Hi Antonio,
Thanks, I'm glad to be able to use the pytables repository. It was
just the cython executable. I hadn't set the path properly in my test
build. I haven't been able to get rid of the warning about the hdf5
runtime--I appear to only have .a's and .dylib's. For future reference
here is the set of tools that are working and some output.
Thanks,
Chris
pytables:
% python
Python 2.7.2 (default, Aug 20 2011, 07:44:38)
[GCC 4.2.1 (Apple Inc. build 5666) (dot 3)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import tables
>>> tables.test()
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
PyTables version: 2.3b1.dev
HDF5 version: 1.8.7
NumPy version: 1.6.2.dev-f21011a
Numexpr version: 1.5.dev (not using Intel's VML/MKL)
Zlib version: 1.2.5 (in Python interpreter)
BZIP2 version: 1.0.5 (10-Dec-2007)
Blosc version: 1.1.2 (2010-11-04)
Cython version: 0.15
Python version: 2.7.2 (default, Aug 20 2011, 07:44:38)
[GCC 4.2.1 (Apple Inc. build 5666) (dot 3)]
Platform: darwin-i386
Byte-ordering: little
Detected cores: 4
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
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 4 hours to complete on a relatively
modern CPU and around 256 MB of main memory.
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
/Users/cekees/src/git-test/proteus/darwin/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/tables/filters.py:264:
FiltersWarning: compression library ``lzo`` is not available; using
``zlib`` instead
% (complib, default_complib), FiltersWarning )
...(and so on ...)
Ran 4723 tests in 223.846s
OK
Machine:
macbook pro (intel) Mac OS X 10.6.8, using the default compilers
(/usr/bin/gcc, etc.).
Python 2.7.2:
./configure --prefix=/Users/cekees/src/git-test/proteus/darwin
--enable-framework=/Users/cekees/src/git-test/proteus/darwin/Library/Frameworks
--enable-toolbox-glue CC=/usr/bin/gcc CXX=/usr/bin/g++
CPPFLAGS=-I//Users/cekees/src/git-test/proteus/darwin/include
CXXFLAGS=-I/Users/cekees/src/git-test/proteus/darwin/include
LD=/usr/bin/gcc
LDFLAGS=-L/Users/cekees/src/git-test/proteus/darwin/lib
HDF5 1.8.7:
SUMMARY OF THE HDF5 CONFIGURATION
=================================
General Information:
-------------------
HDF5 Version: 1.8.7
Configured on: Sat Aug 20 07:48:53 CDT 2011
Configured by: cekees@minikees-3.local
Configure mode: production
Host system: i386-apple-darwin10.8.0
Uname information: Darwin minikees-3.local 10.8.0 Darwin
Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011;
root:xnu-1504.15.3~1/RELEASE_I386 i386
Byte sex: little-endian
Libraries:
Installation point: /Users/cekees/src/git-test/proteus/darwin
Compiling Options:
------------------
Compilation Mode: production
C Compiler: /usr/bin/gcc ( (GCC) 4.2.1 (Apple
Inc. build 5666) (dot 3))
CFLAGS:
-I/Users/cekees/src/git-test/proteus/darwin/include
H5_CFLAGS: -std=c99 -pedantic -Wall -Wextra
-Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wcast-qual
-Wcast-align -Wwrite-strings -Wconversion -Waggregate-return
-Wstrict-prototypes -Wmissing-prototypes -Wmissing-declarations
-Wredundant-decls -Wnested-externs -Winline -Wno-long-long
-Wfloat-equal -Wmissing-format-attribute -Wmissing-noreturn -Wpacked
-Wdisabled-optimization -Wformat=2 -Wunreachable-code -Wendif-labels
-Wdeclaration-after-statement -Wold-style-definition -Winvalid-pch
-Wvariadic-macros -Wnonnull -Winit-self -Wmissing-include-dirs
-Wswitch-default -Wswitch-enum -Wunused-macros
-Wunsafe-loop-optimizations -Wc++-compat -Wvolatile-register-var
-Wstrict-overflow -O3 -fomit-frame-pointer -finline-functions
AM_CFLAGS:
CPPFLAGS:
H5_CPPFLAGS: -DNDEBUG -UH5_DEBUG_API
AM_CPPFLAGS:
-I/Users/cekees/src/git-test/proteus/darwin/include
-I/Users/cekees/src/git-test/proteus/darwin/include
Shared C Library: yes
Static C Library: yes
Statically Linked Executables: no
LDFLAGS:
-L/Users/cekees/src/git-test/proteus/darwin/lib
H5_LDFLAGS:
AM_LDFLAGS:
-L/Users/cekees/src/git-test/proteus/darwin/lib
-L/Users/cekees/src/git-test/proteus/darwin/lib
Extra libraries: -lpthread -lsz -lz -lm -lsz -lz
Archiver: ar
Ranlib: ranlib
Debugged Packages:
API Tracing: no
Languages:
----------
Fortran: no
C++: no
Features:
---------
Parallel HDF5: no
High Level library: yes
Threadsafety: yes
Default API Mapping: v18
With Deprecated Public Symbols: yes
I/O filters (external): deflate(zlib),szip(encoder)
I/O filters (internal): shuffle,fletcher32,nbit,scaleoffset
MPE: no
Direct VFD: no
dmalloc: no
Clear file buffers before write: yes
Using memory checker: no
Function Stack Tracing: no
GPFS: no
Strict File Format Checks: no
Optimization Instrumentation: no
Large File Support (LFS): yes
H5dump Packed Bits: yes
Contents of lib dir:
% ls $PROTEUS_PREFIX/lib
libdaetk.a libhdf5.settings libmetis.a
libsuperlu.a libsz.dylib libz.a
libhdf5.7.dylib libhdf5_hl.7.dylib libparmetis.a
libsuperlu_dist_2.4.a libsz.la libz.dylib
libhdf5.a libhdf5_hl.a libpetsc.a
libsz.2.0.0.dylib libtri.a pkgconfig
libhdf5.dylib libhdf5_hl.dylib libpetsc.dylib
libsz.2.dylib libz.1.2.5.dylib
libhdf5.la libhdf5_hl.la libpetsc.dylib.dSYM libsz.a
libz.1.dylib
On Sat, Aug 20, 2011 at 3:10 AM, Antonio Valentino
<antonio.valent...@tiscali.it> wrote:
> Hi Chris,
>
> Il giorno 20/ago/2011, alle ore 03.57, Chris Kees ha scritto:
>
>> Hi,
>>
>> We use pytables and numexpr, and I'd like to add them as submodules to
>> our project so that I can easily keep updated with pytables
>> improvements and pass changes back up stream if I can be of any help
>> (we do a lot of HPC work with pytables). Is there a plan to add 2.3 as
>> a release branch fairly soon or some other stable point in the git
>> repository that I could point my submodule to? I could also stick with
>> 2.2 for the time being but noticed below that 2.3beta had been used in
>> EPD so I thought there must be a branch or fork somewhere that is
>
> The master branch should be beta quality at the moment. We plan to pack a
> beta release soon.
> If you look at
>
> https://github.com/PyTables/PyTables/issues?milestone=2&state=open
>
> there are still a few bugs to close and they are mainly related to the setup
> process which seems to be your problem too.
>
>
>
>> relatively stable. I would just go with the head of the master
>> branch, but compiling with Cython 0.15 and numpy 1.6.1 gave me the
>> error below.
>>
>> Thanks,
>> Chris
>
> Chris, I'm setting up a virtual environment to reproduce your issue.
> Can you confirm that the cython executable is in your path?
>
> Looking at the error message below it seems that the setup script is unable
> to find the HDF5 runtime:
>
> ".. WARNING:: Could not find the HDF5 runtime."
>
> Can you please post more detail on your system setup and the exact command
> line you used?
>
>
>> * Found numpy 1.6.2.dev-f21011a package installed.
>> * Found numexpr 1.5.dev package installed.
>> * Found Cython 0.15 package installed.
>> * Found HDF5 headers at
>> ``/Users/cekees/src/proteus-git/darwin/include``, library at
>> ``/Users/cekees/src/proteus-git/darwin/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``.
>> cythoning tables/utilsExtension.pyx to tables/utilsExtension.c
>> Traceback (most recent call last):
>> File "setup.py", line 464, in <module>
>> cython_extfiles = get_cython_extfiles(cython_extnames)
>> File "setup.py", line 455, in get_cython_extfiles
>> retcode = subprocess.call(["cython", extpfile])
>> File
>> "/Users/cekees/src/proteus-git/darwin/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py",
>> line 493, in call
>> return Popen(*popenargs, **kwargs).wait()
>> File
>> "/Users/cekees/src/proteus-git/darwin/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py",
>> line 679, in __init__
>> errread, errwrite)
>> File
>> "/Users/cekees/src/proteus-git/darwin/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py",
>> line 1228, in _execute_child
>> raise child_exception
>
> regards
>
> --
> Antonio Valentino
>
>
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