I'm a very experienced Linux admin, but new to the Mac and am trying to figure
out a good way to install various scientific python tools on a 10.6 Mac.
Following recommendation from the SciPy/NumPy I installed the Mac OS X binary
python package from python.org and used the NumPy and SciPy binary mac
installers. So far so good.
I downloaded the OS X binary hdf5/szip bits and put them in /usr/local/hdf5,
/usr/local/szip. Then compiled pytables with:
export MACOSX_DEPLOYMENT_TARGET=10.6
python setup.py build_ext --inplace --hdf5=/usr/local/hdf5-1.6
--library-dirs=/usr/local/szip/lib --libraries=sz
When I run the tests though I get tons of errors, starting with:
$ PYTHONPATH=.:$PYTHONPATH python tables/tests/test_all.py
*Warning*: HDF5 version is lower than recommended: 1.6.10 < 1.6.5
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
PyTables version: 2.1.2
HDF5 version: 1.6.10
NumPy version: 1.4.1
Zlib version: 1.2.3
BZIP2 version: 1.0.5 (10-Dec-2007)
Python version: 2.6.5 (r265:79359, Mar 24 2010, 01:32:55)
[GCC 4.0.1 (Apple Inc. build 5493)]
Platform: darwin-i386
Byte-ordering: little
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
Performing only a light (yet comprehensive) subset of the test suite.
If you want a more complete test, try passing the --heavy flag to this script
(or set the 'heavy' parameter in case you are using tables.test() call).
The whole suite will take more than 2 minutes to complete on a relatively
modern CPU and around 80 MB of main memory.
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
Skipping Numeric test suite.
Skipping numarray test suite.
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
/Users/orion/tables-2.1.2/tables/filters.py:258: FiltersWarning: compression
library ``lzo`` is not available; using ``zlib`` instead
% (complib, default_complib), FiltersWarning )
HDF5-DIAG: Error detected in HDF5 library version: 1.6.10 thread 0. Back
trace follows.
#000: H5A.c line 181 in H5Acreate(): not a type
major(01): Function arguments
minor(03): Inappropriate type
HDF5-DIAG: Error detected in HDF5 library version: 1.6.10 thread 0. Back
trace follows.
#000: H5A.c line 585 in H5Awrite(): not an attribute
major(01): Function arguments
minor(03): Inappropriate type
EHDF5-DIAG: Error detected in HDF5 library version: 1.6.10 thread 0. Back
trace follows.
#000: H5A.c line 181 in H5Acreate(): not a type
major(01): Function arguments
minor(03): Inappropriate type
HDF5-DIAG: Error detected in HDF5 library version: 1.6.10 thread 0. Back
trace follows.
#000: H5A.c line 585 in H5Awrite(): not an attribute
major(01): Function arguments
minor(03): Inappropriate type
EHDF5-DIAG: Error detected in HDF5 library version: 1.6.10 thread 0. Back
trace follows.
#000: H5A.c line 181 in H5Acreate(): not a type
major(01): Function arguments
minor(03): Inappropriate type
HDF5-DIAG: Error detected in HDF5 library version: 1.6.10 thread 0. Back
trace follows.
#000: H5A.c line 585 in H5Awrite(): not an attribute
major(01): Function arguments
minor(03): Inappropriate type
EHDF5-DIAG: Error detected in HDF5 library version: 1.6.10 thread 0. Back
trace follows.
#000: H5A.c line 181 in H5Acreate(): not a type
major(01): Function arguments
minor(03): Inappropriate type
HDF5-DIAG: Error detected in HDF5 library version: 1.6.10 thread 0. Back
trace follows.
#000: H5A.c line 585 in H5Awrite(): not an attribute
major(01): Function arguments
minor(03): Inappropriate type
EHDF5-DIAG: Error detected in HDF5 library version: 1.6.10 thread 0. Back
trace follows.
#000: H5A.c line 181 in H5Acreate(): not a type
major(01): Function arguments
minor(03): Inappropriate type
HDF5-DIAG: Error detected in HDF5 library version: 1.6.10 thread 0. Back
trace follows.
#000: H5A.c line 585 in H5Awrite(): not an attribute
major(01): Function arguments
minor(03): Inappropriate type
......
Full build and test logs are here:
http://www.cora.nwra.com/~orion/build.log
http://www.cora.nwra.com/~orion/test.log
Any suggestions?
Thanks!
--
Orion Poplawski
Technical Manager 303-415-9701 x222
NWRA/CoRA Division FAX: 303-415-9702
3380 Mitchell Lane or...@cora.nwra.com
Boulder, CO 80301 http://www.cora.nwra.com
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