Also add the new feature to the serial-io module.

src/common_io.c

@@ -415,7 +415,6 @@ void io_write_cell_offsets(hid_t h_grp, const int cdim[3],
   offset_spart[0] = 0;
 
   /* Collect the cell information of *local* cells */
-  int count_local_cells = 0;
   long long local_offset_part = 0;
   long long local_offset_gpart = 0;
   long long local_offset_spart = 0;
@@ -443,8 +442,6 @@ void io_write_cell_offsets(hid_t h_grp, const int cdim[3],
       offset_gpart[i] = local_offset_gpart + global_offsets[swift_type_dark_matter];
       offset_spart[i] = local_offset_spart + global_offsets[swift_type_stars];
 
-      ++count_local_cells;
-
       local_offset_part += count_part[i];
       local_offset_gpart += count_gpart[i];
       local_offset_spart += count_spart[i];
@@ -468,7 +465,7 @@ void io_write_cell_offsets(hid_t h_grp, const int cdim[3],
   }
 
 #ifdef WITH_MPI
-    /* Now, reduce all the arrays. Note that we use a bit-by-bit OR here. This
+    /* Now, reduce all the arrays. Note that we use a bit-wise OR here. This
        is safe as we made sure only local cells have non-zero values. */
   if (nodeID == 0) {
     MPI_Reduce(MPI_IN_PLACE, count_part, nr_cells, MPI_LONG_LONG_INT, MPI_BOR,
@@ -513,8 +510,7 @@ void io_write_cell_offsets(hid_t h_grp, const int cdim[3],
 	       0, MPI_COMM_WORLD);
   }
 
-
-  /* For the centres we use a sum as MPI does not like bitwise operations
+  /* For the centres we use a sum as MPI does not like bit-wise operations
      on floating point numbers */
   if (nodeID == 0) {
      MPI_Reduce(MPI_IN_PLACE, centres, 3 * nr_cells, MPI_DOUBLE, MPI_SUM,
@@ -552,7 +548,6 @@ void io_write_cell_offsets(hid_t h_grp, const int cdim[3],
   H5Dclose(h_data);
   H5Sclose(h_space);
 
-
   /* Group containing the offsets for each particle type */
   h_subgrp = H5Gcreate(h_grp, "Offsets", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
   if (h_subgrp < 0) error("Error while creating offsets sub-group");

src/parallel_io.c

@@ -1282,22 +1282,27 @@ void write_output_parallel(struct engine* e, const char* baseName,
     snprintf(fileName, FILENAME_BUFFER_SIZE, "%s_%04i.hdf5", baseName,
              e->snapshot_output_count);
 
-  hid_t h_file_cells, h_grp_cells;
-  if (e->nodeID == 0) {
+  /* Now write the top-level cell structure */
+  hid_t h_file_cells = 0, h_grp_cells = 0;
+  if (mpi_rank == 0) {
+
+    /* Open the snapshot on rank 0 */
     h_file_cells = H5Fopen(fileName, H5F_ACC_RDWR, H5P_DEFAULT);
     if (h_file_cells < 0)
       error("Error while opening file '%s' on rank %d.", fileName, mpi_rank);
+
+    /* Create the group we want in the file */
     h_grp_cells = H5Gcreate(h_file_cells, "/Cells", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
     if (h_grp_cells < 0) 
       error("Error while creating cells group");
-  } else {
-    h_file_cells = 0;
   }
 
+  /* Write the location of the particles in the arrays */
   io_write_cell_offsets(h_grp_cells, e->s->cdim, e->s->cells_top, e->s->nr_cells,
                         e->s->width, mpi_rank, N_total, offset);
 
-  if (e->nodeID == 0) {
+  /* Close everything */
+  if (mpi_rank == 0) {
     H5Gclose(h_grp_cells);
     H5Fclose(h_file_cells);
   }

src/serial_io.c

@@ -1028,6 +1028,31 @@ void write_output_serial(struct engine* e, const char* baseName,
     H5Fclose(h_file);
   }
 
+  /* Now write the top-level cell structure */
+  hid_t h_file_cells = 0, h_grp_cells = 0;
+  if (mpi_rank == 0) {
+
+    /* Open the snapshot on rank 0 */
+    h_file_cells = H5Fopen(fileName, H5F_ACC_RDWR, H5P_DEFAULT);
+    if (h_file_cells < 0)
+      error("Error while opening file '%s' on rank %d.", fileName, mpi_rank);
+
+    /* Create the group we want in the file */
+    h_grp_cells = H5Gcreate(h_file_cells, "/Cells", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+    if (h_grp_cells < 0) 
+      error("Error while creating cells group");
+  }
+
+  /* Write the location of the particles in the arrays */
+  io_write_cell_offsets(h_grp_cells, e->s->cdim, e->s->cells_top, e->s->nr_cells,
+                        e->s->width, mpi_rank, N_total, offset);
+
+  /* Close everything */
+  if (mpi_rank == 0) {
+    H5Gclose(h_grp_cells);
+    H5Fclose(h_file_cells);
+  }
+
   /* Now loop over ranks and write the data */
   for (int rank = 0; rank < mpi_size; ++rank) {
 

src/single_io.c

@@ -826,10 +826,12 @@ void write_output_single(struct engine* e, const char* baseName,
   /* Print the system of Units used internally */
   io_write_unit_system(h_file, internal_units, "InternalCodeUnits");
 
-  /* Write the location of the particles in the arrays */
+  /* Now write the top-level cell structure */
   long long global_offsets[swift_type_count] = {0};
   h_grp = H5Gcreate(h_file, "/Cells", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
   if (h_grp < 0) error("Error while creating cells group");
+
+  /* Write the location of the particles in the arrays */
   io_write_cell_offsets(h_grp, e->s->cdim, e->s->cells_top, e->s->nr_cells,
                         e->s->width, e->nodeID, N_total, global_offsets);
   H5Gclose(h_grp);