Bump Parthenon and Kokkos

CHANGELOG.md

@@ -12,13 +12,20 @@
 ### Fixed (not changing behavior/API/variables/...)
 
 ### Infrastructure
+- [[PR 114]](https://github.com/parthenon-hpc-lab/athenapk/pull/114) Bump Parthenon 24.08 and Kokkos to 4.4.00
 - [[PR 112]](https://github.com/parthenon-hpc-lab/athenapk/pull/112) Add dev container configuration
 - [[PR 105]](https://github.com/parthenon-hpc-lab/athenapk/pull/105) Bump Parthenon to latest develop (2024-03-13)
 - [[PR 84]](https://github.com/parthenon-hpc-lab/athenapk/pull/84) Added `CHANGELOG.md`
 
 ### Removed (removing behavior/API/varaibles/...)
 
 ### Incompatibilities (i.e. breaking changes)
+- [[PR 114]](https://github.com/parthenon-hpc-lab/athenapk/pull/114) Bump Parthenon 24.08 and Kokkos to 4.4.00
+  - Changed signature of `UserWorkBeforeOutput` to include `SimTime` as last paramter
+  - Fixes bitwise idential restarts for AMR simulations (the derefinement counter is now included)
+  - Order of operations in flux-correction has changed (expect round-off error differences to previous results for AMR sims)
+  - History outputs now carry the output block number, i.e., a file previously called parthenon.hst might now be called parthenon.out1.hst
+  - History outputs now contain two additional columns (cycle number and meshblock counts), which changes/shifts the column indices (hint: use the column headers to parse the contents and do not rely on fixed indices as they may also vary between different pgen due to custom/pgen-dependent content in the history file)
 - [[PR 97]](https://github.com/parthenon-hpc-lab/athenapk/pull/97)
   - Removes original `schure.cooling` cooling curve as it had unknown origin.
   - To avoid confusion, only cooling table for a single solar metallicity are supported

src/pgen/cloud.cpp

@@ -229,9 +229,10 @@ void InflowWindX2(std::shared_ptr<MeshBlockData<Real>> &mbd, bool coarse) {
   const auto Bx_ = Bx;
   const auto By_ = By;
   const auto Bz_ = Bz;
+  const bool fine = false;
   pmb->par_for_bndry(
       "InflowWindX2", nb, IndexDomain::inner_x2, parthenon::TopologicalElement::CC,
-      coarse, KOKKOS_LAMBDA(const int, const int &k, const int &j, const int &i) {
+      coarse, fine, KOKKOS_LAMBDA(const int &, const int &k, const int &j, const int &i) {
         cons(IDN, k, j, i) = rho_wind_;
         cons(IM2, k, j, i) = mom_wind_;
         cons(IEN, k, j, i) = rhoe_wind_ + 0.5 * mom_wind_ * mom_wind_ / rho_wind_;

src/pgen/cluster.cpp

@@ -812,7 +812,8 @@ void ProblemGenerator(Mesh *pmesh, ParameterInput *pin, MeshData<Real> *md) {
   }
 }
 
-void UserWorkBeforeOutput(MeshBlock *pmb, ParameterInput *pin) {
+void UserWorkBeforeOutput(MeshBlock *pmb, ParameterInput *pin,
+                          const parthenon::SimTime & /*tm*/) {
   // get hydro
   auto pkg = pmb->packages.Get("Hydro");
   const Real gam = pin->GetReal("hydro", "gamma");

src/pgen/pgen.hpp

@@ -99,7 +99,8 @@ using namespace parthenon::driver::prelude;
 void ProblemInitPackageData(ParameterInput *pin, parthenon::StateDescriptor *pkg);
 void InitUserMeshData(ParameterInput *pin);
 void ProblemGenerator(Mesh *pmesh, ParameterInput *pin, MeshData<Real> *md);
-void UserWorkBeforeOutput(MeshBlock *pmb, ParameterInput *pin);
+void UserWorkBeforeOutput(MeshBlock *pmb, ParameterInput *pin,
+                          const parthenon::SimTime &tm);
 void ClusterUnsplitSrcTerm(MeshData<Real> *md, const parthenon::SimTime &tm,
                            const Real beta_dt);
 void ClusterSplitSrcTerm(MeshData<Real> *md, const parthenon::SimTime &tm,
@@ -120,7 +121,8 @@ void ProblemGenerator(Mesh *pm, parthenon::ParameterInput *pin, MeshData<Real> *
 void ProblemInitPackageData(ParameterInput *pin, parthenon::StateDescriptor *pkg);
 void Driving(MeshData<Real> *md, const parthenon::SimTime &tm, const Real dt);
 void SetPhases(MeshBlock *pmb, ParameterInput *pin);
-void UserWorkBeforeOutput(MeshBlock *pmb, ParameterInput *pin);
+void UserWorkBeforeOutput(MeshBlock *pmb, ParameterInput *pin,
+                          const parthenon::SimTime &tm);
 void Cleanup();
 } // namespace turbulence
 

src/pgen/turbulence.cpp

@@ -450,7 +450,8 @@ void Driving(MeshData<Real> *md, const parthenon::SimTime &tm, const Real dt) {
   Perturb(md, dt);
 }
 
-void UserWorkBeforeOutput(MeshBlock *pmb, ParameterInput *pin) {
+void UserWorkBeforeOutput(MeshBlock *pmb, ParameterInput *pin,
+                          const parthenon::SimTime & /*tm*/) {
   auto hydro_pkg = pmb->packages.Get("Hydro");
 
   // Store (common) acceleration field in spectral space

tst/regression/test_suites/field_loop/field_loop.py

@@ -135,7 +135,7 @@ def Analyse(self, parameters):
 
         for step in range(len(all_cfgs)):
             outname = get_outname(all_cfgs[step])
-            data_filename = f"{parameters.output_path}/{outname}.hst"
+            data_filename = f"{parameters.output_path}/{outname}.out1.hst"
             data = np.genfromtxt(data_filename)
 
             res, method = all_cfgs[step]

tst/regression/test_suites/turbulence/turbulence.py

@@ -40,7 +40,7 @@ def Analyse(self, parameters):
 
         success = True
 
-        data_filename = f"{parameters.output_path}/parthenon.hst"
+        data_filename = f"{parameters.output_path}/parthenon.out1.hst"
         data = np.genfromtxt(data_filename)
 
         # Check Ms