Merge pull request #3 from Ouranosinc/growing-season-length

Benchmarking Growing Season Length

scripts/bench_gsl.py

@@ -0,0 +1,174 @@
+# Growing season length benchmarks
+# Comparing different implementations
+import glob
+import argparse
+import numpy as np
+import xclim as xc
+import pandas as pd
+import xarray as xr
+import datetime as dt
+from xclim import run_length as rl
+from distributed import Client
+testfile = 'testdata_i{i}.nc'
+outfile = 'testout_{}.nc'
+window = 6
+thresh = 5
+
+
+def read_mprofile(filename):
+    times = []
+    mem = []
+    name = filename.split('.')[0]
+    with open(filename, 'r') as f:
+        for line in f:
+            if line.startswith('CMDLINE'):
+                name = line.strip().split()[-1]
+            elif line.startswith('MEM'):
+                _, m, t = line.strip().split()
+                times.append(dt.datetime.fromtimestamp(float(t)))
+                mem.append(float(m))
+    times = [(t - times[0]).total_seconds() for t in times]
+    return name, times, mem
+
+
+def exp_smallchange(tas):
+    c = ((tas > thresh) * 1).rolling(time=window).sum(allow_lazy=True, skipna=False)
+
+    def compute_gsl(c):
+        nt = c.time.size
+        i = xr.DataArray(np.arange(nt), dims="time")
+        ind = xr.broadcast(i, c)[0].chunk(c.chunks)
+        i1 = ind.where(c == window).min(dim="time")
+        i2 = ind.where((c == 0) & (c.time.dt.month >= 7)).min(dim='time')
+        d = (i2 - i1)
+        d = d.where(d > 0)
+        return d
+
+    return c.resample(time='YS').apply(compute_gsl)
+
+
+def exp_firstrun(tas):
+    def func(group):
+        deb = rl.first_run(group.where(group.time.dt.month < 7) > thresh, window, 'time')
+        fin = rl.first_run(group.where(group.time.dt.month >= 7) < thresh, window, 'time')
+        return fin - deb
+
+    return tas.resample(time='YS').apply(func)
+
+
+def exp_firstrunnocheck(tas):
+    def func(group):
+        deb = rl.first_run(group > thresh, window, 'time')
+        fin = rl.first_run(group.where(group.time.dt.month >= 7) < thresh, window, 'time')
+        return fin - deb
+
+    return tas.resample(time='YS').apply(func)
+
+
+def exp_firstruncheck(tas):
+    def func(group):
+        sl = rl.first_run(group.where(group.time.dt.month >= 7) < thresh, window, 'time') - rl.first_run(group > thresh, window, 'time')
+        return sl.where(sl > 0)
+
+    return tas.resample(time='YS').apply(func)
+
+
+def exp_firstrunisel(tas):
+    def func(group):
+        fin = rl.first_run(group.where(group.time.dt.month >= 7) < thresh, window, 'time')
+        deb = rl.first_run(group.where(group.time.dt.dayofyear < fin) > thresh, window, 'time')
+        return fin - deb
+
+    return tas.resample(time='YS').apply(func)
+
+
+def exp_xcdef(tas, window=6, thresh=5):
+    return xc.indices.growing_season_length(tas)
+
+
+all_exps = {name.split('_')[1]: func for name, func in globals().items() if name.startswith('exp')}
+
+
+if __name__ == '__main__':
+    parser = argparse.ArgumentParser(description='Profile memory for rolling functions')
+    parser.add_argument('-c', '--with-client', action='store_true', help='whether to use a dask client')
+    parser.add_argument('-N', '--nthreads', default=10, type=int, help='When using a dask client, number of threads per worker')
+    parser.add_argument('-m', '--max-mem', default='2GB', help='When using a dask client, memory limit')
+    parser.add_argument('exp', type=str, help='which exp to run')
+    parser.add_argument('-i', '--files', default='*.dat', nargs='*', help='Dat files to plot')
+    parser.add_argument('-n', '--chunk-size', default=[3, 100, 100, 1], nargs='*', help='Size of the random data to generate. 1, 2, 3 or 4 values for t (n years), x, y and nchunks/yr. Data is daily.')
+    args = parser.parse_args()
+
+    if args.exp == 'gendata':
+        if isinstance(args.chunk_size, list):
+            if len(args.chunk_size) == 2:
+                Nt, Nc = map(int, args.chunk_size)
+                Ny = Nx = Nt
+            elif len(args.chunk_size) == 3:
+                Nt, Nx, Nc = map(int, args.chunk_size)
+                Ny = Nt
+            else:
+                Nt, Nx, Ny, Nc = map(int, args.chunk_size)
+        else:
+            Nt = Nx = Ny = int(args.chunk_size)
+            Nc = 10
+        times = pd.date_range('2000-01-01', f'20{Nt:02d}-12-31', freq='D')
+        times = xr.DataArray(times, coords={'time': times}, dims=('time',), name='time')
+        chunkSize = 365 // Nc
+        for i in range(Nt):
+            data = np.random.random((times.sel(time=f'20{i:02d}').size, Nx, Ny)) - 20 * np.cos(2 * np.pi * times.sel(time=f'20{i:02d}').dt.dayofyear.values / 366)[:, np.newaxis, np.newaxis]
+            for c in range(Nc):
+                print(f'Generating data {i * Nc + c + 1:02d}/{Nc * Nt}')
+                data = xr.DataArray(data=data[slice(c * chunkSize, (c + 1) * chunkSize if c + 1 < Nc else None)],
+                                    dims=('time', 'x', 'y'),
+                                    coords={'time': times.sel(time=f'20{i:02d}').isel(time=slice(c * chunkSize, (c + 1) * chunkSize if c + 1 < Nc else None)),
+                                            'x': np.arange(Nx), 'y': np.arange(Ny)},
+                                    name='data',
+                                    attrs={'units': 'degC'})
+                data[chunkSize // 2, 0, 0] = np.nan
+                data.to_netcdf(testfile.format(i=f'{i:02d}'))
+
+    elif args.exp == 'plot':
+        import matplotlib.pyplot as plt
+        try:
+            plt.style.use('dark_background')
+        except OSError:
+            pass
+        if not isinstance(args.files, list):
+            if '*' in args.files:
+                files = glob.glob(args.files)
+            else:
+                files = [args.files]
+        else:
+            files = args.files
+        colors = {exp: col for exp, col in zip(all_exps.keys(),
+                                               plt.matplotlib.rcParams['axes.prop_cycle'].by_key()['color'])}
+        fig, ax = plt.subplots(figsize=(10, 5))
+        for file in files:
+            name, times, mem = read_mprofile(file)
+            ax.plot(times, mem, label=name, color=colors[name])
+        ax.legend()
+        ax.set_xlabel('Computation time [s]')
+        ax.set_ylabel('Memory usage [MiB]')
+        ax.set_title('Memory usage of different percentile calculations')
+        plt.show()
+
+    else:
+        if args.with_client:
+            c = Client(n_workers=1, threads_per_worker=args.nthreads, memory_limit=args.max_mem)
+
+        # num_real = len(glob.glob(testfile.format(r='*', i=0)))
+
+        ds = xr.open_mfdataset(testfile.format(i='*'))
+        ds.data.attrs.update(units='degC')
+        print(f'Running rolling with exp: {args.exp}')
+        ds_out = all_exps[args.exp](ds.data)
+
+        print('Writing to file')
+
+        r = ds_out.to_netcdf(outfile.format(args.exp), compute=False)
+        r.compute()
+        ds_out.close()
+
+        if args.with_client:
+            c.close()