Make tests smaller but run more of them in CI (#300)

* dont fillpatch react data in derives when not doing reactions

* remove extraneous file in flamesheet

* make flamesheet tests smaller

* peleLM uses amr.max_step not max_step

* update flowcontrol header name in TripleFlame case

* make tests smaller

* do more tests in CI

* fix no EB checkl for Efield

* add some mass conservation verification

* add EFIELD and EBBFS tests

* fix new tests

* fix unused variables

* more fixes for TripleFlame case

* remove commented code

.github/workflows/linux.yml

@@ -83,6 +83,63 @@ jobs:
       run: |
         mpirun -n 2 ./PeleLMeX3d.gnu.MPI.ex input.3d-regt amr.max_step=2 amr.plot_int=-1 amr.check_int=-1 amr.n_cell=128 32 32
 
+
+  # Build and Run the EB_BackwardStepFlame RegTest with GNU9.3 and MPI support
+  EBBFS:
+    name: [email protected] MPI Run [EBBFS]
+    runs-on: ubuntu-latest
+    env:
+      {CXXFLAGS: "-Werror -Wshadow -Woverloaded-virtual -Wunreachable-code"}
+    steps:
+    - uses: actions/checkout@v3
+    - name: System Dependencies
+      run: .github/workflows/dependencies/dependencies_gcc10.sh
+    - name: Repo Dependencies
+      run: Utils/CloneDeps.sh
+    - name: Build
+      env:
+         AMREX_HOME: ${GITHUB_WORKSPACE}/build/amrex
+         PELE_PHYSICS_HOME: ${GITHUB_WORKSPACE}/build/PelePhysics
+         PELELMEX_HOME: ${GITHUB_WORKSPACE}
+         AMREX_HYDRO_HOME: ${GITHUB_WORKSPACE}/build/AMReX-Hydro
+         SUNDIALS_HOME : ${GITHUB_WORKSPACE}/build/sundials
+      working-directory: ./Exec/RegTests/EB_BackwardStepFlame/
+      run: |
+        make TPL COMP=gnu USE_MPI=TRUE
+        make -j 2 COMP=gnu USE_MPI=TRUE
+    - name: Run
+      working-directory: ./Exec/RegTests/EB_BackwardStepFlame/
+      run: |
+        mpirun -n 2 ./PeleLMeX2d.gnu.MPI.ex input.2d amr.max_step=2 amr.plot_int=-1 amr.check_int=-1
+
+  # Build and Run the Efield flamesheet with GNU9.3 and MPI support
+  EFIELD:
+    name: [email protected] MPI Run [EFIELD]
+    runs-on: ubuntu-latest
+    env:
+      {CXXFLAGS: "-Werror -Wshadow -Woverloaded-virtual -Wunreachable-code"}
+    steps:
+    - uses: actions/checkout@v3
+    - name: System Dependencies
+      run: .github/workflows/dependencies/dependencies_gcc10.sh
+    - name: Repo Dependencies
+      run: Utils/CloneDeps.sh
+    - name: Build
+      env:
+         AMREX_HOME: ${GITHUB_WORKSPACE}/build/amrex
+         PELE_PHYSICS_HOME: ${GITHUB_WORKSPACE}/build/PelePhysics
+         PELELMEX_HOME: ${GITHUB_WORKSPACE}
+         AMREX_HYDRO_HOME: ${GITHUB_WORKSPACE}/build/AMReX-Hydro
+         SUNDIALS_HOME : ${GITHUB_WORKSPACE}/build/sundials
+      working-directory: ./Exec/Efield/FlameSheetIons
+      run: |
+        make TPL COMP=gnu USE_MPI=TRUE
+        make -j 2 COMP=gnu USE_MPI=TRUE
+    - name: Run
+      working-directory: ./Exec/Efield/FlameSheetIons
+      run: |
+        mpirun -n 2 ./PeleLMeX2d.gnu.MPI.EF.ex input.2d-regt amr.max_step=2 amr.plot_int=-1 amr.check_int=-1
+
   # Build and Run the TurbInflow RegTest in DEBUG with GNU9.3 and MPI support
   TI3D:
     name: [email protected] MPI Run [TI3DDBG]

Exec/RegTests/CMakeLists.txt

@@ -11,7 +11,7 @@ add_subdirectory(HotBubble)
 add_subdirectory(PeriodicCases)
 #add_subdirectory(SprayTest)
 add_subdirectory(TaylorGreen)
-#add_subdirectory(TripleFlame)
+add_subdirectory(TripleFlame)
 if(PELELMEX_DIM GREATER 2)
   add_subdirectory(TurbInflow)
 endif()

Exec/RegTests/EnclosedFlame/enclosedflame-2d.inp

@@ -12,7 +12,7 @@ peleLM.hi_bc = NoSlipWallAdiab NoSlipWallAdiab
 
 
 #-------------------------AMR CONTROL----------------------------
-amr.n_cell          = 128 128 32      # Level 0 number of cells in each direction   
+amr.n_cell          = 128 128 8      # Level 0 number of cells in each direction
 amr.v               = 1                # AMR verbose
 amr.max_level       = 2                # maximum level number allowed
 amr.ref_ratio       = 2 2 2 2 2         # refinement ratio
@@ -48,7 +48,7 @@ peleLM.do_mass_balance = 1
 amr.check_int = 100
 amr.plot_int = 100
 amr.max_step = 10
-amr.dt_shrink = 0.0001
+amr.dt_shrink = 0.01
 amr.stop_time = 1.0
 #amr.stop_time = 1.00
 amr.cfl = 0.15
@@ -59,8 +59,8 @@ peleLM.chem_integrator = "ReactorCvode"
 peleLM.use_typ_vals_chem = 1          # Use species/temp typical values in CVODE
 ode.rtol = 1.0e-6                     # Relative tolerance of the chemical solve
 ode.atol = 1.0e-5                     # Absolute tolerance factor applied on typical values
-cvode.solve_type = denseAJ_direct     # CVODE Linear solve type (for Newton direction) 
-cvode.max_order  = 4                  # CVODE max BDF order. 
+cvode.solve_type = denseAJ_direct     # CVODE Linear solve type (for Newton direction)
+cvode.max_order  = 4                  # CVODE max BDF order.
 
 #--------------------REFINEMENT CONTROL------------------------
 #amr.refinement_indicators = temp

Exec/RegTests/EnclosedFlame/enclosedflame-3d.inp

@@ -12,9 +12,9 @@ peleLM.hi_bc = NoSlipWallAdiab NoSlipWallAdiab NoSlipWallAdiab
 
 
 #-------------------------AMR CONTROL----------------------------
-amr.n_cell          = 128 128 128      # Level 0 number of cells in each direction   
+amr.n_cell          = 32 32 32      # Level 0 number of cells in each direction
 amr.v               = 1                # AMR verbose
-amr.max_level       = 1                # maximum level number allowed
+amr.max_level       = 0                # maximum level number allowed
 amr.ref_ratio       = 2 2 2 2 2         # refinement ratio
 amr.regrid_int      = 5                # how often to regrid
 amr.n_error_buf     = 2 2 2 2          # number of buffer cells in error est
@@ -47,7 +47,7 @@ peleLM.do_mass_balance = 1
 amr.check_int = 5
 amr.plot_int = 100
 amr.max_step = 10
-amr.dt_shrink = 0.0001
+amr.dt_shrink = 0.01
 amr.stop_time = 1.0
 #amr.stop_time = 1.00
 amr.cfl = 0.15
@@ -58,8 +58,8 @@ peleLM.chem_integrator = "ReactorCvode"
 #peleLM.use_typ_vals_chem = 1          # Use species/temp typical values in CVODE
 #ode.rtol = 1.0e-6                     # Relative tolerance of the chemical solve
 #ode.atol = 1.0e-5                     # Absolute tolerance factor applied on typical values
-cvode.solve_type = denseAJ_direct     # CVODE Linear solve type (for Newton direction) 
-cvode.max_order  = 4                  # CVODE max BDF order. 
+cvode.solve_type = denseAJ_direct     # CVODE Linear solve type (for Newton direction)
+cvode.max_order  = 4                  # CVODE max BDF order.
 
 #--------------------REFINEMENT CONTROL------------------------
 #amr.refinement_indicators = temp

Exec/RegTests/FlameSheet/flamesheet-drm19-2d.inp

@@ -2,7 +2,7 @@
 geometry.is_periodic = 1 0                # For each dir, 0: non-perio, 1: periodic
 geometry.coord_sys   = 0                  # 0 => cart, 1 => RZ
 geometry.prob_lo     = 0.0 0.0 0.0        # x_lo y_lo (z_lo)
-geometry.prob_hi     = 0.016 0.032 0.016  # x_hi y_hi (z_hi)
+geometry.prob_hi     = 0.008 0.032 0.008  # x_hi y_hi (z_hi)
 
 #---------------------- BC FLAGS ---------------------------------
 # Interior, Inflow, Outflow, Symmetry,
@@ -12,13 +12,13 @@ peleLM.hi_bc = Interior Outflow           # bc in x_hi y_hi (z_hi)
 
 
 #---------------------- AMR CONTROL ------------------------------
-amr.n_cell          = 32 64 32            # Level 0 number of cells in each direction
+amr.n_cell          = 16 64 16            # Level 0 number of cells in each direction
 amr.max_level       = 2                   # maximum level number allowed
 amr.ref_ratio       = 2 2 2 2             # refinement ratio
 amr.regrid_int      = 5                   # how often to regrid
 amr.n_error_buf     = 1 1 2 2             # number of buffer cells in error est
 amr.grid_eff        = 0.7                 # what constitutes an efficient grid
-amr.blocking_factor = 16                  # block factor in grid generation (min box size)
+amr.blocking_factor = 8                   # block factor in grid generation (min box size)
 amr.max_grid_size   = 256                 # max box size
 
 #---------------------- Problem ----------------------------------
@@ -29,7 +29,7 @@ prob.pertlength = 0.016
 pmf.datafile = "drm19_pmf.dat"
 
 #---------------------- PeleLMeX CONTROL -------------------------
-peleLM.v = 1                              # PeleLMeX version
+peleLM.v = 1                              # PeleLMeX verbose
 peleLM.use_wbar = 1                       # Include Wbar term in species diffusion fluxes
 peleLM.sdc_iterMax = 2                    # Number of SDC iterations
 peleLM.num_init_iter = 3                  # Number of initial iterations

Exec/RegTests/FlameSheet/flamesheet-drm19-3d.inp

@@ -2,7 +2,7 @@
 geometry.is_periodic = 1 1 0              # For each dir, 0: non-perio, 1: periodic
 geometry.coord_sys   = 0                  # 0 => cart, 1 => RZ
 geometry.prob_lo     = 0.0 0.0 0.0        # x_lo y_lo (z_lo)
-geometry.prob_hi     = 0.016 0.016 0.032        # x_hi y_hi (z_hi)
+geometry.prob_hi     = 0.008 0.008 0.032        # x_hi y_hi (z_hi)
 
 # >>>>>>>>>>>>>  BC FLAGS <<<<<<<<<<<<<<<<
 # Interior, Inflow, Outflow, Symmetry,
@@ -11,14 +11,14 @@ peleLM.lo_bc = Interior Interior Inflow
 peleLM.hi_bc = Interior Interior Outflow
 
 #-------------------------AMR CONTROL----------------------------
-amr.n_cell          = 32 32 64      # Level 0 number of cells in each direction
+amr.n_cell          = 16 16 64      # Level 0 number of cells in each direction
 amr.v               = 1                # AMR verbose
 amr.max_level       = 1                # maximum level number allowed
 amr.ref_ratio       = 2 2 2 2          # refinement ratio
 amr.regrid_int      = 5                # how often to regrid
 amr.n_error_buf     = 1 1 2 2          # number of buffer cells in error est
 amr.grid_eff        = 0.7              # what constitutes an efficient grid
-amr.blocking_factor = 16               # block factor in grid generation (min box size)
+amr.blocking_factor = 8                # block factor in grid generation (min box size)
 amr.max_grid_size   = 64               # max box size
 
 

Exec/RegTests/HotBubble/hotbubble-3d.inp

@@ -12,8 +12,7 @@ peleLM.hi_bc = SlipWallAdiab Outflow       SlipWallAdiab
 
 
 #-------------------------AMR CONTROL----------------------------
-amr.n_cell          = 32 64 32      # Level 0 number of cells in each direction   
-amr.n_cell          = 64 128 64      # Level 0 number of cells in each direction   
+amr.n_cell          = 16 32 16      # Level 0 number of cells in each direction
 amr.v               = 1                # AMR verbose
 amr.max_level       = 1               # maximum level number allowed
 amr.ref_ratio       = 2 2 2 2          # refinement ratio
@@ -51,14 +50,14 @@ amr.stop_time = 0.07
 amr.cfl = 0.5
 amr.derive_plot_vars = avg_pressure mag_vort mass_fractions
 
-cvode.solve_type = dense               # CVODE Linear solve type (for Newton direction) 
-ode.analytical_jacobian = 0            # Provide analytical jacobian (from Fuego) 
+cvode.solve_type = dense               # CVODE Linear solve type (for Newton direction)
+ode.analytical_jacobian = 0            # Provide analytical jacobian (from Fuego)
 
 #------------  INPUTS TO CONSTANT TRANSPORT -----------------
-transport.const_viscosity        = 0.0 
-transport.const_bulk_viscosity   = 0.0 
-transport.const_conductivity     = 0.0 
-transport.const_diffusivity      = 0.0 
+transport.const_viscosity        = 0.0
+transport.const_bulk_viscosity   = 0.0
+transport.const_conductivity     = 0.0
+transport.const_diffusivity      = 0.0
 
 #--------------------REFINEMENT CONTROL------------------------
 #amr.refinement_indicators = temp

Exec/RegTests/PeriodicCases/covo-3d.inp

@@ -12,14 +12,14 @@ peleLM.hi_bc = Interior Interior Interior
 
 
 #-------------------------AMR CONTROL----------------------------
-amr.n_cell          = 64 64 64         # Level 0 number of cells in each direction   
+amr.n_cell          = 16 16 16         # Level 0 number of cells in each direction
 amr.v               = 1                # AMR verbose
 amr.max_level       = 0                # maximum level number allowed
 amr.ref_ratio       = 2 2 2 2          # refinement ratio
 amr.regrid_int      = 2                # how often to regrid
 amr.n_error_buf     = 1 1 2 2          # number of buffer cells in error est
 amr.grid_eff        = 0.7              # what constitutes an efficient grid
-amr.blocking_factor = 16               # block factor in grid generation (min box size)
+amr.blocking_factor = 8                # block factor in grid generation (min box size)
 amr.max_grid_size   = 64               # max box size
 
 
@@ -32,10 +32,10 @@ prob.rvort       = 0.07
 prob.forcevort   = 6.0
 
 #------------  INPUTS TO CONSTANT TRANSPORT -----------------
-transport.const_viscosity        = 0.0 
-transport.const_bulk_viscosity   = 0.0 
-transport.const_conductivity     = 0.0 
-transport.const_diffusivity      = 0.0 
+transport.const_viscosity        = 0.0
+transport.const_bulk_viscosity   = 0.0
+transport.const_conductivity     = 0.0
+transport.const_diffusivity      = 0.0
 
 #-------------------------PeleLM CONTROL----------------------------
 peleLM.v = 1

Exec/RegTests/TripleFlame/pelelmex_prob.H

@@ -10,7 +10,7 @@
 #include <AMReX_FArrayBox.H>
 #include <AMReX_SPACE.H>
 
-AMREX_GPU_DEVICE
+AMREX_GPU_HOST_DEVICE
 AMREX_FORCE_INLINE
 void
 set_Y_from_Phi(
@@ -29,7 +29,7 @@ set_Y_from_Phi(
   eos.X2Y(Xt, Y);
 }
 
-AMREX_GPU_DEVICE
+AMREX_GPU_HOST_DEVICE
 AMREX_FORCE_INLINE
 void
 set_Y_from_Ksi(
@@ -53,18 +53,13 @@ pelelmex_initdata(
   amrex::Array4<amrex::Real> const& /*aux*/,
   amrex::GeometryData const& geomdata,
   ProbParm const& prob_parm,
-  pele::physics::PMF::PmfData::DataContainer const* pmf_data)
+  pele::physics::PMF::PmfData::DataContainer const* /*pmf_data*/)
 {
   const amrex::Real* prob_lo = geomdata.ProbLo();
-  const amrex::Real* prob_hi = geomdata.ProbHi();
   const amrex::Real* dx = geomdata.CellSize();
 
-  AMREX_D_TERM(const amrex::Real x = prob_lo[0] + (i + 0.5) * dx[0];
-               , const amrex::Real y = prob_lo[1] + (j + 0.5) * dx[1];
-               , const amrex::Real z = prob_lo[2] + (k + 0.5) * dx[2];);
-
-  AMREX_D_TERM(, const amrex::Real L_x = prob_hi[0] - prob_lo[0];
-               , const amrex::Real L_y = prob_hi[1] - prob_lo[1]);
+  const amrex::Real x = prob_lo[0] + (i + 0.5) * dx[0];
+  const amrex::Real y = prob_lo[1] + (j + 0.5) * dx[1];
 
   auto eos = pele::physics::PhysicsType::eos();
   amrex::Real massfrac[NUM_SPECIES] = {0.0};
@@ -128,19 +123,19 @@ bcnormal(
   const amrex::Real x[AMREX_SPACEDIM],
   const int /*m_nAux*/,
   amrex::Real s_ext[NVAR],
-  const int idir,
+  const int /*idir*/,
   const int sgn,
   const amrex::Real time,
-  amrex::GeometryData const& geomdata,
+  amrex::GeometryData const& /*geomdata*/,
   ProbParm const& prob_parm,
-  pele::physics::PMF::PmfData::DataContainer const* pmf_data)
+  pele::physics::PMF::PmfData::DataContainer const* /*pmf_data*/)
 {
   auto eos = pele::physics::PhysicsType::eos();
   amrex::Real massfrac[NUM_SPECIES] = {0.0};
 
   if (sgn == 1) {
 
-    if ((prob_parm.FCData.ctrl_active == 0u) || time <= 0.0) {
+    if ((prob_parm.FCData.ctrl_active == 0U) || time <= 0.0) {
       s_ext[VELX] = 0.0;
 #if (AMREX_SPACEDIM == 2)
       s_ext[VELY] = prob_parm.V_in;