[Numpy-discussion] Strange crash in numpy.linalg.lstsq.
josef.pktd at gmail.com
josef.pktd at gmail.com
Mon Aug 17 13:55:08 EDT 2009
On Mon, Aug 17, 2009 at 1:42 PM, Jonathan
Taylor<jonathan.taylor at utoronto.ca> wrote:
> Hi,
>
> I am getting a strange crash in numpy.linalg.lstsq. I have put the code
> that causes the crash along with two data files on my website at:
>
> http://www.cs.toronto.edu/~jtaylor/crash/
>
> I would be interested to know if this bug can be duplicated and/or if anyone
> has any suggestions as to why:
>
> import numpy as np
> A = np.load('A.npy')
> b = np.load('b.npy')
> rc = np.linalg.lstsq(A,b)
>
> produces:
>
> *** glibc detected *** /usr/bin/python: free(): invalid next size (normal):
> 0x091793c0 ***
> ======= Backtrace: =========
> /lib/tls/i686/cmov/libc.so.6[0xb7dc7a85]
> /lib/tls/i686/cmov/libc.so.6(cfree+0x90)[0xb7dcb4f0]
> /u/jtaylor/lib/python2.5/site-packages/numpy/core/multiarray.so[0xb795403e]
> /usr/bin/python[0x811247a]
> /usr/bin/python(PyEval_EvalCodeEx+0x323)[0x80cae33]
> /usr/bin/python(PyEval_EvalFrameEx+0x565e)[0x80c93fe]
> /usr/bin/python(PyEval_EvalCodeEx+0x6e7)[0x80cb1f7]
> /usr/bin/python(PyEval_EvalCode+0x57)[0x80cb347]
> /usr/bin/python(PyRun_FileExFlags+0xf8)[0x80ea818]
> /usr/bin/python[0x80c1f5a]
> /usr/bin/python(PyObject_Call+0x27)[0x805cb97]
> /usr/bin/python(PyEval_EvalFrameEx+0x4064)[0x80c7e04]
> /usr/bin/python(PyEval_EvalCodeEx+0x6e7)[0x80cb1f7]
> /usr/bin/python[0x8113696]
> /usr/bin/python(PyObject_Call+0x27)[0x805cb97]
> /usr/bin/python(PyEval_EvalFrameEx+0x4064)[0x80c7e04]
> /usr/bin/python(PyEval_EvalCodeEx+0x6e7)[0x80cb1f7]
> /usr/bin/python(PyEval_EvalFrameEx+0x565e)[0x80c93fe]
> /usr/bin/python(PyEval_EvalCodeEx+0x6e7)[0x80cb1f7]
> /usr/bin/python[0x8113696]
> /usr/bin/python(PyObject_Call+0x27)[0x805cb97]
> /usr/bin/python[0x8062bfb]
> /usr/bin/python(PyObject_Call+0x27)[0x805cb97]
> /usr/bin/python(PyEval_EvalFrameEx+0x3d07)[0x80c7aa7]
> /usr/bin/python(PyEval_EvalCodeEx+0x6e7)[0x80cb1f7]
> /usr/bin/python(PyEval_EvalFrameEx+0x565e)[0x80c93fe]
> /usr/bin/python(PyEval_EvalFrameEx+0x5945)[0x80c96e5]
> /usr/bin/python(PyEval_EvalCodeEx+0x6e7)[0x80cb1f7]
> /usr/bin/python(PyEval_EvalFrameEx+0x6d09)[0x80caaa9]
> /usr/bin/python(PyEval_EvalCodeEx+0x6e7)[0x80cb1f7]
> /usr/bin/python(PyEval_EvalFrameEx+0x565e)[0x80c93fe]
> /usr/bin/python(PyEval_EvalCodeEx+0x6e7)[0x80cb1f7]
> /usr/bin/python(PyEval_EvalFrameEx+0x565e)[0x80c93fe]
> /usr/bin/python(PyEval_EvalFrameEx+0x5945)[0x80c96e5]
> /usr/bin/python(PyEval_EvalCodeEx+0x6e7)[0x80cb1f7]
> /usr/bin/python(PyEval_EvalFrameEx+0x565e)[0x80c93fe]
> /usr/bin/python(PyEval_EvalCodeEx+0x6e7)[0x80cb1f7]
> /usr/bin/python(PyEval_EvalFrameEx+0x565e)[0x80c93fe]
> /usr/bin/python(PyEval_EvalCodeEx+0x6e7)[0x80cb1f7]
> /usr/bin/python(PyEval_EvalFrameEx+0x565e)[0x80c93fe]
> /usr/bin/python(PyEval_EvalCodeEx+0x6e7)[0x80cb1f7]
> /usr/bin/python(PyEval_EvalCode+0x57)[0x80cb347]
> /usr/bin/python(PyRun_FileExFlags+0xf8)[0x80ea818]
> /usr/bin/python(PyRun_SimpleFileExFlags+0x199)[0x80eaab9]
> /usr/bin/python(Py_Main+0xa35)[0x8059335]
> /usr/bin/python(main+0x22)[0x80587f2]
> /lib/tls/i686/cmov/libc.so.6(__libc_start_main+0xe0)[0xb7d72450]
> /usr/bin/python[0x8058761]
> ======= Memory map: ========
> 08048000-08140000 r-xp 00000000 08:06 83501 /usr/bin/python2.5
> 08140000-08165000 rw-p 000f7000 08:06 83501 /usr/bin/python2.5
> 08165000-0919a000 rw-p 08165000 00:00 0 [heap]
> b5200000-b5221000 rw-p b5200000 00:00 0
> b5221000-b5300000 ---p b5221000 00:00 0
> b53fc000-b5499000 r-xp 00000000 00:1a 552170
> /h/44/jtaylor/lib/python2.5/site-packages/Cython/Compiler/Parsing.so
> b5499000-b54a2000 rw-p 0009d000 00:1a 552170
> /h/44/jtaylor/lib/python2.5/site-packages/Cython/Compiler/Parsing.so
> b54a2000-b5624000 rw-p b54a2000 00:00 0
> b5624000-b568f000 r-xp 00000000 00:1a 553542
> /h/44/jtaylor/build/matplotlib/lib/matplotlib/backends/_backend_agg.so
> b568f000-b5691000 rw-p 0006a000 00:1a 553542
> /h/44/jtaylor/build/matplotlib/lib/matplotlib/backends/_backend_agg.so
> b5691000-b56f6000 r-xp 00000000 08:06 90831
> /usr/lib/python2.5/lib-dynload/unicodedata.so
> b56f6000-b5705000 rw-p 00065000 08:06 90831
> /usr/lib/python2.5/lib-dynload/unicodedata.so
> b5705000-b5725000 r-xp 00000000 00:1a 553545
> /h/44/jtaylor/build/matplotlib/lib/matplotlib/backends/_tkagg.so
> b5725000-b5726000 rw-p 00020000 00:1a 553545
> /h/44/jtaylor/build/matplotlib/lib/matplotlib/backends/_tkagg.so
> b5726000-b5727000 ---p b5726000 00:00 0
> b5727000-b5f27000 rwxp b5727000 00:00 0
> b5f27000-b5f3e000 r-xp 00000000 08:06 85532 /usr/lib/libxcb.so.1.0.0
> b5f3e000-b5f3f000 rw-p 00016000 08:06 85532 /usr/lib/libxcb.so.1.0.0
> b5f3f000-b5f53000 r-xp 00000000 08:06 1187870
> /lib/tls/i686/cmov/libnsl-2.7.so
> b5f53000-b5f55000 rw-p 00013000 08:06 1187870
> /lib/tls/i686/cmov/libnsl-2.7.so
> b5f55000-b5f57000 rw-p b5f55000 00:00 0
> b5f57000-b603b000 r-xp 00000000 08:06 85536 /usr/lib/libX11.so.6.2.0
> b603b000-b603e000 rw-p 000e4000 08:06 85536 /usr/lib/libX11.so.6.2.0
> b603e000-b60e7000 r-xp 00000000 08:06 85098 /usr/lib/libtcl8.4.so.0
> b60e7000-b60f1000 rw-p 000a8000 08:06 85098 /usr/lib/libtcl8.4.so.0
> b60f1000-b60f2000 rw-p b60f1000 00:00 0
> b60f2000-b61c4000 r-xp 00000000 08:06 85102 /usr/lib/libtk8.4.so.0
> b61c4000-b61cf000 rw-p 000d2000 08:06 85102 /usr/lib/libtk8.4.so.0
> b61cf000-b61d0000 rw-p b61cf000 00:00 0
> b61d0000-b62a8000 r-xp 00000000 08:06 85103 /usr/lib/libBLT.2.4.so.8.4
> b62a8000-b62b9000 rw-p 000d8000 08:06 85103 /usr/lib/libBLT.2.4.so.8.4
> b62b9000-b62ba000 rw-p b62b9000 00:00 0
> b62ba000-b62dc000 r-xp 00000000 08:06 180469 /usr/lib/libpng12.so.0.15.0
> b62dc000-b62dd000 rw-p 00022000 08:06 180469 /usr/lib/libpng12.so.0.15.0
> b62f5000-b62f6000 rw-p b62f5000 00:00 0
> b62f6000-b631d000 r-xp 00000000 00:1a 553544
> /h/44/jtaylor/build/matplotlib/lib/matplotlib/_png.so
> b631d000-b631e000 rw-p 00027000 00:1a 553544
> /h/44/jtaylor/build/matplotlib/lib/matplotlib/_png.so
> b631e000-b6367000 r-xp 00000000 00:1a 553543
> /h/44/jtaylor/build/matplotlib/lib/matplotlib/_image.so
> b6367000-b6369000 rw-p 00049000 00:1a 553543
> /h/44/jtaylor/build/matplotlib/lib/matplotlib/_image.so
> b6369000-b63d3000 r-xp 00000000 08:06 83795
> /usr/lib/libfreetype.so.6.3.16
> b63d3000-b63d6000 rw-p 0006a000 08:06 83795
> /usr/lib/libfreetype.so.6.3.16
> b63d6000-b6424000 r-xp 00000000 00:1a 553535
> /h/44/jtaylor/build/matplotlib/lib/matplotlib/ft2font.so
> b6424000-b6427000 rw-p 0004e000 00:1a 553535
> /h/44/jtaylor/build/matplotlib/lib/matplotlib/ft2font.so
> b6427000-b650f000 r-xp 00000000 08:06 88506 /usr/lib/libstdc++.so.6.0.9
> b650f000-b6512000 r--p 000e8000 08:06 88506 /usr/lib/libstdc++.so.6.0.9
> b6512000-b6514000 rw-p 000eb000 08:06 88506 /usr/lib/libstdc++.so.6.0.9
> b6514000-b651a000 rw-p b6514000 00:00 0
> b651e000-b6528000 r-xp 00000000 08:06 313979
> /usr/lib/python2.5/lib-dynload/_tkinter.so
> b6528000-b6529000 rw-p 0000a000 08:06 313979
> /usr/lib/python2.5/lib-dynload/_tkinter.so
> b6529000-b652d000 r-xp 00000000 08:06 90832
> /usr/lib/python2.5/lib-dynload/zlib.so
> b652d000-b652e000 rw-p 00004000 08:06 90832
> /usr/lib/python2.5/lib-dynload/zlib.so
> b652e000-b6532000 r-xp 00000000 00:1a 553538
> /h/44/jtaylor/build/matplotlib/lib/matplotlib/_cntr.so
> b6532000-b6533000 rw-p 00004000 00:1a 553538
> /h/44/jtaylor/build/matplotlib/lib/matplotlib/_cntr.so
> b6533000-b6577000 r-xp 00000000 00:1a 553541
> /h/44/jtaylor/build/matplotlib/lib/matplotlib/_path.so
> b6577000-b6578000 rw-p 00044000 00:1a 553541
> /h/44/jtaylor/build/matplotlib/lib/matplotlib/_path.so
> b6578000-b6587000 r-xp 00000000 08:06 92419
> /usr/lib/python2.5/lib-dynload/datetime.so
> b6587000-b658a000 rw-p 0000e000 08:06 92419
> /usr/lib/python2.5/lib-dynload/datetime.so
> b658a000-b65b9000 r-xp 00000000 00:1a 532925
> /h/44/jtaylor/lib/python2.5/site-packages/numpy/random/mtrand.so
> b65b9000-b65cb000 rw-p 0002e000 00:1a 532925
> /h/44/jtaylor/lib/python2.5/site-packages/numpy/random/mtrand.so
> b65cb000-b6923000 r-xp 00000000 08:06 517267
> /usr/lib/atlas/libblas.so.3.0
> b6923000-b6927000 rw-p 00358000 08:06 517267
> /usr/lib/atlas/libblas.so.3.0
> b6927000-b6e6f000 r-xp 00000000 08:06 517268
> /usr/lib/atlas/liblapack.so.3.0
> b6e6f000-b6e72000 rw-p 00548000 08:06 517268
> /usr/lib/atlas/liblapack.so.3.0
> b6e72000-b6f76000 rw-p b6e72000 00:00 0
> b6f76000-b6f7a000 r-xp 00000000 08:06 85530 /usr/lib/libXdmcp.so.6.0.0
> b6f7a000-b6f7b000 rw-p 00003000 08:06 85530 /usr/lib/libXdmcp.so.6.0.0
> b6f7b000-b6f7f000 r-xp 00000000 08:06 92437
> /usr/lib/python2.5/lib-dynload/_csv.so
> b6f7f000-b6f81000 rw-p 00004000 08:06 92437
> /usr/lib/python2.5/lib-dynload/_csv.so
> b6f81000-b6f84000 r-xp 00000000 08:06 92427
> /usr/lib/python2.5/lib-dynload/_locale.so
> b6f84000-b6f85000 rw-p 00003000 08:06 92427
> /usr/lib/python2.5/lib-dynload/_locale.so
> b6f85000-b6f8e000 r-xp 00000000 00:1a 533113
> /h/44/jtaylor/lib/python2.5/site-packages/numpy/fft/fftpack_lite.so
> b6f8e000-b6f8f000 rw-p 00008000 00:1a 533113
> /h/44/jtaylor/lib/python2.5/site-packages/numpy/fft/fftpack_lite.so
> b6f8f000-b6fad000 r-xp 00000000 00:1a 533028
> /h/44/jtaylor/lib/python2.5/site-packages/numpy/core/scalarmath.so
> b6fad000-b6fae000 rw-p 0001e000 00:1a 533028
> /h/44/jtaylor/lib/python2.Aborted
>
>
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>
>
no problem here, with official Windows numpy
Josef
>>> np.version.version
'1.3.0'
>python -i why_crash.py
>>> print rc
(array([ -5.23462841, -4.85584394, -2.99233015, -7.54676368,
-10.15455332, 7.074554 , 8.4043877 , 2.79661679,
3.41336578, 5.29202285, 2.70716181, 15.53449435,
9.34557621, 17.32209602, 18.16994838, -50.98017437,
-50.96547959, -17.51283078, 7.68637678, 13.53704022,
20.66278929, -23.64368007, -4.70942583, 18.2568222 ,
2.45709374, 12.97156815, 15.47026211, -44.93348725,
7.7558192 , -39.13996758, 1.20214959, 23.61872159,
-20.21198664, -7.87137325, -4.20255668, -45.24948722,
12.49507108, 24.22157348, 23.46404032, 18.62294373,
-26.31401828, 24.35842929, -37.5578372 , 18.24079679,
28.90693972, -40.40246853, 23.85976491, 11.70965078,
17.38628028, 6.14989021, 0.19683346, 11.57781284,
-6.70961655, -21.98525308, -11.30257635, 31.16804751,
5.08794164, 0.26279222, -27.78390652, -26.3151511 ,
14.89172102, 29.02572416, -10.84227516, 3.20577699,
-34.73738042, 24.90588989, 37.92166034, -30.30146211,
37.28852751, -16.03146259, -30.87415056, -33.02832669,
-21.63514384, 11.15711455, 10.43855884, -7.08345237,
31.50460928, -28.64336727, -12.32269443, -24.59112645,
41.71351395, -29.85091349, -4.07409268, 0.82708638,
14.67839587, 41.58165228, -29.44030397, 31.13279856,
-28.46626932, 31.21863319, -30.50159697, -6.26718832,
-26.41654876, -2.42547434, 44.00738912, -10.94028372,
-0.65862359, -25.08227995, -26.04263867, 13.25529043,
-7.41115206, 36.11891076, 47.22737694, 23.39250661,
-16.59126536, 37.75596345, 12.59698144, 9.15952276,
-22.0567611 , -27.79573887, -30.57535286, 28.71831817,
-21.38243352, 19.30944773, 49.81583705, -19.59172648]), array([ 1063.81
458595]), 116, array([ 10.77032961, 3.02162267, 3.02054405, 3.0010756 ,
2.96191492, 2.94807426, 2.94230063, 2.93906657,
2.92832506, 2.91399677, 2.88159001, 2.86294336,
2.85790349, 2.84497487, 2.82744239, 2.81275744,
2.78836986, 2.77119523, 2.76422221, 2.75861982,
2.75015801, 2.72908307, 2.68445243, 2.67800314,
2.666536 , 2.65671856, 2.64826304, 2.63879427,
2.6296631 , 2.60120053, 2.59118748, 2.58256916,
2.57264941, 2.56585886, 2.53898947, 2.53365513,
2.52103196, 2.49959127, 2.47968021, 2.46456052,
2.46068247, 2.44924031, 2.43199483, 2.41963211,
2.41515001, 2.40937849, 2.39016287, 2.3762653 ,
2.35560428, 2.34357138, 2.3260469 , 2.30884773,
2.29027418, 2.27944481, 2.27465575, 2.25660949,
2.21410648, 2.20263598, 2.1791073 , 2.15789688,
2.14225592, 2.13043072, 2.09846149, 2.07491627,
2.06112946, 2.04336228, 2.02056257, 1.99107297,
1.98856298, 1.97039638, 1.9575191 , 1.93587212,
1.91997992, 1.85665009, 1.84338407, 1.79610228,
1.79328928, 1.78429932, 1.74123465, 1.7241243 ,
1.7010803 , 1.64746663, 1.62765943, 1.62303706,
1.61800823, 1.60531761, 1.52425119, 1.50620662,
1.485018 , 1.45765932, 1.40861388, 1.39268607,
1.3483904 , 1.32025766, 1.31350522, 1.28517948,
1.25950863, 1.23770526, 1.18665953, 1.15504454,
1.14088912, 1.11336858, 1.01682096, 0.9791356 ,
0.93161774, 0.90834728, 0.8611552 , 0.82261935,
0.79141265, 0.64055544, 0.60890393, 0.58578707,
0.4948037 , 0.38776132, 0.35580931, 0.20854201]))
>>>
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