Merge branch 'develop' into lroberts36/add-fine-variables

CHANGELOG.md

@@ -25,6 +25,7 @@
 - [[PR 1004]](https://github.com/parthenon-hpc-lab/parthenon/pull/1004) Allow parameter modification from an input file for restarts
 
 ### Fixed (not changing behavior/API/variables/...)
+- [[PR 1104]](https://github.com/parthenon-hpc-lab/parthenon/pull/1104) Fix reading restarts due to hidden ghost var
 - [[PR 1098]](https://github.com/parthenon-hpc-lab/parthenon/pull/1098) Move to symmetrized logical coordinates and fix SMR bug
 - [[PR 1095]](https://github.com/parthenon-hpc-lab/parthenon/pull/1095) Add missing include guards in hdf5 restart
 - [[PR 1093]](https://github.com/parthenon-hpc-lab/parthenon/pull/1093) Fix forest size for symmetry dimensions

src/outputs/restart.hpp

@@ -132,8 +132,7 @@ class RestartReader {
   // perhaps belongs in a destructor?
   void Close();
 
-  // Does file have ghost cells?
-  int hasGhost;
+  [[nodiscard]] virtual int HasGhost() const = 0;
 };
 
 } // namespace parthenon

src/outputs/restart_hdf5.cpp

@@ -53,7 +53,7 @@ RestartReaderHDF5::RestartReaderHDF5(const char *filename) : filename_(filename)
   fh_ = H5F::FromHIDCheck(H5Fopen(filename, H5F_ACC_RDONLY, H5P_DEFAULT));
   params_group_ = H5G::FromHIDCheck(H5Oopen(fh_, "Params", H5P_DEFAULT));
 
-  hasGhost = GetAttr<int>("Info", "IncludesGhost");
+  has_ghost = GetAttr<int>("Info", "IncludesGhost");
 #endif // ENABLE_HDF5
 }
 
@@ -224,7 +224,7 @@ void RestartReaderHDF5::ReadBlocks(const std::string &name, IndexRange range,
 
   offset[0] = static_cast<hsize_t>(range.s);
   count[0] = static_cast<hsize_t>(range.e - range.s + 1);
-  const IndexDomain domain = hasGhost ? IndexDomain::entire : IndexDomain::interior;
+  const IndexDomain domain = has_ghost != 0 ? IndexDomain::entire : IndexDomain::interior;
 
   // Currently supports versions 3 and 4.
   if (file_output_format_version >= HDF5::OUTPUT_VERSION_FORMAT - 1) {
@@ -245,8 +245,6 @@ void RestartReaderHDF5::ReadBlocks(const std::string &name, IndexRange range,
                            "Buffer (size " + std::to_string(dataVec.size()) +
                                ") is too small for dataset " + name + " (size " +
                                std::to_string(total_count) + ")");
-  PARTHENON_HDF5_CHECK(
-      H5Sselect_hyperslab(hdl.dataspace, H5S_SELECT_SET, offset, NULL, count, NULL));
 
   const H5S memspace = H5S::FromHIDCheck(H5Screate_simple(total_dim, count, NULL));
   PARTHENON_HDF5_CHECK(

src/outputs/restart_hdf5.hpp

@@ -58,6 +58,8 @@ class RestartReaderHDF5 : public RestartReader {
   // Return output format version number. Return -1 if not existent.
   [[nodiscard]] int GetOutputFormatVersion() const override;
 
+  [[nodiscard]] int HasGhost() const override { return has_ghost; };
+
  private:
 #ifdef ENABLE_HDF5
   struct DatasetHandle {
@@ -225,12 +227,12 @@ class RestartReaderHDF5 : public RestartReader {
   // perhaps belongs in a destructor?
   void Close();
 
-  // Does file have ghost cells?
-  int hasGhost;
-
  private:
   const std::string filename_;
 
+  // Does file have ghost cells?
+  int has_ghost;
+
 #ifdef ENABLE_HDF5
   // Currently all restarts are HDF5 files
   // when that changes, this will be revisited

src/parthenon_manager.cpp

@@ -250,7 +250,7 @@ void ParthenonManager::RestartPackages(Mesh &rm, RestartReader &resfile) {
   // Restart packages with information for blocks in ids from the restart file
   // Assumption: blocks are contiguous in restart file, may have to revisit this.
   const IndexDomain theDomain =
-      (resfile.hasGhost ? IndexDomain::entire : IndexDomain::interior);
+      (resfile.HasGhost() != 0 ? IndexDomain::entire : IndexDomain::interior);
   // Get block list and temp array size
   auto &mb = *(rm.block_list.front());
   int nb = rm.GetNumMeshBlocksThisRank(Globals::my_rank);
@@ -364,7 +364,7 @@ void ParthenonManager::RestartPackages(Mesh &rm, RestartReader &resfile) {
       // we update the HDF5 infrastructure!
       if (file_output_format_ver >= HDF5::OUTPUT_VERSION_FORMAT - 1) {
         OutputUtils::PackOrUnpackVar(
-            v_info, resfile.hasGhost, index,
+            v_info, resfile.HasGhost() != 0, index,
             [&](auto index, int topo, int t, int u, int v, int k, int j, int i) {
               v_h(topo, t, u, v, k, j, i) = tmp[index];
             });