Hi
It could be that you just have to much data for the stack. You can see/set
your stack size with ulimit -s (on linux/solaris at least). Try to set it to
unlimited:
ulimit -s unlimited
This has solved similar problems for me in the past.
Best Regards
Troels Kofoed Jacobsen
On Saturday 25 April 2009 16:53:27 Adam Ginsburg wrote:
> Yep, I'm running on a 64 bit machine. I've been dealing with larger
> than 4GB data files in IDL, but I'd rather use python/numpy/matplotlib
> if possible.
>
> Here's the gdb session. The error didn't happen in imshow, only when
> I specified show(); I guess that means I must have had ioff() set
> although I don't think that was my default choice last time I used
> matplotlib.
>
>
> milkyway /data/glimpseii $ gdb /usr/local/python/bin/python
> GNU gdb Red Hat Linux (6.3.0.0-1.159.el4rh)
> Copyright 2004 Free Software Foundation, Inc.
> GDB is free software, covered by the GNU General Public License, and you
> are welcome to change it and/or distribute copies of it under certain
> conditions. Type "show copying" to see the conditions.
> There is absolutely no warranty for GDB. Type "show warranty" for details.
> This GDB was configured as "x86_64-redhat-linux-gnu"...Using host
> libthread_db library "/lib64/tls/libthread_db.so.1".
>
> (gdb) run
> Starting program: /usr/local/python/bin/python
> [Thread debugging using libthread_db enabled]
> [New Thread 182900715072 (LWP 18039)]
> Python 2.5 (r25:51908, Dec 22 2006, 16:08:43)
> [GCC 3.4.6 20060404 (Red Hat 3.4.6-3)] on linux2
> Type "help", "copyright", "credits" or "license" for more information.
>
> >>> import matplotlib,scipy,numpy,pyfits
> >>> from pylab import *
> >>> f = pyfits.open('GLM_00600+0000_mosaic_I3.fits')
> >>> imshow(f[0].data)
>
> <matplotlib.image.AxesImage object at 0x2aa3f45890>
>
> >>> show()
>
> Program received signal SIGSEGV, Segmentation fault.
> [Switching to Thread 182900715072 (LWP 18039)]
> 0x0000002aa3170ab5 in _image_module::fromarray (this=Variable "this"
> is not available.
> ) at src/image.cpp:872
> 872 src/image.cpp: No such file or directory.
> in src/image.cpp
> Current language: auto; currently c++
> (gdb)
>
>
> I've never used gdb before, so is there anything else I should be
> doing at this point?
>
> Thanks,
> Adam
>
> On Fri, Apr 24, 2009 at 7:52 AM, Michael Droettboom <md...@stsci.edu>
wrote:
> > On my machine (32-bit Fedora 10 with 2GB RAM), it chugs along swapping
> > for a loooong time and then fails with a Python MemoryError exception --
> > which is at least reasonable.
> >
> > I suspect you're running on a 64-bit machine and we're running into some
> > sort of non-64-bit-clean issue. We try to be 64-bit clean, but it
> > doesn't get verified on a regular basis, and not all of us (myself
> > included) are running 64-bit OSes.
> >
> > Can you try running python inside of gdb and getting a traceback? That
> > might provide some clues.
> >
> > We can estimate a little bit as to the memory requirements -- though it's
> > hard to account for everything.
> >
> > Input array is (10370, 9320) x 4 = 386MB
> > This array is always converted to doubles to convert to colors (this is
> > probably a place ripe for opimtization) so you get also 786MB. Then this
> > gets converted to an RGBA array for another 386MB
> >
> > Mike
> >
> > Adam Ginsburg wrote:
> >> Hi, I've been getting a segmentation fault when trying to display
> >> large images. A transcript of a sample session is below. I'm using
> >> the TkAgg backend, and I am using numpy, but otherwise I have made no
> >> modifications to the matplotlib setup.
> >>
> >>
> >> milkyway /data/glimpseii $ alias pylab
> >> alias pylab='/usr/local/adm/config/python/bin/ipython -pylab -log'
> >> milkyway /data/glimpseii $ pylab
> >> Activating auto-logging. Current session state plus future input saved.
> >> Filename : ipython_log.py
> >> Mode : rotate
> >> Output logging : False
> >> Raw input log : False
> >> Timestamping : False
> >> State : active
> >> Python 2.5 (r25:51908, Dec 22 2006, 16:08:43)
> >> Type "copyright", "credits" or "license" for more information.
> >>
> >> IPython 0.9.1 -- An enhanced Interactive Python.
> >> ? -> Introduction and overview of IPython's features.
> >> %quickref -> Quick reference.
> >> help -> Python's own help system.
> >> object? -> Details about 'object'. ?object also works, ?? prints more.
> >>
> >> Welcome to pylab, a matplotlib-based Python environment.
> >> For more information, type 'help(pylab)'.
> >>
> >> In [1]: import matplotlib,pyfits,numpy,scipy
> >>
> >> In [2]: scipy.__version__
> >> Out[2]: '0.7.0'
> >>
> >> In [3]: numpy.__version__
> >> Out[3]: '1.3.0'
> >>
> >> In [4]: matplotlib.__version__
> >> Out[4]: '0.98.5.2'
> >>
> >> In [5]: f = pyfits.open('GLM_00600+0000_mosaic_I3.fits')
> >>
> >> In [6]: f[0].data.shape
> >> Out[6]: (10370, 9320)
> >>
> >> In [7]: f[0].data.dtype
> >> Out[7]: dtype('>f4')
> >>
> >> In [8]: imshow(f[0].data)
> >> Segmentation fault
> >>
> >>
> >> Any ideas?
> >>
> >> Thanks,
> >> Adam
>
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