Multi-threading support for MCMC samplers #39
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…bject to orbitize's Sampler object (as part of initialization) emcee v3.0 will no longer support the PT Sampler, using ptemcee instead (designed to be drop-in replacement) this commit still has some issues...not parallel yet;
…rallelization (still failing)
…C and PTMCMC classes to allow for parallelization. Added block to try to do the same for python3, but it doesn't seem to work yet
…objects - this allows paralellization with DFM's emcee - run_sampler now returns emcee.sampler object (for both orbitize.sampler MCMC classes) - test_mcmc.py tests passing in python 2 and 3
Pull Request Test Coverage Report for Build 244
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semaphoreP
approved these changes
Jul 17, 2018
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Looks good to me!
We could in the future try importing either emcee.PTSampler or ptemcee and see which one imports successfully and use the one that does. I believe they have the example same interface.
For the affine invariant sampler to be effective, I think it needs to either only run on fits where we limit \omega and \Omega to be < 180 (i.e., posterior is unimodal) or run one sampler for each mode.
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Okay, the new version of emcee actually deletes their PTSampler and instead checks if you have ptemcee installed and if so, imports that instead. |
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Thanks, @henry-ngo! Milestone! |
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sampler object's initialization can specify
nthreadsfor parallelization.Since
emceewill remove their PT sampler in the next release, I've added the Ensemble Sampler fromemceeas an alternative (a good replacement might beptemcee)Addresses Issue #30