To be fair, in the supercomputing community (or, more generally "high performance computing"--HPC), certain acronyms for libraries are very well-known: MPI, HDF5, FFTW, BLAS, MKL--no one is going to bat their eyes at seeing those names without an acronym expansion.
Think you could make it one day without using those acronyms?
Use of acronyms is usually an audience dependent thing. I am frequently in the in the audience of talks/papers where I don't know all the acronyms. I think the general rule should be, for writing, if there is a reasonable percentage (say more than 10%) of readers who don't know the acronyms, define it on first use. When speaking, give some context or define the terms early in your talk, to help folks along.
I say in a meeting the other day with marketing folks. They may be the worst offenders. Techies are pretty bad too.
