Merge pull request #1230 from nouiz/fix_align

.mailmap

@@ -8,6 +8,7 @@
 # # This file is up-to-date if the command git log --format="%aN <%aE>" | sort -u
 # # gives no duplicates.
 
+Rami Al-Rfou' <rmyeid@gmail.com> Rami Al-Rfou <rmyeid@gmail.com>
 <abergeron@gmail.com> <anakha@kami.(none)>
 David Warde-Farley <wardefar@iro.umontreal.ca> David Warde-Farley <dwf@cs.toronto.edu>
 David Warde-Farley <wardefar@iro.umontreal.ca> David Warde Farley <dwf@cs.toronto.edu>

.travis.yml

@@ -23,6 +23,8 @@ env:
 script:
   - export THEANO_FLAGS=warn.ignore_bug_before=all,on_opt_error=raise,on_shape_error=raise
   - python --version
+  - uname -a
+  - free
   - echo $PART
   - theano-nose $PART
 

theano/printing.py

@@ -478,14 +478,15 @@ default_colorCodes = {'GpuFromHost': 'red',
               'Scan': 'yellow',
               'Shape': 'cyan',
               'IfElse': 'magenta',
-              'Elemwise': '#FFAABB',
-              'Subtensor': '#FFAAFF'}
+              'Elemwise': '#FFAABB',  # dark pink
+              'Subtensor': '#FFAAFF',  # purple
+              'Alloc': '#FFAA22'}  # orange
 
 
 def pydotprint(fct, outfile=None,
                compact=True, format='png', with_ids=False,
                high_contrast=True, cond_highlight=None, colorCodes=None,
-               max_label_size=50, scan_graphs=False,
+               max_label_size=70, scan_graphs=False,
                var_with_name_simple=False,
                print_output_file=True,
                assert_nb_all_strings=-1

theano/tensor/basic.py

@@ -1062,23 +1062,24 @@ class TensorType(Type):
         type_num_%(name)s = ((PyArrayObject*)py_%(name)s)->descr->type_num;
         if (!PyArray_ISALIGNED(py_%(name)s)) {
             PyErr_Format(PyExc_NotImplementedError,
-                         "expected an aligned array of type %%d "
-                         "(%(type_num)s), got non-aligned array of type %%d"
-                         " with %%d dimensions, with 3 last dims %%d, %%d, %%d"
-                         " and 3 last strides %%d %%d, %%d.",
-                         %(type_num)s, type_num_%(name)s,
-                         PyArray_NDIM(py_%(name)s),
-                         PyArray_NDIM(py_%(name)s) >= 3 ?
+                         "expected an aligned array of type %%ld "
+                         "(%(type_num)s), got non-aligned array of type %%ld"
+                         " with %%ld dimensions, with 3 last dims %%ld, %%ld, %%ld"
+                         " and 3 last strides %%ld %%ld, %%ld.",
+                         (long int) %(type_num)s,
+                         (long int) type_num_%(name)s,
+                         (long int) PyArray_NDIM(py_%(name)s),
+                         (long int) PyArray_NDIM(py_%(name)s) >= 3 ?
         PyArray_DIMS(py_%(name)s)[PyArray_NDIM(py_%(name)s)-3] : -1,
-                         PyArray_NDIM(py_%(name)s) >= 2 ?
+                         (long int) PyArray_NDIM(py_%(name)s) >= 2 ?
         PyArray_DIMS(py_%(name)s)[PyArray_NDIM(py_%(name)s)-2] : -1,
-                         PyArray_NDIM(py_%(name)s) >= 1 ?
+                         (long int) PyArray_NDIM(py_%(name)s) >= 1 ?
         PyArray_DIMS(py_%(name)s)[PyArray_NDIM(py_%(name)s)-1] : -1,
-                         PyArray_NDIM(py_%(name)s) >= 2 ?
+                         (long int) PyArray_NDIM(py_%(name)s) >= 3 ?
         PyArray_STRIDES(py_%(name)s)[PyArray_NDIM(py_%(name)s)-3] : -1,
-                         PyArray_NDIM(py_%(name)s) >= 3 ?
+                         (long int) PyArray_NDIM(py_%(name)s) >= 2 ?
         PyArray_STRIDES(py_%(name)s)[PyArray_NDIM(py_%(name)s)-2] : -1,
-                         PyArray_NDIM(py_%(name)s) >= 1 ?
+                         (long int) PyArray_NDIM(py_%(name)s) >= 1 ?
         PyArray_STRIDES(py_%(name)s)[PyArray_NDIM(py_%(name)s)-1] : -1
         );
             %(fail)s
@@ -1105,6 +1106,8 @@ class TensorType(Type):
 
     def c_sync(self, name, sub):
         """Override `CLinkerOp.c_sync` """
+        fail = sub['fail']
+        type_num = self.dtype_specs()[2]
         return """
         {Py_XDECREF(py_%(name)s);}
         if (!%(name)s) {
@@ -1114,7 +1117,33 @@ class TensorType(Type):
         else if ((void*)py_%(name)s != (void*)%(name)s) {
             py_%(name)s = (PyObject*)%(name)s;
         }
+
         {Py_XINCREF(py_%(name)s);}
+
+        if (!PyArray_ISALIGNED(py_%(name)s)) {
+            PyErr_Format(PyExc_NotImplementedError,
+                         "c_sync: expected an aligned array of type %%ld "
+                         "(%(type_num)s), got non-aligned array of type %%ld"
+                         " with %%ld dimensions, with 3 last dims %%ld, %%ld, %%ld"
+                         " and 3 last strides %%ld %%ld, %%ld.",
+                         (long int) %(type_num)s,
+                         (long int) type_num_%(name)s,
+                         (long int) PyArray_NDIM(py_%(name)s),
+                         (long int) PyArray_NDIM(py_%(name)s) >= 3 ?
+        PyArray_DIMS(py_%(name)s)[PyArray_NDIM(py_%(name)s)-3] : -1,
+                         (long int) PyArray_NDIM(py_%(name)s) >= 2 ?
+        PyArray_DIMS(py_%(name)s)[PyArray_NDIM(py_%(name)s)-2] : -1,
+                         (long int) PyArray_NDIM(py_%(name)s) >= 1 ?
+        PyArray_DIMS(py_%(name)s)[PyArray_NDIM(py_%(name)s)-1] : -1,
+                         (long int) PyArray_NDIM(py_%(name)s) >= 3 ?
+        PyArray_STRIDES(py_%(name)s)[PyArray_NDIM(py_%(name)s)-3] : -1,
+                         (long int) PyArray_NDIM(py_%(name)s) >= 2 ?
+        PyArray_STRIDES(py_%(name)s)[PyArray_NDIM(py_%(name)s)-2] : -1,
+                         (long int) PyArray_NDIM(py_%(name)s) >= 1 ?
+        PyArray_STRIDES(py_%(name)s)[PyArray_NDIM(py_%(name)s)-1] : -1
+        );
+            %(fail)s
+        }
         """ % locals()
 
     def c_headers(self):
@@ -1134,7 +1163,7 @@ class TensorType(Type):
     def c_code_cache_version(self):
         scalar_version = scal.Scalar(self.dtype).c_code_cache_version()
         if scalar_version:
-            return (7,) + scalar_version
+            return (9,) + scalar_version
         else:
             return ()
 
@@ -6148,6 +6177,8 @@ class Reshape(Op):
         except Exception:
             raise ValueError('Cannot reshape input of shape %s to shape %s' %
                              (x.shape, shp))
+        if not out[0].flags.aligned:
+            raise RuntimeError("numpy.reshape returned a not aligned tensor.")
 
     def connection_pattern(self, node):
         return [[True], [False]]
@@ -6214,7 +6245,7 @@ class Reshape(Op):
             return [tuple(oshape)]
 
     def c_code_cache_version(self):
-        return (2,)
+        return (4,)
 
     def c_code(self, node, name, inputs, outputs, sub):
         if isinstance(node.inputs[0], TensorVariable):
@@ -6247,6 +6278,10 @@ class Reshape(Op):
                              "Could not reshape array.");
                 %(fail)s;
             }
+            if (!PyArray_ISALIGNED(%(z)s)) {
+                PyErr_Format(PyExc_RuntimeError, "PyArray_Newshape returned an object that isn't aligned!");
+                %(fail)s;
+            }
             """ % locals()
         else:
             return Op.c_code(self, node, name, inputs, outputs, sub)
@@ -6795,6 +6830,9 @@ class AdvancedSubtensor1(Op):
     def __eq__(self, other):
         return type(self) == type(other)
 
+    def __str__(self):
+        return self.__class__.__name__
+
     def make_node(self, x, ilist):
         x_ = as_tensor_variable(x)
         ilist_ = as_tensor_variable(ilist)

theano/tensor/elemwise.py

@@ -308,7 +308,8 @@ class DimShuffle(Op):
         for i, o in enumerate(self.new_order):
             if o != 'x':
                 strides_statements += [('strides[' + str(i)
-                     + '] = PyArray_STRIDES(%(basename)s)[' + str(o) + ']')]
+                     + '] = PyArray_DIMS(%(basename)s)[' + str(o)
+                     + '] == 1? 0 : PyArray_STRIDES(%(basename)s)[' + str(o) + ']')]
             else:
                 strides_statements += [('strides[' + str(i) + '] = 0')]