Re: [Pytables-users] openFile seems to hang
On Tue, Aug 7, 2012 at 11:50 AM, Daniel Wheeler daniel.wheel...@gmail.comwrote: On Tue, Aug 7, 2012 at 12:46 PM, Anthony Scopatz scop...@gmail.comwrote: On Tue, Aug 7, 2012 at 11:43 AM, Daniel Wheeler daniel.wheel...@gmail.com wrote: They should know what do do and how to fix it. Maybe mpi init issues with either pytrilinos or mpi4py as a wild guess. Both are imported by fipy. Your guess is as good, or much better, than mine. Thanks for your questions and answers. BTW If it turns out that you need us to change something in PyTables to play nicely with fipy, please let us know! -- Daniel Wheeler -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Pytables-users mailing list Pytables-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pytables-users -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___ Pytables-users mailing list Pytables-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pytables-users
Re: [Pytables-users] openFile seems to hang
Hi Daniel,
Does this always happen when opening files? or just occasionally?
Be Well
Anthony
On Mon, Aug 6, 2012 at 11:08 AM, Daniel Wheeler
daniel.wheel...@gmail.comwrote:
The following just seems to hang indefinitely.
In [1]: import tables
In [2]: f = tables.openFile('tmp.h5', mode='a')
The tests hang as well.
In [3]: tables.test()
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
PyTables version: 2.4.0
HDF5 version: 1.8.4-patch1
NumPy version: 1.6.1
Numexpr version: 2.0.1 (not using Intel's VML/MKL)
Zlib version: 1.2.3.4 (in Python interpreter)
BZIP2 version: 1.0.5 (10-Dec-2007)
Blosc version: 1.1.3 (2010-11-16)
Cython version:0.15.1
Python version:2.6.6 (r266:84292, Dec 26 2010, 22:31:48)
[GCC 4.4.5]
Platform: linux2-x86_64
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 512 MB of main memory.
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
/users/wd15/.virtualenvs/trunk/lib/python2.6/site-packages/tables/filters.py:253:
FiltersWarning: compression library ``lzo`` is not available; using
``zlib`` instead
% (complib, default_complib), FiltersWarning )
Any ideas are greatly appreciated.
Thanks.
--
Daniel Wheeler
--
Live Security Virtual Conference
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Re: [Pytables-users] openFile seems to hang
On Mon, Aug 6, 2012 at 12:13 PM, Anthony Scopatz scop...@gmail.com wrote: Hi Daniel, Does this always happen when opening files? or just occasionally? I just installed pytables this morning and it happens every time so far. I was using pytables a lot about a year ago without any issues. This morning, I installed it in a virtualenv with a lot of other packages. I might try it in a completely clean virtualenv and see if that helps any. -- Daniel Wheeler -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___ Pytables-users mailing list Pytables-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pytables-users
Re: [Pytables-users] openFile seems to hang
On Mon, Aug 6, 2012 at 12:20 PM, Anthony Scopatz scop...@gmail.com wrote: Hmm What if you try opening in 'r' or 'w' mode, rather than 'a'? Doesn't make a difference. I am not an expert in virtualenv, but I have heard of people having problems with it with other packages. Let us know if there is anything that we can do. Starting with a clean virtualenv seems to have worked. The new configuration is -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= PyTables version: 2.4.0 HDF5 version: 1.8.4-patch1 NumPy version: 1.6.2 Numexpr version: 2.0.1 (not using Intel's VML/MKL) Zlib version: 1.2.3.4 (in Python interpreter) BZIP2 version: 1.0.5 (10-Dec-2007) Blosc version: 1.1.3 (2010-11-16) Cython version:0.16 Python version:2.6.6 (r266:84292, Dec 26 2010, 22:31:48) [GCC 4.4.5] Platform: linux2-x86_64 Byte-ordering: little Detected cores:4 -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= The only difference seems to cython and numpy. Tests run to completion. -- Daniel Wheeler -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___ Pytables-users mailing list Pytables-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pytables-users
