Try to update the code to Julia1.10

aux02_plotting.py

@@ -258,6 +258,7 @@ def truncate_colormap(cmap, minval=0.0, maxval=1.0, n=100):
                       "v"         : dict(vmin=-0.01, vmax=+0.01, cmap=plt.cm.RdBu_r),
                       "v̂"         : dict(vmin=-1.2, vmax=+1.2, cmap=cm.balance),
                       "w"         : dict(vmin=-0.003, vmax=+0.003, cmap=plt.cm.RdBu_r),
+                      "∂u∂z"      : dict(robust=True, cmap=plt.cm.RdBu_r),
                       "PV_norm"   : dict(vmin=-5, vmax=5, cmap="RdBu_r"),
                       "PVᶻ_norm"  : dict(vmin=-5, vmax=5, cmap="RdBu_r"),
                       "PVʰ_norm"  : dict(vmin=-5, vmax=5, cmap="RdBu_r"),
@@ -302,6 +303,7 @@ def truncate_colormap(cmap, minval=0.0, maxval=1.0, n=100):
               "PV_norm" : r"Normalized Ertel PV (PV$/f N^2_\infty$)",
               "v"       : r"$v$-velocity [m/s]",
               "v̂"       : r"Normalized $v$-velocity ($v/V_\infty$)",
+              "∂u∂z"    : r"$\partial u / \partial z$",
               }
 #---
 

diagnostics.jl

@@ -35,9 +35,17 @@ using Oceananigans.Operators
 import NCDatasets as NCD
 function write_to_ds(dsname, varname, data; coords=("xC", "yC", "zC"), dtype=Float64)
     ds = NCD.NCDataset(dsname, "a")
-    if varname ∉ ds
+    if varname ∉ keys(ds)
         newvar = NCD.defVar(ds, varname, dtype, coords)
-        newvar[:,:,:] = Array(data)
+        if length(size(data)) == 3
+            newvar[:,:,:] = Array(data)
+        elseif length(size(data)) == 2
+            newvar[:,:] = Array(data)
+        elseif length(size(data)) == 1
+            newvar[:] = Array(data)
+        else
+            newvar = data
+        end
     end
     NCD.close(ds)
 end

grid_metrics.jl

@@ -1,4 +1,5 @@
 using Oceananigans.Grids: xspacing, yspacing, zspacing, xnode, ynode, znode, boundary_node, inactive_node, destantiate
+using Oceananigans: location
 
 flip_loc(::Center) = Face()
 flip_loc(::Face) = Center()
@@ -36,9 +37,9 @@ using Oceananigans.OutputWriters: fetch_and_convert_output, drop_output_dims,
 using Oceananigans.Fields: AbstractField
 using NCDatasets: defVar
 
-define_timeconstant_variable!(dataset, output::AbstractField, name, array_type, compression, output_attributes, dimensions) =
+define_timeconstant_variable!(dataset, output::AbstractField, name, array_type, deflatelevel, output_attributes, dimensions) =
     defVar(dataset, name, eltype(array_type), netcdf_spatial_dimensions(output),
-           compression=compression, attrib=output_attributes)
+           deflatelevel=deflatelevel, attrib=output_attributes)
 
 function save_output!(ds, output, model, ow, name)
 
@@ -123,8 +124,7 @@ function write_grid_metrics!(ow, metrics; user_indices = (:, :, :), with_halos=f
     for (metric_name, metric_operation) in metrics
         indices = output_indices(metric_operation, metric_operation.grid, user_indices, with_halos)
         sliced_metric = Field(metric_operation, indices=indices)
-
-        if metric_name ∉ ds
+        if metric_name ∉ keys(ds)
             define_timeconstant_variable!(ds, sliced_metric, metric_name, ow.array_type, 0, Dict(), ("xC", "yC", "zC"))
             save_output!(ds, sliced_metric, model, ow, metric_name)
         end
@@ -134,6 +134,7 @@ end
 
 function add_grid_metrics_to!(ow; kwargs...)
     Δξ_list = grid_spacings(grid, ow)
+    @info "Got Δξ_list"
     write_grid_metrics!(ow, Δξ_list; kwargs...)
 end
 

h00_runall.py

@@ -32,7 +32,7 @@
                  "NPN-R1F1",
                  ]
 modifiers = ["-f4", "-f2", "-S-f4", "-S-f2","-AMD-f4", "-AMD-f2",]
-modifiers = ["-f4", "-f2", ""]
+modifiers = ["-f2", "-S-f2", "", "-S"]
 #---
 
 

h01_energy_transfer.py

@@ -36,7 +36,7 @@
     from cycler import cycler
     names = cycler(name=simnames)
     modifiers = cycler(modifier = ["-f4", "-S-f4", "-f2", "-S-f2", "", "-S"])
-    modifiers = cycler(modifier = ["-f4",])
+    modifiers = cycler(modifier = ["-f2",])
     simnames = [ nr["name"] + nr["modifier"] for nr in modifiers * names ]
 #---
 

headland_simulations/headland.jl

@@ -1,4 +1,8 @@
 if ("PBS_JOBID" in keys(ENV))  @info "Job ID" ENV["PBS_JOBID"] end # Print job ID if this is a PBS simulation
+#using Pkg
+#Pkg.instantiate()
+using InteractiveUtils
+println(versioninfo())
 using DrWatson
 using ArgParse
 using Oceananigans
@@ -271,7 +275,8 @@ model = NonhydrostaticModel(grid = grid, timestepper = :RungeKutta3,
                             closure = closure,
                             boundary_conditions = bcs,
                             forcing = (u=Fᵤ, v=Fᵥ, w=Fw, b=Fb),
-                           )
+                            hydrostatic_pressure_anomaly = CenterField(grid),
+                            )
 @info "" model
 if has_cuda_gpu() run(`nvidia-smi -i $(ENV["CUDA_VISIBLE_DEVICES"])`) end
 
@@ -282,15 +287,15 @@ set!(model, b=(x, y, z) -> b∞(x, y, z, 0, f_params), v=params.V_inf)
 params = (; params..., T_advective_max = params.T_advective_spinup + params.T_advective_statistics)
 simulation = Simulation(model, Δt=0.2*minimum_zspacing(grid.underlying_grid)/params.V_inf,
                         stop_time=params.T_advective_max * params.T_advective,
-                        wall_time_limit=23.5hours,
+                        wall_time_limit=23hours,
                         )
 
 using Oceanostics.ProgressMessengers
 walltime_per_timestep = StepDuration(with_prefix=false) # This needs to instantiated here, and not in the function below
 walltime = Walltime()
 progress(simulation) = @info (PercentageProgress(with_prefix=false, with_units=false)
                               + "$(round(time(simulation)/params.T_advective; digits=2)) adv periods" + walltime
-                              + TimeStep() + MaxVelocities() + "CFL = "*AdvectiveCFLNumber(with_prefix=false)
+                              + TimeStep() + "CFL = "*AdvectiveCFLNumber(with_prefix=false)
                               + "step dur = "*walltime_per_timestep)(simulation)
 simulation.callbacks[:progress] = Callback(progress, IterationInterval(40))
 
@@ -324,7 +329,7 @@ checkpointer = construct_outputs(simulation,
                                  write_xyz = true,
                                  write_xiz = true,
                                  write_xyi = true,
-                                 write_iyz = false,
+                                 write_iyz = true,
                                  write_ttt = true,
                                  write_tti = true,
                                  debug = false,

headland_simulations/run_all.py

@@ -23,8 +23,9 @@
 from cycler import cycler
 names = cycler(name=simnames)
 resolutions = cycler(resolution = ["-f4", "-f2", ""])
+resolutions = cycler(resolution = ["-f2", ""])
 modifiers = cycler(rotation = ["", "-S", "-AMD"])
-modifiers = cycler(rotation = ["",])
+modifiers = cycler(rotation = ["", "-S"])
 simnames = [ nr["name"] + nr["rotation"] + nr["resolution"] for nr in modifiers * resolutions * names ]
 #---
 
@@ -58,7 +59,7 @@
 module li
 module --force purge
 module load ncarenv/23.10
-module load julia/1.9.2 cuda
+module load julia/1.10.2 cuda
 module li
 
 #/glade/u/apps/ch/opt/usr/bin/dumpenv # Dumps environment (for debugging with CISL support)

hplot04_v_snapshots.py → hplot04_dudz_snapshots.py

@@ -26,7 +26,7 @@
 slice_names = ["iyz",]
 modifiers = ["-f2", "",]
 
-varnames = ["v̂"]
+varnames = ["∂u∂z",]
 contour_variable_name = None #"water_mask_buffered"
 contour_kwargs = dict(colors="y", linewidths=0.8, linestyles="--", levels=[0])
 #---

hplot08_dissip_scalings.py

@@ -121,7 +121,7 @@
         ax.grid(True)
         ax.set_title("")
         ax.set_xlabel("$S_h$")
-    
+
     letterize(axesf, x=0.05, y=0.9, fontsize=14)
     fig.savefig(f"figures/dissip_scalings_buffer={buffer}m{modifier}.pdf")
     #---

hplot13_SPR_components.py

@@ -29,7 +29,7 @@
 figsize = (8, 7)
 
 #plot_kwargs = dict(vmin=-0.005, vmax=0.005, cmap=plt.cm.RdBu_r, rasterized=True)
-plot_kwargs = dict(vmin=-8e-9, vmax=8e-9, cmap=cm.balance, rasterized=True)
+plot_kwargs = dict(vmin=-8e-10, vmax=8e-10, cmap=cm.balance, rasterized=True)
 #---
 
 #+++ Create ageostrophic variables and pick subset of simulations