Revision 4f75faeded2cb284dedbc856a8b2ae56075ea158 authored by Collin Capano on 20 June 2020, 18:27:09 UTC, committed by GitHub on 20 June 2020, 18:27:09 UTC
* use different acl for every chain in epsie * create base burn in class, move common functions to there; rename MCMCBurnInTests EnsembleMCMC, first stab at creating MCMC tests for independent chains * more changes to burn in module * simplify the attributes in the burn in classes * add write method to burn in classes * add write_data method to base_hdf * remove write_burn_in method from mcmc io; use the write method in burn in module instead * make use of new burn in functions in sampler/base_mcmc * have emcee and emcee pt use ensemble burn in tests * add compute_acf function to epsie * start separating ensemble and mcmc io methods * stop saving thin settings to file; just return on the fly * make read/write samples stand alone functions, and update emcee * rename write functions; update emcee * move multi temper read/write functions to stand alone and update emcee_pt * pass kwargs from emcee(_pt) io functions * simplify get_slice method * add function to base_mcmc to calculate the number of samples in a chain * use nsamples_in_chain function to calculate effective number of samples * add read_raw_samples function that can handle differing number of samples from different chains * add forgotten import * use write/read functions from base_multitemper in epsie io * use stand alone functions for computing ensemble acf/acls * separate out ensemble-specific attributes in sampler module; update emcee and emcee_pt * add acl and effective_nsample methods to epsie * simplify writing acls and burn in * fix various bugs and typos * use a single function for writing both acl and raw_acls * add some more logging info to burn in * reduce identical blocks of code in burn in module * fix self -> fp in read_raw_samples * reduce code duplication in base io and simplify read raw samples function * fix missed rename * reduce code redundacy in sampler/base_multitemper * whitespace * fix bugs and typos in burn_in module * fix code climate issues * use map in compute_acl * more code climate fixes * remove unused variable; try to silence pylint * fix issues reading epsie samples * only load samples from burned in chains by default * add act property to mcmc files * fix act logging message * fix effective number of samples calculation in epsie * remap walkers option to chains for reading samples * fix thinning update * fix acceptance ratio and temperature data thinning in epsie * allow for different fields to have differing number of temperatures when loading * don't try to figure out how many samples will be loaded ahead of time * store acts in file instead of acls * write burn in status to file before computing acls * drop write_acts function * fix issue with getting specific chains * fix typo * code climate issues * fix plot_acl
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test_fftw_pthreads.py
# Copyright (C) 2012 Josh Willis, Andrew Miller
#
# This program is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by the
# Free Software Foundation; either version 3 of the License, or (at your
# option) any later version.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General
# Public License for more details.
#
# You should have received a copy of the GNU General Public License along
# with this program; if not, write to the Free Software Foundation, Inc.,
# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
#
# =============================================================================
#
# Preamble
#
# =============================================================================
#
"""
These are the unit-tests for the pycbc.fft.fftw subpackage, testing only the pthreads
threading backend.
"""
import pycbc.fft
from pycbc.scheme import CPUScheme
import unittest
from sys import exit as _exit
from utils import parse_args_cpu_only, simple_exit
from fft_base import _BaseTestFFTClass
parse_args_cpu_only("FFTW pthreads backend")
# See if we can get set the FFTW backend to 'pthreads'; if not, say so and exit.
if 'fftw' in pycbc.fft.get_backend_names():
import pycbc.fft.fftw
try:
pycbc.fft.fftw.set_threads_backend('pthreads')
except:
print("Unable to import pthreads threads backend to FFTW; skipping pthreads thread tests")
_exit(0)
else:
print("FFTW does not seem to be an available CPU backend; skipping pthreads thread tests")
_exit(0)
# Most of the work is now done in fft_base.
FFTTestClasses = []
kdict = {'backends' : ['fftw'],
'scheme' : 'cpu',
'context' : CPUScheme(num_threads=2)}
klass = type('FFTW_pthreads_test',
(_BaseTestFFTClass,),kdict)
FFTTestClasses.append(klass)
# Finally, we create suites and run them
if __name__ == '__main__':
suite = unittest.TestSuite()
for klass in FFTTestClasses:
suite.addTest(unittest.TestLoader().loadTestsFromTestCase(klass))
results = unittest.TextTestRunner(verbosity=2).run(suite)
simple_exit(results)
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