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Fix allocations + add interactive profiler
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| name = "OceanTransportMatrixBuilder" | ||
| uuid = "c2b4a04e-6049-4fc4-aa6a-5508a29a1e1c" | ||
| authors = ["Benoit Pasquier <[email protected]> and contributors"] | ||
| version = "0.5.0" | ||
| version = "0.5.1" | ||
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| [deps] | ||
| Distances = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7" | ||
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| Original file line number | Diff line number | Diff line change |
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| using Pkg | ||
| Pkg.activate(".") | ||
| Pkg.instantiate() | ||
| using TestEnv | ||
| TestEnv.activate(); | ||
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| using Test | ||
| using OceanTransportMatrixBuilder | ||
| using NetCDF | ||
| using YAXArrays | ||
| using GibbsSeaWater | ||
| using DimensionalData | ||
| using NaNStatistics | ||
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| # stdlib | ||
| using SparseArrays | ||
| using LinearAlgebra | ||
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| # My local directory for input files | ||
| model = "ACCESS-ESM1-5" | ||
| member = "r1i1p1f1" | ||
| inputdir = "/Users/benoitpasquier/Data/TMIP/data/$model/historical/$member/Jan1990-Dec1999" | ||
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| # and for output files | ||
| @show version = "v$(pkgversion(OceanTransportMatrixBuilder))" | ||
| outputdir = joinpath("plots", version) | ||
| mkpath(outputdir) | ||
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| # Load datasets | ||
| umo_ds = open_dataset(joinpath(inputdir, "umo.nc")) | ||
| vmo_ds = open_dataset(joinpath(inputdir, "vmo.nc")) | ||
| uo_ds = open_dataset(joinpath(inputdir, "uo.nc")) | ||
| vo_ds = open_dataset(joinpath(inputdir, "vo.nc")) | ||
| mlotst_ds = open_dataset(joinpath(inputdir, "mlotst.nc")) | ||
| volcello_ds = open_dataset(joinpath(inputdir, "volcello.nc")) | ||
| areacello_ds = open_dataset(joinpath(inputdir, "areacello.nc")) | ||
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| # Load variables in memory | ||
| umo = readcubedata(umo_ds.umo) | ||
| vmo = readcubedata(vmo_ds.vmo) | ||
| umo_lon = readcubedata(umo_ds.lon) | ||
| umo_lat = readcubedata(umo_ds.lat) | ||
| vmo_lon = readcubedata(vmo_ds.lon) | ||
| vmo_lat = readcubedata(vmo_ds.lat) | ||
| mlotst = readcubedata(mlotst_ds.mlotst) | ||
| areacello = readcubedata(areacello_ds.areacello) | ||
| volcello = readcubedata(volcello_ds.volcello) | ||
| lon = readcubedata(volcello_ds.lon) | ||
| lat = readcubedata(volcello_ds.lat) | ||
| lev = volcello_ds.lev | ||
| lon_vertices = readcubedata(volcello_ds.lon_verticies) # xmip issue: https://github.com/jbusecke/xMIP/issues/369 | ||
| lat_vertices = readcubedata(volcello_ds.lat_verticies) # xmip issue: https://github.com/jbusecke/xMIP/issues/369 | ||
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| # Make makegridmetrics | ||
| gridmetrics = makegridmetrics(; areacello, volcello, lon, lat, lev, lon_vertices, lat_vertices) | ||
| (; lon_vertices, lat_vertices, Z3D, v3D, zt, thkcello) = gridmetrics | ||
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| uo = readcubedata(uo_ds.uo) | ||
| vo = readcubedata(vo_ds.vo) | ||
| uo_lon = readcubedata(uo_ds.lon) | ||
| uo_lat = readcubedata(uo_ds.lat) | ||
| vo_lon = readcubedata(vo_ds.lon) | ||
| vo_lat = readcubedata(vo_ds.lat) | ||
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| # Load thetato and so to compute density | ||
| thetao_ds = open_dataset(joinpath(inputdir, "thetao.nc")) | ||
| so_ds = open_dataset(joinpath(inputdir, "so.nc")) | ||
| # Load variables in memory | ||
| thetao = readcubedata(thetao_ds.thetao) | ||
| @test 0 < nanmean(thetao) < 20 | ||
| so = readcubedata(so_ds.so) | ||
| @show 30 < nanmean(so) < 40 | ||
| # Convert thetao and so to density | ||
| ct = gsw_ct_from_pt.(so, thetao) | ||
| ρ = gsw_rho.(so, ct, Z3D) | ||
| # TODO: Check if this is correct usage of gsw functions! | ||
| # Alternatively use a fixed density: | ||
| # ρ = 1035.0 # kg/m^3 | ||
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| # Below is commented out but should eventually be teseted for neutral/potential density | ||
| # @show nanmean(ct) | ||
| ρθ = gsw_rho.(so, ct, 1000) | ||
| # @show nanmean(ρθ) | ||
| # from MATLAB GSW toolbox: | ||
| # gsw_rho.(so, ct, p) | ||
| # so = Absolute Salinity (g/kg) | ||
| # ct = Conservative Temperature (ITS-90) (°C) | ||
| # p = sea pressure (dbar) (here using 0 pressure to get potential density | ||
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| # Diffusivites | ||
| κH = 500.0 # m^2/s | ||
| κVML = 0.1 # m^2/s | ||
| κVdeep = 1e-5 # m^2/s | ||
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| # Make indices | ||
| indices = makeindices(gridmetrics.v3D) | ||
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| @test all(.!isnan.(ρ[indices.wet3D])) == true | ||
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| # Make fuxes from all directions | ||
| ϕ = facefluxesfrommasstransport(; umo, vmo, gridmetrics, indices) | ||
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| # Make fuxes from all directions from velocities | ||
| ϕ_bis = facefluxesfromvelocities(; uo, uo_lon, uo_lat, vo, vo_lon, vo_lat, gridmetrics, indices, ρ) | ||
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| # Make transport matrix | ||
| (; T, Tadv, TκH, TκVML, TκVdeep) = transportmatrix(; ϕ, mlotst, gridmetrics, indices, ρ, κH, κVML, κVdeep) | ||
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| @profview transportmatrix(; ϕ, mlotst, gridmetrics, indices, ρ, κH, κVML, κVdeep) | ||
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| @profview_allocs transportmatrix(; ϕ, mlotst, gridmetrics, indices, ρ, κH, κVML, κVdeep) sample_rate=0.9 |
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@JuliaRegistrator register
Release notes:
sizehint!. TODO: pre-allocate the sparse matrices themselves, or some other process to sum over indices/valuesded800dThere was a problem hiding this comment.
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Registration pull request created: JuliaRegistries/General/118354
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