A Wednesday 26 May 2010 06:21:15 escriguéreu:
> Hi Francesc,
>
> I'm not having any trouble with tables-2.2 and hdf5-1.8.4-patch, but 2.2rc1
> is producing some errors, which I've included below. Should I be disabling
> blosc somehow?
Damn! It seems that Mac OSX does not have support for pthreads barriers :-/
Unfortunately, you cannot disable blosc in PyTables and we should find a
workaround for Mac OSX instead. Meanwhile, you should be using PyTables 2.1.
If anybody here knows about a way to simulate barriers in Mac OSX by using
another pthreads weapons supported by Mac OSX (like mutex or condition vars),
I'm all ears!
Francesc
>
> -Chris
>
> % python setup.py build --hdf5=${MY_PREFIX} --lflags="-L${MY_PREFIX}/lib
> -lhdf5 -lz -lsz"
> * Found numpy 1.4.1 package installed.
> * Found numexpr 1.3.1 package installed.
> * Found HDF5 headers at ``/Users/cekees/src/proteus/darwin64/include``,
> library at ``/Users/cekees/src/proteus/darwin64/lib``.
> .. WARNING:: Could not find the HDF5 runtime.
> The HDF5 shared library was *not* found in the default library
> paths. In case of runtime problems, please remember to install it.
> * Could not find LZO 2 headers and library; disabling support for it.
> * Could not find LZO 1 headers and library; disabling support for it.
> * Found bzip2 headers at ``/usr/include``, library at ``/usr/lib``.
> * Found pthreads headers at ``/usr/include``, library at ``/usr/lib``.
> running build
> running build_py
> running build_ext
> building 'tables.utilsExtension' extension
> C compiler: /usr/bin/mpicc -arch x86_64 -fno-strict-aliasing -fno-common
> -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes
>
> compile options: '-DNDEBUG=1 -DHAVE_BZ2_LIB=1 -Iblosc
> -I/Users/cekees/src/proteus/darwin64/Python.framework/Versions/2.6/lib/pyth
> on2.6/site-packages/numpy/core/include -I/usr/include -I/usr/local/include
> -I/Users/cekees/src/proteus/darwin64/include
> -I/Users/cekees/src/proteus/darwin64/Python.framework/Versions/2.6/include/
> python2.6 -c'
> extra options: '-Isrc -DH5_USE_16_API'
> mpicc: tables/utilsExtension.c
> tables/utilsExtension.c: In function
> ‘__pyx_pf_6tables_14utilsExtension_AtomToHDF5Type’:
> tables/utilsExtension.c:5229: warning: ‘__pyx_v_tid’ may be used
> uninitialized in this function
> mpicc: blosc/shuffle.c
> mpicc: blosc/blosclz.c
> mpicc: src/utils.c
> /Users/cekees/src/proteus/darwin64/Python.framework/Versions/2.6/lib/python
> 2.6/site-packages/numpy/core/include/numpy/__multiarray_api.h:1188:
> warning: ‘_import_array’ defined but not used
> mpicc: blosc/blosc.c
> blosc/blosc.c:65: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’
> before ‘barr_init’
> blosc/blosc.c:66: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’
> before ‘barr_inter’
> blosc/blosc.c:67: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’
> before ‘barr_finish’
> blosc/blosc.c: In function ‘parallel_blosc’:
> blosc/blosc.c:304: warning: implicit declaration of function
> ‘pthread_barrier_wait’
> blosc/blosc.c:304: error: ‘barr_init’ undeclared (first use in this
> function)
> blosc/blosc.c:304: error: (Each undeclared identifier is reported only once
> blosc/blosc.c:304: error: for each function it appears in.)
> blosc/blosc.c:305: error: ‘PTHREAD_BARRIER_SERIAL_THREAD’ undeclared (first
> use in this function)
> blosc/blosc.c:310: error: ‘barr_finish’ undeclared (first use in this
> function)
> blosc/blosc.c: In function ‘t_blosc’:
> blosc/blosc.c:649: error: ‘barr_init’ undeclared (first use in this
> function)
> blosc/blosc.c:650: error: ‘PTHREAD_BARRIER_SERIAL_THREAD’ undeclared (first
> use in this function)
> blosc/blosc.c:774: error: ‘barr_finish’ undeclared (first use in this
> function)
> blosc/blosc.c: In function ‘init_threads’:
> blosc/blosc.c:797: warning: implicit declaration of function
> ‘pthread_barrier_init’
> blosc/blosc.c:797: error: ‘barr_init’ undeclared (first use in this
> function)
> blosc/blosc.c:798: error: ‘barr_inter’ undeclared (first use in this
> function)
> blosc/blosc.c:799: error: ‘barr_finish’ undeclared (first use in this
> function)
> blosc/blosc.c: In function ‘blosc_set_nthreads’:
> blosc/blosc.c:841: error: ‘barr_init’ undeclared (first use in this
> function)
> blosc/blosc.c:842: error: ‘PTHREAD_BARRIER_SERIAL_THREAD’ undeclared (first
> use in this function)
> blosc/blosc.c: In function ‘blosc_free_resources’:
> blosc/blosc.c:884: error: ‘barr_init’ undeclared (first use in this
> function)
> blosc/blosc.c:885: error: ‘PTHREAD_BARRIER_SERIAL_THREAD’ undeclared (first
> use in this function)
> blosc/blosc.c:902: warning: implicit declaration of function
> ‘pthread_barrier_destroy’
> blosc/blosc.c:903: error: ‘barr_inter’ undeclared (first use in this
> function)
> blosc/blosc.c:904: error: ‘barr_finish’ undeclared (first use in this
> function)
> blosc/blosc.c:65: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’
> before ‘barr_init’
> blosc/blosc.c:66: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’
> before ‘barr_inter’
> blosc/blosc.c:67: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’
> before ‘barr_finish’
> blosc/blosc.c: In function ‘parallel_blosc’:
> blosc/blosc.c:304: warning: implicit declaration of function
> ‘pthread_barrier_wait’
> blosc/blosc.c:304: error: ‘barr_init’ undeclared (first use in this
> function)
> blosc/blosc.c:304: error: (Each undeclared identifier is reported only once
> blosc/blosc.c:304: error: for each function it appears in.)
> blosc/blosc.c:305: error: ‘PTHREAD_BARRIER_SERIAL_THREAD’ undeclared (first
> use in this function)
> blosc/blosc.c:310: error: ‘barr_finish’ undeclared (first use in this
> function)
> blosc/blosc.c: In function ‘t_blosc’:
> blosc/blosc.c:649: error: ‘barr_init’ undeclared (first use in this
> function)
> blosc/blosc.c:650: error: ‘PTHREAD_BARRIER_SERIAL_THREAD’ undeclared (first
> use in this function)
> blosc/blosc.c:774: error: ‘barr_finish’ undeclared (first use in this
> function)
> blosc/blosc.c: In function ‘init_threads’:
> blosc/blosc.c:797: warning: implicit declaration of function
> ‘pthread_barrier_init’
> blosc/blosc.c:797: error: ‘barr_init’ undeclared (first use in this
> function)
> blosc/blosc.c:798: error: ‘barr_inter’ undeclared (first use in this
> function)
> blosc/blosc.c:799: error: ‘barr_finish’ undeclared (first use in this
> function)
> blosc/blosc.c: In function ‘blosc_set_nthreads’:
> blosc/blosc.c:841: error: ‘barr_init’ undeclared (first use in this
> function)
> blosc/blosc.c:842: error: ‘PTHREAD_BARRIER_SERIAL_THREAD’ undeclared (first
> use in this function)
> blosc/blosc.c: In function ‘blosc_free_resources’:
> blosc/blosc.c:884: error: ‘barr_init’ undeclared (first use in this
> function)
> blosc/blosc.c:885: error: ‘PTHREAD_BARRIER_SERIAL_THREAD’ undeclared (first
> use in this function)
> blosc/blosc.c:902: warning: implicit declaration of function
> ‘pthread_barrier_destroy’
> blosc/blosc.c:903: error: ‘barr_inter’ undeclared (first use in this
> function)
> blosc/blosc.c:904: error: ‘barr_finish’ undeclared (first use in this
> function)
> error: Command "/usr/bin/mpicc -arch x86_64 -fno-strict-aliasing
> -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes
> -DNDEBUG=1 -DHAVE_BZ2_LIB=1 -Iblosc
> -I/Users/cekees/src/proteus/darwin64/Python.framework/Versions/2.6/lib/pyth
> on2.6/site-packages/numpy/core/include -I/usr/include -I/usr/local/include
> -I/Users/cekees/src/proteus/darwin64/include
> -I/Users/cekees/src/proteus/darwin64/Python.framework/Versions/2.6/include/
> python2.6 -c blosc/blosc.c -o
> build/temp.macosx-10.6-x86_64-2.6/blosc/blosc.o -Isrc -DH5_USE_16_API"
> failed with exit status 1
>
> On Tue, May 25, 2010 at 4:12 AM, Francesc Alted <[email protected]> wrote:
> > A Monday 24 May 2010 20:48:03 Chris Kees escrigué:
> > > Hi,
> > >
> > > I depend on pytables and need it running on mac os x 10.6 and several
> > > different flavors of linux (I also have to compile hdf5 and tables from
> > > source on all these). I'm currently lagging behind the latest releases
> > > of hdf5 and pytables but am trying to upgrade. Can anybody recommend a
> >
> > fairly
> >
> > > solid pairing (e.g. hdf5-1.8.4-patch1 and tables-2.1.2)? Or is 2.2rc1
> >
> > solid
> >
> > > enough to go ahead and switch to it while I'm going through the pain of
> > > upgrading?
> >
> > I'd say that 2.2rc1 is stable enough for production use (except for the
> > Blosc
> > compressor, that I'm still testing heavily, but that is a new feature, so
> > no
> > worries for backward compatibility). And I'd also strongly recommend
> > using hdf5-1.8.4-patch1 with 2.2rc1 (so that you can access the external
> > link new feature).
> >
> > I'm not a Mac guy, but there is currently a thread about installing
> > PyTables
> > on a Mac in the list, so feel free to chime in there if you are having
> > difficulties.
> >
> > Luck,
> >
> > --
> > Francesc Alted
> >
> >
> > -------------------------------------------------------------------------
> >-----
> >
> > _______________________________________________
> > Pytables-users mailing list
> > [email protected]
> > https://lists.sourceforge.net/lists/listinfo/pytables-users
>
--
Francesc Alted
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