You probably should be using a database, but if you are dead set against that for some reason...
My first thought is how have you determined that this record matches another? By looking at other records? If so, why break the "clumping" into a seperate pass?
Tailoring a better solution will depend on what your data is. What changes, what doesn't etc. Should all output records contain all fields that every other matching record contains?
If you on nix or are using cygwin, maybe you should make match the first key in the file and then pipe it into GNU sort (Good at handling large files and pretty fast.) Then all you reads should be sequential and you'll only have to hold the current match data in memory. Hope this helps.
-Lee
"To be civilized is to deny one's nature."
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