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

[Anthony S. <sc...@gm...>]

Hmmm That all looks correct.  Have you tried linking PyTables against the
HDF5 from MacPorts?  This has worked for me in the past...

On Mon, Jun 18, 2012 at 9:37 PM, David Donovan <don...@gm...> 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?
>
> 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
> >>
> >>
> >>
> ------------------------------------------------------------------------------
> >> Live Security Virtual Conference
> >> Exclusive live event will cover all the ways today's security and
> >> threat landscape has changed and how IT managers can respond.
> Discussions
> >> will include endpoint security, mobile security and the latest in
> malware
> >> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> >> _______________________________________________
> >> Pytables-users mailing list
> >> Pyt...@li...
> >> https://lists.sourceforge.net/lists/listinfo/pytables-users
> >
> >
> >
> >
> ------------------------------------------------------------------------------
> > Live Security Virtual Conference
> > Exclusive live event will cover all the ways today's security and
> > threat landscape has changed and how IT managers can respond. Discussions
> > will include endpoint security, mobile security and the latest in malware
> > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> > _______________________________________________
> > Pytables-users mailing list
> > Pyt...@li...
> > https://lists.sourceforge.net/lists/listinfo/pytables-users
> >
>
>
> ------------------------------------------------------------------------------
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and
> threat landscape has changed and how IT managers can respond. Discussions
> will include endpoint security, mobile security and the latest in malware
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> _______________________________________________
> Pytables-users mailing list
> Pyt...@li...
> https://lists.sourceforge.net/lists/listinfo/pytables-users
>