Theano TypeError

marcio · April 1, 2018, 1:39pm

Hi all, after try to sample I’m receiving this (for every model):

Auto-assigning NUTS sampler…
Initializing NUTS using jitter+adapt_diag…
/usr/local/lib/python3.5/dist-packages/pymc3/model.py:384: FutureWarning: Conversion of the second argument of issubdtype from float to np.floating is deprecated. In future, it will be treated as np.float64 == np.dtype(float).type.
if not np.issubdtype(var.dtype, float):
Multiprocess sampling (4 chains in 4 jobs)
NUTS: [beta3, beta2, beta1, intercept_price, imp, sd_b1_log__, nu_log__, epsilon_log__, e]
Process ForkPoolWorker-1:
Traceback (most recent call last):
File “/usr/lib/python3.5/multiprocessing/process.py”, line 249, in _bootstrap
self.run()
File “/usr/lib/python3.5/multiprocessing/process.py”, line 93, in run
self._target(*self._args, **self._kwargs)
File “/usr/lib/python3.5/multiprocessing/pool.py”, line 108, in worker
task = get()
File “/usr/local/lib/python3.5/dist-packages/joblib/pool.py”, line 362, in get
return recv()
File “/usr/lib/python3.5/multiprocessing/connection.py”, line 251, in recv
return ForkingPickler.loads(buf.getbuffer())
File “/usr/local/lib/python3.5/dist-packages/theano/compile/function_module.py”, line 1082, in _constructor_Function
f = maker.create(input_storage, trustme=True)
File “/usr/local/lib/python3.5/dist-packages/theano/compile/function_module.py”, line 1715, in create
input_storage=input_storage_lists, storage_map=storage_map)
File “/usr/local/lib/python3.5/dist-packages/theano/gof/link.py”, line 699, in make_thunk
storage_map=storage_map)[:3]
File “/usr/local/lib/python3.5/dist-packages/theano/gof/vm.py”, line 1084, in make_all
impl=impl))
File “/usr/local/lib/python3.5/dist-packages/theano/gof/op.py”, line 955, in make_thunk
no_recycling)
File “/usr/local/lib/python3.5/dist-packages/theano/gof/op.py”, line 833, in make_c_thunk
e = FunctionGraph(node.inputs, node.outputs)
File “/usr/local/lib/python3.5/dist-packages/theano/gof/fg.py”, line 137, in init
inputs, outputs = graph.clone(inputs, outputs)
File “/usr/local/lib/python3.5/dist-packages/theano/gof/graph.py”, line 862, in clone
equiv = clone_get_equiv(i, o, copy_inputs, copy_orphans)
File “/usr/local/lib/python3.5/dist-packages/theano/gof/graph.py”, line 899, in clone_get_equiv
cpy = input.clone()
File “/usr/local/lib/python3.5/dist-packages/theano/gof/graph.py”, line 607, in clone
cp = self.class(self.type, self.data, self.name)
File “/usr/local/lib/python3.5/dist-packages/theano/tensor/var.py”, line 961, in init
Constant.init(self, type, data, name)
File “/usr/local/lib/python3.5/dist-packages/theano/gof/graph.py”, line 579, in init
self.data = type.filter(data)
File “/usr/local/lib/python3.5/dist-packages/theano/tensor/type.py”, line 189, in filter
“object dtype”, data.dtype)
TypeError: (‘The following error happened while compiling the node’, Elemwise{Composite{(i0 - (i1 + (i2 * i3) + (i4 * i5) + (i6 * i3) + i7))}}[(0, 1)](TensorConstant{[999. 899…299. 299.]}, AdvancedSubtensor1.0, AdvancedSubtensor1.0, TensorConstant{[ 31. 5…04. 794.]}, AdvancedSubtensor1.0, TensorConstant{[ 961. … -24924.]}, AdvancedSubtensor1.0, InplaceDimShuffle{x}.0), ‘\n’, ‘The numpy.ndarray object is not aligned. Theano C code does not support that.’, ‘object buffer<memory at 0x7f13bb452888>’, ‘object shape’, (2935849,), ‘object strides’, (8,), ‘object dtype’, dtype(‘float64’))
Process ForkPoolWorker-2:
Traceback (most recent call last):
File “/usr/lib/python3.5/multiprocessing/process.py”, line 249, in _bootstrap
self.run()
File “/usr/lib/python3.5/multiprocessing/process.py”, line 93, in run
self._target(*self._args, **self._kwargs)
File “/usr/lib/python3.5/multiprocessing/pool.py”, line 108, in worker
task = get()
File “/usr/local/lib/python3.5/dist-packages/joblib/pool.py”, line 362, in get
return recv()
File “/usr/lib/python3.5/multiprocessing/connection.py”, line 251, in recv
return ForkingPickler.loads(buf.getbuffer())
File “/usr/local/lib/python3.5/dist-packages/theano/compile/function_module.py”, line 1082, in _constructor_Function
f = maker.create(input_storage, trustme=True)
File “/usr/local/lib/python3.5/dist-packages/theano/compile/function_module.py”, line 1715, in create
input_storage=input_storage_lists, storage_map=storage_map)
File “/usr/local/lib/python3.5/dist-packages/theano/gof/link.py”, line 699, in make_thunk
storage_map=storage_map)[:3]
File “/usr/local/lib/python3.5/dist-packages/theano/gof/vm.py”, line 1084, in make_all
impl=impl))
File “/usr/local/lib/python3.5/dist-packages/theano/gof/op.py”, line 955, in make_thunk
no_recycling)
File “/usr/local/lib/python3.5/dist-packages/theano/gof/op.py”, line 833, in make_c_thunk
e = FunctionGraph(node.inputs, node.outputs)
File “/usr/local/lib/python3.5/dist-packages/theano/gof/fg.py”, line 137, in init
inputs, outputs = graph.clone(inputs, outputs)
File “/usr/local/lib/python3.5/dist-packages/theano/gof/graph.py”, line 862, in clone
equiv = clone_get_equiv(i, o, copy_inputs, copy_orphans)
File “/usr/local/lib/python3.5/dist-packages/theano/gof/graph.py”, line 899, in clone_get_equiv
cpy = input.clone()
File “/usr/local/lib/python3.5/dist-packages/theano/gof/graph.py”, line 607, in clone
cp = self.class(self.type, self.data, self.name)
File “/usr/local/lib/python3.5/dist-packages/theano/tensor/var.py”, line 961, in init
Constant.init(self, type, data, name)
File “/usr/local/lib/python3.5/dist-packages/theano/gof/graph.py”, line 579, in init
self.data = type.filter(data)
File “/usr/local/lib/python3.5/dist-packages/theano/tensor/type.py”, line 189, in filter
“object dtype”, data.dtype)
TypeError: (‘The following error happened while compiling the node’, Elemwise{Composite{(i0 - (i1 + (i2 * i3) + (i4 * i5) + (i6 * i3) + i7))}}[(0, 1)](TensorConstant{[999. 899…299. 299.]}, AdvancedSubtensor1.0, AdvancedSubtensor1.0, TensorConstant{[ 31. 5…04. 794.]}, AdvancedSubtensor1.0, TensorConstant{[ 961. … -24924.]}, AdvancedSubtensor1.0, InplaceDimShuffle{x}.0), ‘\n’, ‘The numpy.ndarray object is not aligned. Theano C code does not support that.’, ‘object buffer<memory at 0x7f13bb452888>’, ‘object shape’, (2935849,), ‘object strides’, (8,), ‘object dtype’, dtype(‘float64’))
Process ForkPoolWorker-3:
Traceback (most recent call last):
File “/usr/lib/python3.5/multiprocessing/process.py”, line 249, in _bootstrap
self.run()
File “/usr/lib/python3.5/multiprocessing/process.py”, line 93, in run
self._target(*self._args, **self._kwargs)
File “/usr/lib/python3.5/multiprocessing/pool.py”, line 108, in worker
task = get()
File “/usr/local/lib/python3.5/dist-packages/joblib/pool.py”, line 362, in get
return recv()
File “/usr/lib/python3.5/multiprocessing/connection.py”, line 251, in recv
return ForkingPickler.loads(buf.getbuffer())
File “/usr/local/lib/python3.5/dist-packages/theano/compile/function_module.py”, line 1082, in _constructor_Function
f = maker.create(input_storage, trustme=True)
File “/usr/local/lib/python3.5/dist-packages/theano/compile/function_module.py”, line 1715, in create
input_storage=input_storage_lists, storage_map=storage_map)
File “/usr/local/lib/python3.5/dist-packages/theano/gof/link.py”, line 699, in make_thunk
storage_map=storage_map)[:3]
File “/usr/local/lib/python3.5/dist-packages/theano/gof/vm.py”, line 1084, in make_all
impl=impl))
File “/usr/local/lib/python3.5/dist-packages/theano/gof/op.py”, line 955, in make_thunk
no_recycling)
File “/usr/local/lib/python3.5/dist-packages/theano/gof/op.py”, line 833, in make_c_thunk
e = FunctionGraph(node.inputs, node.outputs)
File “/usr/local/lib/python3.5/dist-packages/theano/gof/fg.py”, line 137, in init
inputs, outputs = graph.clone(inputs, outputs)
File “/usr/local/lib/python3.5/dist-packages/theano/gof/graph.py”, line 862, in clone
equiv = clone_get_equiv(i, o, copy_inputs, copy_orphans)
File “/usr/local/lib/python3.5/dist-packages/theano/gof/graph.py”, line 899, in clone_get_equiv
cpy = input.clone()

File “/usr/local/lib/python3.5/dist-packages/theano/gof/graph.py”, line 607, in clone
cp = self.class(self.type, self.data, self.name)
File “/usr/local/lib/python3.5/dist-packages/theano/tensor/var.py”, line 961, in init
Constant.init(self, type, data, name)
File “/usr/local/lib/python3.5/dist-packages/theano/gof/graph.py”, line 579, in init
self.data = type.filter(data)
File “/usr/local/lib/python3.5/dist-packages/theano/tensor/type.py”, line 189, in filter
“object dtype”, data.dtype)
TypeError: (‘The following error happened while compiling the node’, Elemwise{Composite{(i0 - (i1 + (i2 * i3) + (i4 * i5) + (i6 * i3) + i7))}}[(0, 1)](TensorConstant{[999. 899…299. 299.]}, AdvancedSubtensor1.0, AdvancedSubtensor1.0, TensorConstant{[ 31. 5…04. 794.]}, AdvancedSubtensor1.0, TensorConstant{[ 961. … -24924.]}, AdvancedSubtensor1.0, InplaceDimShuffle{x}.0), ‘\n’, ‘The numpy.ndarray object is not aligned. Theano C code does not support that.’, ‘object buffer<memory at 0x7f13bb452888>’, ‘object shape’, (2935849,), ‘object strides’, (8,), ‘object dtype’, dtype(‘float64’))
Process ForkPoolWorker-4:
Traceback (most recent call last):
File “/usr/lib/python3.5/multiprocessing/process.py”, line 249, in _bootstrap
self.run()
File “/usr/lib/python3.5/multiprocessing/process.py”, line 93, in run
self._target(*self._args, **self._kwargs)
File “/usr/lib/python3.5/multiprocessing/pool.py”, line 108, in worker
task = get()
File “/usr/local/lib/python3.5/dist-packages/joblib/pool.py”, line 362, in get
return recv()
File “/usr/lib/python3.5/multiprocessing/connection.py”, line 251, in recv
return ForkingPickler.loads(buf.getbuffer())
File “/usr/local/lib/python3.5/dist-packages/theano/compile/function_module.py”, line 1082, in _constructor_Function
f = maker.create(input_storage, trustme=True)
File “/usr/local/lib/python3.5/dist-packages/theano/compile/function_module.py”, line 1715, in create
input_storage=input_storage_lists, storage_map=storage_map)
File “/usr/local/lib/python3.5/dist-packages/theano/gof/link.py”, line 699, in make_thunk
storage_map=storage_map)[:3]
File “/usr/local/lib/python3.5/dist-packages/theano/gof/vm.py”, line 1084, in make_all
impl=impl))
File “/usr/local/lib/python3.5/dist-packages/theano/gof/op.py”, line 955, in make_thunk
no_recycling)
File “/usr/local/lib/python3.5/dist-packages/theano/gof/op.py”, line 833, in make_c_thunk
e = FunctionGraph(node.inputs, node.outputs)
File “/usr/local/lib/python3.5/dist-packages/theano/gof/fg.py”, line 137, in init
inputs, outputs = graph.clone(inputs, outputs)
File “/usr/local/lib/python3.5/dist-packages/theano/gof/graph.py”, line 862, in clone
equiv = clone_get_equiv(i, o, copy_inputs, copy_orphans)
File “/usr/local/lib/python3.5/dist-packages/theano/gof/graph.py”, line 899, in clone_get_equiv
cpy = input.clone()
File “/usr/local/lib/python3.5/dist-packages/theano/gof/graph.py”, line 607, in clone
cp = self.class(self.type, self.data, self.name)
File “/usr/local/lib/python3.5/dist-packages/theano/tensor/var.py”, line 961, in init
Constant.init(self, type, data, name)
File “/usr/local/lib/python3.5/dist-packages/theano/gof/graph.py”, line 579, in init
self.data = type.filter(data)
File “/usr/local/lib/python3.5/dist-packages/theano/tensor/type.py”, line 189, in filter
“object dtype”, data.dtype)
TypeError: (‘The following error happened while compiling the node’, Elemwise{Composite{(i0 - (i1 + (i2 * i3) + (i4 * i5) + (i6 * i3) + i7))}}[(0, 1)](TensorConstant{[999. 899…299. 299.]}, AdvancedSubtensor1.0, AdvancedSubtensor1.0, TensorConstant{[ 31. 5…04. 794.]}, AdvancedSubtensor1.0, TensorConstant{[ 961. … -24924.]}, AdvancedSubtensor1.0, InplaceDimShuffle{x}.0), ‘\n’, ‘The numpy.ndarray object is not aligned. Theano C code does not support that.’, ‘object buffer<memory at 0x7f13bb452888>’, ‘object shape’, (2935849,), ‘object strides’, (8,), ‘object dtype’, dtype(‘float64’))

Thank you all!

Versions and main components

PyMC3 Version: 3.3.2
Theano Version: 1.01
Python Version: 3.5
Operating system: Ubuntu 16.04
How did you install PyMC3: pip

junpenglao · April 1, 2018, 4:13pm

Following github issue https://github.com/pymc-devs/pymc3/issues/2913
What is the size of your model (number of data point, number or parameters). I think it is running out of memory.

Jihad · December 5, 2021, 3:06am

Hi I am getting an error similar to this,

Exception: ('The following error happened while compiling the node', CGemv{inplace}(AllocEmpty{dtype='float64'}.0, TensorConstant{1.0}, Reshape{2}.0, Elemwise{Composite{((i0 * i1) / i2)}}[(0, 1)].0, TensorConstant{0.0}), '\n', "Compilation failed (return status=1): <command-line>:0:1: error: macro names must be identifiers\r. cc1plus.exe: warning: unrecognized command line option '-Wno-c++11-narrowing'\r. ", 'FunctionGraph(CGemv{inplace}(<TensorType(float64, vector)>, TensorConstant{1.0}, <TensorType(float64, matrix)>, <TensorType(float64, vector)>, TensorConstant{0.0}))')

I am not sure how to check the size of my data, but if it was running out of memory how could I fix this. Thanks.

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Theano TypeError

Versions and main components

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