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Date: Sun, 17 Nov 2024 19:32:58 +0000 (UTC)
To: "cygwin AT cygwin DOT com" <cygwin AT cygwin DOT com>
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Subject: Thread memory allocation issue
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From: Teepean via Cygwin <cygwin AT cygwin DOT com>
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Hello!

I raised this issue couple of years ago on cygwin-developer but now when the problem has manifested again with recent versions of Cygwin I decided to post this to general discussion list.

Steps to Reproduce

1. Compile BWA normally

https://github.com/lh3/bwa/

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


3. Run both versions with the following command:
time ./bwa mem -t 11 chr19_KI270866v1_alt.fasta test_1.fastq test_2.fastq > testorigsingle.sam


Without Patch (Default malloc):


[M::mem_process_seqs] Processed 120000 reads in 30.296 CPU sec, 3.743 real sec
[main] Real time: 3.883 sec; CPU: 30.436 sec
real    0m3.907s
user    0m19.186s
sys     0m11.265s


With Patch (rpmalloc):


[M::mem_process_seqs] Processed 120000 reads in 7.530 CPU sec, 0.702 real sec
[main] Real time: 0.830 sec; CPU: 7.640 sec
real    0m0.868s
user    0m7.343s
sys     0m0.327s


Analysis

1. The default malloc implementation shows extremely high system time (11.265s) compared to the rpmalloc version (0.327s)
2. Total real time is about 4.5x slower with default malloc
3. The dramatic difference in system time suggests heavy contention in the memory allocation subsystem
4. The issue only manifests on Cygwin with bwa; the same code performs normally on native Linux and MacOS
5. The issue manifests with recent versions of Cygwin but does work with older versions

The issue becomes more pronounced with higher thread counts


The patched code is located here in branch Cygwin:


https://github.com/WGSExtract/bwa.git


Simple testsuite. Run bash testsuite.sh. The testsuite includes a version compiled with an older version of Cygwin called bwa_working.exe


https://drive.google.com/file/d/1jtbQVUAcCmpJM-8Exi0C6pzDXcEo4cV6/view?usp=drive_link

Regards,
Teemu Nätkinniemi

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