We are running GATK on a multi-core Intel Xeon that does not have AVX. We have just upgraded from running 3.4-46 to running 3.8, and HaplotypeCaller runs much more slowly. I noticed that our logs used to say:
Using SSE4.1 accelerated implementation of PairHMM
INFO 06:18:09,932 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
INFO 06:18:09,933 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
But now they say:
WARN 07:10:21,304 PairHMMLikelihoodCalculationEngine$1 - OpenMP multi-threaded AVX-accelerated native PairHMM implementation is not supported
WARN 07:10:21,310 PairHMMLikelihoodCalculationEngine$1 - AVX-accelerated native PairHMM implementation is not supported. Falling back to slower LOGLESS_CACHING implementation
I'm guessing the newfangled Intel GKL isn't working so well for us. Note that I had a very similar problem with GATK 3.4-0, in http://gatk.vanillaforums.com/entry/passwordreset/21436/OrxbD0I4oRDaj8y1hDSE and this was resolved in GATK 3.4-46.
