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IntelDeflater problem on Kernel Update
Dear members of the GATK Team,
we ran into a curious problem after updating the Kernel of our machines from 4.4 to 4.12.
Our pool of computing nodes has Xeon E5-2697 v4 and Xeon Gold 6148 CPUs.
In the machines equipped with the latter CPU (Xeon 6148) the GATK HaplotypeCaller and other tools using IntelDeflater stopped working, hanging just before printing the message:
INFO 15:41:08,160 GenomeAnalysisEngine - Deflater: IntelDeflater
INFO 15:41:08,161 GenomeAnalysisEngine - Inflater: IntelInflater
If I set use-jdk-inflater (and deflater) they go through, but terribly slow. On the machines with E5-2697 (older CPU) everything works fine.
This problem occurs using GATK 3.8, while doesn't appear into GATK4. Is there a way to fix that other than updating? We wanted to be consistent for now with analysed data.
Thanks for the support!