Hi again,
Thanks for your help. I followed your directions. First, I checked the file
type of python (which I installed from python.org):
$ file /Library/Frameworks/Python.framework/Versions/2.6/bin/python
/Library/Frameworks/Python.framework/Versions/2.6/bin/python: Mach-O
universal binary with 2 architectures
/Library/Frameworks/Python.framework/Versions/2.6/bin/python (for
architecture ppc): Mach-O executable ppc
/Library/Frameworks/Python.framework/Versions/2.6/bin/python (for
architecture i386): Mach-O executable i386
I assumed this was the first case you mentioned.
I then did export CC=gcc-4.0 CFLAGS='-arch i386' and LDFLAGS='-arch i386'
Then I ran hdf5 configure with ./configure --enable-shared
--prefix=/usr/local
This gave no errors, so I did make and make install, and everything appeared
to work fine.
I checked the arch of hdf5's libraries:
$ file /usr/local/lib/libhdf5.dylib
/usr/local/lib/libhdf5.dylib: Mach-O dynamically linked shared library i386
I then tried installing pytables 4 different ways: the stable release from
easy_install and from source, and the newest trunk from easy_install and
from source. None of these worked.
When I do easy_install tables, it appeared to work, giving no errors, but
when I import tables I get this message:
Python 2.6.3 (r263:75184, Oct 2 2009, 07:56:03)
[GCC 4.0.1 (Apple Inc. build 5493)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import tables
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File
"/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/tables-2.1.2-py2.6-macosx-10.3-fat.egg/tables/__init__.py",
line 56, in <module>
from tables.utilsExtension import getPyTablesVersion, getHDF5Version
ImportError:
dlopen(/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/tables-2.1.2-py2.6-macosx-10.3-fat.egg/tables/utilsExtension.so,
2): Symbol not found: _H5T_STD_I64LE_g
Referenced from:
/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/tables-2.1.2-py2.6-macosx-10.3-fat.egg/tables/utilsExtension.so
Expected in: dynamic lookup
When I run sudo easy_install http://pytables.org/svn/pytables/trunk I get
this message:
$ sudo easy_install http://pytables.org/svn/pytables/trunk
Password:
Downloading http://pytables.org/svn/pytables/trunk
Doing subversion checkout from http://pytables.org/svn/pytables/trunk to
/tmp/easy_install-UvJ1oB/trunk
Processing trunk
Running setup.py -q bdist_egg --dist-dir
/tmp/easy_install-UvJ1oB/trunk/egg-dist-tmp-aBRfFR
* Found numpy 1.3.0 package installed.
* Found numexpr 1.3.1 package installed.
* Found HDF5 headers at ``/usr/local/include``, library at
``/usr/local/lib``.
* 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``.
warning: no files found matching '*.pdf' under directory 'doc'
warning: no files found matching '*.html' under directory 'doc'
powerpc-apple-darwin10-gcc-4.0.1: tables/utilsExtension.c: No such file or
directory
powerpc-apple-darwin10-gcc-4.0.1: no input files
i686-apple-darwin10-gcc-4.0.1: tables/utilsExtension.c: No such file or
directory
i686-apple-darwin10-gcc-4.0.1: no input files
lipo: can't figure out the architecture type of: /var/tmp//cc37vcGT.out
powerpc-apple-darwin10-gcc-4.0.1: tables/utilsExtension.c: No such file or
directory
powerpc-apple-darwin10-gcc-4.0.1: no input files
i686-apple-darwin10-gcc-4.0.1: tables/utilsExtension.c: No such file or
directory
i686-apple-darwin10-gcc-4.0.1: no input files
lipo: can't figure out the architecture type of: /var/tmp//cc37vcGT.out
error: Setup script exited with error: Command "gcc-4.0 -arch ppc -arch i386
-isysroot /Developer/SDKs/MacOSX10.4u.sdk -fno-strict-aliasing -fno-common
-dynamic -DNDEBUG -g -O3 -DNDEBUG=1 -DHAVE_BZ2_LIB=1 -Iblosc
-I/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/numpy/core/include
-I/usr/include -I/usr/local/include
-I/Library/Frameworks/Python.framework/Versions/2.6/include/python2.6 -c
tables/utilsExtension.c -o
build/temp.macosx-10.3-fat-2.6/tables/utilsExtension.o -Isrc
-DH5_USE_16_API" failed with exit status 1
/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/numpy/distutils/misc_util.py:219:
RuntimeWarning: Parent module 'numpy.distutils' not found while handling
absolute import
from numpy.distutils import log
When I install v2.1.2 from source, the most current stable version, it
appears to work until I import tables:
Python 2.6.3 (r263:75184, Oct 2 2009, 07:56:03)
[GCC 4.0.1 (Apple Inc. build 5493)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import tables
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "tables/__init__.py", line 56, in <module>
from tables.utilsExtension import getPyTablesVersion, getHDF5Version
ImportError: dlopen(tables/utilsExtension.so, 2): Symbol not found:
_H5T_STD_I64LE_g
Referenced from:
/Users/brandtbelson/Documents/src/tables-2.1.2/tables/utilsExtension.so
Expected in: dynamic lookup
And lastly, the newest pytables from trunk from source gave:
python setup.py build
* Found numpy 1.3.0 package installed.
* Found numexpr 1.3.1 package installed.
* Found HDF5 headers at ``/usr/local/include``, library at
``/usr/local/lib``.
* 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: gcc-4.0 -DNDEBUG -g -O3 -arch i386
compile options: '-DNDEBUG=1 -DHAVE_BZ2_LIB=1 -Iblosc
-I/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/numpy/core/include
-I/usr/include -I/usr/local/include
-I/Library/Frameworks/Python.framework/Versions/2.6/include/python2.6 -c'
extra options: '-arch i386 -Isrc -DH5_USE_16_API'
gcc-4.0: blosc/blosc.c
blosc/blosc.c:65: error: syntax error before ‘barr_init’
blosc/blosc.c:65: warning: data definition has no type or storage class
blosc/blosc.c:66: error: syntax error before ‘barr_inter’
blosc/blosc.c:66: warning: data definition has no type or storage class
blosc/blosc.c:67: error: syntax error before ‘barr_finish’
blosc/blosc.c:67: warning: data definition has no type or storage class
blosc/blosc.c: In function ‘parallel_blosc’:
blosc/blosc.c:305: error: ‘PTHREAD_BARRIER_SERIAL_THREAD’ undeclared (first
use in this function)
blosc/blosc.c:305: error: (Each undeclared identifier is reported only once
blosc/blosc.c:305: error: for each function it appears in.)
blosc/blosc.c: In function ‘t_blosc’:
blosc/blosc.c:650: error: ‘PTHREAD_BARRIER_SERIAL_THREAD’ undeclared (first
use in this function)
blosc/blosc.c: In function ‘blosc_set_nthreads’:
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:885: error: ‘PTHREAD_BARRIER_SERIAL_THREAD’ undeclared (first
use in this function)
blosc/blosc.c:65: error: syntax error before ‘barr_init’
blosc/blosc.c:65: warning: data definition has no type or storage class
blosc/blosc.c:66: error: syntax error before ‘barr_inter’
blosc/blosc.c:66: warning: data definition has no type or storage class
blosc/blosc.c:67: error: syntax error before ‘barr_finish’
blosc/blosc.c:67: warning: data definition has no type or storage class
blosc/blosc.c: In function ‘parallel_blosc’:
blosc/blosc.c:305: error: ‘PTHREAD_BARRIER_SERIAL_THREAD’ undeclared (first
use in this function)
blosc/blosc.c:305: error: (Each undeclared identifier is reported only once
blosc/blosc.c:305: error: for each function it appears in.)
blosc/blosc.c: In function ‘t_blosc’:
blosc/blosc.c:650: error: ‘PTHREAD_BARRIER_SERIAL_THREAD’ undeclared (first
use in this function)
blosc/blosc.c: In function ‘blosc_set_nthreads’:
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:885: error: ‘PTHREAD_BARRIER_SERIAL_THREAD’ undeclared (first
use in this function)
error: Command "gcc-4.0 -DNDEBUG -g -O3 -arch i386 -DNDEBUG=1
-DHAVE_BZ2_LIB=1 -Iblosc
-I/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/numpy/core/include
-I/usr/include -I/usr/local/include
-I/Library/Frameworks/Python.framework/Versions/2.6/include/python2.6 -c
blosc/blosc.c -o build/temp.macosx-10.3-fat-2.6/blosc/blosc.o -arch i386
-Isrc -DH5_USE_16_API" failed with exit status 1
Does anyone have any other ideas?
Thank you.
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