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Merge pull request #2773 from CliMA/gb/bench_io
Add job to benchmark IO
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| Original file line number | Diff line number | Diff line change |
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| ClimaAtmos.jl Release Notes | ||
| ============================ | ||
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| Main | ||
| ------- | ||
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| - ![][badge-🚀performance] Reduced the number of allocations in the NetCDF | ||
| writer. PRs [#2772](https://github.com/CliMA/ClimaAtmos.jl/pull/2772), | ||
| [#2773](https://github.com/CliMA/ClimaAtmos.jl/pull/2773). | ||
| - Added a new script, `perf/benchmark_netcdf_io.jl` to test IO performance for | ||
| the NetCDF writer. PR [#2773](https://github.com/CliMA/ClimaAtmos.jl/pull/2773). | ||
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| <!-- | ||
| Contributors are welcome to begin the description of changelog items with badge(s) below. Here is a brief description of when to use badges for a particular pull request / set of changes: | ||
| - 🔥behavioralΔ - behavioral changes. For example: a new model is used, yielding more accurate results. | ||
| - 🤖precisionΔ - machine-precision changes. For example, swapping the order of summed arguments can result in machine-precision changes. | ||
| - 💥breaking - breaking changes. For example: removing deprecated functions/types, removing support for functionality, API changes. | ||
| - 🚀performance - performance improvements. For example: improving type inference, reducing allocations, or code hoisting. | ||
| - ✨feature - new feature added. For example: adding support for a cubed-sphere grid | ||
| - 🐛bugfix - bugfix. For example: fixing incorrect logic, resulting in incorrect results, or fixing code that otherwise might give a `MethodError`. | ||
| --> | ||
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| [badge-🔥behavioralΔ]: https://img.shields.io/badge/🔥behavioralΔ-orange.svg | ||
| [badge-🤖precisionΔ]: https://img.shields.io/badge/🤖precisionΔ-black.svg | ||
| [badge-💥breaking]: https://img.shields.io/badge/💥BREAKING-red.svg | ||
| [badge-🚀performance]: https://img.shields.io/badge/🚀performance-green.svg | ||
| [badge-✨feature/enhancement]: https://img.shields.io/badge/feature/enhancement-blue.svg | ||
| [badge-🐛bugfix]: https://img.shields.io/badge/🐛bugfix-purple.svg |
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| import ClimaAtmos as CA | ||
| import ClimaAtmos.Diagnostics as CAD | ||
| import ClimaComms | ||
| import Profile, ProfileCanvas | ||
| import NCDatasets | ||
| import Base: rm | ||
| using BenchmarkTools | ||
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| # This script runs our NetCDF writer and compares its performance with | ||
| # NCDatasets. It also produces a flamegraph for IO. | ||
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| # Number of target interpolation point along each dimension | ||
| const NUM = 100 | ||
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| timings = Dict{ClimaComms.AbstractDevice, Any}( | ||
| ClimaComms.CPUSingleThreaded() => missing, | ||
| ) | ||
| # If a GPU is available, runs on CPU and GPU | ||
| if ClimaComms.device() isa ClimaComms.CUDADevice | ||
| timings[ClimaComms.CUDADevice()] = missing | ||
| end | ||
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| timings_ncdataset = copy(timings) | ||
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| function add_nc(nc, outarray) | ||
| v = nc["rhoa"] | ||
| temporal_size, spatial_size... = size(v) | ||
| time_index = temporal_size + 1 | ||
| nc["time"][time_index] = 10.0 * time_index | ||
| v[time_index, :, :, :] = outarray | ||
| end | ||
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| for device in keys(timings) | ||
| device_name = nameof(typeof(device)) | ||
| config = CA.AtmosConfig(; comms_ctx = ClimaComms.context(device)) | ||
| config.parsed_args["diagnostics"] = | ||
| [Dict("short_name" => "rhoa", "period" => config.parsed_args["dt"])] | ||
| config.parsed_args["netcdf_interpolation_num_points"] = [NUM, NUM, NUM] | ||
| config.parsed_args["job_id"] = "flame_perf_io" | ||
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| simulation = CA.get_simulation(config) | ||
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| # Cleanup pre-existing NC files | ||
| foreach( | ||
| rm, | ||
| filter(endswith(".nc"), readdir(simulation.output_dir, join = true)), | ||
| ) | ||
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| atmos_model = simulation.integrator.p.atmos | ||
| cspace = axes(simulation.integrator.u.c) | ||
| diagnostics, _ = CA.get_diagnostics(config.parsed_args, atmos_model, cspace) | ||
| rhoa_diag = diagnostics[end] | ||
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| netcdf_writer = simulation.output_writers[2] | ||
| field = simulation.integrator.u.c.ρ | ||
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| integrator = simulation.integrator | ||
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| # Run once to create the file | ||
| CAD.write_field!( | ||
| netcdf_writer, | ||
| field, | ||
| rhoa_diag, | ||
| integrator.u, | ||
| integrator.p, | ||
| integrator.t, | ||
| simulation.output_dir, | ||
| ) | ||
| # Now, profile | ||
| @info "Profiling ($device_name)" | ||
| prof = Profile.@profile CAD.save_diagnostic_to_disk!( | ||
| netcdf_writer, | ||
| field, | ||
| rhoa_diag, | ||
| integrator.u, | ||
| integrator.p, | ||
| integrator.t, | ||
| simulation.output_dir, | ||
| ) | ||
| results = Profile.fetch() | ||
| flame_path = joinpath(simulation.output_dir, "flame_$device_name.html") | ||
| ProfileCanvas.html_file(flame_path, results) | ||
| @info "Flame saved in $flame_path" | ||
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| @info "Benchmarking our NetCDF writer (only IO) ($device_name)" | ||
| timings[device] = @benchmark CAD.save_diagnostic_to_disk!( | ||
| $netcdf_writer, | ||
| $field, | ||
| $rhoa_diag, | ||
| $(integrator.u), | ||
| $(integrator.p), | ||
| $(integrator.t), | ||
| $(simulation.output_dir), | ||
| ) | ||
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| @info "Benchmarking NCDatasets ($device_name)" | ||
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| output_path = joinpath(simulation.output_dir, "clean_netcdf.nc") | ||
| nc = NCDatasets.NCDataset(output_path, "c") | ||
| NCDatasets.defDim(nc, "time", Inf) | ||
| NCDatasets.defVar(nc, "time", Float32, ("time",)) | ||
| NCDatasets.defDim(nc, "x", NUM) | ||
| NCDatasets.defDim(nc, "y", NUM) | ||
| NCDatasets.defDim(nc, "z", NUM) | ||
| v = NCDatasets.defVar(nc, "rhoa", Float32, ("time", "x", "y", "z")) | ||
| outarray = Array(netcdf_writer.remappers["rhoa"]._interpolated_values) | ||
| v[1, :, :, :] = outarray | ||
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| timings_ncdataset[device] = @benchmark $add_nc($nc, $outarray) | ||
| end | ||
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| for device in keys(timings) | ||
| println("DEVICE: ", device) | ||
| println("Our writer") | ||
| show(stdout, MIME"text/plain"(), timings[device]) | ||
| println() | ||
| println("NCDatasets") | ||
| show(stdout, MIME"text/plain"(), timings_ncdataset[device]) | ||
| println() | ||
| end |
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