Memory error in memory, 256 GB of RAM, 64-bit python and 64-bit memory. ulimit problem?

There are many numpy memory error messages on google land, but I cannot find one that solves my problem. I am running someone else's software using a high performance server with 256GB of RAM, 64-bit opensuse 13.1, 64-bit python, and 64-bit numpy (as far as I can tell). See below.

The original author is not available for help requests, so I did my best to figure out the memory size for the numpy object it is trying to create. First, here's the stack trace:

File "/home/<me>/cmsRelease/trunk/Classes/DotData.py", line 193, in __new__
  DataObj = numpy.rec.fromarrays(Columns,names = names)
File "/usr/lib64/python2.7/site-packages/numpy/core/records.py", line 562, in fromarrays
  _array = recarray(shape, descr)
File "/usr/lib64/python2.7/site-packages/numpy/core/records.py", line 400, in __new__
  self = ndarray.__new__(subtype, shape, (record, descr), order=order)
MemoryError

      

        
        
        
      

    

I used the following for a loop to estimate the size of an object as far as I know how:

size = 0
for i in Columns:  # Columns is the list passed into numpy.rec.fromarrays
    size += sys.getsizeof(i)
print "Columns size: " + str(size)

      

        
        
        
      

    

Result Columns size: 12051648

. If I'm not mistaken, it's only 12MB, but it's far from 256GB anyway.

Based on this information, I suspect there is a system limit (ulimit) preventing python from accessing memory. Startup ulimit -a

reports the following (I installed ulimit -s 256000000

before running the program):

core file size          (blocks, -c) 0
data seg size           (kbytes, -d) unlimited
scheduling priority             (-e) 0
file size               (blocks, -f) unlimited
pending signals                 (-i) 2065541
max locked memory       (kbytes, -l) 64
max memory size         (kbytes, -m) unlimited
open files                      (-n) 10000
pipe size            (512 bytes, -p) 8
POSIX message queues     (bytes, -q) 819200
real-time priority              (-r) 0
stack size              (kbytes, -s) 256000000
cpu time               (seconds, -t) unlimited
max user processes              (-u) 2065541
virtual memory          (kbytes, -v) unlimited
file locks                      (-x) unlimited

      

        
        
        
      

    

Questions

• What am I missing?
• Couldn't you measure the size of the list object correctly Columns
  
  ?
• Is there any other system property that I need to set?

I would like to Memory Error

be more specific. I appreciate your help.

Supportive system information :

System memory:

> free -h
             total       used       free     shared    buffers     cached
Mem:          252G       1.6G       250G       4.2M        12M        98M
-/+ buffers/cache:       1.5G       250G
Swap:         2.0G        98M       1.9G

      

        
        
        
      

    

OS version:

> cat /etc/os-release
NAME=openSUSE
VERSION="13.1 (Bottle)"
VERSION_ID="13.1"
PRETTY_NAME="openSUSE 13.1 (Bottle) (x86_64)"
ID=opensuse
ANSI_COLOR="0;32"
CPE_NAME="cpe:/o:opensuse:opensuse:13.1"
BUG_REPORT_URL="https://bugs.opensuse.org"
HOME_URL="https://opensuse.org/"
ID_LIKE="suse"

      

        
        
        
      

    

Python version:

Python 2.7.6 (default, Nov 21 2013, 15:55:38) [GCC] on linux2
>>> import platform; platform.architecture()
('64bit', 'ELF')

      

        
        
        
      

    

Multiple species version:

>>> numpy.version
<module 'numpy.version' from '/usr/lib64/python2.7/site-packages/numpy/version.pyc'>
>>> numpy.version.version
'1.7.1'