OK, I added an issue on github. I think for me all I need is a switch I can
use to force the setting (or not) of _POSIX_BARRIERS_MINE. The reason
-U_POSIX_BARRIERS_MINE didn't work is that the logic in blosc.c overwrites
it...
On Thu, Mar 8, 2012 at 9:31 AM, Francesc Alted <fal...@pytables.org> wrote:
> Excellent! I still have to figure out why your system does not support
> posix threads barriers properly, but most probably the patch is a good
> workaround for your case. Please feel free to file a bug so that this is
> not lost.
>
> Thanks,
>
> Francesc
>
> On Mar 7, 2012, at 11:46 PM, Chris Kees wrote:
>
> > Hi Francesc,
> >
> > _POSIX_BARRIERS is 200112L in that machine's standard headers. I put in
> the hack below in blosc.c (the last conditional) and pytables compiled
> fine. I will run the test set tomorrow.
> >
> > Thanks,
> > Chris
> >
> > #if defined(_POSIX_BARRIERS) && ( (_POSIX_BARRIERS - 20012L) >= 0 &&
> _POSIX_BARRIERS != 200112L)
> >
> > On Mar 7, 2012, at 8:25 PM, Francesc Alted wrote:
> >
> >> On Mar 7, 2012, at 6:05 PM, Chris Kees wrote:
> >>> On Wed, Mar 7, 2012 at 5:18 PM, Francesc Alted <fal...@pytables.org>
> wrote:
> >>> On Mar 7, 2012, at 3:14 PM, Francesc Alted wrote:
> >>>
> >>>> On Mar 7, 2012, at 1:57 PM, Chris Kees wrote:
> >>>>
> >>>>> Hi Anthony,
> >>>>>
> >>>>> I'm using 1.8.7 on ranger. Here is the topmost error:
> >>>>>
> >>>>> compile options: '-DNDEBUG=1 -DHAVE_BZ2_LIB=1 -Iblosc
> -I/work/01020/cekees/ranger.gnu/build/ranger.gnu/lib/python2.7/site-packages/numpy/core/include
> -I/work/01020/cekee
> >>>>> s/ranger.gnu/build/ranger.gnu/include
> -I/work/01020/cekees/ranger.gnu/build/ranger.gnu/include/python2.7 -c'
> >>>>> extra options: '-Isrc -DH5_USE_16_API'
> >>>>> gcc: blosc/blosclz.c
> >>>>> gcc: src/H5ARRAY.c
> >>>>> In file included from
> /work/01020/cekees/ranger.gnu/build/ranger.gnu/include/python2.7/Python.h:8,
> >>>>> from src/utils.h:1,
> >>>>> from src/H5ARRAY.c:4:
> >>>>>
> /work/01020/cekees/ranger.gnu/build/ranger.gnu/include/python2.7/pyconfig.h:1155:1:
> warning: "_POSIX_C_SOURCE" redefined
> >>>>> In file included from
> /work/01020/cekees/ranger.gnu/build/ranger.gnu/include/H5public.h:37,
> >>>>> from
> /work/01020/cekees/ranger.gnu/build/ranger.gnu/include/hdf5.h:24,
> >>>>> from src/H5ATTR.h:19,
> >>>>> from src/H5ARRAY.c:1:
> >>>>>
> /share/apps/gcc_amd/4.4.5/bin/../lib/gcc/x86_64-unknown-linux-gnu/4.4.5/include-fixed/features.h:199:1:
> warning: this is the location of the previous definition
> >>>>> In file included from
> /work/01020/cekees/ranger.gnu/build/ranger.gnu/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1972,
> >>>>> from
> /work/01020/cekees/ranger.gnu/build/ranger.gnu/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:17,
> >>>>> from
> /work/01020/cekees/ranger.gnu/build/ranger.gnu/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:15,
> >>>>> from src/utils.h:2,
> >>>>> from src/H5ARRAY.c:4:
> >>>>>
> /work/01020/cekees/ranger.gnu/build/ranger.gnu/lib/python2.7/site-packages/numpy/core/include/numpy/npy_deprecated_api.h:11:2:
> warning: #warning "Using deprecated NumPy
> >>>>> API, disable it by #defining NPY_NO_DEPRECATED_API"
> >>>>>
> /work/01020/cekees/ranger.gnu/build/ranger.gnu/lib/python2.7/site-packages/numpy/core/include/numpy/__multiarray_api.h:1666:
> warning: '_import_array' defined but not use
> >>>>> d
> >>>>> gcc: blosc/blosc.c
> >>>>> blosc/blosc.c:79: error: expected '=', ',', ';', 'asm' or
> '__attribute__' before 'barr_init'
> >>>>
> >>>> Uf, that looks really ugly. Which compiler and version are you
> using? Can you look in this machine's thread.h and tell us the value of
> _POSIX_BARRIERS symbol?
> >>>
> >>> BTW, numexpr also uses the same parallel engine than blosc. As
> numexpr is a requisite for PyTables, I'm curious about if you have been
> able to compile it too.
> >>>
> >>>
> >>> Yes, I was able to compiler numexpr. The versions of pytables
> dependencies I'm using are:
> >>>
> >>> * Found numpy 1.7.0.dev-0b400cb package installed.
> >>> * Found numexpr 1.5.dev package installed.
> >>
> >> Hmm, this is a good sign. Blosc has probably some more hacks for the
> threading code, so this is probably why your compiler is behaving
> differently. The compiler version should be fine too. Do you have
> internally an expert in posix threading that can have a look at the
> offending line? I'm a bit out of ideas.
> >>
> >> -- Francesc Alted
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> ------------------------------------------------------------------------------
> >> Virtualization & Cloud Management Using Capacity Planning
> >> Cloud computing makes use of virtualization - but cloud computing
> >> also focuses on allowing computing to be delivered as a service.
> >> http://www.accelacomm.com/jaw/sfnl/114/51521223/
> >> _______________________________________________
> >> Pytables-users mailing list
> >> Pytables-users@lists.sourceforge.net
> >> https://lists.sourceforge.net/lists/listinfo/pytables-users
> >
> >
> >
> ------------------------------------------------------------------------------
> > Virtualization & Cloud Management Using Capacity Planning
> > Cloud computing makes use of virtualization - but cloud computing
> > also focuses on allowing computing to be delivered as a service.
> > http://www.accelacomm.com/jaw/sfnl/114/51521223/
> > _______________________________________________
> > Pytables-users mailing list
> > Pytables-users@lists.sourceforge.net
> > https://lists.sourceforge.net/lists/listinfo/pytables-users
>
> -- Francesc Alted
>
>
>
>
>
>
>
>
> ------------------------------------------------------------------------------
> Virtualization & Cloud Management Using Capacity Planning
> Cloud computing makes use of virtualization - but cloud computing
> also focuses on allowing computing to be delivered as a service.
> http://www.accelacomm.com/jaw/sfnl/114/51521223/
> _______________________________________________
> Pytables-users mailing list
> Pytables-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/pytables-users
>
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Cloud computing makes use of virtualization - but cloud computing
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