Add support for setting HDF5 alignment property when creating a file

re: Unidata#2177
re: Unidata#2178

Provide get/set functions to store global data alignment
information and apply it when a file is created.

The api is as follows:
````
int nc_set_alignment(int threshold, int alignment);
int nc_get_alignment(int* thresholdp, int* alignmentp);
````

If defined, then for every file created opened after the call to
nc_set_alignment, for every new variable added to the file, the
most recently set threshold and alignment values will be applied
to that variable.

The nc_get_alignment function return the last values set by
nc_set_alignment.  If nc_set_alignment has not been called, then
it returns the value 0 for both threshold and alignment.

The alignment parameters are stored in the NCglobalstate object
(see below) for use as needed. Repeated calls to nc_set_alignment
will overwrite any existing values in NCglobalstate.

The alignment parameters are applied in libhdf5/hdf5create.c
and libhdf5/hdf5open.c

The set/get alignment functions are defined in libsrc4/nc4internal.c.

A test program was added as nc_test4/tst_alignment.c.

## Misc. Changes Unrelated to Alignment

* The NCRCglobalstate type was renamed to NCglobalstate to
  indicate that it represented more general global state than
  just .rc data.  It was also moved to nc4internal.h.  This led
  to a large number of small changes: mostly renaming. The
  global state management functions were moved to nc4internal.c.

* The global chunk cache variables have been moved into
  NCglobalstate.  As warranted, other global state will be moved
  as well.

* Some misc. problems with the nczarr performance tests were corrected.

RELEASE_NOTES.md

@@ -7,6 +7,7 @@ This file contains a high-level description of this package's evolution. Release
 
 ## 4.8.2 - TBD
 
+* [Enhancement] Add ability to set dataset alignment for netcdf-4/HDF5 files. See [Github #????](https://github.com/Unidata/netcdf-c/pull/????).
 * [Enhancement] Add complete bitgroom support to NCZarr. See [Github #2197](https://github.com/Unidata/netcdf-c/pull/2197).
 * [Bug Fix] Clean up the handling of deeply nested VLEN types. Marks nc_free_vlen() and nc_free_string as deprecated in favor of ncaux_reclaim_data(). See [Github #2179(https://github.com/Unidata/netcdf-c/pull/2179).
 * [Bug Fix] Make sure that netcdf.h accurately defines the flags in the open/create mode flags. See [Github #2183](https://github.com/Unidata/netcdf-c/pull/2183).

acinclude.m4

@@ -384,4 +384,6 @@ MOSTLYCLEANFILES += $(valgrind_log_files)
 	AC_SUBST([VALGRIND_CHECK_RULES])
 	m4_ifdef([_AM_SUBST_NOTMAKE], [_AM_SUBST_NOTMAKE([VALGRIND_CHECK_RULES])])
 ])
+
 AC_DEFUN([_AC_FINALIZE],[])
+

dap4_test/test_data.c

@@ -12,7 +12,7 @@ Test the netcdf-4 data building process.
 #include <stdio.h>
 #include "netcdf.h"
 
-#define DEBUG
+#undef DEBUG
 
 static void
 fail(int code)

docs/Doxyfile.in

@@ -781,7 +781,6 @@ INPUT = \
     @abs_top_srcdir@/libdispatch/derror.c \
     @abs_top_srcdir@/libdispatch/dv2i.c \
     @abs_top_srcdir@/libdispatch/dcopy.c \
-    @abs_top_srcdir@/libdispatch/daux.c \
     @abs_top_srcdir@/libsrc4/nc4var.c \
     @abs_top_srcdir@/libhdf5/nc4hdf.c \
     @abs_top_srcdir@/libsrc4/nc4internal.c \

include/nc4internal.h

@@ -118,6 +118,7 @@ typedef enum {NC_FALSE = 0, NC_TRUE = 1} nc_bool_t;
 /* Forward declarations. */
 struct NC_GRP_INFO;
 struct NC_TYPE_INFO;
+struct NCRCinfo;
 
 /**
  * This struct provides indexed Access to Meta-data objects. See the
@@ -205,9 +206,11 @@ typedef struct NC_VAR_INFO
     int parallel_access;         /**< Type of parallel access for I/O on variable (collective or independent). */
     nc_bool_t shuffle;           /**< True if var has shuffle filter applied. */
     nc_bool_t fletcher32;        /**< True if var has fletcher32 filter applied. */
-    size_t chunk_cache_size;     /**< Size in bytes of the var chunk cache. */
-    size_t chunk_cache_nelems;   /**< Number of slots in var chunk cache. */
-    float chunk_cache_preemption; /**< Chunk cache preemtion policy. */
+    struct ChunkCache {
+        size_t size;     /**< Size in bytes of the var chunk cache. */
+        size_t nelems;   /**< Number of slots in var chunk cache. */
+        float preemption; /**< Chunk cache preemtion policy. */
+    } chunkcache;
     int quantize_mode;           /**< Quantize mode. NC_NOQUANTIZE is 0, and means no quantization. */
     int nsd;                     /**< Number of significant digits if quantization is used, 0 if not. */
     void *format_var_info;       /**< Pointer to any binary format info. */
@@ -327,6 +330,24 @@ typedef struct NC_FILE_INFO
     } mem;
 } NC_FILE_INFO_T;
 
+/* Collect global state info in one place */
+typedef struct NCglobalstate {
+    int initialized;
+    char* tempdir; /* track a usable temp dir */
+    char* home; /* track $HOME */
+    char* cwd; /* track getcwd */
+    struct NCRCinfo* rcinfo; /* Currently only one rc file per session */
+    struct GlobalZarr { /* Zarr specific parameters */
+	char dimension_separator;
+    } zarr;
+    struct Alignment { /* H5Pset_alignment parameters */
+        int defined; /* 1 => threshold and alignment explicitly set */
+	int threshold;
+	int alignment;
+    } alignment;
+    struct ChunkCache chunkcache;
+} NCglobalstate;
+
 /** Variable Length Datatype struct in memory. Must be identical to
  * HDF5 hvl_t. (This is only used for VL sequences, not VL strings,
  * which are stored in char *'s) */
@@ -460,6 +481,10 @@ extern const char* nc4_atomic_name[NUM_ATOMIC_TYPES];
 /* Binary searcher for reserved attributes */
 extern const NC_reservedatt* NC_findreserved(const char* name);
 
+/* Global State Management */
+extern NCglobalstate* NC_getglobalstate(void);
+extern void NC_freeglobalstate(void);
+
 /* Generic reserved Attributes */
 #define NC_ATT_REFERENCE_LIST "REFERENCE_LIST"
 #define NC_ATT_CLASS "CLASS"

include/ncrc.h

@@ -33,40 +33,26 @@ typedef struct NCRCentry {
         char* value;
 } NCRCentry;
 
-/* collect all the relevant info around the rc file */
+struct AWSentry {
+    char* key;
+    char* value;
+};
+
+struct AWSprofile {
+    char* name;
+    NClist* entries; /* NClist<struct AWSentry*> */
+};
+
+/* collect all the relevant info around the rc file and AWS */
 typedef struct NCRCinfo {
 	int ignore; /* if 1, then do not use any rc file */
 	int loaded; /* 1 => already loaded */
         NClist* entries; /* the rc file entry store fields*/
         char* rcfile; /* specified rcfile; overrides anything else */
         char* rchome; /* Overrides $HOME when looking for .rc files */
+	NClist* s3profiles; /* NClist<struct AWSprofile*> */
 } NCRCinfo;
 
-/* Collect global state info in one place */
-typedef struct NCRCglobalstate {
-    int initialized;
-    char* tempdir; /* track a usable temp dir */
-    char* home; /* track $HOME */
-    char* cwd; /* track getcwd */
-    NCRCinfo rcinfo; /* Currently only one rc file per session */
-    struct GlobalZarr { /* Zarr specific parameters */
-	char dimension_separator;
-    } zarr;
-    struct S3credentials {
-	NClist* profiles; /* NClist<struct AWSprofile*> */
-    } s3creds;
-} NCRCglobalstate;
-
-struct AWSprofile {
-    char* name;
-    NClist* entries; /* NClist<struct AWSentry*> */
-};
-
-struct AWSentry {
-    char* key;
-    char* value;
-};
-
 typedef struct NCS3INFO {
     char* host; /* non-null if other*/
     char* region; /* region */
@@ -80,9 +66,7 @@ extern "C" {
 #endif
 
 /* From drc.c */
-EXTERNL int ncrc_createglobalstate(void);
 EXTERNL void ncrc_initialize(void);
-EXTERNL void ncrc_freeglobalstate(void);
 EXTERNL int NC_rcfile_insert(const char* key, const char* value, const char* hostport, const char* path);
 EXTERNL char* NC_rclookup(const char* key, const char* hostport, const char* path);
 EXTERNL char* NC_rclookupx(NCURI* uri, const char* key);
@@ -94,7 +78,6 @@ EXTERNL size_t NC_rcfile_length(NCRCinfo*);
 EXTERNL NCRCentry* NC_rcfile_ith(NCRCinfo*,size_t);
 
 /* For internal use */
-EXTERNL NCRCglobalstate* ncrc_getglobalstate(void);
 EXTERNL void NC_rcclear(NCRCinfo* info);
 EXTERNL void NC_rcclear(NCRCinfo* info);
 

include/netcdf.h

@@ -560,6 +560,14 @@ nc_def_user_format(int mode_flag, NC_Dispatch *dispatch_table, char *magic_numbe
 EXTERNL int
 nc_inq_user_format(int mode_flag, NC_Dispatch **dispatch_table, char *magic_number);
 
+/* Set the global alignment property */
+EXTERNL int
+nc_set_alignment(int threshold, int alignment);
+
+/* Get the global alignment property */
+EXTERNL int
+nc_get_alignment(int* thresholdp, int* alignmentp);
+
 EXTERNL int
 nc__create(const char *path, int cmode, size_t initialsz,
          size_t *chunksizehintp, int *ncidp);

libdap2/dceconstraints.c

@@ -13,7 +13,7 @@
 #include "dapincludes.h"
 #include "dceparselex.h"
 
-#define DEBUG
+#undef DEBUG
 
 #define LBRACE "{"
 #define RBRACE "}"

libdap4/d4file.c

@@ -367,7 +367,7 @@ set_curl_properties(NCD4INFO* d4info)
         char* newpath = NULL;
         int len;
 	errno = 0;
-	NCRCglobalstate* globalstate = ncrc_getglobalstate();
+	NCglobalstate* globalstate = NC_getglobalstate();
 
 	/* Create the unique cookie file name */
         len =

libdispatch/ddispatch.c

@@ -12,6 +12,7 @@ See LICENSE.txt for license information.
 #include "ncoffsets.h"
 #include "ncpathmgr.h"
 #include "ncxml.h"
+#include "nc4internal.h"
 
 /* Required for getcwd, other functions. */
 #ifdef HAVE_UNISTD_H
@@ -48,16 +49,15 @@ NCDISPATCH_initialize(void)
 {
     int status = NC_NOERR;
     int i;
-    NCRCglobalstate* globalstate = NULL;
+    NCglobalstate* globalstate = NULL;
 
     for(i=0;i<NC_MAX_VAR_DIMS;i++) {
         NC_coord_zero[i] = 0;
         NC_coord_one[i]  = 1;
         NC_stride_one[i] = 1;
     }
 
-    status = ncrc_createglobalstate(); /* will allocate and clear */
-    globalstate = ncrc_getglobalstate(); /* will allocate and clear */
+    globalstate = NC_getglobalstate(); /* will allocate and clear */
 
     /* Capture temp dir*/
     {
@@ -123,7 +123,7 @@ int
 NCDISPATCH_finalize(void)
 {
     int status = NC_NOERR;
-    ncrc_freeglobalstate();
+    NC_freeglobalstate();
 #if defined(ENABLE_BYTERANGE) || defined(ENABLE_DAP) || defined(ENABLE_DAP4)
     curl_global_cleanup();
 #endif

libdispatch/dpathmgr.c

@@ -42,7 +42,7 @@
 
 #undef DEBUGPATH
 static int pathdebug = -1;
-#define DEBUG
+#undef DEBUG
 
 #ifdef DEBUG
 #define REPORT(e,msg) report((e),(msg),__LINE__)