Re: [Pytables-users] segmentation fault on Mac OS X Lion when running tables.test()

[Josh M. <jos...@gm...>]

On Jun 19, 2012, at 4:37 AM, David Donovan wrote:

> 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?


Hi David,

I always use homebrew for any of my prerequisites:

  http://mxcl.github.com/homebrew/


Cheers
~Josh


> 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
>>>