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ViewsFastest way to write numpy array in arrow format
I'm looking for fast ways to store and retrieve numpy array using pyarrow. I'm pretty satisfied with retrieval. It takes less than 1 second to extract columns from my .arrow file that contains 1.000.000.000 integers of dtype = np.uint16.
import pyarrow as pa
import numpy as np
def write(arr, name):
arrays = [pa.array(col) for col in arr]
names = [str(i) for i in range(len(arrays))]
batch = pa.RecordBatch.from_arrays(arrays, names=names)
with pa.OSFile(name, 'wb') as sink:
with pa.RecordBatchStreamWriter(sink, batch.schema) as writer:
writer.write_batch(batch)
def read(name):
source = pa.memory_map(name, 'r')
table = pa.ipc.RecordBatchStreamReader(source).read_all()
for i in range(table.num_columns):
yield table.column(str(i)).to_numpy()
arr = np.random.randint(65535, size=(250, 4000000), dtype=np.uint16)
%%timeit -r 1 -n 1
write(arr, 'test.arrow')
>>> 25.6 s ± 0 ns per loop (mean ± std. dev. of 1 run, 1 loop each)
%%timeit -r 1 -n 1
for n in read('test.arrow'): n
>>> 901 ms ± 0 ns per loop (mean ± std. dev. of 1 run, 1 loop each)
Can efficiency of writing to .arrow format be improved? In addition, I tested np.save:
%%timeit -r 1 -n 1
np.save('test.npy', arr)
>>> 18.5 s ± 0 ns per loop (mean ± std. dev. of 1 run, 1 loop each)
It looks a little bit faster. Can we optimise Apache Arrow for better writing into .arrow format further?
2 answers
Answer question0
It may be the case that the performance issue is mainly due to IO/disk speed. In this case, there isn't much you can improve.
I ran a few tests on my device. The numbers I get are different from yours. But the bottom line is the same, writing is slower than reading.
The resulting file is 1.9 GB (2000023184 bytes):
$ ls test.arrow -l
-rw-rw-r-- 1 0x26res 0x26res 2000023184 Nov 15 10:01 test.arrow
In the code below I generate 1.9 GB of random bytes, and save them, then compare to the time it took to save with arrow:
import secrets
data = b"\x00" + secrets.token_bytes(2000023184) + b"\x00"
def write_bytes(data, name):
with open(name, 'wb') as fp:
fp.write(data)
%%timeit -r 1 -n 1 write_bytes(data, 'test.bytes')
>>> 2.29 s ± 0 ns per loop (mean ± std. dev. of 1 run, 1 loop each)
%%timeit -r 1 -n 1 write(arr, 'test.arrow')
>>> 2.52 s ± 0 ns per loop (mean ± std. dev. of 1 run, 1 loop each)
On my device, it takes 2.52 seconds to write the data using arrow. If I try to write that amount of random bytes it takes 2.29 seconds. It means the overhead or arrow is about 10% of the write time, so there isn't much that can be done to speed it up.
0
Indeed, it appears to be some kind of limitations of my RAM/IO/disk. Very silent ones... It slows down my writing 3 - 8 times after arr exceeds 200M items and that's why I'm experiencing a drop of speed from 2.5 seconds to 20. I would be glad to know if this could be resolved in pyarrow.
def pyarrow_write_arrow_Batch(arr, name):
arrays = [pa.array(col) for col in arr]
names = [str(i) for i in range(len(arrays))]
batch = pa.RecordBatch.from_arrays(arrays, names=names)
with pa.OSFile(name, 'wb') as sink:
with pa.RecordBatchStreamWriter(sink, batch.schema) as writer:
writer.write_batch(batch)
%matplotlib notebook
import benchit
benchit.setparams(environ='notebook')
benchit.setparams(rep=5)
arr = np.random.randint(65535, size=(int(1e9),), dtype=np.uint16)
size = [4, 8, 12, 20, 32, 48, 64, 100, 160, 256, 400, 600, 1000]
def pwa_Batch_10000(arr, name): return pyarrow_write_arrow_Batch(arr.reshape(-1, 10000), name)
def pwa_Batch_100000(arr, name): return pyarrow_write_arrow_Batch(arr.reshape(-1, 100000), name)
def pwa_Batch_1000000(arr, name): return pyarrow_write_arrow_Batch(arr.reshape(-1, 1000000), name)
def pwa_Batch_4000000(arr, name): return pyarrow_write_arrow_Batch(arr.reshape(-1, 4000000), name)
fns = [pwa_Batch_10000, pwa_Batch_100000, pwa_Batch_1000000, pwa_Batch_4000000]
in_ = {s: (arr[:s*int(1e6)], 'test.arrow') for s in size}
t = benchit.timings(fns, in_, multivar=True, input_name='Millions of items')
t.plot(logx=True, figsize=(8,4), fontsize=10)
