Why did my "yum upgrade" result in "emergency mode"?
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  1. #1
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    Jul 2005
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    Orlando, FL
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    Why did my "yum upgrade" result in "emergency mode"?

    Hello friends!

    Okay... I have a question. Yesterday, I did a "yum upgrade" from the root account on promised. (It had 576 packages, I believe...)

    I knew I'd be shutting it down overnight and rebooting it, this morning.

    This is NOT posted from promise, because it didn't boot.

    When I attempted to boot it, I see:

    <<>>
    Booting 'Fedora (3.15.6-200.fc20.x86_64) 20 (Heisenbug)'

    Welcome to emergency mode! After logging in, type 'journalctl -xb' to view
    system logs, "systemctl reboot" to reboot, "systemctl default" to try again
    to boot into default mode.
    <<>>

    And then it has what I regard as a "standard/typical" give root password for maintenance prompt.

    Okay... what happened?

    I was logged into GNOME as barry, and after doing a <Ctrl>-<Alt>-<F2>, I logged in there are root.

    I don't believe I had anything running from barry/GNOME, other than a firefox and I had 1 terminal window where I had listed the printer reply and posted that, with a "cut and paste".

    In root, I did "yum upgrade". It listed and asked for a "Y", which I did.

    By the time I returned to the office, right before bed, it had finished successfully. I just chose the [Power Off] button, as I typically do. (It says it will power off in 60 seconds, and I nearly always just go ahead and press that button so it powers off immediately. By appearance, it was normal. I didn't power off by holding the power button in.)

    What did I do wrong? I DEFINITELY do not want to do this again!

    Barry
    Barry L. Bond

  2. #2
    Join Date
    Jan 2011
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    1,116

    Re: Why did my "yum upgrade" result in "emergency mode"?

    Linux will try to tell you through the log files in /var/log.

    Honestly I have no idea, my best guess is that Kernel and drivers updates didn't agree, still dmesg, /var/log/messages/Xorg.0.log or journatlctl could tell you what went wrong.

    Maybe even "yum history" would show if any updates had errors.

    If it was me I just do and undo.

    http://www.if-not-true-then-false.co...redo-undo-new/

    With very large updates touching a lot of packages at once I would take a system snapshot or be with the yum undo command at hand for such occasions.

  3. #3
    Join Date
    Aug 2011
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    899

    Re: Why did my "yum upgrade" result in "emergency mode"?

    Did you try selecting an older kernel from the boot loader menu?

  4. #4
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    Re: Why did my "yum upgrade" result in "emergency mode"?

    Greetings!

    I'm posting this from my Windows browser. I haven't had time to really do much on this yet. (Yesterday was an unfortunately long day. I didn't really get enough sleep last night, and it's really going to hurt tonight/tomorrow [Friday/Saturday], since I almost never get more than 4 hours of sleep -- if that -- Saturday morning. My eyes are burning already.)

    When I power on promised, there are 4 lines in the grub.conf (or grub2.conf or whatever F20 is). There were 3 before.

    I *expect* that the top line is the new one, and the bottom three were there. (Though I cannot absolutely guarantee that. The boot screen goes by, normally, quickly, and I don't have the 3 lines that used to be there in writing and haven't confirmed they are the same.)

    Here are the lines, which I'll try to type error free:

    Fedora (3.15.6-200.fc20.x86_64) 20 (Heisenbug)
    Fedora (3.12.6-300.fc20.x86_64) 20 (Heisenbug)
    Fedora, with Linux 3.11.10-301.fc20.x86_64
    Fedora, with Linux 0-rescue-22ff9da4ae0c44fab2c3aca661deb67
    Last night, close to 11:00 PM, HOURS after I should have been in bed, in a quick try, I saw that the first 3 boot with what I have above.

    The bottom boots... possibly normally.

    I will boot it via the bottom one, and post the other couple of things I have ready to post right now from promised.

    Barry
    Barry L. Bond

  5. #5
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    Re: Why did my "yum upgrade" result in "emergency mode"?

    Hi again....

    Having booted promised, by choosing the last Fedora with "rescue" in it, I appear to be using Fedora normally at the moment.

    I will attach a "journal -xb" that I did last night. It seems to have had problems mounting /tmp and some other filesystems.

    I want to thank everyone who looks over this and provides their suggestions/comments/etc. very much! How I need you all!

    Barry
    Attached Files Attached Files
    Barry L. Bond

  6. #6
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    Re: Why did my "yum upgrade" result in "emergency mode"?

    Do you have /usr/bin/, /usr/sbin and /var on separate filesystems/partitions?

  7. #7
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    Re: Why did my "yum upgrade" result in "emergency mode"?

    Hi Ahmad and whomever else!

    This weekend was a VERY rough weekend. :-( I only had about 20 to
    30 minutes. I was going to see whether I could get my ssh port or the
    backup worked out.

    I attempted to boot promised. I got the emergency mode message even
    on the last Fedora with rescue in it! I didn't have time and I didn't
    know what to do.

    Sunday late afternoon, right before going to bed, I was going to try
    something else. I powered promised on.

    I just let it do the default boot, the top-most line.

    (That has been getting errors.)

    It booted! :-O

    I left it on! :-O (I'm afraid to try to reboot it, with it working
    at the moment!) :-D

    Ahmad, thank you for your question.

    Yes! Here is my /etc/fstab:

    #
    # /etc/fstab
    # Created by anaconda on Tue Jan 7 17:31:20 2014
    #
    # Accessible filesystems, by reference, are maintained under '/dev/disk'
    # See man pages fstab(5), findfs(8), mount(8) and/or blkid(8) for more info
    #
    UUID=e591d5dd-f0c7-4462-8f65-e4a5d3ffa8cb / ext4 defaults 1 1
    UUID=3c126371-7111-4bb0-b11b-9de65176279d /boot ext4 defaults 1 2
    UUID=5eac869b-b805-4fd2-ba57-3d165b4771c5 /home ext4 defaults 1 2
    UUID=d8cfc83a-e3ff-4831-9931-8539f1a0ba17 /multimedia ext4 defaults 1 2
    UUID=2cba2877-0f36-41ad-a55d-611dd86a010b /tmp ext4 defaults 1 2
    UUID=933e88cb-1c59-4e7a-bf76-f303406240a6 /var ext4 defaults 1 2
    UUID=a3d3deb0-0dea-4cb4-91bb-9444ad40a937 /vmware ext4 defaults 1 2
    UUID=6d188951-23e1-44c1-b376-3975a1aaff12 swap swap defaults 0 0
    /dev/sda1 /usr/bin ext4 nodev,noatime,nodiratime,discard 0 2
    /dev/sda2 /usr/sbin ext4 nodev,noatime,nodiratime,discard 0 2
    #/dev/sda3 /FMS ext4 nodev,noatime,nodiratime,discard 0 2
    #/dev/sda5 /PRINTERS ext4 nodev,noatime,nodiratime,discard 0 2
    #/dev/sda6 /PUBLIC ext4 nodev,noatime,nodiratime,discard 0 2
    #/dev/sda7 /local/bin ext4 nodev,noatime,nodiratime,discard 0 2
    /dev/sda8 /usr/lib ext4 nodev,noatime,nodiratime,discard 0 2
    /dev/sda9 /usr/lib64 ext4 nodev,noatime,nodiratime,discard 0 2
    Yes! All of them are separate filesystems/partitions!

    In 2012, having installed new Linux systems for our customer, security
    is you wouldn't believe how high! They MUST be installed in separate disk
    partitions and therefore filesystems!

    A couple of things, such as the root filesystem not filling up and
    causing a crash if /tmp or /var/tmp got full, seemed quite nice to me, so I
    chose for Puget Systems to put them as my fstab represents.

    Is that a problem?

    Barry
    Barry L. Bond

  8. #8
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    Re: Why did my "yum upgrade" result in "emergency mode"?

    I think it's the splitting of /usr/bin/, /usr/sbin and /usr/lib* on separate filesystems that's causing the issues you saw; for example /usr/bin/mount can't work because the libs it links against aren't available before /usr/lib* partitions are mounted... etc. Have a look at http://freedesktop.org/wiki/Software...usr-is-broken/

    You can have /var and /tmp on different filesystems, that should work, AFAIK.

    Personally I don't see the point or benefits of having /usr/bin/, /usr/sbin, /usr/lib* on separate filesystems.... I suggest you put all the /usr/* stuff on one filesystem otherwise it's a race condition at boot of what gets mounted first. The wiki page I linked above talks about making the initramfs mounts /usr before 'init' is executed, but it doesn't say how to achieve that; if you want to continue using that partitioning scheme you'll have to make the initramfs mount all the /usr/* filesystems at very early boot.

    A bit off-topic: I see the "discard" mount option in your fstab; according to Theodore Ts'o, the ext4 upstream developer (and possibly other filesystem developers), enabling the "discard" mount option isn't recommended for most SATA SSD drives; instead it's better to run the fstrim command as a cron job[1].

    [1] http://lkml.iu.edu//hypermail/linux/...2.2/03739.html

  9. #9
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    Re: Why did my "yum upgrade" result in "emergency mode"?

    Dear Ahmad -- thank you so much!

    Quote Originally Posted by Ahmad Samir
    I think it's the splitting of /usr/bin/, /usr/sbin and /usr/lib* on separate filesystems that's causing the issues you saw; for example /usr/bin/mount can't work because the libs it links against aren't available before /usr/lib* partitions are mounted... etc. Have a look at http://freedesktop.org/wiki/Software...usr-is-broken/

    You can have /var and /tmp on different filesystems, that should work, AFAIK.
    I am VERY GRATEFUL that people like you read and reply to my messages and provide such wonderful articles that explains to me what is going on. Looking over my journal file and knowing this now, I agree it is likely that.

    So, I guess it is a "race condition" that allows it to boot sometimes and sometimes not? That may help to explain to me why "sometimes it boots and seems to run 100% normally" and sometimes I get the "emergency mode" comment! :-O

    Now I know that any of the four, including the top, newest one -- which booted my currently running promised, would work. The race condition could occur on any of them.

    And, yet, I guess this race condition was so much less likely before I did the "yum upgrade" that this never occurred then! :-O

    I do not know whether you have been following other posts from me, but I'll just say that I'm only asking for help here because if I don't get help from people who understand (such as yourself) how things work these days, I will never get this new F20 computer working! (I'm afraid I have not one but two absolutely critical things that require time -- time that if I don't serve those things immediately either my mother will not have "basic existence" things needed or I won't have much I can eat the next week!)

    Therefore, now that I know about this -- thanks to you -- here are my thoughts/comments/questions...

    I'm afraid whatever is fastest has to come at or very near the top of my list now, unfortunately. (It sat here for just over 6 months and nothing at all had been done until I decided to get help from the Fedora Forum.)

    However, I most certainly will want this promised computer to be "set up well" -- including in the details underneath. It is destined to become my existing Linux computer.

    I'm wondering whether I should Google or search other places in order to understand exactly what needs to be done to the intraramfs to also allow "makes all existing setups work properly".

    Last year, from about November onward, I was emailing Puget Systems and I did provide the explicit filesystem/partitioning information they did for me.

    The way I normally am, if I were to move /usr/* filesystems into the rootfs, that would involve completely removing some disk partitions, and possibly increasing the size of the root partition. This would be a partition the disk and install F20 from scratch.

    At this point, I haven't decided I'm not going to be doing that, anyway! But, I would want to know more about the intraramfs fix. If that fixes it, and it sounds like it would sure be faster -- if that fixes it and truly this wouldn't be a problem after, that may become at least a possible alternative to me.

    A bit off-topic: I see the "discard" mount option in your fstab; according to Theodore Ts'o, the ext4 upstream developer (and possibly other filesystem developers), enabling the "discard" mount option isn't recommended for most SATA SSD drives; instead it's better to run the fstrim command as a cron job[1].

    [1] http://lkml.iu.edu//hypermail/linux/...2.2/03739.html
    And thank you! I personally don't care whether it is off-topic or not, I sure appreciate this comment, as well! :-)

    I was able to give the Puget Systems techs info on how to add to /mnt and a copy command that would copy whatever to wherever, without even checking it. But, I didn't have a CLUE about an SSD drive!

    I even said no. But, the main guy with whom I was emailing told me about the benefits. For whatever reason, I decided to try it.

    I spent as much time as I could, back in Nov/Dec of last year (this was November I believe) and I gave those mount options, but NONE of that was based on personal experience! I have 0 personal experience with SSDs!

    I have a Samsung SSD. I may try to determine whether it does the "trim" efficiently, or else I'll just remove the discard and figure out how often to run the "fstrim" command from (probably root's) cron. :-)

    Again I want to be sure you know how grateful I am for people like you! Your helpful replies allows me to at least continue making a little bit of progress, almost every week (even if it is only a half hour or so) on my "new" F20 computer! :-)

    Barry
    Barry L. Bond

  10. #10
    Join Date
    Aug 2011
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    899

    Re: Why did my "yum upgrade" result in "emergency mode"?

    I don't really know how to mount stuff early using the initramfs/dracut, never tried that before...

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