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January 13, 2024 13:29
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dask h5py lifecycle issue
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import dask | |
import dask.array as da | |
import distributed | |
from distributed.protocol.serialize import dask_deserialize, dask_serialize | |
from dask.distributed import Client | |
import h5py | |
import numpy as np | |
import logging | |
logger = logging.Logger(__name__) | |
def register_custom_deserializer(): | |
dask._h5py_files = {} | |
@dask_deserialize.register(h5py.File) | |
def deserialize_h5py_file(header, frames): | |
import h5py | |
file = h5py.File(header["filename"], mode="r") | |
dask._h5py_files[header["filename"]] = file | |
print('stashed', dask._h5py_files) | |
return file | |
@dask_deserialize.register((h5py.Group, h5py.Dataset)) | |
def deserialize_h5py_dataset(header, frames): | |
file = deserialize_h5py_file(header, frames) | |
print('deserialized dataset') | |
return file[header["name"]] | |
print('registered') | |
def close_all_files(): | |
print("CLOSING!!", dask._h5py_files) | |
while dask._h5py_files: | |
filename, file = dask._h5py_files.popitem() | |
file.close() | |
import time; time.sleep(0.1) | |
if __name__ == "__main__": | |
print(f"Version of Dask: {dask.__version__}") | |
print(f"Version of Distributed: {distributed.__version__}") | |
print(f"===============================") | |
# Create HDF5 file | |
print("Creating HDF5 file") | |
fln = "test.h5" | |
with h5py.File(fln, "w") as f: | |
dset = f.create_dataset("data", data=np.random.random(size=(100, 100)), chunks=(10, 10), dtype="float64") | |
print("Creating client") | |
client = Client() | |
client.run(register_custom_deserializer) | |
# Process the file | |
print("Loading and processing data") | |
with h5py.File(fln, "r") as f: | |
data = da.from_array(f["data"], chunks=(10, 10)) | |
sm_fut = da.sum(data, axis=0).persist(scheduler=client) | |
sm = sm_fut.compute(scheduler=client) | |
print(f"sm={sm}") | |
client.run(close_all_files) | |
# Try to open file for writing | |
print("Attempting to open file for writing") | |
try: | |
with h5py.File(fln, "r+") as f: | |
print("File was opened for writing !!!") | |
except OSError as ex: | |
logger.exception("Failed to open file for writing: %s", ex) | |
print("Closing client") | |
client.close() |
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