Re: pynio crash

Hi Juerg and anyone trying to use PyNIO with Python 2.5.

PyNIO has calls to the C API function PyMem_DEL that were tolerated
(without any complaints) in
versions of Python prior to 2.5, even though they should, according
to the docs,
have been calls to PyObject_DEL. With Python 2.5 this is no longer
allowed.
I think this is most likely the cause of your problem. It is fixed in
our development code.
Mary Haley can get you a current binary.
  -dave

On Sep 24, 2007, at 5:55 PM, Juerg Schmidli wrote:

> Hi
>
> I'm experiencing problems with PyNIO after upgrading my system to
> pyngl-1.2.0 (PyNGL-1.2.0.Linux-i686-gcc4-2.5.tar.gz),
> numpy-1.0.3.1, and python-2.5.1 (gcc-4.1.2). Reading netcdf files
> works ok, but trying to create a netcdf file leads to a crash (see
> attachment). Any ideas what the problem could be. Might it be
> releated to the version of gcc that I am using (gcc-4.1.2)?
>
> Thanks for any suggestions,
> Juerg
>
>
> Python 2.5.1 (r251:54863, Sep 24 2007, 17:35:03)
> [GCC 4.1.2 (Gentoo 4.1.2 p1.0.1)] on linux2
> Type "help", "copyright", "credits" or "license" for more information.
>>>> import PyNGL.Nio as Nio
>>>> f = Nio.open_file('/tmp/test.nc' ,'c')
> fatal:Could not create (/tmp/test.nc)
> *** glibc detected *** python: free(): invalid pointer: 0x081a9ae8 ***
> ======= Backtrace: =========
> /lib/libc.so.6[0xb7d0d9c0]
> /lib/libc.so.6(__libc_free+0x89)[0xb7d0f029]
> /usr/lib/python2.5/site-packages/PyNGL/nio.so[0xb7362620]
> /usr/lib/python2.5/site-packages/PyNGL/nio.so[0xb736565f]
> /usr/lib/python2.5/site-packages/PyNGL/nio.so[0xb7367124]
> /usr/lib/libpython2.5.so.1.0(PyCFunction_Call+0x12a)[0xb7e69c3a]
> /usr/lib/libpython2.5.so.1.0(PyEval_EvalFrameEx+0x5531)[0xb7eb1a01]
> /usr/lib/libpython2.5.so.1.0(PyEval_EvalCodeEx+0x7a0)[0xb7eb2e40]
> /usr/lib/libpython2.5.so.1.0(PyEval_EvalCode+0x55)[0xb7eb2eb5]
> /usr/lib/libpython2.5.so.1.0[0xb7ecb306]
> /usr/lib/libpython2.5.so.1.0(PyRun_InteractiveOneFlags+0x195)
> [0xb7ecce25]
> /usr/lib/libpython2.5.so.1.0(PyRun_InteractiveLoopFlags+0x63)
> [0xb7ecd013]
> /usr/lib/libpython2.5.so.1.0(PyRun_AnyFileExFlags+0x4e)[0xb7ecd13e]
> /usr/lib/libpython2.5.so.1.0(Py_Main+0xa67)[0xb7ed6527]
> python(main+0x32)[0x80485b2]
> /lib/libc.so.6(__libc_start_main+0xd8)[0xb7cbf838]
> python[0x80484f1]
> ======= Memory map: ========
> 08048000-08049000 r-xp 00000000 08:07 3473567 /usr/bin/python2.5
> 08049000-0804a000 rw-p 00000000 08:07 3473567 /usr/bin/python2.5
> 0804a000-08264000 rw-p 0804a000 00:00 0 [heap]
> b6f00000-b6f21000 rw-p b6f00000 00:00 0
> b6f21000-b7000000 ---p b6f21000 00:00 0
> b7045000-b704f000 r-xp 00000000 08:07 3851093 /usr/lib/gcc/i686-
> pc-linux-gnu/4.1.2/libgcc_s.so.1
> b704f000-b7050000 rw-p 00009000 08:07 3851093 /usr/lib/gcc/i686-
> pc-linux-gnu/4.1.2/libgcc_s.so.1
> b7068000-b706d000 r-xp 00000000 08:07 4161927 /usr/lib/python2.5/
> lib-dynload/_struct.so
> b706d000-b706e000 rw-p 00005000 08:07 4161927 /usr/lib/python2.5/
> lib-dynload/_struct.so
> b706e000-b7081000 r-xp 00000000 08:07 4161686 /usr/lib/python2.5/
> lib-dynload/_ctypes.so
> b7081000-b7083000 rw-p 00013000 08:07 4161686 /usr/lib/python2.5/
> lib-dynload/_ctypes.so
> b7083000-b70b4000 r-xp 00000000 08:07 2818096 /usr/lib/python2.5/
> site-packages/numpy/random/mtrand.so
> b70b4000-b70b8000 rw-p 00031000 08:07 2818096 /usr/lib/python2.5/
> site-packages/numpy/random/mtrand.so
> b70b8000-b70c1000 r-xp 00000000 08:07 2785570 /usr/lib/python2.5/
> site-packages/numpy/fft/fftpack_lite.so
> b70c1000-b70c2000 rw-p 00008000 08:07 2785570 /usr/lib/python2.5/
> site-packages/numpy/fft/fftpack_lite.so
> b70c2000-b7163000 r-xp 00000000 08:07 2801765 /usr/lib/python2.5/
> site-packages/numpy/linalg/lapack_lite.so
> b7163000-b7164000 rw-p 000a0000 08:07 2801765 /usr/lib/python2.5/
> site-packages/numpy/linalg/lapack_lite.so
> b7164000-b71cb000 rw-p b7164000 00:00 0
> b71cb000-b71e5000 r-xp 00000000 08:07 2671723 /usr/lib/python2.5/
> site-packages/numpy/core/scalarmath.so
> b71e5000-b71e6000 rw-p 0001a000 08:07 2671723 /usr/lib/python2.5/
> site-packages/numpy/core/scalarmath.so
> b71e6000-b71f5000 r-xp 00000000 08:07 4161827 /usr/lib/python2.5/
> lib-dynload/cPickle.so
> b71f5000-b71f6000 rw-p 0000e000 08:07 4161827 /usr/lib/python2.5/
> lib-dynload/cPickle.so
> b71f6000-b721c000 r-xp 00000000 08:07 2671721 /usr/lib/python2.5/
> site-packages/numpy/core/umath.so
> b721c000-b721f000 rw-p 00026000 08:07 2671721 /usr/lib/python2.5/
> site-packages/numpy/core/umath.so
> b721f000-b7260000 rw-p b721f000 00:00 0
> b7264000-b7267000 r-xp 00000000 08:07 2703428 /usr/lib/python2.5/
> site-packages/numpy/lib/_compiled_base.so
> b7267000-b7268000 rw-p 00002000 08:07 2703428 /usr/lib/python2.5/
> site-packages/numpy/lib/_compiled_base.so
> b7268000-b726b000 r-xp 00000000 08:07 4161691 /usr/lib/python2.5/
> lib-dynload/math.so
> b726b000-b726c000 rw-p 00002000 08:07 4161691 /usr/lib/python2.5/
> lib-dynload/math.so
> b726c000-b727b000 r-xp 00000000 08:07 2671722 /usr/lib/python2.5/
> site-packages/numpy/core/_sort.so
> b727b000-b727c000 rw-p 0000e000 08:07 2671722 /usr/lib/python2.5/
> site-packages/numpy/core/_sort.so
> b727c000-b72d6000 r-xp 00000000 08:07 2671725 /usr/lib/python2.5/
> site-packages/numpy/core/multiarray.so
> b72d6000-b72dc000 rw-p 00059000 08:07 2671725 /usr/lib/python2.5/
> site-packages/Aborted
>
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Received on Mon Sep 24 2007 - 18:27:11 MDT