Moved ECCO downloading to beginning of code in examples/one_degree_simulation.jl (#364)

* Changed the ECCO Password/Username error to have the correct directory for the README

* Made a mistake in the file path -- fixed now

* Some changes idk

* Added the latest version of ClimaOcean

* Swapped ECCO download to front of code and added messages to show directory of download

* Removed Jupyter Notebooks

* Changed the file path for saving outputs back to generic

* Removed Jupyter Notebooks

* Remove .ipynb files from tracking

* Remove .ipynb checkpoint files from tracking

* Remove .gitignore from tracking

* Added ECCO downloading instructions

* Added gitignore and other files back

* Added ECCO downloading instructions

* Added everything back

* code alignment + comment for #363

comment related to #363

* Removed dual conditionals, added missing_files variable

* Update ECCO_metadata.jl

Co-authored-by: Simone Silvestri <[email protected]>

* Update .gitignore

* Update .gitignore

Co-authored-by: Navid C. Constantinou <[email protected]>

* fix bug

* fix bug

---------

Co-authored-by: Navid C. Constantinou <[email protected]>
Co-authored-by: Simone Silvestri <[email protected]>

Author: 3 people

.gitignore

@@ -32,6 +32,8 @@ docs/src/literated/
 # Password files
 *.netrc
 
+# Jupyter notebooks
+.ipynb_checkpoints/*
 # File generated by Pkg, the package manager, based on a corresponding Project.toml
 # It records a fixed state of all packages used by the project. As such, it should not be
 # committed for packages, but should be committed for applications that require a static

examples/one_degree_simulation.jl

@@ -14,9 +14,21 @@ using OrthogonalSphericalShellGrids
 using CFTime
 using Dates
 using Printf
+using ClimaOcean.ECCO: download_dataset
 
 arch = GPU()
 
+# ### Download necessary files to run the code
+
+# ### ECCO files
+
+dates = DateTimeProlepticGregorian(1993, 1, 1) : Month(1) : DateTimeProlepticGregorian(1994, 1, 1)
+temperature = ECCOMetadata(:temperature; dates, version=ECCO4Monthly(), dir="./")
+salinity    = ECCOMetadata(:salinity;    dates, version=ECCO4Monthly(), dir="./")
+
+download_dataset(temperature)
+download_dataset(salinity)
+
 # ### Grid and Bathymetry
 
 Nx = 360
@@ -35,8 +47,8 @@ underlying_grid = TripolarGrid(arch;
 
 bottom_height = regrid_bathymetry(underlying_grid;
                                   minimum_depth = 10,
-                                  interpolation_passes = 75,
-                                  major_basins = 2)
+                                  interpolation_passes = 75, # 75 interpolation passes smooth the bathymetry near Florida so that the Gulf Stream is able to flow
+				  major_basins = 2)
 
 # For this bathymetry at this horizontal resolution we need to manually open the Gibraltar strait.
 view(bottom_height, 102:103, 124, 1) .= -400
@@ -45,16 +57,11 @@ grid = ImmersedBoundaryGrid(underlying_grid, GridFittedBottom(bottom_height); ac
 # ### Restoring
 #
 # We include temperature and salinity surface restoring to ECCO data.
-
 restoring_rate  = 1 / 10days
 z_below_surface = r_faces[end-1]
 
 mask = LinearlyTaperedPolarMask(southern=(-80, -70), northern=(70, 90), z=(z_below_surface, 0))
 
-dates = DateTimeProlepticGregorian(1993, 1, 1) : Month(1) : DateTimeProlepticGregorian(1994, 1, 1)
-temperature = ECCOMetadata(:temperature; dates, version=ECCO4Monthly(), dir="./")
-salinity    = ECCOMetadata(:salinity;    dates, version=ECCO4Monthly(), dir="./")
-
 FT = ECCORestoring(temperature, grid; mask, rate=restoring_rate)
 FS = ECCORestoring(salinity,    grid; mask, rate=restoring_rate)
 forcing = (T=FT, S=FS)
@@ -163,7 +170,6 @@ ocean.output_writers[:surface] = JLD2OutputWriter(ocean.model, outputs;
                                                   with_halos = true,
                                                   overwrite_existing = true,
                                                   array_type = Array{Float32})
-                                                  overwrite_existing = true)
 
 # ### Ready to run
 

src/DataWrangling/ECCO/ECCO_metadata.jl

@@ -235,13 +235,16 @@ function download_dataset(metadata::ECCOMetadata; url = urls(metadata))
         # Write down the username and password in a .netrc file
         downloader = netrc_downloader(username, password, "ecco.jpl.nasa.gov", tmp)
         ntasks = Threads.nthreads()
-        
+       
+	missing_files = false
+
         asyncmap(metadata; ntasks) do metadatum # Distribute the download among tasks
 
             fileurl  = metadata_url(url, metadatum) 
             filepath = metadata_path(metadatum)
 
-            if !isfile(filepath)
+	    if !isfile(filepath)
+	    	missing_files = true
                 instructions_msg = "\n See ClimaOcean.jl/src/DataWrangling/ECCO/README.md for instructions."
                 if isnothing(username)
                     msg = "Could not find the ECCO_PASSWORD environment variable. \
@@ -254,10 +257,13 @@ function download_dataset(metadata::ECCOMetadata; url = urls(metadata))
                            and setting your ECCO_USERNAME and ECCO_PASSWORD." * instructions_msg
                     throw(ArgumentError(msg))
                 end
-
+		println("Downloading ECCO data: $(metadatum.name)")
                 Downloads.download(fileurl, filepath; downloader, progress=download_progress)
-            end
+	    end
         end
+	if !missing_files
+            @info "Note: ECCO $(metadata.name) data is in $(metadata.dir)."
+	end
     end
 
     return nothing