Also create key.seq and key.cnt for zero-size groups

Also fix fill mode setting
NU-CUCIS · Jan 31, 2020 · ed501ff · ed501ff
1 parent 5d395ab
commit ed501ff
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Showing 2 changed files with 26 additions and 13 deletions.
diff --git a/file_partition.cpp b/file_partition.cpp
@@ -26,9 +26,6 @@ int Concatenator::write_partition_key_datasets()
     herr_t err;
     hsize_t ii, jj, kk, start[2]={0,0}, count[2]={1,1};
     hsize_t *seq_offs, *seq_lens, *cnt_offs, *cnt_lens, *extents;
-#if defined PROFILE && PROFILE
-    double ts;
-#endif
 
     /* some groups may not contain key-base datasets */
     cnt_lens = new hsize_t[num_groups_have_key * 5];
@@ -160,6 +157,9 @@ int Concatenator::write_partition_key_datasets()
          * consecutive elements sharing the same key.
          */
         if (set_extent) {
+#if defined PROFILE && PROFILE
+            double ts;
+#endif
             SET_TIMER(ts)
             count[0] = extents[kk];
             err = H5Dset_extent(cnt_dset->out_dset_id, count);
@@ -186,6 +186,9 @@ int Concatenator::write_partition_key_datasets()
          * Below, we use a separate loop to call H5Dset_extent() altogether
          * after all calls to H5Dwrite() are complete.
          */
+#if defined PROFILE && PROFILE
+        double ts;
+#endif
         SET_TIMER(ts)
         kk = 0;
         for (ii=0; ii<num_groups; ii++) {

diff --git a/ph5_concat.cpp b/ph5_concat.cpp
@@ -296,11 +296,14 @@ int Concatenator::create_partition_keys(GrpInfo &grp)
     seq.is_key_seq = true;
     seq.is_key_cnt = false;
     seq.name       = part_key_base + ".key.seq";
-#ifndef DELAY_KEY_DSET_CREATION
-    /* delay creation until writing it in write_partition_key_datasets() */
-    herr_t err = create_dataset(grp.id, seq, true);
-    if (err < 0) RETURN_ERROR("create_dataset", "key.seq")
+#ifdef DELAY_KEY_DSET_CREATION
+    if (seq.global_dims[0] == 0)
 #endif
+    {
+        /* delay creation until writing it in write_partition_key_datasets() */
+        herr_t err = create_dataset(grp.id, seq, false);
+        if (err < 0) RETURN_ERROR("create_dataset", "key.seq")
+    }
     grp.seq_dset = &seq;
     total_num_datasets++;
 
@@ -310,11 +313,14 @@ int Concatenator::create_partition_keys(GrpInfo &grp)
     cnt.is_key_cnt = true;
     cnt.is_key_seq = false;
     cnt.name       = part_key_base + ".key.cnt";
-#ifndef DELAY_KEY_DSET_CREATION
-    /* delay creation until writing it in write_partition_key_datasets() */
-    err = create_dataset(grp.id, cnt, true);
-    if (err < 0) RETURN_ERROR("create_dataset", "key.cnt")
+#ifdef DELAY_KEY_DSET_CREATION
+    if (cnt.global_dims[0] == 0)
 #endif
+    {
+        /* delay creation until writing it in write_partition_key_datasets() */
+        herr_t err = create_dataset(grp.id, cnt, !set_extent);
+        if (err < 0) RETURN_ERROR("create_dataset", "key.cnt")
+    }
     grp.cnt_dset = &cnt;
     total_num_datasets++;
 
@@ -950,8 +956,12 @@ int Concatenator::create_dataset(hid_t     group_id,
             if (err < 0) HANDLE_ERROR("H5Pset_deflate")
         }
 
-        /* HDF5 default fill value is 0 */
-        if (!toFill) {
+        if (toFill) {
+            /* HDF5 default fill value is 0, skip call H5Pset_fill_value() */
+            err = H5Pset_fill_time(dcpl_id, H5D_FILL_TIME_ALLOC);
+            if (err < 0) HANDLE_ERROR("H5Pset_fill_time")
+        }
+        else {
             /* Never fill in the chunk in advance. */
             err = H5Pset_fill_time(dcpl_id, H5D_FILL_TIME_NEVER);
             if (err < 0) HANDLE_ERROR("H5Pset_fill_time")