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coo.todense() segfaults (Trac #1654) #2179
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@stefanv wrote on 2012-05-03 With 0.11.0.dev I get a MemoryError instead. It looks like the row and column coordinates are within bounds:
But the output array would have a prohibitively large memory footprint:
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This is very much still an issue. While the memory footprint may have been "prohibitively large" on rlm's machine, mine has 250GB of ram. This matrix is approximately 19GB. In [4]: import numpy as np In [5]: np.dtype(float).itemsize * np.prod(prM.shape) / 1024.**3 In [6]: badM = cPickle.load(open('/var/xxx/badM.obj', 'rb')) In [7]: badM.todense() xxx@xxx:~/xxx$ free -m -g xxx@xxx:~/xxx$ ipython What gives? |
OK, reopening. This is with scipy 0.12.0 or master I assume? |
@rgommers: Thanks! Yes, this is SciPy 0.12.0. This is Ubuntu 12.04LTS, 230GB ram, 18 2.2Ghz Intel Xeon Virtual Cores. Python 2.7.3 from apt. What other information can I provide you? Here's my show_config(): In [11]: sp.show_config() In [12]: sp.test() ..............................................................................................................................................................................................................................K..............................................................................................................K....................................................................K..K............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................SSSSSS......SSSSSS......SSSS.......................................................................................................K..............................................................................................................................................................................................................................................................................................K..........................................................................................................................................................................................................................K.........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................K....................................................................K......................................................................................................................................................................KK..............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................K.K..........................K................................................................................................................................................................................................................................................................................................................................................................................K........K......................SSSSSSSS.........................................................................................................................................................................................S...................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................Ran 6136 tests in 75.327s OK (KNOWNFAIL=16, SKIP=25) |
That should be enough info. It'll just be hard to reproduce, given that very few people have that much RAM. I just get a ValueError with current master:
If you can produce a segfault with an array that would fit into 8Gb, that would help a lot. |
I will experiment and see if I can make it happen with 8GB. If not, I'm We're using SciPy for some big data ML applications and working with dense On Wed, Jun 5, 2013 at 12:07 PM, Ralf Gommers notifications@github.comwrote:
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Could you try to get a backtrace with gdb? http://www.scipy.org/scipylib/bug-report.html describes how to do that. |
Out of interest, what company/application (if you're allowed to share that)? |
(Have now a machine with enough memory to test this:) This is a 32-bit integer overflow issue, and fixed by PR gh-3224 |
Is this fixed? |
gh-3224 was merged, so yes. |
Original ticket http://projects.scipy.org/scipy/ticket/1654 on 2012-05-03 by trac user rlm, assigned to unknown.
Zipped pickle (~7MB) of a COO matrix can be found here:
http://rlmiller.org/badM.obj.zip
To reproduce:
The setup:
$ uname -a
Darwin dev-rmiller.local 11.3.0 Darwin Kernel Version 11.3.0: Thu Jan 12 18:47:41 PST 2012; root:xnu-1699.24.23~1/RELEASE_X86_64 x86_64
scipy-0.10.0-py2.7-macosx-10.7-intel
Python 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
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