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Ndv dont share mi clr but still lock per bootstrap #63

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Ndv dont share mi clr but still lock per bootstrap #63

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d9526d4
calculate mi and clr on each worker
nickdeveaux May 10, 2018
39babaa
don't calculate your own kvs
nickdeveaux May 10, 2018
42f9096
flush output
nickdeveaux May 10, 2018
dd8795f
removed unused import and key
nickdeveaux May 10, 2018
b4ea275
missing import added
nickdeveaux May 10, 2018
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10 changes: 7 additions & 3 deletions inferelator_ng/bbsr_tfa_workflow.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,7 @@

import numpy as np
import os
import sys
from workflow import WorkflowBase
import design_response_translation #added python design_response
from tfa import TFA
Expand Down Expand Up @@ -41,14 +42,17 @@ def run(self):

for idx, bootstrap in enumerate(self.get_bootstraps()):
print('Bootstrap {} of {}'.format((idx + 1), self.num_bootstraps))

X = self.activity.ix[:, bootstrap]
Y = self.response.ix[:, bootstrap]
print('Calculating MI, Background MI, and CLR Matrix')
(self.clr_matrix, self.mi_matrix) = self.mi_clr_driver.run(X, Y)
# Force stdout to flush so that the output is readable from all workers
sys.stdout.flush()
if 0 == rank:
(self.clr_matrix, self.mi_matrix) = self.mi_clr_driver.run(X, Y)
kvs.put('mi %d'%idx, (self.clr_matrix, self.mi_matrix))
kvs.put('bootstrap %d'%idx, 'This is how we stop workers from moving ahead on a new bootstrap')
else:
(self.clr_matrix, self.mi_matrix) = kvs.view('mi %d'%idx)
kvs.view('bootstrap %d'%idx)
print('Calculating betas using BBSR')
ownCheck = utils.ownCheck(kvs, rank, chunk=25)
current_betas,current_rescaled_betas = self.regression_driver.run(X, Y, self.clr_matrix, self.priors_data,kvs,rank, ownCheck)
Expand Down