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Re: [Pytables-users] segmentation fault on Mac OS X Lion when running tables.test()
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From: David D. <don...@gm...> - 2012-06-19 02:37:25
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Hi Anthony,
Thanks for the response. Installed HDF5 1.8.9 using the following
flags for configure.
`./configure --prefix=/usr/local
--with-szlib=/Library/Frameworks/Python.framework/Versions/Current
CPPFLAGS=-I/Library/Frameworks/Python.framework/Versions/Current/include
LDFLAGS=-L/Library/Frameworks/Python.framework/Versions/Current/lib`
Also, I had to modify the optimization flag for gcc-4 in order to pass
the make check part (as noted on the HDF5 page).
`Conversion Tests fail on Mac OS X 10.7 (Lion) Users have reported
that when building HDF5, the conversion tests failed (make check) in
dt_arith.chk. A workaround is to edit ./< HDF5source
>/config/gnu-flags, search for PROD_CFLAGS under "gcc-4.*", and change
the value for PROD_CFLAGS to "-O0".`
Then:
'make'
'make check'
'sudo make install'
Is there a better way? Is tables somehow having a hard time finding
the HDF5 library do you think?
Thanks!
Best Regards,
David
On Sat, Jun 16, 2012 at 12:57 AM, Anthony Scopatz <sc...@gm...> wrote:
> Hi David,
>
> How did you build / install HDF5?
>
> Be Well
> Anthony
>
> On Fri, Jun 15, 2012 at 7:14 PM, David Donovan <don...@gm...> wrote:
>>
>> Hi Everyone,
>>
>> I am having problems running the tests for PyTables on Mac OS X Lion.
>> I have tried HDF5 version 1.8.5 as well, but I still get the same issue.
>>
>> Any thoughts would be helpful...
>>
>> Thanks for any help you can provide.
>>
>> Best Regards,
>> David Donovan
>>
>>
>> impPython 2.7.1 (r271:86832, Jul 31 2011, 19:30:53)
>> [GCC 4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2335.15.00)] on
>> darwin
>> Type "help", "copyright", "credits" or "license" for more information.
>> >>> import tables
>> table>>> tables.test()
>>
>> -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
>> PyTables version: 2.3.1
>> HDF5 version: 1.8.9
>> NumPy version: 1.7.0.dev-0c5f480
>> Numexpr version: 2.0.1 (not using Intel's VML/MKL)
>> Zlib version: 1.2.5 (in Python interpreter)
>> LZO version: 2.06 (Aug 12 2011)
>> BZIP2 version: 1.0.6 (6-Sept-2010)
>> Blosc version: 1.1.2 (2010-11-04)
>> Cython version: 0.16
>> Python version: 2.7.1 (r271:86832, Jul 31 2011, 19:30:53)
>> [GCC 4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2335.15.00)]
>> Platform: darwin-i386
>> Byte-ordering: little
>> Detected cores: 2
>>
>> -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
>> Performing only a light (yet comprehensive) subset of the test suite.
>> If you want a more complete test, try passing the --heavy flag to this
>> script
>> (or set the 'heavy' parameter in case you are using tables.test() call).
>> The whole suite will take more than 4 hours to complete on a relatively
>> modern CPU and around 512 MB of main memory.
>>
>> -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
>>
>> .....................................................................................................................................FSegmentation
>> fault: 11
>>
>>
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>
>
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> will include endpoint security, mobile security and the latest in malware
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