On Karmic the results of the two experiments are the same:
LD_LIBRARY_PATH=/usr/lib;LD_PRELOAD=/usr/lib/liblapack.so.3gf;./atlas-test
gives me
(8968.96,26706.4) correct result = 110541
just like
LD_LIBRARY_PATH=/usr/lib/sse2/atlas;LD_PRELOAD=/usr/lib/sse2/atlas/liblapack.so.3gf;./atlas-test
Is this what you see, too?
** Changed in: atlas (Ubuntu)
Status: New => Incomplete
** Changed in: atlas (Ubuntu)
Importance: Undecided => High
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matrix multiplication with libatlas gives wrong result for big matrices
https://bugs.launchpad.net/bugs/376739
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