Model split perf

[Huite]

For @jdelsman

Sample script:

# %%

import imod

# %%
path = "Z:/tmp/joost/v5_composiet_v1b_v2_nodsp_aut/v5_composiet_v1b_v2_nodsp.toml"
sim = imod.mf6.Modflow6Simulation.from_file(path)
submodel_labels = sim.create_partition_labels(npartitions=24)

# %%

sim_partitions = sim.split(submodel_labels, ignore_time_purge_empty=True)

The sim.split() takes about 70 seconds here, which seems reasonable (compared to 2 hours before?).

[Huite]

This script will re-order the data to a locality preserving order, and them dump everything to TOML + Zarr:

# %%

import numpy as np
import imod
import xarray as xr

# %%

def morton_encode_2d(x, y):
    """
    Encode 2D coordinates to Morton codes.
    Uses 32 bits per dimension for 64-bit Morton codes.

    Parameters
    ----------
    x: np.ndarray of floats
    y: np.ndarray of floats

    Returns
    -------
    codes: np.ndarray
        Morton codes as uint64
    """
    x = np.asarray(x, dtype=np.float64)
    y = np.asarray(y, dtype=np.float64)

    min_x, max_x = np.min(x), np.max(x)
    min_y, max_y = np.min(y), np.max(y)

    # Add small padding to avoid edge cases
    x_range = max_x - min_x
    y_range = max_y - min_y
    padding = 1e-12  # Smaller padding for maximum resolution

    if x_range == 0:
        x_range = 1.0
        padding = 0.5
    if y_range == 0:
        y_range = 1.0
        padding = 0.5

    min_x -= x_range * padding
    max_x += x_range * padding
    min_y -= y_range * padding
    max_y += y_range * padding

    # Scale coordinates to [0, 2^32 - 1] for maximum resolution
    max_coord = 0xFFFFFFFF  # 2^32 - 1

    x_scaled = ((x - min_x) / (max_x - min_x) * max_coord).astype(np.uint64)
    y_scaled = ((y - min_y) / (max_y - min_y) * max_coord).astype(np.uint64)

    # Clamp to valid range
    x_scaled = np.clip(x_scaled, 0, max_coord)
    y_scaled = np.clip(y_scaled, 0, max_coord)

    # Dilate bits for 32-bit values - maximum resolution bit interleaving
    def dilate_bits_32(vals):
        """Dilate 32-bit values by inserting zeros between bits"""
        vals = vals & 0xFFFFFFFF  # Ensure 32-bit
        vals = (vals | (vals << 32)) & 0x00000000FFFFFFFF
        vals = (vals | (vals << 16)) & 0x0000FFFF0000FFFF
        vals = (vals | (vals << 8)) & 0x00FF00FF00FF00FF
        vals = (vals | (vals << 4)) & 0x0F0F0F0F0F0F0F0F
        vals = (vals | (vals << 2)) & 0x3333333333333333
        vals = (vals | (vals << 1)) & 0x5555555555555555
        return vals

    # Dilate and interleave: x gets odd positions, y gets even positions
    x_dilated = dilate_bits_32(x_scaled)
    y_dilated = dilate_bits_32(y_scaled)

    # Interleave by shifting y left by 1 and OR-ing with x
    morton_codes = x_dilated | (y_dilated << 1)

    return morton_codes


def reorder_morton(data):
    grid = data.ugrid.grid
    x, y = grid.centroids.T
    codes = morton_encode_2d(x, y)
    order = np.argsort(codes)
    return data.isel({grid.face_dimension: order})


def reorder_and_rechunk_simulation(
    sim: imod.mf6.Modflow6Simulation,
    dimension: str = "mesh2d_nFaces",
    chunks: dict[str, int]=None,
):
    if chunks is None:
        chunks = {"time": 10, dimension: 20_000}

    for model in sim.values():
        if isinstance(model, imod.mf6.model.Modflow6Model):
            for package in model.values():
                dims = package.dataset.dims
                if dimension in dims:
                    package_chunks = {k: v for k, v in chunks.items() if k in dims}
                    package.dataset = reorder_morton(package.dataset)
                    # Set encoding chunks which will end up in the zarr file.
                    if package_chunks:
                        package.dataset.encoding = {"chunks": package_chunks}

    return



# %%

path = "Z:/tmp/joost/v5_composiet_v1b_v2_nodsp_aut/v5_composiet_v1b_v2_nodsp.toml"
sim = imod.mf6.Modflow6Simulation.from_file(path)
reorder_and_rechunk_simulation(sim)
sim.dump("rechunked_zarrsim", validate=False, engine="zarr")
 

[Huite]

Annoyingly, I get an error inside the function calls that .item() isn't supported on dask arrays. Though when I access the variable through the REPL it seems to work fine. (EDIT: the reason this works is almost certainly because the REPL calls the __repr__ method which forces a compute somewhere.) Also, it becomes unhappy when it comes across the well package. Anyway, we can sidestep this by forcing all non spatial data into memory:

# %%
import imod

# %%

def load_non_spatial_data(sim, dimension: str = "mesh2d_nFaces"):
    for model in sim.values():
        if isinstance(model, imod.mf6.model.Modflow6Model):
            for package in model.values():
                if dimension not in package.dataset.dims:
                    package.dataset.load()
                for var in package.dataset.data_vars:
                    if dimension not in package.dataset[var].dims:
                        package.dataset[var].load()
        else:
            model.dataset.load()
    return

# %%

path = "rechunked-simulation/v5_composiet_v1b_v2_nodsp.toml"
sim = imod.mf6.Modflow6Simulation.from_file(path)
load_non_spatial_data(sim)
sim._validation_context = imod.mf6.ValidationSettings(strict_well_validation=False, ignore_time=True)

# %%

# Serial test
# sim.write("serial_simulation", validate=False)

submodel_labels = sim.create_partition_labels(npartitions=8)
sim_partitions = sim.split(submodel_labels, ignore_time_purge_empty=True)

sim_partitions._validation_context = imod.mf6.ValidationSettings(strict_well_validation=False, ignore_time=True)
sim_partitions.write("partitioned_simulation", validate=False)
# %%

For future to do's: the morton curve ordering should become a part of xugrid. See: Deltares/xugrid#389

It may make sense to wrap the ordering on the simulation levels, as a method instead of a free function.
We should investigate the zarr stuff; I'm running into an issue here where I cannot re-open a zip store of the recharge while the other packages work fine; the only reason I can think of now is the size. We also need to investigate the .item() thing which seems related to zarr as well -- I think zarr causes more aggressive chunking, whereas the netCDF engine might treat scalars somewhat differently? Not sure.

[Huite]

Some general thoughts (I've had a little time to mull it over); we a minior optimization in the from_file method, which is to simply load all variables that are non-spatial. For these variables, having it dask backed will only increase overhead. This'll also solve the .item() issue.

Secondly, in the get_unfiltered_options; we should probably use is_scalar as a predicate.

[Manangka]

This issue has been addressed in #1693

[Manangka]

Accidently closed this PR.
Keeping it open because it still contains relevant code for optimizing the sim write process

[sonarqubecloud]

Quality Gate passed

Issues
12 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarQube Cloud

[Manangka]

The second part of this issue has been addressed in #1700