CarpetIOHDF5: Use string instead of char[] in HDF5 for large attributes

2 files changed, 52 insertions, 18 deletions

diff --git a/Carpet/CarpetIOHDF5/src/CarpetIOHDF5.cc b/Carpet/CarpetIOHDF5/src/CarpetIOHDF5.cc
index 9d3403d91..0ce40eee4 100644
--- a/Carpet/CarpetIOHDF5/src/CarpetIOHDF5.cc
+++ b/Carpet/CarpetIOHDF5/src/CarpetIOHDF5.cc
@@ -1007,10 +1007,10 @@ static void Checkpoint (const cGH* const cctkGH, int called_from)
         int const len = Util_TableGetString (gdata.tagstable, 0, NULL,
                                              "checkpoint");
         if (len > 0) {
-          char* value = new char[len + 1];
+          vector<char> value_buf(len+1);
+          char* value = &value_buf[0];
           Util_TableGetString (gdata.tagstable, len + 1, value, "checkpoint");
           if (len == sizeof ("no") - 1 and CCTK_Equals (value, "no")) {
-            delete[] value;
             continue;
           } else if (not CCTK_Equals (value, "yes")) {
             char* groupname = CCTK_GroupName (group);
@@ -1019,7 +1019,6 @@ static void Checkpoint (const cGH* const cctkGH, int called_from)
                         value, groupname);
             free (groupname);
           }
-          delete[] value;
         }
 
         /* get the number of active timelevels */
@@ -1512,18 +1511,22 @@ static int WriteLargeAttribute (hid_t const group,
                                 char const * const name,
                                 char const * const svalue)
 {
-  hid_t dataspace, dataset;
+  hid_t dataspace, dataset, datatype;
   int error_count = 0;
   
   // Create a dataset, since the data may not fit into an attribute
   hsize_t const size = strlen (svalue) + 1;
-  HDF5_ERROR (dataspace = H5Screate_simple (1, & size, NULL));
-  HDF5_ERROR (dataset = H5Dcreate (group, name, H5T_NATIVE_CHAR,
-                                   dataspace, H5P_DEFAULT));
-  HDF5_ERROR (H5Dwrite (dataset, H5T_NATIVE_CHAR, H5S_ALL, H5S_ALL,
+  HDF5_ERROR (datatype = H5Tcopy (H5T_C_S1));
+  HDF5_ERROR (H5Tset_size (datatype, size));
+
+  HDF5_ERROR (dataspace = H5Screate (H5S_SCALAR));
+  HDF5_ERROR (dataset   = H5Dcreate (group, name, datatype,
+                                     dataspace, H5P_DEFAULT));
+  HDF5_ERROR (H5Dwrite (dataset, datatype, H5S_ALL, H5S_ALL,
                         H5P_DEFAULT, svalue));
   HDF5_ERROR (H5Dclose (dataset));
   HDF5_ERROR (H5Sclose (dataspace));
+  HDF5_ERROR (H5Tclose (datatype));
   
   return error_count;
 }
diff --git a/Carpet/CarpetIOHDF5/src/Input.cc b/Carpet/CarpetIOHDF5/src/Input.cc
index e50acf1c9..efd5f3199 100644
--- a/Carpet/CarpetIOHDF5/src/Input.cc
+++ b/Carpet/CarpetIOHDF5/src/Input.cc
@@ -470,12 +470,12 @@ int Recover (cGH* cctkGH, const char *basefilename, int called_from)
       int tagstable = CCTK_GroupTagsTableI (gindex);
       int const len = Util_TableGetString (tagstable, 0, NULL, "checkpoint");
       if (len > 0) {
-        char* value = new char[len + 1];
+        vector<char> value_buf(len+1);
+        char* value = &value_buf[0];
         Util_TableGetString (tagstable, len + 1, value, "checkpoint");
         if (len == sizeof ("no") - 1 and CCTK_Equals (value, "no")) {
           not_checkpointed[vindex] = true;
         }
-        delete[] value;
       }
     }
   }
@@ -972,15 +972,29 @@ static list<fileset_t>::iterator OpenFileSet (const cGH* const cctkGH,
       CCTK_VInfo (CCTK_THORNSTRING, "Recovering parameters from checkpoint "
                   "file '%s'", file.filename);
     }
-    hid_t dataset;
+    hid_t dataset, datatype;
+    size_t len;
+    htri_t old_data;
+
     HDF5_ERROR (dataset = H5Dopen (file.file,
                                    METADATA_GROUP "/" ALL_PARAMETERS));
-    char *parameters = new char[H5Dget_storage_size (dataset) + 1];
-    HDF5_ERROR (H5Dread (dataset, H5T_NATIVE_CHAR, H5S_ALL, H5S_ALL,
+    HDF5_ERROR (datatype = H5Dget_type(dataset));
+    HDF5_ERROR (old_data = H5Tequal(datatype, H5T_NATIVE_CHAR));
+    if (old_data) {
+        /* old data that stored this as an array of chars */
+        CCTK_WARN (CCTK_WARN_ALERT, "Old-style checkpoint data found.");
+        HDF5_ERROR (len = H5Dget_storage_size(dataset) + 1);
+    } else {
+        HDF5_ERROR (len = H5Tget_size(datatype));
+    }
+    vector<char> parameter_buf(len);
+    char* parameters = &parameter_buf[0];
+
+    HDF5_ERROR (H5Dread (dataset, datatype, H5S_ALL, H5S_ALL,
                          H5P_DEFAULT, parameters));
     HDF5_ERROR (H5Dclose (dataset));
+    HDF5_ERROR (H5Tclose (datatype));
     IOUtil_SetAllParameters (parameters);
-    delete[] parameters;
 
     num_reflevels = fileset.num_reflevels;
   }
@@ -1062,11 +1076,28 @@ static void ReadMetadata (fileset_t& fileset, hid_t file)
     dataset = H5Dopen (metadata, GRID_STRUCTURE);
   } H5E_END_TRY;
   if (dataset >= 0) {
-    vector<char> gs_cstr (H5Dget_storage_size (dataset) + 1);
-    HDF5_ERROR (H5Dread (dataset, H5T_NATIVE_CHAR, H5S_ALL, H5S_ALL,
-                         H5P_DEFAULT, &gs_cstr.front()));
+    hid_t datatype;
+    htri_t old_data;
+    size_t len;
+
+    HDF5_ERROR (datatype = H5Dget_type(dataset));
+    HDF5_ERROR (datatype = H5Dget_type(dataset));
+    HDF5_ERROR (old_data = H5Tequal(datatype, H5T_NATIVE_CHAR));
+    if (old_data) {
+        /* old data that stored this as an array of chars */
+        CCTK_WARN (CCTK_WARN_ALERT, "Old-style checkpoint data found.");
+        HDF5_ERROR (len = H5Dget_storage_size(dataset) + 1);
+    } else {
+        HDF5_ERROR (len = H5Tget_size(datatype));
+    }
+    vector<char> gs_str_buf(len);
+    char* gs_str = &gs_str_buf[0];
+
+    HDF5_ERROR (H5Dread (dataset, datatype, H5S_ALL, H5S_ALL,
+                         H5P_DEFAULT, gs_str));
     HDF5_ERROR (H5Dclose (dataset));
-    istringstream gs_buf (&gs_cstr.front());
+    HDF5_ERROR (H5Tclose (datatype));
+    istringstream gs_buf (gs_str);
     
     skipws (gs_buf);
     consume (gs_buf, "grid_superstructure:");