Merge pull request #7 from OceanParcels/benchmark-MOi_curvilinear

Benchmark MOi curvilinear

Author: erikvansebille

MOi-Curvilinear/benchmark_moi_curvilinear.py

@@ -0,0 +1,189 @@
+from argparse import ArgumentParser
+from pathlib import Path
+import xarray as xr
+import tracemalloc
+import time
+
+from glob import glob
+
+import numpy as np
+
+import parcels
+
+runtime = np.timedelta64(2, "D")
+dt = np.timedelta64(15, "m")
+
+parcelsv4 = True
+try:
+    import xgcm
+    from parcels.interpolators import XLinear
+except ImportError:
+    parcelsv4 = False
+
+DATA_ROOT = "/storage/shared/oceanparcels/input_data/MOi"
+
+def run_benchmark(interpolator: str, trace_memory: bool = False, surface_simulation: bool =False, preload: bool = False, cycle_chunks: bool = False):
+
+    lon0_expected, lat0_expected = -10.128929, -29.721205  # values from v3 using from_netcf (so assuming A-grid!)
+
+    if cycle_chunks:
+        xy_chunks = [64, 128, 256, 512, 1024, 2084, 32, 16, 8, 4]
+        nparts = [10_000]
+    else:
+        xy_chunks = [256]
+        nparts = [1, 10, 100, 1_000, 5_000, 10_000, 50_000, 100_000, 500_000, 1_000_000]
+    fileU = f"{DATA_ROOT}/GLO12/psy4v3r1-daily_U_2010-01-0[1-3].nc"
+    filenames = {"U": glob(fileU), "V": glob(fileU.replace("_U_", "_V_")), "W": glob(fileU.replace("_U_", "_W_"))}
+    mesh_mask = f"{DATA_ROOT}/domain_ORCA0083-N006/PSY4V3R1_mesh_hgr.nc"
+
+    for chunk in xy_chunks:
+        if parcelsv4:
+            if interpolator == "XLinear":
+                interp_method = XLinear
+            else:
+                raise ValueError(f"Unknown interpolator: {interpolator}")
+
+            fileargs = {"concat_dim": "time_counter",
+                "combine": "nested",
+                "data_vars": 'minimal',
+                "coords": 'minimal',
+                "compat": 'override',
+            }
+            if chunk:
+                fileargs["chunks"] = {"time_counter": 1, "depth":2, "y": chunk, "x": chunk}
+
+            ds_u = xr.open_mfdataset(filenames["U"], **fileargs)[["vozocrtx"]].drop_vars(["nav_lon", "nav_lat"])
+            ds_v = xr.open_mfdataset(filenames["V"], **fileargs)[["vomecrty"]].drop_vars(["nav_lon", "nav_lat"])
+            ds_depth = xr.open_mfdataset(filenames["W"], **fileargs)[["depthw"]]
+            ds_mesh = xr.open_dataset(mesh_mask)[["glamf", "gphif"]].isel(t=0)
+
+            ds = xr.merge([ds_u, ds_v, ds_depth, ds_mesh], compat="identical").rename({"vozocrtx": "U", "vomecrty": "V"}).rename({"glamf": "lon", "gphif": "lat", "time_counter": "time", "depthw": "depth"})
+            ds = xr.merge([ds_u, ds_v, ds_depth, ds_mesh], compat="identical")
+            ds = ds.rename({"vozocrtx": "U", "vomecrty": "V", "glamf": "lon", "gphif": "lat", "time_counter": "time", "depthw": "depth"})
+            ds.deptht.attrs["c_grid_axis_shift"] = -0.5
+
+            coords={"X": {"left": "x"}, "Y": {"left": "y"}, "T": {"center": "time"}}
+
+            coords={
+                "X": {"left": "x"},
+                "Y": {"left": "y"},
+                "T": {"center": "time"},
+            }
+            if surface_simulation:
+                ds = ds.isel(depth=0, deptht=0)
+            else:
+                coords["Z"] = {"center": "deptht", "left": "depth"}
+            print(ds)
+
+            grid = parcels._core.xgrid.XGrid(xgcm.Grid(ds, coords=coords, autoparse_metadata=False, periodic=False), mesh="spherical")
+
+            U = parcels.Field("U", ds["U"], grid, interp_method=interp_method)
+            V = parcels.Field("V", ds["V"], grid, interp_method=interp_method)
+            U.units = parcels.GeographicPolar()
+            V.units = parcels.Geographic()
+            UV = parcels.VectorField("UV", U, V)
+
+            fieldset = parcels.FieldSet([U, V, UV])
+        else:
+            filenames = {
+                "U": {"lon": mesh_mask, "lat": mesh_mask, "depth": filenames["W"][0], "data": filenames["U"]},
+                "V": {"lon": mesh_mask, "lat": mesh_mask, "depth": filenames["W"][0], "data": filenames["V"]},
+            }
+            interpolator = "v3_default"
+            if surface_simulation:
+                indices={"depth": range(2)}
+            else:
+                indices=None
+
+            fieldset = parcels.FieldSet.from_netcdf(
+                filenames,
+                variables={"U": "vozocrtx", "V": "vomecrty"},
+                dimensions={"time": "time_counter", "lat": "gphif", "lon": "glamf", "depth": "depthw"},
+                indices=indices,
+            )
+
+        pclass = parcels.Particle if parcelsv4 else parcels.JITParticle
+
+        if parcelsv4 and preload:
+            fieldset.U.data.load()
+            fieldset.V.data.load()
+
+        for npart in nparts:
+            if cycle_chunks:
+                X, Y = np.meshgrid(np.linspace(-10, 10, int(np.sqrt(npart))), np.linspace(-30, -20, int(np.sqrt(npart))))
+                lon = X.flatten()
+                lat = Y.flatten()
+            else:
+                lon = np.linspace(-10, 10, npart)
+                lat = np.linspace(-30, -20, npart)
+
+            pset = parcels.ParticleSet(fieldset=fieldset, pclass=pclass, lon=lon, lat=lat)
+
+            print(f"Running {len(lon):_} particles on {"surface" if surface_simulation else "3D"} with parcels v{4 if parcelsv4 else 3}, chunksize {chunk} ({'preloaded' if preload else 'not preloaded'}) and {interpolator} interpolator")
+
+            if trace_memory:
+                tracemalloc.start()
+            else:
+                start = time.time()
+
+            pset.execute(parcels.kernels.AdvectionEE, runtime=runtime, dt=dt, verbose_progress=False)
+
+            if trace_memory:
+                current, peak = tracemalloc.get_traced_memory()
+                tracemalloc.stop()
+                print(f"Memory usage: current={current / 1e6:.0f} MB, peak={peak / 1e6:.0f} MB")
+            else:
+                elapsed_time = time.time() - start
+                print(f"Execution time: {elapsed_time:.0f} seconds")
+
+            print("")
+
+            if not cycle_chunks:
+                assert np.allclose(pset[0].lon, lon0_expected, atol=1e-5), f"Expected lon {lon0_expected}, got {pset[0].lon}"
+                assert np.allclose(pset[0].lat, lat0_expected, atol=1e-5), f"Expected lat {lat0_expected}, got {pset[0].lat}"
+
+
+def main(args=None):
+    p = ArgumentParser()
+
+    p.add_argument(
+        "-i",
+        "--Interpolator",
+        choices=("XLinear", "BiRectiLinear", "PureXarrayInterp", "NoFieldAccess"),
+        default="XLinear",
+    )
+
+    p.add_argument(
+        "-m",
+        "--memory",
+        action="store_true",
+        help="Enable memory tracing (default: False)",
+    )
+
+    p.add_argument(
+        "-s",
+        "--surface",
+        action="store_true",
+        help="Run surface simulation with only 1 or 2 depth levels (default: False)",
+    )
+
+    p.add_argument(
+        "-l",
+        "--preload",
+        action="store_true",
+        help="Preload data into memory (default: False)",
+    )
+
+    p.add_argument(
+        "-c",
+        "--chunks",
+        action="store_true",
+        help="Cycle through different chunk sizes (default: False)",
+    )
+
+    args = p.parse_args(args)
+    run_benchmark(args.Interpolator, args.memory, args.surface, args.preload, args.chunks)
+
+
+if __name__ == "__main__":
+    main()