Many thanks for the suggestion. I tried the setting and got the folowing error log. Do you have any further suggestion?
---------------------------------------------------------------------------
RemoteTraceback Traceback (most recent call last)
RemoteTraceback:
"""
Traceback (most recent call last):
File "/home/user/miniforge3/envs/pymc_env0/lib/python3.11/site-packages/pytensor/link/vm.py", line 1235, in make_all
node.op.make_thunk(node, storage_map, compute_map, [], impl=impl)
File "/home/user/miniforge3/envs/pymc_env0/lib/python3.11/site-packages/pytensor/link/c/op.py", line 119, in make_thunk
return self.make_c_thunk(node, storage_map, compute_map, no_recycling)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/user/miniforge3/envs/pymc_env0/lib/python3.11/site-packages/pytensor/link/c/op.py", line 84, in make_c_thunk
outputs = cl.make_thunk(
^^^^^^^^^^^^^^
File "/home/user/miniforge3/envs/pymc_env0/lib/python3.11/site-packages/pytensor/link/c/basic.py", line 1209, in make_thunk
cthunk, module, in_storage, out_storage, error_storage = self.__compile__(
^^^^^^^^^^^^^^^^^
File "/home/user/miniforge3/envs/pymc_env0/lib/python3.11/site-packages/pytensor/link/c/basic.py", line 1129, in __compile__
thunk, module = self.cthunk_factory(
^^^^^^^^^^^^^^^^^^^^
File "/home/user/miniforge3/envs/pymc_env0/lib/python3.11/site-packages/pytensor/link/c/basic.py", line 1653, in cthunk_factory
module = cache.module_from_key(key=key, lnk=self)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/user/miniforge3/envs/pymc_env0/lib/python3.11/site-packages/pytensor/link/c/cmodule.py", line 1197, in module_from_key
module = self._get_from_hash(module_hash, key)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/user/miniforge3/envs/pymc_env0/lib/python3.11/site-packages/pytensor/link/c/cmodule.py", line 1100, in _get_from_hash
with lock_ctx():
File "/home/user/miniforge3/envs/pymc_env0/lib/python3.11/contextlib.py", line 137, in __enter__
return next(self.gen)
^^^^^^^^^^^^^^
File "/home/user/miniforge3/envs/pymc_env0/lib/python3.11/site-packages/pytensor/compile/compilelock.py", line 74, in lock_ctx
fl.acquire(timeout=timeout)
File "/home/user/miniforge3/envs/pymc_env0/lib/python3.11/site-packages/filelock/_api.py", line 264, in acquire
raise Timeout(lock_filename) # noqa: TRY301
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
filelock._error.Timeout: The file lock '/home/user/.pytensor/compiledir_Linux-3.10-el7.x86_64-x86_64-with-glibc2.17-x86_64-3.11.7-64/.lock' could not be acquired.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/user/miniforge3/envs/pymc_env0/lib/python3.11/multiprocessing/pool.py", line 125, in worker
result = (True, func(*args, **kwds))
^^^^^^^^^^^^^^^^^^^
File "/tmp/ipykernel_259166/1255918468.py", line 59, in single_round_simulation
idata = pm.sample(draws=chain_len, chains=1)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/user/miniforge3/envs/pymc_env0/lib/python3.11/site-packages/pymc/sampling/mcmc.py", line 689, in sample
step = assign_step_methods(model, step, methods=pm.STEP_METHODS, step_kwargs=kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/user/miniforge3/envs/pymc_env0/lib/python3.11/site-packages/pymc/sampling/mcmc.py", line 239, in assign_step_methods
return instantiate_steppers(model, steps, selected_steps, step_kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/user/miniforge3/envs/pymc_env0/lib/python3.11/site-packages/pymc/sampling/mcmc.py", line 140, in instantiate_steppers
step = step_class(vars=vars, model=model, **args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/user/miniforge3/envs/pymc_env0/lib/python3.11/site-packages/pymc/step_methods/hmc/nuts.py", line 180, in __init__
super().__init__(vars, **kwargs)
File "/home/user/miniforge3/envs/pymc_env0/lib/python3.11/site-packages/pymc/step_methods/hmc/base_hmc.py", line 109, in __init__
super().__init__(vars, blocked=blocked, model=self._model, dtype=dtype, **pytensor_kwargs)
File "/home/user/miniforge3/envs/pymc_env0/lib/python3.11/site-packages/pymc/step_methods/arraystep.py", line 164, in __init__
func = model.logp_dlogp_function(vars, dtype=dtype, **pytensor_kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/user/miniforge3/envs/pymc_env0/lib/python3.11/site-packages/pymc/model/core.py", line 618, in logp_dlogp_function
return ValueGradFunction(costs, grad_vars, extra_vars_and_values, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/user/miniforge3/envs/pymc_env0/lib/python3.11/site-packages/pymc/model/core.py", line 350, in __init__
self._pytensor_function = compile_pymc(inputs, outputs, givens=givens, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/user/miniforge3/envs/pymc_env0/lib/python3.11/site-packages/pymc/pytensorf.py", line 991, in compile_pymc
pytensor_function = pytensor.function(
^^^^^^^^^^^^^^^^^^
File "/home/user/miniforge3/envs/pymc_env0/lib/python3.11/site-packages/pytensor/compile/function/__init__.py", line 315, in function
fn = pfunc(
^^^^^^
File "/home/user/miniforge3/envs/pymc_env0/lib/python3.11/site-packages/pytensor/compile/function/pfunc.py", line 469, in pfunc
return orig_function(
^^^^^^^^^^^^^^
File "/home/user/miniforge3/envs/pymc_env0/lib/python3.11/site-packages/pytensor/compile/function/types.py", line 1762, in orig_function
fn = m.create(defaults)
^^^^^^^^^^^^^^^^^^
File "/home/user/miniforge3/envs/pymc_env0/lib/python3.11/site-packages/pytensor/compile/function/types.py", line 1654, in create
_fn, _i, _o = self.linker.make_thunk(
^^^^^^^^^^^^^^^^^^^^^^^
File "/home/user/miniforge3/envs/pymc_env0/lib/python3.11/site-packages/pytensor/link/basic.py", line 245, in make_thunk
return self.make_all(
^^^^^^^^^^^^^^
File "/home/user/miniforge3/envs/pymc_env0/lib/python3.11/site-packages/pytensor/link/vm.py", line 1244, in make_all
raise_with_op(fgraph, node)
File "/home/user/miniforge3/envs/pymc_env0/lib/python3.11/site-packages/pytensor/link/utils.py", line 531, in raise_with_op
raise exc_value.with_traceback(exc_trace)
File "/home/user/miniforge3/envs/pymc_env0/lib/python3.11/site-packages/pytensor/link/vm.py", line 1235, in make_all
node.op.make_thunk(node, storage_map, compute_map, [], impl=impl)
File "/home/user/miniforge3/envs/pymc_env0/lib/python3.11/site-packages/pytensor/link/c/op.py", line 119, in make_thunk
return self.make_c_thunk(node, storage_map, compute_map, no_recycling)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/user/miniforge3/envs/pymc_env0/lib/python3.11/site-packages/pytensor/link/c/op.py", line 84, in make_c_thunk
outputs = cl.make_thunk(
^^^^^^^^^^^^^^
File "/home/user/miniforge3/envs/pymc_env0/lib/python3.11/site-packages/pytensor/link/c/basic.py", line 1209, in make_thunk
cthunk, module, in_storage, out_storage, error_storage = self.__compile__(
^^^^^^^^^^^^^^^^^
File "/home/user/miniforge3/envs/pymc_env0/lib/python3.11/site-packages/pytensor/link/c/basic.py", line 1129, in __compile__
thunk, module = self.cthunk_factory(
^^^^^^^^^^^^^^^^^^^^
File "/home/user/miniforge3/envs/pymc_env0/lib/python3.11/site-packages/pytensor/link/c/basic.py", line 1653, in cthunk_factory
module = cache.module_from_key(key=key, lnk=self)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/user/miniforge3/envs/pymc_env0/lib/python3.11/site-packages/pytensor/link/c/cmodule.py", line 1197, in module_from_key
module = self._get_from_hash(module_hash, key)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/user/miniforge3/envs/pymc_env0/lib/python3.11/site-packages/pytensor/link/c/cmodule.py", line 1100, in _get_from_hash
with lock_ctx():
File "/home/user/miniforge3/envs/pymc_env0/lib/python3.11/contextlib.py", line 137, in __enter__
return next(self.gen)
^^^^^^^^^^^^^^
File "/home/user/miniforge3/envs/pymc_env0/lib/python3.11/site-packages/pytensor/compile/compilelock.py", line 74, in lock_ctx
fl.acquire(timeout=timeout)
File "/home/user/miniforge3/envs/pymc_env0/lib/python3.11/site-packages/filelock/_api.py", line 264, in acquire
raise Timeout(lock_filename) # noqa: TRY301
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
filelock._error.Timeout: The file lock 'The file lock '/home/user/.pytensor/compiledir_Linux-3.10-el7.x86_64-x86_64-with-glibc2.17-x86_64-3.11.7-64/.lock' could not be acquired.
Apply node that caused the error: Composite{(i5 - (i2 + (i3 * i4) + (i0 * i1)))}(ExpandDims{axis=0}.0, [-4.045692 ... 74900e+00], ExpandDims{axis=0}.0, ExpandDims{axis=0}.0, [0. 1. 1. ... 1. 0. 0.], Y_obs1{[-2.025834 ... 00053e+00]})
Toposort index: 6
Inputs types: [TensorType(float64, shape=(1,)), TensorType(float64, shape=(1000,)), TensorType(float64, shape=(1,)), TensorType(float64, shape=(1,)), TensorType(float64, shape=(1000,)), TensorType(float64, shape=(1000,))]
HINT: Use a linker other than the C linker to print the inputs' shapes and strides.
HINT: Re-running with most PyTensor optimizations disabled could provide a back-trace showing when this node was created. This can be done by setting the PyTensor flag 'optimizer=fast_compile'. If that does not work, PyTensor optimizations can be disabled with 'optimizer=None'.
HINT: Use the PyTensor flag `exception_verbosity=high` for a debug print-out and storage map footprint of this Apply node.' could not be acquired.
"""
The above exception was the direct cause of the following exception:
Timeout Traceback (most recent call last)
Cell In[8], line 25
12 temp_reses = [ # return
13 pool.apply_async(
14 single_round_simulation, # function
(...)
17 for RANDOM_SEED in range(nrepeat) # 随机种子
18 ]
19 for temp_resi in tqdm(temp_reses, desc="Pipeline: "):
20 ( # 函数的return
21 mcmc_betas_mean,
22 mcmc_betas_std,
23 ols_betas_mean,
24 ols_betas_std
---> 25 ) = temp_resi.get()
26 mcmc_betas_mean_l.append(mcmc_betas_mean)
27 mcmc_betas_std_l.append(mcmc_betas_std)
File ~/miniforge3/envs/pymc_env0/lib/python3.11/multiprocessing/pool.py:774, in ApplyResult.get(self, timeout)
772 return self._value
773 else:
--> 774 raise self._value
Timeout: The file lock 'The file lock '/home/user/.pytensor/compiledir_Linux-3.10-el7.x86_64-x86_64-with-glibc2.17-x86_64-3.11.7-64/.lock' could not be acquired.
Apply node that caused the error: Composite{(i5 - (i2 + (i3 * i4) + (i0 * i1)))}(ExpandDims{axis=0}.0, [-4.045692 ... 74900e+00], ExpandDims{axis=0}.0, ExpandDims{axis=0}.0, [0. 1. 1. ... 1. 0. 0.], Y_obs1{[-2.025834 ... 00053e+00]})
Toposort index: 6
Inputs types: [TensorType(float64, shape=(1,)), TensorType(float64, shape=(1000,)), TensorType(float64, shape=(1,)), TensorType(float64, shape=(1,)), TensorType(float64, shape=(1000,)), TensorType(float64, shape=(1000,))]
HINT: Use a linker other than the C linker to print the inputs' shapes and strides.
HINT: Re-running with most PyTensor optimizations disabled could provide a back-trace showing when this node was created. This can be done by setting the PyTensor flag 'optimizer=fast_compile'. If that does not work, PyTensor optimizations can be disabled with 'optimizer=None'.
HINT: Use the PyTensor flag `exception_verbosity=high` for a debug print-out and storage map footprint of this Apply node.' could not be acquired.