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KrishnaswamyLab / MAGIC

MAGIC (Markov Affinity-based Graph Imputation of Cells), is a method for imputing missing values restoring structure of large biological datasets.
GNU General Public License v2.0
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Suggestions for Unable to allocate 276. GiB for an array with shape (161877, 228942) and data type float64 #203

Open bitcometz opened 2 years ago

bitcometz commented 2 years ago

Hello， Thanks for this great software !!! But I run with some errors:

Code:

magic_operator = magic.MAGIC(n_jobs=80, random_state=1)

Error:

--> 758     data_imputed = diff_op_t.dot(data_imputed)
    760 # fast magic
    761 # a while loop is used when the dimensions of the diffusion matrix
    762 # are greater than those of the data matrix, or when t is not specified
    763 # (so as to allow for the calculation of the optimal t value)
    764 else:
    765     i = 0

MemoryError: Unable to allocate 276. GiB for an array with shape (161877, 228942) and data type float64

Could you give some suggestions ? Thanks !!