Looks like the same error even with the extra flag:
compile options: '-DNDEBUG=1 -DHAVE_BZ2_LIB=1 -Iblosc
-I/share/home/01020/cekees/proteus/ranger.gnu/lib/python2.7/site-package
s/numpy/core/include -I/share/home/01020/cekees/proteus/ranger.gnu/include
-I/share/home/01020/cekees/proteus/ranger.gnu/inclu
de/python2.7 -c'
extra options: '-U_POSIX_BARRIERS_MINE -Isrc -DH5_USE_16_API'
gcc: blosc/blosclz.c
gcc: src/H5ARRAY.c
In file included from
/share/home/01020/cekees/proteus/ranger.gnu/include/python2.7/Python.h:8,
from src/utils.h:1,
from src/H5ARRAY.c:4:
/share/home/01020/cekees/proteus/ranger.gnu/include/python2.7/pyconfig.h:1155:1:
warning: "_POSIX_C_SOURCE" redefined
In file included from
/share/home/01020/cekees/proteus/ranger.gnu/include/H5public.h:37,
from
/share/home/01020/cekees/proteus/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 l
ocation of the previous definition
In file included from
/share/home/01020/cekees/proteus/ranger.gnu/lib/python2.7/site-packages/numpy/core/include/numpy/ndarray
types.h:1972,
from
/share/home/01020/cekees/proteus/ranger.gnu/lib/python2.7/site-packages/numpy/core/include/numpy/ndarray
object.h:17,
from
/share/home/01020/cekees/proteus/ranger.gnu/lib/python2.7/site-packages/numpy/core/include/numpy/arrayob
ject.h:15,
from src/utils.h:2,
from src/H5ARRAY.c:4:
/share/home/01020/cekees/proteus/ranger.gnu/lib/python2.7/site-packages/numpy/core/include/numpy/npy_deprecated_api.h:11:2:
wa
rning: #warning "Using deprecated NumPy API, disable it by #defining
NPY_NO_DEPRECATED_API"
/share/home/01020/cekees/proteus/ranger.gnu/lib/python2.7/site-packages/numpy/core/include/numpy/__multiarray_api.h:1666:
warn
ing: '_import_array' defined but not used
gcc: blosc/blosc.c
blosc/blosc.c:79: error: expected '=', ',', ';', 'asm' or '__attribute__'
before 'barr_init'
On Wed, Mar 7, 2012 at 4:44 PM, Anthony Scopatz <scop...@gmail.com> wrote:
> 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
>>>> 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
>>>
>>>
>>
>>
>> ------------------------------------------------------------------------------
>> 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
>
>
------------------------------------------------------------------------------
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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