Maybe consider rpmalloc

[Mark Geisert]

Hi Teemu,

Teemu Nätkinniemi wrote:
> Hello,
> 
> Thanks for testing! I found a better test case with smaller files
> which should clearly show the issue.
> 
> https://drive.google.com/drive/folders/1jOilHtKrr6CHn7zg__DE93RCDyseoTB1?usp=sharing
> 
> Here's the results. Bwa_working is the one with rpmalloc and
> bwa_original is unpatched. As you can see the unpatched version with
> several threads takes a  whole lot more time to finish even when
> compared with unpatched exe running with a single thread. I am not the
> only one experiencing the issue so I doubt it is my system.
[...]

Well this certainly does show the issue(s) you're seeing.  Short runs but long 
enough for me to get decent profiling.  Yes, malloc code shows up a lot in the 
profiles.

I'm going to research some stuff and ask some questions of the Cygwin gurus to see 
if we can do something about this.
Thanks a bunch,

..mark