Perfect. Thank you! On Mar 9, 2012, at 9:11 AM, Chris Kees wrote:
> 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 > > ------------------------------------------------------------------------------ > 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
