Set default PnetCDF header alignment to 128 KiB

Increase the default Parallel NetCDF header alignment to 128 KiB when
creating new files with SMIOL. This size is sufficiently larger than the
header of a typical MPAS restart file to reduce the likelihood of header
reallocation during ncmpi_enddef, which can lead to I O hangs when
overwriting string attributes or variables with larger values. This
change addresses the hang reported in MPAS Workflow issue 384 and does
not affect calculation results or I O performance in preliminary tests.
The alignment hint may be overridden via the PNETCDF_HINTS environment
variable.

Author: Andy Stokely

src/external/SMIOL/smiol.c

@@ -12,6 +12,7 @@
 #define PNETCDF_DEFINE_MODE 0
 #define PNETCDF_DATA_MODE 1
 #define MAX_REQS 256
+#define PNETCDF_HEADER_ALIGN_SIZE_STR "131072"
 #endif
 
 #define START_COUNT_READ 0
@@ -324,6 +325,7 @@ int SMIOL_open_file(struct SMIOL_context *context, const char *filename,
 			/*
 			 * Convert fformat to a PNetCDF file creation mode
 			 */
+			MPI_Info info = MPI_INFO_NULL;
 			int filecmode;
 			if (fformat == SMIOL_FORMAT_CDF2) {
 				filecmode = NC_64BIT_OFFSET;
@@ -336,11 +338,14 @@ int SMIOL_open_file(struct SMIOL_context *context, const char *filename,
 				MPI_Comm_free(&io_group_comm);
 				return SMIOL_INVALID_FORMAT;
 			}
-
+			MPI_Info_create(&info);
+			MPI_Info_set(info, "nc_header_align_size",
+			             PNETCDF_HEADER_ALIGN_SIZE_STR);
 			ierr = ncmpi_create(io_file_comm, filename,
 			                    (filecmode | NC_CLOBBER),
-			                    MPI_INFO_NULL,
+			                    info,
 			                    &((*file)->ncidp));
+			MPI_Info_free(&info);
 		}
 		(*file)->state = PNETCDF_DEFINE_MODE;
 #endif