EXODUS: Add support for lossy compression via netCDF quantize method

sandialabs · Jun 19, 2024 · 47474bd · 47474bd
1 parent 18cd027
commit 47474bd
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Showing 4 changed files with 16 additions and 5 deletions.
diff --git a/packages/seacas/libraries/exodus/include/exodusII.h b/packages/seacas/libraries/exodus/include/exodusII.h
@@ -55,12 +55,12 @@
 #endif
 
 /* EXODUS version number */
-#define EXODUS_VERSION       "9.00"
+#define EXODUS_VERSION       "9.01"
 #define EXODUS_VERSION_MAJOR 9
-#define EXODUS_VERSION_MINOR 0
+#define EXODUS_VERSION_MINOR 1
 #define EXODUS_RELEASE_DATE  "May 30, 2024"
 
-#define EX_API_VERS       9.00f
+#define EX_API_VERS       9.01f
 #define EX_API_VERS_NODOT (100 * EXODUS_VERSION_MAJOR + EXODUS_VERSION_MINOR)
 #define EX_VERS           EX_API_VERS
 
@@ -242,9 +242,11 @@ 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. */

diff --git a/packages/seacas/libraries/exodus/include/exodusII_int.h b/packages/seacas/libraries/exodus/include/exodusII_int.h
@@ -696,6 +696,8 @@ struct exi_file_item
       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 */
+  unsigned int quantize_nsd : 4;      /**< 0 (disabled) to 15 (maximum) number of significant digits
+                                         retained for lossy quanitzation compression */
   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

diff --git a/packages/seacas/libraries/exodus/src/ex_conv.c b/packages/seacas/libraries/exodus/src/ex_conv.c
@@ -240,6 +240,7 @@ 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;
@@ -454,6 +455,7 @@ int ex_set_option(int exoid, ex_option_type option, int option_value)
       file->compression_level = 0;
     }
     break;
+  case EX_OPT_QUANTIZE_NSD: file->quantize_nsd = option_value; break;
   case EX_OPT_COMPRESSION_SHUFFLE: /* 0 (disabled); 1 (enabled) */
     file->shuffle = option_value != 0 ? 1 : 0;
     break;

diff --git a/packages/seacas/libraries/exodus/src/ex_utils.c b/packages/seacas/libraries/exodus/src/ex_utils.c
@@ -1763,6 +1763,11 @@ void exi_compress_variable(int exoid, int varid, int type)
         ex_err_fn(exoid, __func__, errmsg, EX_BADPARAM);
 #endif
       }
+
+      if (type == 2 && file->quantize_nsd > 0) {
+        // Lossy compression using netCDF quantize methods.
+        nc_def_var_quantize(exoid, varid, NC_QUANTIZE_GRANULARBR, file->quantize_nsd);
+      }
     }
 #if defined(PARALLEL_AWARE_EXODUS)
     if (file->is_parallel) {