR_LENGTH,
+                   "ERROR: invalid value %d for BZIP2 Compression.  Must be between 0 and 9 "
+                   "inclusive. Setting value to 1.",
+                   value);
+          ex_err_fn(exoid, __func__, errmsg, EX_BADPARAM);
+          value = 1;
+        }
+#else
+        char errmsg[MAX_ERR_LENGTH];
+        snprintf(errmsg, MAX_ERR_LENGTH,
+                 "ERROR: Bzip2 compression is not supported in this version of netCDF library.");
+        ex_err_fn(exoid, __func__, errmsg, EX_BADPARAM);
+#endif
       }
       file->compression_level = value;
-      assert(value == file->compression_level);
     }
     else {
       file->compression_level = 0;
     }
     break;
+  case EX_OPT_QUANTIZE_NSD:
+#if NC_HAS_QUANTIZE == 1
+    if (option_value > 15) {
+      char errmsg[MAX_ERR_LENGTH];
+      snprintf(errmsg, MAX_ERR_LENGTH,
+               "ERROR: invalid value %d for Quantize NSD.  Must be less than or equal to 15.  "
+               "Setting value to 15.",
+               option_value);
+      ex_err_fn(exoid, __func__, errmsg, EX_BADPARAM);
+      option_value = 15;
+    }
+    file->quantize_nsd = option_value;
+#else
+  {
+    char errmsg[MAX_ERR_LENGTH];
+    snprintf(errmsg, MAX_ERR_LENGTH,
+             "ERROR: Quanitzation is not supported in this version of netCDF library.");
+    ex_err_fn(exoid, __func__, errmsg, EX_BADPARAM);
+  }
+#endif
+    break;
   case EX_OPT_COMPRESSION_SHUFFLE: /* 0 (disabled); 1 (enabled) */
     file->shuffle = option_value != 0 ? 1 : 0;
     break;
@@ -486,10 +550,10 @@ int exi_comp_ws(int exoid)
     char errmsg[MAX_ERR_LENGTH];
     snprintf(errmsg, MAX_ERR_LENGTH, "ERROR: unknown file id %d", exoid);
     ex_err(__func__, errmsg, EX_BADFILEID);
-    return (EX_FATAL);
+    return EX_FATAL;
   }
   /* Stored as 0 for 4-byte; 1 for 8-byte */
-  return ((file->user_compute_wordsize + 1) * 4);
+  return (file->user_compute_wordsize + 1) * 4;
 }
 
 /*!

ThirdParty/exodusII/vtkexodusII/src/ex_copy.c

 /*
- * 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.
  *
@@ -21,7 +21,7 @@
 #define EXCHECKI(funcall)                                                                          \
   if ((funcall) != NC_NOERR) {                                                                     \
     fprintf(stderr, "Error calling %s\n", TOSTRING(funcall));                                      \
-    return (EX_FATAL);                                                                             \
+    return EX_FATAL;                                                                               \
   }
 
 #define EXCHECKF(funcall)                                                                          \
@@ -66,7 +66,7 @@ static int is_truth_table_variable(const char *var_name)
   /* If copying just the "mesh" or "non-transient" portion of the
    * input DB, these are the variables that won't be copied:
    */
-  return (strstr(var_name, "_var_tab") != NULL);
+  return strstr(var_name, "_var_tab") != NULL;
 }
 
 static int is_non_mesh_variable(const char *var_name)
@@ -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));
@@ -176,6 +176,7 @@ int ex_copy_transient(int in_exoid, int out_exoid)
 static int cpy_variable_data(int in_exoid, int out_exoid, int in_large, int mesh_only)
 {
   int nvars; /* number of variables */
+  /* NOTE: This is incorrect for files containing groups */
   EXCHECKI(nc_inq(in_exoid, NULL, &nvars, NULL, NULL));
   for (int varid = 0; varid < nvars; varid++) {
     bool         is_filtered;
@@ -216,6 +217,7 @@ static int cpy_variables(int in_exoid, int out_exoid, int in_large, int mesh_onl
 {
   int recdimid; /* id of unlimited dimension */
   int nvars;    /* number of variables */
+  /* NOTE: This is incorrect for files containing groups */
   EXCHECKI(nc_inq(in_exoid, NULL, &nvars, NULL, &recdimid));
   for (int varid = 0; varid < nvars; varid++) {
     struct ncvar var; /* variable */
@@ -259,10 +261,11 @@ static int cpy_dimension(int in_exoid, int out_exoid, int mesh_only)
 
   int ndims;    /* number of dimensions */
   int recdimid; /* id of unlimited dimension */
+  /* NOTE: This is incorrect for files containing groups */
   EXCHECKI(nc_inq(in_exoid, &ndims, NULL, NULL, &recdimid));
   for (int dimid = 0; dimid < ndims; dimid++) {
 
-    char   dim_nm[NC_MAX_NAME + 1];
+    char   dim_nm[EX_MAX_NAME + 1];
     size_t dim_sz;
     EXCHECK(nc_inq_dim(in_exoid, dimid, dim_nm, &dim_sz));
 
@@ -344,6 +347,7 @@ static int cpy_global_att(int in_exoid, int out_exoid)
   struct ncatt att; /* attribute */
 
   int ngatts;
+  /* NOTE: This is incorrect for files containing groups */
   EXCHECKI(nc_inq(in_exoid, NULL, NULL, &ngatts, NULL));
 
   /* copy global attributes */
@@ -413,7 +417,7 @@ static int cpy_att(int in_id, int out_id, int var_in_id, int var_out_id)
     nc_copy_att(in_id, var_in_id, att_nm, out_id, var_out_id);
   }
 
-  return (EX_NOERR);
+  return EX_NOERR;
 }
 /*! \endcond */
 
@@ -510,7 +514,7 @@ static int cpy_var_def(int in_id, int out_id, int rec_dim_id, char *var_nm)
   /* Get the dimension sizes and names */
   int dim_out_id[NC_MAX_VAR_DIMS];
   for (int idx = 0; idx < nbr_dim; idx++) {
-    char   dim_nm[NC_MAX_NAME + 1];
+    char   dim_nm[EX_MAX_NAME + 1];
     size_t dim_sz;
 
     EXCHECKI(nc_inq_dim(in_id, dim_in_id[idx], dim_nm, &dim_sz));
@@ -718,11 +722,11 @@ static int cpy_var_val(int in_id, int out_id, char *var_nm)
   /* Free the space that held the variable */
   free(void_ptr);
 
-  return (EX_NOERR);
+  return EX_NOERR;
 
 err_ret:
   free(void_ptr);
-  return (EX_FATAL);
+  return EX_FATAL;
 
 } /* end cpy_var_val() */
 
@@ -789,7 +793,7 @@ static int cpy_coord_val(int in_id, int out_id, char *var_nm, int in_large)
 
   /* Free the space that held the variable */
   free(void_ptr);
-  return (EX_NOERR);
+  return EX_NOERR;
 
 } /* end cpy_coord_val() */
 

ThirdParty/exodusII/vtkexodusII/src/ex_create_group.c

 /*
- * 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);

ThirdParty/exodusII/vtkexodusII/src/ex_create_par.c

@@ -192,15 +192,31 @@ int ex_create_par_int(const char *path, int cmode, int *comp_ws, int *io_ws, MPI
   }
 #endif
 
+#if NC_HAS_PNETCDF
+  bool i_created_info = false;
+  if (info == MPI_INFO_NULL) {
+    MPI_Info_create(&info);
+    i_created_info = true;
+  }
+  MPI_Info_set(info, "nc_header_align_size", "1048576");
+#endif
   /* There is an issue on some versions of mpi that limit the length of the path to <250 characters
    * Check for that here and use `path` if `canon_path` is >=250 characters...
    */
+
   if (strlen(canon_path) >= 250) {
     status = nc_create_par(path, nc_mode, comm, info, &exoid);
   }
   else {
     status = nc_create_par(canon_path, nc_mode, comm, info, &exoid);
   }
+
+#if NC_HAS_PNETCDF
+  if (i_created_info) {
+    MPI_Info_free(&info);
+  }
+#endif
+
   if (status != NC_NOERR) {
     if (my_mode & EX_NETCDF4) {
 #if NC_HAS_PARALLEL4

ThirdParty/exodusII/vtkexodusII/src/ex_cvt_nodes_to_sides.c

 /*
- * Copyright(C) 1999-2020, 2023 National Technology & Engineering Solutions
+ * Copyright(C) 1999-2020, 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.
  *
@@ -171,7 +171,6 @@ int ex_cvt_nodes_to_sides(int exoid, void_int *num_elem_per_set, void_int *num_n
                           void_int *side_sets_elem_list, void_int *side_sets_node_list,
                           void_int *side_sets_side_list)
 {
-  size_t    i, j, k, n;
   int       num_side_sets, num_elem_blks;
   int64_t   tot_num_elem = 0, tot_num_ss_elem = 0, elem_num = 0, ndim;
   void_int *elem_blk_ids     = NULL;
@@ -179,7 +178,7 @@ int ex_cvt_nodes_to_sides(int exoid, void_int *num_elem_per_set, void_int *num_n
   void_int *ss_elem_ndx      = NULL;
   void_int *ss_elem_node_ndx = NULL;
   void_int *ss_parm_ndx      = NULL;
-  size_t    elem_ctr, node_ctr, elem_num_pos;
+  int64_t   elem_ctr, node_ctr, elem_num_pos;
   int       num_nodes_per_elem, num_node_per_side;
 
   int *same_elem_type = NULL;
@@ -255,12 +254,12 @@ int ex_cvt_nodes_to_sides(int exoid, void_int *num_elem_per_set, void_int *num_n
 
   /* First count up # of elements in the side sets*/
   if (ints_64) {
-    for (i = 0; i < num_side_sets; i++) {
+    for (int i = 0; i < num_side_sets; i++) {
       tot_num_ss_elem += ((int64_t *)num_elem_per_set)[i];
     }
   }
   else {
-    for (i = 0; i < num_side_sets; i++) {
+    for (int i = 0; i < num_side_sets; i++) {
       tot_num_ss_elem += ((int *)num_elem_per_set)[i];
     }
   }
@@ -279,7 +278,7 @@ int ex_cvt_nodes_to_sides(int exoid, void_int *num_elem_per_set, void_int *num_n
   if (int_size == sizeof(int64_t)) {
     /* Sort side set element list into index array  - non-destructive */
     int64_t *elems = (int64_t *)ss_elem_ndx;
-    for (i = 0; i < tot_num_ss_elem; i++) {
+    for (int i = 0; i < tot_num_ss_elem; i++) {
       elems[i] = i; /* init index array to current position */
     }
     exi_iqsort64(side_sets_elem_list, elems, tot_num_ss_elem);
@@ -287,7 +286,7 @@ int ex_cvt_nodes_to_sides(int exoid, void_int *num_elem_per_set, void_int *num_n
   else {
     /* Sort side set element list into index array  - non-destructive */
     int *elems = (int *)ss_elem_ndx;
-    for (i = 0; i < tot_num_ss_elem; i++) {
+    for (int i = 0; i < tot_num_ss_elem; i++) {
       elems[i] = i; /* init index array to current position */
     }
     exi_iqsort(side_sets_elem_list, elems, tot_num_ss_elem);
@@ -325,7 +324,7 @@ int ex_cvt_nodes_to_sides(int exoid, void_int *num_elem_per_set, void_int *num_n
     goto cleanup;
   }
   elem_ctr = 0;
-  for (i = 0; i < num_elem_blks; i++) {
+  for (int i = 0; i < num_elem_blks; i++) {
     ex_entity_id id;
     if (ints_64) {
       id = ((int64_t *)elem_blk_ids)[i];
@@ -383,9 +382,10 @@ int ex_cvt_nodes_to_sides(int exoid, void_int *num_elem_per_set, void_int *num_n
   same_elem_type[0] = true;
   if (ints_64) {
     elem_ctr = ((int64_t *)num_elem_per_set)[0];
-    for (i = 0, k = 0; i < tot_num_ss_elem; i++) {
+    for (int64_t i = 0, k = 0; i < tot_num_ss_elem; i++) {
       int64_t elem = ((int64_t *)side_sets_elem_list)[i];
-      for (j = 0; j < num_elem_blks; j++) {
+      int     j    = 0;
+      for (; j < num_elem_blks; j++) {
         if (elem <= elem_blk_parms[j].elem_ctr) {
           break;
         }
@@ -420,10 +420,12 @@ int ex_cvt_nodes_to_sides(int exoid, void_int *num_elem_per_set, void_int *num_n
     */
     node_ctr = 0;
     elem_ctr = ((int64_t *)num_elem_per_set)[0];
-    for (i = 0, k = 0; i < tot_num_ss_elem; i++) {
+    int i    = 0;
+    for (int k = 0; i < tot_num_ss_elem; i++) {
       int64_t elem = ((int64_t *)side_sets_elem_list)[i];
 
-      for (j = 0; j < num_elem_blks; j++) {
+      int j = 0;
+      for (; j < num_elem_blks; j++) {
         if (elem <= elem_blk_parms[j].elem_ctr) {
           break;
         }
@@ -460,10 +462,11 @@ int ex_cvt_nodes_to_sides(int exoid, void_int *num_elem_per_set, void_int *num_n
   }
   else {
     elem_ctr = ((int *)num_elem_per_set)[0];
-    for (i = 0, k = 0; i < tot_num_ss_elem; i++) {
+    for (int i = 0, k = 0; i < tot_num_ss_elem; i++) {
       int elem = ((int *)side_sets_elem_list)[i];
 
-      for (j = 0; j < num_elem_blks; j++) {
+      int j = 0;
+      for (; j < num_elem_blks; j++) {
         if (elem <= elem_blk_parms[j].elem_ctr) {
           break;
         }
@@ -498,10 +501,12 @@ int ex_cvt_nodes_to_sides(int exoid, void_int *num_elem_per_set, void_int *num_n
     */
     node_ctr = 0;
     elem_ctr = ((int *)num_elem_per_set)[0];
-    for (i = 0, k = 0; i < tot_num_ss_elem; i++) {
+    int i    = 0;
+    for (int k = 0; i < tot_num_ss_elem; i++) {
       int elem = ((int *)side_sets_elem_list)[i];
 
-      for (j = 0; j < num_elem_blks; j++) {
+      int j = 0;
+      for (; j < num_elem_blks; j++) {
         if (elem <= elem_blk_parms[j].elem_ctr) {
           break;
         }
@@ -541,7 +546,7 @@ int ex_cvt_nodes_to_sides(int exoid, void_int *num_elem_per_set, void_int *num_n
 
   elem_ctr = 0;
 
-  for (j = 0; j < tot_num_ss_elem; j++) {
+  for (int j = 0; j < tot_num_ss_elem; j++) {
     int64_t elem;
     int64_t idx;
     int64_t ss_node0, ss_node1;
@@ -617,7 +622,8 @@ int ex_cvt_nodes_to_sides(int exoid, void_int *num_elem_per_set, void_int *num_n
 
     num_nodes_per_elem = elem_blk_parms[p_ndx].num_nodes_per_elem;
 
-    for (n = 0; n < num_nodes_per_elem; n++) {
+    int n = 0;
+    for (; n < num_nodes_per_elem; n++) {
       /* find node in connectivity array that matches first node in side set */
       if (((int_size == sizeof(int64_t)) &&
            (ss_node0 == ((int64_t *)connect)[num_nodes_per_elem * (elem_num_pos) + n])) ||

ThirdParty/exodusII/vtkexodusII/src/ex_err.c

 /*
- * Copyright(C) 1999-2020, 2023 National Technology & Engineering Solutions
+ * Copyright(C) 1999-2025 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.
  *
@@ -225,6 +225,7 @@ void ex_err_fn(int exoid, const char *module_name, const char *message, int err_
 
     fprintf(stderr, "    exerrval = %d\n", EX_ERR_NUM);
     fprintf(stderr, "\t%s\n", ex_strerror(EX_ERR_NUM));
+    fflush(stderr);
     EX_FUNC_VOID();
   }
 
@@ -239,6 +240,7 @@ void ex_err_fn(int exoid, const char *module_name, const char *message, int err_
   if (err_num == EX_NULLENTITY) {
     if (exoptval & EX_NULLVERBOSE) {
       fprintf(stderr, "\nExodus Library Warning: [%s]\n\t%s\n", module_name, message);
+      fflush(stderr);
     }
   }
 
@@ -262,8 +264,8 @@ void ex_err_fn(int exoid, const char *module_name, const char *message, int err_
       fprintf(stderr, "\nExodus Library Warning/Error: [%s]\n\t%s\n", module_name, message);
     }
     fprintf(stderr, "\t%s\n", ex_strerror(err_num));
+    fflush(stderr);
   }
-  fflush(stderr);
 
   /* with netCDF 3.4, (fatal) system error codes are > 0;
      so all EXODUS fatal error codes are > 0    */
@@ -333,7 +335,8 @@ const char *ex_strerror(int err_num)
   case EX_MEMFAIL: return "Memory allocation failure";
   case EX_BADFILEMODE: return "Bad file mode -- cannot specify both EX_READ and EX_WRITE";
   case EX_BADFILEID: return "Bad file id. Could not find exodus file associated with file id.";
-  case EX_WRONGFILETYPE: return "Integer sizes must match for input and output file in ex_copy.";
+  case EX_WRONGFILETYPE:
+    return "File does not exist or is not of a supported type (netcdf3, netcdf4, netcdf5).";
   case EX_LOOKUPFAIL:
     return "Id lookup failed for specified entity type. Could not find entity with specified id.";
   case EX_BADFILENAME: return "Empty or null filename specified.";
@@ -344,6 +347,8 @@ const char *ex_strerror(int err_num)
   case EX_INTERNAL: return "Internal logic error in exodus library.";
   case EX_NOTROOTID: return "File id is not the root id; it is a subgroup id.";
   case EX_NULLENTITY: return "Null entity found.";
+  case EX_NOTFOUND: return "Could not find requested variable on database.";
+  case EX_INTSIZEMISMATCH: return "Integer sizes must match for input and output file in ex_copy.";
   case EX_MSG: return "Message printed; no error implied.";
   default: return nc_strerror(err_num);
   }

ThirdParty/exodusII/vtkexodusII/src/ex_field_utils.c

@@ -9,7 +9,6 @@
 #include "exodusII.h"     // for ex_err, etc
 #include "exodusII_int.h" // for EX_FATAL, etc
 #include <assert.h>
-#include <math.h>
 #define _GNU_SOURCE
 #include <string.h>
 
@@ -43,19 +42,25 @@ static size_t my_strlcat(char *dst, const char *src, size_t maxlen)
   return dstlen + srclen;
 }
 
-static int number_width(const size_t number)
+static int number_width(size_t number)
 {
+  /* Could use `(int)floor(log10(number)) + 1`, but that requires math library... */
   if (number == 0) {
     return 1;
   }
-  int width = (int)floor(log10(number)) + 1;
-  return width;
+  int count = 0;
+  // Iterate till n has digits remaining
+  while (number != 0) {
+    number /= 10;
+    ++count;
+  }
+  return count;
 }
 
 static void verify_valid_component(int component, size_t cardinality, size_t suffix_size)
 {
   assert(cardinality == suffix_size);
-  assert(component - 1 < suffix_size);
+  assert(component - 1 < (int)suffix_size);
 }
 
 const char *ex_component_field_name(ex_field *field, int component[EX_MAX_FIELD_NESTING])
@@ -71,7 +76,7 @@ const char *ex_component_field_name(ex_field *field, int component[EX_MAX_FIELD_
   }
 
   // Build up name incrementally which makes it easier to handle an empty component_separator...
-  sprintf(field_name, "%s", field->name);
+  snprintf(field_name, EX_MAX_NAME + 1, "%s", field->name);
 
   for (int i = 0; i < field->nesting; i++) {
     if (field->component_separator[i]) {
@@ -327,8 +332,8 @@ const char *ex_field_component_suffix(ex_field *field, int nest_level, int compo
     static char user_suffix[32];
     static char format[8];
     int         width = number_width(field->cardinality[nest_level]);
-    sprintf(format, "%c%d%dd", '%', 0, width);
-    sprintf(user_suffix, format, component);
+    snprintf(format, 8, "%c%d%dd", '%', 0, width);
+    snprintf(user_suffix, 32, format, component);
     return user_suffix;
   }
 
@@ -338,8 +343,8 @@ const char *ex_field_component_suffix(ex_field *field, int nest_level, int compo
     static char user_suffix[32];
     static char format[8];
     int         width = number_width(field->cardinality[nest_level]);
-    sprintf(format, "%c%d%dd", '%', 0, width);
-    sprintf(user_suffix, format, component - 1);
+    snprintf(format, 8, "%c%d%dd", '%', 0, width);
+    snprintf(user_suffix, 32, format, component - 1);
     return user_suffix;
   }
 

ThirdParty/exodusII/vtkexodusII/src/ex_get_assemblies.c

 /*
- * Copyright(C) 1999-2022 National Technology & Engineering Solutions
+ * Copyright(C) 1999-2022, 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_get_assemblies(int exoid, ex_assembly *assembly)
     snprintf(errmsg, MAX_ERR_LENGTH, "ERROR: failed to inquire ASSEMBLY count in file id %d",
              exoid);
     ex_err_fn(exoid, __func__, errmsg, num_assembly);
-    return (EX_FATAL);
+    return EX_FATAL;
   }
 
   if (ex_int64_status(exoid) & EX_IDS_INT64_API) {

ThirdParty/exodusII/vtkexodusII/src/ex_get_attribute.c

@@ -113,7 +113,7 @@ int ex_get_attribute_count(int exoid, ex_entity_type obj_type, ex_entity_id id)
   /* Get names of each attribute and see if it is an 'internal' name */
   int count = att_count;
   for (int i = 0; i < count; i++) {
-    char name[NC_MAX_NAME + 1];
+    char name[EX_MAX_NAME + 1];
     int  status;
     if ((status = nc_inq_attname(exoid, varid, i, name)) != NC_NOERR) {
       char errmsg[MAX_ERR_LENGTH];
@@ -162,7 +162,7 @@ int ex_get_attribute_param(int exoid, ex_entity_type obj_type, ex_entity_id id,
   */
   count = 0;
   for (int i = 0; i < att_count; i++) {
-    char name[NC_MAX_NAME + 1];
+    char name[EX_MAX_NAME + 1];
     int  status;
     if ((status = nc_inq_attname(exoid, varid, i, name)) != NC_NOERR) {
       snprintf(errmsg, MAX_ERR_LENGTH,

ThirdParty/exodusII/vtkexodusII/src/ex_get_blobs.c

 /*
- * Copyright(C) 1999-2020 National Technology & Engineering Solutions
+ * Copyright(C) 1999-2020, 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.
  *
@@ -23,7 +23,7 @@ int ex_get_blobs(int exoid, ex_blob *blob)
     char errmsg[MAX_ERR_LENGTH];
     snprintf(errmsg, MAX_ERR_LENGTH, "ERROR: failed to inquire BLOB count in file id %d", exoid);
     ex_err_fn(exoid, __func__, errmsg, num_blob);
-    return (EX_FATAL);
+    return EX_FATAL;
   }
 
   if (ex_int64_status(exoid) & EX_IDS_INT64_API) {