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Is the compilation result of exactly the same code the same under different versions of software? For example
# Quartus II
# Version 10.1 Build 197 01/19/2011 Service Pack 1 SJ Full Version
and
# Quartus II
# Version 10.1 Build 15311/19/2010 Service Pack 1 SJ Full Version.
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Since you aren't showing what is supposedly different, and I have no idea what Quartus is, I'll just direct you to Improving Numerical Reproducibility in C/C++/Fortran

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