Hello Chris,
I just tried recompiling with v1.8.7 from the hdf group website on ubuntu
and everything worked great.
If we look at the line 79 of
blosc.c<https://github.com/PyTables/PyTables/blob/master/blosc/blosc.c#L79>,
we see that it is inside of a #ifdef block related to posix threads. Since
you are on ranger,I imagine that something special might be going on.
Would it be possible for you to try to compile it with the symbol
'_POSIX_BARRIERS_MINE' undefined? You can do this by setting CFLAGS on
the command line:
CFLAGS='-U_POSIX_BARRIERS_MINE' python setup.py build
Hopefully this will be a quick fix to at least get something up and running.
Be Well
Anthony
On Wed, Mar 7, 2012 at 3:57 PM, Chris Kees <cek...@gmail.com> 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'
>
>
>
> On Wed, Mar 7, 2012 at 3:38 PM, Anthony Scopatz <scop...@gmail.com> wrote:
>
>> Hi Chris,
>>
>> PyTables should work with HDF5 v1.8.7. (Apparently v1.8.8 is out but I
>> haven't tested it with that.) What version are you using at TACC?
>>
>> Also, what is the top most build error that you are getting?
>>
>> Be Well
>> Anthony
>>
>> On Wed, Mar 7, 2012 at 3:35 PM, Chris Kees <cek...@gmail.com> wrote:
>>
>>> Hi,
>>>
>>> I'm having some trouble building pytables on an HPC machine (ranger at
>>> the texas advanced computing center). If I do a git checkout of v.2.1.2
>>> pytables builds/installs fine. Anything more recent gives errors compiling
>>> (related to blosc...). I would like to help get the main branch working on
>>> this machine and was hoping I could get a recommendation of which version
>>> of hdf5 I should be using to go with the main pytables branch.
>>>
>>> Thanks,
>>> Chris
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Virtualization & Cloud Management Using Capacity Planning
>>> Cloud computing makes use of virtualization - but cloud computing
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>>> 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/
>> _______________________________________________
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>> Pytables-users@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/pytables-users
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>>
>
>
> ------------------------------------------------------------------------------
> 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.
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>
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