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This is a duplicate of #22 opened by @fedden. It was apparently resolved by passing correct parameters, but no specific details are mentioned.
Some things I am adding upon which were unresolved in that issue:
Expanded stack trace
/project/csbio/envs_dirs/viz/lib/python3.6/site-packages/umap/umap_.py:1052: RuntimeWarning: divide by zero encountered in power
return 1.0 / (1.0 + a * x ** (2 * b))
Traceback (most recent call last):
File "pipeline.py", line 271, in <module>
coords, nodes = umap(new_gi_df, args, out_dir)
File "pipeline.py", line 141, in umap
embedding = reducer.fit_transform(gi_df.values)
File "/project/csbio/envs_dirs/viz/lib/python3.6/site-packages/umap/umap_.py", line 1598, in fit_transform
self.fit(X, y)
File "/project/csbio/envs_dirs/viz/lib/python3.6/site-packages/umap/umap_.py", line 1429, in fit
self.verbose,
File "/project/csbio/envs_dirs/viz/lib/python3.6/site-packages/umap/umap_.py", line 281, in nearest_neighbors
verbose=verbose,
File "/project/csbio/envs_dirs/viz/lib/python3.6/site-packages/numba/core/dispatcher.py", line 401, in _compile_for_args
error_rewrite(e, 'typing')
File "/project/csbio/envs_dirs/viz/lib/python3.6/site-packages/numba/core/dispatcher.py", line 344, in error_rewrite
reraise(type(e), e, None)
File "/project/csbio/envs_dirs/viz/lib/python3.6/site-packages/numba/core/utils.py", line 80, in reraise
raise value.with_traceback(tb)
numba.core.errors.TypingError: Failed in nopython mode pipeline (step: nopython frontend)
Failed in nopython mode pipeline (step: nopython frontend)
Invalid use of Function(<built-in function empty>) with argument(s) of type(s): (float64, dtype=class(int64))
* parameterized
In definition 0:
All templates rejected with literals.
In definition 1:
All templates rejected without literals.
This error is usually caused by passing an argument of a type that is unsupported by the named function.
[1] During: resolving callee type: Function(<built-in function empty>)
[2] During: typing of call at /project/csbio/envs_dirs/viz/lib/python3.6/site-packages/umap/utils.py (94)
File "../../../envs_dirs/viz/lib/python3.6/site-packages/umap/utils.py", line 94:
def rejection_sample(n_samples, pool_size, rng_state):
<source elided>
"""
result = np.empty(n_samples, dtype=np.int64)
^
[1] During: resolving callee type: type(CPUDispatcher(<function rejection_sample at 0x7f51f9e38950>))
[2] During: typing of call at /project/csbio/envs_dirs/viz/lib/python3.6/site-packages/umap/nndescent.py (63)
[3] During: resolving callee type: type(CPUDispatcher(<function rejection_sample at 0x7f51f9e38950>))
[4] During: typing of call at /project/csbio/envs_dirs/viz/lib/python3.6/site-packages/umap/nndescent.py (63)
[5] During: resolving callee type: type(CPUDispatcher(<function rejection_sample at 0x7f51f9e38950>))
[6] During: typing of call at /project/csbio/envs_dirs/viz/lib/python3.6/site-packages/umap/nndescent.py (63)
[7] During: resolving callee type: type(CPUDispatcher(<function rejection_sample at 0x7f51f9e38950>))
[8] During: typing of call at /project/csbio/envs_dirs/viz/lib/python3.6/site-packages/umap/nndescent.py (63)
[9] During: resolving callee type: type(CPUDispatcher(<function rejection_sample at 0x7f51f9e38950>))
[10] During: typing of call at /project/csbio/envs_dirs/viz/lib/python3.6/site-packages/umap/nndescent.py (63)
File "../../../envs_dirs/viz/lib/python3.6/site-packages/umap/nndescent.py", line 63:
def nn_descent(
<source elided>
for i in range(data.shape[0]):
indices = rejection_sample(n_neighbors, data.shape[0], rng_state)
^
Reproducible Parameters
Output when verbose=True:
UMAP(a=None, angular_rp_forest=False, b=None, init='spectral',
learning_rate=1.0, local_connectivity=1.0, metric='correlation',
metric_kwds=None, min_dist=0.1, n_components=2, n_epochs=None,
n_neighbors=2.0, negative_sample_rate=5, random_state=None,
repulsion_strength=1.0, set_op_mix_ratio=1.0, spread=0.1,
target_metric='categorical', target_metric_kwds=None,
target_n_neighbors=-1, target_weight=0.5, transform_queue_size=4.0,
transform_seed=42, verbose=True)
Construct fuzzy simplicial set
Wed Jul 22 23:28:22 2020 Finding Nearest Neighbors
Wed Jul 22 23:28:22 2020 Building RP forest with 9 trees
Wed Jul 22 23:28:24 2020 NN descent for 12 iterations
Same error occurs when spread is changed to 1 or 10. Same error also occurs when min_dist is 0.0, 0.1, or 0.99 while spread is default.
It may be helpful to add a more informative error message.
The text was updated successfully, but these errors were encountered:
This is a duplicate of #22 opened by @fedden. It was apparently resolved by passing correct parameters, but no specific details are mentioned.
Some things I am adding upon which were unresolved in that issue:
Expanded stack trace
Reproducible Parameters
Output when
verbose=True
:Same error occurs when
spread
is changed to 1 or 10. Same error also occurs whenmin_dist
is 0.0, 0.1, or 0.99 whilespread
is default.It may be helpful to add a more informative error message.
The text was updated successfully, but these errors were encountered: