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Journaling problem

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  Journaling problem Haines Brown <haines@histomat.net> - 2014-11-30 16:30 -0500
    Re: Journaling problem Marc Haber <mh+usenetspam1118@zugschl.us> - 2014-11-30 22:55 +0100
    Re: Journaling problem philo  <philo@privacy.net> - 2014-11-30 16:11 -0600
    Re: Journaling problem Richard Kettlewell <rjk@greenend.org.uk> - 2014-11-30 22:28 +0000
      Re: Journaling problem Haines Brown <haines@histomat.net> - 2014-12-01 06:29 -0500
        Re: Journaling problem Richard Kettlewell <rjk@greenend.org.uk> - 2014-12-01 19:05 +0000
          Re: Journaling problem Haines Brown <haines@histomat.net> - 2014-12-02 10:09 -0500
            Re: Journaling problem Thomas Richter <thor@math.tu-berlin.de> - 2014-12-02 16:48 +0100
              Re: Journaling problem Haines Brown <haines@histomat.net> - 2014-12-02 16:44 -0500

#2560 — Journaling problem

I'm runing a new machine with a Seagate Constellation hard disk
formatted ext4. 

Although I installed Debian Wheezy on the drive, but after a couple
weeks changed my mind and upgraded it to testing (Jessie). Since that
upgrade I've had regular system freezes more or less every day after
booting, followed by a beep every minute. I was not touching the machine
at the time of freeze. I've been running Memtest86+ for while, and so
far no errors in first pass.

Once I had this error message: 

  [1634.207083] Buffer I/O error on device sdb1, logical block 928015
  [1634.207092] JBD2: Error -5 when updating journal superblock for
    sdb1-8

I should note that the only devices on the machine is the hard disk,
which naturally is sda. /dev/sdb does not exist as a physical device.   

Dmesg say:
  
  Nov 30 14:12:53 engels systemd[1]: /usr appears to be on its own 
  filesytem and is not already mounted. This is not a supported setup. 
  Some things will probably break (sometimes even silently) in
  mysterious ways. Consult 
  http://freedesktop.org/wiki/Software/systemd/separate-usr-is-broken 
  for more information.

  I find that /usr must be premounted, but Linux is not in the habit
  of doing that. This error is supposed to be harmless, but it causes
  problems with udev rules. Could this be the source of an imaginary
  sdb device?

  Nov 30 14:12:53 engels kernel: ACPI: Power Button [PWRF]
  Nov 30 14:12:53 engels kernel: sd 6:0:0:0: [sdb] 15364416 512-byte
    logical blocks: (7.86 GB/7.32 GiB)
  Nov 30 14:12:53 engels kernel: sd 6:0:0:0: [sdb] Write Protect is off
  Nov 30 14:12:53 engels kernel: sd 6:0:0:0: [sdb] Mode Sense: 
    23 00 00 00 
  Nov 30 14:12:53 engels kernel: sd 6:0:0:0: [sdb] No Caching mode page 
    found
  Nov 30 14:12:53 engels kernel: sd 6:0:0:0: [sdb] Assuming drive cache: 
    write through
  Nov 30 14:12:53 engels kernel:  sdb: sdb1
  Nov 30 14:12:53 engels kernel: sd 6:0:0:0: [sdb] Attached SCSI
    removable disk 
  
This following seems unrelated, but I include just in case:

  Nov 30 14:12:53 engels kernel: i915 0000:00:02.0: fb0: inteldrmfb
    frame buffer device
  Nov 30 14:12:53 engels kernel: i915 0000:00:02.0: registered panic 
    notifier
  Nov 30 14:12:54 engels systemd-remount-fs[291]: mount: /usr not
    mounted or bad option
  Nov 30 14:12:54 engels systemd-remount-fs[291]: In some cases useful 
    info is found in syslog - try
  Nov 30 14:12:54 engels systemd-remount-fs[291]: dmesg | tail or so.
  Nov 30 14:12:54 engels systemd-remount-fs[291]: /bin/mount for /usr 
    exited with exit status 32.

I should note that in fact /usr is mounted and accessible despite this
message. 

  Nov 30 14:12:54 engels systemd-udevd[364]: failed to execute 
    '/usr/share/usbmount/usbmount' '/usr/share/usbmount/usbmount add': 
    No such file or directory
  Nov 30 14:12:54 engels systemd[1]: systemd-remount-fs.service: main 
    process exited, code=exited, status=1/FAILURE
  Nov 30 14:12:54 engels systemd[1]: Failed to start Remount Root and 
    Kernel File Systems.
  Nov 30 14:12:54 engels systemd[1]: Unit systemd-remount-fs.service 
    entered failed state.
  Nov 30 14:12:54 engels kernel: EXT4-fs (sda1): re-mounted. Opts: 
    errors=remount-ro
  ...
  Nov 30 14:12:56 engels kernel: FAT-fs (sda2): Volume was not properly 
    unmounted. Some data may be corrupt. Please run fsck.

The sda2 partition is a throw-away DOS partition that I don't use at
this point. There's no data on it.

I can't do a Seagate diagnostic, which is only for Mac and Windows
machines. 

Haines Brown

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#2561

Haines Brown <haines@histomat.net> wrote:
>  Nov 30 14:12:53 engels kernel: sd 6:0:0:0: [sdb] 15364416 512-byte
>    logical blocks: (7.86 GB/7.32 GiB)
>  Nov 30 14:12:53 engels kernel: sd 6:0:0:0: [sdb] Write Protect is off
>  Nov 30 14:12:53 engels kernel: sd 6:0:0:0: [sdb] Mode Sense: 
>    23 00 00 00 
>  Nov 30 14:12:53 engels kernel: sd 6:0:0:0: [sdb] No Caching mode page 
>    found
>  Nov 30 14:12:53 engels kernel: sd 6:0:0:0: [sdb] Assuming drive cache: 
>    write through
>  Nov 30 14:12:53 engels kernel:  sdb: sdb1
>  Nov 30 14:12:53 engels kernel: sd 6:0:0:0: [sdb] Attached SCSI
>    removable disk 

Are you sure this ist not an USB storage device or some other device
like a wireless broadband modem that shows itself as an USB storage
device to deliver its Windows drivers?

The size of just below 8 GB might give a hint.

Just out of curiosity , what does ls -al /dev/disk/by-id | grep sdb
say?

Greetings
Marc
-- 
-------------------------------------- !! No courtesy copies, please !! -----
Marc Haber         |   " Questions are the         | Mailadresse im Header
Mannheim, Germany  |     Beginning of Wisdom "     | http://www.zugschlus.de/
Nordisch by Nature | Lt. Worf, TNG "Rightful Heir" | Fon: *49 621 72739834

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#2562

On 11/30/2014 03:30 PM, Haines Brown wrote:
> I'm runing a new machine with a Seagate Constellation hard disk
> formatted ext4.
>
> Although I installed Debian Wheezy on the drive, but after a couple
> weeks changed my mind and upgraded it to testing (Jessie).


<snip>


In my book moving to a "testing" distribution is not an upgrade.


Why are you surprised there are problems.

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#2563

Haines Brown <haines@histomat.net> writes:
> I'm runing a new machine with a Seagate Constellation hard disk
> formatted ext4. 
>
> Although I installed Debian Wheezy on the drive, but after a couple
> weeks changed my mind and upgraded it to testing (Jessie). Since that
> upgrade I've had regular system freezes more or less every day after
> booting, followed by a beep every minute.

Your new machine probably has a hardware fault of some kind.

Have a look through http://www.biosflash.com/e/bios-beeps.htm or
similar.  Or take it back to whoever sold it ask for a working computer.

-- 
http://www.greenend.org.uk/rjk/

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#2564

Richard Kettlewell <rjk@greenend.org.uk> writes:

> Haines Brown <haines@histomat.net> writes:
>> I'm runing a new machine with a Seagate Constellation hard disk
>> formatted ext4. 
>>
>> Although I installed Debian Wheezy on the drive, but after a couple
>> weeks changed my mind and upgraded it to testing (Jessie). Since that
>> upgrade I've had regular system freezes more or less every day after
>> booting, followed by a beep every minute.
>
> Your new machine probably has a hardware fault of some kind.
>
> Have a look through http://www.biosflash.com/e/bios-beeps.htm or
> similar.  Or take it back to whoever sold it ask for a working computer.

Richard, I have to confess that I built this machine. Except a now
antiquated laptop the last ready made computer I purchased was an IBM
PS/2 to run DOS. I've built many machines over the years without
problems because I have tried to choose top quality components that are
compatible. Perhaps I've just been lucky.

As for the beeps, I assumed that because they don't show up for a day,
they have nothing to do with booting and BIOS. Am I wrong? A beep
exactly once a second does not seem like a BIOS code. I did a RAM test
and so that does not seem the cause. For some reason lm-sensors is not
reporting fan speeds (at last with Debian testing), although the case
and CPU fans are in fact running.

Relevant also is that I originally installed Debian Wheezy, which sat
there unused for a couple weeks without freezing until I upgraded to
Debian testing (with its systemd and DBus). I suspected the freeze was
of the X windows system, and so yesterday I booted without starting X,
and so far no freeze (though I'll be more confident by this evening).

I had not noticed the ~8 Gb size of sdb, and that may hint the 8 Gb USB
key that I've been using to transfer files. I make it a point not to
boot with a USB key inserted, but perhaps I erred. I can't reboot now to
see if the sdb issue persists because I'm waiting a day to see if the
system freezes without having started the X system.

Given that the problem arose when I upgraded from Wheezy to testing, I
suspect the problem is with systemd (with its udev and DBus) or more
simply that testing is meant only for testing. So I'll reinstall Wheezy
and not upgrade it to Jessie in the Spring of '15.
    
Haines Brown

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#2565

Haines Brown <haines@histomat.net> writes:
> Richard Kettlewell <rjk@greenend.org.uk> writes:
>> Haines Brown <haines@histomat.net> writes:
>>> I'm runing a new machine with a Seagate Constellation hard disk
>>> formatted ext4. 
>>>
>>> Although I installed Debian Wheezy on the drive, but after a couple
>>> weeks changed my mind and upgraded it to testing (Jessie). Since that
>>> upgrade I've had regular system freezes more or less every day after
>>> booting, followed by a beep every minute.
>>
>> Your new machine probably has a hardware fault of some kind.
>>
>> Have a look through http://www.biosflash.com/e/bios-beeps.htm or
>> similar.  Or take it back to whoever sold it ask for a working computer.
>
> Richard, I have to confess that I built this machine. Except a now
> antiquated laptop the last ready made computer I purchased was an IBM
> PS/2 to run DOS. I've built many machines over the years without
> problems because I have tried to choose top quality components that are
> compatible. Perhaps I've just been lucky.
>
> As for the beeps, I assumed that because they don't show up for a day,
> they have nothing to do with booting and BIOS. Am I wrong?
> A beep exactly once a second does not seem like a BIOS code.

The BIOS can run at any time, not just during boot.  In particular it is
likely to run when certain hardware problems are detected.  See
https://en.wikipedia.org/wiki/System_Management_Mode for more
information.

Beeping is a common way for the BIOS to report errors.  I don’t know of
anything else that uses this particular strategy.

-- 
http://www.greenend.org.uk/rjk/

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#2567

Richard Kettlewell <rjk@greenend.org.uk> writes:

> Haines Brown <haines@histomat.net> writes:
>> Richard Kettlewell <rjk@greenend.org.uk> writes:

> The BIOS can run at any time, not just during boot.  In particular it is
> likely to run when certain hardware problems are detected.  See
> https://en.wikipedia.org/wiki/System_Management_Mode for more
> information.
>
> Beeping is a common way for the BIOS to report errors.  I don’t know of
> anything else that uses this particular strategy.

The BIOS is an American Megatrends F3, and I don't see that it allows me
to set acceptable ranges for fan speeds, temperature, voltage, etc. DRAM
latency values set a bit higher (for example, 11 vs 9) than recommended
by the manufacturer (Skill), but I suppose this only means I'm getting
a little more stability at the cost of performance. 

The DRAM passed memtest OK, the power supply voltage is correct. The CPU
is running cool, case fans all seem to be spinning up to speed. Although
the hang followed by beeps suggests hardware problems, I suspect that
the hang is of X not getting along with systemd in the testing version
of my linux distribution. I ran the hardware two weeks without systemd
and there were no problems; I could well be wrong, but the beeps seem
quieter than BIOS warning or code beeps, about as if do DEL at a
terminal prompt.

I will now try to do a fsck on the hard disk. If it passes, I'll install
my old distribution that lacked systemd. If after a week or two there is
no freeze, I'll conclude that problem not hardware, but if there is a
freeze, then I'll know what has to be done next.

My HD manufacturer (Seagate) has a diagnostic utility that I'll trying
to run on the drive.   

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#2568

Am 02.12.2014 um 16:09 schrieb Haines Brown:

>>
>> Beeping is a common way for the BIOS to report errors.  I don’t know of
>> anything else that uses this particular strategy.
>
> The BIOS is an American Megatrends F3, and I don't see that it allows me
> to set acceptable ranges for fan speeds, temperature, voltage, etc. DRAM
> latency values set a bit higher (for example, 11 vs 9) than recommended
> by the manufacturer (Skill), but I suppose this only means I'm getting
> a little more stability at the cost of performance.

No, the bios usually does not allow you to set such thresholds, yet they 
exist. The CPU may initiate throttling if it runs to hot, or stop 
completely. To diagnose such errors, install the "mcelog" daemon, and 
check /var/log/mcelog periodically. As long as only thermal throttling 
is enabled, such events will be recorded in this file. If that doesn't 
help, the machine will still shut down.

> The DRAM passed memtest OK, the power supply voltage is correct. The CPU
> is running cool, case fans all seem to be spinning up to speed. Although
> the hang followed by beeps suggests hardware problems, I suspect that
> the hang is of X not getting along with systemd in the testing version
> of my linux distribution. I ran the hardware two weeks without systemd
> and there were no problems; I could well be wrong, but the beeps seem
> quieter than BIOS warning or code beeps, about as if do DEL at a
> terminal prompt.

You can also try to log in remotely in the machine (via SSH) and run a 
tail -f on various log scripts, e.g. /var/log/messages and/or 
/var/log/Xorg.0.log and check whether anything suspicious is showing up 
there.


> I will now try to do a fsck on the hard disk. If it passes, I'll install
> my old distribution that lacked systemd. If after a week or two there is
> no freeze, I'll conclude that problem not hardware, but if there is a
> freeze, then I'll know what has to be done next.
>
> My HD manufacturer (Seagate) has a diagnostic utility that I'll trying
> to run on the drive.

I would suggest to use smartctl from the smartmontools. This will run 
(likely) the same self-test as the vendor-specific program, but it will 
provide a standard output. Read "man smartctl" how to initiate a long 
drive self-test.

Greetings,
	Thomas

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#2569

Thomas Richter <thor@math.tu-berlin.de> writes:

> I would suggest to use smartctl from the smartmontools. This will run
> (likely) the same self-test as the vendor-specific program, but it will
> provide a standard output. Read "man smartctl" how to initiate a long drive
> self-test.

I couldn't get the vender testing software to boot and so did as you
suggested, which is to have run smarttcl long test. The drive passed
it without failure.

Thanks for the suggestion.

Haines

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