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Created June 11, 2013 12:00
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gistfile1.txt
.../Users/bayerj/devel/Theano/theano/compile/debugmode.py:1610: UserWarning: FunctionGraph.nodes is deprecated, it has been renamed 'apply_nodes'
e.toposort = lambda: e.nodes # WARNING: STOCHASTIC ORDER
...........S........................K............../Users/bayerj/devel/Theano/theano/compile/tests/test_inplace_opt_for_value.py:170: UserWarning: theano modules are deprecated and will be removed in release 0.7
super(ExampleRNN, self).__init__()
.............................................................................................WARNING (theano.gof.cmodule): Cache leak due to unpickle-able key data set([(((1,), (10, '1.8.0.dev-dff8c94'), (10, '1.8.0.dev-dff8c94')), ('CLinker.cmodule_key', ('-O3', '-Wno-unused-label', '-Wno-unused-variable', '-Wno-write-strings', '-fno-math-errno'), (), (), 'NPY_ABI_VERSION=0x1000009', 'c_compiler_str=g++ 4.2.1', 'md5:b9113ad2b1dcb7629164b394f0809469', (<theano.gof.tests.test_compute_test_value.IncOneC object at 0x109c0cb10>, ((Scalar(int32), ((-1, 0), False)),), (1, (False,)))))])
............................................................................./Users/bayerj/devel/Theano/theano/gof/tests/test_opt.py:406: UserWarning: FunctionGraph.nodes is deprecated, it has been renamed 'apply_nodes'
max_use_ratio = 1. / len(g.nodes)) # each opt can only be applied once
.....................................SS../Users/bayerj/devel/Theano/theano/misc/pycuda_init.py:34: UserWarning: PyCUDA import failed in theano.misc.pycuda_init
warnings.warn("PyCUDA import failed in theano.misc.pycuda_init")
SSSSSSSSSSSS.SSSS............................................KK...................S00001 #include <Python.h>
00002 #include <iostream>
00003 #include <numpy/arrayobject.h>
00004 #include <math.h>
00005 #include <numpy/arrayscalars.h>
00006 //////////////////////
00007 //// Support Code
00008 //////////////////////
00009
00010
00011 struct __struct_compiled_op_79c73b3e175b1d9cb29b3031285ce238 {
00012 PyObject* __ERROR;
00013
00014 PyObject* storage_V3;
00015 PyObject* storage_V5;
00016 PyObject* storage_V1;
00017
00018
00019 __struct_compiled_op_79c73b3e175b1d9cb29b3031285ce238() {}
00020 ~__struct_compiled_op_79c73b3e175b1d9cb29b3031285ce238(void) {
00021 cleanup();
00022 }
00023
00024 int init(PyObject* __ERROR, PyObject* storage_V3, PyObject* storage_V5, PyObject* storage_V1) {
00025 Py_XINCREF(storage_V3);
00026 Py_XINCREF(storage_V5);
00027 Py_XINCREF(storage_V1);
00028 this->storage_V3 = storage_V3;
00029 this->storage_V5 = storage_V5;
00030 this->storage_V1 = storage_V1;
00031 int __failure = 0;
00032
00033 {
00034
00035 {
00036
00037 {
00038
00039 this->__ERROR = __ERROR;
00040 return 0;
00041 __label_5:
00042
00043 double __DUMMY_5;
00044
00045 }
00046 __label_3:
00047
00048 double __DUMMY_3;
00049
00050 }
00051 __label_1:
00052
00053 double __DUMMY_1;
00054
00055 }
00056
00057 Py_XDECREF(this->storage_V3);
00058 Py_XDECREF(this->storage_V5);
00059 Py_XDECREF(this->storage_V1);
00060
00061 if (__failure) {
00062 // When there is a failure, this code puts the exception
00063 // in __ERROR.
00064 PyObject* err_type = NULL;
00065 PyObject* err_msg = NULL;
00066 PyObject* err_traceback = NULL;
00067 PyErr_Fetch(&err_type, &err_msg, &err_traceback);
00068 if (!err_type) {err_type = Py_None;Py_INCREF(Py_None);}
00069 if (!err_msg) {err_msg = Py_None; Py_INCREF(Py_None);}
00070 if (!err_traceback) {err_traceback = Py_None; Py_INCREF(Py_None);}
00071 PyObject* old_err_type = PyList_GET_ITEM(__ERROR, 0);
00072 PyObject* old_err_msg = PyList_GET_ITEM(__ERROR, 1);
00073 PyObject* old_err_traceback = PyList_GET_ITEM(__ERROR, 2);
00074 PyList_SET_ITEM(__ERROR, 0, err_type);
00075 PyList_SET_ITEM(__ERROR, 1, err_msg);
00076 PyList_SET_ITEM(__ERROR, 2, err_traceback);
00077 {Py_XDECREF(old_err_type);}
00078 {Py_XDECREF(old_err_msg);}
00079 {Py_XDECREF(old_err_traceback);}
00080 }
00081 // The failure code is returned to index what code block failed.
00082 return __failure;
00083
00084 }
00085 void cleanup(void) {
00086 __label_1:
00087
00088 double __DUMMY_1;
00089 __label_3:
00090
00091 double __DUMMY_3;
00092 __label_5:
00093
00094 double __DUMMY_5;
00095
00096 Py_XDECREF(this->storage_V3);
00097 Py_XDECREF(this->storage_V5);
00098 Py_XDECREF(this->storage_V1);
00099 }
00100 int run(void) {
00101 int __failure = 0;
00102
00103 PyObject* py_V1;
00104
00105 PyArrayObject* V1;
00106 int type_num_V1;
00107 typedef npy_float64 dtype_V1;
00108
00109 PyObject* py_V3;
00110
00111 PyArrayObject* V3;
00112 int type_num_V3;
00113 typedef npy_float64 dtype_V3;
00114
00115 PyObject* py_V5;
00116
00117 PyArrayObject* V5;
00118 int type_num_V5;
00119 typedef npy_int64 dtype_V5;
00120
00121 {
00122
00123 py_V1 = PyList_GET_ITEM(storage_V1, 0);
00124 {Py_XINCREF(py_V1);}
00125
00126 if (py_V1 == Py_None)
00127 {
00128
00129 V1 = NULL;
00130 type_num_V1 = NPY_FLOAT64;
00131
00132 }
00133 else
00134 {
00135
00136 V1 = NULL;
00137 if (py_V1 == Py_None) {
00138 // We can either fail here or set V1 to NULL and rely on Ops
00139 // using tensors to handle the NULL case, but if they fail to do so
00140 // they'll end up with nasty segfaults, so this is public service.
00141 PyErr_SetString(PyExc_ValueError, "expected an ndarray, not None");
00142 {__failure = 2; goto __label_2;}
00143 }
00144 if (!PyArray_Check(py_V1)) {
00145 PyErr_SetString(PyExc_ValueError, "expected an ndarray");
00146 {__failure = 2; goto __label_2;}
00147 }
00148 // We expect NPY_FLOAT64
00149 type_num_V1 = ((PyArrayObject*)py_V1)->descr->type_num;
00150 if (!PyArray_ISALIGNED(py_V1)) {
00151 PyErr_Format(PyExc_NotImplementedError,
00152 "expected an aligned array of type %d "
00153 "(NPY_FLOAT64), got non-aligned array of type %d",
00154 NPY_FLOAT64, type_num_V1);
00155 {__failure = 2; goto __label_2;}
00156 }
00157 // This is a TypeError to be consistent with DEBUG_MODE
00158 // Note: DEBUG_MODE also tells the name of the container
00159 if (type_num_V1 != NPY_FLOAT64) {
00160 PyErr_Format(PyExc_TypeError,
00161 "expected type_num %d (NPY_FLOAT64) got %d",
00162 NPY_FLOAT64, type_num_V1);
00163 {__failure = 2; goto __label_2;}
00164 }
00165 V1 = (PyArrayObject*)(py_V1);
00166 Py_XINCREF(V1);
00167
00168 }
00169
00170 {
00171
00172 py_V3 = PyList_GET_ITEM(storage_V3, 0);
00173 {Py_XINCREF(py_V3);}
00174
00175 V3 = NULL;
00176 if (py_V3 == Py_None) {
00177 // We can either fail here or set V3 to NULL and rely on Ops
00178 // using tensors to handle the NULL case, but if they fail to do so
00179 // they'll end up with nasty segfaults, so this is public service.
00180 PyErr_SetString(PyExc_ValueError, "expected an ndarray, not None");
00181 {__failure = 4; goto __label_4;}
00182 }
00183 if (!PyArray_Check(py_V3)) {
00184 PyErr_SetString(PyExc_ValueError, "expected an ndarray");
00185 {__failure = 4; goto __label_4;}
00186 }
00187 // We expect NPY_FLOAT64
00188 type_num_V3 = ((PyArrayObject*)py_V3)->descr->type_num;
00189 if (!PyArray_ISALIGNED(py_V3)) {
00190 PyErr_Format(PyExc_NotImplementedError,
00191 "expected an aligned array of type %d "
00192 "(NPY_FLOAT64), got non-aligned array of type %d",
00193 NPY_FLOAT64, type_num_V3);
00194 {__failure = 4; goto __label_4;}
00195 }
00196 // This is a TypeError to be consistent with DEBUG_MODE
00197 // Note: DEBUG_MODE also tells the name of the container
00198 if (type_num_V3 != NPY_FLOAT64) {
00199 PyErr_Format(PyExc_TypeError,
00200 "expected type_num %d (NPY_FLOAT64) got %d",
00201 NPY_FLOAT64, type_num_V3);
00202 {__failure = 4; goto __label_4;}
00203 }
00204 V3 = (PyArrayObject*)(py_V3);
00205 Py_XINCREF(V3);
00206
00207 {
00208
00209 py_V5 = PyList_GET_ITEM(storage_V5, 0);
00210 {Py_XINCREF(py_V5);}
00211
00212 V5 = NULL;
00213 if (py_V5 == Py_None) {
00214 // We can either fail here or set V5 to NULL and rely on Ops
00215 // using tensors to handle the NULL case, but if they fail to do so
00216 // they'll end up with nasty segfaults, so this is public service.
00217 PyErr_SetString(PyExc_ValueError, "expected an ndarray, not None");
00218 {__failure = 6; goto __label_6;}
00219 }
00220 if (!PyArray_Check(py_V5)) {
00221 PyErr_SetString(PyExc_ValueError, "expected an ndarray");
00222 {__failure = 6; goto __label_6;}
00223 }
00224 // We expect NPY_INT64
00225 type_num_V5 = ((PyArrayObject*)py_V5)->descr->type_num;
00226 if (!PyArray_ISALIGNED(py_V5)) {
00227 PyErr_Format(PyExc_NotImplementedError,
00228 "expected an aligned array of type %d "
00229 "(NPY_INT64), got non-aligned array of type %d",
00230 NPY_INT64, type_num_V5);
00231 {__failure = 6; goto __label_6;}
00232 }
00233 // This is a TypeError to be consistent with DEBUG_MODE
00234 // Note: DEBUG_MODE also tells the name of the container
00235 if (type_num_V5 != NPY_INT64) {
00236 PyErr_Format(PyExc_TypeError,
00237 "expected type_num %d (NPY_INT64) got %d",
00238 NPY_INT64, type_num_V5);
00239 {__failure = 6; goto __label_6;}
00240 }
00241 V5 = (PyArrayObject*)(py_V5);
00242 Py_XINCREF(V5);
00243
00244 {
00245
00246 assert (PyArray_NDIM(V5) == 1);
00247 npy_intp new_dims[4];
00248 PyArray_Dims newshape;
00249 newshape.ptr = new_dims;
00250 newshape.len = 4;
00251 for (int ii = 0; ii < 4; ++ii)
00252 {
00253 // -- We do not want an explicit cast here. the shp can be any
00254 // -- int* dtype. The compiler will explicitly upcast it, but
00255 // -- will err if this will downcast. This could happen if the
00256 // -- user pass an int64 dtype, but npy_intp endup being int32.
00257 new_dims[ii] = ((dtype_V5*)(
00258 PyArray_DATA(V5) + ii * PyArray_STRIDES(V5)[0]))[0];
00259 }
00260 Py_XDECREF(V1);
00261 V1 = (PyArrayObject *) PyArray_Newshape(V3, &newshape,
00262 PyArray_CORDER);
00263 if (!V1)
00264 {
00265 PyErr_Format(PyExc_ValueError,
00266 "Could not reshape array.");
00267 {__failure = 7; goto __label_7;};
00268 }
00269 __label_7:
00270
00271 double __DUMMY_7;
00272
00273 }
00274 __label_6:
00275
00276 if (V5) {
00277 Py_XDECREF(V5);
00278 }
00279
00280 {Py_XDECREF(py_V5);}
00281
00282 double __DUMMY_6;
00283
00284 }
00285 __label_4:
00286
00287 if (V3) {
00288 Py_XDECREF(V3);
00289 }
00290
00291 {Py_XDECREF(py_V3);}
00292
00293 double __DUMMY_4;
00294
00295 }
00296 __label_2:
00297
00298 if (!__failure) {
00299
00300 {Py_XDECREF(py_V1);}
00301 if (!V1) {
00302 Py_INCREF(Py_None);
00303 py_V1 = Py_None;
00304 }
00305 else if ((void*)py_V1 != (void*)V1) {
00306 py_V1 = (PyObject*)V1;
00307 }
00308 {Py_XINCREF(py_V1);}
00309
00310 PyObject* old = PyList_GET_ITEM(storage_V1, 0);
00311 {Py_XINCREF(py_V1);}
00312 PyList_SET_ITEM(storage_V1, 0, py_V1);
00313 {Py_XDECREF(old);}
00314 }
00315
00316 if (V1) {
00317 Py_XDECREF(V1);
00318 }
00319
00320 {Py_XDECREF(py_V1);}
00321
00322 double __DUMMY_2;
00323
00324 }
00325
00326
00327 if (__failure) {
00328 // When there is a failure, this code puts the exception
00329 // in __ERROR.
00330 PyObject* err_type = NULL;
00331 PyObject* err_msg = NULL;
00332 PyObject* err_traceback = NULL;
00333 PyErr_Fetch(&err_type, &err_msg, &err_traceback);
00334 if (!err_type) {err_type = Py_None;Py_INCREF(Py_None);}
00335 if (!err_msg) {err_msg = Py_None; Py_INCREF(Py_None);}
00336 if (!err_traceback) {err_traceback = Py_None; Py_INCREF(Py_None);}
00337 PyObject* old_err_type = PyList_GET_ITEM(__ERROR, 0);
00338 PyObject* old_err_msg = PyList_GET_ITEM(__ERROR, 1);
00339 PyObject* old_err_traceback = PyList_GET_ITEM(__ERROR, 2);
00340 PyList_SET_ITEM(__ERROR, 0, err_type);
00341 PyList_SET_ITEM(__ERROR, 1, err_msg);
00342 PyList_SET_ITEM(__ERROR, 2, err_traceback);
00343 {Py_XDECREF(old_err_type);}
00344 {Py_XDECREF(old_err_msg);}
00345 {Py_XDECREF(old_err_traceback);}
00346 }
00347 // The failure code is returned to index what code block failed.
00348 return __failure;
00349
00350 }
00351 };
00352
00353
00354 int __struct_compiled_op_79c73b3e175b1d9cb29b3031285ce238_executor(__struct_compiled_op_79c73b3e175b1d9cb29b3031285ce238* self) {
00355 return self->run();
00356 }
00357
00358 void __struct_compiled_op_79c73b3e175b1d9cb29b3031285ce238_destructor(void* executor, void* self) {
00359 //printf("doing cleanup\n");
00360 //fflush(stdout);
00361 // ((__struct_compiled_op_79c73b3e175b1d9cb29b3031285ce238*)self)->cleanup();
00362 // free(self);
00363 delete ((__struct_compiled_op_79c73b3e175b1d9cb29b3031285ce238*)self);
00364 //printf("done cleanup\n");
00365 //fflush(stdout);
00366 }
00367
00368 //////////////////////
00369 //// Functions
00370 //////////////////////
00371 static PyObject * instantiate(PyObject * self, PyObject *argtuple) {
00372 assert(PyTuple_Check(argtuple));
00373 if (4 != PyTuple_Size(argtuple)){
00374 PyErr_Format(PyExc_TypeError, "Wrong number of arguments, expected 4, got %i", (int)PyTuple_Size(argtuple));
00375 return NULL;
00376 }
00377 __struct_compiled_op_79c73b3e175b1d9cb29b3031285ce238* struct_ptr = new __struct_compiled_op_79c73b3e175b1d9cb29b3031285ce238();
00378 struct_ptr->init( PyTuple_GET_ITEM(argtuple, 0),PyTuple_GET_ITEM(argtuple, 1),PyTuple_GET_ITEM(argtuple, 2),PyTuple_GET_ITEM(argtuple, 3) );
00379 PyObject* thunk = PyCObject_FromVoidPtrAndDesc((void*)(&__struct_compiled_op_79c73b3e175b1d9cb29b3031285ce238_executor), struct_ptr, __struct_compiled_op_79c73b3e175b1d9cb29b3031285ce238_destructor);
00380 return thunk; }
00381
00382 //////////////////////
00383 //// Module init
00384 //////////////////////
00385 static PyMethodDef MyMethods[] = {
00386 {"instantiate", instantiate, METH_VARARGS, "undocumented"} ,
00387 {NULL, NULL, 0, NULL}
00388 };
00389 PyMODINIT_FUNC init79c73b3e175b1d9cb29b3031285ce238(void){
00390 import_array();
00391 (void) Py_InitModule("79c73b3e175b1d9cb29b3031285ce238", MyMethods);
00392 }
00393
Problem occurred during compilation with the command line below:
g++ -dynamiclib -g -O3 -Wno-write-strings -Wno-unused-label -Wno-unused-variable -fno-math-errno -fPIC -undefined dynamic_lookup -m64 -I/Library/Python/2.7/site-packages/numpy-1.8.0.dev_dff8c94_20130602-py2.7-macosx-10.8-intel.egg/numpy/core/include -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -o /Users/bayerj/.theano/compiledir_Darwin-12.4.0-x86_64-i386-64bit-i386-2.7.2/tmpdVJ2qq/79c73b3e175b1d9cb29b3031285ce238.so /Users/bayerj/.theano/compiledir_Darwin-12.4.0-x86_64-i386-64bit-i386-2.7.2/tmpdVJ2qq/mod.cpp -L/System/Library/Frameworks/Python.framework/Versions/2.7/lib
E
======================================================================
ERROR: test_grad_ignore_border (theano.sandbox.test_neighbours.T_Images2Neibs)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/Users/bayerj/devel/Theano/theano/sandbox/test_neighbours.py", line 321, in test_grad_ignore_border
eps=0.1)
File "/Users/bayerj/devel/Theano/theano/tests/unittest_tools.py", line 77, in verify_grad
T.verify_grad(op, pt, n_tests, rng, *args, **kwargs)
File "/Users/bayerj/devel/Theano/theano/gradient.py", line 1389, in verify_grad
grad_fn = function(tensor_pt, symbolic_grad)
File "/Users/bayerj/devel/Theano/theano/gradient.py", line 1338, in function
on_unused_input='ignore')
File "/Users/bayerj/devel/Theano/theano/compile/function.py", line 206, in function
profile=profile)
File "/Users/bayerj/devel/Theano/theano/compile/pfunc.py", line 482, in pfunc
on_unused_input=on_unused_input)
File "/Users/bayerj/devel/Theano/theano/compile/function_module.py", line 1427, in orig_function
defaults)
File "/Users/bayerj/devel/Theano/theano/compile/function_module.py", line 1255, in create
_fn, _i, _o = self.linker.make_thunk(input_storage=input_storage_lists)
File "/Users/bayerj/devel/Theano/theano/gof/link.py", line 380, in make_thunk
output_storage = output_storage)[:3]
File "/Users/bayerj/devel/Theano/theano/gof/vm.py", line 796, in make_all
for node in order]
File "/Users/bayerj/devel/Theano/theano/gof/op.py", line 579, in make_thunk
output_storage=node_output_storage)
File "/Users/bayerj/devel/Theano/theano/gof/cc.py", line 911, in make_thunk
keep_lock=keep_lock)
File "/Users/bayerj/devel/Theano/theano/gof/cc.py", line 854, in __compile__
keep_lock=keep_lock)
File "/Users/bayerj/devel/Theano/theano/gof/cc.py", line 1278, in cthunk_factory
key=key, fn=self.compile_cmodule_by_step, keep_lock=keep_lock)
File "/Users/bayerj/devel/Theano/theano/gof/cmodule.py", line 963, in module_from_key
module = compile_steps.next()
File "/Users/bayerj/devel/Theano/theano/gof/cc.py", line 1200, in compile_cmodule_by_step
preargs=preargs)
File "/Users/bayerj/devel/Theano/theano/gof/cmodule.py", line 1617, in compile_str
(status, compile_stderr.replace('\n', '. ')))
Exception: ('Compilation failed (return status=1): In file included from /Library/Python/2.7/site-packages/numpy-1.8.0.dev_dff8c94_20130602-py2.7-macosx-10.8-intel.egg/numpy/core/include/numpy/ndarraytypes.h:1736,. from /Library/Python/2.7/site-packages/numpy-1.8.0.dev_dff8c94_20130602-py2.7-macosx-10.8-intel.egg/numpy/core/include/numpy/ndarrayobject.h:17,. from /Library/Python/2.7/site-packages/numpy-1.8.0.dev_dff8c94_20130602-py2.7-macosx-10.8-intel.egg/numpy/core/include/numpy/arrayobject.h:4,. from /Users/bayerj/.theano/compiledir_Darwin-12.4.0-x86_64-i386-64bit-i386-2.7.2/tmpdVJ2qq/mod.cpp:3:. /Library/Python/2.7/site-packages/numpy-1.8.0.dev_dff8c94_20130602-py2.7-macosx-10.8-intel.egg/numpy/core/include/numpy/npy_deprecated_api.h:11:2: warning: #warning "Using deprecated NumPy API, disable it by #defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION". /Users/bayerj/.theano/compiledir_Darwin-12.4.0-x86_64-i386-64bit-i386-2.7.2/tmpdVJ2qq/mod.cpp: In member function \xe2\x80\x98int __struct_compiled_op_79c73b3e175b1d9cb29b3031285ce238::run()\xe2\x80\x99:. /Users/bayerj/.theano/compiledir_Darwin-12.4.0-x86_64-i386-64bit-i386-2.7.2/tmpdVJ2qq/mod.cpp:258: error: pointer of type \xe2\x80\x98void *\xe2\x80\x99 used in arithmetic. ', '[Reshape{4}(<TensorType(float64, matrix)>, <TensorType(int64, vector)>)]')
-------------------- >> begin captured stdout << ---------------------
===============================
===============================
In file included from /Library/Python/2.7/site-packages/numpy-1.8.0.dev_dff8c94_20130602-py2.7-macosx-10.8-intel.egg/numpy/core/include/numpy/ndarraytypes.h:1736,
from /Library/Python/2.7/site-packages/numpy-1.8.0.dev_dff8c94_20130602-py2.7-macosx-10.8-intel.egg/numpy/core/include/numpy/ndarrayobject.h:17,
from /Library/Python/2.7/site-packages/numpy-1.8.0.dev_dff8c94_20130602-py2.7-macosx-10.8-intel.egg/numpy/core/include/numpy/arrayobject.h:4,
from /Users/bayerj/.theano/compiledir_Darwin-12.4.0-x86_64-i386-64bit-i386-2.7.2/tmpdVJ2qq/mod.cpp:3:
/Library/Python/2.7/site-packages/numpy-1.8.0.dev_dff8c94_20130602-py2.7-macosx-10.8-intel.egg/numpy/core/include/numpy/npy_deprecated_api.h:11:2: warning: #warning "Using deprecated NumPy API, disable it by #defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION"
/Users/bayerj/.theano/compiledir_Darwin-12.4.0-x86_64-i386-64bit-i386-2.7.2/tmpdVJ2qq/mod.cpp: In member function \u2018int __struct_compiled_op_79c73b3e175b1d9cb29b3031285ce238::run()\u2019:
/Users/bayerj/.theano/compiledir_Darwin-12.4.0-x86_64-i386-64bit-i386-2.7.2/tmpdVJ2qq/mod.cpp:258: error: pointer of type \u2018void *\u2019 used in arithmetic
--------------------- >> end captured stdout << ----------------------
----------------------------------------------------------------------
Ran 349 tests in 20.186s
FAILED (KNOWNFAIL=3, SKIP=20, errors=1)
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