Merge pull request #3288 from abergeron/nouiz_mixed

doc/LICENSE.txt

@@ -9,6 +9,9 @@ All rights reserved.
 Contains code from NumPy, Copyright (c) 2005-2011, NumPy Developers.
 All rights reserved.
 
+Contain CnMeM under the same license with this copyright:
+Copyright (c) 2015, NVIDIA CORPORATION. All rights reserved.
+
 Redistribution and use in source and binary forms, with or without
 modification, are permitted provided that the following conditions are met:
 

doc/index.txt

@@ -21,6 +21,8 @@ Montreal).
 News
 ====
 
+* We added support for :ref:`CuDNN v3 <libdoc_cuda_dnn>`.
+
 * We added support for :attr:`CNMeM <config.lib.cnmem>` to speed up
   the GPU memory allocation.
 

doc/install.txt

@@ -308,6 +308,18 @@ to your ``Theano`` folder and execute the following command:
 You should update frequently, bugs are fixed on a very regular basis.
 
 
+Specific git commit
+~~~~~~~~~~~~~~~~~~~
+
+You can install a specific git commit by using the bleeding edge
+instruction and adding @COMMIT_ID to the pip command like:
+
+.. code-block:: bash
+
+    pip install --upgrade --no-deps git+git://github.com/Theano/Theano.git@07e9332a0932e90c47ed2a70fc3c7f8a55d2aa23
+
+
+
 .. _testing_installation:
 
 Testing your installation

doc/library/config.txt

@@ -705,6 +705,25 @@ import theano and print the config variable, as in:
     Generate a warning when the destroy_map or view_map tell that an op work
     inplace, but the op did not reuse the input for its output.
 
+.. attribute:: config.NanGuardMode.nan_is_error
+
+    Bool value, default: True
+
+    Controls whether NanGuardMode generates an error when it sees a nan.
+
+.. attribute:: config.NanGuardMode.inf_is_error
+
+    Bool value, default: True
+
+    Controls whether NanGuardMode generates an error when it sees an inf.
+
+.. attribute:: config.NanGuardMode.nan_is_error
+
+    Bool value, default: True
+
+    Controls whether NanGuardMode generates an error when it sees a
+    big value (>1e10).
+
 .. attribute:: numpy
 
     This section contains different attributes for configuring numpy's

doc/tutorial/examples.txt

@@ -500,8 +500,8 @@ It will be used repeatedly.
   training_steps = 10000
   
   # Declare Theano symbolic variables
-  x = T.matrix("x")
-  y = T.vector("y")
+  x = T.dmatrix("x")
+  y = T.dvector("y")
   w = theano.shared(rng.randn(feats), name="w")
   b = theano.shared(0., name="b")
   print "Initial model:"

theano/compile/builders.py

@@ -171,11 +171,6 @@ class OpFromGraph(gof.Op):
         return ret
 
     def grad(self, inputs, output_grads):
-        # OpFromGraph doesn't implement a connection_pattern, so for
-        # now we regard all inputs and outputs as connected. This will
-        # compute the right numerical value for the gradients but
-        # could fail to raise the disconnected inputs error in some
-        # cases.
         if hasattr(self, "grad_ops"):
             grad_ops = self.grad_ops
         else:

theano/compile/mode.py

@@ -387,12 +387,17 @@ def get_mode(orig_string):
                 default_mode_class):
             return instanciated_default_mode
 
-    if string in ['Mode', 'ProfileMode', 'DebugMode']:
+    if string in ['Mode', 'ProfileMode', 'DebugMode', 'NanGuardMode']:
         if string == 'DebugMode':
             # need to import later to break circular dependency.
             from .debugmode import DebugMode
             # DebugMode use its own linker.
             ret = DebugMode(optimizer=config.optimizer)
+        elif string == 'NanGuardMode':
+            # need to import later to break circular dependency.
+            from .nanguardmode import NanGuardMode
+            # DebugMode use its own linker.
+            ret = NanGuardMode(True, True, True, optimizer=config.optimizer)
         else:
             # This might be required if the string is 'ProfileMode'
             from .profilemode import ProfileMode  # noqa

theano/compile/nanguardmode.py

-import logging
 import collections
+import logging
+
 import numpy as np
+
 import theano
+from theano.configparser import config, AddConfigVar, BoolParam
 import theano.tensor as T
 import theano.sandbox.cuda as cuda
 from theano.compile import Mode
 
+AddConfigVar('NanGuardMode.nan_is_error',
+             "Default value for nan_is_error",
+             BoolParam(True),
+             in_c_key=False)
+
+AddConfigVar('NanGuardMode.inf_is_error',
+             "Default value for inf_is_error",
+             BoolParam(True),
+             in_c_key=False)
+
+AddConfigVar('NanGuardMode.big_is_error',
+             "Default value for big_is_error",
+             BoolParam(True),
+             in_c_key=False)
+
 
 logger = logging.getLogger("theano.compile.nanguardmode")
 
@@ -110,26 +128,60 @@ class NanGuardMode(Mode):
     big_is_error : bool
         If True, raise an error when a value greater than 1e10 is encountered.
 
+    Note
+    ----
+        We ignore the linker parameter
     """
+    # We currently loose the 3 first params frequently, when calling
+    # mode.including() and variant.
+    def __init__(self, nan_is_error=None, inf_is_error=None, big_is_error=None,
+                 optimizer=None, linker=None):
+        self.provided_optimizer = optimizer
+        cuda_compile_failed = False
+        if nan_is_error is None:
+            nan_is_error = config.NanGuardMode.nan_is_error
+        if inf_is_error is None:
+            inf_is_error = config.NanGuardMode.inf_is_error
+        if big_is_error is None:
+            big_is_error = config.NanGuardMode.big_is_error
+
+        assert nan_is_error or inf_is_error or big_is_error
 
-    def __init__(self, nan_is_error, inf_is_error, big_is_error=True):
         if cuda.cuda_available:
             self.guard_input = cuda.fvector('nan_guard')
             if nan_is_error or inf_is_error:
+                try:
                     self.gpumin = theano.function(
                         [self.guard_input], T.min(self.guard_input),
                         mode='FAST_RUN'
                     )
-            if inf_is_error:
+                except RuntimeError:
+                    # This can happen if cuda is available, but the
+                    # device is in exclusive mode and used by another
+                    # process.
+                    cuda_compile_failed = True
+            if inf_is_error and not cuda_compile_failed:
+                try:
                     self.gpumax = theano.function(
                         [self.guard_input], T.max(self.guard_input),
                         mode='FAST_RUN'
                     )
-            if big_is_error:
+                except RuntimeError:
+                    # This can happen if cuda is available, but the
+                    # device is in exclusive mode and used by another
+                    # process.
+                    cuda_compile_failed = True
+            if big_is_error and not cuda_compile_failed:
+                try:
                     self.gpuabsmax = theano.function(
                         [self.guard_input], T.max(T.abs_(self.guard_input)),
                         mode='FAST_RUN'
                     )
+                except RuntimeError:
+                    # This can happen if cuda is available, but the
+                    # device is in exclusive mode and used by another
+                    # process.
+                    cuda_compile_failed = True
 
         def do_check_on(var, nd, f, is_input):
             """
@@ -154,6 +206,9 @@ class NanGuardMode(Mode):
             if nan_is_error:
                 err = False
                 if cuda.cuda_available and isinstance(var, cuda.CudaNdarray):
+                    if not isinstance(nd.op,
+                                      # It store ints in float container
+                                      theano.sandbox.rng_mrg.GPU_mrg_uniform):
                         err = np.isnan(self.gpumin(var.reshape(var.size)))
                 else:
                     err = contains_nan(var)
@@ -227,4 +282,4 @@ class NanGuardMode(Mode):
         wrap_linker = theano.gof.WrapLinker([theano.gof.OpWiseCLinker()],
                                             nan_check)
         super(NanGuardMode, self).__init__(wrap_linker,
-                                           optimizer=theano.config.optimizer)
+                                           optimizer=self.provided_optimizer)

theano/configdefaults.py

@@ -150,6 +150,7 @@ AddConfigVar(
     'mode',
     "Default compilation mode",
     EnumStr('Mode', 'ProfileMode', 'DebugMode', 'FAST_RUN',
+            'NanGuardMode',
             'FAST_COMPILE', 'PROFILE_MODE', 'DEBUG_MODE'),
     in_c_key=False)
 

theano/gof/optdb.py

@@ -290,6 +290,7 @@ class SequenceDB(DB):
 
     def register(self, name, obj, position, *tags):
         super(SequenceDB, self).register(name, obj, *tags)
+        assert isinstance(position, (int, float))
         self.__position__[name] = position
 
     def query(self, *tags, **kwtags):

theano/gof/tests/test_opt.py

@@ -6,7 +6,6 @@ from theano.gof.opt import *  # noqa
 from theano.gof.fg import FunctionGraph as Env
 from theano.gof.toolbox import *  # noqa
 
-from theano.tensor.opt import Assert
 from theano import tensor as T
 
 

theano/misc/elemwise_openmp_speedup.py

@@ -49,7 +49,12 @@ if __name__ == '__main__':
     else:
         costlySpeed = costlyTimeOpenmp / costlyTime
         costlySpeedstring = "slowdown"
+    print("Timed with vector of %d elements" % options.N)
+    print("Fast op time without openmp %fs with openmp %fs %s %2.2f" % (
+        cheapTime, cheapTimeOpenmp, cheapSpeedstring, cheapSpeed))
 
-    print("Fast op time without openmp %fs with openmp %fs %s %2.2f" % (cheapTime, cheapTimeOpenmp, cheapSpeedstring, cheapSpeed))
+    print("Fast op time without openmp %fs with openmp %fs %s %2.2f" % (
+        cheapTime, cheapTimeOpenmp, cheapSpeedstring, cheapSpeed))
 
-    print("Slow op time without openmp %fs with openmp %fs %s %2.2f" % (costlyTime, costlyTimeOpenmp, costlySpeedstring, costlySpeed))
+    print("Slow op time without openmp %fs with openmp %fs %s %2.2f" % (
+        costlyTime, costlyTimeOpenmp, costlySpeedstring, costlySpeed))

theano/misc/pycuda_example.py

@@ -285,6 +285,11 @@ class PycudaElemwiseSourceModuleMakeThunkOp(Op):
         self.scalar_op = scalar_op
         self.inplace_pattern = inplace_pattern
 
+    # As we have a dict in props, we need to implement __hash__
+    def __hash__(self):
+        return hash(type(self), hash(self.scalar_op),
+                    hash_from_dict(self.inplace_pattern))
+
     def __str__(self):
         if self.name is None:
             if self.inplace_pattern:

theano/sandbox/cuda/elemwise.py

@@ -66,7 +66,7 @@ class NaiveAlgo(object):
     def cache_version(self):
         ver = self.scalar_op.c_code_cache_version()
         if ver:
-            return (17, self.verbose, self.sync, ver)
+            return (18, self.verbose, self.sync, ver)
         else:
             return ver
 
@@ -142,6 +142,8 @@ class NaiveAlgo(object):
 
         # perform the scalar operation on the input and output references
         # TODO: What if the scalar_op needs support_code??
+        for ipos, i in enumerate(node.outputs):
+            print("npy_%s o%d_i;" % (i.dtype, ipos), file=sio)
         task_code = self.scalar_op.c_code(
             Apply(self.scalar_op,
                   [scalar.Scalar(dtype=input.type.dtype).make_variable()
@@ -150,9 +152,11 @@ class NaiveAlgo(object):
                    for output in node.outputs]),
             nodename + '_scalar_',
             get_str_list_logical_scalar(node),
-            ['ii_o%i_data[0]' % ipos for ipos, i in enumerate(node.outputs)],
+            ['o%i_i' % ipos for ipos, i in enumerate(node.outputs)],
             sub=dict(fail='return;'))  # TODO: set a failure code somehow!!!
         print("       ", task_code, file=sio)
+        for ipos, _ in enumerate(node.outputs):
+            print("o%i_data[i] = o%i_i;" % (ipos, ipos), file=sio)
         print("    }", file=sio)
 
         #indent = " "*(4*d+7)
@@ -477,6 +481,8 @@ class NaiveAlgo(object):
         print("    for (int i = idx; i < numEls; i += numThreads) {", file=sio)
         # perform the scalar operation on the input and output references
         # TODO: What if the scalar_op needs support_code??
+        for ipos, i in enumerate(node.outputs):
+            print("npy_%s o%d_i;" % (i.dtype, ipos), file=sio)
         task_code = self.scalar_op.c_code(
                 Apply(self.scalar_op,
                     [scalar.Scalar(dtype=input.type.dtype).make_variable()
@@ -486,9 +492,11 @@ class NaiveAlgo(object):
                 , nodename + '_scalar_'
                 #, ['i%i_data[i]'%ipos for ipos, i in enumerate(node.inputs)]
                 , get_str_list_logical_scalar(node, data_str='i%i_data[i]')
-                , ['o%i_data[i]'%ipos for ipos, i in enumerate(node.outputs)]
+                , ['o%i_i'%ipos for ipos, i in enumerate(node.outputs)]
                 , sub=dict(fail='return;'))  # TODO: set a failure code somehow!!!
         print("       ", task_code, file=sio)
+        for ipos, _ in enumerate(node.outputs):
+            print("o%i_data[i] = o%i_i;" % (ipos, ipos), file=sio)
         print("    }", file=sio)
         print("}", file=sio)
 

theano/sandbox/cuda/opt.py

@@ -279,7 +279,8 @@ def local_gpu_elemwise_0(node):
                     # TODO: change this when fusion makes Elemwise with
                     # multiple outputs
                     gpu_elemwise = new_op(*(gpu_from_host(i)
-                                            for i in node.inputs))
+                                            for i in node.inputs),
+                                          return_list=True)
                 # case 2 - it is still ok if some inputs were upcast to float32
                 elif all([i.type.dtype in upcastable
                           for i in node.inputs]):
@@ -292,18 +293,19 @@ def local_gpu_elemwise_0(node):
 
                         new_inputs = [gpu_from_host(tensor.cast(i, 'float32'))
                                       for i in node.inputs]
-                        gpu_elemwise = new_op(*new_inputs)
+                        gpu_elemwise = new_op(*new_inputs, return_list=True)
                     else:
                         return False
                 else:
                     return False
 
-                gpu_elemwise = split_huge_add_or_mul(gpu_elemwise.owner)
+                gpu_elemwise = split_huge_add_or_mul(gpu_elemwise[0].owner)
                 if not gpu_elemwise:
                     return False
-                if max_inputs_to_GpuElemwise(node) < len(gpu_elemwise.inputs):
+                if (max_inputs_to_GpuElemwise(node) <
+                        len(gpu_elemwise.inputs)):
                     return False
-                return [host_from_gpu(gpu_elemwise.outputs[0])]
+                return [host_from_gpu(out) for out in gpu_elemwise.outputs]
 
 
 @register_opt()
@@ -785,7 +787,7 @@ def local_gpu_careduce(node):
             x, = node.inputs
             # Otherwise, is some corner case, we will try to move it
             # to the GPU later and this cause not wanted user warning.
-            if x.dtype != 'float32':
+            if x.dtype != 'float32' or node.outputs[0].dtype != "float32":
                 return
             replace = False
             if x.owner and isinstance(x.owner.op, HostFromGpu):
@@ -1114,6 +1116,13 @@ def local_gpu_incsubtensor(node):
             incsubt = host_output.owner.op
             x, y = host_output.owner.inputs[0:2]
             coords = host_output.owner.inputs[2:]
+            if x.dtype != "float32":
+                return
+            if y.dtype != "float32":
+                # The IncSubtensor upcast to float32 y, so we do it
+                # explicitly to move it to the GPU.
+                y = y.astype('float32')
+
             return [GpuIncSubtensor(
                 incsubt.idx_list,
                 inplace=incsubt.inplace,
@@ -1124,7 +1133,7 @@ def local_gpu_incsubtensor(node):
     # Incrementing a float32 x results in a float32
     # output even if y is float64, so we can downcast
     # y to put it on GPU
-    if type(node.op) == tensor.IncSubtensor and \
+    elif type(node.op) == tensor.IncSubtensor and \
        node.inputs[0].dtype == "float32":
         x, y = node.inputs[0:2]
         assert isinstance(x.type, tensor.TensorType)

theano/sandbox/cuda/tests/test_opt.py

@@ -599,11 +599,11 @@ def test_local_gpu_elemwise_0():
 
     # Due to optimization order, this composite is created when all
     # the op are on the gpu.
-    f = theano.function([a, b, c], [a + b + c], mode=mode_with_gpu)
+    f = theano.function([a, b, c], a + b + c, mode=mode_with_gpu)
     topo = f.maker.fgraph.toposort()
     assert sum(isinstance(node.op, cuda.GpuElemwise) for node in topo) == 1
     assert sum(isinstance(node.op, tensor.Elemwise) for node in topo) == 1
-    f(a_v, b_v, c_v)
+    utt.assert_allclose(f(a_v, b_v, c_v), a_v + b_v + c_v)
 
     # Now test with the composite already on the cpu before we move it
     # to the gpu
@@ -612,11 +612,46 @@ def test_local_gpu_elemwise_0():
     c_s = theano.scalar.float32()
     out_s = theano.scalar.Composite([a_s, b_s, c_s], [a_s + b_s + c_s])
     out_op = tensor.Elemwise(out_s)
-    f = theano.function([a, b, c], [out_op(a, b, c)], mode=mode_with_gpu)
+    f = theano.function([a, b, c], out_op(a, b, c), mode=mode_with_gpu)
     topo = f.maker.fgraph.toposort()
     assert sum(isinstance(node.op, cuda.GpuElemwise) for node in topo) == 1
     assert sum(isinstance(node.op, tensor.Elemwise) for node in topo) == 1
-    f(a_v, b_v, c_v)
+    utt.assert_allclose(f(a_v, b_v, c_v), a_v + b_v + c_v)
+
+    # Test multiple output
+    a_s = theano.scalar.float32()
+    a = tensor.fmatrix()
+    from theano.scalar.basic import identity
+    out_s = theano.scalar.Composite([a_s, b_s, c_s],
+                                    [identity(a_s), identity(c_s), identity(b_s)])
+    outs_op = tensor.Elemwise(out_s)
+    f = theano.function([a, b, c], outs_op(a, b, c), mode=mode_with_gpu)
+    topo = f.maker.fgraph.toposort()
+    assert sum(isinstance(node.op, cuda.GpuElemwise) for node in topo) == 1
+    assert sum(isinstance(node.op, tensor.Elemwise) for node in topo) == 0
+    out = f(a_v, b_v, c_v)
+    utt.assert_allclose(out[0], a_v)
+    utt.assert_allclose(out[1], c_v)
+    utt.assert_allclose(out[2], b_v)
+
+    # Test multiple output
+    out_s = theano.scalar.Composite([a_s, b_s, c_s], [a_s + b_s, a_s * c_s])
+    outs_op = tensor.Elemwise(out_s)
+    f = theano.function([a, b, c], outs_op(a, b, c), mode=mode_with_gpu)
+    topo = f.maker.fgraph.toposort()
+    assert sum(isinstance(node.op, cuda.GpuElemwise) for node in topo) == 1
+    assert sum(isinstance(node.op, tensor.Elemwise) for node in topo) == 0
+    out = f(a_v, b_v, c_v)
+    utt.assert_allclose(out[0], a_v + b_v)
+    utt.assert_allclose(out[1], a_v * c_v)
+
+    # Test non-contiguous input
+    c = cuda.shared_constructor(c_v)
+    f = theano.function([a, b], outs_op(a[::2], b[::2], c[::2]),
+                        mode=mode_with_gpu)
+    out = f(a_v, b_v)
+    utt.assert_allclose(out[0], a_v[::2] + b_v[::2])
+    utt.assert_allclose(out[1], a_v[::2] * c_v[::2])
 
 
 def test_elemwise_fusion():

theano/sandbox/gpuarray/elemwise.py

@@ -72,6 +72,8 @@ class GpuElemwise(HideC, Elemwise):
         res = Elemwise.make_node(self, *inputs)
         outputs = [GpuArrayType(broadcastable=o.type.broadcastable,
                                 dtype=o.type.dtype)() for o in res.outputs]
+        if len(outputs) > 1:
+            raise NotImplementedError()
         inputs = [as_gpuarray_variable(i) for i in inputs]
         node = Apply(self, inputs, outputs)
 

theano/sandbox/gpuarray/opt.py

@@ -270,7 +270,8 @@ def local_gpu_elemwise(node):
     name = op.name
     if name:
         name = 'Gpu' + name
-
+    if len(node.outputs) > 1:
+        return
     res = GpuElemwise(scal_op, name=name,
                       inplace_pattern=copy.copy(op.inplace_pattern),
                       nfunc_spec=op.nfunc_spec)

theano/sandbox/gpuarray/tests/test_opt.py

@@ -255,3 +255,73 @@ def test_local_gpu_subtensor():
     assert any([type(node.op) is tensor.Subtensor for node in topo])
     assert not any([isinstance(node.op, GpuSubtensor) for node in topo])
     assert any([isinstance(node.op, GpuElemwise) for node in topo])
+
+
+def test_local_gpu_elemwise():
+    """
+    Test local_gpu_elemwise when there is a dtype upcastable to float32
+    """
+    a = tensor.bmatrix()
+    b = tensor.fmatrix()
+    c = tensor.fmatrix()
+
+    a_v = (numpy.random.rand(4, 5) * 10).astype("int8")
+    b_v = (numpy.random.rand(4, 5) * 10).astype("float32")
+    c_v = (numpy.random.rand(4, 5) * 10).astype("float32")
+
+    # Due to optimization order, this composite is created when all
+    # the op are on the gpu.
+    f = theano.function([a, b, c], a + b + c, mode=mode_with_gpu)
+    topo = f.maker.fgraph.toposort()
+    assert sum(isinstance(node.op, GpuElemwise) for node in topo) == 1
+    assert sum(type(node.op) == tensor.Elemwise for node in topo) == 0
+    utt.assert_allclose(f(a_v, b_v, c_v), a_v + b_v + c_v)
+
+    # Now test with the composite already on the cpu before we move it
+    # to the gpu
+    a_s = theano.scalar.int8()
+    b_s = theano.scalar.float32()
+    c_s = theano.scalar.float32()
+    out_s = theano.scalar.Composite([a_s, b_s, c_s], [a_s + b_s + c_s])
+    out_op = tensor.Elemwise(out_s)
+    f = theano.function([a, b, c], out_op(a, b, c), mode=mode_with_gpu)
+    topo = f.maker.fgraph.toposort()
+    assert sum(isinstance(node.op, GpuElemwise) for node in topo) == 1
+    assert sum(type(node.op) == tensor.Elemwise for node in topo) == 0
+    utt.assert_allclose(f(a_v, b_v, c_v), a_v + b_v + c_v)
+
+    return  # Not yet implemeted
+    # Test multiple output
+    a_s = theano.scalar.float32()
+    a = tensor.fmatrix()
+    from theano.scalar.basic import identity
+    out_s = theano.scalar.Composite([a_s, b_s, c_s],
+                                    [identity(a_s), identity(c_s), identity(b_s)])
+    outs_op = tensor.Elemwise(out_s)
+    f = theano.function([a, b, c], outs_op(a, b, c), mode=mode_with_gpu)
+    topo = f.maker.fgraph.toposort()
+    assert sum(isinstance(node.op, GpuElemwise) for node in topo) == 1
+    assert sum(type(node.op) == tensor.Elemwise for node in topo) == 0
+    out = f(a_v, b_v, c_v)
+    utt.assert_allclose(out[0], a_v)
+    utt.assert_allclose(out[1], c_v)
+    utt.assert_allclose(out[2], b_v)
+
+    # Test multiple output
+    out_s = theano.scalar.Composite([a_s, b_s, c_s], [a_s + b_s, a_s * b_s])
+    outs_op = tensor.Elemwise(out_s)
+    f = theano.function([a, b, c], outs_op(a, b, c), mode=mode_with_gpu)
+    topo = f.maker.fgraph.toposort()
+    assert sum(isinstance(node.op, GpuElemwise) for node in topo) == 1
+    assert sum(type(node.op) == tensor.Elemwise for node in topo) == 0
+    out = f(a_v, b_v, c_v)
+    utt.assert_allclose(out[0], a_v + b_v)
+    utt.assert_allclose(out[1], a_v * c_v)
+
+    # Test non-contiguous input
+    c = cuda.shared_constructor(numpy.asarray(c_v, dtype='float32'))
+    f = theano.function([a, b], outs_op(a[::2], b[::2], c[::2]),
+                        mode=mode_with_gpu)
+    out = f(a_v, b_v)
+    utt.assert_allclose(out[0], a_v[::2] + b_v[::2])
+    utt.assert_allclose(out[1], a_v[::2] * c_v[::2])

theano/scalar/basic.py

@@ -724,7 +724,7 @@ def same_out_float_only(type):
 
 class transfer_type(gof.utils.object2):
     def __init__(self, *transfer):
-        assert all(type(x) == int for x in transfer)
+        assert all(type(x) in [int, str] or x is None for x in transfer)
         self.transfer = transfer
 
     def __str__(self):
@@ -736,6 +736,8 @@ class transfer_type(gof.utils.object2):
         for i in self.transfer:
             if i is None:
                 retval += [upcast]
+            elif isinstance(i, str):
+                retval += [i]
             else:
                 retval += [types[i]]
         return retval
@@ -3410,7 +3412,10 @@ class Composite(ScalarOp):
                 return lambda inputs: r.data
             node = r.owner
             producers = [compose_impl(input) for input in node.inputs]
-            return lambda inputs: node.op.impl(*[p(inputs) for p in producers])
+
+            def f(inputs):
+                return node.op.impl(*[p(inputs) for p in producers])
+            return f
         self._impls = [compose_impl(r) for r in self.fgraph.outputs]
 
     def init_name(self):
@@ -3467,6 +3472,8 @@ class Composite(ScalarOp):
         # that will flatten Composite. We don't need to do this
         # recusively, as the way the fusion optimizer work, we have
         # only 1 new Composite each time at the output.
+        for i in inputs:
+            assert i not in outputs  # This isn't supported, use identity
         if len(outputs) > 1 or not any([isinstance(var.owner.op, Composite)
                                         for var in outputs]):
             # No inner Composite
@@ -3538,8 +3545,11 @@ class Composite(ScalarOp):
     def impl(self, *inputs):
         output_storage = [[None] for i in xrange(self.nout)]
         self.perform(None, inputs, output_storage)
-        return utils.to_return_values([storage[0] for storage in
+        ret = utils.to_return_values([storage[0] for storage in
                                       output_storage])
+        if self.nout > 1:
+            ret = tuple(ret)
+        return ret
 
     def grad(self, inputs, output_grads):
         raise NotImplementedError("grad is not implemented for Composite")

theano/tensor/opt.py

@@ -296,6 +296,7 @@ def inplace_elemwise_optimizer_op(OP):
             # gpuarray GpuElemwise inherit from Elemwise
             if not type(op) == OP:
                 continue
+
             baseline = op.inplace_pattern
             protected_inputs = [
                 f.protected for f in node.fgraph._features if
@@ -331,8 +332,8 @@ def inplace_elemwise_optimizer_op(OP):
                         if hasattr(op.scalar_op, "make_new_inplace"):
                             new_scal = op.scalar_op.make_new_inplace(
                                 scalar.transfer_type(
-                                    *[inplace_pattern.get(i, None)
-                                      for i in xrange(len(node.outputs))]))
+                                    *[inplace_pattern.get(i, o.dtype)
+                                      for i, o in enumerate(node.outputs)]))
                         else:
                             new_scal = op.scalar_op.__class__(
                                 scalar.transfer_type(
@@ -1507,7 +1508,11 @@ def local_subtensor_make_vector(node):
                     # Python 2.4 wants to index only with Python integers
                     v = int(v)
                 # We don't need to copy over any stack traces here
-                return [x.owner.inputs[v]]
+                try:
+                    ret = [x.owner.inputs[v]]
+                except IndexError:
+                    raise NotScalarConstantError("Bad user graph!")
+                return ret
             except NotScalarConstantError:
                 pass
         elif idx.ndim == 1 and isinstance(idx, T.Constant):
@@ -5867,15 +5872,17 @@ def local_elemwise_fusion_op(OP, max_input_fct=lambda node: 32,
                             tmp_s_input.append(tmp)
                             tmp_input.append(ii)
                             tmp_scalar.append(tmp_s_input[-1])
-                    s_op = i.owner.op.scalar_op(*tmp_s_input)
+                    s_op = i.owner.op.scalar_op(*tmp_s_input,
+                                                return_list=True)
 
                     # if the scalar_op don't have a c implementation,
                     # we skip its fusion to allow the fusion of the
                     # other ops.
-                    i.owner.op.scalar_op.c_code(s_op.owner,
+                    i.owner.op.scalar_op.c_code(s_op[0].owner,
                                                 "test_presence_of_c_code",
                                                 ["x" for x in i.owner.inputs],
-                                                "z", {})
+                                                ["z" for z in i.owner.outputs],
+                                                {})
                 except MethodNotDefined:
                     catch = True
                 except NotImplementedError:
@@ -5906,7 +5913,7 @@ def local_elemwise_fusion_op(OP, max_input_fct=lambda node: 32,
                 new_nb_input = new_nb_input_
                 inputs.extend(tmp_input)
                 s_inputs.extend(tmp_scalar)
-                s_g.append(s_op)
+                s_g.extend(s_op)
             else:
                 # We must support the case where the same variable appear many
                 # time in the inputs
@@ -5934,25 +5941,26 @@ def local_elemwise_fusion_op(OP, max_input_fct=lambda node: 32,
 fusion optimization. We skip this optimization. You can ignore this message,
 your code will run correctly, but may be slower.""")
 
-        s_new_out = node.op.scalar_op(*s_g)
+        s_new_out = node.op.scalar_op(*s_g, return_list=True)
         try:
-            s_new_out.owner.op.c_code(s_new_out.owner,
+            s_new_out[0].owner.op.c_code(s_new_out[0].owner,
                                          "test_presence_of_c_code",
                                          ["x" for x in s_g],
-                                      "z", {})
+                                         ["z" for x in s_new_out], {})
         except MethodNotDefined:
             _logger.info(("%s does not implement the c_code function."
                           " As well as being potentially slow, this disables "
-                          "loop fusion of this op.") % str(s_new_out.owner.op))
+                          "loop fusion of this op.") % str(
+                              s_new_out[0].owner.op))
             return False
         except NotImplementedError:
             _logger.info(("%s does not implement the c_code function. As well"
                           " as being potentially slow, this disables loop"
-                          " fusion of this op.") % str(s_new_out.owner.op))
+                          " fusion of this op.") % str(s_new_out[0].owner.op))
             return False
 
         # create the composite op.
-        C = scalar.Composite(s_inputs, [s_new_out])
+        C = scalar.Composite(s_inputs, s_new_out)
 
         # create the new node.
         # Do not call make_node to have test_value

theano/tensor/tests/test_gc.py

-import sys
 import numpy
 import six.moves.cPickle as pickle
 from six.moves import xrange
@@ -120,4 +119,4 @@ def test_merge_opt_runtime():
     dt = time.time() - t
 
     # it should never take longer than 5 seconds to compile this graph
-    assert dt < 5.0
+    assert dt < 5.0, dt

theano/tests/test_flake8.py

@@ -205,18 +205,6 @@ whitelist_flake8 = [
     "sparse/sandbox/sp.py",
     "gof/unify.py",
     "gof/__init__.py",
-    "gof/tests/test_cmodule.py",
-    "gof/tests/test_destroyhandler.py",
-    "gof/tests/test_opt.py",
-    "gof/tests/test_lazy.py",
-    "gof/tests/test_toolbox.py",
-    "gof/tests/test_link.py",
-    "gof/tests/test_fg.py",
-    "gof/tests/test_sched.py",
-    "gof/tests/test_graph_opt_caching.py",
-    "gof/tests/test_graph.py",
-    "gof/tests/test_cc.py",
-    "gof/tests/test_compute_test_value.py",
     "gof/sandbox/equilibrium.py",
 ]