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biod / sambamba

Tools for working with SAM/BAM data
http://thebird.nl/blog/D_Dragon.html
GNU General Public License v2.0
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Intel Xeon bug may segfault Sambamba #335

Closed pjotrp closed 6 years ago

pjotrp commented 6 years ago

See #219

It is called BDF76 An Intel® Hyper-Threading Technology Enabled Processor May Exhibit Internal Parity Errors or Unpredictable System Behavior”. The symptoms described for this issue are very broad (“unpredictable system behavior may occur”), but what we were observing seemed to match the description of this issue better than any other.

A microcode update is available. Also switching off hyperthreading in the bios should fix it. There is no LLVM fix that I can find (Intel says there is no possible fix available).

See also

https://www.intel.co.uk/content/www/uk/en/processors/xeon/xeon-e5-v4-spec-update.html https://www.digitaltrends.com/computing/intel-hyperthreading-bug-kaby-skylake/

pjotrp commented 6 years ago

As this is an intel bug without a fix in llvm or gcc I'll close it. It is here for reference.