CarpetIOHDF5: close all HDF5 objects when output file is closed

also garbage collect HDF5 at each H5close

3 files changed, 35 insertions, 10 deletions

diff --git a/Carpet/CarpetIOHDF5/src/CarpetIOHDF5.cc b/Carpet/CarpetIOHDF5/src/CarpetIOHDF5.cc
index 40a2a5d56..27ce292c4 100644
--- a/Carpet/CarpetIOHDF5/src/CarpetIOHDF5.cc
+++ b/Carpet/CarpetIOHDF5/src/CarpetIOHDF5.cc
@@ -839,13 +839,17 @@ static int OutputVarAs (const cGH* const cctkGH, const char* const fullname,
     }
 
     if (is_new_file) {
+      hid_t fapl_id;
+      HDF5_ERROR (fapl_id = H5Pcreate (H5P_FILE_ACCESS));
+      HDF5_ERROR (H5Pset_fclose_degree (fapl_id, H5F_CLOSE_STRONG));
       HDF5_ERROR (file = H5Fcreate (c_filename, H5F_ACC_TRUNC, H5P_DEFAULT,
-                                    H5P_DEFAULT));
+                                    fapl_id));
       if (output_index) {
         HDF5_ERROR (index_file = H5Fcreate (index_filename.c_str(),
                                             H5F_ACC_TRUNC, H5P_DEFAULT,
-                                            H5P_DEFAULT));
+                                            fapl_id));
       }
+      HDF5_ERROR (H5Pclose (fapl_id));
       // write metadata information
       error_count +=
         WriteMetadata (cctkGH, nioprocs, firstvar, numvars, false, file);
@@ -855,9 +859,13 @@ static int OutputVarAs (const cGH* const cctkGH, const char* const fullname,
           WriteMetadata (cctkGH, nioprocs, firstvar, numvars, false, index_file);
       }
     } else {
-      HDF5_ERROR (file = H5Fopen (c_filename, H5F_ACC_RDWR, H5P_DEFAULT));
+      hid_t fapl_id;
+      HDF5_ERROR (fapl_id = H5Pcreate (H5P_FILE_ACCESS));
+      HDF5_ERROR (H5Pset_fclose_degree (fapl_id, H5F_CLOSE_STRONG));
+      HDF5_ERROR (file = H5Fopen (c_filename, H5F_ACC_RDWR, fapl_id));
       if (output_index)
-        HDF5_ERROR (index_file = H5Fopen (index_filename.c_str(), H5F_ACC_RDWR, H5P_DEFAULT));
+        HDF5_ERROR (index_file = H5Fopen (index_filename.c_str(), H5F_ACC_RDWR, fapl_id));
+      HDF5_ERROR (H5Pclose (fapl_id));
     }
     io_files += 1;
   }
@@ -902,6 +910,7 @@ static int OutputVarAs (const cGH* const cctkGH, const char* const fullname,
     if (output_index)
       HDF5_ERROR (H5Fclose (index_file));
   }
+  HDF5_ERROR (H5garbage_collect());
   {
     CCTK_REAL local[2], global[2];
     local[0] = io_files;
@@ -956,8 +965,11 @@ static void Checkpoint (const cGH* const cctkGH, int called_from)
                   tempname);
     }
 
+    hid_t fapl_id;
+    HDF5_ERROR (fapl_id = H5Pcreate (H5P_FILE_ACCESS));
+    HDF5_ERROR (H5Pset_fclose_degree (fapl_id, H5F_CLOSE_STRONG));
     HDF5_ERROR (file = H5Fcreate (tempname, H5F_ACC_TRUNC, H5P_DEFAULT,
-                                  H5P_DEFAULT));
+                                  fapl_id));
 
     // write metadata information
     error_count += WriteMetadata (cctkGH, nioprocs, -1, -1, true, file);
@@ -966,10 +978,11 @@ static void Checkpoint (const cGH* const cctkGH, int called_from)
 
       HDF5_ERROR (index_file = H5Fcreate (index_tempname,
                                           H5F_ACC_TRUNC, H5P_DEFAULT,
-                                          H5P_DEFAULT));
+                                          fapl_id));
       error_count +=
         WriteMetadata (cctkGH, nioprocs, -1, -1, true, index_file);
     }
+    HDF5_ERROR (H5Pclose (fapl_id));
   }
 
   // remember the current wall time
@@ -1103,6 +1116,7 @@ static void Checkpoint (const cGH* const cctkGH, int called_from)
   if (index_file >= 0) {
     HDF5_ERROR (H5Fclose(index_file));
   }
+  HDF5_ERROR (H5garbage_collect());
 
 
   // get global error count
diff --git a/Carpet/CarpetIOHDF5/src/Output.cc b/Carpet/CarpetIOHDF5/src/Output.cc
index 44f9df478..7288c9bc2 100644
--- a/Carpet/CarpetIOHDF5/src/Output.cc
+++ b/Carpet/CarpetIOHDF5/src/Output.cc
@@ -68,6 +68,7 @@ int WriteVarUnchunked (const cGH* const cctkGH,
   hid_t plist;
   HDF5_ERROR (plist = H5Pcreate (H5P_FILE_ACCESS));
   HDF5_ERROR (H5Pset_fapl_core (plist, 0, 0));
+  HDF5_ERROR (H5Pset_fclose_degree (plist, H5F_CLOSE_STRONG));
 
   // Traverse all maps
   BEGIN_MAP_LOOP (cctkGH, group.grouptype) {
@@ -135,6 +136,7 @@ int WriteVarUnchunked (const cGH* const cctkGH,
         // than recombining an HDF5 dataset on a disk file.
         HDF5_ERROR (memfile = H5Fcreate ("tempfile", H5F_ACC_EXCL, H5P_DEFAULT,
                                          plist));
+        HDF5_ERROR (H5Pclose (plist));
         HDF5_ERROR (dataspace = H5Screate_simple (group.dim, shape, NULL));
         HDF5_ERROR (memdataset = H5Dcreate (memfile, datasetname.str().c_str(),
                                          filedatatype, dataspace, H5P_DEFAULT));
diff --git a/Carpet/CarpetIOHDF5/src/OutputSlice.cc b/Carpet/CarpetIOHDF5/src/OutputSlice.cc
index acc94493c..57f3e046f 100644
--- a/Carpet/CarpetIOHDF5/src/OutputSlice.cc
+++ b/Carpet/CarpetIOHDF5/src/OutputSlice.cc
@@ -817,13 +817,17 @@ namespace CarpetIOHDF5 {
       }
 
       if (truncate_file or not file_exists) {
+        hid_t fapl_id;
+        HDF5_ERROR (fapl_id = H5Pcreate (H5P_FILE_ACCESS));
+        HDF5_ERROR (H5Pset_fclose_degree (fapl_id, H5F_CLOSE_STRONG));
         HDF5_ERROR(file = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT,
-                                    H5P_DEFAULT));
+                                    fapl_id));
         if (output_index) {
           HDF5_ERROR (index_file = H5Fcreate (index_filename.c_str(),
                                               H5F_ACC_TRUNC, H5P_DEFAULT,
-                                              H5P_DEFAULT));
+                                              fapl_id));
         }
+        HDF5_ERROR (H5Pclose (fapl_id));
         // write metadata information
         error_count +=
           WriteMetadata(cctkGH, nioprocs, vindex, numvars, false, file);
@@ -833,9 +837,13 @@ namespace CarpetIOHDF5 {
             WriteMetadata (cctkGH, nioprocs, vindex, numvars, false, index_file);
         }
       } else {
-        HDF5_ERROR (file = H5Fopen(filename, H5F_ACC_RDWR, H5P_DEFAULT));
+        hid_t fapl_id;
+        HDF5_ERROR (fapl_id = H5Pcreate (H5P_FILE_ACCESS));
+        HDF5_ERROR (H5Pset_fclose_degree (fapl_id, H5F_CLOSE_STRONG));
+        HDF5_ERROR (file = H5Fopen(filename, H5F_ACC_RDWR, fapl_id));
+        HDF5_ERROR (H5Pclose (fapl_id));
         if (output_index)
-          HDF5_ERROR (index_file = H5Fopen (index_filename.c_str(), H5F_ACC_RDWR, H5P_DEFAULT));
+          HDF5_ERROR (index_file = H5Fopen (index_filename.c_str(), H5F_ACC_RDWR,fapl_id));
       }
       io_files += 1;
 
@@ -859,6 +867,7 @@ namespace CarpetIOHDF5 {
       if (output_index and index_file >= 0) {
         HDF5_ERROR (H5Fclose (index_file));
       }
+      HDF5_ERROR (H5garbage_collect());
     }
     if (nioprocs > 1) {
       CCTK_REAL local[2], global[2];