From 9a34533d018c4f7e6270ab3b7bc7683472e44cf5 Mon Sep 17 00:00:00 2001
From: Matthew Pitkin <matthew.pitkin@ligo.org>
Date: Thu, 22 Aug 2024 15:19:55 +0000
Subject: [PATCH] Resolve "patch to speed the MCMC"
---
AUTHORS.md | 1 +
bilby/core/sampler/emcee.py | 16 +++++++++-------
2 files changed, 10 insertions(+), 7 deletions(-)
diff --git a/AUTHORS.md b/AUTHORS.md
index 8c227ed6f..17b09070f 100644
--- a/AUTHORS.md
+++ b/AUTHORS.md
@@ -16,6 +16,7 @@ Bruce Edelman
Carl-Johan Haster
Cecilio Garcia-Quiros
Charlie Hoy
+Chentao Yang
Christopher Philip Luke Berry
Christos Karathanasis
Colm Talbot
diff --git a/bilby/core/sampler/emcee.py b/bilby/core/sampler/emcee.py
index 76e4dd1eb..2c12ee354 100644
--- a/bilby/core/sampler/emcee.py
+++ b/bilby/core/sampler/emcee.py
@@ -1,7 +1,6 @@
import os
import shutil
from collections import namedtuple
-from shutil import copyfile
import numpy as np
from packaging import version
@@ -333,16 +332,19 @@ class Emcee(MCMCSampler):
def write_chains_to_file(self, sample):
chain_file = self.checkpoint_info.chain_file
temp_chain_file = chain_file + ".temp"
- if os.path.isfile(chain_file):
- 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(temp_chain_file, "a") as ff:
- for ii, point in enumerate(points):
- ff.write(self.checkpoint_info.chain_template.format(ii, *point))
- shutil.move(temp_chain_file, chain_file)
+ data_to_write = "\n".join(
+ self.checkpoint_info.chain_template.format(ii, *point)
+ for ii, point in enumerate(points)
+ )
+ with open(temp_chain_file, "w") as ff:
+ ff.write(data_to_write)
+ with open(temp_chain_file, "rb") as ftemp, open(chain_file, "ab") as fchain:
+ shutil.copyfileobj(ftemp, fchain)
+ os.remove(temp_chain_file)
@property
def _previous_iterations(self):
--
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