GKL hangs on kernel update

[jonn-smith]

It looks like a GATK user is experiencing a GKL hang since they updated their kernel (4.4 -> 4.12, SUSE Linux, SLES15, CPUs: Xeon E5-2697 v4 and Xeon Gold 6148 CPUs). They detailed their findings in a forum post:

https://gatkforums.broadinstitute.org/gatk/discussion/23342/inteldeflater-problem-on-kernel-update/p1

@gspowley - Can you take a look and see if you can make more sense of it?

[gspowley]

@mepowers, can you please take a look at this issue?

[rpomaris]

@jonn-smith I replied on the thread, asking berutti to provide any updates here. Apologies for the lag time on this.

[rpomaris]

Haven't heard back from the user. On GATK 3.X as well. Sync'd with Broad; closing this.