On Aug 21, 2014, at 14:46 , Bob Handsaker <[email protected]> wrote: > This is a shot in the dark, but I notice you are running with -Xmx100g. > You might try a less aggressive heap allocation. > The stochastic nature of the failures might be due to contention over system > resources. > It looks like some of your runs are, in fact, growing the java heap to 100g.
Thanks for the suggestion. I scaled it back yesterday to 25g (and added -Xms25g) and still see crashes. The server has 128g of RAM and is otherwise completely unloaded. I've monitored resources during runs and nothing ever reaches close to capacity, RAM, CPU, or I/O wise. Still looking... ------------------------------------------------------------------------------ Slashdot TV. Video for Nerds. Stuff that matters. http://tv.slashdot.org/ _______________________________________________ Samtools-help mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/samtools-help
