From: Panagiotis Atmatzidis <ml@...>
Date: 2012-09-09T02:39:25+09:00
Subject: Re: Using ruby for scientific computing

Hello,

On 8 Σεπ 2012, at 18:06 , Olivier Saut <osaut@airpost.net> wrote:

> Hi all,
> 
> For pedagogic purposes, I am trying to solve simple partial differential
> equations (say a diffusion equation on a regular mesh in 2D) with Ruby.
> Using the NArray gem, I have built a satisfactory tool from an interface
> (and ease of use) point of view but the performance are suboptimal. 

Is the code available on a public repo?

> I am now wondering what is the right way to improve my code
> performance-wise. I am doing a lot of matrix-vector and vector-vector
> products. 
> 
> From 2 2D NArrays describing two scalar fields, dot-product is implemented as :
> 
> def dot_product(vec_a, vec_b) 
>        dot_product=(vec_a*vec_b">vec_a*vec_b).sum 
> end
> 
> and as I am working with sparse matrices, (for the time being) a matrix
> is an Array of Hashes. Each key of the hash contains the index of the
> non-vanishing coefficients (the value of this coefficient is the value
> of the Hash) of the matrix. For the identity matrix it gives
> 
> def identity(sizeX, sizeY)
>        mat=[]
>        (0..sizeX*sizeY">sizeX*sizeY).each { |ind|
>            mat << {ind=>1.0}
>        }
>        mat
> end
> 
> 
> Matrix vector product is then defined as
> 
> def matrix_vector_product(mat, vector) 
>        ff=NArray.float(100,100)
>        (0..100*100).each { |ind|
>            matrix[ind].each do |key,value|
>                ff[[ind]]+=value*vector[[key]][0]
>            end
>        }
>        ff
> end
> 
> I am wondering what is the best way to tackle this performance problem :
> 1. Improve the ruby code (and how? :) Should I avoid using hashes?
> 2. Write an extension to perform these operations in C. BTW is there a
> way to access directly NArray data (without copy) from a C extension?
> 3. Use a wrapper like Ruby-lapack
> (
> https://rubyforge.org/projects/ruby-lapack/
> ).
> 
> What do you think? 
> 
> Thanks for your help !
> 
> -- 
>  Olivier Saut
> 
> osaut@airpost.net
> 						       	                	- Olivier
> 
> 


Panagiotis Atmatzidis
-----------------------------
Pharmacy Student at VFU

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The wise man said: "Never argue with an idiot, he brings you down to his level and beat you with experience."