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BKM to init matrix for FFT transform

I have large arrays that I need to do FFT transform many times. The Vtune shows the memset as the hottest spot. I used memset to zero init all array values before I assign. Not all matrix elements got assigned values. It is more like a sparse matrix. If I don't use memset and use for loop instead, the program runs even slower. How do I init the array more efficiently? Thanks.
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