Segmentation fault at "from libtiff import TIFF" / dlopen(...tif_lzw.so") with python 2.6

[GoogleCodeExporter]

What steps will reproduce the problem?
1. run enthought python distribution 6.3-2 on scientific linux 5
2. build/install pylibtiff (revision 70)
3. run python -c "from libtiff import TIFF"

What is the expected output? What do you see instead?
$ python -v -d -c "from libtiff import TIFF"
....

import copy # precompiled from /scratch/epd-6.3-2-rh5-x86/lib/python2.6/copy.pyc
# /scratch/pylibtiff.i386/lib/python/libtiff/tiff_base.pyc matches 
/scratch/pylibtiff.i386/lib/python/libtiff/tiff_base.py
import libtiff.tiff_base # precompiled from 
/scratch/pylibtiff.i386/lib/python/libtiff/tiff_base.pyc
# /scratch/pylibtiff.i386/lib/python/libtiff/lsm.pyc matches 
/scratch/pylibtiff.i386/lib/python/libtiff/lsm.py
import libtiff.lsm # precompiled from 
/scratch/pylibtiff.i386/lib/python/libtiff/lsm.pyc
dlopen("/scratch/pylibtiff.i386/lib/python/libtiff/tif_lzw.so", 102);
Segmentation fault



What version of the product are you using? On what operating system?

$ python -V
Python 2.6.6 -- EPD 6.3-2 (32-bit)

$ uname -a
Linux pc6490 2.6.18-194.26.1.el5 #1 SMP Tue Nov 9 12:56:26 EST 2010 i686 i686 
i386 GNU/Linux


Please provide any additional information below.

Works o.k. with python 2.7. 

Original issue reported on code.google.com by heiner.b...@gmail.com on 19 Jan 2011 at 2:17

[GoogleCodeExporter]

Importing tif_lzw works fine with Python 2.6.5 on Ubuntu Linux.

Could you try importing libtiff to python via gdb or ddd to get more
information about the segmentation fault. Also check that the libtiff 
build/install
is clean (no build/ directory when running the build command).

Original comment by pearu.peterson on 19 Jan 2011 at 7:40

[GoogleCodeExporter]

Same issue here.  It could be a bug in EPD.

$ python -V
Python 2.6.6 -- EPD 6.3-2 (64-bit)

$ uname -a
Linux 2.6.37-12-generic #26-Ubuntu SMP Wed Jan 5 18:38:48 UTC 2011 x86_64 
GNU/Linux

Stack trace attached.

Problem occurs on call to import_array().  Copying the tif_lzw.so into the 
current directory and importing directly works fine.

Original comment by jon.beez...@gmail.com on 9 Feb 2011 at 12:41

Attachments:

• libtiff_bug.txt

[GoogleCodeExporter]

How was libtiff built? If with Python 2.7 then try rebuilding it
with Python 2.6 and against numpy that EPD provides.

Original comment by pearu.peterson on 9 Feb 2011 at 9:08

[GoogleCodeExporter]

The only version on python I have installed is 2.6.6.  I do have a system 
python 2.6.6, but numpy is not installed there.  I have rebuilt from a fresh 
directory.  Also:


$ ldd 
/opt/epd/epd-6.3-2-rh5-x86_64/lib/python2.6/site-packages/libtiff/tif_lzw.so 
    linux-vdso.so.1 =>  (0x00007fff3f192000)
    libpython2.6.so.1.0 => /opt/epd/epd-6.3-2-rh5-x86_64/lib/libpython2.6.so.1.0 (0x00007f3de03e4000)
    libpthread.so.0 => /lib/libpthread.so.0 (0x00007f3de01a1000)
    libc.so.6 => /lib/libc.so.6 (0x00007f3ddfe1d000)
    libdl.so.2 => /lib/libdl.so.2 (0x00007f3ddfc19000)
    libutil.so.1 => /lib/libutil.so.1 (0x00007f3ddfa16000)
    libm.so.6 => /lib/libm.so.6 (0x00007f3ddf792000)
    /lib64/ld-linux-x86-64.so.2 (0x00007f3de0980000)

Original comment by jon.beez...@gmail.com on 9 Feb 2011 at 9:29

[GoogleCodeExporter]

I wonder if you can build and import any numpy based extension module in your 
system.
For example, try

echo -e "subroutine foo\nend" > foo.f90
f2py -c -m bar foo.f90
python -c 'import bar; print bar.__doc__'

Does it work?

Original comment by pearu.peterson on 9 Feb 2011 at 9:45

[GoogleCodeExporter]

Yes, I have never had problems with numpy extensions using EPD in the past.

Original comment by jon.beez...@gmail.com on 9 Feb 2011 at 10:35

Attachments:

• test_module.txt

[GoogleCodeExporter]

Hmm, then I have no idea what could be wrong.

Try importing numpy before importing libtiff.

You can also edit libtiff/src/tif_lzw.c by removing its
code until it will import successfully; this might give some ideas
what is going on.

Original comment by pearu.peterson on 10 Feb 2011 at 6:05

[GoogleCodeExporter]

Here's an idea. In the header of tif_lzw.c try to change the following line

  #define PY_ARRAY_UNIQUE_SYMBOL PyArray_API

to

  #define PY_ARRAY_UNIQUE_SYMBOL PyArray_API_tif_lzw

and rebuild libtiff.

Original comment by pearu.peterson on 10 Feb 2011 at 6:23

[pearu]

Oudated.