merge

5 files changed, 71 insertions, 8 deletions

diff --git a/Carpet/CarpetIOHDF5/src/CarpetIOHDF5.cc b/Carpet/CarpetIOHDF5/src/CarpetIOHDF5.cc
index 12c9a68ea..c3053c332 100644
--- a/Carpet/CarpetIOHDF5/src/CarpetIOHDF5.cc
+++ b/Carpet/CarpetIOHDF5/src/CarpetIOHDF5.cc
@@ -229,6 +229,28 @@ void CarpetIOHDF5_TerminationCheckpoint (CCTK_ARGUMENTS)
 }
 
 
+CCTK_INT CarpetIOHDF5_SetCheckpointGroups (CCTK_INT const * const groups,
+                                           CCTK_INT const ngroups)
+{
+  if (ngroups == -1) {
+    // Checkpoint all groups
+    groups_to_checkpoint.clear();
+  } else {
+    assert (ngroups >= 0);
+    groups_to_checkpoint.resize(CCTK_NumGroups());
+    for (int n=0; n<CCTK_NumGroups(); ++n) {
+      groups_to_checkpoint.at(n) = false;
+    }
+    for (int n=0; n<ngroups; ++n) {
+      groups_to_checkpoint.at(groups[n]) = true;
+    }
+  }
+  return 0;
+}
+
+vector<bool> groups_to_checkpoint;
+
+
 hid_t CCTKtoHDF5_Datatype (const cGH* const cctkGH,
                            int cctk_type, bool single_precision)
 {
@@ -938,9 +960,16 @@ static void Checkpoint (const cGH* const cctkGH, int called_from)
       }
 
       for (int group = CCTK_NumGroups () - 1; group >= 0; group--) {
+        /* skip variables which have been disabled for checkpointing */
+        if (not groups_to_checkpoint.empty() and
+            not groups_to_checkpoint.at(group))
+        {
+          continue;
+        }
         /* only dump groups which have storage assigned */
         if (CCTK_QueryGroupStorageI (cctkGH, group) <= 0 or
-          CCTK_NumVarsInGroupI(group) == 0) {
+            CCTK_NumVarsInGroupI(group) == 0)
+        {
           continue;
         }
 
diff --git a/Carpet/CarpetIOHDF5/src/CarpetIOHDF5.hh b/Carpet/CarpetIOHDF5/src/CarpetIOHDF5.hh
index dfa6a276e..3cff7bf3b 100644
--- a/Carpet/CarpetIOHDF5/src/CarpetIOHDF5.hh
+++ b/Carpet/CarpetIOHDF5/src/CarpetIOHDF5.hh
@@ -247,7 +247,8 @@ namespace CarpetIOHDF5
 
   };                            // struct IOHDF5
 
-  // scheduled routines (must be declared as C according to schedule.ccl)
+  // scheduled and aliased routines (must be declared as C according
+  // to schedule.ccl)
   extern "C" {
 
     int CarpetIOHDF5_RecoverParameters (void);
@@ -261,8 +262,15 @@ namespace CarpetIOHDF5
     void CarpetIOHDF5_EvolutionCheckpoint (CCTK_ARGUMENTS);
     void CarpetIOHDF5_TerminationCheckpoint (CCTK_ARGUMENTS);
 
+    CCTK_INT CarpetIOHDF5_SetCheckpointGroups (CCTK_INT const *groups,
+                                               CCTK_INT ngroups);
+
   } // extern "C"
 
+  // Which groups should be checkpointed. If empty, all variables
+  // should be checkpointed (default).
+  extern vector<bool> groups_to_checkpoint;
+
 } // namespace CarpetIOHDF5
 
 #endif // !defined(CARPETIOHDF5_HH)
diff --git a/Carpet/CarpetIOHDF5/src/Output.cc b/Carpet/CarpetIOHDF5/src/Output.cc
index 1b5bf8eec..d77324860 100644
--- a/Carpet/CarpetIOHDF5/src/Output.cc
+++ b/Carpet/CarpetIOHDF5/src/Output.cc
@@ -203,7 +203,8 @@ int WriteVarUnchunked (const cGH* const cctkGH,
         processor_component->allocate (overlap, 0);
         for (comm_state state; not state.done(); state.step()) {
           int const p = hh->processor(refinementlevel,component);
-          processor_component->copy_from (state, data, overlap, 0, p);
+          processor_component->copy_from
+            (state, data, overlap, overlap, NULL, 0, p);
         }
 
         // Write data
@@ -380,7 +381,7 @@ int WriteVarChunkedSequential (const cGH* const cctkGH,
       processor_component->allocate (bbox, 0);
       for (comm_state state; not state.done(); state.step()) {
         int const p = hh->processor(refinementlevel,component);
-        processor_component->copy_from (state, data, bbox, 0, p);
+        processor_component->copy_from (state, data, bbox, bbox, NULL, 0, p);
       }
 
       // Write data on I/O processor 0
diff --git a/Carpet/CarpetIOHDF5/src/OutputSlice.cc b/Carpet/CarpetIOHDF5/src/OutputSlice.cc
index 8c4c42295..f0d570ced 100644
--- a/Carpet/CarpetIOHDF5/src/OutputSlice.cc
+++ b/Carpet/CarpetIOHDF5/src/OutputSlice.cc
@@ -648,7 +648,8 @@ namespace CarpetIOHDF5 {
               for (comm_state state; not state.done(); state.step()) {
                 for (size_t n=0; n<datas.size(); ++n) {
                   tmpdatas.at(n)->copy_from
-                    (state, datas.at(n), data_ext, ioproc, proc);
+                    (state, datas.at(n), data_ext, data_ext, NULL,
+                     ioproc, proc);
                 }
               }
 
@@ -1420,11 +1421,23 @@ namespace CarpetIOHDF5 {
         datasetname.append (datasetname_suffix.str());
   
         // remove an already existing dataset of the same name
-        if (slice_requests.at(vi + n)->check_exist) {
+        ioRequest* request = slice_requests.at(vi + n);
+        if (not request) {
+#ifdef IOUTIL_PARSER_HAS_OUT_DT
+        request = IOUtil_DefaultIORequest (cctkGH, vi + n, 1, -1.0);
+#else
+        request = IOUtil_DefaultIORequest (cctkGH, vi + n, 1);
+#endif
+        }
+        if (request->check_exist) {
           H5E_BEGIN_TRY {
             H5Gunlink(file, datasetname.c_str());
           } H5E_END_TRY;
         }
+        // free I/O request structure
+        if (request != slice_requests.at(vi + n)) {
+          IOUtil_FreeIORequest (&request);
+        }
 
         // write the dataset
         hid_t dataset;
@@ -1516,11 +1529,23 @@ namespace CarpetIOHDF5 {
         datasetname.append (datasetname_suffix.str());
 
         // remove an already existing dataset of the same name
-        if (slice_requests[vi + n]->check_exist) {
+        ioRequest* request = slice_requests.at(vi + n);
+        if (not request) {
+#ifdef IOUTIL_PARSER_HAS_OUT_DT
+        request = IOUtil_DefaultIORequest (cctkGH, vi + n, 1, -1.0);
+#else
+        request = IOUtil_DefaultIORequest (cctkGH, vi + n, 1);
+#endif
+        }
+        if (request->check_exist) {
           H5E_BEGIN_TRY {
             H5Gunlink(file, datasetname.c_str());
           } H5E_END_TRY;
         }
+        // free I/O request structure
+        if (request != slice_requests.at(vi + n)) {
+          IOUtil_FreeIORequest (&request);
+        }
 
         // write the dataset
         hid_t dataset;
diff --git a/Carpet/CarpetIOHDF5/src/make.configuration.deps b/Carpet/CarpetIOHDF5/src/make.configuration.deps
index 74b2a2aa6..b118cf3b9 100644
--- a/Carpet/CarpetIOHDF5/src/make.configuration.deps
+++ b/Carpet/CarpetIOHDF5/src/make.configuration.deps
@@ -23,4 +23,4 @@ $(UTIL_DIR)/%: $(CARPETIOHDF5_BUILD_DIR)/%.o
 $(CARPETIOHDF5_BUILD_DIR)/%.o: $(CARPETIOHDF5_SRC_DIR)/%.cc
 	@echo Compiling $<
 	if [ ! -d $(CARPETIOHDF5_BUILD_DIR) ]; then $(MKDIR) $(MKDIRFLAGS) $(CARPETIOHDF5_BUILD_DIR) ; fi
-	$(CXX) $< $(CARPETIOHDF5_CXXFLAGS) -c -o $@
+	$(CXX) $< $(CARPETIOHDF5_CXXFLAGS) -DTHORN_IS_CarpetIOHDF5 -c -o $@