The dot product implementation might differ according to the input, i.e. dot product between two vectors as opposed between two matrices. Also, a quick search on the web exposes a few implementations of the dot product in the BLAS routines themselves and Matlab might be picking one or another according to different needs.
edit([matlabroot '/extern/examples/refbook/dotProductComplex.c']);
However, this doesn't tell us much about the dot product between matrices.
The difference in the results after startup calculation seems to be just chance. In fact, if you vary the number of random draws, the difference is not 0 anymore. To reset the state of the random generator without restarting, simply use
To address such a big discrepancy, we need to see what are the values of the dot products.
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