Increase HDF5 chunk size and set shuffle filter for single and serial output...

Increase HDF5 chunk size and set shuffle filter for single and serial output when compression is switched on.

src/serial_io.c

@@ -197,13 +197,13 @@ void prepareArray(const struct engine* e, hid_t grp, char* fileName,
     rank = 2;
     shape[0] = N_total;
     shape[1] = props.dimension;
-    chunk_shape[0] = 1 << 16; /* Just a guess...*/
+    chunk_shape[0] = 1 << 20; /* Just a guess...*/
     chunk_shape[1] = props.dimension;
   } else {
     rank = 1;
     shape[0] = N_total;
     shape[1] = 0;
-    chunk_shape[0] = 1 << 16; /* Just a guess...*/
+    chunk_shape[0] = 1 << 20; /* Just a guess...*/
     chunk_shape[1] = 0;
   }
 
@@ -211,7 +211,7 @@ void prepareArray(const struct engine* e, hid_t grp, char* fileName,
   if (chunk_shape[0] > N_total) chunk_shape[0] = N_total;
 
   /* Change shape of data space */
-  hid_t h_err = H5Sset_extent_simple(h_space, rank, shape, NULL);
+  hid_t h_err = H5Sset_extent_simple(h_space, rank, shape, shape);
   if (h_err < 0) {
     error("Error while changing data space shape for field '%s'.", props.name);
   }
@@ -228,11 +228,15 @@ void prepareArray(const struct engine* e, hid_t grp, char* fileName,
 
   /* Impose data compression */
   if (e->snapshotCompression > 0) {
+    h_err = H5Pset_shuffle(h_prop);
+    if (h_err < 0)
+      error("Error while setting shuffling options for field '%s'.",
+            props.name);
+
     h_err = H5Pset_deflate(h_prop, e->snapshotCompression);
-    if (h_err < 0) {
+    if (h_err < 0)
       error("Error while setting compression options for field '%s'.",
             props.name);
-    }
   }
 
   /* Create dataset */

src/single_io.c

@@ -204,13 +204,13 @@ void writeArray(const struct engine* e, hid_t grp, char* fileName,
     rank = 2;
     shape[0] = N;
     shape[1] = props.dimension;
-    chunk_shape[0] = 1 << 16; /* Just a guess...*/
+    chunk_shape[0] = 1 << 20; /* Just a guess...*/
     chunk_shape[1] = props.dimension;
   } else {
     rank = 1;
     shape[0] = N;
     shape[1] = 0;
-    chunk_shape[0] = 1 << 16; /* Just a guess...*/
+    chunk_shape[0] = 1 << 20; /* Just a guess...*/
     chunk_shape[1] = 0;
   }
 
@@ -218,7 +218,7 @@ void writeArray(const struct engine* e, hid_t grp, char* fileName,
   if (chunk_shape[0] > N) chunk_shape[0] = N;
 
   /* Change shape of data space */
-  hid_t h_err = H5Sset_extent_simple(h_space, rank, shape, NULL);
+  hid_t h_err = H5Sset_extent_simple(h_space, rank, shape, shape);
   if (h_err < 0) {
     error("Error while changing data space shape for field '%s'.", props.name);
   }
@@ -235,11 +235,15 @@ void writeArray(const struct engine* e, hid_t grp, char* fileName,
 
   /* Impose data compression */
   if (e->snapshotCompression > 0) {
+    h_err = H5Pset_shuffle(h_prop);
+    if (h_err < 0)
+      error("Error while setting shuffling options for field '%s'.",
+            props.name);
+
     h_err = H5Pset_deflate(h_prop, e->snapshotCompression);
-    if (h_err < 0) {
+    if (h_err < 0)
       error("Error while setting compression options for field '%s'.",
             props.name);
-    }
   }
 
   /* Create dataset */