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Change format of netCDF metedata file
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Athena Elafrou committed Sep 13, 2022
1 parent 0a0ed6c commit d2dd202
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126 changes: 77 additions & 49 deletions Partitioner.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -156,39 +156,49 @@ void Partitioner::save_metadata(const std::string& filename) const
NC_CHECK(nc_def_dim(nc_id, "L", left_dim, &left_dimid));
NC_CHECK(nc_def_dim(nc_id, "R", right_dim, &right_dimid));

// Define groups in netCDF file
int bbox_gid, connectivity_gid;
NC_CHECK(nc_def_grp(nc_id, "bounding_boxes", &bbox_gid));
NC_CHECK(nc_def_grp(nc_id, "connectivity", &connectivity_gid));

// Define variables in netCDF file
int top_x_vid, top_y_vid;
int cnt_x_vid, cnt_y_vid;
int top_num_vid, bottom_num_vid, left_num_vid, right_num_vid;
int top_ids_vid, bottom_ids_vid, left_ids_vid, right_ids_vid;
int top_halos_vid, bottom_halos_vid, left_halos_vid, right_halos_vid;
NC_CHECK(nc_def_var(nc_id, "global_x", NC_INT, 1, &dimid, &top_x_vid));
NC_CHECK(nc_def_var(nc_id, "global_y", NC_INT, 1, &dimid, &top_y_vid));
NC_CHECK(nc_def_var(nc_id, "local_extent_x", NC_INT, 1, &dimid, &cnt_x_vid));
NC_CHECK(nc_def_var(nc_id, "local_extent_y", NC_INT, 1, &dimid, &cnt_y_vid));
NC_CHECK(nc_def_var(nc_id, "top_neighbors", NC_INT, 1, &dimid, &top_num_vid));
NC_CHECK(nc_def_var(nc_id, "top_neighbor_ids", NC_INT, 1, &top_dimid,
&top_ids_vid));
NC_CHECK(nc_def_var(nc_id, "top_neighbor_halos", NC_INT, 1, &top_dimid,
&top_halos_vid));
NC_CHECK(nc_def_var(nc_id, "bottom_neighbors", NC_INT, 1, &dimid,
&bottom_num_vid));
NC_CHECK(nc_def_var(nc_id, "bottom_neighbor_ids", NC_INT, 1, &bottom_dimid,
&bottom_ids_vid));
NC_CHECK(nc_def_var(nc_id, "bottom_neighbor_halos", NC_INT, 1, &bottom_dimid,
&bottom_halos_vid));
// Bounding boxes group
NC_CHECK(nc_def_var(bbox_gid, "global_x", NC_INT, 1, &dimid, &top_x_vid));
NC_CHECK(nc_def_var(bbox_gid, "global_y", NC_INT, 1, &dimid, &top_y_vid));
NC_CHECK(
nc_def_var(nc_id, "left_neighbors", NC_INT, 1, &dimid, &left_num_vid));
NC_CHECK(nc_def_var(nc_id, "left_neighbor_ids", NC_INT, 1, &left_dimid,
&left_ids_vid));
NC_CHECK(nc_def_var(nc_id, "left_neighbor_halos", NC_INT, 1, &left_dimid,
&left_halos_vid));
nc_def_var(bbox_gid, "local_extent_x", NC_INT, 1, &dimid, &cnt_x_vid));
NC_CHECK(
nc_def_var(nc_id, "right_neighbors", NC_INT, 1, &dimid, &right_num_vid));
NC_CHECK(nc_def_var(nc_id, "right_neighbor_ids", NC_INT, 1, &right_dimid,
&right_ids_vid));
NC_CHECK(nc_def_var(nc_id, "right_neighbor_halos", NC_INT, 1, &right_dimid,
&right_halos_vid));
nc_def_var(bbox_gid, "local_extent_y", NC_INT, 1, &dimid, &cnt_y_vid));
// Connectivity group
NC_CHECK(nc_def_var(connectivity_gid, "top_neighbors", NC_INT, 1, &dimid,
&top_num_vid));
NC_CHECK(nc_def_var(connectivity_gid, "top_neighbor_ids", NC_INT, 1,
&top_dimid, &top_ids_vid));
NC_CHECK(nc_def_var(connectivity_gid, "top_neighbor_halos", NC_INT, 1,
&top_dimid, &top_halos_vid));
NC_CHECK(nc_def_var(connectivity_gid, "bottom_neighbors", NC_INT, 1, &dimid,
&bottom_num_vid));
NC_CHECK(nc_def_var(connectivity_gid, "bottom_neighbor_ids", NC_INT, 1,
&bottom_dimid, &bottom_ids_vid));
NC_CHECK(nc_def_var(connectivity_gid, "bottom_neighbor_halos", NC_INT, 1,
&bottom_dimid, &bottom_halos_vid));
NC_CHECK(nc_def_var(connectivity_gid, "left_neighbors", NC_INT, 1, &dimid,
&left_num_vid));
NC_CHECK(nc_def_var(connectivity_gid, "left_neighbor_ids", NC_INT, 1,
&left_dimid, &left_ids_vid));
NC_CHECK(nc_def_var(connectivity_gid, "left_neighbor_halos", NC_INT, 1,
&left_dimid, &left_halos_vid));
NC_CHECK(nc_def_var(connectivity_gid, "right_neighbors", NC_INT, 1, &dimid,
&right_num_vid));
NC_CHECK(nc_def_var(connectivity_gid, "right_neighbor_ids", NC_INT, 1,
&right_dimid, &right_ids_vid));
NC_CHECK(nc_def_var(connectivity_gid, "right_neighbor_halos", NC_INT, 1,
&right_dimid, &right_halos_vid));

// Write metadata to file
NC_CHECK(nc_enddef(nc_id));
Expand All @@ -198,42 +208,60 @@ void Partitioner::save_metadata(const std::string& filename) const

// Store data
start = _rank;
NC_CHECK(nc_var_par_access(nc_id, top_x_vid, NC_COLLECTIVE));
NC_CHECK(nc_put_var1_int(nc_id, top_x_vid, &start, &_global_0_new));
NC_CHECK(nc_var_par_access(nc_id, top_y_vid, NC_COLLECTIVE));
NC_CHECK(nc_put_var1_int(nc_id, top_y_vid, &start, &_global_1_new));
NC_CHECK(nc_var_par_access(nc_id, cnt_x_vid, NC_COLLECTIVE));
NC_CHECK(nc_put_var1_int(nc_id, cnt_x_vid, &start, &_local_ext_0_new));
NC_CHECK(nc_var_par_access(nc_id, cnt_y_vid, NC_COLLECTIVE));
NC_CHECK(nc_put_var1_int(nc_id, cnt_y_vid, &start, &_local_ext_1_new));
NC_CHECK(nc_put_var1_int(nc_id, top_num_vid, &start, &top_num_neighbors));
NC_CHECK(
nc_put_var1_int(nc_id, bottom_num_vid, &start, &bottom_num_neighbors));
NC_CHECK(nc_put_var1_int(nc_id, left_num_vid, &start, &left_num_neighbors));
NC_CHECK(nc_put_var1_int(nc_id, right_num_vid, &start, &right_num_neighbors));
NC_CHECK(nc_var_par_access(bbox_gid, top_x_vid, NC_COLLECTIVE));
NC_CHECK(nc_put_var1_int(bbox_gid, top_x_vid, &start, &_global_0_new));
NC_CHECK(nc_var_par_access(bbox_gid, top_y_vid, NC_COLLECTIVE));
NC_CHECK(nc_put_var1_int(bbox_gid, top_y_vid, &start, &_global_1_new));
NC_CHECK(nc_var_par_access(bbox_gid, cnt_x_vid, NC_COLLECTIVE));
NC_CHECK(nc_put_var1_int(bbox_gid, cnt_x_vid, &start, &_local_ext_0_new));
NC_CHECK(nc_var_par_access(bbox_gid, cnt_y_vid, NC_COLLECTIVE));
NC_CHECK(nc_put_var1_int(bbox_gid, cnt_y_vid, &start, &_local_ext_1_new));

NC_CHECK(nc_var_par_access(connectivity_gid, top_num_vid, NC_COLLECTIVE));
NC_CHECK(nc_put_var1_int(connectivity_gid, top_num_vid, &start,
&top_num_neighbors));
NC_CHECK(nc_var_par_access(connectivity_gid, bottom_num_vid, NC_COLLECTIVE));
NC_CHECK(nc_put_var1_int(connectivity_gid, bottom_num_vid, &start,
&bottom_num_neighbors));
NC_CHECK(nc_var_par_access(connectivity_gid, left_num_vid, NC_COLLECTIVE));
NC_CHECK(nc_put_var1_int(connectivity_gid, left_num_vid, &start,
&left_num_neighbors));
NC_CHECK(nc_var_par_access(connectivity_gid, right_num_vid, NC_COLLECTIVE));
NC_CHECK(nc_put_var1_int(connectivity_gid, right_num_vid, &start,
&right_num_neighbors));

start = top_offset;
count = top_num_neighbors;
NC_CHECK(nc_put_vara_int(nc_id, top_ids_vid, &start, &count, top_ids.data()));
NC_CHECK(
nc_put_vara_int(nc_id, top_halos_vid, &start, &count, top_halos.data()));
NC_CHECK(nc_var_par_access(connectivity_gid, top_ids_vid, NC_COLLECTIVE));
NC_CHECK(nc_put_vara_int(connectivity_gid, top_ids_vid, &start, &count,
top_ids.data()));
NC_CHECK(nc_var_par_access(connectivity_gid, top_halos_vid, NC_COLLECTIVE));
NC_CHECK(nc_put_vara_int(connectivity_gid, top_halos_vid, &start, &count,
top_halos.data()));
start = bottom_offset;
count = bottom_num_neighbors;
NC_CHECK(nc_put_vara_int(nc_id, bottom_ids_vid, &start, &count,
NC_CHECK(nc_var_par_access(connectivity_gid, bottom_ids_vid, NC_COLLECTIVE));
NC_CHECK(nc_put_vara_int(connectivity_gid, bottom_ids_vid, &start, &count,
bottom_ids.data()));
NC_CHECK(nc_put_vara_int(nc_id, bottom_halos_vid, &start, &count,
NC_CHECK(
nc_var_par_access(connectivity_gid, bottom_halos_vid, NC_COLLECTIVE));
NC_CHECK(nc_put_vara_int(connectivity_gid, bottom_halos_vid, &start, &count,
bottom_halos.data()));
start = left_offset;
count = left_num_neighbors;
NC_CHECK(
nc_put_vara_int(nc_id, left_ids_vid, &start, &count, left_ids.data()));
NC_CHECK(nc_put_vara_int(nc_id, left_halos_vid, &start, &count,
NC_CHECK(nc_var_par_access(connectivity_gid, left_ids_vid, NC_COLLECTIVE));
NC_CHECK(nc_put_vara_int(connectivity_gid, left_ids_vid, &start, &count,
left_ids.data()));
NC_CHECK(nc_var_par_access(connectivity_gid, left_halos_vid, NC_COLLECTIVE));
NC_CHECK(nc_put_vara_int(connectivity_gid, left_halos_vid, &start, &count,
left_halos.data()));
start = right_offset;
count = right_num_neighbors;
NC_CHECK(
nc_put_vara_int(nc_id, right_ids_vid, &start, &count, right_ids.data()));
NC_CHECK(nc_put_vara_int(nc_id, right_halos_vid, &start, &count,
NC_CHECK(nc_var_par_access(connectivity_gid, right_ids_vid, NC_COLLECTIVE));
NC_CHECK(nc_put_vara_int(connectivity_gid, right_ids_vid, &start, &count,
right_ids.data()));
NC_CHECK(nc_var_par_access(connectivity_gid, right_halos_vid, NC_COLLECTIVE));
NC_CHECK(nc_put_vara_int(connectivity_gid, right_halos_vid, &start, &count,
right_halos.data()));

NC_CHECK(nc_close(nc_id));
Expand Down
37 changes: 22 additions & 15 deletions README.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -127,11 +127,22 @@ dimensions:
B = 1 ;
L = UNLIMITED ; // (0 currently)
R = UNLIMITED ; // (0 currently)
variables:
group: bounding_boxes {
variables:
int global_x(P) ;
int global_y(P) ;
int local_extent_x(P) ;
int local_extent_y(P) ;
data:
global_x = 0, 16 ;
global_y = 0, 0 ;
local_extent_x = 16, 14 ;
local_extent_y = 30, 30 ;
} // group bounding_boxes
group: connectivity {
variables:
int top_neighbors(P) ;
int top_neighbor_ids(T) ;
int top_neighbor_halos(T) ;
Expand All @@ -144,20 +155,16 @@ variables:
int right_neighbors(P) ;
int right_neighbor_ids(R) ;
int right_neighbor_halos(R) ;
data:
global_x = 0, 16 ;
global_y = 0, 0 ;
local_extent_x = 16, 14 ;
local_extent_y = 30, 30 ;
top_neighbors = 0, 1 ;
top_neighbor_ids = 0 ;
top_neighbor_halos = 30 ;
bottom_neighbors = 1, 0 ;
bottom_neighbor_ids = 1 ;
bottom_neighbor_halos = 30 ;
left_neighbors = 0, 0 ;
right_neighbors = 0, 0 ;
data:
top_neighbors = 0, 1 ;
top_neighbor_ids = 0 ;
top_neighbor_halos = 30 ;
bottom_neighbors = 1, 0 ;
bottom_neighbor_ids = 1 ;
bottom_neighbor_halos = 30 ;
left_neighbors = 0, 0 ;
right_neighbors = 0, 0 ;
} // group connectivity
}
```
Expand Down

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