segmentation fault on Mac OS X Lion when running tables.test()

Discussion:

David Donovan

2012-06-16 00:14:32 UTC

Hi Everyone,

I am having problems running the tests for PyTables on Mac OS X Lion.
I have tried HDF5 version 1.8.5 as well, but I still get the same issue.

Any thoughts would be helpful...

Thanks for any help you can provide.

Best Regards,
David Donovan

impPython 2.7.1 (r271:86832, Jul 31 2011, 19:30:53)
[GCC 4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2335.15.00)] on darwin
Type "help", "copyright", "credits" or "license" for more information.

import tables

Anthony Scopatz

2012-06-16 07:57:35 UTC

Permalink

Hi David,

How did you build / install HDF5?

Be Well
Anthony

Post by David Donovan
Hi Everyone,
I am having problems running the tests for PyTables on Mac OS X Lion.
I have tried HDF5 version 1.8.5 as well, but I still get the same issue.
Any thoughts would be helpful...
Thanks for any help you can provide.
Best Regards,
David Donovan
impPython 2.7.1 (r271:86832, Jul 31 2011, 19:30:53)
[GCC 4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2335.15.00)] on darwin
Type "help", "copyright", "credits" or "license" for more information.

import tables

table>>> tables.test()
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
PyTables version: 2.3.1
HDF5 version: 1.8.9
NumPy version: 1.7.0.dev-0c5f480
Numexpr version: 2.0.1 (not using Intel's VML/MKL)
Zlib version: 1.2.5 (in Python interpreter)
LZO version: 2.06 (Aug 12 2011)
BZIP2 version: 1.0.6 (6-Sept-2010)
Blosc version: 1.1.2 (2010-11-04)
Cython version: 0.16
Python version: 2.7.1 (r271:86832, Jul 31 2011, 19:30:53)
[GCC 4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2335.15.00)]
Platform: darwin-i386
Byte-ordering: little
Detected cores: 2
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
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.
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
.....................................................................................................................................FSegmentation
fault: 11
------------------------------------------------------------------------------
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David Donovan

2012-06-19 02:37:18 UTC

Permalink

Hi Anthony,

Thanks for the response. Installed HDF5 1.8.9 using the following
flags for configure.

`./configure --prefix=/usr/local
--with-szlib=/Library/Frameworks/Python.framework/Versions/Current
CPPFLAGS=-I/Library/Frameworks/Python.framework/Versions/Current/include
LDFLAGS=-L/Library/Frameworks/Python.framework/Versions/Current/lib`

Also, I had to modify the optimization flag for gcc-4 in order to pass
the make check part (as noted on the HDF5 page).
`Conversion Tests fail on Mac OS X 10.7 (Lion) Users have reported
that when building HDF5, the conversion tests failed (make check) in
dt_arith.chk. A workaround is to edit ./< HDF5source

/config/gnu-flags, search for PROD_CFLAGS under "gcc-4.*", and change

the value for PROD_CFLAGS to "-O0".`

Then:
'make'
'make check'
'sudo make install'

Is there a better way? Is tables somehow having a hard time finding
the HDF5 library do you think?

Thanks!

Best Regards,
David

Hi David,
How did you build / install HDF5?
Be Well
Anthony

import tables

------------------------------------------------------------------------------
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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/
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Anthony Scopatz

2012-06-19 03:10:27 UTC

Permalink

Hmmm That all looks correct. Have you tried linking PyTables against the
HDF5 from MacPorts? This has worked for me in the past...

Post by David Donovan
Hi Anthony,
Thanks for the response. Installed HDF5 1.8.9 using the following
flags for configure.
`./configure --prefix=/usr/local
--with-szlib=/Library/Frameworks/Python.framework/Versions/Current
CPPFLAGS=-I/Library/Frameworks/Python.framework/Versions/Current/include
LDFLAGS=-L/Library/Frameworks/Python.framework/Versions/Current/lib`
Also, I had to modify the optimization flag for gcc-4 in order to pass
the make check part (as noted on the HDF5 page).
`Conversion Tests fail on Mac OS X 10.7 (Lion) Users have reported
that when building HDF5, the conversion tests failed (make check) in
dt_arith.chk. A workaround is to edit ./< HDF5source

/config/gnu-flags, search for PROD_CFLAGS under "gcc-4.*", and change

the value for PROD_CFLAGS to "-O0".`
'make'
'make check'
'sudo make install'
Is there a better way? Is tables somehow having a hard time finding
the HDF5 library do you think?
Thanks!
Best Regards,
David

Hi David,
How did you build / install HDF5?
Be Well
Anthony

import tables

table>>> tables.test()

-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=

Post by David Donovan
PyTables version: 2.3.1
HDF5 version: 1.8.9
NumPy version: 1.7.0.dev-0c5f480
Numexpr version: 2.0.1 (not using Intel's VML/MKL)
Zlib version: 1.2.5 (in Python interpreter)
LZO version: 2.06 (Aug 12 2011)
BZIP2 version: 1.0.6 (6-Sept-2010)
Blosc version: 1.1.2 (2010-11-04)
Cython version: 0.16
Python version: 2.7.1 (r271:86832, Jul 31 2011, 19:30:53)
[GCC 4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2335.15.00)]
Platform: darwin-i386
Byte-ordering: little
Detected cores: 2

-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=

Post by David Donovan
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.

-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
.....................................................................................................................................FSegmentation

Post by David Donovan
fault: 11

------------------------------------------------------------------------------

Post by David Donovan
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

Post by David Donovan
will include endpoint security, mobile security and the latest in

malware

Post by David Donovan
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
_______________________________________________
Pytables-users mailing list
https://lists.sourceforge.net/lists/listinfo/pytables-users

------------------------------------------------------------------------------

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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
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Josh Moore

2012-06-22 14:46:56 UTC

Permalink

/config/gnu-flags, search for PROD_CFLAGS under "gcc-4.*", and change

the value for PROD_CFLAGS to "-O0".`
'make'
'make check'
'sudo make install'
Is there a better way? Is tables somehow having a hard time finding
the HDF5 library do you think?

Hi David,

I always use homebrew for any of my prerequisites:

http://mxcl.github.com/homebrew/

Cheers
~Josh

Post by David Donovan
Thanks!
Best Regards,
David

Hi David,
How did you build / install HDF5?
Be Well
Anthony

import tables

Olana Missura

2016-04-01 16:17:59 UTC

Permalink

Hi guys,

I have a segmentation fault as well when running tables.test() after some

Post by Anthony Scopatz

Post by David Donovan

import tables

Problems initializing LZO library

Post by Anthony Scopatz

Post by David Donovan

tables.test()

-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
PyTables version: 3.2.2
HDF5 version: 1.8.14
NumPy version: 1.11.0
Numexpr version: 2.5.1 (not using Intel's VML/MKL)
Zlib version: 1.2.8 (in Python interpreter)
BZIP2 version: 1.0.6 (6-Sept-2010)
Blosc version: 1.5.2 (2014-12-30)
Blosc compressors: blosclz (1.0.3), lz4 (1.5.0), lz4hc (1.5.0), snappy
(1.1.1), zlib (1.2.8)
Cython version: 0.23.5
Python version: 2.7.11 |Continuum Analytics, Inc.| (default, Dec 6
2015, 18:57:58)
[GCC 4.2.1 (Apple Inc. build 5577)]
Platform: Darwin-15.0.0-x86_64-i386-64bit
Byte-ordering: little
Detected cores: 4
Default encoding: ascii
Default FS encoding: utf-8
Default locale: (en_US, UTF-8)
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
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/Olana/anaconda/envs/choosito-familiarity/lib/python2.7/site-packages/tables/filters.py:292:
FiltersWarning: compression library ``lzo`` is not available; using
``zlib`` instead
% (complib, default_complib), FiltersWarning)
......................................................................................................................................................................................................................................................................................................................................................................................................................................................................ssss.........Segmentation
fault: 11

Any help would be much appreciated!

Best,
Olana

Post by Anthony Scopatz

/config/gnu-flags, search for PROD_CFLAGS under "gcc-4.*", and change

the value for PROD_CFLAGS to "-O0".`
'make'
'make check'
'sudo make install'
Is there a better way? Is tables somehow having a hard time finding
the HDF5 library do you think?

Hi David,
http://mxcl.github.com/homebrew/
Cheers
~Josh

Post by David Donovan
Thanks!
Best Regards,
David

Hi David,
How did you build / install HDF5?
Be Well
Anthony

Post by David Donovan
Hi Everyone,
I am having problems running the tests for PyTables on Mac OS X Lion.
I have tried HDF5 version 1.8.5 as well, but I still get the same

issue.

Post by David Donovan

Post by David Donovan
Any thoughts would be helpful...
Thanks for any help you can provide.
Best Regards,
David Donovan
impPython 2.7.1 (r271:86832, Jul 31 2011, 19:30:53)
[GCC 4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2335.15.00)]

Post by David Donovan

Post by David Donovan
darwin
Type "help", "copyright", "credits" or "license" for more information.

import tables

table>>> tables.test()

-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=

Post by David Donovan

-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=

Post by David Donovan

call).

Post by David Donovan

Post by David Donovan
The whole suite will take more than 4 hours to complete on a

relatively

Post by David Donovan

Post by David Donovan
modern CPU and around 512 MB of main memory.

Post by David Donovan

Post by David Donovan
fault: 11

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Antonio Valentino

2016-04-02 07:01:49 UTC

Permalink

Hi Olana,

Post by Olana Missura
Hi guys,

import tables

Problems initializing LZO library

tables.test()

-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
PyTables version: 3.2.2
HDF5 version: 1.8.14
NumPy version: 1.11.0
Numexpr version: 2.5.1 (not using Intel's VML/MKL)
Zlib version: 1.2.8 (in Python interpreter)
BZIP2 version: 1.0.6 (6-Sept-2010)
Blosc version: 1.5.2 (2014-12-30)
Blosc compressors: blosclz (1.0.3), lz4 (1.5.0), lz4hc (1.5.0), snappy (1.1.1), zlib (1.2.8)
Cython version: 0.23.5
Python version: 2.7.11 |Continuum Analytics, Inc.| (default, Dec 6 2015, 18:57:58)
[GCC 4.2.1 (Apple Inc. build 5577)]
Platform: Darwin-15.0.0-x86_64-i386-64bit
Byte-ordering: little
Detected cores: 4
Default encoding: ascii
Default FS encoding: utf-8
Default locale: (en_US, UTF-8)
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
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/Olana/anaconda/envs/choosito-familiarity/lib/python2.7/site-packages/tables/filters.py:292: FiltersWarning: compression library ``lzo`` is not available; using ``zlib`` instead
% (complib, default_complib), FiltersWarning)
......................................................................................................................................................................................................................................................................................................................................................................................................................................................................ssss.........Segmentation fault: 11
Any help would be much appreciated!
Best,
Olana

the problem seems to be related to the github issue #532 [1].
It is fixed now.
Can you please make a test with the current development version of PyTables (develop branch on github [2])?

cheers
Antonio

[1] https://github.com/PyTables/PyTables/issues/532
[2] https://github.com/PyTables/PyTables.git

â
Antonio Valentino

Olana Missura

2016-04-02 11:52:34 UTC

Permalink

I will give it a try when I get back to the office on Monday. Thank you!

Post by Antonio Valentino
Hi Olana,

Post by Olana Missura
Hi guys,
I have a segmentation fault as well when running tables.test() after

import tables

Problems initializing LZO library

tables.test()

-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=

Post by Olana Missura
PyTables version: 3.2.2
HDF5 version: 1.8.14
NumPy version: 1.11.0
Numexpr version: 2.5.1 (not using Intel's VML/MKL)
Zlib version: 1.2.8 (in Python interpreter)
BZIP2 version: 1.0.6 (6-Sept-2010)
Blosc version: 1.5.2 (2014-12-30)
Blosc compressors: blosclz (1.0.3), lz4 (1.5.0), lz4hc (1.5.0), snappy

(1.1.1), zlib (1.2.8)

Post by Olana Missura
Cython version: 0.23.5
Python version: 2.7.11 |Continuum Analytics, Inc.| (default, Dec 6

2015, 18:57:58)

Post by Olana Missura
[GCC 4.2.1 (Apple Inc. build 5577)]
Platform: Darwin-15.0.0-x86_64-i386-64bit
Byte-ordering: little
Detected cores: 4
Default encoding: ascii
Default FS encoding: utf-8
Default locale: (en_US, UTF-8)

-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=

Post by Olana Missura
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

Post by Olana Missura
(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.

-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
FiltersWarning: compression library ``lzo`` is not available; using
``zlib`` instead

Post by Olana Missura
% (complib, default_complib), FiltersWarning)

......................................................................................................................................................................................................................................................................................................................................................................................................................................................................ssss.........Segmentation
fault: 11

Post by Olana Missura
Any help would be much appreciated!
Best,
Olana

the problem seems to be related to the github issue #532 [1].
It is fixed now.
Can you please make a test with the current development version of
PyTables (develop branch on github [2])?
cheers
Antonio
[1] https://github.com/PyTables/PyTables/issues/532
[2] https://github.com/PyTables/PyTables.git
â
Antonio Valentino