Swap memory in Python ? - three questions

[Robert LaMarca]

Hi,

I am using numpy and wish to create very large arrays. My system is AMD 64 x 2 Ubuntu 8.04. Ubuntu should be 64 bit. I have 3gb RAM and a 15 GB swap drive.

The command I have been trying to use is;
g=numpy.ones([1000,1000,1000],numpy.int32)

This returns a memory error.
A smaller array ([500,500,500]) worked fine..
Two smaller arrays again crashed the system.

So... I did the math. a 1000x1000x1000 array at 32 bits should be around 4gb RAM... Obviously larger than RAM, but much smaller than the swap drive.

1. So... does Numpy have a really lot of overhead? Or is my system just not somehow getting to make use of the 15gb swap area.
2. Is there a way I can access the swap area, or direct numpy to do so? Or do I have to write out my own numpy cache system...
3. How difficult is it to use data compression internally on numpy arrays?

thanks very much
Robert

[Scott David Daniels]

Re: Swap memory in Python ? - three questions

Robert LaMarca wrote:

Hi,
>
I am using numpy and wish to create very large arrays. My system is AMD 64 x 2 Ubuntu 8.04. Ubuntu should be 64 bit. I have 3gb RAM and a 15 GB swap drive.
>
The command I have been trying to use is;
g=numpy.ones([1000,1000,1000],numpy.int32)
>
This returns a memory error.
A smaller array ([500,500,500]) worked fine..
Two smaller arrays again crashed the system.
>
So... I did the math. a 1000x1000x1000 array at 32 bits should be around 4gb RAM... Obviously larger than RAM, but much smaller than the swap drive.
>
1. So... does Numpy have a really lot of overhead? Or is my system just not somehow getting to make use of the 15gb swap area.
2. Is there a way I can access the swap area, or direct numpy to do so? Or do I have to write out my own numpy cache system...
3. How difficult is it to use data compression internally on numpy arrays?
>
thanks very much
Robert

There are architectural issues that you should not expect (and really
do not want) the libraries / languages / os to handle for you
automatically. The reason you don't even _want_ an automatic solution
is that the computer has no understanding of the problem you are trying
to solve. If the machine guesses wrong, it will be doing computations
at I/O speeds, and for 4G of data, that will result in geological
computing times.

On big problems the programming issue is how to break the problem into
tractable sub-problems (of feasible computing size), and how to stitch
those results together. This is a place to apply human intellect, not
machine effort. So, sorry, there is no way to solve the problem without
understanding the field it occurs in and the question being addressed
by the code.

--Scott David Daniels
Scott.Daniels@A cm.Org

[Marc Christiansen]

Re: Swap memory in Python ? - three questions

Robert LaMarca <robertmlamarca @yahoo.comwrote :

Hi,
>
I am using numpy and wish to create very large arrays. My system is
AMD 64 x 2 Ubuntu 8.04. Ubuntu should be 64 bit. I have 3gb RAM and a
15 GB swap drive.
>
The command I have been trying to use is;
g=numpy.ones([1000,1000,1000],numpy.int32)
>
This returns a memory error.

Works for me on AMD64x2, 2GB RAM, 3GB swap. With much paging of course
;) Process size of python 4019508kB.

A smaller array ([500,500,500]) worked fine..

About 0.5GB.. no surprise.

Two smaller arrays again crashed the system.

Crash as in "computer reboots"? Strange. And you say, that two [500,
500, 500] arrays are two much?

So... I did the math. a 1000x1000x1000 array at 32 bits should be
around 4gb RAM... Obviously larger than RAM, but much smaller than the
swap drive.

Sounds like either your kernel or python are not 64bit.
For the kernel, have a look at /proc/meminfo, which value you get for
VmallocTotal. I have VmallocTotal: 34359738367 kB.
For python, check sys.maxint. If it's 2147483647, then you have a 32bit
python. Mine says 922337203685477 5807.

1. So... does Numpy have a really lot of overhead? Or is my system
just not somehow getting to make use of the 15gb swap area.

No. Yes.

2. Is there a way I can access the swap area, or direct numpy to do
so? Or do I have to write out my own numpy cache system...
3. How difficult is it to use data compression internally on numpy
arrays?

2 + 3: Should not be necessary.

I just tried a 32bit python on my 64bit system, using Numeric instead of
numpy (don't have a 32bit numpy ready):

g=Numeric.zeros ([1000,1000,1000],Numeric.Int32)
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
MemoryError: can't allocate memory for array

g=Numeric.zeros ([1000,1000,500],Numeric.Int32) succeeds.

So it looks like you have a 32bit kernel.

Marc

[John Nagle]

Re: Swap memory in Python ? - three questions

Robert LaMarca wrote:

Hi,
>
I am using numpy and wish to create very large arrays. My system is AMD 64
x 2 Ubuntu 8.04. Ubuntu should be 64 bit. I have 3gb RAM and a 15 GB swap
drive.

Does a full 64-bit version of CPython, one where all pointers
and sizes are 64 bits, even exist?

John Nagle

[Tim Roberts]

Re: Swap memory in Python ? - three questions

John Nagle <nagle@animats. comwrote:

>Robert LaMarca wrote:

>>
>I am using numpy and wish to create very large arrays. My system is AMD 64
>x 2 Ubuntu 8.04. Ubuntu should be 64 bit. I have 3gb RAM and a 15 GB swap
>drive.

>
Does a full 64-bit version of CPython, one where all pointers
>and sizes are 64 bits, even exist?

Absolutely.

[timr@naxier ~]# uname -a
Linux naxier.xxxxxx.c om 2.6.9-42.0.3.ELsmp #1 SMP Mon Sep 25 17:24:31 EDT
2006 x86_64 x86_64 x86_64 GNU/Linux
[timr@naxier ~]# python
Python 2.3.4 (#1, Feb 18 2008, 17:16:53)
[GCC 3.4.6 20060404 (Red Hat 3.4.6-9)] on linux2
Type "help", "copyright" , "credits" or "license" for more information.

>>import sys
>>sys.maxint

922337203685477 5807

>>>

--
Tim Roberts, timr@probo.com
Providenza & Boekelheide, Inc.