[theano-users] Error after sudo apt-get upgrade

Xu Zhang

2017-05-18 23:56:20 UTC

My theano and lasagne works well yesterday. Today, after I type sudo
apt-get upgrade and installed some others dependencies for VLC. My Theano
doesn't work anymore. Error is below when I run my code. The screen keep
printing similar errors without stopping.

my nvidia info:

+-----------------------------------------------------------------------------+
| NVIDIA-SMI 361.93.02 Driver Version:
361.93.02 |
|-------------------------------+----------------------+----------------------+
| GPU Name Persistence-M| Bus-Id Disp.A | Volatile Uncorr.
ECC |
| Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util Compute
M. |
|===============================+======================+======================|
| 0 Tesla K40m On | 0000:81:00.0 Off |
0 |
| N/A 37C P8 20W / 235W | 0MiB / 11441MiB | 0%
Default |
+-------------------------------+----------------------+----------------------+

+-----------------------------------------------------------------------------+
| Processes: GPU
Memory |
| GPU PID Type Process name
Usage |
|=============================================================================|
| No running processes
found |
+-----------------------------------------------------------------------------+
cuda version:

nvcc: NVIDIA (R) Cuda compiler driver
Copyright (c) 2005-2016 NVIDIA Corporation
Built on Tue_Jan_10_13:22:03_CST_2017
Cuda compilation tools, release 8.0, V8.0.61

Ubuntu version:

Distributor ID: Ubuntu
Description: Ubuntu 14.04.5 LTS
Release: 14.04
Codename: trusty

WARNING (theano.sandbox.cuda): The cuda backend is deprecated and will be
removed in the next release (v0.10). Please switch to the gpuarray
backend. You can get more information about how to switch at this URL:
https://github.com/Theano/Theano/wiki/Converting-to-the-new-gpu-back-end%28gpuarray%29

1 #include <Python.h>
2 #include <iostream>
3 #include "theano_mod_helper.h"
4 #include "cudnn.h"
5 //////////////////////
6 //// Support Code
7 //////////////////////
8
9 #if PY_MAJOR_VERSION >= 3
10 #define PyInt_FromLong PyLong_FromLong
11 #endif
12
13
14 namespace {
15 struct __struct_compiled_op_3442132e74e76f61361fb1c73112eef4 {
16 PyObject* __ERROR;
17
18 PyObject* storage_V1;
19
20
21 __struct_compiled_op_3442132e74e76f61361fb1c73112eef4() {
22 // This is only somewhat safe because we:
23 // 1) Are not a virtual class
24 // 2) Do not use any virtual classes in the members
25 // 3) Deal with mostly POD and pointers
26
27 // If this changes, we would have to revise this, but for
28 // now I am tired of chasing segfaults because
29 // initialization code had an error and some pointer has
30 // a junk value.
31 memset(this, 0, sizeof(*this));
32 }
33 ~__struct_compiled_op_3442132e74e76f61361fb1c73112eef4(void) {
34 cleanup();
35 }
36
37 int init(PyObject* __ERROR, PyObject* storage_V1) {
38 Py_XINCREF(storage_V1);
39 this->storage_V1 = storage_V1;
40
41
42
43 this->__ERROR = __ERROR;
44 return 0;
45 }
46 void cleanup(void) {
47 __label_1:
48
49 double __DUMMY_1;
50 __label_4:
51
52 double __DUMMY_4;
53
54 Py_XDECREF(this->storage_V1);
55 }
56 int run(void) {
57 int __failure = 0;
58
59 PyObject* py_V1;
60
61 PyObject* V1;
62
63 {
64
65 py_V1 = Py_None;
66 {Py_XINCREF(py_V1);}
67
68 V1 = NULL;
69
70 {
71 // Op class DnnVersion
72
73 #if defined(CUDNN_VERSION)
74 V1 = PyTuple_Pack(2, PyInt_FromLong(CUDNN_VERSION),
PyInt_FromLong(cudnnGetVersion()));
75 #else
76 V1 = PyInt_FromLong(-1);
77 #endif
78 __label_3:
79
80 double __DUMMY_3;
81
82 }
83 __label_2:
84
85 if (!__failure) {
86
87 assert(py_V1->ob_refcnt > 1);
88 Py_DECREF(py_V1);
89 py_V1 = V1 ? V1 : Py_None;
90 Py_INCREF(py_V1);
91
92 PyObject* old = PyList_GET_ITEM(storage_V1, 0);
93 {Py_XINCREF(py_V1);}
94 PyList_SET_ITEM(storage_V1, 0, py_V1);
95 {Py_XDECREF(old);}
96 }
97
98 Py_XDECREF(V1);
99
100 {Py_XDECREF(py_V1);}
101
102 double __DUMMY_2;
103
104 }
105
106
107 if (__failure) {
108 // When there is a failure, this code puts the exception
109 // in __ERROR.
110 PyObject* err_type = NULL;
111 PyObject* err_msg = NULL;
112 PyObject* err_traceback = NULL;
113 PyErr_Fetch(&err_type, &err_msg, &err_traceback);
114 if (!err_type) {err_type = Py_None;Py_INCREF(Py_None);}
115 if (!err_msg) {err_msg = Py_None; Py_INCREF(Py_None);}
116 if (!err_traceback) {err_traceback = Py_None;
Py_INCREF(Py_None);}
117 PyObject* old_err_type = PyList_GET_ITEM(__ERROR, 0);
118 PyObject* old_err_msg = PyList_GET_ITEM(__ERROR, 1);
119 PyObject* old_err_traceback = PyList_GET_ITEM(__ERROR, 2);
120 PyList_SET_ITEM(__ERROR, 0, err_type);
121 PyList_SET_ITEM(__ERROR, 1, err_msg);
122 PyList_SET_ITEM(__ERROR, 2, err_traceback);
123 {Py_XDECREF(old_err_type);}
124 {Py_XDECREF(old_err_msg);}
125 {Py_XDECREF(old_err_traceback);}
126 }
127 // The failure code is returned to index what code block failed.
128 return __failure;
129
130 }
131 };
132 }
133
134
135 static int
__struct_compiled_op_3442132e74e76f61361fb1c73112eef4_executor(__struct_compiled_op_3442132e74e76f61361fb1c73112eef4*
self) {
136 return self->run();
137 }
138
139 static void
__struct_compiled_op_3442132e74e76f61361fb1c73112eef4_destructor(void*
executor, void* self) {
140 delete
((__struct_compiled_op_3442132e74e76f61361fb1c73112eef4*)self);
141 }
142
143 //////////////////////
144 //// Functions
145 //////////////////////
146 static PyObject * instantiate(PyObject * self, PyObject *argtuple) {
147 assert(PyTuple_Check(argtuple));
148 if (2 != PyTuple_Size(argtuple)){
149 PyErr_Format(PyExc_TypeError, "Wrong number of arguments, expected
2, got %i", (int)PyTuple_Size(argtuple));
150 return NULL;
151 }
152 __struct_compiled_op_3442132e74e76f61361fb1c73112eef4* struct_ptr =
new __struct_compiled_op_3442132e74e76f61361fb1c73112eef4();
153 if (struct_ptr->init( PyTuple_GET_ITEM(argtuple,
0),PyTuple_GET_ITEM(argtuple, 1) ) != 0) {
154 delete struct_ptr;
155 return NULL;
156 }
157 PyObject* thunk =
PyCObject_FromVoidPtrAndDesc((void*)(&__struct_compiled_op_3442132e74e76f61361fb1c73112eef4_executor),
struct_ptr,
__struct_compiled_op_3442132e74e76f61361fb1c73112eef4_destructor);
158 return thunk; }
159
160 //////////////////////
161 //// Module init
162 //////////////////////
163 static PyMethodDef MyMethods[] = {
164 {"instantiate", instantiate, METH_VARARGS, "undocumented"} ,
165 {NULL, NULL, 0, NULL}
166 };
167 PyMODINIT_FUNC init3442132e74e76f61361fb1c73112eef4(void){
168 (void) Py_InitModule("3442132e74e76f61361fb1c73112eef4", MyMethods);
169 }
170
===============================
nvcc warning : The 'compute_20', 'sm_20', and 'sm_21' architectures are
deprecated, and may be removed in a future release (Use
-Wno-deprecated-gpu-targets to suppress warning).
/usr/bin/ld: cannot find -lcudnn
/usr/bin/ld: cannot find -lcudart
/usr/bin/ld: cannot find -lcudadevrt
/usr/bin/ld: cannot find -lcudart_static
collect2: error: ld returned 1 exit status
Using gpu device 0: Tesla K40m (CNMeM is enabled with initial size: 95.0%
of memory, cuDNN None)

['nvcc', '-shared', '-O3', '-Xlinker', '-rpath,/usr/local/cuda-8.0/lib64',
'-m64', '-Xcompiler',
'-fno-math-errno,-Wno-unused-label,-Wno-unused-variable,-Wno-write-strings,-DCUDA_NDARRAY_CUH=c72d035fdf91890f3b36710688069b2e,-DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION,-fPIC,-fvisibility=hidden',
'-Xlinker',
'-rpath,/space/xzhang/.theano/compiledir_Linux-3.19--generic-x86_64-with-Ubuntu-14.04-trusty-x86_64-2.7.6-64/cuda_ndarray',
'-I/usr/local/cuda-8.0/include',
'-I/usr/local/lib/python2.7/dist-packages/numpy/core/include',
'-I/usr/include/python2.7',
'-I/usr/local/lib/python2.7/dist-packages/theano/gof',
'-I/usr/local/lib/python2.7/dist-packages/theano/sandbox/cuda',
'-L/usr/lib', '-o',
'/space/xzhang/.theano/compiledir_Linux-3.19--generic-x86_64-with-Ubuntu-14.04-trusty-x86_64-2.7.6-64/tmpjR_LxZ/3442132e74e76f61361fb1c73112eef4.so',
'mod.cu', '-lcudnn', '-lpython2.7', '-lcudart']
Loading data...
Building model and compiling functions...
number of parameters in model: 145376

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Xu Zhang

2017-05-20 00:50:31 UTC

Permalink

I check online. There is one guy who had the same problem as me. But he
didn't say how he fixed it.
https://github.com/Theano/Theano/issues/5330

Post by Xu Zhang
My theano and lasagne works well yesterday. Today, after I type sudo
apt-get upgrade and installed some others dependencies for VLC. My Theano
doesn't work anymore. Error is below when I run my code. The screen keep
printing similar errors without stopping.
+-----------------------------------------------------------------------------+
361.93.02 |
|-------------------------------+----------------------+----------------------+
| GPU Name Persistence-M| Bus-Id Disp.A | Volatile Uncorr.
ECC |
| Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util Compute
M. |
|===============================+======================+======================|
| 0 Tesla K40m On | 0000:81:00.0 Off
| 0 |
| N/A 37C P8 20W / 235W | 0MiB / 11441MiB | 0%
Default |
+-------------------------------+----------------------+----------------------+
+-----------------------------------------------------------------------------+
| Processes: GPU
Memory |
| GPU PID Type Process name
Usage |
|=============================================================================|
| No running processes
found |
+-----------------------------------------------------------------------------+
nvcc: NVIDIA (R) Cuda compiler driver
Copyright (c) 2005-2016 NVIDIA Corporation
Built on Tue_Jan_10_13:22:03_CST_2017
Cuda compilation tools, release 8.0, V8.0.61
Distributor ID: Ubuntu
Description: Ubuntu 14.04.5 LTS
Release: 14.04
Codename: trusty
WARNING (theano.sandbox.cuda): The cuda backend is deprecated and will be
removed in the next release (v0.10). Please switch to the gpuarray
https://github.com/Theano/Theano/wiki/Converting-to-the-new-gpu-back-end%28gpuarray%29
1 #include <Python.h>
2 #include <iostream>
3 #include "theano_mod_helper.h"
4 #include "cudnn.h"
5 //////////////////////
6 //// Support Code
7 //////////////////////
8
9 #if PY_MAJOR_VERSION >= 3
10 #define PyInt_FromLong PyLong_FromLong
11 #endif
12
13
14 namespace {
15 struct __struct_compiled_op_3442132e74e76f61361fb1c73112eef4 {
16 PyObject* __ERROR;
17
18 PyObject* storage_V1;
19
20
21 __struct_compiled_op_3442132e74e76f61361fb1c73112eef4() {
23 // 1) Are not a virtual class
24 // 2) Do not use any virtual classes in the members
25 // 3) Deal with mostly POD and pointers
26
27 // If this changes, we would have to revise this, but for
28 // now I am tired of chasing segfaults because
29 // initialization code had an error and some pointer has
30 // a junk value.
31 memset(this, 0, sizeof(*this));
32 }
33 ~__struct_compiled_op_3442132e74e76f61361fb1c73112eef4(void) {
34 cleanup();
35 }
36
37 int init(PyObject* __ERROR, PyObject* storage_V1) {
38 Py_XINCREF(storage_V1);
39 this->storage_V1 = storage_V1;
40
41
42
43 this->__ERROR = __ERROR;
44 return 0;
45 }
46 void cleanup(void) {
48
49 double __DUMMY_1;
51
52 double __DUMMY_4;
53
54 Py_XDECREF(this->storage_V1);
55 }
56 int run(void) {
57 int __failure = 0;
58
59 PyObject* py_V1;
60
61 PyObject* V1;
62
63 {
64
65 py_V1 = Py_None;
66 {Py_XINCREF(py_V1);}
67
68 V1 = NULL;
69
70 {
71 // Op class DnnVersion
72
73 #if defined(CUDNN_VERSION)
74 V1 = PyTuple_Pack(2, PyInt_FromLong(CUDNN_VERSION),
PyInt_FromLong(cudnnGetVersion()));
75 #else
76 V1 = PyInt_FromLong(-1);
77 #endif
79
80 double __DUMMY_3;
81
82 }
84
85 if (!__failure) {
86
87 assert(py_V1->ob_refcnt > 1);
88 Py_DECREF(py_V1);
89 py_V1 = V1 ? V1 : Py_None;
90 Py_INCREF(py_V1);
91
92 PyObject* old = PyList_GET_ITEM(storage_V1, 0);
93 {Py_XINCREF(py_V1);}
94 PyList_SET_ITEM(storage_V1, 0, py_V1);
95 {Py_XDECREF(old);}
96 }
97
98 Py_XDECREF(V1);
99
100 {Py_XDECREF(py_V1);}
101
102 double __DUMMY_2;
103
104 }
105
106
107 if (__failure) {
108 // When there is a failure, this code puts the exception
109 // in __ERROR.
110 PyObject* err_type = NULL;
111 PyObject* err_msg = NULL;
112 PyObject* err_traceback = NULL;
113 PyErr_Fetch(&err_type, &err_msg, &err_traceback);
114 if (!err_type) {err_type = Py_None;Py_INCREF(Py_None);}
115 if (!err_msg) {err_msg = Py_None; Py_INCREF(Py_None);}
116 if (!err_traceback) {err_traceback = Py_None;
Py_INCREF(Py_None);}
117 PyObject* old_err_type = PyList_GET_ITEM(__ERROR, 0);
118 PyObject* old_err_msg = PyList_GET_ITEM(__ERROR, 1);
119 PyObject* old_err_traceback = PyList_GET_ITEM(__ERROR, 2);
120 PyList_SET_ITEM(__ERROR, 0, err_type);
121 PyList_SET_ITEM(__ERROR, 1, err_msg);
122 PyList_SET_ITEM(__ERROR, 2, err_traceback);
123 {Py_XDECREF(old_err_type);}
124 {Py_XDECREF(old_err_msg);}
125 {Py_XDECREF(old_err_traceback);}
126 }
127 // The failure code is returned to index what code block failed.
128 return __failure;
129
130 }
131 };
132 }
133
134
135 static int
__struct_compiled_op_3442132e74e76f61361fb1c73112eef4_executor(__struct_compiled_op_3442132e74e76f61361fb1c73112eef4*
self) {
136 return self->run();
137 }
138
139 static void
__struct_compiled_op_3442132e74e76f61361fb1c73112eef4_destructor(void*
executor, void* self) {
140 delete
((__struct_compiled_op_3442132e74e76f61361fb1c73112eef4*)self);
141 }
142
143 //////////////////////
144 //// Functions
145 //////////////////////
146 static PyObject * instantiate(PyObject * self, PyObject *argtuple) {
147 assert(PyTuple_Check(argtuple));
148 if (2 != PyTuple_Size(argtuple)){
149 PyErr_Format(PyExc_TypeError, "Wrong number of arguments,
expected 2, got %i", (int)PyTuple_Size(argtuple));
150 return NULL;
151 }
152 __struct_compiled_op_3442132e74e76f61361fb1c73112eef4* struct_ptr =
new __struct_compiled_op_3442132e74e76f61361fb1c73112eef4();
153 if (struct_ptr->init( PyTuple_GET_ITEM(argtuple,
0),PyTuple_GET_ITEM(argtuple, 1) ) != 0) {
154 delete struct_ptr;
155 return NULL;
156 }
157 PyObject* thunk =
PyCObject_FromVoidPtrAndDesc((void*)(&__struct_compiled_op_3442132e74e76f61361fb1c73112eef4_executor),
struct_ptr,
__struct_compiled_op_3442132e74e76f61361fb1c73112eef4_destructor);
158 return thunk; }
159
160 //////////////////////
161 //// Module init
162 //////////////////////
163 static PyMethodDef MyMethods[] = {
164 {"instantiate", instantiate, METH_VARARGS, "undocumented"} ,
165 {NULL, NULL, 0, NULL}
166 };
167 PyMODINIT_FUNC init3442132e74e76f61361fb1c73112eef4(void){
168 (void) Py_InitModule("3442132e74e76f61361fb1c73112eef4", MyMethods);
169 }
170
===============================
nvcc warning : The 'compute_20', 'sm_20', and 'sm_21' architectures are
deprecated, and may be removed in a future release (Use
-Wno-deprecated-gpu-targets to suppress warning).
/usr/bin/ld: cannot find -lcudnn
/usr/bin/ld: cannot find -lcudart
/usr/bin/ld: cannot find -lcudadevrt
/usr/bin/ld: cannot find -lcudart_static
collect2: error: ld returned 1 exit status
Using gpu device 0: Tesla K40m (CNMeM is enabled with initial size: 95.0%
of memory, cuDNN None)
['nvcc', '-shared', '-O3', '-Xlinker', '-rpath,/usr/local/cuda-8.0/lib64',
'-m64', '-Xcompiler',
'-fno-math-errno,-Wno-unused-label,-Wno-unused-variable,-Wno-write-strings,-DCUDA_NDARRAY_CUH=c72d035fdf91890f3b36710688069b2e,-DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION,-fPIC,-fvisibility=hidden',
'-Xlinker',
'-rpath,/space/xzhang/.theano/compiledir_Linux-3.19--generic-x86_64-with-Ubuntu-14.04-trusty-x86_64-2.7.6-64/cuda_ndarray',
'-I/usr/local/cuda-8.0/include',
'-I/usr/local/lib/python2.7/dist-packages/numpy/core/include',
'-I/usr/include/python2.7',
'-I/usr/local/lib/python2.7/dist-packages/theano/gof',
'-I/usr/local/lib/python2.7/dist-packages/theano/sandbox/cuda',
'-L/usr/lib', '-o',
'/space/xzhang/.theano/compiledir_Linux-3.19--generic-x86_64-with-Ubuntu-14.04-trusty-x86_64-2.7.6-64/tmpjR_LxZ/3442132e74e76f61361fb1c73112eef4.so',
'mod.cu', '-lcudnn', '-lpython2.7', '-lcudart']
Loading data...
Building model and compiling functions...
number of parameters in model: 145376