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Bug 378733 - gentoo-sources-2.6.38-r6 - slow I/O
Summary: gentoo-sources-2.6.38-r6 - slow I/O
Status: RESOLVED TEST-REQUEST
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: [OLD] Core system (show other bugs)
Hardware: x86 Linux
: High normal (vote)
Assignee: Gentoo Kernel Bug Wranglers and Kernel Maintainers
URL:
Whiteboard:
Keywords:
Depends on:
Blocks:
 
Reported: 2011-08-11 06:25 UTC by brad
Modified: 2011-11-01 14:52 UTC (History)
1 user (show)

See Also:
Package list:
Runtime testing required: ---


Attachments

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Description brad 2011-08-11 06:25:04 UTC
Brand new gentoo install of 2.6.38-gentoo-r6. on first boot using this http://www.gentoo.org/doc/en/gentoo-x86-quickinstall.xml installation method, the boot took forever.
Had a few other issues, reformatted the filesystem and did the complete install again. Same problem.
Started disabling drivers like usb etc in the kernel and traced it back to ext3 readonly as the only possible source for my system drag.



*****************dmesg****************
[    0.788165] ata3: SATA link down (SStatus 0 SControl 300)
[    0.788405] ata1: SATA link up 1.5 Gbps (SStatus 113 SControl 300)
[    0.789528] ata1.00: ACPI cmd ef/10:03:00:00:00:a0 (SET FEATURES) filtered out
[    0.793187] ata1.00: ATA-8: Hitachi HTS545025B9A300, PB2OC64G, max UDMA/133
[    0.793353] ata1.00: 488397168 sectors, multi 16: LBA48 NCQ (depth 31/32), AA
[    0.795377] ata1.00: ACPI cmd ef/10:03:00:00:00:a0 (SET FEATURES) filtered out
[    0.796273] ata1.00: configured for UDMA/133
[    0.796698] scsi 0:0:0:0: Direct-Access     ATA      Hitachi HTS54502 PB2O PQ: 0 ANSI: 5
[    0.797627] sd 0:0:0:0: [sda] 488397168 512-byte logical blocks: (250 GB/232 GiB)
[    0.797952] sd 0:0:0:0: Attached scsi generic sg0 type 0
[    0.798136] sd 0:0:0:0: [sda] Write Protect is off
[    0.798299] sd 0:0:0:0: [sda] Mode Sense: 00 3a 00 00
[    0.798386] sd 0:0:0:0: [sda] Write cache: enabled, read cache: enabled, doesn't support DPO or FUA
[    0.855100]  sda: sda1 sda2 sda3 sda4
[    0.856748] sd 0:0:0:0: [sda] Attached SCSI disk
[    1.682458] input: PS/2 Mouse as /devices/platform/i8042/serio1/input/input4
[    1.740756] input: AlpsPS/2 ALPS GlidePoint as /devices/platform/i8042/serio1/input/input5
[    1.753921] md: Waiting for all devices to be available before autodetect
[    1.754131] md: If you don't use raid, use raid=noautodetect
[    1.754814] md: Autodetecting RAID arrays.
[    1.754961] md: Scanned 0 and added 0 devices.
[    1.755131] md: autorun ...
[    1.755280] md: ... autorun DONE.
[    1.781213] EXT3-fs (sda4): recovery required on readonly filesystem
[    1.781390] EXT3-fs (sda4): write access will be enabled during recovery
[    1.841252] EXT3-fs: barriers not enabled
[  135.715247] kjournald starting.  Commit interval 5 seconds
[  135.715390] EXT3-fs (sda4): recovery complete
[  135.715830] EXT3-fs (sda4): mounted filesystem with writeback data mode
[  135.716067] VFS: Mounted root (ext3 filesystem) readonly on device 8:4.
[  135.808526] devtmpfs: mounted
[  135.808804] Freeing unused kernel memory: 400k freed
[  135.809229] Write protecting the kernel text: 4572k
[  135.809437] Write protecting the kernel read-only data: 1832k
[  218.760104] kbd_mode used greatest stack depth: 6888 bytes left
[  223.777935] loadkeys used greatest stack depth: 5984 bytes left
[  223.778493] init-early.sh used greatest stack depth: 5792 bytes left
[  371.009409] udev[1025]: starting version 164
[  387.324140] EXT3-fs (sda4): using internal journal


**************************************************

At:
135.715247] kjournald starting.

is where she starts to drag but I am highly suspicious it is the ext3 readonly issue?

Reproducible: Always

Steps to Reproduce:
1. this installation method http://www.gentoo.org/doc/en/gentoo-x86-quickinstall.xml
2.
3.
Comment 1 brad 2011-08-11 06:25:56 UTC
emerge --info
Portage 2.1.10.3 (default/linux/x86/10.0, gcc-4.4.5, glibc-2.12.2-r0, 2.6.38-gentoo-r6 i686)
=================================================================
System uname: Linux-2.6.38-gentoo-r6-i686-Intel-R-_Atom-TM-_CPU_N280_@_1.66GHz-with-gentoo-2.0.3
Timestamp of tree: Wed, 10 Aug 2011 13:00:01 +0000
app-shells/bash:          4.1_p9
dev-lang/python:          2.7.1-r1, 3.1.3-r1
dev-util/cmake:           2.8.4-r1
dev-util/pkgconfig:       0.26
sys-apps/baselayout:      2.0.3
sys-apps/openrc:          0.8.3-r1
sys-apps/sandbox:         2.4
sys-devel/autoconf:       2.68
sys-devel/automake:       1.9.6-r3, 1.11.1
sys-devel/binutils:       2.20.1-r1
sys-devel/gcc:            4.4.5
sys-devel/gcc-config:     1.4.1-r1
sys-devel/libtool:        2.4-r1
sys-devel/make:           3.82
sys-kernel/linux-headers: 2.6.36.1 (virtual/os-headers)
sys-libs/glibc:           2.12.2
Repositories: gentoo
ACCEPT_KEYWORDS="x86 ~x86"
ACCEPT_LICENSE="* -@EULA"
CBUILD="i486-pc-linux-gnu"
CFLAGS="-O2 -march=i486 -pipe"
CHOST="i486-pc-linux-gnu"
CONFIG_PROTECT="/etc"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/sandbox.d /etc/terminfo"
CXXFLAGS="-O2 -march=i486 -pipe"
DISTDIR="/usr/portage/distfiles"
EMERGE_DEFAULT_OPTS="--autounmask=n"
FEATURES="assume-digests binpkg-logs distlocks ebuild-locks fixlafiles fixpackages news parallel-fetch protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch"
FFLAGS=""
GENTOO_MIRRORS="http://gentoo.localhost.net.ar/ ftp://mirrors.localhost.net.ar/pub/mirrors/gentoo/ http://ftp.swin.edu.au/gentoo ftp://ftp.swin.edu.au/gentoo http://gentoo.inode.at/ ftp://gentoo.inode.at/source/ rsync://gentoo.lagis.at/gentoo-distfiles/ http://gentoo.lagis.at/"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
MAKEOPTS="-j2"
PKGDIR="/usr/portage/packages"
PORTAGE_CONFIGROOT="/"
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --stats --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages"
PORTAGE_TMPDIR="/var/tmp"
PORTDIR="/usr/portage"
PORTDIR_OVERLAY=""
SYNC="rsync://rsync1.au.gentoo.org/gentoo-portage"
USE="X acl berkdb bzip2 cli consolekit cracklib crypt cups cxx dbus dri extras fortran gdbm gpm iconv ipv6 jpeg lcms modules mudflap ncurses nls nptl nptlonly openmp pam pcre perl png policykit pppd python readline session ssl sysfs tcpd threads tiff unicode utils x86 xorg xpdf-headers zlib" ALSA_CARDS="ali5451 als4000 atiixp atiixp-modem bt87x ca0106 cmipci emu10k1 emu10k1x ens1370 ens1371 es1938 es1968 fm801 hda-intel intel8x0 intel8x0m maestro3 trident usb-audio via82xx via82xx-modem ymfpci" ALSA_PCM_PLUGINS="adpcm alaw asym copy dmix dshare dsnoop empty extplug file hooks iec958 ioplug ladspa lfloat linear meter mmap_emul mulaw multi null plug rate route share shm softvol" APACHE2_MODULES="actions alias auth_basic authn_alias authn_anon authn_dbm authn_default authn_file authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache cgi cgid dav dav_fs dav_lock deflate dir disk_cache env expires ext_filter file_cache filter headers include info log_config logio mem_cache mime mime_magic negotiation rewrite setenvif speling status unique_id userdir usertrack vhost_alias" CALLIGRA_FEATURES="braindump flow karbon kexi kpresenter krita tables words" CAMERAS="ptp2" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" ELIBC="glibc" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock itrax mtk3301 nmea ntrip navcom oceanserver oldstyle oncore rtcm104v2 rtcm104v3 sirf superstar2 timing tsip tripmate tnt ubx" INPUT_DEVICES="keyboard mouse evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" PHP_TARGETS="php5-3" RUBY_TARGETS="ruby18" USERLAND="GNU" VIDEO_CARDS="fbdev glint intel mach64 mga neomagic nouveau nv r128 radeon savage sis tdfx trident vesa via vmware dummy v4l" XTABLES_ADDONS="quota2 psd pknock lscan length2 ipv4options ipset ipp2p iface geoip fuzzy condition tee tarpit sysrq steal rawnat logmark ipmark dhcpmac delude chaos account"
Unset:  CPPFLAGS, CTARGET, INSTALL_MASK, LANG, LC_ALL, LINGUAS, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS
Comment 2 brad 2011-08-11 06:26:29 UTC
cat /etc/fstab
# /etc/fstab: static file system information.
#
# noatime turns off atimes for increased performance (atimes normally aren't
# needed); notail increases performance of ReiserFS (at the expense of storage
# efficiency).  It's safe to drop the noatime options if you want and to
# switch between notail / tail freely.
#
# The root filesystem should have a pass number of either 0 or 1.
# All other filesystems should have a pass number of 0 or greater than 1.
#
# See the manpage fstab(5) for more information.
#

# <fs>                  <mountpoint>    <type>          <opts>          <dump/pass>

# NOTE: If your BOOT partition is ReiserFS, add the notail option to opts.
/dev/sda4               /boot           ext3            noauto,noatime  1 2
/dev/sda4               /               ext3            noatime         0 1
/dev/sda3               none            swap            sw              0 0
/dev/cdrom              /mnt/cdrom      auto            noauto,ro       0 0
/dev/fd0                /mnt/floppy     auto            noauto          0 0
Comment 3 brad 2011-08-11 06:27:07 UTC
cat /boot/grub/grub.conf
# This is a sample grub.conf for use with Genkernel, per the Gentoo handbook
# http://www.gentoo.org/doc/en/handbook/handbook-x86.xml?part=1&chap=10#doc_chap2
# If you are not using Genkernel and you need help creating this file, you
# should consult the handbook. Alternatively, consult the grub.conf.sample that
# is included with the Grub documentation.

default 0
timeout 5
splashimage=(hd0,3)/boot/grub/splash.xpm.gz

title Homie's Winblows
rootnoverify (hd0,1)
makeactive
chainloader --force +1
#boot

title Homie's Gentoo
root (hd0,3)
kernel /boot/myKernel3 root=/dev/sda4
#initrd /boot/initramfs-genkernel-x86-2.6.24-gentoo-r5
Comment 4 brad 2011-08-11 06:27:44 UTC
fdisk -l

Disk /dev/sda: 250.1 GB, 250059350016 bytes
255 heads, 63 sectors/track, 30401 cylinders, total 488397168 sectors
Units = sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 512 bytes
I/O size (minimum/optimal): 512 bytes / 512 bytes
Disk identifier: 0x74457445

   Device Boot      Start         End      Blocks   Id  System
/dev/sda1            2048     3074047     1536000   27  Hidden NTFS WinRE
/dev/sda2   *     3074048   328132607   162529280    7  HPFS/NTFS/exFAT
/dev/sda3       328132608   330229759     1048576   82  Linux swap / Solaris
/dev/sda4       330229760   488397167    79083704   83  Linux
Comment 5 brad 2011-08-11 06:28:36 UTC
df
Filesystem           1K-blocks      Used Available Use% Mounted on
rootfs                77841568   3760052  70127332   6% /
/dev/root             77841568   3760052  70127332   6% /
devtmpfs               1030988       216   1030772   1% /dev
rc-svcdir                 1024        44       980   5% /lib/rc/init.d
shm                    1031188         0   1031188   0% /dev/shm
Comment 6 Jeroen Roovers (RETIRED) gentoo-dev 2011-08-11 19:38:08 UTC
What if you used the ext4 driver instead of the ext3 driver?

Also, it looks like between the first and 135th second it's actually doing "recovery" on sda4. It should really not do this on the next boot.

Also, it looks like / and /boot are pointing to the same block device (/dev/sda4) in your fstab. This is wrong and should be corrected, although it doesn't explain the kernel lag, unless this somehow influences how the root fs is unmounted on the previous boot.
Comment 7 brad 2011-08-12 11:14:22 UTC
my boot is sda4 so the setting is correct.
sd1a/ = some proprietary toshiba crap which is left alone
sda2/ = winblows
sda3/ = linux swap
sda4/ = gentoo with /boot

it's not just lagging at boot, it's lagging the entire system.
I left the system on for a day and trying to compile the kernel now. At this pace the compile is going to take 5 to 7 hrs. 2 hrs have already passed.
Compared to if I booted up on the livecd, this exact same process would take 5 min.
The OS is shot before I even have a chance to use it.
Its REALLY bad.

Toshiba NB205 with a 1.6 atom and 2 gigs of ram
Comment 8 Jeroen Roovers (RETIRED) gentoo-dev 2011-08-12 16:32:18 UTC
/dev/sda4               /boot           ext3            noauto,noatime  1 2
/dev/sda4               /               ext3            noatime         0 1

Look, that is wrong. /dev/sda4 is mentioned twice. Please correct that.
Comment 9 brad 2011-08-12 18:18:34 UTC
I commented '#' out one of the fstab entries.
Same exact behavior.
Comment 10 Jeroen Roovers (RETIRED) gentoo-dev 2011-08-12 18:33:23 UTC
You could run top(1) and see what is making the system slow.
Comment 11 brad 2011-08-12 18:47:47 UTC
Top says the computer is sleeping.
Even worse, when I compile the kernel, you know how your disk access light goes nuts? Not mine. It blinks at a snails pace.
Comment 12 Jeroen Roovers (RETIRED) gentoo-dev 2011-08-12 19:14:13 UTC
Your lspci output and kernel configuration might help here.
Comment 13 brad 2011-08-13 21:02:44 UTC
I am thinking the fstab adjustment fixed it, but not 100% sure.
I am sitting at a desktop, updating the system normally.
I still have a very slow boot but the system runs fine.
Comment 14 brad 2011-08-13 22:24:57 UTC
lspci
00:00.0 Host bridge: Intel Corporation Mobile 945GME Express Memory Controller H                                                                             ub (rev 03)
00:02.0 VGA compatible controller: Intel Corporation Mobile 945GME Express Integ                                                                             rated Graphics Controller (rev 03)
00:02.1 Display controller: Intel Corporation Mobile 945GM/GMS/GME, 943/940GML E                                                                             xpress Integrated Graphics Controller (rev 03)
00:1b.0 Audio device: Intel Corporation 82801G (ICH7 Family) High Definition Aud                                                                             io Controller (rev 02)
00:1c.0 PCI bridge: Intel Corporation 82801G (ICH7 Family) PCI Express Port 1 (r                                                                             ev 02)
00:1c.1 PCI bridge: Intel Corporation 82801G (ICH7 Family) PCI Express Port 2 (r                                                                             ev 02)
00:1c.2 PCI bridge: Intel Corporation 82801G (ICH7 Family) PCI Express Port 3 (r                                                                             ev 02)
00:1c.3 PCI bridge: Intel Corporation 82801G (ICH7 Family) PCI Express Port 4 (r                                                                             ev 02)
00:1d.0 USB Controller: Intel Corporation 82801G (ICH7 Family) USB UHCI Controll                                                                             er #1 (rev 02)
00:1d.1 USB Controller: Intel Corporation 82801G (ICH7 Family) USB UHCI Controll                                                                             er #2 (rev 02)
00:1d.2 USB Controller: Intel Corporation 82801G (ICH7 Family) USB UHCI Controll                                                                             er #3 (rev 02)
00:1d.3 USB Controller: Intel Corporation 82801G (ICH7 Family) USB UHCI Controll                                                                             er #4 (rev 02)
00:1d.7 USB Controller: Intel Corporation 82801G (ICH7 Family) USB2 EHCI Control                                                                             ler (rev 02)
00:1e.0 PCI bridge: Intel Corporation 82801 Mobile PCI Bridge (rev e2)
00:1f.0 ISA bridge: Intel Corporation 82801GBM (ICH7-M) LPC Interface Bridge (re                                                                             v 02)
00:1f.1 IDE interface: Intel Corporation 82801G (ICH7 Family) IDE Controller (re                                                                             v 02)
00:1f.2 SATA controller: Intel Corporation 82801GBM/GHM (ICH7 Family) SATA AHCI                                                                              Controller (rev 02)
00:1f.3 SMBus: Intel Corporation 82801G (ICH7 Family) SMBus Controller (rev 02)
03:00.0 Network controller: Atheros Communications Inc. AR9285 Wireless Network                                                                              Adapter (PCI-Express) (rev 01)
04:00.0 Ethernet controller: Realtek Semiconductor Co., Ltd. RTL8101E/RTL8102E P                                                                             CI Express Fast Ethernet controller (rev 02)
Comment 15 brad 2011-08-13 22:26:32 UTC
notice the delay in dmesg
:(

[    1.561597] md: Waiting for all devices to be available before autodetect
[    1.561765] md: If you don't use raid, use raid=noautodetect
[    1.562530] md: Autodetecting RAID arrays.
[    1.562677] md: Scanned 0 and added 0 devices.
[    1.562820] md: autorun ...
[    1.562958] md: ... autorun DONE.
[    1.865830] EXT3-fs: barriers not enabled
[    5.712393] kjournald starting.  Commit interval 5 seconds
[    5.712513] EXT3-fs (sda4): mounted filesystem with ordered data mode
[    5.712550] VFS: Mounted root (ext3 filesystem) readonly on device 8:4.
[   11.711617] devtmpfs: mounted
[   11.711859] Freeing unused kernel memory: 400k freed
[   11.712370] Write protecting the kernel text: 4780k
[   11.712582] Write protecting the kernel read-only data: 1884k
[   29.879331] kworker/u:7 used greatest stack depth: 7092 bytes left
[  140.806731] kbd_mode used greatest stack depth: 6888 bytes left
[  145.723082] loadkeys used greatest stack depth: 5984 bytes left
[  145.723610] init-early.sh used greatest stack depth: 5788 bytes left
[  361.068210] <30>udevd[1031]: starting version 171
[  462.361133] EXT3-fs (sda4): using internal journal
[  485.463057] Adding 1048572k swap on /dev/sda3.  Priority:-1 extents:1 across:
Comment 16 brad 2011-08-14 14:33:32 UTC
The comment about it working?
scratch that. firefox is taking 9+ hours to install.
Laptop ran out of power and puter blinked.
Initial boot took 1.2 hrs. I could see it journaling the filesystem so I gave it a little bit of credit.
Rebooted her the next day and boot only took 40min, this was an improvement.
Lastnight before I went to bed I started the install for firefox. It's still running now.
Comment 17 brad 2011-08-14 16:30:33 UTC
I changed fstab to ext4 to try and force the ext4 drivers at reboot it loaded the 'ext3 drivers' instead but something 'broke' in udev during boot, some timeout, and my system began to boot at a normal speed and run fine for the very first time. "After waiting on it to break"
I emerged java jre in a matter of 10 min or less which is completely acceptable.
I don't know what broke, dmesg is clean and does not indicate the timeout that occurred.
I am installing syslog-ng in hopes of getting more output.
Comment 18 brad 2011-08-14 17:56:42 UTC
after installing syslog-ng and rebooting, the 'breakage' did not occur again and my puter is back to running like a broke snail again.
:(
Comment 19 Mike Pagano gentoo-dev 2011-10-13 14:48:02 UTC
Do you still have issues with a 3.0.6 kernel?
Comment 20 Mike Pagano gentoo-dev 2011-11-01 14:52:35 UTC
Please test 3.1, and let us know if there is any change. Reopen if still a problem.