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Date: Sun, 24 Nov 2024 01:44:38 -0800
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Subject: Re: Thread memory allocation issue
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From: Mark Geisert via Cygwin <cygwin@cygwin.com>
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Hi Teemu,

On 11/18/2024 10:59 PM, Teepean via Cygwin wrote:
>>> 2. Compile BWA with rpmalloc and the following patch:
>>>
>>>
>>> // In thread worker function:
>>> #ifdef __CYGWIN__
>>> rpmalloc_thread_initialize();
>>> #endif
>>>
>>>
>>> // ... thread work ...
>>> #ifdef __CYGWIN__
>>> rpmalloc_thread_finalize(1);
>>> #endif

How, exactly, did you compile BWA with rpmalloc?  I ask because of the 
three bwa* executables in the test_data directory, only bwa.exe is 
purely Cygwin.  The other two have both Cygwin and MSVCRT runtimes 
associated, something that is not supported by us.  Was your rpmalloc 
compiled by Visual Studio?

BTW where exactly did you get rpmalloc from?  Just so I do the same.

In spite of the different runtime libraries, all three executables have 
similar run- and cpu-times on my test system (9-10s and 37-39s 
respectively).  That might indicate the Cygwin runtime is being used in 
preference to MSVCRT here.  Maybe that's different on your system?

Another BTW: are the input data files and output files on a hard disk or 
an SSD on your system?  They're on an SSD on mine.
Curiouser and curiouser,

..mark

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