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htm-community / nupic.studio

NuPIC Studio is a powerful all­-in-­one tool that allows users create a HTM neural network from scratch, train it, collect statistics, and share it among the members of the community.
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Fatal Python error: PyThreadState_Get: no current thread #22

Closed kkittel closed 9 years ago

kkittel commented 9 years ago

Hello,

I have installed nustudio successfully on OS X Yosemite, but when I run it I get the following hard crash: nustudio Fatal Python error: PyThreadState_Get: no current thread zsh: abort nustudio

I had a hard time installing all the dependencies under Yosemite first I tried macports then switched to homebrew. After much problems, homebrew now seems to be working correctly on my system. One of the other posts suggested that the libray links might not match the version of Python running on my system, but that doesn't seem to be an issue with mine.

python Python 2.7.9 (default, Jan 31 2015, 04:25:24) [GCC 4.2.1 Compatible Apple LLVM 6.0 (clang-600.0.56)] on darwin Type "help", "copyright", "credits" or "license" for more information.

I also have the dump from the crash:

Process: Python [35875] Path: /usr/local/Cellar/python/2.7.9/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python Identifier: Python Version: 2.7.9 (2.7.9) Code Type: X86-64 (Native) Parent Process: zsh [29366] Responsible: iTerm [1067] User ID: 501

Date/Time: 2015-02-09 08:11:03.495 -0500 OS Version: Mac OS X 10.10.2 (14C109) Report Version: 11 Anonymous UUID: B16CB0A6-AA57-F152-BD5F-1A012A1D4EFD

Sleep/Wake UUID: 42BA06E0-4BEB-42D6-8BA9-73096ED11DCD

Time Awake Since Boot: 300000 seconds Time Since Wake: 1600 seconds

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

Exception Type: EXC_CRASH (SIGABRT) Exception Codes: 0x0000000000000000, 0x0000000000000000

Application Specific Information: abort() called

Thread 0 Crashed:: Dispatch queue: com.apple.main-thread 0 libsystem_kernel.dylib 0x00007fff9262c286 pthread_kill + 10 1 libsystem_c.dylib 0x00007fff8b0edb53 abort + 129 2 org.python.python 0x000000010f12e901 Py_FatalError + 49 3 org.python.python 0x000000010f12d96c PyThreadState_Get + 44 4 org.python.python 0x000000010f129cbb Py_InitModule4_64 + 75 5 _math.so 0x000000010ebc8e95 init_math + 687 6 org.python.python 0x000000010b2302f7 _PyImport_LoadDynamicModule + 140 7 org.python.python 0x000000010b22ec1a imp_load_module + 243 8 org.python.python 0x000000010b21b80e PyEval_EvalFrameEx + 14392 9 org.python.python 0x000000010b21e656 fast_function + 262 10 org.python.python 0x000000010b21b428 PyEval_EvalFrameEx + 13394 11 org.python.python 0x000000010b217da2 PyEval_EvalCodeEx + 1409 12 org.python.python 0x000000010b21781b PyEval_EvalCode + 54 13 org.python.python 0x000000010b22c85e PyImport_ExecCodeModuleEx + 241 14 org.python.python 0x000000010b22f53e load_source_module + 1091 15 org.python.python 0x000000010b22ffdf import_submodule + 270 16 org.python.python 0x000000010b22fba9 load_next + 280 17 org.python.python 0x000000010b22dde9 PyImport_ImportModuleLevel + 1191 18 org.python.python 0x000000010b213403 builtin___import + 135 19 org.python.python 0x000000010b19e19a PyObject_Call + 99 20 org.python.python 0x000000010b21ddb3 PyEval_CallObjectWithKeywords + 93 21 org.python.python 0x000000010b21a08d PyEval_EvalFrameEx + 8375 22 org.python.python 0x000000010b217da2 PyEval_EvalCodeEx + 1409 23 org.python.python 0x000000010b21781b PyEval_EvalCode + 54 24 org.python.python 0x000000010b22c85e PyImport_ExecCodeModuleEx + 241 25 org.python.python 0x000000010b22f53e load_source_module + 1091 26 org.python.python 0x000000010b22ffdf import_submodule + 270 27 org.python.python 0x000000010b22fba9 load_next + 280 28 org.python.python 0x000000010b22dde9 PyImport_ImportModuleLevel + 1191 29 org.python.python 0x000000010b213403 builtin_import + 135 30 org.python.python 0x000000010b19e19a PyObject_Call + 99 31 org.python.python 0x000000010b21ddb3 PyEval_CallObjectWithKeywords + 93 32 org.python.python 0x000000010b21a08d PyEval_EvalFrameEx + 8375 33 org.python.python 0x000000010b217da2 PyEval_EvalCodeEx + 1409 34 org.python.python 0x000000010b21781b PyEval_EvalCode + 54 35 org.python.python 0x000000010b22c85e PyImport_ExecCodeModuleEx + 241 36 org.python.python 0x000000010b22f53e load_source_module + 1091 37 org.python.python 0x000000010b22ffdf import_submodule + 270 38 org.python.python 0x000000010b22fba9 load_next + 280 39 org.python.python 0x000000010b22dde9 PyImport_ImportModuleLevel + 1191 40 org.python.python 0x000000010b213403 builtin_import + 135 41 org.python.python 0x000000010b19e19a PyObject_Call + 99 42 org.python.python 0x000000010b21ddb3 PyEval_CallObjectWithKeywords + 93 43 org.python.python 0x000000010b21a08d PyEval_EvalFrameEx + 8375 44 org.python.python 0x000000010b217da2 PyEval_EvalCodeEx + 1409 45 org.python.python 0x000000010b21781b PyEval_EvalCode + 54 46 org.python.python 0x000000010b22c85e PyImport_ExecCodeModuleEx + 241 47 org.python.python 0x000000010b22f53e load_source_module + 1091 48 org.python.python 0x000000010b22ffdf import_submodule + 270 49 org.python.python 0x000000010b22fba9 load_next + 280 50 org.python.python 0x000000010b22dde9 PyImport_ImportModuleLevel + 1191 51 org.python.python 0x000000010b213403 builtin_import + 135 52 org.python.python 0x000000010b19e19a PyObject_Call + 99 53 org.python.python 0x000000010b21ddb3 PyEval_CallObjectWithKeywords + 93 54 org.python.python 0x000000010b21a08d PyEval_EvalFrameEx + 8375 55 org.python.python 0x000000010b217da2 PyEval_EvalCodeEx + 1409 56 org.python.python 0x000000010b21781b PyEval_EvalCode + 54 57 org.python.python 0x000000010b22c85e PyImport_ExecCodeModuleEx + 241 58 org.python.python 0x000000010b22f53e load_source_module + 1091 59 org.python.python 0x000000010b22ffdf import_submodule + 270 60 org.python.python 0x000000010b22fba9 load_next + 280 61 org.python.python 0x000000010b22dde9 PyImport_ImportModuleLevel + 1191 62 org.python.python 0x000000010b213403 builtin_import + 135 63 org.python.python 0x000000010b21c211 PyEval_EvalFrameEx + 16955 64 org.python.python 0x000000010b217da2 PyEval_EvalCodeEx + 1409 65 org.python.python 0x000000010b21e5c5 fast_function + 117 66 org.python.python 0x000000010b21b428 PyEval_EvalFrameEx + 13394 67 org.python.python 0x000000010b217da2 PyEval_EvalCodeEx + 1409 68 org.python.python 0x000000010b21e5c5 fast_function + 117 69 org.python.python 0x000000010b21b428 PyEval_EvalFrameEx + 13394 70 org.python.python 0x000000010b217da2 PyEval_EvalCodeEx + 1409 71 org.python.python 0x000000010b21e5c5 fast_function + 117 72 org.python.python 0x000000010b21b428 PyEval_EvalFrameEx + 13394 73 org.python.python 0x000000010b217da2 PyEval_EvalCodeEx + 1409 74 org.python.python 0x000000010b21e5c5 fast_function + 117 75 org.python.python 0x000000010b21b428 PyEval_EvalFrameEx + 13394 76 org.python.python 0x000000010b217da2 PyEval_EvalCodeEx + 1409 77 org.python.python 0x000000010b21781b PyEval_EvalCode + 54 78 org.python.python 0x000000010b2378ca run_mod + 53 79 org.python.python 0x000000010b23796d PyRun_FileExFlags + 133 80 org.python.python 0x000000010b23750a PyRun_SimpleFileExFlags + 769 81 org.python.python 0x000000010b248c83 Py_Main + 3051 82 libdyld.dylib 0x00007fff960825c9 start + 1

Thread 0 crashed with X86 Thread State (64-bit): rax: 0x0000000000000000 rbx: 0x0000000000000006 rcx: 0x00007fff54a6dc38 rdx: 0x0000000000000000 rdi: 0x0000000000000513 rsi: 0x0000000000000006 rbp: 0x00007fff54a6dc60 rsp: 0x00007fff54a6dc38 r8: 0x00007fff54a6dc50 r9: 0x00007fff7b20a300 r10: 0x0000000008000000 r11: 0x0000000000000206 r12: 0x00000000000003f5 r13: 0x0000000000000000 r14: 0x00007fff7b20a300 r15: 0x000000010eef27f0 rip: 0x00007fff9262c286 rfl: 0x0000000000000206 cr2: 0x00007fff7b00ffd8

Logical CPU: 0 Error Code: 0x02000148 Trap Number: 133

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External Modification Summary: Calls made by other processes targeting this process: task_for_pid: 0 thread_create: 0 thread_set_state: 0 Calls made by this process: task_for_pid: 0 thread_create: 0 thread_set_state: 0 Calls made by all processes on this machine: task_for_pid: 108396 thread_create: 0 thread_set_state: 0

VM Region Summary: ReadOnly portion of Libraries: Total=222.5M resident=115.4M(52%) swapped_out_or_unallocated=107.1M(48%) Writable regions: Total=40.8M written=11.9M(29%) resident=18.5M(45%) swapped_out=0K(0%) unallocated=22.3M(55%)

REGION TYPE VIRTUAL =========== ======= Kernel Alloc Once 4K MALLOC 30.4M MALLOC (admin) 32K STACK GUARD 56.0M Stack 8192K VM_ALLOCATE 16K DATA 17.9M IMAGE 528K LINKEDIT 81.8M TEXT 140.7M __UNICODE 544K shared memory 4K =========== ======= TOTAL 335.9M

Model: iMac8,1, BootROM IM81.00C1.B00, 2 processors, Intel Core 2 Duo, 2.4 GHz, 2 GB, SMC 1.29f1 Graphics: ATI Radeon HD 2400 XT, ATI Radeon HD 2400, PCIe, 128 MB Memory Module: BANK 0/DIMM0, 1 GB, DDR2 SDRAM, 800 MHz, 0xAD00000000000000, 0x48594D503131325336344352362D53362020 Memory Module: BANK 1/DIMM1, 1 GB, DDR2 SDRAM, 800 MHz, 0x7F7F7F7F7F510000, 0x36345431323830323145444C322E35423220 AirPort: spairport_wireless_card_type_airport_extreme (0x14E4, 0x8C), Broadcom BCM43xx 1.0 (5.10.131.36.16) Bluetooth: Version 4.3.2f6 15235, 3 services, 27 devices, 1 incoming serial ports Network Service: AirPort, AirPort, en1 Serial ATA Device: Hitachi HDP725025GLA380, 250.06 GB Parallel ATA Device: MATSHITADVD-R UJ-875 USB Device: Built-in iSight USB Device: Keyboard Hub USB Device: USB Receiver USB Device: Apple Keyboard USB Device: BRCM2046 Hub USB Device: Bluetooth USB Host Controller USB Device: IR Receiver Thunderbolt Bus:

rcrowder commented 9 years ago

Hi Karl. Thanks for this update. There's some tracking of this issue, or similar, at https://github.com/numenta/nupic/issues/1813

[GCC 4.2.1 Compatible Apple LLVM 6.0 (clang-600.0.56)] on darwin

If this is Python startup output, can you update with the GCC/CLANG --version installed?

kkittel commented 9 years ago

Can you give me detailed instructions to get the version of GCC/CLANG please?

kkittel commented 9 years ago

The other post suggested this:

If I replace /System/Library/Frameworks/Python.framework/Versions/2.7/Python (system python) with a soft link to /usr/local/Cellar/python/2.7.9/Frameworks/Python.framework/Versions/2.7/Python (homebrew python), running python -c "import nupic.bindings.math" produces no error.

Can someone give me some help explaining how to set up the soft link? My UNIX skills are a bit rusty but coming back slowly the more I use it.

kkittel commented 9 years ago

Is this what you wanted?

karl-kittels-imac% gcc --version Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/c++/4.2.1 Apple LLVM version 6.0 (clang-600.0.56) (based on LLVM 3.5svn) Target: x86_64-apple-darwin14.1.0 Thread model: posix

rhyolight commented 9 years ago

Yeah as @rcrowder said, this may be a NuPIC issue.

kkittel commented 9 years ago

No, I think it is a Python issue. I get this same error from anything that uses Python.

rhyolight commented 9 years ago

Then you probably have multiple versions of python installed on your machine that are conflicting somehow. I would recommend uninstalling all but one.

Matt Taylor OS Community Flag-Bearer Numenta

On Mon, Feb 9, 2015 at 2:46 PM, Karl Kittel notifications@github.com wrote:

No, I think it is a Python issue. I get this same error from anything that uses Python.

— Reply to this email directly or view it on GitHub https://github.com/nupic-community/nupic.studio/issues/22#issuecomment-73607449 .

kkittel commented 9 years ago

That is what I have been trying to do. How do I remove all versions of Python. The real problem is that Yosemite sucks.

kkittel commented 9 years ago

I found that Python 3.x and Python 2.7.x were installed on my system. Maybe they are interfering with each other. I tried uninstalling them both and reinstalling Python 2.7.9 but I still get the same error.

kkittel commented 9 years ago

The other post suggested this:

If I replace /System/Library/Frameworks/Python.framework/Versions/2.7/Python (system python) with a soft link to /usr/local/Cellar/python/2.7.9/Frameworks/Python.framework/Versions/2.7/Python (homebrew python), running python -c "import nupic.bindings.math" produces no error.

I get this same exact error. Can someone give me some help explaining how to set up the soft link?

kkittel commented 9 years ago

ln -s /System/Library/Frameworks/Python.framework/Versions/2.7/Python /usr/local/Cellar/python/2.7.9/Frameworks/Python.framework/Versions/2.7/Python ln: /usr/local/Cellar/python/2.7.9/Frameworks/Python.framework/Versions/2.7/Python: File exists

So what does this mean? I already have the soft link set up?

rcrowder commented 9 years ago

I'm keen to get a Mac, but languishing in Windows land at the moment. It does look like a minefield with Python on OS X. Potentially need to compare Root PATH, User PATH, and PythonPath env variables. http://stackoverflow.com/questions/14117945/too-many-different-python-versions-on-my-system-and-causing-problems

kkittel commented 9 years ago

OK, so the python interpreter runs on my system, I can do things like interactive help() ok, it doesn't crash right away. But it does crash when I do python -c "import nupic.bindings.math" or when I try to run nustudio.

david-ragazzi commented 9 years ago

Hey @kkittel, have you solved this problem? As said before, this is a nupic issue due to the command python -c "import nupic.bindings.math" present error. I recommend you create a issue on nupic repo (https://github.com/numenta/nupic/issues)?

@rcrowder @rhyolight Thanks for the help!

kkittel commented 9 years ago

Thanks, I opened a new issue on the other forum.

Regards,

Karl

Date: Wed, 18 Feb 2015 16:15:07 -0800 From: notifications@github.com To: nupic.studio@noreply.github.com CC: klkittel@hotmail.com Subject: Re: [nupic.studio] Fatal Python error: PyThreadState_Get: no current thread (#22)

Hey @kkittel, have you solved this problem? As said before, this is a nupic issue due to python -c "import nupic.bindings.math" error, i.e. nupic.bindings.math is nupic stuff. I recommend you create a issue on nupic repo (https://github.com/numenta/nupic/issues)?

@rcrowder @rhyolight Thanks for the help!

— Reply to this email directly or view it on GitHub.

david-ragazzi commented 9 years ago

BTW Once this problem is solved, I believe you will enjoy nupic.studio without problems.. :-)