Maybe consider rpmalloc

[Mark Geisert]

Hi Teemu,

Teemu Nätkinniemi via Cygwin-developers wrote:
> Sorry, hurt my back yesterday and looks like I am not thinking clearly.

Hope you are feeling better by this time.

> ./bwa mem -t 10 bwa_reference/hs37d5.fa ERS4238880_1.fastq > test1.sam

Thanks.  It was my unfamiliarity with Google Drive which prevented my finding all 
the data files you had stored there.  After a while I did find all I needed.

I rebuilt bwa.exe alternately using the provided Makefile and Makefile.cygwin. 
When building with the latter I made sure your #ifdef patches were enabled so that 
rpmalloc was pulled in for the build.  When building with the former I made sure 
your patches were disabled, so the Cygwin malloc would be used for this case.

I had no difficulty running either version of bwa to completion.  On one smallish 
test machine the rpmalloc version finished in a bit less elapsed time but with the 
same CPU time as the Cygwin malloc version.

I also ran on a larger system; here both versions ran with similar elapsed and CPU 
times.  I also ran the Cygwin malloc version with '-t 32' to add some stress but 
still your test case ran to successful completion.

So I'm afraid I can't explain the results you were seeing.  Is it possible that 
you might have given up too soon running the Cygwin malloc version, thinking you 
should be seeing output as quickly as you would on Linux?  You won't, unfortunately.

You might try backing out your changes, or I think, building again on your main 
branch, to see if waiting longer proves successful.  If you have any other 
suggestions, please let us know.
Thanks & Regards,

..mark

P.S. Here's Cygwin malloc version's output from my smallish system
(i5, 2.3GHz, 2C/4T)...
./bwa mem -t 10 bwa_reference/hs37d5.fa /tmp/ERS4238880_1.fastq > test1.sam
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 1712342 sequences (100000087 bp)...
[M::process] read 1103688 sequences (64503600 bp)...
[M::mem_process_seqs] Processed 1712342 reads in 2157.077 CPU sec, 2214.871 real sec
[M::mem_process_seqs] Processed 1103688 reads in 1541.766 CPU sec, 1591.704 real sec
[main] Version: 0.7.17-r1198-dirty
[main] CMD: ./bwa mem -t 10 bwa_reference/hs37d5.fa /tmp/ERS4238880_1.fastq
[main] Real time: 3831.624 sec; CPU: 3713.937 sec