Make sure the HDF5 dataset chunks are smaller than the dataset itself.

That solves issue #116 (closed). Thanks !

No need to do anything for the parallel-HDF5 version as there is no chunking there.

src/serial_io.c

@@ -201,6 +201,9 @@ void prepareArray(hid_t grp, char* fileName, FILE* xmfFile, char* name,
chunk_shape[1] = 0;
}
+  /* Make sure the chunks are not larger than the dataset */
+  if (chunk_shape[0] > N_total) chunk_shape[0] = N_total;
+
/* Change shape of data space */
h_err = H5Sset_extent_simple(h_space, rank, shape, NULL);
if (h_err < 0) {