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numenta / nupic-legacy

Numenta Platform for Intelligent Computing is an implementation of Hierarchical Temporal Memory (HTM), a theory of intelligence based strictly on the neuroscience of the neocortex.
http://numenta.org/
GNU Affero General Public License v3.0
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unit and integration tests fail on MacBookPro after building nupic per official instructions #1569

Closed vitaly-krugl closed 9 years ago

vitaly-krugl commented 9 years ago

OS: Mac OS-X Mavericks Python 2.7.5 clang version:

Apple LLVM version 5.1 (clang-503.0.40) (based on LLVM 3.4svn)
Target: x86_64-apple-darwin13.4.0
Thread model: posix

gcc version:

Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/usr/include/c++/4.2.1
Apple LLVM version 5.1 (clang-503.0.40) (based on LLVM 3.4svn)
Target: x86_64-apple-darwin13.4.0
Thread model: posix

I performed a clean build (and repeated several times), resulting in unit and integration test failures:

The failures are SIGSEGV in C++ code in the nta::algorithms module.

I performed the build as follows per instructions on https://github.com/numenta/nupic:

  1. pip install --allow-all-external --allow-unverified PIL --allow-unverified psutil -r external/common/requirements.txt --target ~/Library/Python/2.7/lib/python/site-packages/
  2. cd $NUPIC
  3. git clean -fdx
  4. mkdir -p $NTA/lib/python2.7/site-packages
  5. python setup.py build
  6. python setup.py develop --install-dir="$NTA/lib/python2.7/site-packages"

NOTE1: if I build nupic.core manually, and then point nupic to the manually-built nupic.core, then the tests pass! (python setup.py develop --install-dir="$NTA/lib/python2.7/site-packages" --cmake_options="-DNUPIC_CORE=/Users/vkruglikov/nta/nupic.core/build/release" per https://github.com/numenta/nupic/wiki/NuPIC's-Dependency-on-nupic.core)

NOTE2: I tried the following build variations and still got the same errors:

The SIGSEGV occur in C++ code in the nta::algorithms module and produce the following dump:

Process:         Python [35749]
Path:            /System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python
Identifier:      Python
Version:         2.7.5 (2.7.5)
Code Type:       X86-64 (Native)
Parent Process:  Python [35653]
Responsible:     Terminal [6743]
User ID:         502

PlugIn Path:       /Users/USER/*/_algorithms.so
PlugIn Identifier: _algorithms.so
PlugIn Version:    ??? (???)

Date/Time:       2014-11-25 13:31:49.989 -0800
OS Version:      Mac OS X 10.9.5 (13F34)
Report Version:  11
Anonymous UUID:  62578250-CF79-759F-0A43-7627816C0464

Sleep/Wake UUID: 6243D231-4234-46CC-99B2-D6B3661D1AE3

Crashed Thread:  0  Dispatch queue: com.apple.main-thread

Exception Type:  EXC_BAD_ACCESS (SIGSEGV)
Exception Codes: KERN_INVALID_ADDRESS at 0x000000000000002a

VM Regions Near 0x2a:
--> 
    __TEXT                 000000010a926000-000000010a927000 [    4K] r-x/rwx SM=COW  /System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python

Application Specific Information:
crashed on child side of fork pre-exec

Thread 0 Crashed:: Dispatch queue: com.apple.main-thread
0   _algorithms.so                  0x000000010c8008fc nta::algorithms::Cells4::Segment::invariants() const + 380
1   _algorithms.so                  0x000000010c8e63e5 nta::algorithms::Cells4::Segment::decaySynapses(float, std::__1::vector<unsigned int, std::__1::allocator<unsigned int> >&, float, bool) + 53
2   _algorithms.so                  0x000000010c8bbe75 nta::algorithms::Cells4::Cells4::trimSegments(float, unsigned int) + 389
3   _algorithms.so                  0x000000010c6b6920 _wrap_Cells4_trimSegments(_object*, _object*, _object*) + 560
4   org.python.python               0x000000010a9b012f PyEval_EvalFrameEx + 16242
5   org.python.python               0x000000010a9ac093 PyEval_EvalCodeEx + 1641
6   org.python.python               0x000000010a9b28c8 0x10a92c000 + 551112
7   org.python.python               0x000000010a9af4d4 PyEval_EvalFrameEx + 13079
8   org.python.python               0x000000010a9ac093 PyEval_EvalCodeEx + 1641
9   org.python.python               0x000000010a9b28c8 0x10a92c000 + 551112
10  org.python.python               0x000000010a9af4d4 PyEval_EvalFrameEx + 13079
11  org.python.python               0x000000010a9ac093 PyEval_EvalCodeEx + 1641
12  org.python.python               0x000000010a9b28c8 0x10a92c000 + 551112
13  org.python.python               0x000000010a9af4d4 PyEval_EvalFrameEx + 13079
14  org.python.python               0x000000010a9ac093 PyEval_EvalCodeEx + 1641
15  org.python.python               0x000000010a9b28c8 0x10a92c000 + 551112
16  org.python.python               0x000000010a9af4d4 PyEval_EvalFrameEx + 13079
17  org.python.python               0x000000010a9ac093 PyEval_EvalCodeEx + 1641
18  org.python.python               0x000000010a953796 0x10a92c000 + 161686
19  org.python.python               0x000000010a935f72 PyObject_Call + 101
20  org.python.python               0x000000010a9b0395 PyEval_EvalFrameEx + 16856
21  org.python.python               0x000000010a9ac093 PyEval_EvalCodeEx + 1641
22  org.python.python               0x000000010a953796 0x10a92c000 + 161686
23  org.python.python               0x000000010a935f72 PyObject_Call + 101
24  org.python.python               0x000000010a9409a7 0x10a92c000 + 84391
25  org.python.python               0x000000010a935f72 PyObject_Call + 101
26  org.python.python               0x000000010a97acad 0x10a92c000 + 322733
27  org.python.python               0x000000010a935f72 PyObject_Call + 101
28  org.python.python               0x000000010a9afdf5 PyEval_EvalFrameEx + 15416
29  org.python.python               0x000000010a9b2864 0x10a92c000 + 551012
30  org.python.python               0x000000010a9af4d4 PyEval_EvalFrameEx + 13079
31  org.python.python               0x000000010a9ac093 PyEval_EvalCodeEx + 1641
32  org.python.python               0x000000010a953796 0x10a92c000 + 161686
33  org.python.python               0x000000010a935f72 PyObject_Call + 101
34  org.python.python               0x000000010a9b0395 PyEval_EvalFrameEx + 16856
35  org.python.python               0x000000010a9b2864 0x10a92c000 + 551012
36  org.python.python               0x000000010a9af4d4 PyEval_EvalFrameEx + 13079
37  org.python.python               0x000000010a9b2864 0x10a92c000 + 551012
38  org.python.python               0x000000010a9af4d4 PyEval_EvalFrameEx + 13079
39  org.python.python               0x000000010a9ac093 PyEval_EvalCodeEx + 1641
40  org.python.python               0x000000010a953796 0x10a92c000 + 161686
41  org.python.python               0x000000010a935f72 PyObject_Call + 101
42  org.python.python               0x000000010a9b0395 PyEval_EvalFrameEx + 16856
43  org.python.python               0x000000010a9ac093 PyEval_EvalCodeEx + 1641
44  org.python.python               0x000000010a953796 0x10a92c000 + 161686
45  org.python.python               0x000000010a935f72 PyObject_Call + 101
46  org.python.python               0x000000010a9b0395 PyEval_EvalFrameEx + 16856
47  org.python.python               0x000000010a9ac093 PyEval_EvalCodeEx + 1641
48  org.python.python               0x000000010a9b28c8 0x10a92c000 + 551112
49  org.python.python               0x000000010a9af4d4 PyEval_EvalFrameEx + 13079
50  org.python.python               0x000000010a9ac093 PyEval_EvalCodeEx + 1641
51  org.python.python               0x000000010a953796 0x10a92c000 + 161686
52  org.python.python               0x000000010a935f72 PyObject_Call + 101
53  org.python.python               0x000000010a9409a7 0x10a92c000 + 84391
54  org.python.python               0x000000010a935f72 PyObject_Call + 101
55  org.python.python               0x000000010a9b201f PyEval_CallObjectWithKeywords + 93
56  org.python.python               0x000000010a93ec59 PyInstance_New + 123
57  org.python.python               0x000000010a935f72 PyObject_Call + 101
58  org.python.python               0x000000010a9afdf5 PyEval_EvalFrameEx + 15416
59  org.python.python               0x000000010a9ac093 PyEval_EvalCodeEx + 1641
60  org.python.python               0x000000010a953796 0x10a92c000 + 161686
61  org.python.python               0x000000010a935f72 PyObject_Call + 101
62  org.python.python               0x000000010a9b0395 PyEval_EvalFrameEx + 16856
63  org.python.python               0x000000010a9ac093 PyEval_EvalCodeEx + 1641
64  org.python.python               0x000000010a9b28c8 0x10a92c000 + 551112
65  org.python.python               0x000000010a9af4d4 PyEval_EvalFrameEx + 13079
66  org.python.python               0x000000010a9ac093 PyEval_EvalCodeEx + 1641
67  org.python.python               0x000000010a9b28c8 0x10a92c000 + 551112
68  org.python.python               0x000000010a9af4d4 PyEval_EvalFrameEx + 13079
69  org.python.python               0x000000010a9ac093 PyEval_EvalCodeEx + 1641
70  org.python.python               0x000000010a953796 0x10a92c000 + 161686
71  org.python.python               0x000000010a935f72 PyObject_Call + 101
72  org.python.python               0x000000010a9b0395 PyEval_EvalFrameEx + 16856
73  org.python.python               0x000000010a9b2864 0x10a92c000 + 551012
74  org.python.python               0x000000010a9af4d4 PyEval_EvalFrameEx + 13079
75  org.python.python               0x000000010a9ac093 PyEval_EvalCodeEx + 1641
76  org.python.python               0x000000010a953796 0x10a92c000 + 161686
77  org.python.python               0x000000010a935f72 PyObject_Call + 101
78  org.python.python               0x000000010a9409a7 0x10a92c000 + 84391
79  org.python.python               0x000000010a935f72 PyObject_Call + 101
80  org.python.python               0x000000010a9b201f PyEval_CallObjectWithKeywords + 93
81  org.python.python               0x000000010a93ec59 PyInstance_New + 123
82  org.python.python               0x000000010a935f72 PyObject_Call + 101
83  org.python.python               0x000000010a9afdf5 PyEval_EvalFrameEx + 15416
84  org.python.python               0x000000010a9ac093 PyEval_EvalCodeEx + 1641
85  org.python.python               0x000000010a9b28c8 0x10a92c000 + 551112
86  org.python.python               0x000000010a9af4d4 PyEval_EvalFrameEx + 13079
87  org.python.python               0x000000010a9ac093 PyEval_EvalCodeEx + 1641
88  org.python.python               0x000000010a953796 0x10a92c000 + 161686
89  org.python.python               0x000000010a935f72 PyObject_Call + 101
90  org.python.python               0x000000010a9b0395 PyEval_EvalFrameEx + 16856
91  org.python.python               0x000000010a9b2864 0x10a92c000 + 551012
92  org.python.python               0x000000010a9af4d4 PyEval_EvalFrameEx + 13079
93  org.python.python               0x000000010a9b2864 0x10a92c000 + 551012
94  org.python.python               0x000000010a9af4d4 PyEval_EvalFrameEx + 13079
95  org.python.python               0x000000010a9ac093 PyEval_EvalCodeEx + 1641
96  org.python.python               0x000000010a953796 0x10a92c000 + 161686
97  org.python.python               0x000000010a935f72 PyObject_Call + 101
98  org.python.python               0x000000010a9409a7 0x10a92c000 + 84391
99  org.python.python               0x000000010a935f72 PyObject_Call + 101
100 org.python.python               0x000000010a93fc70 0x10a92c000 + 81008
101 org.python.python               0x000000010a935f72 PyObject_Call + 101
102 org.python.python               0x000000010a9afdf5 PyEval_EvalFrameEx + 15416
103 org.python.python               0x000000010a9ac093 PyEval_EvalCodeEx + 1641
104 org.python.python               0x000000010a953796 0x10a92c000 + 161686
105 org.python.python               0x000000010a935f72 PyObject_Call + 101
106 org.python.python               0x000000010a9b0395 PyEval_EvalFrameEx + 16856
107 org.python.python               0x000000010a9b2864 0x10a92c000 + 551012
108 org.python.python               0x000000010a9af4d4 PyEval_EvalFrameEx + 13079
109 org.python.python               0x000000010a9b2864 0x10a92c000 + 551012
110 org.python.python               0x000000010a9af4d4 PyEval_EvalFrameEx + 13079
111 org.python.python               0x000000010a9ac093 PyEval_EvalCodeEx + 1641
112 org.python.python               0x000000010a953796 0x10a92c000 + 161686
113 org.python.python               0x000000010a935f72 PyObject_Call + 101
114 org.python.python               0x000000010a9409a7 0x10a92c000 + 84391
115 org.python.python               0x000000010a935f72 PyObject_Call + 101
116 org.python.python               0x000000010a93fc70 0x10a92c000 + 81008
117 org.python.python               0x000000010a935f72 PyObject_Call + 101
118 org.python.python               0x000000010a9afdf5 PyEval_EvalFrameEx + 15416
119 org.python.python               0x000000010a9b2864 0x10a92c000 + 551012
120 org.python.python               0x000000010a9af4d4 PyEval_EvalFrameEx + 13079
121 org.python.python               0x000000010a9b2864 0x10a92c000 + 551012
122 org.python.python               0x000000010a9af4d4 PyEval_EvalFrameEx + 13079
123 org.python.python               0x000000010a9ac093 PyEval_EvalCodeEx + 1641
124 org.python.python               0x000000010a953796 0x10a92c000 + 161686
125 org.python.python               0x000000010a935f72 PyObject_Call + 101
126 org.python.python               0x000000010a9b0395 PyEval_EvalFrameEx + 16856
127 org.python.python               0x000000010a9b2864 0x10a92c000 + 551012
128 org.python.python               0x000000010a9af4d4 PyEval_EvalFrameEx + 13079
129 org.python.python               0x000000010a9b2864 0x10a92c000 + 551012
130 org.python.python               0x000000010a9af4d4 PyEval_EvalFrameEx + 13079
131 org.python.python               0x000000010a9ac093 PyEval_EvalCodeEx + 1641
132 org.python.python               0x000000010a953796 0x10a92c000 + 161686
133 org.python.python               0x000000010a935f72 PyObject_Call + 101
134 org.python.python               0x000000010a9409a7 0x10a92c000 + 84391
135 org.python.python               0x000000010a935f72 PyObject_Call + 101
136 org.python.python               0x000000010a93fc70 0x10a92c000 + 81008
137 org.python.python               0x000000010a935f72 PyObject_Call + 101
138 org.python.python               0x000000010a9afdf5 PyEval_EvalFrameEx + 15416
139 org.python.python               0x000000010a9ac093 PyEval_EvalCodeEx + 1641
140 org.python.python               0x000000010a9b28c8 0x10a92c000 + 551112
141 org.python.python               0x000000010a9af4d4 PyEval_EvalFrameEx + 13079
142 org.python.python               0x000000010a9b2864 0x10a92c000 + 551012
143 org.python.python               0x000000010a9af4d4 PyEval_EvalFrameEx + 13079
144 org.python.python               0x000000010a9ac093 PyEval_EvalCodeEx + 1641
145 org.python.python               0x000000010a9aba24 PyEval_EvalCode + 54
146 org.python.python               0x000000010a9cac2c 0x10a92c000 + 650284
147 org.python.python               0x000000010a9cacd3 PyRun_FileExFlags + 137
148 org.python.python               0x000000010a9ca821 PyRun_SimpleFileExFlags + 718
149 org.python.python               0x000000010a9db363 Py_Main + 2995
150 libdyld.dylib                   0x00007fff8a7445fd start + 1

Thread 0 crashed with X86 Thread State (64-bit):
  rax: 0x000000000000000a  rbx: 0x0000000000000002  rcx: 0x000000000000000a  rdx: 0x0000000000000022
  rdi: 0x0000000000000002  rsi: 0x000000010ca2c7e0  rbp: 0x00007fff552d1e90  rsp: 0x00007fff552d1bf0
   r8: 0x0000000000000040   r9: 0x00007fff552d2200  r10: 0x0000000000000200  r11: 0x0000000000c9e6bf
  r12: 0x00007fff552d25e0  r13: 0x0000000000000000  r14: 0x0000000000000000  r15: 0x000000010ca2c7e0
  rip: 0x000000010c8008fc  rfl: 0x0000000000010206  cr2: 0x000000000000002a

Logical CPU:     6
Error Code:      0x00000004
Trap Number:     14

Binary Images:
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VM Region Summary:
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REGION TYPE                      VIRTUAL
===========                      =======
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MALLOC (admin)                       16K
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Stack                              64.0M
VM_ALLOCATE                          16K
__DATA                             2612K
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__TEXT                             37.8M
__UNICODE                           544K
shared memory                         4K
===========                      =======
TOTAL                             445.4M
vitaly-krugl commented 9 years ago

CC @oxtopus, @rhyolight

rhyolight commented 9 years ago

@vitaly-krugl Can you re-install with the latest code / instructions and try running tests again? (The test commands have changed).

vitaly-krugl commented 9 years ago

@rhyolight: trying it now, will post an update

vitaly-krugl commented 9 years ago

work-in-progress comments: Build/Install:

  1. git clean -fdx
  2. pip install --user --allow-all-external --allow-unverified PIL --allow-unverified psutil -r external/common/requirements.txt
  3. python setup.py build
  4. python setup.py develop --install-dir=~/Library/Python/2.7/lib/python/site-packages/ --script-dir=~/Library/Python/2.7/bin/

There is a fatal error reported during the build regarding capnp (but the build completes with 0 return code) while running pip install --user -r external/common/requirements.txt:

    /var/folders/kn/xpy4z9wx001_zwmfyzcgxcg40000gp/T/tmpsAym2b/vers.cpp:4:10: fatal error: 'capnp/common.h' file not found
    #include "capnp/common.h"

$NUPIC/scripts/run_nupic_tests -u --coverage failed:

tests/unit/nupic/algorithms/tp10x2_test.py:242: TP10X2Test.testTPs FAILED
/Users/vkruglikov/nta/nupic/tests/unit/nupic/algorithms/tp10x2_test.py:241: running the test CRASHED with signal 11

$NUPIC/scripts/run_nupic_tests -i --coverage failed:

tests/integration/nupic/algorithms/tp_likelihood_test.py:414: TPLikelihoodTest.testLikelihood1Long FAILED
/Users/vkruglikov/nta/nupic/tests/integration/nupic/algorithms/tp_likelihood_test.py:413: running the test CRASHED with signal 11
breznak commented 9 years ago

'capnp/common.h' file not found

i've seen and reported this one, at least my installation works fine even with this err.

On Tue, Jan 13, 2015 at 8:58 PM, vitaly-krugl notifications@github.com wrote:

work-in-progress comments:

There is a fatal error reported during the build regarding capnp (but the build completes with 0 return code):

/var/folders/kn/xpy4z9wx001_zwmfyzcgxcg40000gp/T/tmpsAym2b/vers.cpp:4:10: fatal error: 'capnp/common.h' file not found
#include "capnp/common.h"

— Reply to this email directly or view it on GitHub https://github.com/numenta/nupic/issues/1569#issuecomment-69808943.

Marek Otahal :o)

rhyolight commented 9 years ago

@scottpurdy Does the error above concern you?

vitaly-krugl commented 9 years ago

@rhyolight: I tried various cleanups and rebuilds, and am still getting those signal 11 (SIGSEGV) crashes as before. Last time it was on Mac OS X Mavericks, this time on Yosemite

rhyolight commented 9 years ago

Thanks, @vitaly-krugl. Let's sit down tomorrow so I can take a look.

scottpurdy commented 9 years ago

@vitaly-krugl - I'd like to check out your system. First, I would like to see if pycapnp works after you install from requirements.txt. I am guessing that it falls back to a workaround when you see that fatal error but if it is an actual error then I want to use your machine to figure out #1719

Second, I am suspicious that your environment variables aren't set right. The NuPIC build has been changing fairly frequently and it looks like it may have to do with this. Although some of the things @breznak has been filing make me think there may be a bigger issue (like #1699).

vitaly-krugl commented 9 years ago

The problem appears to be due to a snarled xcode install on my dev laptop. At the time of the failures, gcc -v was reporting the LLVM version of 5.x (don't remember the exact value of the x), and App Store was stuck trying to update Xcode to v6.1.1 (it would periodically report "this item is temporarily unavailable"). In an effort to remedy the App Store issue, I dragged /Applications/xcode to Trash and emptied the Trash folder. After this, gcc -v started reporting LLVM version 6.0. It appears that the full xcode installation was somehow obscuring the more recent version of command-line developer tools (that might have been installed the other day when I ran xcode-select --install). I hope this write-up helps someone else who might be running into a similar snafu.

rhyolight commented 9 years ago

facepalm