python 2.7 + RHEL 6.5 + Shapely-1.4.4 : MemoryError

Question

I am facing this problem over two of my deployments on RHEL 6.5 . Could not find any answers over Google search

Base Installation Packages

(nout)$ sudo rpm -qa | grep geos
geos-devel-3.3.2-1.el6.x86_64
geos-3.3.2-1.el6.x86_64
geos-python-3.3.2-1.el6.x86_64

Shapely Installation

(nout)$ easy_install -Z Shapely-1.4.4.tar.gz 
Processing Shapely-1.4.4.tar.gz
Writing /tmp/easy_install-iLylTY/Shapely-1.4.4/setup.cfg
Running Shapely-1.4.4/setup.py -q bdist_egg --dist-dir /tmp/easy_install-iLylTY/Shapely-1.4.4/egg-dist-tmp-xFmed4
Numpy or Cython not available, shapely.vectorized submodule not being built.
shapely/speedups/_speedups.c: In function ‘__pyx_pf_7shapely_8speedups_9_speedups_2geos_linestring_from_py’:
shapely/speedups/_speedups.c:1603: warning: assignment discards qualifiers from pointer target type
shapely/speedups/_speedups.c:2087: warning: assignment discards qualifiers from pointer target type
shapely/speedups/_speedups.c:2553: warning: assignment discards qualifiers from pointer target type
shapely/speedups/_speedups.c: In function ‘__pyx_pf_7shapely_8speedups_9_speedups_4geos_linearring_from_py’:
shapely/speedups/_speedups.c:3118: warning: assignment discards qualifiers from pointer target type
shapely/speedups/_speedups.c:3127: warning: pointer targets in passing argument 3 of ‘GEOSCoordSeq_getSize_r’ differ in signedness
/usr/include/geos_c.h:321: note: expected ‘unsigned int *’ but argument is of type ‘int *’
shapely/speedups/_speedups.c:3614: warning: assignment discards qualifiers from pointer target type
shapely/speedups/_speedups.c:4158: warning: assignment discards qualifiers from pointer target type
shapely/speedups/_speedups.c: At top level:
shapely/speedups/_speedups.c:924: warning: ‘__pyx_f_7shapely_8speedups_9_speedups_get_geos_context_handle’ defined but not used
shapely/speedups/_speedups.c:1010: warning: ‘__pyx_f_7shapely_8speedups_9_speedups_geos_from_prepared’ defined but not used
zip_safe flag not set; analyzing archive contents...
shapely.geos: module references __file__
Adding Shapely 1.4.4 to easy-install.pth file

Python Shell

(nout)$ python
Python 2.7.8 (default, Sep 12 2014, 14:39:38) 
[GCC 4.4.7 20120313 (Red Hat 4.4.7-4)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> from shapely.geometry import Polygon, Point
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/omd/nocout/nout/lib/python2.7/site-packages/Shapely-1.4.4-py2.7-linux-x86_64.egg/shapely/geometry/__init__.py", line 4, in <module>
    from .base import CAP_STYLE, JOIN_STYLE
  File "/omd/nocout/nout/lib/python2.7/site-packages/Shapely-1.4.4-py2.7-linux-x86_64.egg/shapely/geometry/base.py", line 9, in <module>
    from shapely.coords import CoordinateSequence
  File "/omd/nocout/nout/lib/python2.7/site-packages/Shapely-1.4.4-py2.7-linux-x86_64.egg/shapely/coords.py", line 8, in <module>
    from shapely.geos import lgeos
  File "/omd/nocout/nout/lib/python2.7/site-packages/Shapely-1.4.4-py2.7-linux-x86_64.egg/shapely/geos.py", line 194, in <module>
    error_h = EXCEPTION_HANDLER_FUNCTYPE(error_handler)
MemoryError

Python Shell

>>> from shapely.ops import transform
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/omd/nocout/nout/lib/python2.7/site-packages/Shapely-1.4.4-py2.7-linux-x86_64.egg/shapely/ops.py", line 13, in <module>
    from shapely.geos import lgeos
  File "/omd/nocout/nout/lib/python2.7/site-packages/Shapely-1.4.4-py2.7-linux-x86_64.egg/shapely/geos.py", line 194, in <module>
    error_h = EXCEPTION_HANDLER_FUNCTYPE(error_handler)
MemoryError

On calling the import MemoryError is received

I am not able to understand the reason.

Answer 1

For RHEL + selinux enabled + /tmp as noexec, any module that tries to access and execute in /tmp would generate a MEMORY ERROR.

in my case, /tmp was noexec and selinux was enforced

The /tmp defaults to defaults,noexec,nosuid,nodev.

I set : looking at : https://bugzilla.redhat.com/show_bug.cgi?id=645193#c11

$ getsebool -a | grep httpd_tmp_exec
httpd_tmp_exec --> on

Still the problem persisted, if I am to understand correctly this was because of : https://bugzilla.redhat.com/show_bug.cgi?id=582009

The libffi library tries to write to /tmp, 
which isn't allowed for the apache user in a default SELinux config   
(https://bugzilla.redhat.com/show_bug.cgi?id=582009). 
In this environment, importing ctypes always throws a MemoryError

So the option httpd_tmp_exec --> on was of no use to me.

I went looking into python lib files, searching for /tmp declaration, and i found tempfile.py line 147 : def _candidate_tempdir_list()

There in I saw that if there are envnames TMPDIR , TEMP, TMP , python will pickup the temp location.

Which variable to set ? For that I went in libffi source code, libffi-3.0.6 . file : src/closures.c line 290 open_temp_exec_file_env, "TMPDIR", 0 .

The TMPDIR was the candidate to be set.

I went ahead with mounting /opt/app/tmp, set export TMPDIR=/opt/app/tmp

Doing all this was working fine, till I used python idle, when I went ahead with nginx + uwsgi deployment, I was caughtup by the same error. Now I am not sure why that was happening, I thought must be a uwsgi execution issue. So I reinstalled uwsgi first, then I modified the /location for nginx.conf and looking at : http://nginx.org/en/docs/http/ngx_http_uwsgi_module.html#uwsgi_temp_path set : uwsgi_temp_path

I restarted all the services, nginx, uwsgi. and tried. It worked.

I also first tried with : (safe) HACK : Python ctypes MemoryError in fcgi process from PIL library

Results were disappointing for me.