pymc (original) (raw)

Auto-assigning NUTS sampler... Initializing NUTS using jitter+adapt_diag... Multiprocess sampling (4 chains in 4 jobs) NUTS: [Intercept, col1, col2, col3, col4, col5, col6, col7, col8, col9, col10, col11, col12, target_sigma]

0.00% [0/8000 00:00<? Sampling 4 chains, 0 divergences]

KeyboardInterrupt Traceback (most recent call last) File ~/anaconda3/lib/python3.9/site-packages/pymc/sampling.py:1522, in _mp_sample(draws, tune, step, chains, cores, random_seed, start, progressbar, trace, model, callback, discard_tuned_samples, mp_ctx, **kwargs) 1521 with sampler: -> 1522 for draw in sampler: 1523 strace = traces[draw.chain]

File ~/anaconda3/lib/python3.9/site-packages/pymc/parallel_sampling.py:458, in ParallelSampler.iter(self) 457 while self._active: --> 458 draw = ProcessAdapter.recv_draw(self._active) 459 proc, is_last, draw, tuning, stats = draw

File ~/anaconda3/lib/python3.9/site-packages/pymc/parallel_sampling.py:328, in ProcessAdapter.recv_draw(processes, timeout) 327 pipes = [proc._msg_pipe for proc in processes] --> 328 ready = multiprocessing.connection.wait(pipes) 329 if not ready:

File ~/anaconda3/lib/python3.9/multiprocessing/connection.py:936, in wait(object_list, timeout) 935 while True: --> 936 ready = selector.select(timeout) 937 if ready:

File ~/anaconda3/lib/python3.9/selectors.py:416, in _PollLikeSelector.select(self, timeout) 415 try: --> 416 fd_event_list = self._selector.poll(timeout) 417 except InterruptedError:

KeyboardInterrupt:

During handling of the above exception, another exception occurred:

KeyboardInterrupt Traceback (most recent call last) File ~/anaconda3/lib/python3.9/site-packages/pymc/sampling.py:1530, in _mp_sample(draws, tune, step, chains, cores, random_seed, start, progressbar, trace, model, callback, discard_tuned_samples, mp_ctx, **kwargs) 1529 if callback is not None: -> 1530 callback(trace=trace, draw=draw) 1532 except ps.ParallelSamplingError as error:

File ~/anaconda3/lib/python3.9/site-packages/pymc/parallel_sampling.py:491, in ParallelSampler.exit(self, *args) 490 def exit(self, *args): --> 491 ProcessAdapter.terminate_all(self._samplers)

File ~/anaconda3/lib/python3.9/site-packages/pymc/parallel_sampling.py:365, in ProcessAdapter.terminate_all(processes, patience) 364 raise multiprocessing.TimeoutError() --> 365 process.join(timeout) 366 except multiprocessing.TimeoutError:

File ~/anaconda3/lib/python3.9/site-packages/pymc/parallel_sampling.py:318, in ProcessAdapter.join(self, timeout) 317 def join(self, timeout=None): --> 318 self._process.join(timeout)

File ~/anaconda3/lib/python3.9/multiprocessing/process.py:149, in BaseProcess.join(self, timeout) 148 assert self._popen is not None, 'can only join a started process' --> 149 res = self._popen.wait(timeout) 150 if res is not None:

File ~/anaconda3/lib/python3.9/multiprocessing/popen_fork.py:40, in Popen.wait(self, timeout) 39 from multiprocessing.connection import wait ---> 40 if not wait([self.sentinel], timeout): 41 return None

File ~/anaconda3/lib/python3.9/multiprocessing/connection.py:936, in wait(object_list, timeout) 935 while True: --> 936 ready = selector.select(timeout) 937 if ready:

File ~/anaconda3/lib/python3.9/selectors.py:416, in _PollLikeSelector.select(self, timeout) 415 try: --> 416 fd_event_list = self._selector.poll(timeout) 417 except InterruptedError:

KeyboardInterrupt:

During handling of the above exception, another exception occurred:

ValueError Traceback (most recent call last) Input In [100], in <cell line: 5>() 43 model = bmb.Model(f'{target} ~ {X}', train) 45 # Fit the model using 1000 on each of 4 chains ---> 46 results = model.fit(draws=1000, chains=4) 48 # Out of sample predictions 49 model.predict(results, data=test)

File ~/anaconda3/lib/python3.9/site-packages/bambi/models.py:277, in Model.fit(self, draws, tune, discard_tuned_samples, omit_offsets, include_mean, inference_method, init, n_init, chains, cores, random_seed, **kwargs) 270 if isinstance(self.family, univariate.Bernoulli): 271 _log.info( 272 "Modeling the probability that %s==%s", 273 self.response.name, 274 str(self.response.success), 275 ) --> 277 return self.backend.run( 278 draws=draws, 279 tune=tune, 280 discard_tuned_samples=discard_tuned_samples, 281 omit_offsets=omit_offsets, 282 include_mean=include_mean, 283 inference_method=inference_method, 284 init=init, 285 n_init=n_init, 286 chains=chains, 287 cores=cores, 288 random_seed=random_seed, 289 **kwargs, 290 )

File ~/anaconda3/lib/python3.9/site-packages/bambi/backend/pymc.py:94, in PyMCModel.run(self, draws, tune, discard_tuned_samples, omit_offsets, include_mean, inference_method, init, n_init, chains, cores, random_seed, **kwargs) 92 # NOTE: Methods return different types of objects (idata, approximation, and dictionary) 93 if inference_method in ["mcmc", "nuts_numpyro", "nuts_blackjax"]: ---> 94 result = self._run_mcmc( 95 draws, 96 tune, 97 discard_tuned_samples, 98 omit_offsets, 99 include_mean, 100 init, 101 n_init, 102 chains, 103 cores, 104 random_seed, 105 inference_method, 106 **kwargs, 107 ) 108 elif inference_method == "vi": 109 result = self._run_vi(**kwargs)

File ~/anaconda3/lib/python3.9/site-packages/bambi/backend/pymc.py:283, in PyMCModel._run_mcmc(self, draws, tune, discard_tuned_samples, omit_offsets, include_mean, init, n_init, chains, cores, random_seed, sampler_backend, **kwargs) 281 if sampler_backend == "mcmc": 282 try: --> 283 idata = pm.sample( 284 draws=draws, 285 tune=tune, 286 discard_tuned_samples=discard_tuned_samples, 287 init=init, 288 n_init=n_init, 289 chains=chains, 290 cores=cores, 291 random_seed=random_seed, 292 **kwargs, 293 ) 294 except (RuntimeError, ValueError): 295 if ( 296 "ValueError: Mass matrix contains" in traceback.format_exc() 297 and init == "auto" 298 ):

File ~/anaconda3/lib/python3.9/site-packages/pymc/sampling.py:617, in sample(draws, step, init, n_init, initvals, trace, chains, cores, tune, progressbar, model, random_seed, discard_tuned_samples, compute_convergence_checks, callback, jitter_max_retries, return_inferencedata, keep_warning_stat, idata_kwargs, mp_ctx, **kwargs) 615 _print_step_hierarchy(step) 616 try: --> 617 mtrace = _mp_sample(**sample_args, **parallel_args) 618 except pickle.PickleError: 619 _log.warning("Could not pickle model, sampling singlethreaded.")

File ~/anaconda3/lib/python3.9/site-packages/pymc/sampling.py:1543, in _mp_sample(draws, tune, step, chains, cores, random_seed, start, progressbar, trace, model, callback, discard_tuned_samples, mp_ctx, **kwargs) 1541 except KeyboardInterrupt: 1542 if discard_tuned_samples: -> 1543 traces, length = _choose_chains(traces, tune) 1544 else: 1545 traces, length = _choose_chains(traces, 0)

File ~/anaconda3/lib/python3.9/site-packages/pymc/sampling.py:1582, in _choose_chains(traces, tune) 1580 lengths = [max(0, len(trace) - tune) for trace in traces] 1581 if not sum(lengths): -> 1582 raise ValueError("Not enough samples to build a trace.") 1584 idxs = np.argsort(lengths) 1585 l_sort = np.array(lengths)[idxs]

ValueError: Not enough samples to build a trace.