Error while building RNN model

[naeemulhassan]

model = RNN(layers=layers, cost='CategoricalCrossEntropy')

I received this error while building the RNN model. Any ideas? The complete error message is very long.

Thanks!

/home/naeemul/anaconda/lib/python2.7/site-packages/theano/tensor/subtensor.py:110: FutureWarning: comparison to None will result in an elementwise object comparison in the future.
start in [None, 0] or
/home/naeemul/anaconda/lib/python2.7/site-packages/theano/tensor/subtensor.py:114: FutureWarning: comparison to None will result in an elementwise object comparison in the future.
stop in [None, length, maxsize] or
/home/naeemul/anaconda/lib/python2.7/site-packages/theano/tensor/opt.py:2165: FutureWarning: comparison to None will result in an elementwise object comparison in the future.
if (replace_x == replace_y and
WARNING (theano.tensor.blas): We did not found a dynamic library into the library_dir of the library we use for blas. If you use ATLAS, make sure to compile it with dynamics library.

WARNING:theano.tensor.blas:We did not found a dynamic library into the library_dir of the library we use for blas. If you use ATLAS, make sure to compile it with dynamics library.

/usr/bin/ld: cannot find -lf77blas
/usr/bin/ld: cannot find -lcblas
/usr/bin/ld: cannot find -latlas
collect2: error: ld returned 1 exit status

---

Exception Traceback (most recent call last)
in ()
----> 1 model = RNN(layers=layers, cost='CategoricalCrossEntropy')
2 model.fit(train_tokens, train.verdict)
3
4 model.predict(tokenizer.transform(test.text))

/home/naeemul/anaconda/lib/python2.7/site-packages/passage/models.pyc in init(self, layers, cost, updater, verbose, Y, iterator)
49 self.updates = self.updater.get_updates(self.params, cost)
50
---> 51 self._train = theano.function([self.X, self.Y], cost, updates=self.updates)
52 self._cost = theano.function([self.X, self.Y], cost)
53 self._predict = theano.function([self.X], self.y_te)

/home/naeemul/anaconda/lib/python2.7/site-packages/theano/compile/function.pyc in function(inputs, outputs, mode, updates, givens, no_default_updates, accept_inplace, name, rebuild_strict, allow_input_downcast, profile, on_unused_input)
221 allow_input_downcast=allow_input_downcast,
222 on_unused_input=on_unused_input,
--> 223 profile=profile)
224 # We need to add the flag check_aliased inputs if we have any mutable or
225 # borrowed used defined inputs

/home/naeemul/anaconda/lib/python2.7/site-packages/theano/compile/pfunc.pyc in pfunc(params, outputs, mode, updates, givens, no_default_updates, accept_inplace, name, rebuild_strict, allow_input_downcast, profile, on_unused_input)
510 return orig_function(inputs, cloned_outputs, mode,
511 accept_inplace=accept_inplace, name=name, profile=profile,
--> 512 on_unused_input=on_unused_input)
513
514

/home/naeemul/anaconda/lib/python2.7/site-packages/theano/compile/function_module.pyc in orig_function(inputs, outputs, mode, accept_inplace, name, profile, on_unused_input)
1310 profile=profile,
1311 on_unused_input=on_unused_input).create(
-> 1312 defaults)
1313
1314 t2 = time.time()

/home/naeemul/anaconda/lib/python2.7/site-packages/theano/compile/function_module.pyc in create(self, input_storage, trustme)
1179 # Get a function instance
1180 start_linker = time.time()
-> 1181 _fn, _i, _o = self.linker.make_thunk(input_storage=input_storage_lists)
1182 end_linker = time.time()
1183

/home/naeemul/anaconda/lib/python2.7/site-packages/theano/gof/link.pyc in make_thunk(self, profiler, input_storage, output_storage)
432 return self.make_all(profiler=profiler,
433 input_storage=input_storage,
--> 434 output_storage=output_storage)[:3]
435
436 def make_all(self, profiler, input_storage, output_storage):

/home/naeemul/anaconda/lib/python2.7/site-packages/theano/gof/vm.pyc in make_all(self, profiler, input_storage, output_storage)
845 storage_map,
846 compute_map,
--> 847 no_recycling))
848 except Exception, e:
849 e.args = ("The following error happened while"

/home/naeemul/anaconda/lib/python2.7/site-packages/theano/gof/op.pyc in make_thunk(self, node, storage_map, compute_map, no_recycling)
604 logger.debug('Trying CLinker.make_thunk')
605 outputs = cl.make_thunk(input_storage=node_input_storage,
--> 606 output_storage=node_output_storage)
607 fill_storage, node_input_filters, node_output_filters = outputs
608

/home/naeemul/anaconda/lib/python2.7/site-packages/theano/gof/cc.pyc in make_thunk(self, input_storage, output_storage, keep_lock)
946 cthunk, in_storage, out_storage, error_storage = self.compile(
947 input_storage, output_storage,
--> 948 keep_lock=keep_lock)
949
950 res = _CThunk(cthunk, init_tasks, tasks, error_storage)

/home/naeemul/anaconda/lib/python2.7/site-packages/theano/gof/cc.pyc in compile(self, input_storage, output_storage, keep_lock)
889 input_storage,
890 output_storage,
--> 891 keep_lock=keep_lock)
892 return (thunk,
893 [link.Container(input, storage) for input, storage in

/home/naeemul/anaconda/lib/python2.7/site-packages/theano/gof/cc.pyc in cthunk_factory(self, error_storage, in_storage, out_storage, keep_lock)
1320 else:
1321 module = get_module_cache().module_from_key(
-> 1322 key=key, fn=self.compile_cmodule_by_step, keep_lock=keep_lock)
1323
1324 vars = self.inputs + self.outputs + self.orphans

/home/naeemul/anaconda/lib/python2.7/site-packages/theano/gof/cmodule.pyc in module_from_key(self, key, fn, keep_lock, key_data)
994 # The module should be returned by the last
995 # step of the compilation.
--> 996 module = next(compile_steps)
997 except StopIteration:
998 break

/home/naeemul/anaconda/lib/python2.7/site-packages/theano/gof/cc.pyc in compile_cmodule_by_step(self, location)
1235 lib_dirs=self.lib_dirs(),
1236 libs=libs,
-> 1237 preargs=preargs)
1238 except Exception, e:
1239 e.args += (str(self.fgraph),)

/home/naeemul/anaconda/lib/python2.7/site-packages/theano/gof/cmodule.pyc in compile_str(module_name, src_code, location, include_dirs, lib_dirs, libs, preargs, py_module)
1969 # difficult to read.
1970 raise Exception('Compilation failed (return status=%s): %s' %
-> 1971 (status, compile_stderr.replace('\n', '. ')))
1972 elif config.cmodule.compilation_warning and compile_stderr:
1973 # Print errors just below the command line.

Exception: ('The following error happened while compiling the node', Dot22(Reshape{2}.0, Reshape{2}.0), '\n', 'Compilation failed (return status=1): /usr/bin/ld: cannot find -lf77blas. /usr/bin/ld: cannot find -lcblas. /usr/bin/ld: cannot find -latlas. collect2: error: ld returned 1 exit status. ', '[Dot22(<TensorType(float64, matrix)>, <TensorType(float64, matrix)>)]')

[Newmu]

This is related to improper configuration/installation of theano. An example of a correct way to install theano is here http://deeplearning.net/software/theano/install_ubuntu.html

More specifically, it looks like you BLAS is improperly configured/linked - the openblas example in the above link should help with setting up a proper BLAS.

Closing as this is not related to Passage but is instead a system setup issue with other libraries.