GRUV
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Published
20 hours ago •
MattVitelli
MattVitelli
Exception: Compilation failed (return status=1)
I am not able to train using any dataset. I always get this error when I run python train.py
Traceback (most recent call last):
File "train.py", line 5, in <module>
import nn_utils.network_utils as network_utils
File "/home/n1amr/GRUV/nn_utils/network_utils.py", line 1, in <module>
from keras.models import Sequential
File "/home/n1amr/.pyenv/versions/env_nn/lib/python2.7/site-packages/keras/models.py", line 3, in <module>
import theano
File "/home/n1amr/.pyenv/versions/env_nn/lib/python2.7/site-packages/theano/__init__.py", line 66, in <module>
from theano.compile import (
File "/home/n1amr/.pyenv/versions/env_nn/lib/python2.7/site-packages/theano/compile/__init__.py", line 10, in <module>
from theano.compile.function_module import *
File "/home/n1amr/.pyenv/versions/env_nn/lib/python2.7/site-packages/theano/compile/function_module.py", line 21, in <module>
import theano.compile.mode
File "/home/n1amr/.pyenv/versions/env_nn/lib/python2.7/site-packages/theano/compile/mode.py", line 10, in <module>
import theano.gof.vm
File "/home/n1amr/.pyenv/versions/env_nn/lib/python2.7/site-packages/theano/gof/vm.py", line 662, in <module>
from . import lazylinker_c
File "/home/n1amr/.pyenv/versions/env_nn/lib/python2.7/site-packages/theano/gof/lazylinker_c.py", line 127, in <module>
preargs=args)
File "/home/n1amr/.pyenv/versions/env_nn/lib/python2.7/site-packages/theano/gof/cmodule.py", line 2316, in compile_str
(status, compile_stderr.replace('\n', '. ')))
Exception: Compilation failed (return status=1): /home/n1amr/.pyenv/versions/2.7.12/lib/libpython2.7.a(posixmodule.o): In function `posix_tmpnam':. /home/n1amr/.pyenv/sources/2.7.12/Python-2.7.12/./Modules/posixmodule.c:7631: warning: the use of `tmpnam_r' is dangerous, better use `mkstemp'. /home/n1amr/.pyenv/versions/2.7.12/lib/libpython2.7.a(posixmodule.o): In function `posix_tempnam':. /home/n1amr/.pyenv/sources/2.7.12/Python-2.7.12/./Modules/posixmodule.c:7578: warning: the use of `tempnam' is dangerous, better use `mkstemp'. /usr/bin/ld: /home/n1amr/.pyenv/versions/2.7.12/lib/libpython2.7.a(classobject.o): relocation R_X86_64_PC32 against symbol `_Py_NotImplementedStruct' can not be used when making a shared object; recompile with -fPIC. /usr/bin/ld: final link failed: Bad value. collect2: error: ld returned 1 exit status.
Complete error message:
00001 #include00002 #include "theano_mod_helper.h" 00003 #include "structmember.h" 00004 #include 00005 00006 #if PY_VERSION_HEX >= 0x03000000 00007 #include "numpy/npy_3kcompat.h" 00008 #define PyCObject_AsVoidPtr NpyCapsule_AsVoidPtr 00009 #define PyCObject_GetDesc NpyCapsule_GetDesc 00010 #define PyCObject_Check NpyCapsule_Check 00011 #endif 00012 00013 #ifndef Py_TYPE 00014 #define Py_TYPE(obj) obj->ob_type 00015 #endif 00016 00017 /** 00018 00019 TODO: 00020 - Check max supported depth of recursion 00021 - CLazyLinker should add context information to errors caught during evaluation. Say what node we were on, add the traceback attached to the node. 00022 - Clear containers of fully-useed intermediate results if allow_gc is 1 00023 - Add timers for profiling 00024 - Add support for profiling space used. 00025 00026 00027 */ 00028 static double pytime(const struct timeval * tv) 00029 { 00030 struct timeval t; 00031 if (!tv) 00032 { 00033 tv = &t; 00034 gettimeofday(&t, NULL); 00035 } 00036 return (double) tv->tv_sec + (double) tv->tv_usec / 1000000.0; 00037 } 00038 00039 /** 00040 Helper routine to convert a PyList of integers to a c array of integers. 00041 */ 00042 static int unpack_list_of_ssize_t(PyObject * pylist, Py_ssize_t **dst, Py_ssize_t *len, 00043 const char* kwname) 00044 { 00045 Py_ssize_t buflen, *buf; 00046 if (!PyList_Check(pylist)) 00047 { 00048 PyErr_Format(PyExc_TypeError, "%s must be list", kwname); 00049 return -1; 00050 } 00051 assert (NULL == *dst); 00052 *len = buflen = PyList_Size(pylist); 00053 *dst = buf = (Py_ssize_t*)calloc(buflen, sizeof(Py_ssize_t)); 00054 assert(buf); 00055 for (int ii = 0; ii owner 00097 int * var_has_owner; // 1 or 0 00098 00099 Py_ssize_t * node_n_inputs; 00100 Py_ssize_t * node_n_outputs; 00101 Py_ssize_t ** node_inputs; 00102 Py_ssize_t ** node_outputs; 00103 Py_ssize_t * node_inputs_outputs_base; // node_inputs and node_outputs point into this 00104 Py_ssize_t * node_n_prereqs; 00105 Py_ssize_t ** node_prereqs; 00106 00107 Py_ssize_t * update_storage; // input cells to update with the last outputs in output_vars 00108 Py_ssize_t n_updates; 00109 00110 void ** thunk_cptr_fn; 00111 void ** thunk_cptr_data; 00112 PyObject * call_times; 00113 PyObject * call_counts; 00114 int do_timing; 00115 int need_update_inputs; 00116 int position_of_error; // -1 for no error, otw the index into `thunks` that failed. 00117 } CLazyLinker; 00118 00119 00120 static void 00121 CLazyLinker_dealloc(PyObject* _self) 00122 { 00123 CLazyLinker* self = (CLazyLinker *) _self; 00124 free(self->thunk_cptr_fn); 00125 free(self->thunk_cptr_data); 00126 00127 free(self->is_lazy); 00128 00129 free(self->update_storage); 00130 00131 if (self->node_n_prereqs) 00132 { 00133 for (int i = 0; i n_applies; ++i) 00134 { 00135 free(self->node_prereqs[i]); 00136 } 00137 } 00138 free(self->node_n_prereqs); 00139 free(self->node_prereqs); 00140 free(self->node_inputs_outputs_base); 00141 free(self->node_n_inputs); 00142 free(self->node_n_outputs); 00143 free(self->node_inputs); 00144 free(self->node_outputs); 00145 00146 if (self->dependencies) 00147 { 00148 for (int i = 0; i n_vars; ++i) 00149 { 00150 free(self->dependencies[i]); 00151 } 00152 free(self->dependencies); 00153 free(self->n_dependencies); 00154 } 00155 00156 free(self->var_owner); 00157 free(self->var_has_owner); 00158 free(self->var_computed); 00159 if (self->var_computed_cells) 00160 { 00161 for (int i = 0; i n_vars; ++i) 00162 { 00163 Py_DECREF(self->var_computed_cells[i]); 00164 Py_DECREF(self->var_value_cells[i]); 00165 } 00166 } 00167 free(self->var_computed_cells); 00168 free(self->var_value_cells); 00169 free(self->output_vars); 00170 00171 Py_XDECREF(self->nodes); 00172 Py_XDECREF(self->thunks); 00173 Py_XDECREF(self->call_times); 00174 Py_XDECREF(self->call_counts); 00175 Py_XDECREF(self->pre_call_clear); 00176 Py_TYPE(self)->tp_free((PyObject*)self); 00177 } 00178 static PyObject * 00179 CLazyLinker_new(PyTypeObject *type, PyObject *args, PyObject *kwds) 00180 { 00181 CLazyLinker *self; 00182 00183 self = (CLazyLinker *)type->tp_alloc(type, 0); 00184 if (self != NULL) { 00185 self->nodes = NULL; 00186 self->thunks = NULL; 00187 self->pre_call_clear = NULL; 00188 00189 self->allow_gc = 1; 00190 self->n_applies = 0; 00191 self->n_vars = 0; 00192 self->var_computed = NULL; 00193 self->var_computed_cells = NULL; 00194 self->var_value_cells = NULL; 00195 self->dependencies = NULL; 00196 self->n_dependencies = NULL; 00197 00198 self->n_output_vars = 0; 00199 self->output_vars = NULL; 00200 00201 self->is_lazy = NULL; 00202 00203 self->var_owner = NULL; 00204 self->var_has_owner = NULL; 00205 00206 self->node_n_inputs = NULL; 00207 self->node_n_outputs = NULL; 00208 self->node_inputs = NULL; 00209 self->node_outputs = NULL; 00210 self->node_inputs_outputs_base = NULL; 00211 self->node_prereqs = NULL; 00212 self->node_n_prereqs = NULL; 00213 00214 self->update_storage = NULL; 00215 self->n_updates = 0; 00216 00217 self->thunk_cptr_data = NULL; 00218 self->thunk_cptr_fn = NULL; 00219 self->call_times = NULL; 00220 self->call_counts = NULL; 00221 self->do_timing = 0; 00222 00223 self->need_update_inputs = 0; 00224 self->position_of_error = -1; 00225 } 00226 return (PyObject *)self; 00227 } 00228 00229 static int 00230 CLazyLinker_init(CLazyLinker *self, PyObject *args, PyObject *kwds) 00231 { 00232 static char *kwlist[] = { 00233 (char*)"nodes", 00234 (char*)"thunks", 00235 (char*)"pre_call_clear", 00236 (char*)"allow_gc", 00237 (char*)"call_counts", 00238 (char*)"call_times", 00239 (char*)"compute_map_list", 00240 (char*)"storage_map_list", 00241 (char*)"base_input_output_list", 00242 (char*)"node_n_inputs", 00243 (char*)"node_n_outputs", 00244 (char*)"node_input_offset", 00245 (char*)"node_output_offset", 00246 (char*)"var_owner", 00247 (char*)"is_lazy_list", 00248 (char*)"output_vars", 00249 (char*)"node_prereqs", 00250 (char*)"node_output_size", 00251 (char*)"update_storage", 00252 (char*)"dependencies", 00253 NULL}; 00254 00255 PyObject *compute_map_list=NULL, 00256 *storage_map_list=NULL, 00257 *base_input_output_list=NULL, 00258 *node_n_inputs=NULL, 00259 *node_n_outputs=NULL, 00260 *node_input_offset=NULL, 00261 *node_output_offset=NULL, 00262 *var_owner=NULL, 00263 *is_lazy=NULL, 00264 *output_vars=NULL, 00265 *node_prereqs=NULL, 00266 *node_output_size=NULL, 00267 *update_storage=NULL, 00268 *dependencies=NULL; 00269 00270 assert(!self->nodes); 00271 if (! PyArg_ParseTupleAndKeywords(args, kwds, "OOOiOOOOOOOOOOOOOOOO", kwlist, 00272 &self->nodes, 00273 &self->thunks, 00274 &self->pre_call_clear, 00275 &self->allow_gc, 00276 &self->call_counts, 00277 &self->call_times, 00278 &compute_map_list, 00279 &storage_map_list, 00280 &base_input_output_list, 00281 &node_n_inputs, 00282 &node_n_outputs, 00283 &node_input_offset, 00284 &node_output_offset, 00285 &var_owner, 00286 &is_lazy, 00287 &output_vars, 00288 &node_prereqs, 00289 &node_output_size, 00290 &update_storage, 00291 &dependencies 00292 )) 00293 return -1; 00294 Py_INCREF(self->nodes); 00295 Py_INCREF(self->thunks); 00296 Py_INCREF(self->pre_call_clear); 00297 Py_INCREF(self->call_counts); 00298 Py_INCREF(self->call_times); 00299 00300 Py_ssize_t n_applies = PyList_Size(self->nodes); 00301 00302 self->n_applies = n_applies; 00303 self->n_vars = PyList_Size(var_owner); 00304 00305 if (PyList_Size(self->thunks) != n_applies) return -1; 00306 if (PyList_Size(self->call_counts) != n_applies) return -1; 00307 if (PyList_Size(self->call_times) != n_applies) return -1; 00308 00309 // allocated and initialize thunk_cptr_data and thunk_cptr_fn 00310 if (n_applies) 00311 { 00312 self->thunk_cptr_data = (void**)calloc(n_applies, sizeof(void*)); 00313 self->thunk_cptr_fn = (void**)calloc(n_applies, sizeof(void*)); 00314 self->is_lazy = (int*)calloc(n_applies, sizeof(int)); 00315 self->node_prereqs = (Py_ssize_t**)calloc(n_applies, sizeof(Py_ssize_t*)); 00316 self->node_n_prereqs = (Py_ssize_t*)calloc(n_applies, sizeof(Py_ssize_t)); 00317 assert(self->node_prereqs); 00318 assert(self->node_n_prereqs); 00319 assert(self->is_lazy); 00320 assert(self->thunk_cptr_fn); 00321 assert(self->thunk_cptr_data); 00322 00323 for (int i = 0; i thunks, i); 00326 //thunk is borrowed 00327 if (PyObject_HasAttrString(thunk, "cthunk")) 00328 { 00329 PyObject * cthunk = PyObject_GetAttrString(thunk, "cthunk"); 00330 //new reference 00331 assert (cthunk && PyCObject_Check(cthunk)); 00332 self->thunk_cptr_fn[i] = PyCObject_AsVoidPtr(cthunk); 00333 self->thunk_cptr_data[i] = PyCObject_GetDesc(cthunk); 00334 Py_DECREF(cthunk); 00335 // cthunk is kept alive by membership in self->thunks 00336 } 00337 00338 PyObject * el_i = PyList_GetItem(is_lazy, i); 00339 self->is_lazy[i] = PyNumber_AsSsize_t(el_i, NULL); 00340 00341 /* now get the prereqs */ 00342 el_i = PyList_GetItem(node_prereqs, i); 00343 assert (PyList_Check(el_i)); 00344 self->node_n_prereqs[i] = PyList_Size(el_i); 00345 if (self->node_n_prereqs[i]) 00346 { 00347 self->node_prereqs[i] = (Py_ssize_t*)malloc( 00348 PyList_Size(el_i)*sizeof(Py_ssize_t)); 00349 for (int j = 0; j node_prereqs[i][j] = N; 00358 } 00359 } 00360 } 00361 } 00362 if (PyList_Check(base_input_output_list)) 00363 { 00364 Py_ssize_t n_inputs_outputs_base = PyList_Size(base_input_output_list); 00365 self->node_inputs_outputs_base = (Py_ssize_t*)calloc(n_inputs_outputs_base,sizeof(Py_ssize_t)); 00366 assert(self->node_inputs_outputs_base); 00367 for (int i = 0; i node_inputs_outputs_base[i] = idx; 00373 } 00374 self->node_n_inputs = (Py_ssize_t*)calloc(n_applies,sizeof(Py_ssize_t)); 00375 assert(self->node_n_inputs); 00376 self->node_n_outputs = (Py_ssize_t*)calloc(n_applies,sizeof(Py_ssize_t)); 00377 assert(self->node_n_outputs); 00378 self->node_inputs = (Py_ssize_t**)calloc(n_applies,sizeof(Py_ssize_t*)); 00379 assert(self->node_inputs); 00380 self->node_outputs = (Py_ssize_t**)calloc(n_applies,sizeof(Py_ssize_t*)); 00381 assert(self->node_outputs); 00382 for (int i = 0; i node_n_inputs[i] = N; 00389 N = PyNumber_AsSsize_t(PyList_GetItem(node_n_outputs, i),PyExc_IndexError); 00390 if (PyErr_Occurred()) return -1; 00391 assert (N node_n_outputs[i] = N; 00393 N = PyNumber_AsSsize_t(PyList_GetItem(node_input_offset, i),PyExc_IndexError); 00394 if (PyErr_Occurred()) return -1; 00395 assert (N node_inputs[i] = &self->node_inputs_outputs_base[N]; 00397 N = PyNumber_AsSsize_t(PyList_GetItem(node_output_offset, i),PyExc_IndexError); 00398 if (PyErr_Occurred()) return -1; 00399 assert (N node_outputs[i] = &self->node_inputs_outputs_base[N]; 00401 } 00402 } 00403 else 00404 { 00405 PyErr_SetString(PyExc_TypeError, "base_input_output_list must be list"); 00406 return -1; 00407 } 00408 00409 // allocation for var_owner 00410 if (PyList_Check(var_owner)) 00411 { 00412 self->var_owner = (Py_ssize_t*)calloc(self->n_vars,sizeof(Py_ssize_t)); 00413 self->var_has_owner = (int*)calloc(self->n_vars,sizeof(int)); 00414 self->var_computed = (int*)calloc(self->n_vars,sizeof(int)); 00415 self->var_computed_cells = (PyObject**)calloc(self->n_vars,sizeof(PyObject*)); 00416 self->var_value_cells = (PyObject**)calloc(self->n_vars,sizeof(PyObject*)); 00417 for (int i = 0; i n_vars; ++i) 00418 { 00419 PyObject * el_i = PyList_GetItem(var_owner, i); 00420 if (el_i == Py_None) 00421 { 00422 self->var_has_owner[i] = 0; 00423 } 00424 else 00425 { 00426 Py_ssize_t N = PyNumber_AsSsize_t(el_i, PyExc_IndexError); 00427 if (PyErr_Occurred()) return -1; 00428 assert (N var_owner[i] = N; 00430 self->var_has_owner[i] = 1; 00431 } 00432 self->var_computed_cells[i] = PyList_GetItem(compute_map_list, i); 00433 Py_INCREF(self->var_computed_cells[i]); 00434 self->var_value_cells[i] = PyList_GetItem(storage_map_list, i); 00435 Py_INCREF(self->var_value_cells[i]); 00436 } 00437 } 00438 else 00439 { 00440 PyErr_SetString(PyExc_TypeError, "var_owner must be list"); 00441 return -1; 00442 } 00443 00444 if (dependencies != Py_None) 00445 { 00446 self->dependencies = (Py_ssize_t**)calloc(self->n_vars, sizeof(Py_ssize_t *)); 00447 self->n_dependencies = (Py_ssize_t*)calloc(self->n_vars, sizeof(Py_ssize_t)); 00448 assert(self->dependencies); 00449 assert(self->n_dependencies); 00450 00451 for (int i = 0; i n_vars; ++i) 00452 { 00453 PyObject *tmp = PyList_GetItem(dependencies, i); 00454 // refcounting - tmp is borrowed 00455 if (unpack_list_of_ssize_t(tmp, &self->dependencies[i], &self->n_dependencies[i], 00456 "dependencies")) 00457 return -1; 00458 } 00459 } 00460 00461 if (unpack_list_of_ssize_t(output_vars, &self->output_vars, &self->n_output_vars, 00462 "output_vars")) 00463 return -1; 00464 for (int i = 0; i n_output_vars; ++i) 00465 { 00466 assert(self->output_vars[i] n_vars); 00467 } 00468 if (unpack_list_of_ssize_t(update_storage, &self->update_storage, &self->n_updates, 00469 "updates_storage")) 00470 return -1; 00471 return 0; 00472 } 00473 static void set_position_of_error(CLazyLinker * self, int owner_idx) 00474 { 00475 if (self->position_of_error == -1) 00476 { 00477 self->position_of_error = owner_idx; 00478 } 00479 } 00480 static PyObject * pycall(CLazyLinker * self, Py_ssize_t node_idx, int verbose) 00481 { 00482 // call thunk to see which inputs it wants 00483 PyObject * thunk = PyList_GetItem(self->thunks, node_idx); 00484 // refcounting - thunk is borrowed 00485 PyObject * rval = NULL; 00486 if (self->do_timing) 00487 { 00488 double t0 = pytime(NULL); 00489 if (verbose) fprintf(stderr, "calling via Python (node %i)\n", (int)node_idx); 00490 rval = PyObject_CallObject(thunk, NULL); 00491 if (rval) 00492 { 00493 double t1 = pytime(NULL); 00494 double ti = PyFloat_AsDouble( 00495 PyList_GetItem(self->call_times, node_idx)); 00496 PyList_SetItem(self->call_times, node_idx, 00497 PyFloat_FromDouble(t1 - t0 + ti)); 00498 PyObject * count = PyList_GetItem(self->call_counts, node_idx); 00499 long icount = PyInt_AsLong(count); 00500 PyList_SetItem(self->call_counts, node_idx, 00501 PyInt_FromLong(icount + 1)); 00502 } 00503 } 00504 else 00505 { 00506 if (verbose) 00507 { 00508 fprintf(stderr, "calling via Python (node %i)\n", (int)node_idx); 00509 } 00510 rval = PyObject_CallObject(thunk, NULL); 00511 } 00512 return rval; 00513 } 00514 static int c_call(CLazyLinker * self, Py_ssize_t node_idx, int verbose) 00515 { 00516 void * ptr_addr = self->thunk_cptr_fn[node_idx]; 00517 int (*fn)(void*) = (int (*)(void*))(ptr_addr); 00518 if (verbose) fprintf(stderr, "calling non-lazy shortcut (node %i)\n", (int)node_idx); 00519 int err = 0; 00520 if (self->do_timing) 00521 { 00522 double t0 = pytime(NULL); 00523 err = fn(self->thunk_cptr_data[node_idx]); 00524 double t1 = pytime(NULL); 00525 double ti = PyFloat_AsDouble(PyList_GetItem(self->call_times, node_idx)); 00526 PyList_SetItem(self->call_times, node_idx, PyFloat_FromDouble(t1 - t0 + ti)); 00527 PyObject * count = PyList_GetItem(self->call_counts, node_idx); 00528 long icount = PyInt_AsLong(count); 00529 PyList_SetItem(self->call_counts, node_idx, PyInt_FromLong(icount+1)); 00530 } 00531 else 00532 { 00533 err = fn(self->thunk_cptr_data[node_idx]); 00534 } 00535 00536 if (err) 00537 { 00538 // cast the argument to a PyList (as described near line 226 of cc.py) 00539 PyObject * __ERROR = ((PyObject**)self->thunk_cptr_data[node_idx])[0]; 00540 assert (PyList_Check(__ERROR)); 00541 assert (PyList_Size(__ERROR) == 3); 00542 PyObject * err_type = PyList_GetItem(__ERROR, 0); //stolen ref 00543 PyObject * err_msg = PyList_GetItem(__ERROR, 1); //stolen ref 00544 PyObject * err_trace = PyList_GetItem(__ERROR, 2); //stolen ref 00545 PyList_SET_ITEM(__ERROR, 0, Py_None); Py_INCREF(Py_None); //clobbers old ref 00546 PyList_SET_ITEM(__ERROR, 1, Py_None); Py_INCREF(Py_None); //clobbers old ref 00547 PyList_SET_ITEM(__ERROR, 2, Py_None); Py_INCREF(Py_None); //clobbers old ref 00548 00549 assert(!PyErr_Occurred()); // because CLinker hid the exception in __ERROR aka data 00550 PyErr_Restore(err_type, err_msg, err_trace); //steals refs to args 00551 } 00552 if (err) set_position_of_error(self, node_idx); 00553 return err; 00554 } 00555 static 00556 int lazy_rec_eval(CLazyLinker * self, Py_ssize_t var_idx, PyObject*one, PyObject*zero) 00557 { 00558 PyObject *rval = NULL; 00559 int verbose = 0; 00560 int err = 0; 00561 00562 if (verbose) fprintf(stderr, "lazy_rec computing %i\n", (int)var_idx); 00563 00564 if (self->var_computed[var_idx] || !self->var_has_owner[var_idx]) 00565 return 0; 00566 00567 Py_ssize_t owner_idx = self->var_owner[var_idx]; 00568 00569 // STEP 1: compute the pre-requirements of the node 00570 // Includes input nodes for non-lazy ops. 00571 for (int i = 0; i node_n_prereqs[owner_idx]; ++i) 00572 { 00573 Py_ssize_t prereq_idx = self->node_prereqs[owner_idx][i]; 00574 if (!self->var_computed[prereq_idx]) 00575 { 00576 err = lazy_rec_eval(self, prereq_idx, one, zero); 00577 if (err) return err; 00578 } 00579 assert (self->var_computed[prereq_idx]); 00580 } 00581 00582 // STEP 2: compute the node itself 00583 if (self->is_lazy[owner_idx]) 00584 { 00585 // update the compute_map cells corresponding to the inputs of this thunk 00586 for (int i = 0; i node_n_inputs[owner_idx]; ++i) 00587 { 00588 int in_idx = self->node_inputs[owner_idx][i]; 00589 if (self->var_computed[in_idx]) 00590 { 00591 Py_INCREF(one); 00592 err = PyList_SetItem(self->var_computed_cells[in_idx], 0, one); 00593 } 00594 else 00595 { 00596 Py_INCREF(zero); 00597 err = PyList_SetItem(self->var_computed_cells[in_idx], 0, zero); 00598 } 00599 if (err) goto fail; 00600 } 00601 00602 rval = pycall(self, owner_idx, verbose); 00603 // refcounting - rval is new ref 00604 //TODO: to prevent infinite loops 00605 // - consider check that a thunk does not ask for an input that is already computed 00606 if (rval == NULL) 00607 { 00608 assert (PyErr_Occurred()); 00609 err = 1; 00610 goto fail; 00611 } 00612 00613 //update the computed-ness of any output cells 00614 for (int i = 0; i node_n_outputs[owner_idx]; ++i) 00615 { 00616 int out_idx = self->node_outputs[owner_idx][i]; 00617 PyObject * el_i = PyList_GetItem(self->var_computed_cells[out_idx], 0); 00618 Py_ssize_t N = PyNumber_AsSsize_t(el_i, PyExc_IndexError); 00619 if (PyErr_Occurred()) 00620 { 00621 err = -1; 00622 goto pyfail; 00623 } 00624 assert (N==0 || N==1); 00625 self->var_computed[out_idx] = N; 00626 } 00627 if (!self->var_computed[var_idx]) 00628 { 00629 /* 00630 * If self is not computed after the call, this means that some 00631 * inputs are needed. Compute the ones on the returned list 00632 * and try to compute the current node again (with recursive call). 00633 * This allows a node to request more nodes more than once before 00634 * finally yielding a result. 00635 */ 00636 if (!PyList_Check(rval)) 00637 { 00638 //TODO: More helpful error to help find *which node* made this 00639 // bad thunk 00640 PyErr_SetString(PyExc_TypeError, 00641 "lazy thunk should return a list"); 00642 err = 1; 00643 goto pyfail; 00644 } 00645 00646 if (!PyList_Size(rval)) 00647 { 00648 PyErr_SetString(PyExc_ValueError, 00649 "lazy thunk returned empty list without computing output"); 00650 err = 1; 00651 goto pyfail; 00652 } 00653 00654 for (int i = 0; i node_n_inputs[owner_idx]); 00664 Py_ssize_t input_idx = self->node_inputs[owner_idx][N]; 00665 err = lazy_rec_eval(self, input_idx, one, zero); 00666 if (err) goto pyfail; 00667 } 00668 00669 Py_DECREF(rval); 00670 /* 00671 * We intentionally skip all the end-of-function processing 00672 * (mark outputs, GC) as it will be performed by the call 00673 * that actually manages to compute the result. 00674 */ 00675 return lazy_rec_eval(self, var_idx, one, zero); 00676 } 00677 00678 Py_DECREF(rval); 00679 } 00680 else //owner is not a lazy op. Ensure all intputs are evaluated. 00681 { 00682 // loop over inputs to owner 00683 // call lazy_rec_eval on each one that is not computed. 00684 // if there's an error, pass it up the stack 00685 for (int i = 0; i node_n_inputs[owner_idx]; ++i) 00686 { 00687 Py_ssize_t input_idx = self->node_inputs[owner_idx][i]; 00688 if (!self->var_computed[input_idx]) 00689 { 00690 err = lazy_rec_eval(self, input_idx, one, zero); 00691 if (err) return err; 00692 } 00693 assert (self->var_computed[input_idx]); 00694 } 00695 00696 // call the thunk for this owner. 00697 if (self->thunk_cptr_fn[owner_idx]) 00698 { 00699 err = c_call(self, owner_idx, verbose); 00700 if (err) goto fail; 00701 } 00702 else 00703 { 00704 rval = pycall(self, owner_idx, verbose); 00705 //rval is new ref 00706 if (rval) //pycall returned normally (no exception) 00707 { 00708 if (rval == Py_None) 00709 { 00710 Py_DECREF(rval); //ignore a return of None 00711 } 00712 else if (PyList_Check(rval)) 00713 { 00714 PyErr_SetString(PyExc_TypeError, 00715 "non-lazy thunk should return None, not list"); 00716 err = 1; 00717 goto pyfail; 00718 } 00719 else // don't know what it returned, but it wasn't right. 00720 { 00721 PyErr_SetObject(PyExc_TypeError, rval); 00722 err = 1; 00723 // We don't release rval since we put it in the error above 00724 goto fail; 00725 } 00726 } 00727 else // pycall returned NULL (internal error) 00728 { 00729 err = 1; 00730 goto fail; 00731 } 00732 } 00733 } 00734 00735 // loop over all outputs and mark them as computed 00736 for (int i = 0; i node_n_outputs[owner_idx]; ++i) 00737 { 00738 self->var_computed[self->node_outputs[owner_idx][i]] = 1; 00739 } 00740 00741 // Free vars that are not needed anymore 00742 if (self->allow_gc) 00743 { 00744 for (int i = 0; i node_n_inputs[owner_idx]; ++i) 00745 { 00746 int cleanup = 1; 00747 Py_ssize_t i_idx = self->node_inputs[owner_idx][i]; 00748 if (!self->var_has_owner[i_idx]) 00749 continue; 00750 00751 for (int j = 0; j n_output_vars; ++j) 00752 { 00753 if (i_idx == self->output_vars[j]) 00754 { 00755 cleanup = 0; 00756 break; 00757 } 00758 } 00759 if (!cleanup) continue; 00760 00761 for (int j = 0; j n_dependencies[i_idx]; ++j) 00762 { 00763 if (!self->var_computed[self->dependencies[i_idx][j]]) 00764 { 00765 cleanup = 0; 00766 break; 00767 } 00768 } 00769 if (!cleanup) continue; 00770 00771 Py_INCREF(Py_None); 00772 err = PyList_SetItem(self->var_value_cells[i_idx], 0, Py_None); 00773 //See the Stack gc implementation for why we change it to 2 and not 0. 00774 self->var_computed[i_idx] = 2; 00775 if (err) goto fail; 00776 } 00777 } 00778 00779 return 0; 00780 pyfail: 00781 Py_DECREF(rval); 00782 fail: 00783 set_position_of_error(self, owner_idx); 00784 return err; 00785 } 00786 00787 static PyObject * 00788 CLazyLinker_call(PyObject *_self, PyObject *args, PyObject *kwds) 00789 { 00790 CLazyLinker * self = (CLazyLinker*)_self; 00791 static char *kwlist[] = { 00792 (char *)"time_thunks", 00793 (char *)"n_calls", 00794 (char *)"output_subset", 00795 NULL}; 00796 int n_calls=1; 00797 PyObject *output_subset_ptr = NULL; 00798 if (! PyArg_ParseTupleAndKeywords(args, kwds, "|iiO", kwlist, 00799 &self->do_timing, 00800 &n_calls, 00801 &output_subset_ptr)) 00802 return NULL; 00803 00804 int err = 0; 00805 // parse an output_subset list 00806 // it is stored as a bool list of length n_output_vars: calculate a var or not 00807 char *output_subset = NULL; 00808 int output_subset_size = -1; 00809 if (output_subset_ptr != NULL) 00810 { 00811 if (! PyList_Check(output_subset_ptr)) 00812 { 00813 err = 1; 00814 PyErr_SetString(PyExc_RuntimeError, "Output_subset is not a list"); 00815 } 00816 else 00817 { 00818 output_subset_size = PyList_Size(output_subset_ptr); 00819 output_subset = (char*)calloc(self->n_output_vars, sizeof(char)); 00820 for (int it = 0; it position_of_error = -1; 00834 // create constants used to fill the var_compute_cells 00835 PyObject * one = PyInt_FromLong(1); 00836 PyObject * zero = PyInt_FromLong(0); 00837 00838 // pre-allocate our return value 00839 Py_INCREF(Py_None); 00840 PyObject * rval = Py_None; 00841 //clear storage of pre_call_clear elements 00842 for (int call_i = 0; call_i pre_call_clear); 00845 assert(PyList_Check(self->pre_call_clear)); 00846 for (int i = 0; i pre_call_clear, i); 00849 Py_INCREF(Py_None); 00850 PyList_SetItem(el_i, 0, Py_None); 00851 } 00852 //clear the computed flag out of all non-input vars 00853 for (int i = 0; i n_vars; ++i) 00854 { 00855 self->var_computed[i] = !self->var_has_owner[i]; 00856 if (self->var_computed[i]) 00857 { 00858 Py_INCREF(one); 00859 PyList_SetItem(self->var_computed_cells[i], 0, one); 00860 } 00861 else 00862 { 00863 Py_INCREF(zero); 00864 PyList_SetItem(self->var_computed_cells[i], 0, zero); 00865 } 00866 } 00867 00868 int first_updated = self->n_output_vars - self->n_updates; 00869 for (int i = 0; i n_output_vars && (!err); ++i) 00870 { 00871 if (i >= first_updated || output_subset == NULL || output_subset[i] == 1) 00872 { 00873 err = lazy_rec_eval(self, self->output_vars[i], one, zero); 00874 } 00875 } 00876 00877 if (!err) 00878 { 00879 // save references to outputs prior to updating storage containers 00880 assert (self->n_output_vars >= self->n_updates); 00881 Py_DECREF(rval); 00882 rval = PyList_New(self->n_output_vars); 00883 for (int i = 0; i n_output_vars); ++i) 00884 { 00885 Py_ssize_t src = self->output_vars[i]; 00886 PyObject * item = PyList_GetItem(self->var_value_cells[src], 0); 00887 if ((output_subset == NULL || output_subset[i]) && 00888 self->var_computed[src] != 1) 00889 { 00890 err = 1; 00891 PyErr_Format(PyExc_AssertionError, 00892 "The compute map of output %d should contain " 00893 "1 at the end of execution, not %d.", 00894 i, self->var_computed[src]); 00895 break; 00896 } 00897 Py_INCREF(item); 00898 PyList_SetItem(rval, i, item); 00899 } 00900 } 00901 00902 if (!err) 00903 { 00904 // Update the inputs that have an update rule 00905 for (int i = 0; i n_updates; ++i) 00906 { 00907 PyObject* tmp = PyList_GetItem(rval, self->n_output_vars - self->n_updates + i); 00908 Py_INCREF(tmp); 00909 Py_ssize_t dst = self->update_storage[i]; 00910 PyList_SetItem(self->var_value_cells[dst], 0, tmp); 00911 } 00912 } 00913 } 00914 00915 /* 00916 Clear everything that is left and not an output. This is needed 00917 for lazy evaluation since the current GC algo is too conservative 00918 with lazy graphs. 00919 */ 00920 if (self->allow_gc && !err) 00921 { 00922 for (Py_ssize_t i = 0; i n_vars; ++i) 00923 { 00924 int do_cleanup = 1; 00925 if (!self->var_has_owner[i] || !self->var_computed[i]) 00926 continue; 00927 for (int j = 0; j n_output_vars; ++j) 00928 { 00929 if (i == self->output_vars[j]) 00930 { 00931 do_cleanup = 0; 00932 break; 00933 } 00934 } 00935 if (!do_cleanup) 00936 continue; 00937 Py_INCREF(Py_None); 00938 PyList_SetItem(self->var_value_cells[i], 0, Py_None); 00939 } 00940 } 00941 if (output_subset != NULL) 00942 free(output_subset); 00943 00944 Py_DECREF(one); 00945 Py_DECREF(zero); 00946 if (err) 00947 { 00948 Py_DECREF(rval); 00949 return NULL; 00950 } 00951 return rval; 00952 } 00953 00954 #if 0 00955 static PyMethodDef CLazyLinker_methods[] = { 00956 { 00957 //"name", (PyCFunction)CLazyLinker_accept, METH_VARARGS, "Return the name, combining the first and last name" 00958 }, 00959 {NULL} /* Sentinel */ 00960 }; 00961 #endif 00962 00963 00964 static PyObject * 00965 CLazyLinker_get_allow_gc(CLazyLinker *self, void *closure) 00966 { 00967 return PyBool_FromLong(self->allow_gc); 00968 } 00969 00970 static int 00971 CLazyLinker_set_allow_gc(CLazyLinker *self, PyObject *value, void *closure) 00972 { 00973 if(!PyBool_Check(value)) 00974 return -1; 00975 00976 if (value == Py_True) 00977 self->allow_gc = true; 00978 else 00979 self->allow_gc = false; 00980 return 0; 00981 } 00982 00983 static PyGetSetDef CLazyLinker_getset[] = { 00984 {(char*)"allow_gc", 00985 (getter)CLazyLinker_get_allow_gc, 00986 (setter)CLazyLinker_set_allow_gc, 00987 (char*)"do this function support allow_gc", 00988 NULL}, 00989 {NULL, NULL, NULL, NULL} /* Sentinel */ 00990 }; 00991 static PyMemberDef CLazyLinker_members[] = { 00992 {(char*)"nodes", T_OBJECT_EX, offsetof(CLazyLinker, nodes), 0, 00993 (char*)"list of nodes"}, 00994 {(char*)"thunks", T_OBJECT_EX, offsetof(CLazyLinker, thunks), 0, 00995 (char*)"list of thunks in program"}, 00996 {(char*)"call_counts", T_OBJECT_EX, offsetof(CLazyLinker, call_counts), 0, 00997 (char*)"number of calls of each thunk"}, 00998 {(char*)"call_times", T_OBJECT_EX, offsetof(CLazyLinker, call_times), 0, 00999 (char*)"total runtime in each thunk"}, 01000 {(char*)"position_of_error", T_INT, offsetof(CLazyLinker, position_of_error), 0, 01001 (char*)"position of failed thunk"}, 01002 {(char*)"time_thunks", T_INT, offsetof(CLazyLinker, do_timing), 0, 01003 (char*)"bool: nonzero means call will time thunks"}, 01004 {(char*)"need_update_inputs", T_INT, offsetof(CLazyLinker, need_update_inputs), 0, 01005 (char*)"bool: nonzero means Function.__call__ must implement update mechanism"}, 01006 {NULL} /* Sentinel */ 01007 }; 01008 01009 static PyTypeObject lazylinker_ext_CLazyLinkerType = { 01010 #if defined(NPY_PY3K) 01011 PyVarObject_HEAD_INIT(NULL, 0) 01012 #else 01013 PyObject_HEAD_INIT(NULL) 01014 0, /*ob_size*/ 01015 #endif 01016 "lazylinker_ext.CLazyLinker", /*tp_name*/ 01017 sizeof(CLazyLinker), /*tp_basicsize*/ 01018 0, /*tp_itemsize*/ 01019 CLazyLinker_dealloc, /*tp_dealloc*/ 01020 0, /*tp_print*/ 01021 0, /*tp_getattr*/ 01022 0, /*tp_setattr*/ 01023 0, /*tp_compare*/ 01024 0, /*tp_repr*/ 01025 0, /*tp_as_number*/ 01026 0, /*tp_as_sequence*/ 01027 0, /*tp_as_mapping*/ 01028 0, /*tp_hash */ 01029 CLazyLinker_call, /*tp_call*/ 01030 0, /*tp_str*/ 01031 0, /*tp_getattro*/ 01032 0, /*tp_setattro*/ 01033 0, /*tp_as_buffer*/ 01034 Py_TPFLAGS_DEFAULT|Py_TPFLAGS_BASETYPE, /*tp_flags*/ 01035 "CLazyLinker object", /* tp_doc */ 01036 0, /* tp_traverse */ 01037 0, /* tp_clear */ 01038 0, /* tp_richcompare */ 01039 0, /* tp_weaklistoffset */ 01040 0, /* tp_iter */ 01041 0, /* tp_iternext */ 01042 0,//CLazyLinker_methods, /* tp_methods */ 01043 CLazyLinker_members, /* tp_members */ 01044 CLazyLinker_getset, /* tp_getset */ 01045 0, /* tp_base */ 01046 0, /* tp_dict */ 01047 0, /* tp_descr_get */ 01048 0, /* tp_descr_set */ 01049 0, /* tp_dictoffset */ 01050 (initproc)CLazyLinker_init,/* tp_init */ 01051 0, /* tp_alloc */ 01052 CLazyLinker_new, /* tp_new */ 01053 }; 01054 01055 static PyObject * get_version(PyObject *dummy, PyObject *args) 01056 { 01057 PyObject *result = PyFloat_FromDouble(0.211); 01058 return result; 01059 } 01060 01061 static PyMethodDef lazylinker_ext_methods[] = { 01062 {"get_version", get_version, METH_VARARGS, "Get extension version."}, 01063 {NULL, NULL, 0, NULL} /* Sentinel */ 01064 }; 01065 01066 #if defined(NPY_PY3K) 01067 static struct PyModuleDef moduledef = { 01068 PyModuleDef_HEAD_INIT, 01069 "lazylinker_ext", 01070 NULL, 01071 -1, 01072 lazylinker_ext_methods, 01073 NULL, 01074 NULL, 01075 NULL, 01076 NULL 01077 }; 01078 #endif 01079 #if defined(NPY_PY3K) 01080 #define RETVAL m 01081 PyMODINIT_FUNC 01082 PyInit_lazylinker_ext(void) { 01083 #else 01084 #define RETVAL 01085 PyMODINIT_FUNC 01086 initlazylinker_ext(void) 01087 { 01088 #endif 01089 PyObject* m; 01090 01091 lazylinker_ext_CLazyLinkerType.tp_new = PyType_GenericNew; 01092 if (PyType_Ready(&lazylinker_ext_CLazyLinkerType) Traceback (most recent call last): File "train.py", line 5, in import nn_utils.network_utils as network_utils File "/home/n1amr/GRUV/nn_utils/network_utils.py", line 1, in from keras.models import Sequential File "/home/n1amr/.pyenv/versions/env_nn/lib/python2.7/site-packages/keras/models.py", line 3, in import theano File "/home/n1amr/.pyenv/versions/env_nn/lib/python2.7/site-packages/theano/init.py", line 66, in from theano.compile import ( File "/home/n1amr/.pyenv/versions/env_nn/lib/python2.7/site-packages/theano/compile/init.py", line 10, in from theano.compile.function_module import * File "/home/n1amr/.pyenv/versions/env_nn/lib/python2.7/site-packages/theano/compile/function_module.py", line 21, in import theano.compile.mode File "/home/n1amr/.pyenv/versions/env_nn/lib/python2.7/site-packages/theano/compile/mode.py", line 10, in import theano.gof.vm File "/home/n1amr/.pyenv/versions/env_nn/lib/python2.7/site-packages/theano/gof/vm.py", line 662, in from . import lazylinker_c File "/home/n1amr/.pyenv/versions/env_nn/lib/python2.7/site-packages/theano/gof/lazylinker_c.py", line 127, in preargs=args) File "/home/n1amr/.pyenv/versions/env_nn/lib/python2.7/site-packages/theano/gof/cmodule.py", line 2316, in compile_str (status, compile_stderr.replace('\n', '. '))) Exception: Compilation failed (return status=1): /home/n1amr/.pyenv/versions/2.7.12/lib/libpython2.7.a(posixmodule.o): In function posix_tmpnam':. /home/n1amr/.pyenv/sources/2.7.12/Python-2.7.12/./Modules/posixmodule.c:7631: warning: the use oftmpnam_r' is dangerous, better usemkstemp'. /home/n1amr/.pyenv/versions/2.7.12/lib/libpython2.7.a(posixmodule.o): In functionposix_tempnam':. /home/n1amr/.pyenv/sources/2.7.12/Python-2.7.12/./Modules/posixmodule.c:7578: warning: the use oftempnam' is dangerous, better usemkstemp'. /usr/bin/ld: /home/n1amr/.pyenv/versions/2.7.12/lib/libpython2.7.a(classobject.o): relocation R_X86_64_PC32 against symbol `_Py_NotImplementedStruct' can not be used when making a shared object; recompile with -fPIC. /usr/bin/ld: final link failed: Bad value. collect2: error: ld returned 1 exit status.
Packages versions:
appdirs (1.4.3) backports.shutil-get-terminal-size (1.0.0) cycler (0.10.0) decorator (4.0.11) enum34 (1.1.6) funcsigs (1.0.2) functools32 (3.2.3.post2) ipython (5.3.0) ipython-genutils (0.2.0) Keras (0.1.0) matplotlib (2.0.0) mock (2.0.0) numpy (1.12.1) packaging (16.8) pathlib2 (2.2.1) pbr (3.0.1) pexpect (4.2.1) pickleshare (0.7.4) pip (9.0.1) prompt-toolkit (1.0.14) protobuf (3.3.0) ptyprocess (0.5.1) py (1.4.33) Pygments (2.2.0) pyparsing (2.2.0) pytest (3.0.7) python-dateutil (2.6.0) pytz (2017.2) PyYAML (3.12) scandir (1.5) scipy (0.19.0) setuptools (36.0.1) simplegeneric (0.8.1) six (1.10.0) subprocess32 (3.2.7) tensorflow (1.1.0) Theano (0.9.0) traitlets (4.3.2) virtualenv (15.1.0) wcwidth (0.1.7) Werkzeug (0.12.2) wheel (0.29.0)
