pymc-devs / pymc-devs/pymc-examples
Error in `examples/samplers/SMC-ABC_Lotka-Volterra_example.ipynb`
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Description
────────────────────────────────────── Error running examples/samplers/SMC-ABC_Lotka-Volterra_example.ipynb ──────────────────────────────────────
---------------------------------------------------------------------------
Exception encountered at "In [12]":
---------------------------------------------------------------------------
_RemoteTraceback Traceback (most recent call last)
_RemoteTraceback:
"""
Traceback (most recent call last):
File "/home/wdean/micromamba/envs/pymc-examples/lib/python3.11/site-packages/pytensor/compile/function/types.py", line 959, in __call__
self.vm()
File "/home/wdean/micromamba/envs/pymc-examples/lib/python3.11/site-packages/pytensor/graph/op.py", line 524, in rval
r = p(n, [x[0] for x in i], o)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/wdean/micromamba/envs/pymc-examples/lib/python3.11/site-packages/pytensor/tensor/random/op.py", line 403, in perform
smpl_val = self.rng_fn(rng, *([*args, size]))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/wdean/micromamba/envs/pymc-examples/lib/python3.11/site-packages/pymc/distributions/simulator.py", line 53, in rng_fn
return cls.fn(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^
File "/tmp/ipykernel_43958/1881729530.py", line 27, in competition_model
return odeint(dX_dt, y0=X0, t=t, rtol=0.01, args=(a, b, c, d))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/wdean/micromamba/envs/pymc-examples/lib/python3.11/site-packages/scipy/integrate/_odepack_py.py", line 243, in odeint
output = _odepack.odeint(func, y0, t, args, Dfun, col_deriv, ml, mu,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
RuntimeError: The array return by func must be one-dimensional, but got ndim=3.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/wdean/micromamba/envs/pymc-examples/lib/python3.11/concurrent/futures/process.py", line 261, in _process_worker
r = call_item.fn(*call_item.args, **call_item.kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/wdean/micromamba/envs/pymc-examples/lib/python3.11/site-packages/pymc/smc/sampling.py", line 303, in _sample_smc_int
smc._initialize_kernel()
File "/home/wdean/micromamba/envs/pymc-examples/lib/python3.11/site-packages/pymc/smc/kernels.py", line 249, in _initialize_kernel
likelihoods =
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/wdean/micromamba/envs/pymc-examples/lib/python3.11/site-packages/pymc/smc/kernels.py", line 249, in <listcomp>
likelihoods =
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/wdean/micromamba/envs/pymc-examples/lib/python3.11/site-packages/pytensor/compile/function/types.py", line 972, in __call__
raise_with_op(
File "/home/wdean/micromamba/envs/pymc-examples/lib/python3.11/site-packages/pytensor/link/utils.py", line 524, in raise_with_op
raise exc_value.with_traceback(exc_trace)
File "/home/wdean/micromamba/envs/pymc-examples/lib/python3.11/site-packages/pytensor/compile/function/types.py", line 959, in __call__
self.vm()
File "/home/wdean/micromamba/envs/pymc-examples/lib/python3.11/site-packages/pytensor/graph/op.py", line 524, in rval
r = p(n, [x[0] for x in i], o)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/wdean/micromamba/envs/pymc-examples/lib/python3.11/site-packages/pytensor/tensor/random/op.py", line 403, in perform
smpl_val = self.rng_fn(rng, *([*args, size]))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/wdean/micromamba/envs/pymc-examples/lib/python3.11/site-packages/pymc/distributions/simulator.py", line 53, in rng_fn
return cls.fn(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^
File "/tmp/ipykernel_43958/1881729530.py", line 27, in competition_model
return odeint(dX_dt, y0=X0, t=t, rtol=0.01, args=(a, b, c, d))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/wdean/micromamba/envs/pymc-examples/lib/python3.11/site-packages/scipy/integrate/_odepack_py.py", line 243, in odeint
output = _odepack.odeint(func, y0, t, args, Dfun, col_deriv, ml, mu,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
RuntimeError: The array return by func must be one-dimensional, but got ndim=3.
Apply node that caused the error: Simulator_sim_rv{"(),()->()"}(simulator_rng, [100 2], Exp.0, Exp.0)
Toposort index: 8
Inputs types: [RandomGeneratorType, TensorType(int64, shape=(2,)), TensorType(float64, shape=(1, 1)), TensorType(float64, shape=(1, 1))]
Inputs shapes: ['No shapes', (2,), (1, 1), (1, 1)]
Inputs strides: ['No strides', (8,), (8, 8), (8, 8)]
Inputs values: [Generator(PCG64) at 0x7F6744184C80, array([100, 2]), array([[0.74738862]]), array([[0.78745484]])]
Outputs clients: [[output[1](Simulator_sim_rv{"(),()->()"}.0)], [Composite{sqr((0.1 * (i0 - i1)))}(sim{[[ 9.52728 ... 47175637]]},
Simulator_sim_rv{"(),()->()"}.out)]]
Backtrace when the node is created (use PyTensor flag traceback__limit=N to make it longer):
File "/home/wdean/micromamba/envs/pymc-examples/lib/python3.11/multiprocessing/process.py", line 314, in _bootstrap
self.run()
File "/home/wdean/micromamba/envs/pymc-examples/lib/python3.11/multiprocessing/process.py", line 108, in run
self._target(*self._args, **self._kwargs)
File "/home/wdean/micromamba/envs/pymc-examples/lib/python3.11/concurrent/futures/process.py", line 261, in _process_worker
r = call_item.fn(*call_item.args, **call_item.kwargs)
File "/home/wdean/micromamba/envs/pymc-examples/lib/python3.11/site-packages/pymc/smc/sampling.py", line 303, in _sample_smc_int
smc._initialize_kernel()
File "/home/wdean/micromamba/envs/pymc-examples/lib/python3.11/site-packages/pymc/smc/kernels.py", line 244, in _initialize_kernel
self.likelihood_logp_func = _logp_forw(
File "/home/wdean/micromamba/envs/pymc-examples/lib/python3.11/site-packages/pymc/smc/kernels.py", line 636, in _logp_forw
out_list, inarray0 = join_nonshared_inputs(
File "/home/wdean/micromamba/envs/pymc-examples/lib/python3.11/site-packages/pymc/pytensorf.py", line 619, in join_nonshared_inputs
new_outputs = [
File "/home/wdean/micromamba/envs/pymc-examples/lib/python3.11/site-packages/pymc/pytensorf.py", line 620, in <listcomp>
pytensor.clone_replace(output, replace, rebuild_strict=False) for output in outputs
HINT: Use the PyTensor flag `exception_verbosity=high` for a debug print-out and storage map footprint of this Apply node.
"""
The above exception was the direct cause of the following exception:
RuntimeError Traceback (most recent call last)
Cell In[12], line 7
3 b = pm.HalfNormal("b", 1.0)
5 sim = pm.Simulator("sim", competition_model, params=(a, b), epsilon=10, observed=observed)
----> 7 idata_lv = pm.sample_smc()
File ~/micromamba/envs/pymc-examples/lib/python3.11/site-packages/pymc/smc/sampling.py:180, in sample_smc(draws, kernel, start, model,
random_seed, chains, cores, compute_convergence_checks, return_inferencedata, idata_kwargs, progressbar, **kernel_kwargs)
171 params = (
172 draws,
173 kernel,
174 start,
175 model,
176 )
178 t1 = time.time()
--> 180 results = run_chains(chains, progressbar, params, random_seed, kernel_kwargs, cores)
182 (
183 traces,
184 sample_stats,
185 sample_settings,
186 ) = zip(*results)
188 trace = MultiTrace(traces)
File ~/micromamba/envs/pymc-examples/lib/python3.11/site-packages/pymc/smc/sampling.py:385, in run_chains(chains, progressbar, params,
random_seed, kernel_kwargs, cores)
378 # update the progress bar for this task:
379 progress.update(
380 status=f"Stage: {stage} Beta: {beta:.3f}",
381 task_id=task_id,
382 refresh=True,
383 )
--> 385 return tuple(cloudpickle.loads(r.result()) for r in done)
File ~/micromamba/envs/pymc-examples/lib/python3.11/site-packages/pymc/smc/sampling.py:385, in <genexpr>(.0)
378 # update the progress bar for this task:
379 progress.update(
380 status=f"Stage: {stage} Beta: {beta:.3f}",
381 task_id=task_id,
382 refresh=True,
383 )
--> 385 return tuple(cloudpickle.loads(r.result()) for r in done)
File ~/micromamba/envs/pymc-examples/lib/python3.11/concurrent/futures/_base.py:449, in Future.result(self, timeout)
447 raise CancelledError()
448 elif self._state == FINISHED:
--> 449 return self.__get_result()
451 self._condition.wait(timeout)
453 if self._state in [CANCELLED, CANCELLED_AND_NOTIFIED]:
File ~/micromamba/envs/pymc-examples/lib/python3.11/concurrent/futures/_base.py:401, in Future.__get_result(self)
399 if self._exception:
400 try:
--> 401 raise self._exception
402 finally:
403 # Break a reference cycle with the exception in self._exception
404 self = None
RuntimeError: The array return by func must be one-dimensional, but got ndim=3.
Apply node that caused the error: Simulator_sim_rv{"(),()->()"}(simulator_rng, [100 2], Exp.0, Exp.0)
Toposort index: 8
Inputs types: [RandomGeneratorType, TensorType(int64, shape=(2,)), TensorType(float64, shape=(1, 1)), TensorType(float64, shape=(1, 1))]
Inputs shapes: ['No shapes', (2,), (1, 1), (1, 1)]
Inputs strides: ['No strides', (8,), (8, 8), (8, 8)]
Inputs values: [Generator(PCG64) at 0x7F6744184C80, array([100, 2]), array([[0.74738862]]), array([[0.78745484]])]
Outputs clients: [[output[1](Simulator_sim_rv{"(),()->()"}.0)], [Composite{sqr((0.1 * (i0 - i1)))}(sim{[[ 9.52728 ... 47175637]]},
Simulator_sim_rv{"(),()->()"}.out)]]
Backtrace when the node is created (use PyTensor flag traceback__limit=N to make it longer):
File "/home/wdean/micromamba/envs/pymc-examples/lib/python3.11/multiprocessing/process.py", line 314, in _bootstrap
self.run()
File "/home/wdean/micromamba/envs/pymc-examples/lib/python3.11/multiprocessing/process.py", line 108, in run
self._target(*self._args, **self._kwargs)
File "/home/wdean/micromamba/envs/pymc-examples/lib/python3.11/concurrent/futures/process.py", line 261, in _process_worker
r = call_item.fn(*call_item.args, **call_item.kwargs)
File "/home/wdean/micromamba/envs/pymc-examples/lib/python3.11/site-packages/pymc/smc/sampling.py", line 303, in _sample_smc_int
smc._initialize_kernel()
File "/home/wdean/micromamba/envs/pymc-examples/lib/python3.11/site-packages/pymc/smc/kernels.py", line 244, in _initialize_kernel
self.likelihood_logp_func = _logp_forw(
File "/home/wdean/micromamba/envs/pymc-examples/lib/python3.11/site-packages/pymc/smc/kernels.py", line 636, in _logp_forw
out_list, inarray0 = join_nonshared_inputs(
File "/home/wdean/micromamba/envs/pymc-examples/lib/python3.11/site-packages/pymc/pytensorf.py", line 619, in join_nonshared_inputs
new_outputs = [
File "/home/wdean/micromamba/envs/pymc-examples/lib/python3.11/site-packages/pymc/pytensorf.py", line 620, in <listcomp>
pytensor.clone_replace(output, replace, rebuild_strict=False) for output in outputs
HINT: Use the PyTensor flag `exception_verbosity=high` for a debug print-out and storage map footprint of this Apply node.
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- Open a pull request that references the issue number.
Research direction
Open examples/samplers/SMC-ABC_Lotka-Volterra_example.ipynb and inspect cell 12, especially competition_model and its odeint call. Reproduce the failure at pm.sample_smc(); the work is done when the notebook runs without the ndim=3 error.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- jupyter-notebook, python
- Domain
- documentation
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 42/100