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' -- PGP Public key ID: 1024D/2DE827B3 fingerprint = 8797 A26D 0854 2EAB 0285 A290 8A67 719C 2DE8 27B3 See http://pgp.mit.edu or any PGP keyserver for public key.
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