From: Tim Walberg <tewalberg@mediaone.net>
To: linux-kernel@vger.kernel.org
Subject: Re: Bug report
Date: Thu, 22 Mar 2001 15:43:45 -0600 [thread overview]
Message-ID: <20010322154345.A18622@mediaone.net> (raw)
In-Reply-To: <Pine.GSO.4.31.0103221257390.10736-100000@cmgm.stanford.edu>
In-Reply-To: <Pine.GSO.4.31.0103221257390.10736-100000@cmgm.stanford.edu> from Craig Cummings on 03/22/2001 14:58
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"User does not understand how *NIX systems utilize memory" is
not the same thing as "bug". What you are seeing is the kernel
using memory for file system cache.
On 03/22/2001 12:58 -0800, Craig Cummings wrote:
>> Hi there,
>>
>> I think this qualifies as a bug but let me know if this could be a
>> configuration or hardware issue.
>>
>> I've been having problems with memory leaks when I run programs on
>> large--up to 250MB text files. (I know this is huge, but that's the 3
>> billion base human genome for you.) At first I though it was a Perl
>> problem but I later found that a completely unrelated C program also
>> caused memory leaks. I recently upgraded to the 2.4 kernel, hoping to
>> solve these problems (see below). However, the memory leaks are still
>> happening and this time I know the problem is at a deeper level than my
>> programs. Some standard UNIX programs are leaking a lot of memory. I
>> would appreciate some advice and ultimately, a fix. Unfortunately, My
>> programming skills are not sufficient for tinkering with the kernel
>> source. Thank you, in advance for your help. Details follow.
>>
>> Regards,
>>
>> Craig Cummings
>>
>>
>> Here are the specs for my system:
>> Dell Precision XPSt700, Pentium III, 512 MB RAM
>> I've recently upgraded from Red Hat 6.2 with the 2.2.14 kernel to
>> Red Hat 7, then built the 2.4.2 kernel on my own.
>>
>> Here's what happens with grep:
>>
>> Output of free, freshly booted system:
>>
>> total used free shared buffers cached
>> Mem: 513616 47516 466100 0 2476 27048
>> -/+ buffers/cache: 17992 495624
>> Swap: 128480 0 128480
>>
>> Output of free after grep 'NT_005289' Data/hs_chr12.fa:
>>
>> total used free shared buffers cached
>> Mem: 513616 183548 330068 0 2624 159616
>> -/+ buffers/cache: 21308 492308
>> Swap: 128480 0 128480
>>
>> Output of grep 'NT_005289' Data/hs_chr2.fa:
>>
>> >gi|12728771|ref|NT_005289.2|Hs2_5446 Homo sapiens chromosome 2 working draft sequence segment
>>
>> Output of free after this grep:
>>
>> total used free shared buffers cached
>> Mem: 513616 424272 89344 0 2860 394232
>> -/+ buffers/cache: 27180 486436
>> Swap: 128480 0 128480
>>
>> Output of grep 'NT_005289' Data/hs_chr2.fa:
>>
>> >gi|12728771|ref|NT_005289.2|Hs2_5446 Homo sapiens chromosome 2 working draft sequence segment
>>
>> Output of free after this grep:
>>
>> total used free shared buffers cached
>> Mem: 513616 424272 89344 0 2860 394232
>> -/+ buffers/cache: 27180 486436
>> Swap: 128480 0 128480
>>
>> File sizes of the two files grep'ed:
>>
>> -rw-rw-r-- 1 cummings genomics 135744469 Mar 12 22:09 Data/hs_chr12.fa
>> -rw-rw-r-- 1 cummings genomics 240244039 Mar 12 22:24 Data/hs_chr2.fa
>>
>> Note that these file sizes are equivalent to the amount of memory leaked
>> when grep is called on that file.
>>
>> When I grep the same file a second time, very little additional memory is
>> leaked.
>>
>>
>> This same phenomenon occurs when I run a different UNIX program, e.g. wc:
>>
>> Output of wc -l Data/hs_chr3.fa:
>>
>> 2915465 Data/hs_chr3.fa
>>
>> Output of free:
>>
>> total used free shared buffers cached
>> Mem: 513616 511520 2096 0 1252 481020
>> -/+ buffers/cache: 29248 484368
>> Swap: 128480 0 128480
>>
>> Interestingly, after running wc a second time on the same file, it goes
>> very fast and very little additional memory is leaked:
>>
>> total used free shared buffers cached
>> Mem: 513616 510732 2884 0 1204 480948
>> -/+ buffers/cache: 28580 485036
>> Swap: 128480 40 128440
>>
>>
>> -------------------------------------------
>> Craig Cummings, Ph.D.
>>
>> Relman Laboratory
>> Stanford University School of Medicine
>> Department of Microbiology and Immunology
>>
>> e-mail: cummings@cmgm.stanford.edu
>> phone: 650-498-5998
>> fax: 650-852-3291
>>
>> -
>> To unsubscribe from this list: send the line "unsubscribe linux-kernel" in
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>> Please read the FAQ at http://www.tux.org/lkml/
End of included message
--
+--------------------------+------------------------------+
| Tim Walberg | tewalberg@mediaone.net |
| 828 Marshall Ct. | www.concentric.net/~twalberg |
| Palatine, IL 60074 | |
+--------------------------+------------------------------+
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next prev parent reply other threads:[~2001-03-22 21:44 UTC|newest]
Thread overview: 184+ messages / expand[flat|nested] mbox.gz Atom feed top
2001-03-22 20:58 Bug report Craig Cummings
2001-03-22 21:43 ` Tim Walberg [this message]
-- strict thread matches above, loose matches on Subject: below --
2023-08-28 12:51 Dexter Pontañeles
2023-06-27 16:02 Bug Report Tiago d'Almeida
2022-12-28 2:43 Bug report Jensen Bean
2022-12-28 5:02 ` Eric Sunshine
2022-12-25 17:26 bug report Eyal Post
2022-12-25 18:12 ` Eric Sunshine
2022-12-08 5:29 Bug Report Jensen Bean
2022-12-08 8:31 ` Bagas Sanjaya
[not found] ` <CANqKdC-gHgQHn5DMoOREY52y7PpRLMpNAjX3qeA5iy9z_GXdzw@mail.gmail.com>
2022-12-26 2:15 ` Bagas Sanjaya
2022-11-19 20:20 Jensen Bean
2022-10-03 15:28 Bug report Alastair Douglas
2022-10-03 16:53 ` Junio C Hamano
2022-10-04 10:15 ` Alastair Douglas
2022-10-05 5:46 ` Junio C Hamano
2022-04-20 19:45 Bug Report Daniel Habenicht
2022-04-20 21:30 ` brian m. carlson
2022-04-20 22:34 ` rsbecker
2022-04-21 13:20 ` Daniel Habenicht
2022-04-21 14:39 ` Torsten Bögershausen
[not found] ` <AS1P190MB175022A7F1264807ECA464A8ECF49@AS1P190MB1750.EURP190.PROD.OUTLOOK.COM>
2022-04-21 17:52 ` Torsten Bögershausen
2021-12-01 22:31 Josh Rampersad
2021-11-12 4:22 bug report Theodore Li
2021-11-12 4:29 ` Junio C Hamano
2021-11-12 6:59 ` Theodore Li
2021-11-12 14:05 ` Paul Smith
2020-03-27 11:53 Bug Report James Yeoman
2020-03-27 12:59 ` Pratyush Yadav
2020-03-21 9:38 bug report aaa
2020-03-22 8:13 ` Leon Romanovsky
[not found] <CA+2sEepTyrK-iH+VBHVF1i9DuYVzDkTNxuM0-yoWbkC9N4f8HA@mail.gmail.com>
2019-04-15 15:18 ` Nick Steinhauser
2018-09-08 9:50 Bug report 李 武刚
2018-09-19 20:46 ` Nicolas Iooss
2018-09-06 20:23 Jianliang Wu
2018-09-07 9:43 ` Luiz Augusto von Dentz
2017-08-30 21:25 Aleksandar Pavic
2017-08-31 6:36 ` Kevin Daudt
2017-08-31 14:19 ` Dov Grobgeld
2017-08-31 14:55 ` Aleksandar Pavic
2017-08-31 16:23 ` Stephan Beyer
2017-09-02 8:49 ` Jeff King
2016-12-22 20:07 Ing. Ricardo Brisighelli
2016-12-23 13:15 ` Wei Liu
2016-05-13 5:04 bug report 李本超
2016-05-13 5:23 ` Pranit Bauva
2016-05-13 5:58 ` 李本超
2016-05-13 6:37 ` Pranit Bauva
2016-05-13 6:57 ` 李本超
2016-05-13 7:10 ` Pranit Bauva
2016-05-13 7:41 ` 李本超
2016-05-13 8:10 ` Jeff King
2016-05-13 12:05 ` 李本超
2016-04-03 0:25 Bug Report Benjamin Sandeen
2016-04-03 2:20 ` Eric N. Vander Weele
2016-04-03 2:22 ` Jacob Keller
2015-05-11 16:57 Alex Newman
2015-05-11 17:14 ` David Ahern
2015-05-11 17:56 ` Alex Newman
2015-05-11 21:42 ` Arnaldo Carvalho de Melo
2015-01-27 14:43 bug report Albert Akhriev
2015-01-27 14:50 ` Jeff King
2014-08-05 5:08 Zhu, Zhengyun
2014-08-05 16:05 ` Vasily Tarasov
2013-05-24 22:32 Bug Report Rajiv Shah
2013-05-28 11:07 ` Bryn M. Reeves
[not found] <CAC34_pT9zwZDnUjo1bTUZabD02M48=_+77-mNCA5adWTgxuYgg@mail.gmail.com>
2013-04-08 5:20 ` Kirk Fraser
2013-03-04 5:44 Roberto CORRADO
2012-10-05 10:13 Bug report Муковников Михаил
2012-10-05 10:32 ` Konstantin Khomoutov
2012-10-05 10:47 ` Carlos Martín Nieto
2012-10-05 11:03 ` Муковников Михаил
2012-10-05 10:52 ` Муковников Михаил
2012-10-04 4:35 John Whitney
2012-10-04 14:19 ` Phil Hord
2012-10-04 16:10 ` John Whitney
2012-10-06 13:31 ` Jeff King
2012-10-07 2:23 ` John Whitney
2012-10-07 23:52 ` Jeff King
2012-10-09 17:17 ` John Whitney
2012-10-09 19:00 ` John Whitney
2012-10-04 15:21 ` Andrew Wong
2012-10-04 16:16 ` John Whitney
2012-10-04 16:28 ` John Whitney
2012-10-04 17:01 ` Andrew Wong
2012-09-01 23:24 bug report Manoel Pedro
2012-08-20 22:31 Bug report mr.shroom
2012-08-20 22:43 ` Randy Dunlap
2012-08-20 23:16 ` Alan Cox
2012-08-21 9:37 ` Borislav Petkov
2012-08-01 10:46 artem rus
2011-10-28 15:55 Hendrik Knackstedt
2011-07-19 17:34 Bug Report Charles Opondo
2011-07-20 15:38 ` Bjorn Helgaas
2011-04-05 4:48 bug report Larry D'Anna
2011-04-05 6:17 ` Helmut Hullen
[not found] <mailman.1.1244602801.14549.users@nilfs.org>
[not found] ` <mailman.1.1244602801.14549.users-JrjvKiOkagjYtjvyW6yDsg@public.gmane.org>
2009-06-11 17:51 ` Bug Report Dipl.-Ing. Michael Niederle
2009-06-12 6:44 ` Ryusuke Konishi
2009-04-03 23:44 bug report Jeremy
2008-11-03 18:30 Todor Gyumyushev
2008-09-25 14:08 Todor Gyumyushev
2008-09-24 9:41 Todor Gyumyushev
2008-09-24 16:38 ` Simon Holm Thøgersen
2008-09-24 17:55 ` Todor Gyumyushev
2008-09-24 18:25 ` Simon Holm Thøgersen
2008-09-29 1:36 ` Tejun Heo
2008-09-29 8:30 ` Todor Gyumyushev
2008-09-30 11:47 ` Tejun Heo
2008-07-26 15:17 Bug report Jachin Spencer
2008-07-27 1:11 ` Pavel Roskin
2008-06-06 19:59 bug report Zsiros Attila
2008-06-07 1:44 ` Oliver Pinter
2008-06-07 1:45 ` Oliver Pinter
2008-06-07 5:56 ` Andrew Morton
2008-06-07 8:47 ` Ilpo Järvinen
2008-06-07 12:50 ` Oliver Pinter
2008-06-07 15:09 ` Phil Oester
2008-06-07 18:53 ` Oliver Pinter
2008-06-08 11:56 ` Zsiros Attila
2008-06-09 17:04 ` Oliver Pinter
2007-09-06 17:05 Bug Report Mark Goodall
2007-09-07 0:23 ` Barry Naujok
2007-09-18 2:27 ` Barry Naujok
2006-07-09 2:04 BUG report Antonio Mignolli
2006-07-12 10:56 ` Markus Rechberger
2005-10-21 8:42 bug report Ian Pratt
2005-10-21 11:28 ` David F Barrera
2005-10-20 16:47 Stephan Böni
2005-10-20 12:47 Stephan Böni
2005-10-20 15:28 ` David F Barrera
2005-05-26 1:09 Jerry DeLisle
2005-05-26 2:12 ` Jerry DeLisle
2005-04-11 14:07 Bug report studdugie
2005-04-11 15:30 ` Vladimir Saveliev
2005-04-12 13:57 ` studdugie
2005-04-13 12:49 ` Vladimir Saveliev
2005-04-14 4:45 ` David Masover
2005-04-14 9:15 ` Vladimir Saveliev
2004-12-25 13:00 Ioannis Fikouras
2004-11-14 12:38 Bug Report Alan Erola
2004-11-29 18:31 ` bug report Muhtar Mahsut
2004-11-30 0:39 ` Greg KH
2004-12-18 11:11 ` Brian Kreulen
2004-12-18 12:06 ` Brian Kreulen
2005-08-21 20:06 ` John Saylor
2005-08-21 20:45 ` Kay Sievers
2006-01-11 11:08 ` Michael Mey
2006-01-11 11:17 ` Kay Sievers
2004-03-03 10:47 Bug report Manivannan Shanmugam
2004-02-21 2:48 Grahame M. Kelly
2004-02-24 9:22 ` Vitaly Fertman
2004-01-13 19:09 BUG REPORT Luca T.
2004-01-13 21:18 ` David D. Huff Jr.
2004-01-14 10:17 ` Vitaly Fertman
2003-11-23 2:09 bug report Stephan Reichel
2003-11-23 12:19 ` Vitaly Fertman
2003-11-25 0:44 ` Stephan Reichel
2003-11-25 0:54 ` Carl-Daniel Hailfinger
2003-11-25 10:54 ` Vitaly Fertman
2003-11-23 12:20 ` Redeeman
2003-08-02 18:10 Russell Whitaker
[not found] ` <3F424BB1.8050400@metavize.com>
2003-08-19 23:44 ` Russell Whitaker
2003-04-28 20:40 robs
2003-04-29 5:49 ` Oleg Drokin
2003-04-29 8:20 ` robs
2003-04-29 8:43 ` Oleg Drokin
2003-04-29 8:41 ` robs
2003-04-29 8:45 ` Oleg Drokin
2002-12-02 19:40 Howard Shane
2002-10-04 15:01 Sander Kamphuis
2002-10-04 15:32 ` Paulo Andre'
2002-10-04 15:35 ` Adrian Bunk
2002-07-12 5:12 Bug Report service
2002-04-24 9:15 bug report Pan,Gaoyong
2002-03-04 16:04 Vitaly Fertman
2001-11-27 15:04 Bug (?) report Matteo Sasso
2001-11-27 15:51 ` Tommy Reynolds
2001-11-10 19:01 Bug Report Logoth Dragon
2001-11-10 19:08 ` Alan Cox
2001-08-02 9:38 Bug report Daniel Glozman
2001-02-01 22:09 Anders S. Buch
2001-02-03 1:44 ` Jens Axboe
1999-06-07 8:54 Alexander Larsson
1999-06-07 13:53 ` Dan Malek
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