Merge branch 'develop' into bprather/flat-set-bounds

CHANGELOG.md

@@ -3,6 +3,7 @@
 ## Current develop
 
 ### Added (new features/APIs/variables/...)
+- [[PR 1103]](https://github.com/parthenon-hpc-lab/parthenon/pull/1103) Add sparsity to vector wave equation test
 - [[PR 1185]](https://github.com/parthenon-hpc-lab/parthenon/pull/1185/files) Bugfix to particle defragmentation
 - [[PR 1184]](https://github.com/parthenon-hpc-lab/parthenon/pull/1184) Fix swarm block neighbor indexing in 1D, 2D
 - [[PR 1183]](https://github.com/parthenon-hpc-lab/parthenon/pull/1183) Fix particle leapfrog example initialization data
@@ -11,6 +12,8 @@
 - [[PR 1161]](https://github.com/parthenon-hpc-lab/parthenon/pull/1161) Make flux field Metadata accessible, add Metadata::CellMemAligned flag, small perfomance upgrades
 
 ### Changed (changing behavior/API/variables/...)
+- [[PR 1209]](https://github.com/parthenon-hpc-lab/parthenon/pull/1209) Ordered history output
+- [[PR 1206]](https://github.com/parthenon-hpc-lab/parthenon/pull/1206) Leapfrog fix
 - [[PR1203]](https://github.com/parthenon-hpc-lab/parthenon/pull/1203) Pin Ubuntu CI image
 - [[PR1177]](https://github.com/parthenon-hpc-lab/parthenon/pull/1177) Make mesh-level boundary conditions usable without the "user" flag
 - [[PR 1187]](https://github.com/parthenon-hpc-lab/parthenon/pull/1187) Make DataCollection::Add safer and generalize MeshBlockData::Initialize
@@ -19,6 +22,8 @@
 - [[PR 1172]](https://github.com/parthenon-hpc-lab/parthenon/pull/1172) Make parthenon manager robust against external MPI init and finalize calls
 
 ### Fixed (not changing behavior/API/variables/...)
+- [[PR 1188]](https://github.com/parthenon-hpc-lab/parthenon/pull/1188) Fix hdf5 output issue for metadata none variables, update test.
+- [[PR 1170]](https://github.com/parthenon-hpc-lab/parthenon/pull/1170) Fixed incorrect initialization of array by a const not constexpr
 - [[PR 1189]](https://github.com/parthenon-hpc-lab/parthenon/pull/1189) Address CUDA MPI/ICP issue with Kokkos <=4.4.1
 - [[PR 1178]](https://github.com/parthenon-hpc-lab/parthenon/pull/1178) Fix issue with mesh pointer when using relative residual tolerance in BiCGSTAB solver.
 - [[PR 1173]](https://github.com/parthenon-hpc-lab/parthenon/pull/1173) Make debugging easier by making parthenon throw an error if ParameterInput is different on multiple MPI ranks.

CMakeLists.txt

@@ -75,9 +75,9 @@ include(cmake/Format.cmake)
 include(cmake/Lint.cmake)
 
 # regression test reference data
-set(REGRESSION_GOLD_STANDARD_VER 24 CACHE STRING "Version of gold standard to download and use")
+set(REGRESSION_GOLD_STANDARD_VER 25 CACHE STRING "Version of gold standard to download and use")
 set(REGRESSION_GOLD_STANDARD_HASH
-  "SHA512=e220df92a335131131e42ddb52dc221a6dbd6bb56361483b4af0292620eeb82ffb21ef3b95fd9a7c5cc158fb754da0bf1a1015bec98b5bbad05f4bceb1ee99bc"
+  "SHA512=314dc8312366d81ba33d1fde25812e9a7697b2f529de29e22662df0d458f1c4bc5b5bb4e649888170f66ffec0df1be20a9cf401944531c1c1ad835e26eaad28f"
   CACHE STRING "Hash of default gold standard file to download")
 option(REGRESSION_GOLD_STANDARD_SYNC "Automatically sync gold standard files." ON)
 

doc/sphinx/src/outputs.rst

@@ -194,7 +194,9 @@ block might look like
 
 This will produce a text file (``.hst``) output file every 1 units of
 simulation time. The content of the file is determined by the functions
-enrolled by specific packages, see :ref:`state history output`.
+enrolled by specific packages, see :ref:`state history output`. Per-package history
+outputs will always be in alphabetical order by package name, which may not match
+the order in which packages were added to a simulation.
 
 Histograms
 ----------

example/advection/advection_package.cpp

@@ -196,6 +196,20 @@ std::shared_ptr<StateDescriptor> Initialize(ParameterInput *pin) {
   m = Metadata({Metadata::Cell, Metadata::OneCopy}, std::vector<int>({1}));
   pkg->AddField("my_derived_var", m);
 
+  // Create a Metadata::None variable for IO testing purposes.
+  // Only load if test_metadata_none is specified in the Advection block
+  auto test_metadata_none =
+      pin->GetOrAddBoolean("Advection", "test_metadata_none", false);
+  pkg->AddParam<bool>("test_metadata_none", test_metadata_none);
+  if (test_metadata_none) {
+    const int nx1 = pin->GetOrAddInteger("parthenon/meshblock", "nx1", 1);
+    const int nx2 = pin->GetOrAddInteger("parthenon/meshblock", "nx2", 1);
+    const int nx3 = pin->GetOrAddInteger("parthenon/meshblock", "nx3", 1);
+    std::vector<int> test_shape = {nx1 + 1, nx2 + 1, nx3 + 1, 3};
+    m = Metadata({Metadata::OneCopy, Metadata::None}, test_shape);
+    pkg->AddField("metadata_none_var", m);
+  }
+
   // List (vector) of HistoryOutputVar that will all be enrolled as output variables
   parthenon::HstVar_list hst_vars = {};
   // Now we add a couple of callback functions
@@ -281,6 +295,7 @@ AmrTag CheckRefinement(MeshBlockData<Real> *rc) {
 void PreFill(MeshBlockData<Real> *rc) {
   auto pmb = rc->GetBlockPointer();
   auto pkg = pmb->packages.Get("advection_package");
+  const bool test_metadata_none = pkg->Param<bool>("test_metadata_none");
   bool fill_derived = pkg->Param<bool>("fill_derived");
 
   if (fill_derived) {
@@ -302,6 +317,24 @@ void PreFill(MeshBlockData<Real> *rc) {
           v(out + n, k, j, i) = 1.0 - v(in + n, k, j, i);
         });
   }
+
+  // Fill the metadata::None var with index gymnastics.
+  if (test_metadata_none) {
+    const int nx1 = pmb->cellbounds.ncellsi(IndexDomain::interior);
+    const int nx2 = pmb->cellbounds.ncellsj(IndexDomain::interior);
+    const int nx3 = pmb->cellbounds.ncellsk(IndexDomain::interior);
+
+    // packing in principle unnecessary/convoluted here and just done for demonstration
+    std::vector<std::string> vars({"metadata_none_var"});
+    PackIndexMap imap;
+    const auto &v = rc->PackVariables(vars, imap);
+
+    pmb->par_for(
+        PARTHENON_AUTO_LABEL, 0, 2, 0, nx3, 0, nx2, 0, nx1,
+        KOKKOS_LAMBDA(const int n, const int k, const int j, const int i) {
+          v(n, k, j, i) = n + k + j + i;
+        });
+  }
 }
 
 // this is the package registered function to fill derived

example/fine_advection/advection_driver.cpp

@@ -21,6 +21,7 @@
 #include "amr_criteria/refinement_package.hpp"
 #include "bvals/comms/bvals_in_one.hpp"
 #include "interface/metadata.hpp"
+#include "interface/state_descriptor.hpp"
 #include "interface/update.hpp"
 #include "mesh/meshblock_pack.hpp"
 #include "parthenon/driver.hpp"
@@ -72,6 +73,12 @@ TaskCollection AdvectionDriver::MakeTaskCollection(BlockList_t &blocks, const in
   TaskCollection tc;
   TaskID none(0);
 
+  std::shared_ptr<parthenon::StateDescriptor> pkg =
+      pmesh->packages.Get("advection_package");
+  const auto do_regular_advection = pkg->Param<bool>("do_regular_advection");
+  const auto do_fine_advection = pkg->Param<bool>("do_fine_advection");
+  const auto do_CT_advection = pkg->Param<bool>("do_CT_advection");
+
   // Build MeshBlockData containers that will be included in MeshData containers. It is
   // gross that this has to be done by hand.
   const auto &stage_name = integrator->stage_name;
@@ -118,35 +125,49 @@ TaskCollection AdvectionDriver::MakeTaskCollection(BlockList_t &blocks, const in
     auto flx = none;
     auto flx_fine = none;
     for (auto face : faces) {
-      flx = flx | tl.AddTask(none, advection_package::CalculateFluxes<pack_desc_t>, desc,
-                             face, parthenon::CellLevel::same, mc0.get());
-      flx_fine = flx_fine |
-                 tl.AddTask(none, advection_package::CalculateFluxes<pack_desc_fine_t>,
-                            desc_fine, face, parthenon::CellLevel::fine, mc0.get());
+      if (do_regular_advection) {
+        flx = flx | tl.AddTask(none, advection_package::CalculateFluxes<pack_desc_t>,
+                               desc, face, parthenon::CellLevel::same, mc0.get());
+      }
+      if (do_fine_advection) {
+        flx_fine = flx_fine |
+                   tl.AddTask(none, advection_package::CalculateFluxes<pack_desc_fine_t>,
+                              desc_fine, face, parthenon::CellLevel::fine, mc0.get());
+      }
     }
 
     auto vf_dep = none;
-    for (auto edge : std::vector<TE>{TE::E1, TE::E2, TE::E3}) {
-      vf_dep = tl.AddTask(vf_dep, advection_package::CalculateVectorFluxes<C, D>, edge,
-                          parthenon::CellLevel::same, 1.0, mc0.get());
-      vf_dep = tl.AddTask(vf_dep, advection_package::CalculateVectorFluxes<D, C>, edge,
-                          parthenon::CellLevel::same, -1.0, mc0.get());
+    if (do_CT_advection) {
+      for (auto edge : std::vector<TE>{TE::E1, TE::E2, TE::E3}) {
+        vf_dep = tl.AddTask(vf_dep, advection_package::CalculateVectorFluxes<C, D>, edge,
+                            parthenon::CellLevel::same, 1.0, mc0.get());
+        vf_dep = tl.AddTask(vf_dep, advection_package::CalculateVectorFluxes<D, C>, edge,
+                            parthenon::CellLevel::same, -1.0, mc0.get());
+      }
     }
 
     auto set_flx = parthenon::AddFluxCorrectionTasks(
         start_flxcor | flx | flx_fine | vf_dep, tl, mc0, pmesh->multilevel);
 
-    auto update =
-        AddUpdateTasks(set_flx, tl, parthenon::CellLevel::same, TT::Cell, beta, dt, desc,
-                       mbase.get(), mc0.get(), mdudt.get(), mc1.get());
+    auto update = set_flx;
+    if (do_regular_advection) {
+      update = AddUpdateTasks(set_flx, tl, parthenon::CellLevel::same, TT::Cell, beta, dt,
+                              desc, mbase.get(), mc0.get(), mdudt.get(), mc1.get());
+    }
 
-    auto update_fine =
-        AddUpdateTasks(set_flx, tl, parthenon::CellLevel::fine, TT::Cell, beta, dt,
-                       desc_fine, mbase.get(), mc0.get(), mdudt.get(), mc1.get());
+    auto update_fine = set_flx;
+    if (do_fine_advection) {
+      update_fine =
+          AddUpdateTasks(set_flx, tl, parthenon::CellLevel::fine, TT::Cell, beta, dt,
+                         desc_fine, mbase.get(), mc0.get(), mdudt.get(), mc1.get());
+    }
 
-    auto update_vec =
-        AddUpdateTasks(set_flx, tl, parthenon::CellLevel::same, TT::Face, beta, dt,
-                       desc_vec, mbase.get(), mc0.get(), mdudt.get(), mc1.get());
+    auto update_vec = set_flx;
+    if (do_CT_advection) {
+      update_vec =
+          AddUpdateTasks(set_flx, tl, parthenon::CellLevel::same, TT::Face, beta, dt,
+                         desc_vec, mbase.get(), mc0.get(), mdudt.get(), mc1.get());
+    }
 
     auto boundaries = parthenon::AddBoundaryExchangeTasks(
         update | update_vec | update_fine | start_send, tl, mc1, pmesh->multilevel);
@@ -155,7 +176,8 @@ TaskCollection AdvectionDriver::MakeTaskCollection(BlockList_t &blocks, const in
         tl.AddTask(boundaries, parthenon::Update::FillDerived<MeshData<Real>>, mc1.get());
 
     if (stage == integrator->nstages) {
-      auto new_dt = tl.AddTask(fill_derived, EstimateTimestep<MeshData<Real>>, mc1.get());
+      auto dealloc = tl.AddTask(fill_derived, SparseDealloc, mc1.get());
+      auto new_dt = tl.AddTask(dealloc, EstimateTimestep<MeshData<Real>>, mc1.get());
       if (pmesh->adaptive) {
         auto tag_refine =
             tl.AddTask(new_dt, parthenon::Refinement::Tag<MeshData<Real>>, mc1.get());