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
