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Segfault in pd.read_csv() using chunksize parameter #11793

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OEP opened this Issue Dec 8, 2015 · 5 comments

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@OEP

OEP commented Dec 8, 2015

Here is my repro script:

import pandas as pd
import sys

for df in pd.read_csv(sys.argv[1], chunksize=1000):
    print(df[['sum']].sum())

and I am attaching small.csv.gz as the smallest data set I know reproduces this segfault. Running python repro.py small.csv.gz reproduces the segfault in 0.17.1 on OSX Yosemite. I can't reproduce with 0.13.1 or 0.17.1 on Ubuntu 14.04. Removing chunksize works normally with that file.

I tried my best to narrow it down. You can edit this file down to under 2000 lines and the segfault does not occur. Once it goes over 2000 lines I start to see the segfault. I can add lines 1000 at a time and notice the segfault is intermittent (I see it again at 6002 lines). It seems like to me if there are a multiple of chunksize items in the file the segfault does not occur.

I installed via pip install pandas. I also repro'd this on latest master (43edd83) on OSX Yosemite.

INSTALLED VERSIONS
------------------
commit: None
python: 2.7.9.final.0
python-bits: 64
OS: Darwin
OS-release: 14.5.0
machine: x86_64
processor: i386
byteorder: little
LC_ALL: None
LANG: en_US.UTF-8

pandas: 0.17.1
nose: 1.3.4
pip: 1.5.6
setuptools: 8.2.1
Cython: 0.23.4
numpy: 1.10.1
scipy: 0.15.1
statsmodels: None
IPython: 2.3.1
sphinx: 1.1.2
patsy: None
dateutil: 2.4.2
pytz: 2015.7
blosc: None
bottleneck: None
tables: None
numexpr: None
matplotlib: 1.4.3
openpyxl: None
xlrd: 0.9.3
xlwt: None
xlsxwriter: None
lxml: None
bs4: None
html5lib: None
httplib2: None
apiclient: None
sqlalchemy: None
pymysql: None
psycopg2: None
Jinja2: None
Exception Type:        EXC_BAD_ACCESS (SIGSEGV)
Exception Codes:       KERN_INVALID_ADDRESS at 0x0000000110bbf0bf

VM Regions Near 0x110bbf0bf:
    MALLOC_LARGE           0000000110b3f000-0000000110bbf000 [  512K] rw-/rwx SM=PRV  
--> 
    MALLOC_LARGE           0000000110cae000-0000000110e2e000 [ 1536K] rw-/rwx SM=PRV  

Thread 0 Crashed:: Dispatch queue: com.apple.main-thread
0   parser.so                       0x000000011069af3f __pyx_f_6pandas_6parser_10TextReader__convert_with_dtype + 2191
1   parser.so                       0x00000001106977ed __pyx_f_6pandas_6parser_10TextReader__convert_tokens + 3293
2   parser.so                       0x00000001106c47fe __pyx_pf_6pandas_6parser_10TextReader_16_convert_column_data + 3006
3   parser.so                       0x000000011069572b __pyx_f_6pandas_6parser_10TextReader__read_rows + 1371
4   parser.so                       0x0000000110693f65 __pyx_f_6pandas_6parser_10TextReader__read_low_memory + 869
5   parser.so                       0x00000001106c2b9e __pyx_pw_6pandas_6parser_10TextReader_9read + 174
6   org.python.python               0x000000010e1f77e6 PyEval_EvalFrameEx + 14392
7   org.python.python               0x000000010e1f3d7a PyEval_EvalCodeEx + 1409
8   org.python.python               0x000000010e1fa59d fast_function + 117
9   org.python.python               0x000000010e1f7400 PyEval_EvalFrameEx + 13394
10  org.python.python               0x000000010e1f3d7a PyEval_EvalCodeEx + 1409
11  org.python.python               0x000000010e1fa59d fast_function + 117
12  org.python.python               0x000000010e1f7400 PyEval_EvalFrameEx + 13394
13  org.python.python               0x000000010e18f67a gen_send_ex + 193
14  org.python.python               0x000000010e1f4525 PyEval_EvalFrameEx + 1399
15  org.python.python               0x000000010e1f3d7a PyEval_EvalCodeEx + 1409
16  org.python.python               0x000000010e1f37f3 PyEval_EvalCode + 54
17  org.python.python               0x000000010e2138a2 run_mod + 53
18  org.python.python               0x000000010e213945 PyRun_FileExFlags + 133
19  org.python.python               0x000000010e2134e2 PyRun_SimpleFileExFlags + 769
20  org.python.python               0x000000010e224c5b Py_Main + 3051
21  libdyld.dylib                   0x00007fff8c26c5c9 start + 1
@jdeschenes

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jdeschenes commented Dec 8, 2015

Were you able to reproduce this bug in 0.17.0 or 0.16.2?

@jreback jreback added the IO CSV label Dec 8, 2015

@OEP

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OEP commented Dec 9, 2015

@jdeschenes Yes, looks like I can reproduce it for OSX Yosemite on 0.17.0 and 0.16.2.

It works fine for both versions on Ubuntu 14.04.

@jreback

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jreback commented Dec 11, 2015

this is prob a dupe of #9726 (though your examples are better!)

@OEP

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OEP commented Dec 15, 2015

I tried to look into this a little more. I think the segfault is occurring in pandas/parser.pyx at line 1606 at a call to kh_get_str(), inside _try_int64_nogil().

...
if na_filter:
    for i in range(lines):
        COLITER_NEXT(it, word)
        k = kh_get_str(na_hashset, word)
        # in the hash table
...

I think word becomes becomes an invalid reference in the COLITER_NEXT() macro but I'm not sure what the issue is.

I thought given the bug is OSX only maybe we ran into a compiler quirk with clang. I can't repro with clang on LInux though on a recent checkout.

@ivannz

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ivannz commented Jul 28, 2016

This one is resolved by PR #13788. I was able to reproduce the crash on 0.18.1 (same crash report as in issue #13703). Running on the build with the mentioned PR did not crash.

edit: The symptoms described by @OEP are exactly the same as in the mentioned issue: same invalid data returned by COLITER_NEXT.

@ivannz ivannz referenced this issue Jul 29, 2016

Closed

TST: A test to cover fault in issue #5291 #13833

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