diff --git a/bilby/core/sampler/pymultinest.py b/bilby/core/sampler/pymultinest.py
index 055d4e14ad969f70da745fa13571db693405784a..9421c8207c09dae938d4b37cf6b61a46c2853a42 100644
--- a/bilby/core/sampler/pymultinest.py
+++ b/bilby/core/sampler/pymultinest.py
@@ -2,7 +2,10 @@ import importlib
import os
import tempfile
import shutil
+import distutils.dir_util
import signal
+import time
+import datetime
import numpy as np
@@ -115,8 +118,15 @@ class Pymultinest(NestedSampler):
# for PyMultiNest >=2.9 the n_params kwarg cannot be None
if self.kwargs["n_params"] is None:
self.kwargs["n_params"] = self.ndim
+ if self.kwargs['dump_callback'] is None:
+ self.kwargs['dump_callback'] = self._dump_callback
NestedSampler._verify_kwargs_against_default_kwargs(self)
+ def _dump_callback(self, *args, **kwargs):
+ if self.use_temporary_directory:
+ self._copy_temporary_directory_contents_to_proper_path()
+ self._calculate_and_save_sampling_time()
+
def _apply_multinest_boundaries(self):
if self.kwargs["wrapped_params"] is None:
self.kwargs["wrapped_params"] = []
@@ -154,10 +164,6 @@ class Pymultinest(NestedSampler):
shutil.copytree(
self.outputfiles_basename, self.temporary_outputfiles_basename
)
- if os.path.islink(self.outputfiles_basename):
- os.unlink(self.outputfiles_basename)
- else:
- shutil.rmtree(self.outputfiles_basename)
def write_current_state_and_exit(self, signum=None, frame=None):
""" Write current state and exit on exit_code """
@@ -166,15 +172,15 @@ class Pymultinest(NestedSampler):
signum, self.exit_code
)
)
+ self._calculate_and_save_sampling_time()
if self.use_temporary_directory:
self._move_temporary_directory_to_proper_path()
os._exit(self.exit_code)
- def _move_temporary_directory_to_proper_path(self):
+ def _copy_temporary_directory_contents_to_proper_path(self):
"""
- Move the temporary back to the proper path
-
- Anything in the proper path at this point is removed including links
+ Copy the temporary back to the proper path.
+ Do not delete the temporary directory.
"""
logger.info(
"Overwriting {} with {}".format(
@@ -185,11 +191,16 @@ class Pymultinest(NestedSampler):
outputfiles_basename_stripped = self.outputfiles_basename[:-1]
else:
outputfiles_basename_stripped = self.outputfiles_basename
- if os.path.islink(outputfiles_basename_stripped):
- os.unlink(outputfiles_basename_stripped)
- elif os.path.isdir(outputfiles_basename_stripped):
- shutil.rmtree(outputfiles_basename_stripped)
- shutil.move(self.temporary_outputfiles_basename, outputfiles_basename_stripped)
+ distutils.dir_util.copy_tree(self.temporary_outputfiles_basename, outputfiles_basename_stripped)
+
+ def _move_temporary_directory_to_proper_path(self):
+ """
+ Copy the temporary back to the proper path
+
+ Anything in the temporary directory at this point is removed
+ """
+ self._copy_temporary_directory_contents_to_proper_path()
+ shutil.rmtree(self.temporary_outputfiles_basename)
def run_sampler(self):
import pymultinest
@@ -197,17 +208,20 @@ class Pymultinest(NestedSampler):
self._verify_kwargs_against_default_kwargs()
self._setup_run_directory()
+ self._check_and_load_sampling_time_file()
# Overwrite pymultinest's signal handling function
pm_run = importlib.import_module("pymultinest.run")
pm_run.interrupt_handler = self.write_current_state_and_exit
+ self.start_time = time.time()
out = pymultinest.solve(
LogLikelihood=self.log_likelihood,
Prior=self.prior_transform,
n_dims=self.ndim,
**self.kwargs
)
+ self._calculate_and_save_sampling_time()
self._clean_up_run_directory()
@@ -222,26 +236,22 @@ class Pymultinest(NestedSampler):
self.result.log_evidence_err = out["logZerr"]
self.calc_likelihood_count()
self.result.outputfiles_basename = self.outputfiles_basename
+ self.result.sampling_time = datetime.timedelta(seconds=self.total_sampling_time)
return self.result
def _setup_run_directory(self):
"""
If using a temporary directory, the output directory is moved to the
- temporary directory and symlinked back.
+ temporary directory.
"""
if self.use_temporary_directory:
temporary_outputfiles_basename = tempfile.TemporaryDirectory().name
self.temporary_outputfiles_basename = temporary_outputfiles_basename
if os.path.exists(self.outputfiles_basename):
- shutil.move(self.outputfiles_basename, self.temporary_outputfiles_basename)
+ distutils.dir_util.copy_tree(self.outputfiles_basename, self.temporary_outputfiles_basename)
check_directory_exists_and_if_not_mkdir(temporary_outputfiles_basename)
- os.symlink(
- os.path.abspath(self.temporary_outputfiles_basename),
- os.path.abspath(self.outputfiles_basename),
- target_is_directory=True,
- )
self.kwargs["outputfiles_basename"] = self.temporary_outputfiles_basename
logger.info("Using temporary file {}".format(temporary_outputfiles_basename))
else:
@@ -249,6 +259,21 @@ class Pymultinest(NestedSampler):
self.kwargs["outputfiles_basename"] = self.outputfiles_basename
logger.info("Using output file {}".format(self.outputfiles_basename))
+ def _check_and_load_sampling_time_file(self):
+ self.time_file_path = self.kwargs["outputfiles_basename"] + '/sampling_time.dat'
+ if os.path.exists(self.time_file_path):
+ with open(self.time_file_path, 'r') as time_file:
+ self.total_sampling_time = float(time_file.readline())
+ else:
+ self.total_sampling_time = 0
+
+ def _calculate_and_save_sampling_time(self):
+ current_time = time.time()
+ new_sampling_time = current_time - self.start_time
+ self.total_sampling_time += new_sampling_time
+ with open(self.time_file_path, 'w') as time_file:
+ time_file.write(str(self.total_sampling_time))
+
def _clean_up_run_directory(self):
if self.use_temporary_directory:
self._move_temporary_directory_to_proper_path()
diff --git a/test/sampler_test.py b/test/sampler_test.py
index 0140b4f7b8a5c5d6d736adc1350e30ae25cf8f41..d9879543cfe8ab5c1413eb85d85b6ef806621f64 100644
--- a/test/sampler_test.py
+++ b/test/sampler_test.py
@@ -767,7 +767,8 @@ class TestPymultinest(unittest.TestCase):
n_iter_before_update=100, null_log_evidence=-1e90,
max_modes=100, mode_tolerance=-1e90, seed=-1,
context=0, write_output=True, log_zero=-1e100,
- max_iter=0, init_MPI=False, dump_callback=None)
+ max_iter=0, init_MPI=False, dump_callback='dumper')
+ self.sampler.kwargs['dump_callback'] = 'dumper' # Check like the dynesty print_func
self.assertListEqual([1, 0], self.sampler.kwargs['wrapped_params']) # Check this separately
self.sampler.kwargs['wrapped_params'] = None # The dict comparison can't handle lists
self.assertDictEqual(expected, self.sampler.kwargs)
@@ -782,7 +783,7 @@ class TestPymultinest(unittest.TestCase):
n_iter_before_update=100, null_log_evidence=-1e90,
max_modes=100, mode_tolerance=-1e90, seed=-1,
context=0, write_output=True, log_zero=-1e100,
- max_iter=0, init_MPI=False, dump_callback=None)
+ max_iter=0, init_MPI=False, dump_callback='dumper')
for equiv in bilby.core.sampler.base_sampler.NestedSampler.npoints_equiv_kwargs:
new_kwargs = self.sampler.kwargs.copy()
@@ -790,6 +791,7 @@ class TestPymultinest(unittest.TestCase):
new_kwargs[
"wrapped_params"
] = None # The dict comparison can't handle lists
+ new_kwargs['dump_callback'] = 'dumper' # Check this like Dynesty print_func
new_kwargs[equiv] = 123
self.sampler.kwargs = new_kwargs
self.assertDictEqual(expected, self.sampler.kwargs)