Improve ptemcee

This is a total rewrite of the ptemcee implementation. Originally, we had based ptemcee on emcee, but emcee has changed quite significantly and I anticipate it will be easier to maintain the two uncoupled from hereon. This adds sufficient functionality to ptemcee for it to be usable on gravitational wave events. Here is a summary of the changes

1. Add automatic convergence to the user interface: users now specify nsamples as a the primary input. The sampler will run until it has nsamples independent samples from the posterior. The user now has access to a reduced set of the ptemcee full functionality (e.g. iterations), but this isn't required given the convergence checking.
2. Add diagnostic plots for the autocorrelation time, e.g.:
3. Improve the traceplots to show the convergence and the current posterior samples
4. Add dumping of posterior samples to a .dat file
5. Add multi-processing support, tested on a 16 core machine to give a significant reduction in compute time (exact timings yet to be calculated).
6. Add regular 10-minute checkpointing

Note, I have intentionally put much of the primary logic into functions rather than class methods. This is because eventually we should port changes to parallel bilby and potentially other samplers and this is most easily done from a functional interface (at least for parallel bilby where inheritance causes issues with the parallel aspects).

bilby/core/sampler/ptemcee.py

@@ -13,7 +13,7 @@ import pandas as pd
 import matplotlib.pyplot as plt
 
 from ..utils import logger
-from .base_sampler import MCMCSampler
+from .base_sampler import SamplerError, MCMCSampler
 
 
 class Ptemcee(MCMCSampler):
@@ -41,15 +41,15 @@ class Ptemcee(MCMCSampler):
         ntemps=20, nwalkers=200, Tmax=None, betas=None,
         a=2.0, loglargs=[], logpargs=[], loglkwargs={},
         logpkwargs={}, adaptation_lag=10000, adaptation_time=100, random=None,
-        iterations=1000, thin=1, storechain=True, adapt=False,
-        swap_ratios=False)
+        adapt=False, swap_ratios=False)
 
     def __init__(self, likelihood, priors, outdir='outdir', label='label',
-                 use_ratio=False, plot=False, skip_import_verification=False,
+                 use_ratio=False, check_point_plot=True, skip_import_verification=False,
                  resume=True, nsamples=5000, burn_in_nact=50, thin_by_nact=1,
-                 autocorr_c=5, safety=1, ncheck=50, nfrac=5, frac_threshold=0.01,
-                 autocorr_tol=50, min_tau=1, check_point_deltaT=600, 
-                 threads=1, **kwargs):
+                 autocorr_c=5, safety=1, frac_threshold=0.01,
+                 autocorr_tol=50, autocorr_tau=5, min_tau=1, check_point_deltaT=600,
+                 threads=1, exit_code=77, plot=False, store_walkers=False,
+                 ignore_keys_for_tau="recalib", pos0="prior", **kwargs):
         super(Ptemcee, self).__init__(
             likelihood=likelihood, priors=priors, outdir=outdir,
             label=label, use_ratio=use_ratio, plot=plot,
@@ -60,25 +60,29 @@ class Ptemcee(MCMCSampler):
         signal.signal(signal.SIGALRM, self.write_current_state_and_exit)
 
         self.resume = resume
-        self.ncheck = ncheck
         self.autocorr_c = autocorr_c
         self.safety = safety
         self.burn_in_nact = burn_in_nact
         self.thin_by_nact = thin_by_nact
-        self.nfrac = nfrac
         self.frac_threshold = frac_threshold
         self.nsamples = nsamples
         self.autocorr_tol = autocorr_tol
+        self.autocorr_tau = autocorr_tau
         self.min_tau = min_tau
         self.check_point_deltaT = check_point_deltaT
 
         self.threads = threads
+        self.store_walkers = store_walkers
+        self.ignore_keys_for_tau = ignore_keys_for_tau
+        self.pos0 = pos0
 
+        self.check_point_plot = check_point_plot
         self.resume_file = "{}/{}_checkpoint_resume.pickle".format(self.outdir, self.label)
+        self.exit_code = exit_code
 
     @property
     def sampler_function_kwargs(self):
-        keys = ['iterations', 'thin', 'storechain', 'adapt', 'swap_ratios']
+        keys = ['adapt', 'swap_ratios']
         return {key: self.kwargs[key] for key in keys}
 
     @property
@@ -94,30 +98,107 @@ class Ptemcee(MCMCSampler):
                  for _ in range(self.sampler_init_kwargs["nwalkers"])]
                 for _ in range(self.kwargs['ntemps'])]
 
+    def get_pos0_from_minimize(self, minimize_list=None):
+        logger.info("Attempting to set pos0 from minimize")
+        from scipy.optimize import minimize
+
+        if minimize_list is None:
+            minimize_list = self.search_parameter_keys
+            pos0 = np.zeros((self.kwargs["ntemps"], self.kwargs["nwalkers"], self.ndim))
+        else:
+            pos0 = np.array(self.get_pos0_from_prior())
+
+        likelihood_copy = copy.copy(self.likelihood)
+
+        def neg_log_like(params):
+            likelihood_copy.parameters.update(
+                {key: val for key, val in zip(minimize_list, params)})
+            try:
+                return -likelihood_copy.log_likelihood()
+            except RuntimeError:
+                return +np.inf
+        bounds = [(self.priors[key].minimum, self.priors[key].maximum)
+                  for key in minimize_list]
+        trials = 0
+        success = []
+        while True:
+            draw = self.priors.sample()
+            likelihood_copy.parameters.update(draw)
+            x0 = [draw[key] for key in minimize_list]
+            res = minimize(
+                neg_log_like, x0, bounds=bounds, method='L-BFGS-B')
+            if res.success:
+                success.append(res.x)
+            if trials > 100:
+                raise SamplerError("Unable to set pos0 from minimize")
+            if len(success) >= 3:
+                break
+
+        success = np.array(success)
+        for i, key in enumerate(minimize_list):
+            pos0_min = np.min(success[:, i])
+            pos0_max = np.max(success[:, i])
+            logger.info("Initialize {} walkers from {}->{}"
+                        .format(key, pos0_min, pos0_max))
+            j = self.search_parameter_keys.index(key)
+            pos0[:, :, j] = np.random.uniform(
+                pos0_min, pos0_max,
+                size=(self.kwargs["ntemps"], self.kwargs["nwalkers"]))
+        return pos0
+
     def setup_sampler(self):
         import ptemcee
         if os.path.isfile(self.resume_file) and self.resume is True:
             logger.info("Resume data {} found".format(self.resume_file))
             with open(self.resume_file, "rb") as file:
                 data = dill.load(file)
+
             self.sampler = data["sampler"]
-            self.sampler.pool = self.pool
-            self.sampler.threads = self.threads
             self.tau_list = data["tau_list"]
             self.tau_list_n = data["tau_list_n"]
+            self.time_per_check = data["time_per_check"]
+
+            self.sampler.pool = self.pool
+            self.sampler.threads = self.threads
+
             pos0 = None
+
             logger.info("Resuming from previous run with time={}".format(self.sampler.time))
 
         else:
-            self.sampler = ptemcee.Sampler(
-                dim=self.ndim, logl=do_nothing_function, logp=do_nothing_function,
-                pool=self.pool, threads=self.threads, **self.sampler_init_kwargs)
-            self.sampler._likeprior = LikePriorEvaluator(
-                self.search_parameter_keys, use_ratio=self.use_ratio)
-            pos0 = self.get_pos0_from_prior()
+            # Initialize the PTSampler
+            if self.threads == 1:
+                self.sampler = ptemcee.Sampler(
+                    dim=self.ndim, logl=self.log_likelihood, logp=self.log_prior,
+                    **self.sampler_init_kwargs)
+            else:
+                self.sampler = ptemcee.Sampler(
+                    dim=self.ndim, logl=do_nothing_function, logp=do_nothing_function,
+                    pool=self.pool, threads=self.threads, **self.sampler_init_kwargs)
+
+                self.sampler._likeprior = LikePriorEvaluator(
+                    self.search_parameter_keys, use_ratio=self.use_ratio)
+
+            # Set up empty lists
+            self.tau_list = []
+            self.tau_list_n = []
+            self.time_per_check = []
+
+            # Initialize the walker postitions
+            pos0 = self.get_pos0()
 
         return self.sampler, pos0
 
+    def get_pos0(self):
+        if isinstance(self.pos0, str) and self.pos0.lower() == "prior":
+            return self.get_pos0_from_prior()
+        elif isinstance(self.pos0, str) and self.pos0.lower() == "minimize":
+            return self.get_pos0_from_minimize()
+        elif isinstance(self.pos0, list):
+            return self.get_pos0_from_minimize(minimize_list=self.pos0)
+        else:
+            raise SamplerError("pos0={} not implemented".format(self.pos0))
+
     def setup_pool(self):
         if self.threads > 1:
             import schwimmbad
@@ -139,24 +220,23 @@ class Ptemcee(MCMCSampler):
     def run_sampler_internal(self):
         import emcee
         sampler, pos0 = self.setup_sampler()
-        self.time_per_check = []
-        self.tau_list = []
-        self.tau_list_n = []
 
         t0 = datetime.datetime.now()
         logger.info("Starting to sample")
-        for (pos0, lnprob, lnlike) in sampler.sample(
-                pos0, **self.sampler_function_kwargs):
-            # Only check convergence every ncheck steps
-            if sampler.time % self.ncheck:
-                continue
+        while True:
+            for (pos0, _, _) in sampler.sample(pos0, **self.sampler_function_kwargs):
+                pass
+
+            # Calculate time per iteration
+            self.time_per_check.append((datetime.datetime.now() - t0).total_seconds())
+            t0 = datetime.datetime.now()
 
             # Compute ACT tau for 0-temperature chains
             samples = sampler.chain[0, :, : sampler.time, :]
             taus = []
             for ii in range(sampler.nwalkers):
                 for jj, key in enumerate(self.search_parameter_keys):
-                    if "recalib" in key:
+                    if self.ignore_keys_for_tau and self.ignore_keys_for_tau in key:
                         continue
                     try:
                         taus.append(
@@ -170,52 +250,58 @@ class Ptemcee(MCMCSampler):
             # Apply multiplicitive safety factor
             tau = self.safety * np.mean(taus)
 
-            if np.isnan(tau) or np.isinf(tau):
-                print("{} | Unable to use tau={}".format(sampler.time, tau), flush=True)
-                continue
-
-            # Convert to an integer and store for plotting
-            tau = int(tau)
+            # Store for convergence checking and plotting
             self.tau_list.append(tau)
             self.tau_list_n.append(sampler.time)
 
+            # Convert to an integer
+            tau_int = int(np.ceil(tau)) if not np.isnan(tau) else tau
+
+            if np.isnan(tau_int) or np.isinf(tau_int):
+                print_progress(
+                    self.sampler,
+                    self.time_per_check,
+                    self.nsamples,
+                    np.nan,
+                    np.nan,
+                    np.nan,
+                    [np.nan],
+                    False)
+                continue
+
             # Calculate the effective number of samples available
-            self.nburn = int(self.burn_in_nact * tau)
-            self.thin = int(np.max([1, self.thin_by_nact * tau]))
-            samples_per_check = self.ncheck * sampler.nwalkers / self.thin
+            self.nburn = int(self.burn_in_nact * tau_int)
+            self.thin = int(np.max([1, self.thin_by_nact * tau_int]))
+            samples_per_check = sampler.nwalkers / self.thin
             self.nsamples_effective = int(sampler.nwalkers * (sampler.time - self.nburn) / self.thin)
 
-            # Calculate fractional change in tau from previous iteration
-            frac = (tau - np.array(self.tau_list)[-self.nfrac - 1: -1]) / tau
-            passes = frac < self.frac_threshold
-
             # Calculate convergence boolean
             converged = self.nsamples < self.nsamples_effective
-            converged &= np.all(passes)
-            if sampler.time < tau * self.autocorr_tol or tau < self.min_tau:
-                converged = False
-                tau_pass = False
+
+            # Calculate fractional change in tau from previous iterations
+            check_taus = np.array(self.tau_list[-tau_int * self.autocorr_tau:])
+            if not np.any(np.isnan(check_taus)):
+                frac = (tau - check_taus) / tau
+                tau_usable = np.all(frac < self.frac_threshold)
             else:
-                tau_pass = True
+                tau_usable = False
 
-            # Calculate time per iteration
-            self.time_per_check.append((datetime.datetime.now() - t0).total_seconds())
-            t0 = datetime.datetime.now()
+            if sampler.time < tau_int * self.autocorr_tol or tau_int < self.min_tau:
+                tau_usable = False
 
             # Print an update on the progress
             print_progress(
                 self.sampler,
-                self.ncheck,
                 self.time_per_check,
                 self.nsamples,
                 self.nsamples_effective,
                 samples_per_check,
-                passes,
-                tau,
-                tau_pass,
+                tau_int,
+                check_taus,
+                tau_usable,
             )
 
-            if converged:
+            if converged and tau_usable:
                 logger.info("Finished sampling")
                 break
 
@@ -226,22 +312,13 @@ class Ptemcee(MCMCSampler):
                 last_checkpoint_s = np.sum(self.time_per_check)
 
             if last_checkpoint_s > self.check_point_deltaT:
-                self.write_current_state()
-
-        # Check if we reached the end without converging
-        if sampler.time == self.sampler_function_kwargs["iterations"]:
-            raise ValueError(
-                "Failed to reach convergence by iterations={}".format(
-                    self.sampler_function_kwargs["iterations"]
-                )
-            )
+                self.write_current_state(plot=self.check_point_plot)
 
         # Run a final checkpoint to update the plots and samples
-        self.write_current_state()
+        self.write_current_state(plot=self.check_point_plot)
 
         # Get 0-likelihood samples and store in the result
         samples = sampler.chain[0, :, :, :]  # nwalkers, nsteps, ndim
-        self.result.walkers = samples[:, :sampler.time:, :]
         self.result.samples = (
             samples[:, self.nburn: sampler.time:self.thin, :].reshape((-1, self.ndim)))
         loglikelihood = sampler.loglikelihood[
@@ -249,7 +326,8 @@ class Ptemcee(MCMCSampler):
         ]  # nwalkers, nsteps
         self.result.log_likelihood_evaluations = loglikelihood.reshape((-1))
 
-        self.result.walkers = self.sampler.chain
+        if self.store_walkers:
+            self.result.walkers = self.sampler.chain
         self.result.nburn = self.nburn
 
         log_evidence, log_evidence_err = compute_evidence(
@@ -264,28 +342,40 @@ class Ptemcee(MCMCSampler):
 
     def write_current_state_and_exit(self, signum=None, frame=None):
         logger.warning("Run terminated with signal {}".format(signum))
-        if self.pool:
+        if getattr(self, 'pool', None):
+            self.write_current_state(plot=False)
+            logger.warning("Closing pool")
             self.pool.close()
-        self.write_current_state()
-        sys.exit(77)
+        sys.exit(self.exit_code)
 
-    def write_current_state(self):
+    def write_current_state(self, plot=True):
         checkpoint(self.outdir, self.label, self.nsamples_effective,
                    self.sampler, self.nburn, self.thin,
                    self.search_parameter_keys, self.resume_file, self.tau_list,
-                   self.tau_list_n)
+                   self.tau_list_n, self.time_per_check)
+
+        if plot and not np.isnan(self.nburn):
+            # Generate the walkers plot diagnostic
+            plot_walkers(
+                self.sampler.chain[0, :, : self.sampler.time, :],
+                self.nburn, self.thin, self.search_parameter_keys, self.outdir,
+                self.label
+            )
+
+            # Generate the tau plot diagnostic
+            plot_tau(self.tau_list_n, self.tau_list, self.outdir, self.label,
+                     self.autocorr_tau)
 
 
 def print_progress(
     sampler,
-    ncheck,
     time_per_check,
     nsamples,
     nsamples_effective,
     samples_per_check,
-    passes,
-    tau,
-    tau_pass,
+    tau_int,
+    tau_list,
+    tau_usable,
 ):
     # Setup acceptance string
     acceptance = sampler.acceptance_fraction[0, :]
@@ -299,30 +389,31 @@ def print_progress(
 
     ave_time_per_check = np.mean(time_per_check[-3:])
     time_left = (
-        (nsamples - nsamples_effective)
-        * ave_time_per_check
-        / samples_per_check
+        (nsamples - nsamples_effective) * ave_time_per_check / samples_per_check
     )
     if time_left > 0:
         time_left = str(datetime.timedelta(seconds=int(time_left)))
     else:
         time_left = "waiting on convergence"
 
-    convergence = "".join([["F", "T"][i] for i in passes])
+    sampling_time = datetime.timedelta(seconds=np.sum(time_per_check))
 
-    tau_str = str(tau)
-    if tau_pass is False:
-        tau_str = tau_str + "(F)"
+    tau_str = "{}:{:0.1f}->{:0.1f}".format(tau_int, np.min(tau_list), np.max(tau_list))
+    if tau_usable:
+        tau_str = "={}".format(tau_str)
+    else:
+        tau_str = "!{}".format(tau_str)
 
-    evals_per_check = sampler.nwalkers * sampler.ntemps * ncheck
+    evals_per_check = sampler.nwalkers * sampler.ntemps
 
     ncalls = "{:1.1e}".format(sampler.time * sampler.nwalkers * sampler.ntemps)
-    eval_timing = "{:1.1f}ms/evl".format(1e3 * ave_time_per_check / evals_per_check)
-    samp_timing = "{:1.2f}ms/smp".format(1e3 * ave_time_per_check / samples_per_check)
+    eval_timing = "{:1.1f}ms/ev".format(1e3 * ave_time_per_check / evals_per_check)
+    samp_timing = "{:1.1f}ms/sm".format(1e3 * ave_time_per_check / samples_per_check)
 
     print(
-        "{}| nc:{}| a0:{}| swp:{}| n:{}<{}| tau:{}| {}| {}| {}".format(
+        "{}| {} | nc:{}| a0:{}| swp:{}| n:{}<{}| tau{}| {}| {}".format(
             sampler.time,
+            str(sampling_time).split(".")[0],
             ncalls,
             acceptance_str,
             tswap_acceptance_str,
@@ -331,14 +422,14 @@ def print_progress(
             tau_str,
             eval_timing,
             samp_timing,
-            convergence,
         ),
         flush=True,
     )
 
 
 def checkpoint(outdir, label, nsamples_effective, sampler, nburn, thin,
-               search_parameter_keys, resume_file, tau_list, tau_list_n):
+               search_parameter_keys, resume_file, tau_list, tau_list_n,
+               time_per_check):
     logger.info("Writing checkpoint and diagnostics")
     ndim = sampler.dim
 
@@ -358,49 +449,52 @@ def checkpoint(outdir, label, nsamples_effective, sampler, nburn, thin,
     sampler_copy._logposterior = sampler._logposterior[:, :, : sampler.time]
     sampler_copy._loglikelihood = sampler._loglikelihood[:, :, : sampler.time]
     sampler_copy._beta_history = sampler._beta_history[:, : sampler.time]
-    data = dict(sampler=sampler_copy, tau_list=tau_list, tau_list_n=tau_list_n)
+
+    data = dict(
+        sampler=sampler_copy, tau_list=tau_list, tau_list_n=tau_list_n,
+        time_per_check=time_per_check)
+
     with open(resume_file, "wb") as file:
         dill.dump(data, file, protocol=4)
     del data, sampler_copy
+    logger.info("Finished writing checkpoint")
 
-    # Generate the walkers plot diagnostic
-    plot_walkers(
-        sampler.chain[0, :, : sampler.time, :], nburn, search_parameter_keys, outdir, label
-    )
 
-    # Generate the tau plot diagnostic
-    plot_tau(tau_list_n, tau_list, outdir, label)
-
-    logger.info("Finished writing checkpoint and diagnostics")
-
-
-def plot_walkers(walkers, nburn, parameter_labels, outdir, label):
+def plot_walkers(walkers, nburn, thin, parameter_labels, outdir, label):
     """ Method to plot the trace of the walkers in an ensemble MCMC plot """
     nwalkers, nsteps, ndim = walkers.shape
     idxs = np.arange(nsteps)
-    fig, axes = plt.subplots(nrows=ndim, figsize=(6, 3 * ndim))
-    scatter_kwargs = dict(lw=0, marker="o", markersize=1, alpha=0.05)
-    for i, ax in enumerate(axes):
+    fig, axes = plt.subplots(nrows=ndim, ncols=2, figsize=(8, 3 * ndim))
+    scatter_kwargs = dict(lw=0, marker="o", markersize=1)
+    # Plot the burn-in
+    for i, (ax, axh) in enumerate(axes):
         ax.plot(
-            idxs[: nburn + 1], walkers[:, : nburn + 1, i].T, color="r", **scatter_kwargs
+            idxs[: nburn + 1], walkers[:, : nburn + 1, i].T, color="C1", **scatter_kwargs
         )
-        ax.set_ylabel(parameter_labels[i])
 
-    for i, ax in enumerate(axes):
-        ax.plot(idxs[nburn:], walkers[:, nburn:, i].T, color="k", **scatter_kwargs)
+    # Plot the thinned posterior samples
+    for i, (ax, axh) in enumerate(axes):
+        ax.plot(idxs[nburn::thin], walkers[:, nburn::thin, i].T, color="C0", **scatter_kwargs)
+        axh.hist(walkers[:, nburn::thin, i].reshape((-1)), bins=50, alpha=0.8)
+        axh.set_xlabel(parameter_labels[i])
+        ax.set_ylabel(parameter_labels[i])
 
     fig.tight_layout()
-    filename = "{}/{}_traceplot.png".format(outdir, label)
+    filename = "{}/{}_checkpoint_trace.png".format(outdir, label)
     fig.savefig(filename)
     plt.close(fig)
 
 
-def plot_tau(tau_list_n, tau_list, outdir, label):
+def plot_tau(tau_list_n, tau_list, outdir, label, autocorr_tau):
     fig, ax = plt.subplots()
-    ax.plot(tau_list_n, tau_list, "-x")
+    ax.plot(tau_list_n, tau_list, "-", color='C1')
+    check_tau_idx = -int(tau_list[-1] * autocorr_tau)
+    check_taus = tau_list[check_tau_idx:]
+    check_taus_n = tau_list_n[check_tau_idx:]
+    ax.plot(check_taus_n, check_taus, "-", color='C0')
     ax.set_xlabel("Iteration")
     ax.set_ylabel(r"$\langle \tau \rangle$")
-    fig.savefig("{}/{}_tau.png".format(outdir, label))
+    fig.savefig("{}/{}_checkpoint_tau.png".format(outdir, label))
     plt.close(fig)