Comments (2)
It happens because your matrix is too large that cannot be fit into the memory.
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Hi, I'm facing the exactly the same issue.
But the issue is weird, because the same code with the same data crashes in my Ubuntu 16.04 LTS with 64GB of RAM, but it runs in my MacOSX with 16GB of RAM.
I have everything set using conda.
The only difference is the numpy version. In the macosx I have numpy 1.11 and in the ubuntu 16.04 I have numpy 1.12.
File "./bin/plot_tsne_one_file.py", line 19, in <module>
sys.exit(context_experiments.script.plot_tsne_one_file.main())
File "/home/tiago-ttt/Documents/redmine/context_experiments/context_experiments/script/plot_tsne_one_file.py", line 126, in main
fig = plot_per_attribute(file_name, seed, perplexity, learning_rate, 200, device, "id")
File "/home/tiago-ttt/Documents/redmine/context_experiments/context_experiments/script/plot_tsne_one_file.py", line 83, in plot_per_attribute
projected_data = model.fit_transform(data)
File "/home/tiago-ttt/miniconda3/envs/context_py27/lib/python2.7/site-packages/sklearn/manifold/t_sne.py", line 884, in fit_transform
embedding = self._fit(X)
File "/home/tiago-ttt/miniconda3/envs/context_py27/lib/python2.7/site-packages/sklearn/manifold/t_sne.py", line 730, in _fit
squared=True)
File "/home/tiago-ttt/miniconda3/envs/context_py27/lib/python2.7/site-packages/sklearn/metrics/pairwise.py", line 1240, in pairwise_distances
return _parallel_pairwise(X, Y, func, n_jobs, **kwds)
File "/home/tiago-ttt/miniconda3/envs/context_py27/lib/python2.7/site-packages/sklearn/metrics/pairwise.py", line 1083, in _parallel_pairwise
return func(X, Y, **kwds)
File "/home/tiago-ttt/miniconda3/envs/context_py27/lib/python2.7/site-packages/sklearn/metrics/pairwise.py", line 245, in euclidean_distances
distances = safe_sparse_dot(X, Y.T, dense_output=True)
File "/home/tiago-ttt/miniconda3/envs/context_py27/lib/python2.7/site-packages/sklearn/utils/extmath.py", line 189, in safe_sparse_dot
return fast_dot(a, b)
MemoryError
from scikit-feature.
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