[theano-users] Cannot run my previous code showing /usr/bin/ld: cannot find -lcudnn

[z***@gmail.com]

The old server crash and trying to run my code on the new server. I
installed theano 0.9.0-dev and lasagne 0.2.0 dev. When I ran my previous
code, it shows me error as below:

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).
In file included from
/var/home/xzhang/anaconda2/include/python2.7/Python.h:8:0,
from mod.cu:1:
/var/home/xzhang/anaconda2/include/python2.7/pyconfig.h:1190:0: warning:
"_POSIX_C_SOURCE" redefined [enabled by default]
#define _POSIX_C_SOURCE 200112L
^
In file included from /usr/local/cuda/include/host_config.h:173:0,
from /usr/local/cuda/include/cuda_runtime.h:78,
from <command-line>:0:
/usr/include/features.h:230:0: note: this is the location of the previous
definition
# define _POSIX_C_SOURCE 200809L
^
In file included from
/var/home/xzhang/anaconda2/include/python2.7/Python.h:8:0,
from mod.cu:1:
/var/home/xzhang/anaconda2/include/python2.7/pyconfig.h:1212:0: warning:
"_XOPEN_SOURCE" redefined [enabled by default]
#define _XOPEN_SOURCE 600
^
In file included from /usr/local/cuda/include/host_config.h:173:0,
from /usr/local/cuda/include/cuda_runtime.h:78,
from <command-line>:0:
/usr/include/features.h:162:0: note: this is the location of the previous
definition
# define _XOPEN_SOURCE 700
^
In file included from
/var/home/xzhang/anaconda2/include/python2.7/Python.h:8:0,
from mod.cu:1:
/var/home/xzhang/anaconda2/include/python2.7/pyconfig.h:1190:0: warning:
"_POSIX_C_SOURCE" redefined [enabled by default]
#define _POSIX_C_SOURCE 200112L
^
In file included from /usr/local/cuda/include/host_config.h:173:0,
from /usr/local/cuda/include/cuda_runtime.h:78,
from <command-line>:0:
/usr/include/features.h:230:0: note: this is the location of the previous
definition
# define _POSIX_C_SOURCE 200809L
^
In file included from
/var/home/xzhang/anaconda2/include/python2.7/Python.h:8:0,
from mod.cu:1:
/var/home/xzhang/anaconda2/include/python2.7/pyconfig.h:1212:0: warning:
"_XOPEN_SOURCE" redefined [enabled by default]
#define _XOPEN_SOURCE 600
^
In file included from /usr/local/cuda/include/host_config.h:173:0,
from /usr/local/cuda/include/cuda_runtime.h:78,
from <command-line>:0:
/usr/include/features.h:162:0: note: this is the location of the previous
definition
# define _XOPEN_SOURCE 700
^
/usr/bin/ld: cannot find -lcudnn
collect2: error: ld returned 1 exit status

['nvcc', '-shared', '-O3', '-Xlinker', '-rpath,/usr/local/cuda/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,/var/home/xzhang/.theano/compiledir_Linux-3.13--generic-x86_64-with-debian-jessie-sid-x86_64-2.7.13-64/cuda_ndarray',
'-I/usr/local/cuda/include',
'-I/var/home/xzhang/anaconda2/lib/python2.7/site-packages/numpy/core/include',
'-I/var/home/xzhang/anaconda2/include/python2.7',
'-I/var/home/xzhang/anaconda2/lib/python2.7/site-packages/theano/gof',
'-I/var/home/xzhang/anaconda2/lib/python2.7/site-packages/theano/sandbox/cuda',
'-L/var/home/xzhang/anaconda2/lib', '-o',
'/var/home/xzhang/.theano/compiledir_Linux-3.13--generic-x86_64-with-debian-jessie-sid-x86_64-2.7.13-64/tmpSrZcvj/3442132e74e76f61361fb1c73112eef4.so',
'mod.cu', '-lcudnn', '-lpython2.7', '-lcudart']
Using gpu device 0: Tesla K80 (CNMeM is disabled, cuDNN None)
Using Theano backend.
Compiling...
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
===============================
In file included from
/var/home/xzhang/anaconda2/include/python2.7/Python.h:8:0,
from mod.cu:1:
/var/home/xzhang/anaconda2/include/python2.7/pyconfig.h:1190:0: warning:
"_POSIX_C_SOURCE" redefined [enabled by default]
#define _POSIX_C_SOURCE 200112L
^
In file included from /usr/local/cuda/include/host_config.h:173:0,
from /usr/local/cuda/include/cuda_runtime.h:78,
from <command-line>:0:
/usr/include/features.h:230:0: note: this is the location of the previous
definition
# define _POSIX_C_SOURCE 200809L
^
In file included from
/var/home/xzhang/anaconda2/include/python2.7/Python.h:8:0,
from mod.cu:1:
/var/home/xzhang/anaconda2/include/python2.7/pyconfig.h:1212:0: warning:
"_XOPEN_SOURCE" redefined [enabled by default]
#define _XOPEN_SOURCE 600
^
In file included from /usr/local/cuda/include/host_config.h:173:0,
from /usr/local/cuda/include/cuda_runtime.h:78,
from <command-line>:0:
/usr/include/features.h:162:0: note: this is the location of the previous
definition
# define _XOPEN_SOURCE 700
^
In file included from
/var/home/xzhang/anaconda2/include/python2.7/Python.h:8:0,
from mod.cu:1:
/var/home/xzhang/anaconda2/include/python2.7/pyconfig.h:1190:0: warning:
"_POSIX_C_SOURCE" redefined [enabled by default]
#define _POSIX_C_SOURCE 200112L
^
In file included from /usr/local/cuda/include/host_config.h:173:0,
from /usr/local/cuda/include/cuda_runtime.h:78,
from <command-line>:0:
/usr/include/features.h:230:0: note: this is the location of the previous
definition
# define _POSIX_C_SOURCE 200809L
^
In file included from
/var/home/xzhang/anaconda2/include/python2.7/Python.h:8:0,
from mod.cu:1:
/var/home/xzhang/anaconda2/include/python2.7/pyconfig.h:1212:0: warning:
"_XOPEN_SOURCE" redefined [enabled by default]
#define _XOPEN_SOURCE 600
^
In file included from /usr/local/cuda/include/host_config.h:173:0,
from /usr/local/cuda/include/cuda_runtime.h:78,
from <command-line>:0:
/usr/include/features.h:162:0: note: this is the location of the previous
definition
# define _XOPEN_SOURCE 700
^
/usr/bin/ld: cannot find -lcudnn
collect2: error: ld returned 1 exit status

['nvcc', '-shared', '-O3', '-Xlinker', '-rpath,/usr/local/cuda/lib64',
'-arch=sm_37', '-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,/var/home/xzhang/.theano/compiledir_Linux-3.13--generic-x86_64-with-debian-jessie-sid-x86_64-2.7.13-64/cuda_ndarray',
'-I/usr/local/cuda/include',
'-I/var/home/xzhang/anaconda2/lib/python2.7/site-packages/numpy/core/include',
'-I/var/home/xzhang/anaconda2/include/python2.7',
'-I/var/home/xzhang/anaconda2/lib/python2.7/site-packages/theano/gof',
'-I/var/home/xzhang/anaconda2/lib/python2.7/site-packages/theano/sandbox/cuda',
'-L/var/home/xzhang/anaconda2/lib', '-o',
'/var/home/xzhang/.theano/compiledir_Linux-3.13--generic-x86_64-with-debian-jessie-sid-x86_64-2.7.13-64/tmpKcdE1p/3442132e74e76f61361fb1c73112eef4.so',
'mod.cu', '-lcudnn', '-lpython2.7', '-lcudart']
Traceback (most recent call last):
File "test_convnet_binary_bias3.py", line 159, in <module>
main(**kargs)
File "test_convnet_binary_bias3.py", line 94, in main
temp, temp1, temp2, temp3,conv1_spikes=second_l.get_output()
File
"/var/home/xzhang/code_repository/binarizednetwork_08_03/timefirstspike/relulastlayer/theano_layers.py",
line 169, in get_output
border_mode=(pad_x, pad_y))
File
"/var/home/xzhang/anaconda2/lib/python2.7/site-packages/theano/sandbox/cuda/dnn.py",
line 1186, in dnn_conv
return GpuDnnConv(algo=algo)(img, kerns, out, desc)
File
"/var/home/xzhang/anaconda2/lib/python2.7/site-packages/theano/sandbox/cuda/dnn.py",
line 359, in __init__
if version() < (5000, 5000):
File
"/var/home/xzhang/anaconda2/lib/python2.7/site-packages/theano/sandbox/cuda/__init__.py",
line 429, in dnn_version
profile=False)
File
"/var/home/xzhang/anaconda2/lib/python2.7/site-packages/theano/compile/function.py",
line 326, in function
output_keys=output_keys)
File
"/var/home/xzhang/anaconda2/lib/python2.7/site-packages/theano/compile/pfunc.py",
line 486, in pfunc
output_keys=output_keys)
File
"/var/home/xzhang/anaconda2/lib/python2.7/site-packages/theano/compile/function_module.py",
line 1795, in orig_function
defaults)
File
"/var/home/xzhang/anaconda2/lib/python2.7/site-packages/theano/compile/function_module.py",
line 1661, in create
input_storage=input_storage_lists, storage_map=storage_map)
File
"/var/home/xzhang/anaconda2/lib/python2.7/site-packages/theano/gof/link.py",
line 699, in make_thunk
storage_map=storage_map)[:3]
File
"/var/home/xzhang/anaconda2/lib/python2.7/site-packages/theano/gof/vm.py",
line 1047, in make_all
impl=impl))
File
"/var/home/xzhang/anaconda2/lib/python2.7/site-packages/theano/gof/op.py",
line 935, in make_thunk
no_recycling)
File
"/var/home/xzhang/anaconda2/lib/python2.7/site-packages/theano/gof/op.py",
line 839, in make_c_thunk
output_storage=node_output_storage)
File
"/var/home/xzhang/anaconda2/lib/python2.7/site-packages/theano/gof/cc.py",
line 1190, in make_thunk
keep_lock=keep_lock)
File
"/var/home/xzhang/anaconda2/lib/python2.7/site-packages/theano/gof/cc.py",
line 1131, in __compile__
keep_lock=keep_lock)
File
"/var/home/xzhang/anaconda2/lib/python2.7/site-packages/theano/gof/cc.py",
line 1586, in cthunk_factory
key=key, lnk=self, keep_lock=keep_lock)
File
"/var/home/xzhang/anaconda2/lib/python2.7/site-packages/theano/gof/cmodule.py",
line 1159, in module_from_key
module = lnk.compile_cmodule(location)
File
"/var/home/xzhang/anaconda2/lib/python2.7/site-packages/theano/gof/cc.py",
line 1489, in compile_cmodule
preargs=preargs)
File
"/var/home/xzhang/anaconda2/lib/python2.7/site-packages/theano/sandbox/cuda/nvcc_compiler.py",
line 405, in compile_str
'for cmd', ' '.join(cmd))
Exception: ('The following error happened while compiling the node',
<theano.sandbox.cuda.DnnVersion object at 0x7f4feef0de50>(), '\n', 'nvcc
return status', 1, 'for cmd', 'nvcc -shared -O3 -Xlinker
-rpath,/usr/local/cuda/lib64 -arch=sm_37 -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,/var/home/xzhang/.theano/compiledir_Linux-3.13--generic-x86_64-with-debian-jessie-sid-x86_64-2.7.13-64/cuda_ndarray
-I/usr/local/cuda/include
-I/var/home/xzhang/anaconda2/lib/python2.7/site-packages/numpy/core/include
-I/var/home/xzhang/anaconda2/include/python2.7
-I/var/home/xzhang/anaconda2/lib/python2.7/site-packages/theano/gof
-I/var/home/xzhang/anaconda2/lib/python2.7/site-packages/theano/sandbox/cuda
-L/var/home/xzhang/anaconda2/lib -o
/var/home/xzhang/.theano/compiledir_Linux-3.13--generic-x86_64-with-debian-jessie-sid-x86_64-2.7.13-64/tmpKcdE1p/3442132e74e76f61361fb1c73112eef4.so
mod.cu -lcudnn -lpython2.7 -lcudart', '[<theano.sandbox.cuda.DnnVersion
object at 0x7f4feef0de50>()]')