Merge branch 'pgrete/bump-parth-for-rr' into pgrete/reflect

.github/workflows/ci.yml

@@ -56,6 +56,6 @@ jobs:
             build/tst/regression/outputs/aniso_therm_cond_gauss_conv/cond.png
             build/tst/regression/outputs/field_loop/field_loop.png
             build/tst/regression/outputs/riemann_hydro/shock_tube.png
-            build/tst/regression/outputs/turbulence/parthenon.hst
+            build/tst/regression/outputs/turbulence/parthenon.out1.hst
           retention-days: 3
 

CHANGELOG.md

@@ -12,18 +12,20 @@
 ### Fixed (not changing behavior/API/variables/...)
 
 ### Infrastructure
-- [[PR 114]](https://github.com/parthenon-hpc-lab/athenapk/pull/109) Bump Parthenon to latest develop (2024-05-29)
+- [[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/109) Bump Parthenon to latest develop (2024-05-29)
+- [[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

tst/regression/test_suites/aniso_therm_cond_gauss_conv/aniso_therm_cond_gauss_conv.py

@@ -137,10 +137,15 @@ def get_ref(x, Bx, field_cfg):
             outname = get_outname(all_cfgs[step])
             data_filename = f"{parameters.output_path}/parthenon.{outname}.final.phdf"
             data_file = phdf.phdf(data_filename)
-            prim = data_file.Get("prim")
             zz, yy, xx = data_file.GetVolumeLocations()
             mask = yy == yy[0]
-            temp = prim[4][mask]
+            # Flatten=true (default) is currently (Sep 24) broken so we manually flatten
+            components = data_file.GetComponents(
+                data_file.Info["ComponentNames"], flatten=False
+            )
+            temp = components["prim_pressure"].ravel()[
+                mask
+            ]  # because of gamma = 2.0 and rho = 1 -> p = e = T
             x = xx[mask]
             res, field_cfg, int_cfg = all_cfgs[step]
             row = res_cfgs.index(res)

tst/regression/test_suites/aniso_therm_cond_ring_conv/aniso_therm_cond_ring_conv.py

@@ -35,7 +35,6 @@
 
 class TestCase(utils.test_case.TestCaseAbs):
     def Prepare(self, parameters, step):
-
         assert parameters.num_ranks <= 4, "Use <= 4 ranks for diffusion test."
 
         res = res_cfgs[step - 1]
@@ -78,8 +77,14 @@ def Analyse(self, parameters):
         for res in res_cfgs:
             data_filename = f"{parameters.output_path}/parthenon.{res}.final.phdf"
             data_file = phdf.phdf(data_filename)
-            prim = data_file.Get("prim")
-            T = prim[4]  # because of gamma = 2.0 and rho = 1 -> p = e = T
+            # Flatten=true (default) is currently (Sep 24) broken so we manually flatten
+            components = data_file.GetComponents(
+                data_file.Info["ComponentNames"], flatten=False
+            )
+            T = components[
+                "prim_pressure"
+            ].ravel()  # because of gamma = 2.0 and rho = 1 -> p = e = T
+
             zz, yy, xx = data_file.GetVolumeLocations()
             r = np.sqrt(xx**2 + yy**2)
 

tst/regression/test_suites/aniso_therm_cond_ring_multid/aniso_therm_cond_ring_multid.py

@@ -35,7 +35,6 @@
 
 class TestCase(utils.test_case.TestCaseAbs):
     def Prepare(self, parameters, step):
-
         assert parameters.num_ranks <= 4, "Use <= 4 ranks for diffusion test."
 
         # 2D reference case again
@@ -110,8 +109,13 @@ def Analyse(self, parameters):
         for step in range(1, 5):
             data_filename = f"{parameters.output_path}/parthenon.{step}.final.phdf"
             data_file = phdf.phdf(data_filename)
-            prim = data_file.Get("prim")
-            T = prim[4]  # because of gamma = 2.0 and rho = 1 -> p = e = T
+            # Flatten=true (default) is currently (Sep 24) broken so we manually flatten
+            components = data_file.GetComponents(
+                data_file.Info["ComponentNames"], flatten=False
+            )
+            T = components[
+                "prim_pressure"
+            ].ravel()  # because of gamma = 2.0 and rho = 1 -> p = e = T
             zz, yy, xx = data_file.GetVolumeLocations()
             if step == 1 or step == 2:
                 r = np.sqrt(xx**2 + yy**2)

tst/regression/test_suites/cluster_hse/cluster_hse.py

@@ -211,21 +211,15 @@ def AnalyseInitPert(self, parameters):
         # flatten array as prim var are also flattended
         cell_vol = cell_vol.ravel()
 
-        prim = data_file.Get("prim")
-
-        # FIXME: For now this is hard coded - a component mapping should be done by phdf
-        prim_col_dict = {
-            "velocity_1": 1,
-            "velocity_2": 2,
-            "velocity_3": 3,
-            "magnetic_field_1": 5,
-            "magnetic_field_2": 6,
-            "magnetic_field_3": 7,
-        }
-
-        vx = prim[prim_col_dict["velocity_1"]]
-        vy = prim[prim_col_dict["velocity_2"]]
-        vz = prim[prim_col_dict["velocity_3"]]
+        # Flatten=true (default) is currently (Sep 24) broken so we manually flatten
+        components = data_file.GetComponents(
+            data_file.Info["ComponentNames"], flatten=False
+        )
+        rho = components["prim_density"].ravel()
+        vx = components["prim_velocity_1"].ravel()
+        vy = components["prim_velocity_2"].ravel()
+        vz = components["prim_velocity_3"].ravel()
+        pres = components["prim_pressure"].ravel()
 
         # volume weighted rms velocity
         rms_v = np.sqrt(
@@ -243,9 +237,9 @@ def AnalyseInitPert(self, parameters):
                 f"Expected {self.sigma_v.in_units('code_velocity')} but got {rms_v}\n"
             )
 
-        bx = prim[prim_col_dict["magnetic_field_1"]]
-        by = prim[prim_col_dict["magnetic_field_2"]]
-        bz = prim[prim_col_dict["magnetic_field_3"]]
+        bx = components["prim_magnetic_field_1"].ravel()
+        by = components["prim_magnetic_field_2"].ravel()
+        bz = components["prim_magnetic_field_3"].ravel()
 
         # volume weighted rms magnetic field
         rms_b = np.sqrt(

tst/regression/test_suites/cluster_tabular_cooling/cluster_tabular_cooling.py

@@ -310,19 +310,16 @@ def zero_corrected_linf_err(gold, test):
                 analyze_status = False
 
             data_file = phdf.phdf(data_filename)
-            prim = data_file.Get("prim")
-
-            # FIXME: TODO(forrestglines) For now this is hard coded - a component mapping should be done by phdf
-            prim_col_dict = {
-                "density": 0,
-                "pressure": 4,
-            }
+            # Flatten=true (default) is currently (Sep 24) broken so we manually flatten
+            components = data_file.GetComponents(
+                data_file.Info["ComponentNames"], flatten=False
+            )
 
             rho = unyt.unyt_array(
-                prim[prim_col_dict["density"], :], "code_mass*code_length**-3"
+                components["prim_density"].ravel(), "code_mass*code_length**-3"
             )
             pres = unyt.unyt_array(
-                prim[prim_col_dict["pressure"], :],
+                components["prim_pressure"].ravel(),
                 "code_mass*code_length**-1*code_time**-2",
             )
 
@@ -364,19 +361,16 @@ def zero_corrected_linf_err(gold, test):
                 analyze_status = False
 
             data_file = phdf.phdf(data_filename)
-            prim = data_file.Get("prim")
-
-            # FIXME: TODO(forrestglines) For now this is hard coded - a component mapping should be done by phdf
-            prim_col_dict = {
-                "density": 0,
-                "pressure": 4,
-            }
+            # Flatten=true (default) is currently (Sep 24) broken so we manually flatten
+            components = data_file.GetComponents(
+                data_file.Info["ComponentNames"], flatten=False
+            )
 
             rho = unyt.unyt_array(
-                prim[prim_col_dict["density"]], "code_mass*code_length**-3"
+                components["prim_density"].ravel(), "code_mass*code_length**-3"
             )
             pres = unyt.unyt_array(
-                prim[prim_col_dict["pressure"]],
+                components["prim_pressure"].ravel(),
                 "code_mass*code_length**-1*code_time**-2",
             )
 

tst/regression/test_suites/field_loop/field_loop.py

@@ -135,13 +135,13 @@ 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]
             row = method_cfgs.index(method)
-            p[row, 0].plot(data[:, 0], data[:, 8] / data[0, 8], label=outname)
-            p[row, 1].plot(data[:, 0], data[:, 10], label=outname)
+            p[row, 0].plot(data[:, 0], data[:, 10] / data[0, 10], label=outname)
+            p[row, 1].plot(data[:, 0], data[:, 12], label=outname)
 
         p[0, 0].set_title("Emag(t)/Emag(0)")
         p[0, 1].set_title("rel DivB")

tst/regression/test_suites/riemann_hydro/riemann_hydro.py

@@ -58,7 +58,6 @@
 
 class TestCase(utils.test_case.TestCaseAbs):
     def Prepare(self, parameters, step):
-
         method, init_cond = all_cfgs[step - 1]
 
         nx1 = method["nx1"]
@@ -126,10 +125,13 @@ def Analyse(self, parameters):
 
             data_filename = f"{parameters.output_path}/parthenon.{step + 1}.final.phdf"
             data_file = phdf.phdf(data_filename)
-            prim = data_file.Get("prim")
-            rho = prim[0]
-            vx = prim[1]
-            pres = prim[4]
+            # Flatten=true (default) is currently (Sep 24) broken so we manually flatten
+            components = data_file.GetComponents(
+                data_file.Info["ComponentNames"], flatten=False
+            )
+            rho = components["prim_density"].ravel()
+            vx = components["prim_velocity_1"].ravel()
+            pres = components["prim_pressure"].ravel()
             zz, yy, xx = data_file.GetVolumeLocations()
 
             label = (

tst/regression/test_suites/turbulence/turbulence.py

@@ -22,7 +22,6 @@
 
 class TestCase(utils.test_case.TestCaseAbs):
     def Prepare(self, parameters, step):
-
         parameters.driver_cmd_line_args = [
             "parthenon/output2/dt=-1",
             "parthenon/output3/dt=-1",
@@ -31,7 +30,6 @@ def Prepare(self, parameters, step):
         return parameters
 
     def Analyse(self, parameters):
-
         sys.path.insert(
             1,
             parameters.parthenon_path
@@ -40,17 +38,17 @@ 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
         if not (data[-1, -3] > 0.45 and data[-1, -3] < 0.50):
-            print("ERROR: Mismatch in Ms")
+            print(f"ERROR: Mismatch in Ms={data[-1, -3]}")
             success = False
 
         # Check Ma
         if not (data[-1, -2] > 12.8 and data[-1, -2] < 13.6):
-            print("ERROR: Mismatch in Ma")
+            print(f"ERROR: Mismatch in Ma={data[-1, -2]}")
             success = False
 
         return success