I am running Python 3.8 on Windows 10 Pro. I am attempting to fit a multinomial fixed effects model to some data. All the packages appear to load fine, the data loads and can be manipulated and viewed. But I get an error when I call a module that my collaborator wrote to fit the model (called contactai). Here is the code for contactai:
Note: tt stands for theano.tensor and pm stands for pymc3
def fixed_effects_model(X, y):
Parameters
X : array contains covariates Design matrix n x p
y : array or shared theano variable Multinomial response variable, n x 3
Returns
pymc3 model object containing fitted model
yarray = y.eval()
else:
yarray = y
if type(X) == tt.sharedvar.TensorSharedVariable:
Xmat = X.eval()
else:
Xmat = X
model = pm.Model()
with model:
# Transformed coefficients
betaD = pm.Normal('betad', mu=0, sd=5, shape=(Xmat.shape[1], 1))
betaI = pm.Normal('betai', mu=0, sd=5, shape=(Xmat.shape[1], 1))
# Softmax transformation with no contact as baseline
etad = tt.exp(tt.dot(X, betaD))
etai = tt.exp(tt.dot(X, betaI))
p_d = etad / (1 + etad + etai)
p_i = etai / (1 + etad + etai)
p_n = 1 - p_d - p_i
ps = tt.stack([p_n, p_d, p_i], axis=1).reshape((len(yarray), 3)) # Stack column-wise
Y_obs = pm.Multinomial("Y_obs", n=1, p=ps, observed=y)
return(model)
When I call contaciai.py in my jupyter notebook using
test_mod = contactai.fixed_effects_model(Xmat1, Yres.values)
I get this error message:
ImportError Traceback (most recent call last)
<ipython-input-6-275ca67d4b63> in <module>
1 # Run Fixed Effects model
----> 2 test_mod = contactai.fixed_effects_model(Xmat1, Yres.values)
3 niter = 1000
4
5 with test_mod:
~\dropbox\Brooke\ai_multinomial_model\contactai.py in fixed_effects_model(X, y)
50 # Transformed coefficients, what are D and I? In other examples this is where priors are
51 #specified.
---> 52 betaD = pm.Normal('betad', mu=0, sd=5, shape=(Xmat.shape[1], 1))
53 betaI = pm.Normal('betai', mu=0, sd=5, shape=(Xmat.shape[1], 1))
54 # First argument is the name of the random variable
c:\users\webblab\appdata\local\programs\python\python38-32\lib\site-packages\pymc3\distributions\distribution.py in __new__(cls, name, *args, **kwargs)
44 raise TypeError("observed needs to be data but got: {}".format(type(data)))
45 total_size = kwargs.pop('total_size', None)
---> 46 dist = cls.dist(*args, **kwargs)
47 return model.Var(name, dist, data, total_size)
48 else:
c:\users\webblab\appdata\local\programs\python\python38-32\lib\site-packages\pymc3\distributions\distribution.py in dist(cls, *args, **kwargs)
55 def dist(cls, *args, **kwargs):
56 dist = object.__new__(cls)
---> 57 dist.__init__(*args, **kwargs)
58 return dist
59
c:\users\webblab\appdata\local\programs\python\python38-32\lib\site-packages\pymc3\distributions\continuous.py in __init__(self, mu, sigma, tau, sd, **kwargs)
468
469 self.mean = self.median = self.mode = self.mu = mu = tt.as_tensor_variable(floatX(mu))
--> 470 self.variance = 1. / self.tau
471
472 assert_negative_support(sigma, 'sigma', 'Normal')
c:\users\webblab\appdata\local\programs\python\python38-32\lib\site-packages\theano\tensor\var.py in __rtruediv__(self, other)
204
205 def __rtruediv__(self, other):
--> 206 return theano.tensor.basic.true_div(other, self)
207
208 def __rfloordiv__(self, other):
c:\users\webblab\appdata\local\programs\python\python38-32\lib\site-packages\theano\gof\op.py in __call__(self, *inputs, **kwargs)
667
668 # compute output value once with test inputs to validate graph
--> 669 thunk = node.op.make_thunk(node, storage_map, compute_map,
670 no_recycling=[])
671 thunk.inputs = [storage_map[v] for v in node.inputs]
c:\users\webblab\appdata\local\programs\python\python38-32\lib\site-packages\theano\gof\op.py in make_thunk(self, node, storage_map, compute_map, no_recycling, impl)
952 compute_map=compute_map, impl='c')
953 try:
--> 954 return self.make_c_thunk(node, storage_map, compute_map,
955 no_recycling)
956 except (NotImplementedError, utils.MethodNotDefined):
c:\users\webblab\appdata\local\programs\python\python38-32\lib\site-packages\theano\gof\op.py in make_c_thunk(self, node, storage_map, compute_map, no_recycling)
855 raise NotImplementedError("float16")
856 _logger.debug('Trying CLinker.make_thunk')
--> 857 outputs = cl.make_thunk(input_storage=node_input_storage,
858 output_storage=node_output_storage)
859 thunk, node_input_filters, node_output_filters = outputs
c:\users\webblab\appdata\local\programs\python\python38-32\lib\site-packages\theano\gof\cc.py in make_thunk(self, input_storage, output_storage, storage_map, keep_lock)
1213 """
1214 init_tasks, tasks = self.get_init_tasks()
-> 1215 cthunk, module, in_storage, out_storage, error_storage = self.__compile__(
1216 input_storage, output_storage, storage_map,
1217 keep_lock=keep_lock)
c:\users\webblab\appdata\local\programs\python\python38-32\lib\site-packages\theano\gof\cc.py in __compile__(self, input_storage, output_storage, storage_map, keep_lock)
1151 input_storage = tuple(input_storage)
1152 output_storage = tuple(output_storage)
-> 1153 thunk, module = self.cthunk_factory(error_storage,
1154 input_storage,
1155 output_storage,
c:\users\webblab\appdata\local\programs\python\python38-32\lib\site-packages\theano\gof\cc.py in cthunk_factory(self, error_storage, in_storage, out_storage, storage_map, keep_lock)
1621 for node in self.node_order:
1622 node.op.prepare_node(node, storage_map, None, 'c')
-> 1623 module = get_module_cache().module_from_key(
1624 key=key, lnk=self, keep_lock=keep_lock)
1625
c:\users\webblab\appdata\local\programs\python\python38-32\lib\site-packages\theano\gof\cmodule.py in module_from_key(self, key, lnk, keep_lock)
1187 try:
1188 location = dlimport_workdir(self.dirname)
-> 1189 module = lnk.compile_cmodule(location)
1190 name = module.__file__
1191 assert name.startswith(location)
c:\users\webblab\appdata\local\programs\python\python38-32\lib\site-packages\theano\gof\cc.py in compile_cmodule(self, location)
1518 try:
1519 _logger.debug("LOCATION %s", str(location))
-> 1520 module = c_compiler.compile_str(
1521 module_name=mod.code_hash,
1522 src_code=src_code,
c:\users\webblab\appdata\local\programs\python\python38-32\lib\site-packages\theano\gof\cmodule.py in compile_str(module_name, src_code, location, include_dirs, lib_dirs, libs, preargs, py_module, hide_symbols)
2418 open(os.path.join(location, "__init__.py"), 'w').close()
2419 assert os.path.isfile(lib_filename)
-> 2420 return dlimport(lib_filename)
2421
2422
c:\users\webblab\appdata\local\programs\python\python38-32\lib\site-packages\theano\gof\cmodule.py in dlimport(fullpath, suffix)
315 warnings.filterwarnings("ignore",
316 message="numpy.ndarray size changed")
--> 317 rval = __import__(module_name, {}, {}, [module_name])
318 t1 = time.time()
319 import_time += t1 - t0
ImportError: DLL load failed while importing m54e1ce4760689129b813fce15fee7f8d468afbe167bc036205eea6bd301309d7: The specified module could not be found.
My collaborator does not get this error when running identical code on their macbook so the issue is not with the code. I installed all packages with pip. Any help would be greatly appreciated, this has brought me to a standstill on this project.
