Numpy Import "Aborted"

Question

I am working on a linux server with a root installed python2.7 (/usr/bin/python2.7). Then I tried to install Numpy into this by downloading the source and doing python2.7 setup.py build; python2.7 setup.py install --user. Numpy neatly installs to ~/.local/lib/python2.7/site-packages/numpy. I get:

$ python2.7
Python 2.7.2+ (default, Dec 22 2011, 12:26:43)
[GCC 4.4.5] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import numpy
Aborted
$

Where do I even start? I've never seen this before!

(FYI, the default python (2.6), has a working numpy install in /usr/lib/pymodules/python2.6/numpy)

As requested, a stacktrace, (and thanks for the instructions on that!). Whole thing here on pastebin.

Program received signal SIGABRT, Aborted.
0x00002aaaabdb31b5 in *__GI_raise (sig=<value optimized out>)
    at ../nptl/sysdeps/unix/sysv/linux/raise.c:64
64  ../nptl/sysdeps/unix/sysv/linux/raise.c: No such file or directory.
    in ../nptl/sysdeps/unix/sysv/linux/raise.c
(gdb) bt
#0  0x00002aaaabdb31b5 in *__GI_raise (sig=<value optimized out>) at ../nptl/sysdeps/unix/sysv/linux/raise.c:64
#1  0x00002aaaabdb5fc0 in *__GI_abort () at abort.c:92
#2  0x00002aaab03fb9bd in free () from /usr/lib/python2.7/lib-dynload/_ctypes.so
#3  0x00002aaab03f8312 in ?? () from /usr/lib/python2.7/lib-dynload/_ctypes.so
#4  0x00002aaab03f8924 in ffi_closure_alloc () from /usr/lib/python2.7/lib-dynload/_ctypes.so
#5  0x00002aaab03f0af2 in _ctypes_alloc_callback () from /usr/lib/python2.7/lib-dynload/_ctypes.so
#6  0x00002aaab03eee68 in ?? () from /usr/lib/python2.7/lib-dynload/_ctypes.so
#7  0x00000000004b6ed5 in ?? ()
#8  0x0000000000425cdc in PyObject_Call ()

Looks like that numpy build is killing python. I would just try to install another version of numpy. If you feel investigative you could "ulimit -c unlimited" to make it create a coredump and then look at it using gdb. — itai
– itai, Commented Mar 12, 2013 at 10:08
A stack trace would go a long way, perhaps. You could also try running python directly in gdb: gdb $(which python2.7) then at the prompt r and then do your import numpy. Then after it aborts, run bt and post the result here. — FatalError
– FatalError, Commented Mar 12, 2013 at 10:14

NPE · Accepted Answer · 2013-03-12 10:39:38Z

1

This looks like a versioning issue. Make sure you are not inadvertently loading into Python 2.7 a module built for Python 2.6.

The first things to check would be $PYTHONPATH and sys.path.

answered Mar 12, 2013 at 10:39

NPE

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1 Comment

noio Over a year ago

I don't see anything pointing to 2.6.

sys.path == ['', '/usr/lib/python2.7', '/usr/lib/python2.7/plat-linux2', '/usr/lib/python2.7/lib-tk', '/usr/lib/python2.7/lib-old', '/usr/lib/python2.7/lib-dynload', '~/.local/lib/python2.7/site-packages', '/usr/local/lib/python2.7/dist-packages', '/usr/lib/python2.7/dist-packages']

noio · Accepted Answer · 2013-06-07 11:16:04Z

0

I never found out what was causing this, but I had the admin install numpy as root and it works now.

answered Jun 7, 2013 at 11:16

noio

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