Add HDF5 backend support for CGNS in SU2 (#1500)

* Add hdf5 subdirectory in CGNS

- hdf5 1.12 source copied in cgns
- add cgns files from 4.2 to support hdf5 backend
- add parallel cgns build detection to meson
- add LICENSE

Co-authored-by: Pedro Gomes <pcarruscag@gmail.com>

Author: MicK7

.lgtm.yml

@@ -1,3 +1,15 @@
+extraction:
+  cpp:
+     prepare:
+        packages: 
+          - libboost-all-dev
+     configure:
+        command:
+        - ./meson.py build --optimization=1
+     index:
+        build_command:
+        - ./ninja -C build
+
 path_classifiers:
   test:
     - TestCases/*

externals/cgns/README

@@ -1,6 +1,6 @@
 **********************************************************************
 https://github.com/CGNS/CGNS/releases, 
-the source files for CGNS v3.3.0 are bundled and build directly into SU2
+the source files for CGNS v4.2.0 are bundled and build directly into SU2
 
 From the CGNS webpage:
 

externals/cgns/adf/ADF.h

@@ -58,6 +58,7 @@ File:	ADF.h
 	ADF core code.  These sizes are provided for reference only!
 ***********************************************************************/
 #define ADF_DATA_TYPE_LENGTH        32
+#define ADF_CGIO_DATA_TYPE_LENGTH    2
 #define ADF_DATE_LENGTH             32
 #define ADF_FILENAME_LENGTH       1024
 #define ADF_FORMAT_LENGTH           20
@@ -249,6 +250,7 @@ EXTERN	void	ADF_Put_Name(
 
 EXTERN	void	ADF_Read_All_Data(
 			const double ID,
+                        const char *m_data_type,
 			char *data,
 			int *error_return ) ;
 
@@ -269,6 +271,7 @@ EXTERN	void	ADF_Read_Data(
 			const cgsize_t m_start[],
 			const cgsize_t m_end[],
 			const cgsize_t m_stride[],
+                        const char *m_data_type,
 			char *data,
 			int *error_return ) ;
 

externals/cgns/adf/ADF_interface.c

@@ -1371,7 +1371,7 @@ ADFI_chase_link( ID, &LID, &file_index,  &block_offset, &node, error_return ) ;
 CHECK_ADF_ABORT( *error_return ) ;
 
 	/** Copy the blank-filled data-type into a C string **/
-ADFI_string_2_C_string( node.data_type, ADF_DATA_TYPE_LENGTH, data_type,
+ADFI_string_2_C_string( node.data_type, ADF_CGIO_DATA_TYPE_LENGTH, data_type,
 		error_return ) ;
 CHECK_ADF_ABORT( *error_return ) ;
 
@@ -2601,6 +2601,7 @@ output: int *error_return	Error return.
 ***********************************************************************/
 void	ADF_Read_All_Data(
 		const double ID,
+                const char *m_data_type,
 		char *data,
 		int *error_return )
 {
@@ -2629,7 +2630,16 @@ if( data == NULL ) {
 ADFI_chase_link( ID, &LID, &file_index,  &block_offset, &node, error_return ) ;
 CHECK_ADF_ABORT( *error_return ) ;
 
+/* if it was provided, check to make sure the data types match */
+if( m_data_type != NULL ) {
+  if(strncmp(m_data_type, node.data_type, 2) != 0){
+    *error_return = INVALID_DATA_TYPE;
+    CHECK_ADF_ABORT( *error_return );
+  }
+}
+
 	/** Get datatype size **/
+
 ADFI_evaluate_datatype( file_index, node.data_type, &file_bytes, &memory_bytes,
 	tokenized_data_type, &file_format, &machine_format, error_return ) ;
 CHECK_ADF_ABORT( *error_return ) ;
@@ -2916,6 +2926,7 @@ void	ADF_Read_Data(
 		const cgsize_t m_start[],
 		const cgsize_t m_end[],
 		const cgsize_t m_stride[],
+                const char *m_data_type,
 		char *data,
 		int *error_return )
 {
@@ -2952,6 +2963,14 @@ if( (s_start == NULL) || (s_end == NULL) || (s_stride == NULL) ||
 ADFI_chase_link( ID, &LID, &file_index,  &block_offset, &node, error_return ) ;
 CHECK_ADF_ABORT( *error_return ) ;
 
+/* if it was provided, check to make sure the data types match */
+if( m_data_type != NULL ) {
+  if(strncmp(m_data_type, node.data_type, 2) != 0){
+    *error_return = INVALID_DATA_TYPE;
+    CHECK_ADF_ABORT( *error_return );
+  }
+}
+
 	/** Get datatype length **/
 ADFI_evaluate_datatype( file_index, node.data_type, &file_bytes, &memory_bytes,
 	tokenized_data_type, &disk_format, &machine_format, error_return ) ;

externals/cgns/adf/ADF_internals.c

@@ -482,7 +482,7 @@ static void ADFI_convert_integers(
 	}
     }
     else {
-        memcpy(to_data, from_data, size * count);
+        memcpy(to_data, from_data, (size_t)size * (size_t)count);
     }
 }
 /*------------------------------------------------------------------------------------*/

externals/cgns/adfh/ADF.h

@@ -0,0 +1,54 @@
+/*-------------------------------------------------------------------
+ * this is a replacement for ADF.h for HDF5 implementation
+ *-------------------------------------------------------------------*/
+
+#ifndef _ADF_H_
+#define _ADF_H_
+
+/* map ADF calls to ADFH calls */
+
+#define ADF_Children_Names		ADFH_Children_Names
+#define ADF_Children_IDs		ADFH_Children_IDs
+#define ADF_Create			ADFH_Create
+#define ADF_Database_Close		ADFH_Database_Close
+#define ADF_Database_Delete		ADFH_Database_Delete
+#define ADF_Database_Garbage_Collection	ADFH_Database_Garbage_Collection
+#define ADF_Database_Get_Format		ADFH_Database_Get_Format
+#define ADF_Database_Open		ADFH_Database_Open
+#define ADF_Database_Valid		ADFH_Database_Valid
+#define ADF_Database_Set_Format		ADFH_Database_Set_Format
+#define ADF_Database_Version		ADFH_Database_Version
+#define ADF_Delete			ADFH_Delete
+#define ADF_Error_Message		ADFH_Error_Message
+#define ADF_Flush_to_Disk		ADFH_Flush_to_Disk
+#define ADF_Get_Data_Type		ADFH_Get_Data_Type
+#define ADF_Get_Dimension_Values	ADFH_Get_Dimension_Values
+#define ADF_Get_Error_State		ADFH_Get_Error_State
+#define ADF_Get_Label			ADFH_Get_Label
+#define ADF_Get_Link_Path		ADFH_Get_Link_Path
+#define ADF_Get_Name			ADFH_Get_Name
+#define ADF_Get_Node_ID			ADFH_Get_Node_ID
+#define ADF_Get_Number_of_Dimensions	ADFH_Get_Number_of_Dimensions
+#define ADF_Get_Root_ID			ADFH_Get_Root_ID
+#define ADF_Is_Link			ADFH_Is_Link
+#define ADF_Library_Version		ADFH_Library_Version
+#define ADF_Link			ADFH_Link
+#define ADF_Move_Child			ADFH_Move_Child
+#define ADF_Number_of_Children		ADFH_Number_of_Children
+#define ADF_Put_Dimension_Information	ADFH_Put_Dimension_Information
+#define ADF_Put_Name			ADFH_Put_Name
+#define ADF_Read_All_Data		ADFH_Read_All_Data
+#define ADF_Read_Block_Data		ADFH_Read_Block_Data
+#define ADF_Read_Data			ADFH_Read_Data
+#define ADF_Set_Error_State		ADFH_Set_Error_State
+#define ADF_Set_Label			ADFH_Set_Label
+#define ADF_Write_All_Data		ADFH_Write_All_Data
+#define ADF_Write_Block_Data		ADFH_Write_Block_Data
+#define ADF_Write_Data			ADFH_Write_Data
+#define ADF_Release_ID			ADFH_Release_ID
+
+/* include ADFH.h */
+
+#include "ADFH.h"
+
+#endif