WIP: Allow users to set data alignment within netcdf4 files

include/nc4dispatch.h

@@ -23,7 +23,8 @@ extern "C" {
     EXTERNL int
     NC4_create(const char *path, int cmode,
                size_t initialsz, int basepe, size_t *chunksizehintp,
-               void* parameters, const NC_Dispatch*, int);
+               void* parameters, const NC_Dispatch*, int,
+               size_t, size_t);
 
     EXTERNL int
     NC4_open(const char *path, int mode,

include/ncdispatch.h

@@ -168,7 +168,8 @@ struct NC;
 
 int NC_create(const char *path, int cmode,
 	      size_t initialsz, int basepe, size_t *chunksizehintp,
-	      int useparallel, void *parameters, int *ncidp);
+	      int useparallel, void *parameters, int *ncidp,
+          size_t alignment_threshold, size_t alignment_interval);
 int NC_open(const char *path, int cmode,
 	    int basepe, size_t *chunksizehintp,
 	    int useparallel, void *parameters, int *ncidp);

include/netcdf_dispatch.h.in

@@ -38,7 +38,8 @@ struct NC_Dispatch
 
     int (*create)(const char *path, int cmode, size_t initialsz,
                   int basepe, size_t *chunksizehintp, void *parameters,
-                  const struct NC_Dispatch *table, int ncid);
+                  const struct NC_Dispatch *table, int ncid,
+                  size_t alignment_threshold, size_t alignment_interval);
     int (*open)(const char *path, int mode, int basepe, size_t *chunksizehintp,
                 void *parameters, const struct NC_Dispatch *table, int ncid);
 

libdispatch/dfile.c

@@ -462,7 +462,7 @@ nc__create(const char *path, int cmode, size_t initialsz,
            size_t *chunksizehintp, int *ncidp)
 {
     return NC_create(path, cmode, initialsz, 0,
-                     chunksizehintp, 0, NULL, ncidp);
+                     chunksizehintp, 0, NULL, ncidp, 1, 1);
 }
 
 /** \ingroup datasets
@@ -508,7 +508,7 @@ nc_create_mem(const char* path, int mode, size_t initialsize, int* ncidp)
 {
     if(mode & NC_MMAP) return NC_EINVAL;
     mode |= NC_INMEMORY; /* Specifically, do not set NC_DISKLESS */
-    return NC_create(path, mode, initialsize, 0, NULL, 0, NULL, ncidp);
+    return NC_create(path, mode, initialsize, 0, NULL, 0, NULL, ncidp, 1, 1);
 }
 
 /**
@@ -535,7 +535,7 @@ nc__create_mp(const char *path, int cmode, size_t initialsz,
               int basepe, size_t *chunksizehintp, int *ncidp)
 {
     return NC_create(path, cmode, initialsz, basepe,
-                     chunksizehintp, 0, NULL, ncidp);
+                     chunksizehintp, 0, NULL, ncidp, 1, 1);
 }
 
 /**
@@ -1815,6 +1815,12 @@ check_create_mode(int mode)
  * @param parameters Pointer to MPI comm and info.
  * @param ncidp Pointer to location where returned netCDF ID is to be
  * stored.
+ * @param alignment_threshold Desired data alignment threshold within
+ * the created file. For HDF5 based files, this is passed to 
+ * H5Pset_alignment. Default value: 1 (no alignment threshold).
+ * @param alignment_interval Desired data alignment interval within
+ * the created file. For HDF5 based files, this is passed to 
+ * H5Pset_alignment. Default value: 1 (no alignment).
  *
  * @returns ::NC_NOERR No error.
  * @ingroup dispatch
@@ -1823,7 +1829,8 @@ check_create_mode(int mode)
 int
 NC_create(const char *path0, int cmode, size_t initialsz,
           int basepe, size_t *chunksizehintp, int useparallel,
-          void* parameters, int *ncidp)
+          void* parameters, int *ncidp,
+          size_t alignment_threshold, size_t alignment_interval)
 {
     int stat = NC_NOERR;
     NC* ncp = NULL;
@@ -1924,7 +1931,8 @@ NC_create(const char *path0, int cmode, size_t initialsz,
 
     /* Assume create will fill in remaining ncp fields */
     if ((stat = dispatcher->create(ncp->path, cmode, initialsz, basepe, chunksizehintp,
-                                   parameters, dispatcher, ncp->ext_ncid))) {
+                                   parameters, dispatcher, ncp->ext_ncid,
+                                   alignment_threshold, alignment_interval))) {
         del_from_NCList(ncp); /* oh well */
         free_NC(ncp);
     } else {

libdispatch/dparallel.c

@@ -128,7 +128,7 @@ int nc_create_par(const char *path, int cmode, MPI_Comm comm,
 
     data.comm = comm;
     data.info = info;
-    return NC_create(path, cmode, 0, 0, NULL, 1, &data, ncidp);
+    return NC_create(path, cmode, 0, 0, NULL, 1, &data, ncidp, 1, 1);
 #endif /* USE_PARALLEL */
 }
 

libhdf5/hdf5create.c

@@ -34,17 +34,20 @@ extern int NC4_create_image_file(NC_FILE_INFO_T* h5, size_t);
  * in-memory netCDF-4/HDF5 files only).
  * @param parameters extra parameter info (like MPI communicator).
  * @param ncid The already-assigned ncid for this file (aka ext_ncid).
+ * @param alignment_threshold The HDF5 alignment threshold. Passed to H5Pset_alignment. Default value: 1.
+ * @param alignment_interval The HDF5 alignment interval. Passed to H5Pset_alignment. Default value: 1.
  *
  * @return ::NC_NOERR No error.
  * @return ::NC_EINVAL Invalid input (check cmode).
  * @return ::NC_EEXIST File exists and NC_NOCLOBBER used.
  * @return ::NC_EHDFERR HDF5 returned error.
  * @ingroup netcdf4
- * @author Ed Hartnett, Dennis Heimbigner
+ * @author Ed Hartnett, Dennis Heimbigner, Mark Harfouche
  */
 static int
 nc4_create_file(const char *path, int cmode, size_t initialsz,
-                void* parameters, int ncid)
+                void* parameters, int ncid,
+                size_t alignment_threshold, size_t alignment_interval)
 {
     hid_t fcpl_id, fapl_id = -1;
     unsigned flags;
@@ -163,6 +166,9 @@ nc4_create_file(const char *path, int cmode, size_t initialsz,
 	     __func__, nc4_chunk_cache_size, nc4_chunk_cache_nelems,
 	     nc4_chunk_cache_preemption));
     }
+    if (H5Pset_alignment(fapl_id, alignment_threshold, alignment_interval) < 0) {
+        BAIL(NC_EHDFERR);
+    }
 
 #if H5_VERSION_GE(1,10,2)
     /* lib versions 1.10.2 and higher */
@@ -281,6 +287,8 @@ nc4_create_file(const char *path, int cmode, size_t initialsz,
  * @param dispatch Pointer to the dispatch table for this file.
  * @param ncid The ncid that has been assigned by the dispatch layer
  * (aka ext_ncid).
+ * @param alignment_threshold The HDF5 alignment threshold. Passed to H5Pset_alignment. Default value: 1.
+ * @param alignment_interval The HDF5 alignment interval. Passed to H5Pset_alignment. Default value: 1.
  *
  * @return ::NC_NOERR No error.
  * @return ::NC_EINVAL Invalid input (check cmode).
@@ -290,7 +298,8 @@ nc4_create_file(const char *path, int cmode, size_t initialsz,
 int
 NC4_create(const char* path, int cmode, size_t initialsz, int basepe,
            size_t *chunksizehintp, void *parameters,
-           const NC_Dispatch *dispatch, int ncid)
+           const NC_Dispatch *dispatch, int ncid,
+           size_t alignment_threshold, size_t alignment_interval)
 {
     int res;
 
@@ -315,7 +324,8 @@ NC4_create(const char* path, int cmode, size_t initialsz, int basepe,
         return NC_EINVAL;
 
     /* Create the netCDF-4/HDF5 file. */
-    res = nc4_create_file(path, cmode, initialsz, parameters, ncid);
+    res = nc4_create_file(path, cmode, initialsz, parameters, ncid,
+                          alignment_threshold, alignment_interval);
 
     return res;
 }