From d807cb4eba77da186dcc629e264084a256c6bf8a Mon Sep 17 00:00:00 2001
From: Gregory Ashton <gregory.ashton@ligo.org>
Date: Wed, 3 Apr 2019 16:10:33 +1100
Subject: [PATCH] Add atomic-writing to emcee chains
---
bilby/core/sampler/emcee.py | 8 +++++++-
1 file changed, 7 insertions(+), 1 deletion(-)
diff --git a/bilby/core/sampler/emcee.py b/bilby/core/sampler/emcee.py
index 993ab4836..355e93ef1 100644
--- a/bilby/core/sampler/emcee.py
+++ b/bilby/core/sampler/emcee.py
@@ -3,6 +3,7 @@ from __future__ import absolute_import, print_function
from collections import namedtuple
import os
import signal
+from shutil import copyfile
import sys
import numpy as np
@@ -285,13 +286,18 @@ class Emcee(MCMCSampler):
return self._sampler
def write_chains_to_file(self, sample):
+ chain_file = self.checkpoint_info.chain_file
+ temp_chain_file = chain_file + '.temp'
+ copyfile(chain_file, temp_chain_file)
+
if self.prerelease:
points = np.hstack([sample.coords, sample.blobs])
else:
points = np.hstack([sample[0], np.array(sample[3])])
- with open(self.checkpoint_info.chain_file, "a") as ff:
+ with open(temp_chain_file, "a") as ff:
for ii, point in enumerate(points):
ff.write(self.checkpoint_info.chain_template.format(ii, *point))
+ os.rename(temp_chain_file, chain_file)
@property
def _previous_iterations(self):
--
GitLab