dask_ml.decomposition.PCA: ValueError with data > 1 TB

When I do dask_ml.decomposition.PCA().fit(x), where the array x has a size > 1 TB, I get the error ValueError: output array is read-only.

I use

dask-ml                   1.1.1
distributed               2.9.0

The script

from dask_jobqueue import SLURMCluster
from dask.distributed import Client
from dask_ml.decomposition import PCA
import dask.array as da

cluster = SLURMCluster()
nb_workers = 58
cluster.scale(nb_workers)
client = Client(cluster)
client.wait_for_workers(nb_workers)

x = da.random.random((1000000, 140000), chunks=(100000, 2000))
pca = PCA(n_components=64)
pca.fit(x)

gives the error

Traceback (most recent call last):
  File "value_error.py", line 48, in <module>
    pca.fit(x)
  File "/home/dheim/miniconda3/lib/python3.7/site-packages/dask_ml/decomposition/pca.py", line 190, in fit
    self._fit(X)
  File "/home/dheim/miniconda3/lib/python3.7/site-packages/dask_ml/decomposition/pca.py", line 338, in _fit
    raise e
  File "/home/dheim/miniconda3/lib/python3.7/site-packages/dask_ml/decomposition/pca.py", line 325, in _fit
    singular_values,
  File "/home/dheim/miniconda3/lib/python3.7/site-packages/dask/base.py", line 436, in compute
    results = schedule(dsk, keys, **kwargs)
  File "/home/dheim/miniconda3/lib/python3.7/site-packages/distributed/client.py", line 2573, in get
    results = self.gather(packed, asynchronous=asynchronous, direct=direct)
  File "/home/dheim/miniconda3/lib/python3.7/site-packages/distributed/client.py", line 1873, in gather
    asynchronous=asynchronous,
  File "/home/dheim/miniconda3/lib/python3.7/site-packages/distributed/client.py", line 768, in sync
    self.loop, func, *args, callback_timeout=callback_timeout, **kwargs
  File "/home/dheim/miniconda3/lib/python3.7/site-packages/distributed/utils.py", line 334, in sync
    raise exc.with_traceback(tb)
  File "/home/dheim/miniconda3/lib/python3.7/site-packages/distributed/utils.py", line 318, in f
    result[0] = yield future
  File "/home/dheim/miniconda3/lib/python3.7/site-packages/tornado/gen.py", line 735, in run
    value = future.result()
  File "/home/dheim/miniconda3/lib/python3.7/site-packages/distributed/client.py", line 1729, in _gather
    raise exception.with_traceback(traceback)
  File "/home/dheim/miniconda3/lib/python3.7/site-packages/sklearn/utils/extmath.py", line 516, in svd_flip
    v *= signs[:, np.newaxis]
ValueError: output array is read-only

Note that

• If I use x = da.random.random((1000000, 130000), chunks=(100000, 2000)) (1.0 TB), the error does not appear.
• When I look at the dashboard, the PCA seems to run fine and the error appears at the very end of the computation.
• I temporarily fixed the error in extmath.py by changing

def svd_flip(u, v, u_based_decision=True):
    if u_based_decision:
        # columns of u, rows of v
        max_abs_cols = np.argmax(np.abs(u), axis=0)
        signs = np.sign(u[max_abs_cols, range(u.shape[1])])
        u *= signs
-        v *= signs[:, np.newaxis]
+        v_copy = np.copy(v)
+        v_copy *= signs[:, np.newaxis]
+        return u, v_copy
    else:

I think this is not a good fix because I assume that the array v is blocked by another function. Is there another way to fix the error?

[TomAugspurger]

Can you reproduce the error on your HPC?

I don’t have access to an HPC machine.

https://github.com/dask/distributed/issues/1978 does sound related. Does ensuring that all your dependencies are built against Cython 0.28 or newer fix things?

https://github.com/dask/distributed/issues/1978#issuecomment-448209604 is using PCA as well. Let’s continue the discussion over there.

[jakirkham]

I also don’t understand why the array is readonly.

Because we send bytes over the wire and bytes are immutable.

In [1]: memoryview(b"abc").readonly                                             
Out[1]: True