From b7d0696756f4485f8d1f0fa3747867acc1324c71 Mon Sep 17 00:00:00 2001
From: Gregory Ashton <gregory.ashton@ligo.org>
Date: Wed, 3 Apr 2019 15:05:32 +1100
Subject: [PATCH] Minor bug fixing
---
bilby/core/sampler/emcee.py | 5 ++++-
bilby/core/sampler/ptemcee.py | 3 ++-
2 files changed, 6 insertions(+), 2 deletions(-)
diff --git a/bilby/core/sampler/emcee.py b/bilby/core/sampler/emcee.py
index 2f76850fe..993ab4836 100644
--- a/bilby/core/sampler/emcee.py
+++ b/bilby/core/sampler/emcee.py
@@ -274,6 +274,8 @@ class Emcee(MCMCSampler):
if hasattr(self, '_sampler'):
pass
elif self.resume and os.path.isfile(self.checkpoint_info.sampler_file):
+ logger.info("Resuming run from checkpoint file {}"
+ .format(self.checkpoint_info.sampler_file))
with open(self.checkpoint_info.sampler_file, 'rb') as f:
self._sampler = pickle.load(f)
self._set_pos0_for_resume()
@@ -335,13 +337,14 @@ class Emcee(MCMCSampler):
iterations = sampler_function_kwargs.pop('iterations')
iterations -= self._previous_iterations
- print('pos0', self.pos0)
sampler_function_kwargs['p0'] = self.pos0
+ # main iteration loop
for sample in tqdm(
self.sampler.sample(iterations=iterations, **sampler_function_kwargs),
total=iterations):
self.write_chains_to_file(sample)
+ self.checkpoint()
self.result.sampler_output = np.nan
blobs_flat = np.array(self.sampler.blobs).reshape((-1, 2))
diff --git a/bilby/core/sampler/ptemcee.py b/bilby/core/sampler/ptemcee.py
index 9bcd9e7f2..37eb22201 100644
--- a/bilby/core/sampler/ptemcee.py
+++ b/bilby/core/sampler/ptemcee.py
@@ -42,7 +42,7 @@ class Ptemcee(Emcee):
label=label, use_ratio=use_ratio, plot=plot,
skip_import_verification=skip_import_verification,
nburn=nburn, burn_in_fraction=burn_in_fraction,
- burn_in_act=burn_in_act, resume=True, **kwargs)
+ burn_in_act=burn_in_act, resume=resume, **kwargs)
@property
def sampler_function_kwargs(self):
@@ -116,6 +116,7 @@ class Ptemcee(Emcee):
**sampler_function_kwargs),
total=iterations):
self.write_chains_to_file(pos, loglike, logpost)
+ self.checkpoint()
self.calculate_autocorrelation(self.sampler.chain.reshape((-1, self.ndim)))
self.result.sampler_output = np.nan
--
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