Re: Quick cluster time and space optimisation

[John Darrington]

That was my idea, yes. 

J'

On Wed, Mar 23, 2011 at 07:35:41AM -0700, Mehmet Hakan Satman wrote:
     Hi John,
     
     the method:
     struct Kmeans *
     kmeans_create (struct casereader *cr, int m, int ngroups, int maxiter);
     
     will read the data from the given casereader and write to gsl_matrix 
directly. 
     We bring the
     
     data = xmalloc (numobs * n * sizeof (double));
     
     away. And we will only use gsl_matrix. Right?
     
      Mehmet Hakan Satman
     http://www.mhsatman.com
     
     
     
     
     
     ________________________________
     From: John Darrington <address@hidden>
     To: Mehmet Hakan Satman <address@hidden>
     Cc: address@hidden
     Sent: Wed, March 23, 2011 12:58:08 PM
     Subject: Quick cluster  time and space optimisation
     
     On Tue, Mar 22, 2011 at 02:53:45AM -0700, Mehmet Hakan Satman wrote:
          Hi friends,
         
          I corrected the source file and prepared the test files as John 
suggested. 
     I 
     
          created the file quick-cluster.at with a test data. I run the "make 
check" 
          command and some of the output of this process is like:
         
          436: T-TEST invalid syntax                           ok
          437: T-TEST string variable                          ok
          438: T-TEST string variable, only one value          ok
          439: T-TEST string variable comparison bug           ok
         
          QUICK CLUSTER
         
          440: QUICK CLUSTER                                   ok
         
     
     Wonderful!
     
     Now that we've got a working autotest we can start optimising the
     algorithm without fear of unwittingly breaking it.   This is where it
     starts to get interesting!
     
     The biggest problem I see at the moment is that it is allocating
     potentially huge blocks of memory.  PSPP (and spss) is designed to 
     cope with extremely large amounts of data.  So we should try to
     accommodate this in the design of quick-cluster.
     
     So imagine for the moment that somebody wants to perform
     quick-cluster 500 variables (m), and 10,000,000 cases (n).  PSPP would
     run out of memory before it even starts to do the calculation.
     There's a number of places where we should eliminate these memory
     allocations, but let's deal with them one at a time.
     
     Firstly, I see that the entire dataset is copied not once, but twice:
     Once before the call to kmeans_create where you copy the casereader
     into the array.  And then again inside kmeans_create where you copy
     the array into a gsl_matrix.  I did some profiling on my system and
     this  accounted for a significant proportion of the time taken to
     perform QUICK CLUSTER.
     
     So,  I suggest that we start by changing the signature of 
     kmeans_create from 
     
     struct Kmeans *
     kmeans_create (double *data, int n, int m, int ngroups, int maxiter);
     
     struct Kmeans *
     kmeans_create (struct casereader *cr, int m, int ngroups, int maxiter);
     
     This will save at least one iteration through the data and one big
     chunk of memory.  Later we can improve on this.
     
     J'
     
     
     
     
     
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