DMARC-Filter: OpenDMARC Filter v1.4.2 delorie.com 4AO9j9sW1172434
Authentication-Results: delorie.com; dmarc=pass (p=none dis=none) header.from=cygwin.com
Authentication-Results: delorie.com; spf=pass smtp.mailfrom=cygwin.com
DKIM-Filter: OpenDKIM Filter v2.11.0 delorie.com 4AO9j9sW1172434
Authentication-Results: delorie.com;
	dkim=pass (1024-bit key, unprotected) header.d=cygwin.com header.i=@cygwin.com header.a=rsa-sha256 header.s=default header.b=E0CVwBt+
X-Recipient: archive-cygwin AT delorie DOT com
DKIM-Filter: OpenDKIM Filter v2.11.0 sourceware.org 8E7F23858C60
DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=cygwin.com;
	s=default; t=1732441507;
	bh=KJUqL/8yTbprTV8mDDgDq4j8i5p8yCjL9GhoTWEGSvc=;
	h=Date:Subject:To:References:In-Reply-To:List-Id:List-Unsubscribe:
	 List-Archive:List-Post:List-Help:List-Subscribe:From:Reply-To:
	 From;
	b=E0CVwBt+3dYrmOlj/vdcUpbkdFWiuP6y5nDWcRrq8Dg9TE/3ThJ61sifnh7W39y1r
	 vvEtgpgtMzHXiH6v5H43yrY2BPSoDsiCwTrbtDDDUgnryWHjb3eltV9/1RL2w7qUML
	 R/jcnCp3GiS+K2FDgMuvy3c3E3a3dWFZLLTlz21U=
X-Original-To: cygwin AT cygwin DOT com
Delivered-To: cygwin AT cygwin DOT com
DMARC-Filter: OpenDMARC Filter v1.4.2 sourceware.org 10EF13858D29
ARC-Filter: OpenARC Filter v1.0.0 sourceware.org 10EF13858D29
ARC-Seal: i=1; a=rsa-sha256; d=sourceware.org; s=key; t=1732441482; cv=none;
 b=DbVG1IFAAMYKyczrD6GoK01cejdAvk0Dib2Q8NlL64fryM+hskR9RMHC8l4e+/Q7Fr3nKxt/qb6i9DiyBUIv6efgJ1S04XPGWBbBD7RL6+ACm0FmJm3P0KPDsrQDdl3AC7vlGjTTGoS2AslqpFYKYAOITo01L7ejTSuJ6D+U4So=
ARC-Message-Signature: i=1; a=rsa-sha256; d=sourceware.org; s=key;
 t=1732441482; c=relaxed/simple;
 bh=7S7rFY44fhrqgcJEmFCVJyPhYJeSWAuQxqnw/+Ko4R4=;
 h=Message-ID:Date:MIME-Version:Subject:To:From;
 b=nSDKnWtpuFRf+ky+ORqkG2fBvawhJNyWH8ynQkerSxFkeoYbz7DliXn1KuvDp6X3MQRKiaYhg4Xcpfh8inx5Kgj5TQpRZjyiOKG5LHWsa0oTXN8/z6p/dRmbSP0qaU7KynLvVhKMMc20XEXtMEyv4tmc4eDhcYeK4wVxdC0e6W0=
ARC-Authentication-Results: i=1; server2.sourceware.org
DKIM-Filter: OpenDKIM Filter v2.11.0 sourceware.org 10EF13858D29
Message-ID: <b1a9db79-0eec-4a2f-a246-c3f1a849244d@maxrnd.com>
Date: Sun, 24 Nov 2024 01:44:38 -0800
MIME-Version: 1.0
User-Agent: Mozilla Thunderbird
Subject: Re: Thread memory allocation issue
To: "cygwin AT cygwin DOT com" <cygwin AT cygwin DOT com>
References: <791865992 DOT 3601338 DOT 1731871978376 DOT ref AT mail DOT yahoo DOT com>
 <791865992 DOT 3601338 DOT 1731871978376 AT mail DOT yahoo DOT com>
 <0bec82b7-503d-4cfd-b940-cb66914b61f1 AT maxrnd DOT com>
 <2093810197 DOT 191568 DOT 1731999559821 AT mail DOT yahoo DOT com>
Content-Language: en-US
In-Reply-To: <2093810197.191568.1731999559821@mail.yahoo.com>
X-BeenThere: cygwin AT cygwin DOT com
X-Mailman-Version: 2.1.30
Precedence: list
List-Id: General Cygwin discussions and problem reports <cygwin.cygwin.com>
List-Unsubscribe: <https://cygwin.com/mailman/options/cygwin>,
 <mailto:cygwin-request AT cygwin DOT com?subject=unsubscribe>
List-Archive: <https://cygwin.com/pipermail/cygwin/>
List-Post: <mailto:cygwin AT cygwin DOT com>
List-Help: <mailto:cygwin-request AT cygwin DOT com?subject=help>
List-Subscribe: <https://cygwin.com/mailman/listinfo/cygwin>,
 <mailto:cygwin-request AT cygwin DOT com?subject=subscribe>
From: Mark Geisert via Cygwin <cygwin AT cygwin DOT com>
Reply-To: Mark Geisert <mark AT maxrnd DOT com>
Content-Transfer-Encoding: 7bit
Content-Type: text/plain; charset="us-ascii"; Format="flowed"
Errors-To: cygwin-bounces~archive-cygwin=delorie DOT com AT cygwin DOT com
Sender: "Cygwin" <cygwin-bounces~archive-cygwin=delorie DOT com AT cygwin DOT com>

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

-- 
Problem reports:      https://cygwin.com/problems.html
FAQ:                  https://cygwin.com/faq/
Documentation:        https://cygwin.com/docs.html
Unsubscribe info:     https://cygwin.com/ml/#unsubscribe-simple