Added a benchmarking module #26
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These returns only return the last result. Did you want to append all the replicates instead?
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No, they are identical.
Am 13/12/15 um 17:42 schrieb John Chodera:
In bhmm/tests/benchmark_hidden.py
#26 (comment):
C = hidden.transition_counts(self.alpha[i], self.beta[i], self.A[i], self.pobs[i], out=out)# comparetime2 = time.time()d = (time2-time1)/(1.0*self.nrep)return (C, d)
- def run_viterbi(self, i, out):
vpath = Nonehidden.set_implementation(self.kernel)time1 = time.time()for k in range(self.nrep):vpath = hidden.viterbi(self.A[i], self.pobs[i], self.pi[i])# comparetime2 = time.time()d = (time2-time1)/(1.0*self.nrep)return (vpath, d)These returns only return the /last/ result. Did you want to append
all the replicates instead?—
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https://github.com/bhmm/bhmm/pull/26/files#r47446997.
Prof. Dr. Frank Noe
Head of Computational Molecular Biology group
Freie Universitaet Berlin
Phone: (+49) (0)30 838 75354
Web: research.franknoe.de
Mail: Arnimallee 6, 14195 Berlin, Germany
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Ah, these are all deterministic computations!
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yup
Am 13/12/15 um 17:46 schrieb John Chodera:
In bhmm/tests/benchmark_hidden.py
#26 (comment):
C = hidden.transition_counts(self.alpha[i], self.beta[i], self.A[i], self.pobs[i], out=out)# comparetime2 = time.time()d = (time2-time1)/(1.0*self.nrep)return (C, d)
- def run_viterbi(self, i, out):
vpath = Nonehidden.set_implementation(self.kernel)time1 = time.time()for k in range(self.nrep):vpath = hidden.viterbi(self.A[i], self.pobs[i], self.pi[i])# comparetime2 = time.time()d = (time2-time1)/(1.0*self.nrep)return (vpath, d)Ah, these are all deterministic computations!
—
Reply to this email directly or view it on GitHub
https://github.com/bhmm/bhmm/pull/26/files#r47447063.
Prof. Dr. Frank Noe
Head of Computational Molecular Biology group
Freie Universitaet Berlin
Phone: (+49) (0)30 838 75354
Web: research.franknoe.de
for testing runtimes of hidden variable operations during development.