CarpetIOHDF5: support indices in sequential chunked output

which happens to be the output method used for single process runs.

3 files changed, 25 insertions, 4 deletions

diff --git a/Carpet/CarpetIOHDF5/src/CarpetIOHDF5.cc b/Carpet/CarpetIOHDF5/src/CarpetIOHDF5.cc
index 909764b46..85b10c229 100644
--- a/Carpet/CarpetIOHDF5/src/CarpetIOHDF5.cc
+++ b/Carpet/CarpetIOHDF5/src/CarpetIOHDF5.cc
@@ -871,7 +871,7 @@ static int OutputVarAs (const cGH* const cctkGH, const char* const fullname,
         groupdata.disttype == CCTK_DISTRIB_CONSTANT) {
       error_count += WriteVarUnchunked (cctkGH, file, io_bytes, r, false);
     } else if (CCTK_EQUALS (out_mode, "onefile")) {
-      error_count += WriteVarChunkedSequential (cctkGH, file, io_bytes, r, false);
+      error_count += WriteVarChunkedSequential (cctkGH, file, io_bytes, r, false, index_file);
     } else {
       error_count += WriteVarChunkedParallel (cctkGH, file, io_bytes, r, false, index_file);
     }
diff --git a/Carpet/CarpetIOHDF5/src/CarpetIOHDF5.hh b/Carpet/CarpetIOHDF5/src/CarpetIOHDF5.hh
index 3cff7bf3b..42c7d6622 100644
--- a/Carpet/CarpetIOHDF5/src/CarpetIOHDF5.hh
+++ b/Carpet/CarpetIOHDF5/src/CarpetIOHDF5.hh
@@ -119,7 +119,8 @@ namespace CarpetIOHDF5
                                  hid_t file,
                                  CCTK_REAL & io_bytes,
                                  const ioRequest* const request,
-                                 bool called_from_checkpoint);
+                                 bool called_from_checkpoint,
+                                 hid_t index = -1);
   int WriteVarChunkedParallel (const cGH* const cctkGH,
                                hid_t file,
                                CCTK_REAL & io_bytes,
diff --git a/Carpet/CarpetIOHDF5/src/Output.cc b/Carpet/CarpetIOHDF5/src/Output.cc
index f8c580335..1df156c16 100644
--- a/Carpet/CarpetIOHDF5/src/Output.cc
+++ b/Carpet/CarpetIOHDF5/src/Output.cc
@@ -307,7 +307,8 @@ int WriteVarChunkedSequential (const cGH* const cctkGH,
                                hid_t outfile,
                                CCTK_REAL & io_bytes,
                                const ioRequest* const request,
-                               bool called_from_checkpoint)
+                               bool called_from_checkpoint,
+                               hid_t indexfile)
 {
   DECLARE_CCTK_PARAMETERS;
 
@@ -353,11 +354,13 @@ int WriteVarChunkedSequential (const cGH* const cctkGH,
 
       // Get the shape of the HDF5 dataset (in Fortran index order)
       hsize_t shape[dim];
+      hsize_t index_shape[dim];
       hsize_t num_elems = 1;
       for (int d = 0; d < group.dim; ++d) {
         assert (group.dim-1-d>=0 and group.dim-1-d<dim);
         shape[group.dim-1-d] = (bbox.shape() / bbox.stride())[d];
         num_elems *= shape[group.dim-1-d];
+        index_shape[group.dim-1-d]  = 1;
       }
 
       // Don't create zero-sized components
@@ -426,6 +429,8 @@ int WriteVarChunkedSequential (const cGH* const cctkGH,
           if (request->check_exist) {
             H5E_BEGIN_TRY {
               H5Gunlink (outfile, datasetname.str().c_str());
+              if (indexfile != -1)
+                H5Gunlink (indexfile, datasetname.str().c_str());
             } H5E_END_TRY;
           }
 
@@ -438,7 +443,7 @@ int WriteVarChunkedSequential (const cGH* const cctkGH,
           }
 
           // Write the component as an individual dataset
-          hid_t plist, dataspace, dataset;
+          hid_t plist, dataspace, dataset, index_dataspace, index_dataset;
           HDF5_ERROR (plist = H5Pcreate (H5P_DATASET_CREATE));
           // enable compression if requested
           const int compression_lvl = request->compression_level >= 0 ?
@@ -456,6 +461,14 @@ int WriteVarChunkedSequential (const cGH* const cctkGH,
           HDF5_ERROR (dataspace = H5Screate_simple (group.dim, shape, NULL));
           HDF5_ERROR (dataset = H5Dcreate (outfile, datasetname.str().c_str(),
                                            filedatatype, dataspace, plist));
+
+          if (indexfile != -1) {
+            HDF5_ERROR (index_dataspace = H5Screate_simple (group.dim,
+                                                            index_shape, NULL));
+            HDF5_ERROR (index_dataset = H5Dcreate (indexfile, datasetname.str().c_str(),
+                                                   filedatatype, index_dataspace, H5P_DEFAULT));
+          }
+
           io_bytes +=
             H5Sget_simple_extent_npoints (dataspace) *
             H5Tget_size (filedatatype);
@@ -466,6 +479,13 @@ int WriteVarChunkedSequential (const cGH* const cctkGH,
           error_count += AddAttributes (cctkGH, fullname, group.dim,
                                         refinementlevel, request, bbox,dataset);
           HDF5_ERROR (H5Dclose (dataset));
+
+          if (indexfile != -1) {
+            HDF5_ERROR (H5Sclose (index_dataspace));
+            error_count += AddAttributes (cctkGH, fullname, group.dim,refinementlevel,
+                                          request, bbox, index_dataset, true);
+            HDF5_ERROR (H5Dclose (index_dataset));
+          }
         }
 
       } // if dist::rank() == 0