如何解决此python解释器崩溃？

Question

I'm running a small script with PANDAS and I get a rather impressive interpreter error. I've included the full stack trace at the end of this question since it's so damn long.

Poking around with ipdb , I've managed to isolate the block that may be at the origin of the error. When executing the code between breakpoints, the following block of code exits with the much less verbose error message “ipython” terminated by signal SIGSEGV (Address boundary error) :

samples = pd.DataFrame(
    re.findall(re_samp, m), columns=('t', 'x', 'y', 'cr')
)

import ipdb; ipdb.set_trace()
# set nans when eyes are not being tracked
for c in samples:
    samples[c][samples[c] == '.'] = pd.np.nan

    # column type conversions
    if c == 't':
        samples[c] = samples[c].astype(int)
    else:
        samples[c] = samples[c].astype(float)
ipdb.set_trace()

In the above snippet, the error occurs between the two ipdb statements, specifically this line: samples[c][samples[c] == '.'] = pd.np.nan .

Beyond the fact that PANDAS and scipy sparse matrixes are involved ( cf traceback below), I am at an absolute loss as to:

1. what the problem is
2. how I should go about fixing it

Any advice is greatly welcomed! Thank you very much in advance!

*** Error in `/usr/bin/python': free(): invalid size: 0x0000000003712f30 ***
======= Backtrace: =========
/lib/x86_64-linux-gnu/libc.so.6(+0x80996)[0x7f3e69f98996]
/usr/lib/python2.7/dist-packages/numpy/core/multiarray.so(+0x86b77)[0x7f3e6599eb77]
/usr/lib/python2.7/dist-packages/numpy/core/multiarray.so(+0x9e99d)[0x7f3e659b699d]
/usr/lib/python2.7/dist-packages/numpy/core/multiarray.so(+0x9e95c)[0x7f3e659b695c]
/usr/bin/python[0x484b53]
/usr/bin/python[0x559f7f]
/usr/bin/python[0x484b53]
/usr/bin/python[0x55988f]
/usr/bin/python[0x484736]
/usr/bin/python[0x55988f]
/usr/bin/python[0x55976f]
/usr/bin/python[0x484736]
/usr/bin/python[0x55aa43]
/usr/bin/python[0x558d90]
/usr/bin/python[0x558ea0]
/usr/bin/python(PyDict_SetItem+0x566)[0x526ec6]
/usr/bin/python(PyDict_SetItemString+0x10d)[0x501aed]
/usr/bin/python(PyEval_EvalFrameEx+0x354d)[0x530f1d]
/usr/bin/python(PyEval_EvalFrameEx+0xca2)[0x52e672]
/usr/bin/python(PyEval_EvalCode+0xfc)[0x567cdc]
/usr/bin/python(PyEval_EvalFrameEx+0x59eb)[0x5333bb]
/usr/bin/python(PyEval_EvalCodeEx+0x2a4)[0x505b24]
/usr/bin/python(PyEval_EvalFrameEx+0x1a22)[0x52f3f2]
/usr/bin/python(PyEval_EvalCodeEx+0x2a4)[0x505b24]
/usr/bin/python(PyEval_EvalFrameEx+0x867)[0x52e237]
/usr/bin/python(PyEval_EvalCodeEx+0x2a4)[0x505b24]
/usr/bin/python(PyEval_EvalFrameEx+0x867)[0x52e237]
/usr/bin/python(PyEval_EvalCodeEx+0x2a4)[0x505b24]
/usr/bin/python(PyEval_EvalFrameEx+0x867)[0x52e237]
/usr/bin/python(PyEval_EvalCodeEx+0x2a4)[0x505b24]
/usr/bin/python(PyEval_EvalFrameEx+0x867)[0x52e237]
/usr/bin/python(PyEval_EvalCodeEx+0x2a4)[0x505b24]
/usr/bin/python(PyEval_EvalFrameEx+0x1a22)[0x52f3f2]
/usr/bin/python(PyEval_EvalCodeEx+0x2a4)[0x505b24]
/usr/bin/python(PyEval_EvalFrameEx+0x1a22)[0x52f3f2]
/usr/bin/python(PyEval_EvalCode+0xfc)[0x567cdc]
/usr/bin/python[0x451adb]
/usr/bin/python(PyRun_FileExFlags+0x92)[0x451e5b]
/usr/bin/python(PyRun_SimpleFileExFlags+0x2ee)[0x452394]
/usr/bin/python(Py_Main+0xb5e)[0x453ead]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf5)[0x7f3e69f39de5]
/usr/bin/python[0x5786be]
======= Memory map: ========
00400000-006ba000 r-xp 00000000 08:06 2491349                            /usr/bin/python2.7
008b9000-008ba000 r--p 002b9000 08:06 2491349                            /usr/bin/python2.7
008ba000-0092f000 rw-p 002ba000 08:06 2491349                            /usr/bin/python2.7
0092f000-00941000 rw-p 00000000 00:00 0 
01499000-09020000 rw-p 00000000 00:00 0                                  [heap]
7f3e53a58000-7f3e54386000 rw-p 00000000 00:00 0 
7f3e54fb8000-7f3e558d0000 rw-p 00000000 00:00 0 
7f3e558d0000-7f3e558d5000 r-xp 00000000 08:06 2626378                    /usr/lib/python2.7/lib-dynload/mmap.x86_64-linux-gnu.so
7f3e558d5000-7f3e55ad4000 ---p 00005000 08:06 2626378                    /usr/lib/python2.7/lib-dynload/mmap.x86_64-linux-gnu.so
7f3e55ad4000-7f3e55ad5000 r--p 00004000 08:06 2626378                    /usr/lib/python2.7/lib-dynload/mmap.x86_64-linux-gnu.so
7f3e55ad5000-7f3e55ad6000 rw-p 00005000 08:06 2626378                    /usr/lib/python2.7/lib-dynload/mmap.x86_64-linux-gnu.so
7f3e55ad8000-7f3e55ae2000 r-xp 00000000 08:06 5247160                    /usr/lib/python2.7/dist-packages/scipy/io/matlab/streams.so
7f3e55ae2000-7f3e55ce1000 ---p 0000a000 08:06 5247160                    /usr/lib/python2.7/dist-packages/scipy/io/matlab/streams.so
7f3e55ce1000-7f3e55ce2000 r--p 00009000 08:06 5247160                    /usr/lib/python2.7/dist-packages/scipy/io/matlab/streams.so
7f3e55ce2000-7f3e55ce3000 rw-p 0000a000 08:06 5247160                    /usr/lib/python2.7/dist-packages/scipy/io/matlab/streams.so
7f3e55ce3000-7f3e55ce4000 rw-p 00000000 00:00 0 
7f3e55ce8000-7f3e55d06000 r-xp 00000000 08:06 5247162                    /usr/lib/python2.7/dist-packages/scipy/io/matlab/mio5_utils.so
7f3e55d06000-7f3e55f06000 ---p 0001e000 08:06 5247162                    /usr/lib/python2.7/dist-packages/scipy/io/matlab/mio5_utils.so
7f3e55f06000-7f3e55f07000 r--p 0001e000 08:06 5247162                    /usr/lib/python2.7/dist-packages/scipy/io/matlab/mio5_utils.so
7f3e55f07000-7f3e55f0b000 rw-p 0001f000 08:06 5247162                    /usr/lib/python2.7/dist-packages/scipy/io/matlab/mio5_utils.so
7f3e55f10000-7f3e55f16000 r-xp 00000000 08:06 5247159                    /usr/lib/python2.7/dist-packages/scipy/io/matlab/mio_utils.so
7f3e55f16000-7f3e56115000 ---p 00006000 08:06 5247159                    /usr/lib/python2.7/dist-packages/scipy/io/matlab/mio_utils.so
7f3e56115000-7f3e56116000 r--p 00005000 08:06 5247159                    /usr/lib/python2.7/dist-packages/scipy/io/matlab/mio_utils.so
7f3e56116000-7f3e56117000 rw-p 00006000 08:06 5247159                    /usr/lib/python2.7/dist-packages/scipy/io/matlab/mio_utils.so
7f3e56118000-7f3e56125000 r-xp 00000000 08:06 5247240                    /usr/lib/python2.7/dist-packages/scipy/sparse/csgraph/_min_spanning_tree.so
7f3e56125000-7f3e56324000 ---p 0000d000 08:06 5247240                    /usr/lib/python2.7/dist-packages/scipy/sparse/csgraph/_min_spanning_tree.so
7f3e56324000-7f3e56325000 r--p 0000c000 08:06 5247240                    /usr/lib/python2.7/dist-packages/scipy/sparse/csgraph/_min_spanning_tree.so
7f3e56325000-7f3e56328000 rw-p 0000d000 08:06 5247240                    /usr/lib/python2.7/dist-packages/scipy/sparse/csgraph/_min_spanning_tree.so
7f3e56328000-7f3e56341000 r-xp 00000000 08:06 5247242                    /usr/lib/python2.7/dist-packages/scipy/sparse/csgraph/_traversal.so
7f3e56341000-7f3e56540000 ---p 00019000 08:06 5247242                    /usr/lib/python2.7/dist-packages/scipy/sparse/csgraph/_traversal.so
7f3e56540000-7f3e56541000 r--p 00018000 08:06 5247242                    /usr/lib/python2.7/dist-packages/scipy/sparse/csgraph/_traversal.so
7f3e56541000-7f3e56546000 rw-p 00019000 08:06 5247242                    /usr/lib/python2.7/dist-packages/scipy/sparse/csgraph/_traversal.so
7f3e56546000-7f3e56547000 rw-p 00000000 00:00 0 
7f3e56548000-7f3e56560000 r-xp 00000000 08:06 5247239                    /usr/lib/python2.7/dist-packages/scipy/sparse/csgraph/_tools.so
7f3e56560000-7f3e5675f000 ---p 00018000 08:06 5247239                    /usr/lib/python2.7/dist-packages/scipy/sparse/csgraph/_tools.so
7f3e5675f000-7f3e56760000 r--p 00017000 08:06 5247239                    /usr/lib/python2.7/dist-packages/scipy/sparse/csgraph/_tools.so
7f3e56760000-7f3e56765000 rw-p 00018000 08:06 5247239                    /usr/lib/python2.7/dist-packages/scipy/sparse/csgraph/_tools.so
7f3e56768000-7f3e56791000 r-xp 00000000 08:06 5247241                    /usr/lib/python2.7/dist-packages/scipy/sparse/csgraph/_shortest_path.so
7f3e56791000-7f3e56991000 ---p 00029000 08:06 5247241                    /usr/lib/python2.7/dist-packages/scipy/sparse/csgraph/_shortest_path.so
7f3e56991000-7f3e56992000 r--p 00029000 08:06 5247241                    /usr/lib/python2.7/dist-packages/scipy/sparse/csgraph/_shortest_path.so
7f3e56992000-7f3e56998000 rw-p 0002a000 08:06 5247241                    /usr/lib/python2.7/dist-packages/scipy/sparse/csgraph/_shortest_path.so
7f3e56998000-7f3e5699e000 r-xp 00000000 08:06 5247214                    /usr/lib/python2.7/dist-packages/scipy/sparse/sparsetools/_csgraph.so
7f3e5699e000-7f3e56b9d000 ---p 00006000 08:06 5247214                    /usr/lib/python2.7/dist-packages/scipy/sparse/sparsetools/_csgraph.so
7f3e56b9d000-7f3e56b9e000 r--p 00005000 08:06 5247214                    /usr/lib/python2.7/dist-packages/scipy/sparse/sparsetools/_csgraph.so
7f3e56b9e000-7f3e56b9f000 rw-p 00006000 08:06 5247214                    /usr/lib/python2.7/dist-packages/scipy/sparse/sparsetools/_csgraph.so
7f3e56ba0000-7f3e56c8f000 r-xp 00000000 08:06 5247213                    /usr/lib/python2.7/dist-packages/scipy/sparse/sparsetools/_bsr.so
7f3e56c8f000-7f3e56e8e000 ---p 000ef000 08:06 5247213                    /usr/lib/python2.7/dist-packages/scipy/sparse/sparsetools/_bsr.so
7f3e56e8e000-7f3e56e8f000 r--p 000ee000 08:06 5247213                    /usr/lib/python2.7/dist-packages/scipy/sparse/sparsetools/_bsr.so
7f3e56e8f000-7f3e56e90000 rw-p 000ef000 08:06 5247213                    /usr/lib/python2.7/dist-packages/scipy/sparse/sparsetools/_bsr.so
7f3e56e90000-7f3e56e9d000 r-xp 00000000 08:06 5247217                    /usr/lib/python2.7/dist-packages/scipy/sparse/sparsetools/_dia.so
7f3e56e9d000-7f3e5709d000 ---p 0000d000 08:06 5247217                    /usr/lib/python2.7/dist-packages/scipy/sparse/sparsetools/_dia.so
7f3e5709d000-7f3e5709e000 r--p 0000d000 08:06 5247217                    /usr/lib/python2.7/dist-packages/scipy/sparse/sparsetools/_dia.so
7f3e5709e000-7f3e5709f000 rw-p 0000e000 08:06 5247217                    /usr/lib/python2.7/dist-packages/scipy/sparse/sparsetools/_dia.so
7f3e570a0000-7f3e570c6000 r-xp 00000000 08:06 5247215                    /usr/lib/python2.7/dist-packages/scipy/sparse/sparsetools/_coo.so
7f3e570c6000-7f3e572c5000 ---p 00026000 08:06 5247215                    /usr/lib/python2.7/dist-packages/scipy/sparse/sparsetools/_coo.so
7f3e572c5000-7f3e572c6000 r--p 00025000 08:06 5247215                    /usr/lib/python2.7/dist-packages/scipy/sparse/sparsetools/_coo.so
7f3e572c6000-7f3e572c7000 rw-p 00026000 08:06 5247215                    /usr/lib/python2.7/dist-packages/scipy/sparse/sparsetools/_coo.so
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7f3e57348000-7f3e57547000 ---p 00080000 08:06 5247218                    /usr/lib/python2.7/dist-packages/scipy/sparse/sparsetools/_csc.so
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7f3e57548000-7f3e57549000 rw-p 00080000 08:06 5247218                    /usr/lib/python2.7/dist-packages/scipy/sparse/sparsetools/_csc.so
7f3e57550000-7f3e57621000 r-xp 00000000 08:06 5247216                    /usr/lib/python2.7/dist-packages/scipy/sparse/sparsetools/_csr.so
7f3e57621000-7f3e57820000 ---p 000d1000 08:06 5247216                    /usr/lib/python2.7/dist-packages/scipy/sparse/sparsetools/_csr.so
7f3e57820000-7f3e57821000 r--p 000d0000 08:06 5247216                    /usr/lib/python2.7/dist-packages/scipy/sparse/sparsetools/_csr.so
7f3e57821000-7f3e57823000 rw-p 000d1000 08:06 5247216                    /usr/lib/python2.7/dist-packages/scipy/sparse/sparsetools/_csr.so
7f3e57828000-7f3e57833000 r-xp 00000000 08:06 2498783                    /usr/lib/x86_64-linux-gnu/libjbig.so.0.0.0
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7f3e57a32000-7f3e57a33000 r--p 0000a000 08:06 2498783                    /usr/lib/x86_64-linux-gnu/libjbig.so.0.0.0
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7f3e57a38000-7f3e57aa6000 r-xp 00000000 08:06 2499073                    /usr/lib/x86_64-linux-gnu/libtiff.so.5.1.0
7f3e57aa6000-7f3e57ca6000 ---p 0006e000 08:06 2499073                    /usr/lib/x86_64-linux-gnu/libtiff.so.5.1.0
7f3e57ca6000-7f3e57ca7000 r--p 0006e000 08:06 2499073                    /usr/lib/x86_64-linux-gnu/libtiff.so.5.1.0
7f3e57ca7000-7f3e57caa000 rw-p 0006f000 08:06 2499073                    /usr/lib/x86_64-linux-gnu/libtiff.so.5.1.0
7f3e57cb0000-7f3e57cf3000 r-xp 00000000 08:06 2496034                    /usr/lib/x86_64-linux-gnu/libjpeg.so.8.0.2
7f3e57cf3000-7f3e57ef3000 ---p 00043000 08:06 2496034                    /usr/lib/x86_64-linux-gnu/libjpeg.so.8.0.2
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7f3e57f08000-7f3e57f49000 r-xp 00000000 08:06 2624064                    /usr/lib/python2.7/dist-packages/_imaging.so
7f3e57f49000-7f3e58148000 ---p 00041000 08:06 2624064                    /usr/lib/python2.7/dist-packages/_imaging.so
7f3e58148000-7f3e5814b000 r--p 00040000 08:06 2624064                    /usr/lib/python2.7/dist-packages/_imaging.so
7f3e5814b000-7f3e5814e000 rw-p 00043000 08:06 2624064                    /usr/lib/python2.7/dist-packages/_imaging.so
7f3e58150000-7f3e58167000 r-xp 00000000 08:06 4337590                    /usr/lib/python2.7/dist-packages/pandas/msgpack.so
7f3e58167000-7f3e58366000 ---p 00017000 08:06 4337590                    /usr/lib/python2.7/dist-packages/pandas/msgpack.so
7f3e58366000-7f3e58367000 r--p 00016000 08:06 4337590                    /usr/lib/python2.7/dist-packages/pandas/msgpack.so
7f3e58367000-7f3e5836b000 rw-p 00017000 08:06 4337590                    /usr/lib/python2.7/dist-packages/pandas/msgpack.so
7f3e58370000-7f3e58374000 r-xp 00000000 08:06 1445743                    /lib/x86_64-linux-gnu/libgpg-error.so.0.10.0
7f3e58374000-7f3e58573000 ---p 00004000 08:06 1445743                    /lib/x86_64-linux-gnu/libgpg-error.so.0.10.0
7f3e58573000-7f3e58574000 r--p 00003000 08:06 1445743                    /lib/x86_64-linux-gnu/libgpg-error.so.0.10.0
7f3e58574000-7f3e58575000 rw-p 00004000 08:06 1445743                    /lib/x86_64-linux-gnu/libgpg-error.so.0.10.0
7f3e58578000-7f3e58599000 r-xp 00000000 08:06 1445760                    /lib/x86_64-linux-gnu/liblzma.so.5.0.0
7f3e58599000-7f3e58798000 ---p 00021000 08:06 1445760                    /lib/x86_64-linux-gnu/liblzma.so.5.0.0
7f3e58798000-7f3e58799000 r--p 00020000 08:06 1445760                    /lib/x86_64-linux-gnu/liblzma.so.5.0.0
7f3e58799000-7f3e5879a000 rw-p 00021000 08:06 1445760                    /lib/x86_64-linux-gnu/liblzma.so.5.0.0
7f3e587a0000-7f3e5881a000 r-xp 00000000 08:06 1445739                    /lib/x86_64-linux-gnu/libgcrypt.so.11.7.0
7f3e5881a000-7f3e58a1a000 ---p 0007a000 08:06 1445739                    /lib/x86_64-linux-gnu/libgcrypt.so.11.7.0
7f3e58a1a000-7f3e58a1b000 r--p 0007a000 08:06 1445739                    /lib/x86_64-linux-gnu/libgcrypt.so.11.7.0
7f3e58a1b000-7f3e58a1e000 rw-p 0007b000 08:06 1445739                    /lib/x86_64-linux-gnu/libgcrypt.so.11.7.0

Answer 1

see the big-bold warning in red:

http://pandas.pydata.org/pandas-docs/dev/whatsnew.html#v0-13-1-february-3-2014

This is an interaction be numpy < 1.8 see in pandas 0.13.0 when doing a chained assignment

do your assignment like this:

samples.loc[samples[c]=='.',c] = np.nan