clarify and implement the precedences of I/O hints

benchmarks/C/aggregation.c

@@ -172,10 +172,9 @@ int benchmark_write(char       *filename,
 
     /* set PnetCDF I/O hints */
     MPI_Info_create(&info);
-    /* disable the header extent alignments
-    MPI_Info_set(info, "nc_header_align_size", "1");    size in bytes
-    */
-    /* disable the fixed-size variable alignments */
+    /* disable the fixed-size variable alignments, which also
+     * disable the header extent alignments
+     */
     MPI_Info_set(info, "nc_var_align_size", "1");
 
     nvars = 0;

benchmarks/C/write_block_read_column.c

@@ -84,7 +84,6 @@ int benchmark_write(char       *filename,
 
     /* set PnetCDF I/O hints */
     MPI_Info_create(&info);
-    MPI_Info_set(info, "nc_header_align_size",      "1");   /* size in bytes */
     MPI_Info_set(info, "nc_var_align_size",         "1");   /* size in bytes */
     MPI_Info_set(info, "nc_header_read_chunk_size", "512"); /* size in bytes */
     /* note that set the above values to 1 to disable the alignment */

examples/C/get_info.c

@@ -15,7 +15,7 @@
  *
  *    Example standard output:
 
-    MPI File Info: nkeys = 35
+    MPI File Info: nkeys = 34
     MPI File Info: [ 0] key =            cb_buffer_size, value = 16777216
     MPI File Info: [ 1] key =             romio_cb_read, value = automatic
     MPI File Info: [ 2] key =            romio_cb_write, value = automatic
@@ -39,18 +39,17 @@
     MPI File Info: [20] key =             striping_unit, value = 0
     MPI File Info: [21] key =           striping_factor, value = 0
     MPI File Info: [22] key =            start_iodevice, value = 0
-    MPI File Info: [23] key =      nc_header_align_size, value = 512
-    MPI File Info: [24] key =         nc_var_align_size, value = 4
-    MPI File Info: [25] key =      nc_record_align_size, value = 4
-    MPI File Info: [26] key = nc_header_read_chunk_size, value = 262144
-    MPI File Info: [27] key =          nc_in_place_swap, value = auto
-    MPI File Info: [28] key =              nc_ibuf_size, value = 16777216
-    MPI File Info: [29] key =         pnetcdf_subfiling, value = disable
-    MPI File Info: [30] key =           nc_num_subfiles, value = 0
-    MPI File Info: [31] key =          nc_hash_size_dim, value = 256
-    MPI File Info: [32] key =          nc_hash_size_var, value = 256
-    MPI File Info: [33] key =        nc_hash_size_gattr, value = 64
-    MPI File Info: [34] key =        nc_hash_size_vattr, value = 8
+    MPI File Info: [23] key =         nc_var_align_size, value = 4
+    MPI File Info: [24] key =      nc_record_align_size, value = 4
+    MPI File Info: [25] key = nc_header_read_chunk_size, value = 262144
+    MPI File Info: [26] key =          nc_in_place_swap, value = auto
+    MPI File Info: [27] key =              nc_ibuf_size, value = 16777216
+    MPI File Info: [28] key =         pnetcdf_subfiling, value = disable
+    MPI File Info: [29] key =           nc_num_subfiles, value = 0
+    MPI File Info: [30] key =          nc_hash_size_dim, value = 256
+    MPI File Info: [31] key =          nc_hash_size_var, value = 256
+    MPI File Info: [32] key =        nc_hash_size_gattr, value = 64
+    MPI File Info: [33] key =        nc_hash_size_vattr, value = 8
  */
 
 #include <stdio.h>

examples/C/hints.c

@@ -7,8 +7,8 @@
 /* $Id$ */
 
 /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
- * This example sets two PnetCDF hints:
- *    nc_header_align_size and nc_var_align_size
+ * This example sets PnetCDF hint:
+ *    nc_var_align_size
  * and prints the hint values as well as the header size, header extent, and
  * two variables' starting file offsets.
  *
@@ -18,7 +18,6 @@
  *
  *    % mpiexec -l -n 4 ./hints /pvfs2/wkliao/testfile.nc
  *
- *    nc_header_align_size      set to = 1024
  *    nc_var_align_size         set to = 512
  *    nc_header_read_chunk_size set to = 256
  *    header size                      = 252
@@ -94,7 +93,7 @@ int print_hints(int ncid,
     char value[MPI_MAX_INFO_VAL];
     int err, len, flag, nerrs=0;
     MPI_Offset header_size, header_extent, var_zy_start, var_yx_start;
-    MPI_Offset h_align=-1, v_align=-1, h_chunk=-1;
+    MPI_Offset v_align=-1, h_chunk=-1;
     MPI_Info info_used;
 
     err = ncmpi_inq_header_size  (ncid, &header_size);      ERR
@@ -103,12 +102,7 @@ int print_hints(int ncid,
     err = ncmpi_inq_varoffset(ncid, varid1, &var_yx_start); ERR
 
     err = ncmpi_inq_file_info(ncid, &info_used); ERR
-    MPI_Info_get_valuelen(info_used, "nc_header_align_size", &len, &flag);
-    if (flag) {
-        MPI_Info_get(info_used, "nc_header_align_size", len+1, value, &flag);
-        h_align = strtoll(value,NULL,10);
-    }
-        MPI_Info_get_valuelen(info_used, "nc_var_align_size", &len, &flag);
+    MPI_Info_get_valuelen(info_used, "nc_var_align_size", &len, &flag);
     if (flag) {
         MPI_Info_get(info_used, "nc_var_align_size", len+1, value, &flag);
         v_align = strtoll(value,NULL,10);
@@ -120,11 +114,6 @@ int print_hints(int ncid,
     }
     MPI_Info_free(&info_used);
 
-    if (h_align == -1)
-        printf("nc_header_align_size      is NOT set\n");
-    else
-        printf("nc_header_align_size      set to = %lld\n", h_align);
-
     if (v_align == -1)
         printf("nc_var_align_size         is NOT set\n");
     else
@@ -171,7 +160,6 @@ int main(int argc, char** argv)
     else                      snprintf(filename, 256, "%s", argv[optind]);
 
     MPI_Info_create(&info);
-    MPI_Info_set(info, "nc_header_align_size",      "1024"); /* size in bytes */
     MPI_Info_set(info, "nc_var_align_size",         "512");  /* size in bytes */
     MPI_Info_set(info, "nc_header_read_chunk_size", "256");  /* size in bytes */
     /* note that set the above values to 1 to disable the alignment */

examples/CXX/get_info.cpp

@@ -15,7 +15,7 @@
  *
  *    Example standard output:
 
-    MPI File Info: nkeys = 18
+    MPI File Info: nkeys = 17
     MPI File Info: [ 0] key =            cb_buffer_size, value = 16777216
     MPI File Info: [ 1] key =             romio_cb_read, value = automatic
     MPI File Info: [ 2] key =            romio_cb_write, value = automatic
@@ -31,9 +31,8 @@
     MPI File Info: [12] key =             romio_ds_read, value = automatic
     MPI File Info: [13] key =            romio_ds_write, value = automatic
     MPI File Info: [14] key =            cb_config_list, value = *:1
-    MPI File Info: [15] key =      nc_header_align_size, value = 512
-    MPI File Info: [16] key =         nc_var_align_size, value = 512
-    MPI File Info: [17] key = nc_header_read_chunk_size, value = 0
+    MPI File Info: [15] key =         nc_var_align_size, value = 512
+    MPI File Info: [16] key = nc_header_read_chunk_size, value = 0
  */
 
 #include <stdio.h>

examples/CXX/hints.cpp

@@ -7,8 +7,8 @@
 /* $Id$ */
 
 /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
- * This example sets two PnetCDF hints:
- *    nc_header_align_size and nc_var_align_size
+ * This example sets PnetCDF hint:
+ *    nc_var_align_size
  * and prints the hint values as well as the header size, header extent, and
  * two variables' starting file offsets.
  *
@@ -18,7 +18,6 @@
  *
  *    % mpiexec -l -n 4 ./hints /pvfs2/wkliao/testfile.nc
  *
- *    nc_header_align_size      set to = 1024
  *    nc_var_align_size         set to = 512
  *    nc_header_read_chunk_size set to = 256
  *    header size                      = 252
@@ -64,7 +63,7 @@ void print_hints(NcmpiFile &ncFile,
     char value[MPI_MAX_INFO_VAL];
     int len, flag;
     MPI_Offset header_size, header_extent, var_zy_start, var_yx_start;
-    MPI_Offset h_align=-1, v_align=-1, h_chunk=-1;
+    MPI_Offset v_align=-1, h_chunk=-1;
     MPI_Info info_used;
 
     ncFile.Inq_header_size(&header_size);
@@ -76,12 +75,7 @@ void print_hints(NcmpiFile &ncFile,
     /* get all the hints used */
     ncFile.Inq_file_info(&info_used);
 
-    MPI_Info_get_valuelen(info_used, (char*)"nc_header_align_size", &len, &flag);
-    if (flag) {
-        MPI_Info_get(info_used, (char*)"nc_header_align_size", len+1, value, &flag);
-        h_align = strtoll(value,NULL,10);
-    }
-        MPI_Info_get_valuelen(info_used, (char*)"nc_var_align_size", &len, &flag);
+    MPI_Info_get_valuelen(info_used, (char*)"nc_var_align_size", &len, &flag);
     if (flag) {
         MPI_Info_get(info_used, (char*)"nc_var_align_size", len+1, value, &flag);
         v_align = strtoll(value,NULL,10);
@@ -93,11 +87,6 @@ void print_hints(NcmpiFile &ncFile,
     }
     MPI_Info_free(&info_used);
 
-    if (h_align == -1)
-        printf("nc_header_align_size      is NOT set\n");
-    else
-        printf("nc_header_align_size      set to = %lld\n", h_align);
-
     if (v_align == -1)
         printf("nc_var_align_size         is NOT set\n");
     else
@@ -141,7 +130,6 @@ int main(int argc, char** argv)
 
     try {
         MPI_Info_create(&info);
-        MPI_Info_set(info, (char*)"nc_header_align_size",      (char*)"1024");
         MPI_Info_set(info, (char*)"nc_var_align_size",         (char*)"512");
         MPI_Info_set(info, (char*)"nc_header_read_chunk_size", (char*)"256");
         /* note that set the above values to 1 to disable the alignment */

examples/F77/get_info.f

@@ -15,7 +15,7 @@
 !
 !    Example standard output:
 !
-!   MPI File Info: nkeys =          18
+!   MPI File Info: nkeys =          17
 !   MPI File Info: [ 0] key =            cb_buffer_size, value =16777216
 !   MPI File Info: [ 1] key =             romio_cb_read, value =automatic
 !   MPI File Info: [ 2] key =            romio_cb_write, value =automatic
@@ -31,9 +31,8 @@
 !   MPI File Info: [12] key =             romio_ds_read, value =automatic
 !   MPI File Info: [13] key =            romio_ds_write, value =automatic
 !   MPI File Info: [14] key =            cb_config_list, value =*:1
-!   MPI File Info: [15] key =      nc_header_align_size, value =0
-!   MPI File Info: [16] key =         nc_var_align_size, value =0
-!   MPI File Info: [17] key = nc_header_read_chunk_size, value =0
+!   MPI File Info: [15] key =         nc_var_align_size, value =0
+!   MPI File Info: [16] key = nc_header_read_chunk_size, value =0
 
 
         program main

examples/F77/hints.f

@@ -6,8 +6,8 @@
 ! $Id$
 
 !
-! This example sets two PnetCDF hints:
-!    nc_header_align_size and nc_var_align_size
+! This example sets PnetCDF hint:
+!    nc_var_align_size
 ! and prints the hint values as well as the header size, header extent, and
 ! two variables' starting file offsets.
 !
@@ -17,7 +17,6 @@
 !
 !    % mpiexec -n 4 ./hints /pvfs2/wkliao/testfile.nc
 !
-!    nc_header_align_size      set to = 1024
 !    nc_var_align_size         set to = 512
 !    nc_header_read_chunk_size set to = 256
 !    header size                      = 252
@@ -54,9 +53,8 @@ subroutine print_hints(ncid, varid0, varid1)
           logical flag
           integer*8 header_size, header_extent
           integer*8 var_zy_start, var_yx_start
-          integer*8 h_align, v_align, h_chunk
+          integer*8 v_align, h_chunk
 
-          h_align=-1
           v_align=-1
           h_chunk=-1
 
@@ -72,13 +70,6 @@ subroutine print_hints(ncid, varid0, varid1)
           err = nfmpi_inq_file_info(ncid, info_used)
           call check(err, 'In nfmpi_inq_file_info : ')
 
-          call MPI_Info_get_valuelen(info_used, "nc_header_align_size",
-     +                               len, flag, err)
-          if (flag) then
-              call MPI_Info_get(info_used, "nc_header_align_size",
-     +                          len+1, value, flag, err)
-              read(value, '(i16)') h_align
-          endif
           call MPI_Info_get_valuelen(info_used, "nc_var_align_size",
      +                               len, flag, err)
           if (flag) then
@@ -96,11 +87,6 @@ subroutine print_hints(ncid, varid0, varid1)
           endif
           call MPI_Info_free(info_used, err)
 
-          if (h_align .EQ. -1) then
-              print*,"nc_header_align_size      is NOT set"
-          else
-              print*,"nc_header_align_size      set to = ", h_align
-          endif
           if (v_align .EQ. -1) then
               print*,"nc_var_align_size         is NOT set"
           else
@@ -178,7 +164,6 @@ program main
      +               MPI_COMM_WORLD, err)
 
       call MPI_Info_create(info, err)
-      call MPI_Info_set(info, "nc_header_align_size",      "1024", err)
       call MPI_Info_set(info, "nc_var_align_size",         "512",  err)
       call MPI_Info_set(info, "nc_header_read_chunk_size", "256",  err)
       ! note that set the above values to 1 to disable the alignment

examples/F90/get_info.f90

@@ -16,7 +16,7 @@
 !
 !    Example standard output:
 !
-!   MPI File Info: nkeys =          18
+!   MPI File Info: nkeys =          17
 !   MPI File Info: [ 0] key =            cb_buffer_size, value =16777216
 !   MPI File Info: [ 1] key =             romio_cb_read, value =automatic
 !   MPI File Info: [ 2] key =            romio_cb_write, value =automatic
@@ -32,9 +32,8 @@
 !   MPI File Info: [12] key =             romio_ds_read, value =automatic
 !   MPI File Info: [13] key =            romio_ds_write, value =automatic
 !   MPI File Info: [14] key =            cb_config_list, value =*:1
-!   MPI File Info: [15] key =      nc_header_align_size, value =0
-!   MPI File Info: [16] key =         nc_var_align_size, value =0
-!   MPI File Info: [17] key = nc_header_read_chunk_size, value =0
+!   MPI File Info: [15] key =         nc_var_align_size, value =0
+!   MPI File Info: [16] key = nc_header_read_chunk_size, value =0
 
 
         program main

examples/F90/hints.f90

@@ -7,8 +7,8 @@
 ! $Id$
 
 !
-! This example sets two PnetCDF hints:
-!    nc_header_align_size and nc_var_align_size
+! This example sets PnetCDF hint:
+!    nc_var_align_size
 ! and prints the hint values as well as the header size, header extent, and
 ! two variables' starting file offsets.
 !
@@ -18,7 +18,6 @@
 !
 !    % mpiexec -n 4 ./hints /pvfs2/wkliao/testfile.nc
 !
-!    nc_header_align_size      set to = 1024
 !    nc_var_align_size         set to = 512
 !    nc_header_read_chunk_size set to = 256
 !    header size                      = 252
@@ -55,9 +54,8 @@ subroutine print_hints(ncid, varid0, varid1)
           logical flag
           integer(kind=MPI_OFFSET_KIND) header_size, header_extent
           integer(kind=MPI_OFFSET_KIND) var_zy_start, var_yx_start
-          integer(kind=MPI_OFFSET_KIND) h_align, v_align, h_chunk
+          integer(kind=MPI_OFFSET_KIND) v_align, h_chunk
 
-          h_align=-1
           v_align=-1
           h_chunk=-1
 
@@ -73,13 +71,6 @@ subroutine print_hints(ncid, varid0, varid1)
           err = nf90mpi_inq_file_info(ncid, info_used)
           call check(err, 'In nf90mpi_inq_file_info : ')
 
-          call MPI_Info_get_valuelen(info_used, "nc_header_align_size", &
-                                     len, flag, err)
-          if (flag) then
-              call MPI_Info_get(info_used, "nc_header_align_size", &
-                                len+1, value, flag, err)
-              read(value, '(i16)') h_align
-          endif
           call MPI_Info_get_valuelen(info_used, "nc_var_align_size", &
                                      len, flag, err)
           if (flag) then
@@ -97,11 +88,6 @@ subroutine print_hints(ncid, varid0, varid1)
           endif
           call MPI_Info_free(info_used, err)
 
-          if (h_align .EQ. -1) then
-              print*,"nc_header_align_size      is NOT set"
-          else
-              print*,"nc_header_align_size      set to = ", h_align
-          endif
           if (v_align .EQ. -1) then
               print*,"nc_var_align_size         is NOT set"
           else
@@ -176,7 +162,6 @@ program main
       call MPI_Bcast(filename, 256, MPI_CHARACTER, 0, MPI_COMM_WORLD, err)
 
       call MPI_Info_create(info, err)
-      call MPI_Info_set(info, "nc_header_align_size",      "1024", err)
       call MPI_Info_set(info, "nc_var_align_size",         "512",  err)
       call MPI_Info_set(info, "nc_header_read_chunk_size", "256",  err)
       ! note that set the above values to 1 to disable the alignment

examples/README.md

@@ -92,8 +92,8 @@ with C, C++, F77, and F90 versions.
   + ./CXX/hints.cpp
   + ./F77/hints.f
   + ./F90/hints.f90
-  + This example sets two PnetCDF hints: `nc_header_align_size` and
-    `nc_var_align_size` and prints the hint values, the header size, header
+  + This example sets PnetCDF hint: `nc_var_align_size`
+    and prints the hint values, the header size, header
     extent, and variables' starting file offsets.
 
 * ./C/mput.c