some more fixes based on Perlmutter

zingale · zingale · commit b00390492fa4 · 2026-02-07T11:25:38.000-05:00
diff --git a/Exec/science/subchandra/GNUmakefile b/Exec/science/subchandra/GNUmakefile
@@ -17,7 +17,10 @@ USE_SHOCK_VAR = TRUE
 
 USE_MODEL_PARSER = TRUE
 
-USE_SIMPLIFIED_SDC=TRUE
+USE_SIMPLIFIED_SDC = TRUE
+
+# for the networks we tend to use, we can still use Jac caching on GPUs
+USE_JACOBIAN_CACHING = TRUE
 
 # This sets the EOS directory in $(MICROPHYSICS_HOME)/EOS
 EOS_DIR     := helmholtz
diff --git a/Exec/science/subchandra/inputs_2d.N14.coarse b/Exec/science/subchandra/inputs_2d.N14.coarse
@@ -1,8 +1,5 @@
 # ------------------  INPUTS TO MAIN PROGRAM  -------------------
 
-amr.plot_files_output = 1
-amr.checkpoint_files_output = 1
-
 max_step = 1000000
 stop_time = 10.0
 
@@ -95,6 +92,12 @@ amr.blocking_factor = 32       # block factor in grid generation
 
 # I/O
 
+amr.plot_files_output = 1
+amr.checkpoint_files_output = 1
+# with the SLURM HUP functionality, we get a checkpoint near
+# the end of the queue window -- don't do a plotfile then too
+amr.write_plotfile_with_checkpoint = 0
+
 amr.check_file      = subch_chk     # root name of checkpoint file
 amr.check_int       = 50     # number of timesteps between checkpoints
 amr.plot_file       = subch_plt     # root name of plot file
diff --git a/Exec/science/subchandra/inputs_2d.NSE b/Exec/science/subchandra/inputs_2d.NSE
@@ -1,7 +1,4 @@
 # ------------------  INPUTS TO MAIN PROGRAM  -------------------
-amr.plot_files_output = 1
-amr.checkpoint_files_output = 1
-
 max_step = 1000000
 stop_time = 10.0
 
@@ -13,8 +10,6 @@ geometry.prob_hi   =  5.12e9 1.024e10
 
 amr.n_cell         = 1280 2560
 
-amr.max_level      = 1       # maximum level number allowed
-
 castro.lo_bc       =  3 2
 castro.hi_bc       =  2 2
 
@@ -63,7 +58,7 @@ castro.sponge_timescale     = 1.e-3
 castro.cfl            = 0.2     # cfl number for hyperbolic system
 castro.init_shrink    = 0.05     # scale back initial timestep by this factor
 castro.change_max     = 1.025    # factor by which dt is allowed to change each timestep
-castro.sum_interval   = 0       # timesteps between computing and printing volume averages
+castro.sum_interval   = 5       # timesteps between computing and printing volume averages
 castro.update_sources_after_reflux = 0
 castro.time_integration_method = 3
 
@@ -73,32 +68,44 @@ castro.max_subcycles = 32
 
 castro.abundance_failure_rho_cutoff = 1.0
 
+amr.v               = 1       # control verbosity in Amr.cpp
+castro.v            = 1       # control verbosity in Castro.cpp
+
+castro.small_dens   = 1.e-5
+castro.small_temp   = 1.e5
+
 #castro.dtnuc_e = 0.25
 #castro.dtnuc_X = 0.25
 
+# gridding
+
+amr.max_level      = 1       # 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     = 2 2 2 2 # number of buffer cells in error est
 amr.grid_eff        = 0.7     # what constitutes an efficient grid
 
+amr.max_grid_size   = 256      # maximum grid size allowed -- used to control parallelism
+amr.blocking_factor = 32       # block factor in grid generation
+
+# I/O
+
+amr.plot_files_output = 1
+amr.checkpoint_files_output = 1
+# with the SLURM HUP functionality, we get a checkpoint near
+# the end of the queue window -- don't do a plotfile then too
+amr.write_plotfile_with_checkpoint = 0
+
 amr.check_file      = subch_chk     # root name of checkpoint file
 amr.check_int       = 50     # number of timesteps between checkpoints
 amr.plot_file       = subch_plt     # root name of plot file
 amr.plot_int        = -1     # number of timesteps between plotfiles
 amr.plot_per        = 2.e-3
 
-amr.max_grid_size   = 256      # maximum grid size allowed -- used to control parallelism
-amr.blocking_factor = 32       # block factor in grid generation
-
-amr.v               = 1       # control verbosity in Amr.cpp
-castro.v            = 1       # control verbosity in Castro.cpp
-
 amr.derive_plot_vars = ALL
 castro.store_burn_weights = 1
 
-castro.small_dens   = 1.e-5
-castro.small_temp   = 1.e5
-
 # problem parameters
 
 problem.pert_temp_factor = 20.0
diff --git a/Exec/science/subchandra/inputs_2d.ONe b/Exec/science/subchandra/inputs_2d.ONe
@@ -1,8 +1,5 @@
 # ------------------  INPUTS TO MAIN PROGRAM  -------------------
 
-amr.plot_files_output = 1
-amr.checkpoint_files_output = 1
-
 max_step = 1000000
 stop_time = 10.0
 
@@ -28,13 +25,13 @@ castro.do_grav  = 1
 castro.do_react = 1
 castro.do_sponge = 1
 
-castro.react_rho_min = 100.0
+castro.react_rho_min = 500.0
 castro.react_T_min = 5.e7
 
 castro.disable_shock_burning = 1
 castro.ppm_type = 1
 castro.ppm_temp_fix = 0
-castro.use_pslope = 1
+castro.ppm_well_balanced = 1
 
 castro.use_flattening = 1
 
@@ -95,6 +92,12 @@ amr.blocking_factor = 32       # block factor in grid generation
 
 # I/O
 
+amr.plot_files_output = 1
+amr.checkpoint_files_output = 1
+# with the SLURM HUP functionality, we get a checkpoint near
+# the end of the queue window -- don't do a plotfile then too
+amr.write_plotfile_with_checkpoint = 0
+
 amr.check_file      = subch_chk     # root name of checkpoint file
 amr.check_int       = 50     # number of timesteps between checkpoints
 amr.plot_file       = subch_plt     # root name of plot file
@@ -167,17 +170,26 @@ integrator.SMALL_X_SAFE = 1.e-30
 integrator.do_species_clip = 0
 
 integrator.rtol_spec = 1.e-5
-integrator.atol_spec = 1.e-5
+integrator.atol_spec = 1.e-8
 integrator.rtol_enuc = 1.e-5
 integrator.atol_enuc = 1.e-5
 integrator.jacobian = 1
 
 integrator.X_reject_buffer = 4.0
 
-# disable jacobian caching in VODE
-integrator.use_jacobian_caching = 0
+integrator.use_jacobian_caching = 1
 
-integrator.ode_max_steps = 20000
+# force a small number of steps to get a retry at the burn level
+# instead of the Castro level
+integrator.ode_max_steps = 5000
 
 integrator.use_burn_retry = 1
 integrator.retry_swap_jacobian = 1
+
+# NSE
+
+nse.nse_molar_independent = 0
+nse.nse_dx_independent = 0
+nse.ase_tol = 0.1
+nse.nse_skip_molar = 0
+nse.solve_nse_e_mode = 1
diff --git a/Exec/science/subchandra/inputs_3d.N14.M_WD1.0_M_He0.05 b/Exec/science/subchandra/inputs_3d.N14.M_WD1.0_M_He0.05
@@ -1,8 +1,5 @@
 # ------------------  INPUTS TO MAIN PROGRAM  -------------------
 
-amr.plot_files_output = 1
-amr.checkpoint_files_output = 1
-
 max_step = 100000
 stop_time = 10.0
 
@@ -98,6 +95,12 @@ amr.blocking_factor = 32       # block factor in grid generation
 
 # I/O
 
+amr.plot_files_output = 1
+amr.checkpoint_files_output = 1
+# with the SLURM HUP functionality, we get a checkpoint near
+# the end of the queue window -- don't do a plotfile then too
+amr.write_plotfile_with_checkpoint = 0
+
 amr.check_file      = subch_chk     # root name of checkpoint file
 amr.check_int       = 100     # number of timesteps between checkpoints
 amr.plot_file       = subch_plt     # root name of plot file
diff --git a/Exec/science/subchandra/inputs_3d.N14.coarse b/Exec/science/subchandra/inputs_3d.N14.coarse
@@ -1,8 +1,5 @@
 # ------------------  INPUTS TO MAIN PROGRAM  -------------------
 
-amr.plot_files_output = 1
-amr.checkpoint_files_output = 1
-
 max_step = 100000
 stop_time = 10.0
 
@@ -98,6 +95,12 @@ amr.blocking_factor = 32       # block factor in grid generation
 
 # I/O
 
+amr.plot_files_output = 1
+amr.checkpoint_files_output = 1
+# with the SLURM HUP functionality, we get a checkpoint near
+# the end of the queue window -- don't do a plotfile then too
+amr.write_plotfile_with_checkpoint = 0
+
 amr.check_file      = subch_chk     # root name of checkpoint file
 amr.check_int       = 25     # number of timesteps between checkpoints
 amr.plot_file       = subch_plt     # root name of plot file
