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Segfault on linux #121

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esc opened this issue Jan 15, 2015 · 12 comments
Closed

Segfault on linux #121

esc opened this issue Jan 15, 2015 · 12 comments

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esc commented Jan 15, 2015

I am using Debian stable:

zsh» uname -a
Linux toolbox 3.9-0.bpo.1-amd64 #1 SMP Debian 3.9.6-1~bpo70+1 x86_64 GNU/Linux
zsh» gcc --version
gcc (Debian 4.7.2-5) 4.7.2
Copyright (C) 2012 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
zsh» cat /etc/debian_version
7.7

zsh» pwd
/tmp/bcolz
zsh» ls -lah
total 144K
drwx------ 10 esc  esc  4.0K Jan 15 23:22 ./
drwxrwxrwt 20 root root  20K Jan 15 23:23 ../
-rw-------  1 esc  esc  3.0K Jan 15 01:13 ANNOUNCE.rst
drwx------  3 esc  esc  4.0K Jan 15 23:23 bcolz/
drwx------  2 esc  esc  4.0K Jan 15 01:13 bench/
-rw-------  1 esc  esc   255 Jan 15 01:13 .binstar.yml
drwx------  3 esc  esc  4.0K Jan 15 23:22 build/
drwx------ 10 esc  esc  4.0K Jan 15 01:13 c-blosc/
drwx------  2 esc  esc  4.0K Jan 15 01:13 conda.recipe/
drwx------  2 esc  esc  4.0K Jan 15 01:13 doc/
drwx------  8 esc  esc  4.0K Jan 15 23:24 .git/
-rw-------  1 esc  esc    71 Jan 15 01:13 .gitignore
drwx------  2 esc  esc  4.0K Jan 15 01:13 LICENSES/
-rw-------  1 esc  esc   439 Jan 15 01:13 .mailmap
-rw-------  1 esc  esc   393 Jan 15 01:13 MANIFEST.in
-rw-------  1 esc  esc  6.2K Jan 15 01:13 pavement.py
-rw-------  1 esc  esc  6.6K Jan 15 01:13 persistence.rst
-rw-------  1 esc  esc  5.0K Jan 15 01:13 README.rst
-rw-------  1 esc  esc   12K Jan 15 01:13 RELEASE_NOTES.rst
-rw-------  1 esc  esc  3.1K Jan 15 01:13 RELEASING.rst
-rw-------  1 esc  esc    11 Jan 15 01:13 requirements.txt
-rw-------  1 esc  esc  7.6K Jan 15 01:45 setup.py
-rwx------  1 esc  esc   994 Jan 15 01:13 subtree-merge-blosc.sh*
-rw-------  1 esc  esc   280 Jan 15 01:13 THANKS.rst
-rw-------  1 esc  esc   329 Jan 15 01:13 .travis.yml
-rw-------  1 esc  esc    10 Jan 15 01:13 VERSION

And I am seeing segfaults, only when running bcolz tests using the builtin test runner and only outside my home directory:

zsh» python -c "import bcolz; bcolz.test(heavy=True)"
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
bcolz version:     0.8.1-dev
bcolz git info:    v0.8.0-4-g36ae3d8a6c
NumPy version:     1.9.1
Blosc version:     1.5.2 ($Date:: 2014-12-30 #$)
Blosc compressors: ['blosclz', 'lz4', 'lz4hc', 'snappy', 'zlib']
Numexpr version:   2.4
Python version:    2.7.9 (default, Jan 10 2015, 18:16:14) 
[GCC 4.7.2]
Platform:          linux2-x86_64
Byte-ordering:     little
Detected cores:    4
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
Performing the complete test suite!
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
.........................................................................................................................................................................................................................................s......s......s......s........................................ss............................................................................................................................................................................................................................................................................................................................................................................................................................................................................s.........................................................................................................................
----------------------------------------------------------------------
Ran 879 tests in 18.352s

OK (skipped=7)
[3]    26271 segmentation fault (core dumped)  python -c "import bcolz; bcolz.test(heavy=True)"
python -c "import bcolz; bcolz.test(heavy=True)"  19.41s user 1.32s system 112% cpu 18.501 total

This was built using a default build of Python from source. It seems like there is something wrong right before exit, as the backtrace confirms:

zsh» gdb python core
GNU gdb (GDB) 7.4.1-debian
Copyright (C) 2012 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.  Type "show copying"
and "show warranty" for details.
This GDB was configured as "x86_64-linux-gnu".
For bug reporting instructions, please see:
<http://www.gnu.org/software/gdb/bugs/>...
Reading symbols from /usr/local/bin/python...done.
[New LWP 26271]
[New LWP 26282]
[New LWP 26281]
[New LWP 26280]
[New LWP 26283]

warning: Can't read pathname for load map: Input/output error.
[Thread debugging using libthread_db enabled]
Using host libthread_db library "/lib/x86_64-linux-gnu/libthread_db.so.1".
Core was generated by `python -c import bcolz; bcolz.test(heavy=True)'.
Program terminated with signal 11, Segmentation fault.
#0  0x00007fc3c96f11f0 in _int_free (av=0x7fc3c9a00e40, p=0x2d2fff0) at malloc.c:5002
5002    malloc.c: No such file or directory.
(gdb) bt
#0  0x00007fc3c96f11f0 in _int_free (av=0x7fc3c9a00e40, p=0x2d2fff0) at malloc.c:5002
#1  0x00007fc3c96f47bc in *__GI___libc_free (mem=<optimized out>) at malloc.c:3738
#2  0x000000000043a699 in PyFloat_ClearFreeList () at Objects/floatobject.c:2240
#3  0x00000000004dee3a in clear_freelists () at Modules/gcmodule.c:848
#4  collect (generation=generation@entry=2) at Modules/gcmodule.c:1020
#5  0x00000000004df5e8 in PyGC_Collect () at Modules/gcmodule.c:1440
#6  0x00000000004ca750 in Py_Finalize () at Python/pythonrun.c:449
#7  Py_Finalize () at Python/pythonrun.c:405
#8  0x00000000004c9708 in Py_Exit (sts=sts@entry=0) at Python/pythonrun.c:1778
#9  0x0000000000416ab4 in handle_system_exit () at Python/pythonrun.c:1152
#10 0x00000000004c984b in handle_system_exit () at Python/pythonrun.c:1108
#11 PyErr_PrintEx (set_sys_last_vars=set_sys_last_vars@entry=1) at Python/pythonrun.c:1162
#12 0x00000000004c9bd7 in PyErr_Print () at Python/pythonrun.c:1065
#13 PyRun_SimpleStringFlags (command=command@entry=0x2752010 "import bcolz; bcolz.test(heavy=True)\n", flags=flags@entry=0x7fff911fd870)
    at Python/pythonrun.c:977
#14 0x0000000000417b28 in Py_Main (argc=<optimized out>, argv=<optimized out>) at Modules/main.c:584
#15 0x00007fc3c9697ead in __libc_start_main (main=<optimized out>, argc=<optimized out>, ubp_av=<optimized out>, init=<optimized out>, fini=<optimized out>, 
    rtld_fini=<optimized out>, stack_end=0x7fff911fda18) at libc-start.c:244
#16 0x0000000000417191 in _start ()

Then, this also is an issue on an Anaconda Python:

zsh» python -c "import bcolz; bcolz.test(heavy=True)"
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
bcolz version:     0.8.1-dev
bcolz git info:    v0.8.0-4-g36ae3d8a6c
NumPy version:     1.9.1
Blosc version:     1.5.2 ($Date:: 2014-12-30 #$)
Blosc compressors: ['blosclz', 'lz4', 'lz4hc', 'snappy', 'zlib']
Numexpr version:   2.3.1
Python version:    2.7.9 |Anaconda 2.1.0 (64-bit)| (default, Dec 15 2014, 10:33:51) 
[GCC 4.4.7 20120313 (Red Hat 4.4.7-1)]
Platform:          linux2-x86_64
Byte-ordering:     little
Detected cores:    4
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
Performing the complete test suite!
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
............................................................................................................................................................................................................................................................................................................*** glibc detected *** python: double free or corruption (out): 0x00000000023a5c70 ***
======= Backtrace: =========
/lib/x86_64-linux-gnu/libc.so.6(+0x76a16)[0x7f097984ba16]
/lib/x86_64-linux-gnu/libc.so.6(cfree+0x6c)[0x7f09798507bc]
/home/esc/anaconda/lib/python2.7/site-packages/numpy/core/multiarray.so(+0x1bb67)[0x7f09774cfb67]
/home/esc/anaconda/lib/python2.7/site-packages/numpy/core/multiarray.so(+0x1ebee)[0x7f09774d2bee]
bcolz/carray_ext.so(+0x1038f)[0x7f0968bce38f]
/home/esc/NOBACKUP/anaconda/bin/../lib/libpython2.7.so.1.0(+0x8d10b)[0x7f097a21110b]
======= Memory map: ========
00400000-00401000 r-xp 00000000 fe:03 9242442                            /home/esc/NOBACKUP/anaconda/bin/python2.7
00600000-00601000 rw-p 00000000 fe:03 9242442                            /home/esc/NOBACKUP/anaconda/bin/python2.7
015b0000-0401c000 rw-p 00000000 00:00 0                                  [heap]
32b9600000-32b9682000 r-xp 00000000 fe:03 9239087                        /home/esc/NOBACKUP/anaconda/lib/libm-2.5.so
32b9682000-32b9881000 ---p 00082000 fe:03 9239087                        /home/esc/NOBACKUP/anaconda/lib/libm-2.5.so
32b9881000-32b9882000 r--p 00081000 fe:03 9239087                        /home/esc/NOBACKUP/anaconda/lib/libm-2.5.so
32b9882000-32b9883000 rw-p 00082000 fe:03 9239087                        /home/esc/NOBACKUP/anaconda/lib/libm-2.5.so
7f0958000000-7f0958022000 rw-p 00000000 00:00 0 
7f0958022000-7f095c000000 ---p 00000000 00:00 0 
7f0960000000-7f0960022000 rw-p 00000000 00:00 0 
7f0960022000-7f0964000000 ---p 00000000 00:00 0 
7f09644ed000-7f09644ee000 ---p 00000000 00:00 0 
7f09644ee000-7f0964cee000 rw-p 00000000 00:00 0                          [stack:27496]
7f0964cee000-7f0964cef000 ---p 00000000 00:00 0 
7f0964cef000-7f09654ef000 rw-p 00000000 00:00 0                          [stack:27497]
7f09654ef000-7f09654f0000 ---p 00000000 00:00 0 
7f09654f0000-7f0965cf0000 rw-p 00000000 00:00 0                          [stack:27498]
7f0965cf0000-7f0965cf1000 ---p 00000000 00:00 0 
7f0965cf1000-7f09664f1000 rw-p 00000000 00:00 0                          [stack:27499]
7f09664f1000-7f09664f2000 ---p 00000000 00:00 0 
7f09664f2000-7f0966cf2000 rw-p 00000000 00:00 0                          [stack:27475]
7f0966cf2000-7f0966cf3000 ---p 00000000 00:00 0 
7f0966cf3000-7f09674f3000 rw-p 00000000 00:00 0                          [stack:27474]
7f09674f3000-7f09674f4000 ---p 00000000 00:00 0 
7f09674f4000-7f0967cf4000 rw-p 00000000 00:00 0                          [stack:27473]
7f0967cf4000-7f0967cf5000 ---p 00000000 00:00 0 
7f0967cf5000-7f0968575000 rw-p 00000000 00:00 0                          [stack:27472]
7f0968635000-7f0968675000 rw-p 00000000 00:00 0 
7f0968835000-7f09688b5000 rw-p 00000000 00:00 0 
7f09688f5000-7f0968935000 rw-p 00000000 00:00 0 
7f09689b5000-7f09689bd000 r-xp 00000000 fe:03 9321382                    /home/esc/NOBACKUP/anaconda/lib/python2.7/lib-dynload/_json.so
7f09689bd000-7f0968bbd000 ---p 00008000 fe:03 9321382                    /home/esc/NOBACKUP/anaconda/lib/python2.7/lib-dynload/_json.so
7f0968bbd000-7f0968bbe000 rw-p 00008000 fe:03 9321382                    /home/esc/NOBACKUP/anaconda/lib/python2.7/lib-dynload/_json.so
7f0968bbe000-7f0968c50000 r-xp 00000000 fe:02 925930                     /tmp/bcolz/bcolz/carray_ext.so
7f0968c50000-7f0968e50000 ---p 00092000 fe:02 925930                     /tmp/bcolz/bcolz/carray_ext.so
7f0968e50000-7f0968e59000 rw-p 00092000 fe:02 925930                     /tmp/bcolz/bcolz/carray_ext.so
7f0968e59000-7f0968f5a000 rw-p 00000000 00:00 0 
7f0968f5a000-7f0968f83000 r-xp 00000000 fe:03 9226170                    /home/esc/NOBACKUP/anaconda/lib/python2.7/site-packages/tables/indexesextension.so
7f0968f83000-7f0969183000 ---p 00029000 fe:03 9226170                    /home/esc/NOBACKUP/anaconda/lib/python2.7/site-packages/tables/indexesextension.so
7f0969183000-7f0969187000 rw-p 00029000 fe:03 9226170                    /home/esc/NOBACKUP/anaconda/lib/python2.7/site-packages/tables/indexesextension.so
7f0969187000-7f09691c7000 rw-p 00000000 00:00 0 
7f09691c7000-7f09691db000 r-xp 00000000 fe:03 9226180                    /home/esc/NOBACKUP/anaconda/lib/python2.7/site-packages/tables/lrucacheextension.so
7f09691db000-7f09693da000 ---p 00014000 fe:03 9226180                    /home/esc/NOBACKUP/anaconda/lib/python2.7/site-packages/tables/lrucacheextension.so
7f09693da000-7f09693dd000 rw-p 00013000 fe:03 9226180                    /home/esc/NOBACKUP/anaconda/lib/python2.7/site-packages/tables/lrucacheextension.so
7f09693dd000-7f0969439000 r-xp 00000000 fe:03 9226220                    /home/esc/NOBACKUP/anaconda/lib/python2.7/site-packages/tables/tableextension.so
7f0969439000-7f0969639000 ---p 0005c000 fe:03 9226220                    /home/esc/NOBACKUP/anaconda/lib/python2.7/site-packages/tables/tableextension.so
7f0969639000-7f096963f000 rw-p 0005c000 fe:03 9226220                    /home/esc/NOBACKUP/anaconda/lib/python2.7/site-packages/tables/tableextension.so
7f096963f000-7f0969682000 rw-p 00000000 00:00 0 
7f0969682000-7f096968e000 r-xp 00000000 fe:03 9226177                    /home/esc/NOBACKUP/anaconda/lib/python2.7/site-packages/tables/linkextension.so
7f096968e000-7f096988d000 ---p 0000c000 fe:03 9226177                    /home/esc/NOBACKUP/anaconda/lib/python2.7/site-packages/tables/linkextension.so
7f096988d000-7f096988f000 rw-p 0000b000 fe:03 9226177                    /home/esc/NOBACKUP/anaconda/lib/python2.7/site-packages/tables/linkextension.so
7f096988f000-7f09698d0000 rw-p 00000000 00:00 0 
7f09698d0000-7f0969944000 r-xp 00000000 fe:03 9226161                    /home/esc/NOBACKUP/anaconda/lib/python2.7/site-packages/tables/hdf5extension.so
7f0969944000-7f0969b43000 ---p 00074000 fe:03 9226161                    /home/esc/NOBACKUP/anaconda/lib/python2.7/site-packages/tables/hdf5extension.so
7f0969b43000-7f0969b4c000 rw-p 00073000 fe:03 9226161                    /home/esc/NOBACKUP/anaconda/lib/python2.7/site-packages/tables/hdf5extension.so
7f0969b4c000-7f0969b4e000 rw-p 00000000 00:00 0 
7f0969b4e000-7f0969b60000 r-xp 00000000 fe:03 9226129                    /home/esc/NOBACKUP/anaconda/lib/python2.7/site-packages/tables/_comp_bzip2.so
7f0969b60000-7f0969d5f000 ---p 00012000 fe:03 9226129                    /home/esc/NOBACKUP/anaconda/lib/python2.7/site-packages/tables/_comp_bzip2.so
7f0969d5f000-7f0969d61000 rw-p 00011000 fe:03 9226129                    /home/esc/NOBACKUP/anaconda/lib/python2.7/site-packages/tables/_comp_bzip2.so
7f0969d61000-7f0969d66000 r-xp 00000000 fe:03 9226130                    /home/esc/NOBACKUP/anaconda/lib/python2.7/site-packages/tables/_comp_lzo.so
7f0969d66000-7f0969f66000 ---p 00005000 fe:03 9226130                    /home/esc/NOBACKUP/anaconda/lib/python2.7/site-packages/tables/_comp_lzo.so
7f0969f66000-7f0969f67000 rw-p 00005000 fe:03 9226130                    /home/esc/NOBACKUP/anaconda/lib/python2.7/site-packages/tables/_comp_lzo.so
7f0969f67000-7f0969fe7000 rw-p 00000000 00:00 0 
7f0969fe7000-7f096a2b5000 r-xp 00000000 fe:03 9212668                    /home/esc/NOBACKUP/anaconda/lib/libhdf5.so.8.0.2
7f096a2b5000-7f096a4b5000 ---p 002ce000 fe:03 9212668                    /home/esc/NOBACKUP/anaconda/lib/libhdf5.so.8.0.2
7f096a4b5000-7f096a4c0000 rw-p 002ce000 fe:03 9212668                    /home/esc/NOBACKUP/anaconda/lib/libhdf5.so.8.0.2
7f096a4c0000-7f096a4c1000 rw-p 00000000 00:00 0 
7f096a4c1000-7f096a51a000 r-xp 00000000 fe:03 9226332                    /home/esc/NOBACKUP/anaconda/lib/python2.7/site-packages/tables/utilsextension.so
7f096a51a000-7f096a719000 ---p 00059000 fe:03 9226332                    /home/esc/NOBACKUP/anaconda/lib/python2.7/site-packages/tables/utilsextension.so
7f096a719000-7f096a721000 rw-p 00058000 fe:03 9226332                    /home/esc/NOBACKUP/anaconda/lib/python2.7/site-packages/tables/utilsextension.so
7f096a721000-7f096a724000 rw-p 00000000 00:00 0 
7f096a724000-7f096a72d000 r-xp 00000000 fe:03 9222247                    /home/esc/NOBACKUP/anaconda/lib/python2.7/site-packages/pandas/_testing.so
7f096a72d000-7f096a92c000 ---p 00009000 fe:03 9222247                    /home/esc/NOBACKUP/anaconda/lib/python2.7/site-packages/pandas/_testing.so
7f096a92c000-7f096a92e000 rw-p 00008000 fe:03 9222247                    /home/esc/NOBACKUP/anaconda/lib/python2.7/site-packages/pandas/_testing.so
7f096a92e000-7f096a96e000 rw-p 00000000 00:00 0 
7f096a96e000-7f096a971000 r-xp 00000000 fe:03 9241692                    /home/esc/NOBACKUP/anaconda/lib/libuuid.so.1.3.0
7f096a971000-7f096ab71000 ---p 00003000 fe:03 9241692                    /home/esc/NOBACKUP/anaconda/lib/libuuid.so.1.3.0
7f096ab71000-7f096ab72000 rw-p 00003000 fe:03 9241692                    /home/esc/NOBACKUP/anaconda/lib/libuuid.so.1.3.0
7f096ab72000-7f096ab73000 ---p 00000000 00:00 0 
7f096ab73000-7f096b373000 rw-p 00000000 00:00 0                          [stack:27464]
7f096b373000-7f096b374000 ---p 00000000 00:00 0 
7f096b374000-7f096bb74000 rw-p 00000000 00:00 0                          [stack:27463]
7f096bb74000-7f096bb75000 ---p 00000000 00:00 0 
7f096bb75000-7f096c375000 rw-p 00000000 00:00 0                          [stack:27462]
7f096c375000-7f096c376000 ---p 00000000 00:00 0 
7f096c376000-7f096cb76000 rw-p 00000000 00:00 0                          [stack:27461]
7f096cb76000-7f096cba0000 r-xp 00000000 fe:03 9961859                    /home/esc/NOBACKUP/anaconda/lib/python2.7/site-packages/blosc/blosc_extension.so
7f096cba0000-7f096cd9f000 ---p 0002a000 fe:03 9961859                    /home/esc/NOBACKUP/anaconda/lib/python2.7/site-packages/blosc/blosc_extension.so
7f096cd9f000-7f096cda1000 rw-p 00029000 fe:03 9961859                    /home/esc/NOBACKUP/anaconda/lib/python2.7/site-packages/blosc/blosc_extension.so
7f096cda1000-7f096cda3000 rw-p 00000000 00:00 0 
7f096cda3000-7f096cdbc000 r-xp 00000000 fe:03 9222501                    /home/esc/NOBACKUP/anaconda/lib/python2.7/site-packages/pandas/msgpack.so
7f096cdbc000-7f096cfbc000 ---p 00019000 fe:03 9222501                    /home/esc/NOBACKUP/anaconda/lib/python2.7/site-packages/pandas/msgpack.so
7f096cfbc000-7f096cfc0000 rw-p 00019000 fe:03 9222501                    /home/esc/NOBACKUP/anaconda/lib/python2.7/site-packages/pandas/msgpack.so
7f096cfc0000-7f096d040000 rw-p 00000000 00:00 0 
7f096d040000-7f096d047000 r-xp 00000000 fe:02 1333572                    /lib/x86_64-linux-gnu/librt-2.13.so
7f096d047000-7f096d246000 ---p 00007000 fe:02 1333572                    /lib/x86_64-linux-gnu/librt-2.13.so
7f096d246000-7f096d247000 r--p 00006000 fe:02 1333572                    /lib/x86_64-linux-gnu/librt-2.13.so
7f096d247000-7f096d248000 rw-p 00007000 fe:02 1333572                    /lib/x86_64-linux-gnu/librt-2.13.so
7f096d248000-7f096d389000 r-xp 00000000 fe:03 9214879                    /home/esc/NOBACKUP/anaconda/lib/libxml2.so.2.9.0
7f096d389000-7f096d588000 ---p 00141000 fe:03 9214879                    /home/esc/NOBACKUP/anaconda/lib/libxml2.so.2.9.0
7f096d588000-7f096d592000 rw-p 00140000 fe:03 9214879                    /home/esc/NOBACKUP/anaconda/lib/libxml2.so.2.9.0
7f096d592000-7f096d593000 rw-p 00000000 00:00 0 
7f096d593000-7f096d5a5000 r-xp 00000000 fe:03 9215128                    /home/esc/NOBACKUP/anaconda/lib/libexslt.so.0.8.17
7f096d5a5000-7f096d7a4000 ---p 00012000 fe:03 9215128                    /home/esc/NOBACKUP/anaconda/lib/libexslt.so.0.8.17
7f096d7a4000-7f096d7a5000 rw-p 00011000 fe:03 9215128                    /home/esc/NOBACKUP/anaconda/lib/libexslt.so.0.8.17
7f096d7a5000-7f096d7de000 r-xp 00000000 fe:03 9215133                    /home/esc/NOBACKUP/anaconda/lib/libxslt.so.1.1.28
7f096d7de000-7f096d9dd000 ---p 00039000 fe:03 9215133                    /home/esc/NOBACKUP/anaconda/lib/libxslt.so.1.1.28
7f096d9dd000-7f096d9df000 rw-p 00038000 fe:03 9215133                    /home/esc/NOBACKUP/anaconda/lib/libxslt.so.1.1.28
7f096d9df000-7f096db4a000 r-xp 00000000 fe:03 9216986                    /home/esc/NOBACKUP/anaconda/lib/python2.7/site-packages/lxml/etree.so
7f096db4a000-7f096dd49000 ---p 0016b000 fe:03 9216986                    /home/esc/NOBACKUP/anaconda/lib/python2.7/site-packages/lxml/etree.so
7f096dd49000-7f096dd7f000 rw-p 0016a000 fe:03 9216986                    /home/esc/NOBACKUP/anaconda/lib/python2.7/site-packages/lxml/etree.so
7f096dd7f000-7f096de84000 rw-p 00000000 00:00 0 
7f096de84000-7f096de98000 r-xp 00000000 fe:03 9222499                    /home/esc/NOBACKUP/anaconda/lib/python2.7/site-packages/pandas/json.so
7f096de98000-7f096e098000 ---p 00014000 fe:03 9222499                    /home/esc/NOBACKUP/anaconda/lib/python2.7/site-packages/pandas/json.so
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7f0977d78000-7f0977d7a000 rw-p 00003000 fe:03 9321379                    /home/esc/NOBACKUP/anaconda/lib/python2.7/lib-dynload/_heapq.so
7f0977d7a000-7f0977d84000 r-xp 00000000 fe:03 9321406                    /home/esc/NOBACKUP/anaconda/lib/python2.7/lib-dynload/itertools.so
7f0977d84000-7f0977f84000 ---p 0000a000 fe:03 9321406                    /home/esc/NOBACKUP/anaconda/lib/python2.7/lib-dynload/itertools.so
7f0977f84000-7f0977f89000 rw-p 0000a000 fe:03 9321406                    /home/esc/NOBACKUP/anaconda/lib/python2.7/lib-dynload/itertools.so
7f0977f89000-7f0977f90000 r-xp 00000000 fe:03 9321370                    /home/esc/NOBACKUP/anaconda/lib/python2.7/lib-dynload/_collections.so
7f0977f90000-7f097818f000 ---p 00007000 fe:03 9321370                    /home/esc/NOBACKUP/anaconda/lib/python2.7/lib-dynload/_collections.so
7f097818f000-7f0978191000 rw-p 00006000 fe:03 9321370                    /home/esc/NOBACKUP/anaconda/lib/python2.7/lib-dynload/_collections.so
7f0978191000-7f09781d1000 rw-p 00000000 00:00 0 
7f09781d1000-7f09781d9000 r-xp 00000000 fe:03 9321411                    /home/esc/NOBACKUP/anaconda/lib/python2.7/lib-dynload/operator.so
7f09781d9000-7f09783d9000 ---p 00008000 fe:03 9321411                    /home/esc/NOBACKUP/anaconda/lib/python2.7/lib-dynload/operator.so
7f09783d9000-7f09783db000 rw-p 00008000 fe:03 9321411                    /home/esc/NOBACKUP/anaconda/lib/python2.7/lib-dynload/operator.so
7f09783db000-7f09783e0000 r-xp 00000000 fe:03 9321419                    /home/esc/NOBACKUP/anaconda/lib/python2.7/lib-dynload/strop.so
7f09783e0000-7f09785df000 ---p 00005000 fe:03 9321419                    /home/esc/NOBACKUP/anaconda/lib/python2.7/lib-dynload/strop.so
7f09785df000-7f09785e1000 rw-p 00004000 fe:03 9321419                    /home/esc/NOBACKUP/anaconda/lib/python2.7/lib-dynload/strop.so
7f09785e1000-7f0978621000 rw-p 00000000 00:00 0 
7f0978621000-7f0978625000 r-xp 00000000 fe:03 9321399                    /home/esc/NOBACKUP/anaconda/lib/python2.7/lib-dynload/cStringIO.so
7f0978625000-7f0978824000 ---p 00004000 fe:03 9321399                    /home/esc/NOBACKUP/anaconda/lib/python2.7/lib-dynload/cStringIO.so
7f0978824000-7f0978826000 rw-p 00003000 fe:03 9321399                    /home/esc/NOBACKUP/anaconda/lib/python2.7/lib-dynload/cStringIO.so
7f0978826000-7f097883c000 r-xp 00000000 fe:03 9245950                    /home/esc/NOBACKUP/anaconda/lib/libz.so.1.2.8
7f097883c000-7f0978a3b000 ---p 00016000 fe:03 9245950                    /home/esc/NOBACKUP/anaconda/lib/libz.so.1.2.8
7f0978a3b000-7f0978a3c000 rw-p 00015000 fe:03 9245950                    /home/esc/NOBACKUP/anaconda/lib/libz.so.1.2.8
7f0978a3c000-7f0978a40000 r-xp 00000000 fe:03 9321396                    /home/esc/NOBACKUP/anaconda/lib/python2.7/lib-dynload/binascii.so
7f0978a40000-7f0978c40000 ---p 00004000 fe:03 9321396                    /home/esc/NOBACKUP/anaconda/lib/python2.7/lib-dynload/binascii.so
7f0978c40000-7f0978c41000 rw-p 00004000 fe:03 9321396                    /home/esc/NOBACKUP/anaconda/lib/python2.7/lib-dynload/binascii.so
7f0978c41000-7f0978c48000 r-xp 00000000 fe:03 9321391                    /home/esc/NOBACKUP/anaconda/lib/python2.7/lib-dynload/_struct.so
7f0978c48000-7f0978e48000 ---p 00007000 fe:03 9321391                    /home/esc/NOBACKUP/anaconda/lib/python2.7/lib-dynload/_struct.so
7f0978e48000-7f0978e4a000 rw-p 00007000 fe:03 9321391                    /home/esc/NOBACKUP/anaconda/lib/python2.7/lib-dynload/_struct.so
7f0978e4a000-7f0978e4d000 r-xp 00000000 fe:03 9321403                    /home/esc/NOBACKUP/anaconda/lib/python2.7/lib-dynload/fcntl.so
7f0978e4d000-7f097904c000 ---p 00003000 fe:03 9321403                    /home/esc/NOBACKUP/anaconda/lib/python2.7/lib-dynload/fcntl.so
7f097904c000-7f097904e000 rw-p 00002000 fe:03 9321403                    /home/esc/NOBACKUP/anaconda/lib/python2.7/lib-dynload/fcntl.so
7f097904e000-7f0979052000 r-xp 00000000 fe:03 9321417                    /home/esc/NOBACKUP/anaconda/lib/python2.7/lib-dynload/select.so
7f0979052000-7f0979252000 ---p 00004000 fe:03 9321417                    /home/esc/NOBACKUP/anaconda/lib/python2.7/lib-dynload/select.so
7f0979252000-7f0979254000 rw-p 00004000 fe:03 9321417                    /home/esc/NOBACKUP/anaconda/lib/python2.7/lib-dynload/select.so
7f0979254000-7f0979258000 r-xp 00000000 fe:03 9321422                    /home/esc/NOBACKUP/anaconda/lib/python2.7/lib-dynload/time.so
7f0979258000-7f0979457000 ---p 00004000 fe:03 9321422                    /home/esc/NOBACKUP/anaconda/lib/python2.7/lib-dynload/time.so
7f0979457000-7f0979459000 rw-p 00003000 fe:03 9321422                    /home/esc/NOBACKUP/anaconda/lib/python2.7/lib-dynload/time.so
7f0979459000-7f09795d0000 r--p 00000000 fe:02 1182649                    /usr/lib/locale/locale-archive
7f09795d0000-7f09795d4000 r-xp 00000000 fe:03 9321383                    /home/esc/NOBACKUP/anaconda/lib/python2.7/lib-dynload/_locale.so
7f09795d4000-7f09797d4000 ---p 00004000 fe:03 9321383                    /home/esc/NOBACKUP/anaconda/lib/python2.7/lib-dynload/_locale.so
7f09797d4000-7f09797d5000 rw-p 00004000 fe:03 9321383                    /home/esc/NOBACKUP/anaconda/lib/python2.7/lib-dynload/_locale.so
7f09797d5000-7f0979957000 r-xp 00000000 fe:02 1332657                    /lib/x86_64-linux-gnu/libc-2.13.so
7f0979957000-7f0979b57000 ---p 00182000 fe:02 1332657                    /lib/x86_64-linux-gnu/libc-2.13.so
7f0979b57000-7f0979b5b000 r--p 00182000 fe:02 1332657                    /lib/x86_64-linux-gnu/libc-2.13.so
7f0979b5b000-7f0979b5c000 rw-p 00186000 fe:02 1332657                    /lib/x86_64-linux-gnu/libc-2.13.so
7f0979b5c000-7f0979b61000 rw-p 00000000 00:00 0 
7f0979b61000-7f0979b63000 r-xp 00000000 fe:02 1333575                    /lib/x86_64-linux-gnu/libutil-2.13.so
7f0979b63000-7f0979d62000 ---p 00002000 fe:02 1333575                    /lib/x86_64-linux-gnu/libutil-2.13.so
7f0979d62000-7f0979d63000 r--p 00001000 fe:02 1333575                    /lib/x86_64-linux-gnu/libutil-2.13.so
7f0979d63000-7f0979d64000 rw-p 00002000 fe:02 1333575                    /lib/x86_64-linux-gnu/libutil-2.13.so
7f0979d64000-7f0979d66000 r-xp 00000000 fe:02 1333560                    /lib/x86_64-linux-gnu/libdl-2.13.so
7f0979d66000-7f0979f66000 ---p 00002000 fe:02 1333560                    /lib/x86_64-linux-gnu/libdl-2.13.so
7f0979f66000-7f0979f67000 r--p 00002000 fe:02 1333560                    /lib/x86_64-linux-gnu/libdl-2.13.so
7f0979f67000-7f0979f68000 rw-p 00003000 fe:02 1333560                    /lib/x86_64-linux-gnu/libdl-2.13.so
7f0979f68000-7f0979f7f000 r-xp 00000000 fe:02 1332653                    /lib/x86_64-linux-gnu/libpthread-2.13.so
7f0979f7f000-7f097a17e000 ---p 00017000 fe:02 1332653                    /lib/x86_64-linux-gnu/libpthread-2.13.so
7f097a17e000-7f097a17f000 r--p 00016000 fe:02 1332653                    /lib/x86_64-linux-gnu/libpthread-2.13.so
7f097a17f000-7f097a180000 rw-p 00017000 fe:02 1332653                    /lib/x86_64-linux-gnu/libpthread-2.13.so
7f097a180000-7f097a184000 rw-p 00000000 00:00 0 
7f097a184000-7f097a319000 r-xp 00000000 fe:03 9242785                    /home/esc/NOBACKUP/anaconda/lib/libpython2.7.so.1.0
7f097a319000-7f097a518000 ---p 00195000 fe:03 9242785                    /home/esc/NOBACKUP/anaconda/lib/libpython2.7.so.1.0
7f097a518000-7f097a557000 rw-p 00194000 fe:03 9242785                    /home/esc/NOBACKUP/anaconda/lib/libpython2.7.so.1.0
7f097a557000-7f097a566000 rw-p 00000000 00:00 0 
7f097a566000-7f097a586000 r-xp 00000000 fe:02 1332654                    /lib/x86_64-linux-gnu/ld-2.13.so
7f097a5b2000-7f097a672000 rw-p 00000000 00:00 0 
7f097a6a3000-7f097a768000 rw-p 00000000 00:00 0 
7f097a77a000-7f097a781000 r--s 00000000 fe:02 1226251                    /usr/lib/x86_64-linux-gnu/gconv/gconv-modules.cache
7f097a781000-7f097a782000 rwxp 00000000 00:00 0 
7f097a782000-7f097a785000 rw-p 00000000 00:00 0 
7f097a785000-7f097a786000 r--p 0001f000 fe:02 1332654                    /lib/x86_64-linux-gnu/ld-2.13.so
7f097a786000-7f097a787000 rw-p 00020000 fe:02 1332654                    /lib/x86_64-linux-gnu/ld-2.13.so
7f097a787000-7f097a788000 rw-p 00000000 00:00 0 
7fff83713000-7fff83734000 rw-p 00000000 00:00 0                          [stack]
7fff837e4000-7fff837e6000 r-xp 00000000 00:00 0                          [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0                  [vsyscall]
[3]    27453 abort (core dumped)  python -c "import bcolz; bcolz.test(heavy=True)"

And the backtrace:

134 zsh» gdb python core
GNU gdb (GDB) 7.4.1-debian
Copyright (C) 2012 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.  Type "show copying"
and "show warranty" for details.
This GDB was configured as "x86_64-linux-gnu".
For bug reporting instructions, please see:
<http://www.gnu.org/software/gdb/bugs/>...
Reading symbols from /home/esc/NOBACKUP/anaconda/bin/python...done.
[New LWP 27453]
[New LWP 27464]
[New LWP 27461]
[New LWP 27462]
[New LWP 27469]
[New LWP 27468]
[New LWP 27463]
[New LWP 27472]
[New LWP 27496]
[New LWP 27497]
[New LWP 27471]
[New LWP 27470]
[New LWP 27498]
[New LWP 27474]
[New LWP 27475]
[New LWP 27499]
[New LWP 27473]

warning: Can't read pathname for load map: Input/output error.
[Thread debugging using libthread_db enabled]
Using host libthread_db library "/lib/x86_64-linux-gnu/libthread_db.so.1".

warning: no loadable sections found in added symbol-file system-supplied DSO at 0x7fff837e4000
Core was generated by `python -c import bcolz; bcolz.test(heavy=True)'.
Program terminated with signal 6, Aborted.
#0  0x00007f0979807165 in *__GI_raise (sig=<optimized out>) at ../nptl/sysdeps/unix/sysv/linux/raise.c:64
64  ../nptl/sysdeps/unix/sysv/linux/raise.c: No such file or directory.
(gdb) bt
#0  0x00007f0979807165 in *__GI_raise (sig=<optimized out>) at ../nptl/sysdeps/unix/sysv/linux/raise.c:64
#1  0x00007f097980a3e0 in *__GI_abort () at abort.c:92
#2  0x00007f09798421cb in __libc_message (do_abort=<optimized out>, fmt=<optimized out>) at ../sysdeps/unix/sysv/linux/libc_fatal.c:189
#3  0x00007f097984ba16 in malloc_printerr (action=3, str=0x7f0979926150 "double free or corruption (out)", ptr=<optimized out>) at malloc.c:6312
#4  0x00007f09798507bc in *__GI___libc_free (mem=<optimized out>) at malloc.c:3738
#5  0x00007f09774cfb67 in PyDataMem_FREE (ptr=0x23a5c70) at numpy/core/src/multiarray/alloc.c:210
#6  _npy_free_cache (dealloc=0x7f09774cf940 <PyDataMem_FREE>, cache=0x7f09778590c0, msz=1024, nelem=<optimized out>, p=0x23a5c70)
    at numpy/core/src/multiarray/alloc.c:58
#7  npy_free_cache (p=0x23a5c70, sz=<optimized out>) at numpy/core/src/multiarray/alloc.c:91
#8  0x00007f09774d2bee in array_dealloc (self=0x7f09688ae350) at numpy/core/src/multiarray/arrayobject.c:423
#9  0x00007f0968bce38f in __pyx_tp_dealloc_5bcolz_10carray_ext_carray (o=0x7f09691a0e60) at bcolz/carray_ext.c:34522
#10 0x00007f097a21110b in dict_dealloc (mp=0x7f0968933d70) at Objects/dictobject.c:1010
#11 0x00007f097a21110b in dict_dealloc (mp=0x7f0968885e88) at Objects/dictobject.c:1010
#12 0x00007f097a230901 in subtype_dealloc (self=0x7f0968925b90) at Objects/typeobject.c:1015
#13 0x00007f097a21110b in dict_dealloc (mp=0x7f0968933b40) at Objects/dictobject.c:1010
#14 0x00007f097a230901 in subtype_dealloc (self=0x7f0968925c10) at Objects/typeobject.c:1015
#15 0x00007f097a1fa452 in frame_dealloc (f=0x2374db0) at Objects/frameobject.c:460
#16 0x00007f097a27d917 in PyEval_EvalCodeEx (co=<optimized out>, globals=<optimized out>, locals=<optimized out>, args=<optimized out>, argcount=1, 
    kws=0x2180990, kwcount=0, defs=0x0, defcount=0, closure=0x0) at Python/ceval.c:3276
#17 0x00007f097a27c2aa in fast_function (nk=<optimized out>, na=1, n=<optimized out>, pp_stack=0x7fff8372fa88, func=0x7f096853d410) at Python/ceval.c:4129
#18 call_function (oparg=<optimized out>, pp_stack=0x7fff8372fa88) at Python/ceval.c:4054
#19 PyEval_EvalFrameEx (f=<optimized out>, throwflag=<optimized out>) at Python/ceval.c:2679
#20 0x00007f097a27dc6e in PyEval_EvalCodeEx (co=0x7f097655c2b0, globals=<optimized out>, locals=<optimized out>, args=<optimized out>, argcount=2, 
    kws=0x7f097a723068, kwcount=0, defs=0x7f09762cab68, defcount=1, closure=0x0) at Python/ceval.c:3265
#21 0x00007f097a1fb958 in function_call (func=0x7f09762d2320, arg=0x7f096852d3b0, kw=0x7f09688aa910) at Objects/funcobject.c:526
#22 0x00007f097a1cc323 in PyObject_Call (func=0x7f09762d2320, arg=<optimized out>, kw=<optimized out>) at Objects/abstract.c:2529
#23 0x00007f097a27a865 in ext_do_call (nk=1750258608, na=<optimized out>, flags=<optimized out>, pp_stack=0x7fff8372fd58, func=0x7f09762d2320)
    at Python/ceval.c:4346
#24 PyEval_EvalFrameEx (f=<optimized out>, throwflag=<optimized out>) at Python/ceval.c:2718
#25 0x00007f097a27dc6e in PyEval_EvalCodeEx (co=0x7f097655c430, globals=<optimized out>, locals=<optimized out>, args=<optimized out>, argcount=2, kws=0x0, 
    kwcount=0, defs=0x0, defcount=0, closure=0x0) at Python/ceval.c:3265
#26 0x00007f097a1fb851 in function_call (func=0x7f09762d2410, arg=0x7f096852d2d8, kw=0x0) at Objects/funcobject.c:526
#27 0x00007f097a1cc323 in PyObject_Call (func=0x7f09762d2410, arg=<optimized out>, kw=<optimized out>) at Objects/abstract.c:2529
#28 0x00007f097a1de95f in instancemethod_call (func=0x7f09762d2410, arg=0x7f096852d2d8, kw=0x0) at Objects/classobject.c:2602
#29 0x00007f097a1cc323 in PyObject_Call (func=0x7f0968f4deb0, arg=<optimized out>, kw=<optimized out>) at Objects/abstract.c:2529
#30 0x00007f097a238aac in slot_tp_call (self=0x7f09685629d0, args=0x7f09684fc5d0, kwds=0x0) at Objects/typeobject.c:5432
#31 0x00007f097a1cc323 in PyObject_Call (func=0x7f09685629d0, arg=<optimized out>, kw=<optimized out>) at Objects/abstract.c:2529
#32 0x00007f097a27b362 in do_call (nk=<optimized out>, na=<optimized out>, pp_stack=0x7fff83730338, func=0x7f09685629d0) at Python/ceval.c:4251
#33 call_function (oparg=<optimized out>, pp_stack=0x7fff83730338) at Python/ceval.c:4056
#34 PyEval_EvalFrameEx (f=<optimized out>, throwflag=<optimized out>) at Python/ceval.c:2679
#35 0x00007f097a27dc6e in PyEval_EvalCodeEx (co=0x7f09762d5330, globals=<optimized out>, locals=<optimized out>, args=<optimized out>, argcount=2, 
---Type <return> to continue, or q <return> to quit---
    kws=0x7f097a723068, kwcount=0, defs=0x7f09762d3fa8, defcount=1, closure=0x0) at Python/ceval.c:3265
#36 0x00007f097a1fb958 in function_call (func=0x7f09762d96e0, arg=0x7f096852d7e8, kw=0x7f09688abc58) at Objects/funcobject.c:526
#37 0x00007f097a1cc323 in PyObject_Call (func=0x7f09762d96e0, arg=<optimized out>, kw=<optimized out>) at Objects/abstract.c:2529
#38 0x00007f097a27a865 in ext_do_call (nk=1750259688, na=<optimized out>, flags=<optimized out>, pp_stack=0x7fff83730608, func=0x7f09762d96e0)
    at Python/ceval.c:4346
#39 PyEval_EvalFrameEx (f=<optimized out>, throwflag=<optimized out>) at Python/ceval.c:2718
#40 0x00007f097a27dc6e in PyEval_EvalCodeEx (co=0x7f09762d50b0, globals=<optimized out>, locals=<optimized out>, args=<optimized out>, argcount=2, kws=0x0, 
    kwcount=0, defs=0x0, defcount=0, closure=0x0) at Python/ceval.c:3265
#41 0x00007f097a1fb851 in function_call (func=0x7f09762d95f0, arg=0x7f09688f8128, kw=0x0) at Objects/funcobject.c:526
#42 0x00007f097a1cc323 in PyObject_Call (func=0x7f09762d95f0, arg=<optimized out>, kw=<optimized out>) at Objects/abstract.c:2529
#43 0x00007f097a1de95f in instancemethod_call (func=0x7f09762d95f0, arg=0x7f09688f8128, kw=0x0) at Objects/classobject.c:2602
#44 0x00007f097a1cc323 in PyObject_Call (func=0x7f0968f31dc0, arg=<optimized out>, kw=<optimized out>) at Objects/abstract.c:2529
#45 0x00007f097a238aac in slot_tp_call (self=0x7f09685628d0, args=0x7f09684fc610, kwds=0x0) at Objects/typeobject.c:5432
#46 0x00007f097a1cc323 in PyObject_Call (func=0x7f09685628d0, arg=<optimized out>, kw=<optimized out>) at Objects/abstract.c:2529
#47 0x00007f097a27b362 in do_call (nk=<optimized out>, na=<optimized out>, pp_stack=0x7fff83730be8, func=0x7f09685628d0) at Python/ceval.c:4251
#48 call_function (oparg=<optimized out>, pp_stack=0x7fff83730be8) at Python/ceval.c:4056
#49 PyEval_EvalFrameEx (f=<optimized out>, throwflag=<optimized out>) at Python/ceval.c:2679
#50 0x00007f097a27dc6e in PyEval_EvalCodeEx (co=0x7f09762d5330, globals=<optimized out>, locals=<optimized out>, args=<optimized out>, argcount=2, 
    kws=0x7f097a723068, kwcount=0, defs=0x7f09762d3fa8, defcount=1, closure=0x0) at Python/ceval.c:3265
#51 0x00007f097a1fb958 in function_call (func=0x7f09762d96e0, arg=0x7f09688fc488, kw=0x7f09688854b0) at Objects/funcobject.c:526
#52 0x00007f097a1cc323 in PyObject_Call (func=0x7f09762d96e0, arg=<optimized out>, kw=<optimized out>) at Objects/abstract.c:2529
#53 0x00007f097a27a865 in ext_do_call (nk=1754252424, na=<optimized out>, flags=<optimized out>, pp_stack=0x7fff83730eb8, func=0x7f09762d96e0)
    at Python/ceval.c:4346
#54 PyEval_EvalFrameEx (f=<optimized out>, throwflag=<optimized out>) at Python/ceval.c:2718
#55 0x00007f097a27dc6e in PyEval_EvalCodeEx (co=0x7f09762d50b0, globals=<optimized out>, locals=<optimized out>, args=<optimized out>, argcount=2, kws=0x0, 
    kwcount=0, defs=0x0, defcount=0, closure=0x0) at Python/ceval.c:3265
#56 0x00007f097a1fb851 in function_call (func=0x7f09762d95f0, arg=0x7f096852d908, kw=0x0) at Objects/funcobject.c:526
#57 0x00007f097a1cc323 in PyObject_Call (func=0x7f09762d95f0, arg=<optimized out>, kw=<optimized out>) at Objects/abstract.c:2529
#58 0x00007f097a1de95f in instancemethod_call (func=0x7f09762d95f0, arg=0x7f096852d908, kw=0x0) at Objects/classobject.c:2602
#59 0x00007f097a1cc323 in PyObject_Call (func=0x7f0968f4de60, arg=<optimized out>, kw=<optimized out>) at Objects/abstract.c:2529
#60 0x00007f097a238aac in slot_tp_call (self=0x7f0968852fd0, args=0x7f09684fc350, kwds=0x0) at Objects/typeobject.c:5432
#61 0x00007f097a1cc323 in PyObject_Call (func=0x7f0968852fd0, arg=<optimized out>, kw=<optimized out>) at Objects/abstract.c:2529
#62 0x00007f097a27b362 in do_call (nk=<optimized out>, na=<optimized out>, pp_stack=0x7fff83731498, func=0x7f0968852fd0) at Python/ceval.c:4251
#63 call_function (oparg=<optimized out>, pp_stack=0x7fff83731498) at Python/ceval.c:4056
#64 PyEval_EvalFrameEx (f=<optimized out>, throwflag=<optimized out>) at Python/ceval.c:2679
#65 0x00007f097a27dc6e in PyEval_EvalCodeEx (co=0x7f09762d5330, globals=<optimized out>, locals=<optimized out>, args=<optimized out>, argcount=2, 
    kws=0x7f097a723068, kwcount=0, defs=0x7f09762d3fa8, defcount=1, closure=0x0) at Python/ceval.c:3265
#66 0x00007f097a1fb958 in function_call (func=0x7f09762d96e0, arg=0x7f0968f48c68, kw=0x7f096892e6e0) at Objects/funcobject.c:526
#67 0x00007f097a1cc323 in PyObject_Call (func=0x7f09762d96e0, arg=<optimized out>, kw=<optimized out>) at Objects/abstract.c:2529
#68 0x00007f097a27a865 in ext_do_call (nk=1760857192, na=<optimized out>, flags=<optimized out>, pp_stack=0x7fff83731768, func=0x7f09762d96e0)
    at Python/ceval.c:4346
---Type <return> to continue, or q <return> to quit---
#69 PyEval_EvalFrameEx (f=<optimized out>, throwflag=<optimized out>) at Python/ceval.c:2718
#70 0x00007f097a27dc6e in PyEval_EvalCodeEx (co=0x7f09762d50b0, globals=<optimized out>, locals=<optimized out>, args=<optimized out>, argcount=2, kws=0x0, 
    kwcount=0, defs=0x0, defcount=0, closure=0x0) at Python/ceval.c:3265
#71 0x00007f097a1fb851 in function_call (func=0x7f09762d95f0, arg=0x7f0968e7ff80, kw=0x0) at Objects/funcobject.c:526
#72 0x00007f097a1cc323 in PyObject_Call (func=0x7f09762d95f0, arg=<optimized out>, kw=<optimized out>) at Objects/abstract.c:2529
#73 0x00007f097a1de95f in instancemethod_call (func=0x7f09762d95f0, arg=0x7f0968e7ff80, kw=0x0) at Objects/classobject.c:2602
#74 0x00007f097a1cc323 in PyObject_Call (func=0x7f0969fa4910, arg=<optimized out>, kw=<optimized out>) at Objects/abstract.c:2529
#75 0x00007f097a238aac in slot_tp_call (self=0x7f0968e66990, args=0x7f097a668bd0, kwds=0x0) at Objects/typeobject.c:5432
#76 0x00007f097a1cc323 in PyObject_Call (func=0x7f0968e66990, arg=<optimized out>, kw=<optimized out>) at Objects/abstract.c:2529
#77 0x00007f097a27b362 in do_call (nk=<optimized out>, na=<optimized out>, pp_stack=0x7fff83731d48, func=0x7f0968e66990) at Python/ceval.c:4251
#78 call_function (oparg=<optimized out>, pp_stack=0x7fff83731d48) at Python/ceval.c:4056
#79 PyEval_EvalFrameEx (f=<optimized out>, throwflag=<optimized out>) at Python/ceval.c:2679
#80 0x00007f097a27c600 in fast_function (nk=<optimized out>, na=<optimized out>, n=<optimized out>, pp_stack=0x7fff83731e98, func=0x7f0976277488)
    at Python/ceval.c:4119
#81 call_function (oparg=<optimized out>, pp_stack=0x7fff83731e98) at Python/ceval.c:4054
#82 PyEval_EvalFrameEx (f=<optimized out>, throwflag=<optimized out>) at Python/ceval.c:2679
#83 0x00007f097a27dc6e in PyEval_EvalCodeEx (co=0x7f0968e5aab0, globals=<optimized out>, locals=<optimized out>, args=<optimized out>, argcount=0, 
    kws=0x7f097a70a1d0, kwcount=1, defs=0x7f0968f48b18, defcount=2, closure=0x0) at Python/ceval.c:3265
#84 0x00007f097a27c2aa in fast_function (nk=<optimized out>, na=0, n=<optimized out>, pp_stack=0x7fff83732098, func=0x7f0968f59758) at Python/ceval.c:4129
#85 call_function (oparg=<optimized out>, pp_stack=0x7fff83732098) at Python/ceval.c:4054
#86 PyEval_EvalFrameEx (f=<optimized out>, throwflag=<optimized out>) at Python/ceval.c:2679
#87 0x00007f097a27dc6e in PyEval_EvalCodeEx (co=0x7f097a609230, globals=<optimized out>, locals=<optimized out>, args=<optimized out>, argcount=0, kws=0x0, 
    kwcount=0, defs=0x0, defcount=0, closure=0x0) at Python/ceval.c:3265
#88 0x00007f097a27dd82 in PyEval_EvalCode (co=<optimized out>, globals=<optimized out>, locals=<optimized out>) at Python/ceval.c:667
#89 0x00007f097a29c11c in run_mod (arena=0x16257a0, flags=<optimized out>, locals=0x7f097a6f8168, globals=0x7f097a6f8168, filename=0x7f097a2cc04d "<string>", 
    mod=<optimized out>) at Python/pythonrun.c:1371
#90 PyRun_StringFlags (str=0x15b0010 "import bcolz; bcolz.test(heavy=True)\n", start=257, globals=0x7f097a6f8168, locals=0x7f097a6f8168, 
    flags=<optimized out>) at Python/pythonrun.c:1334
#91 0x00007f097a29d440 in PyRun_SimpleStringFlags (command=0x15b0010 "import bcolz; bcolz.test(heavy=True)\n", flags=0x7fff83732320) at Python/pythonrun.c:975
#92 0x00007f097a2b2f47 in Py_Main (argc=<optimized out>, argv=<optimized out>) at Modules/main.c:589
#93 0x00007f09797f3ead in __libc_start_main (main=<optimized out>, argc=<optimized out>, ubp_av=<optimized out>, init=<optimized out>, fini=<optimized out>, 
    rtld_fini=<optimized out>, stack_end=0x7fff83732438) at libc-start.c:244
#94 0x0000000000400649 in _start ()

Works fine with nosetests on both Pythons.

Amazingly enough, it also works with Blosc 1.4.1:

zsh» LD_LIBRARY_PATH=/home/esc/gw/c-blosc/build/install/lib python -c "import bcolz; bcolz.test(heavy=True)"
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
bcolz version:     0.8.1-dev
bcolz git info:    v0.8.0-4-g36ae3d8a6c
NumPy version:     1.9.1
Blosc version:     1.4.1 ($Date:: 2014-07-08 #$)
Blosc compressors: ['blosclz', 'lz4', 'lz4hc', 'snappy', 'zlib']
Numexpr version:   2.4
Python version:    2.7.9 (default, Jan 10 2015, 18:16:14) 
[GCC 4.7.2]
Platform:          linux2-x86_64
Byte-ordering:     little
Detected cores:    4
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
Performing the complete test suite!
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
.........................................................................................................................................................................................................................................s......s......s......s........................................ss............................................................................................................................................................................................................................................................................................................................................................................................................................................................................s.........................................................................................................................
----------------------------------------------------------------------
Ran 879 tests in 14.350s

OK (skipped=7)

And with anaconda python:

zsh» LD_LIBRARY_PATH=/home/esc/gw/c-blosc/build/install/lib python -c "import bcolz; bcolz.test()"
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
bcolz version:     0.8.1-dev
bcolz git info:    v0.8.0-4-g36ae3d8a6c
NumPy version:     1.9.1
Blosc version:     1.4.1 ($Date:: 2014-07-08 #$)
Blosc compressors: ['blosclz', 'lz4', 'lz4hc', 'snappy', 'zlib']
Numexpr version:   2.3.1
Python version:    2.7.9 |Anaconda 2.1.0 (64-bit)| (default, Dec 15 2014, 10:33:51) 
[GCC 4.4.7 20120313 (Red Hat 4.4.7-1)]
Platform:          linux2-x86_64
Byte-ordering:     little
Detected cores:    4
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
Performing only a light (yet comprehensive) subset of the test suite.
If you want a more complete test, try passing the '-heavy' flag to this
script (or set the 'heavy' parameter in case you are using bcolz.test()
call).  The whole suite will take more than 30 seconds to complete on a
relatively modern CPU and around 300 MB of RAM and 500 MB of disk
[32-bit platforms will always run significantly more lightly].

-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................ssssss.........................................................................................................................
----------------------------------------------------------------------
Ran 879 tests in 3.993s

OK (skipped=6)
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esc commented Jan 15, 2015

Happens with bcolz 0.7.3 and `0.8.0``but not with 0.7.2

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esc commented Jan 15, 2015

@FrancescAlted 0.7.2 is also the version with Blosc 1.4.1 do you think this might have something to do with the Blosc 1.5.x series?

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That's possible yes. I would say that downgrading to 1.4.x would be a sensible action until 1.5 is fixed.

Enviat des del meu iPhone

El 15/01/2015, a les 23:37, Valentin Haenel notifications@github.com va escriure:

@FrancescAlted 0.7.2 is also the version with Blosc 1.4.1 do you think this might have something to do with the Blosc 1.5.x series?

—
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This was referenced Jan 16, 2015
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@FrancescAlted FrancescAlted mentioned this issue Mar 9, 2015
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@ARF1 ARF1 mentioned this issue Mar 9, 2015
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This is a bit crazy because I cannot reproduce the problem on my Ubuntu 14.10 machine.

With Ubuntu system Python:

-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
bcolz version:     0.9.0-dev
bcolz git info:    v0.8.1-38-g56f1e59
NumPy version:     1.8.2
Blosc version:     1.5.3.dev ($Date:: 2014-12-30 #$)
Blosc compressors: ['blosclz', 'lz4', 'lz4hc', 'snappy', 'zlib']
Numexpr version:   2.4
Python version:    2.7.8 (default, Oct 20 2014, 15:05:19) 
[GCC 4.9.1]
Platform:          linux2-x86_64
Byte-ordering:     little
Detected cores:    4
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
Performing the complete test suite!
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
......s......s......s......s................................................................................................................................................................................................................s..............................................................................................................................................................................................................................................................................................................................................................................................................................ss...................................................................................................................................................................................................................................................
----------------------------------------------------------------------
Ran 896 tests in 20.668s

OK (skipped=7)

With Anaconda Python:

-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
bcolz version:     0.9.0-dev
bcolz git info:    v0.8.1-38-g56f1e59
NumPy version:     1.9.2
Blosc version:     1.5.3.dev ($Date:: 2014-12-30 #$)
Blosc compressors: ['blosclz', 'lz4', 'lz4hc', 'snappy', 'zlib']
Numexpr version:   2.3.1
Python version:    2.7.9 |Anaconda 2.1.0 (64-bit)| (default, Mar  9 2015, 16:20:48) 
[GCC 4.4.7 20120313 (Red Hat 4.4.7-1)]
Platform:          linux2-x86_64
Byte-ordering:     little
Detected cores:    4
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
Performing the complete test suite!
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
............................................................................................................................................................................................................................................s...................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
----------------------------------------------------------------------
Ran 896 tests in 18.516s

OK (skipped=1)

Hmm, tricky...

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I continue to have the feeling that perhaps some recent optimization in the default blosclz has something to do with the problem. Could you please use the next branch (basically master but using blosclz 1.0.2):

https://github.com/Blosc/c-blosc/tree/blosclz-1.0.2

and tell me how it goes with your machine?

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In case the above works, and to make sure that the problem is in blosclz 1.0.3 I have created another branch using blosc 1.4.1 but with blosclz 1.0.3 (instead of 1.0.2):

https://github.com/Blosc/c-blosc/tree/blosc-1.4.1-blosclz-1.0.3

Please check it out and tell me how it goes. This can also be done with #120 and #122.

@FrancescAlted FrancescAlted mentioned this issue Mar 25, 2015
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esc commented Mar 26, 2015

#166 by itself doesn't fix this with blosc v1.5.2

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esc commented Mar 26, 2015

#166 + blosc master at Blosc/c-blosc@8250362 doesn't fix it either

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esc commented Mar 26, 2015

Hmm #166 + https://github.com/Blosc/c-blosc/tree/blosc-1.4.1-blosclz-1.0.3 seems to be fine,

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esc commented Mar 26, 2015

But #166 with https://github.com/Blosc/c-blosc/tree/blosclz-1.0.2 doesn't

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Well, that excludes blosclz 1.0.3 for being guilty, so that's something. Uh, I wonder I can't reproduce the crash on my laptop. Would that be a problem with the compiler or pthreads implementation? Here are my versions:

faltet@francesc-Latitude-E6430:~/blosc/bcolz$ dpkg -l libc6 gcc
Desitjat=desconegUt/Instaŀla/supRimeix/Purga/retín(H)
| Estat=Not/Inst/Conf-files/Unpacked/halF-conf/Half-inst/trig-aWait/Trig-pend
|/ Err?=(none)/Reinst-required (Estat,Err: majúsc.=dolent)
||/ Nom                           Versió              Arquitectura        Descripció
+++-=============================-===================-===================-================================================================
ii  gcc                           4:4.9.1-4ubuntu2    amd64               GNU C compiler
ii  libc6:amd64                   2.19-10ubuntu2.3    amd64               GNU C Library: Shared libraries
ii  libc6:i386                    2.19-10ubuntu2.3    i386                GNU C Library: Shared libraries

Can you paste yours?

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esc commented Jun 11, 2015

This no longer happends with 2.7.10 from anaconda and current master at e23e79f

@esc esc closed this as completed Jun 11, 2015
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