up vote 8 down vote favorite
4

A disaster just occurred to me after I ran the command "yum remove python" and now I can't boot the server up anymore.

How it happened: I tried updating some apps via yum on my CentOS 5 vps and the command was failing due to some weird python 2.4 error. I noticed that my version of python was old and I tried reinstalling it by first removing it, and so I did yum remove python.

After that it asked me something about removing dependencies and it looked like nothing I could miss so I clicked [Y].

So the aftermath of that was that I was unable to run any command what so ever. I even tried cd /var/www but it said something like "command does not exist in /usr/bin". When I used tab to see folder navigation suggestions, the file structure still seemed to be there (at least the /var/www bit which is really important to me). After that I tried restarting the vps (from the admin panel since "reboot" command did not work) and now it doesn't boot anymore.

Now my question is: how can a command like that possibly destroy my server like this?

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what kind of error do you have at boot ? – olivierg yesterday
6  
Incidentally, apt-get remove apt works. I haven't tried dpkg --remove dpkg yet. I bet that's really bad. – joshudson yesterday
2  
You do have a backup, right? – vasin1987 17 hours ago
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@joshudson I just spun up a Debian 8.4 live CD in a VM and tried it. Result: # dpkg --remove dpkg spits out dpkg: error processing dpkg (--remove): this is an essential package; it should not be removed. If I add --force-all to dpkg's command line, dpkg spits out a whole bundle of warnings and proceeds to remove itself, along with breaking about two dozen other packages that depend on dpkg. On a real system, I'm pretty sure you'd have some trouble recovering from that, but you probably could (there's little magic to .debs); CentOS may or may not be similar in this regard. – Michael Kjörling 14 hours ago
1  
@joshudson It works because there's a copy of apt running in memory when you issue the command... as soon as it's finished (and the program terminates), you won't be able to use apt any longer. – SnakeDoc 13 hours ago
up vote 40 down vote

Frankly, because you did something you didn't fully understand. Python is an essential part of the OS and the things you considered unimportant are very important. Restore from backup.

When you removed Python, yum showed you a long list of packages that would also be removed. This list contains such essentials as yum itself, coreutils, net-tools and others. You confirmed to yum that you know what you are doing and want to proceed anyway. The result of this is a non-working system. This shouldn't be surprising.

For the record, on newer CentOS version this isnt't possible anymore, as certain packages are now marked as protected and can't be removed, only reinstalled or upgraded. And since CentOS 5 is now EOL anyway, this is a good time to upgrade to a newer version.

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1  
Restore is something you need to consider before it's necessary. Do you have backups? – yoonix yesterday
4  
@tadoman: If you can boot into some kind of rescue system, you will be able to mount the disk and recover data from it (this should be all of your user data, including config files). You have to contact your provider to discuss what is possible in their environment. – Sven♦ yesterday
3  
If you are really interested why removing python wiped your system, try installing this particular linux distro - LFS - after you finish, most of your questions about linux would be answered... – Anubioz yesterday
2  
@RussellBorogove: I don't say either of this. yum works by walking down the dependency graph and it removes packages until all dependencies are satisfied. If package A depends on package B and package B depends on package C, yum will also remove package B and in turn, package A to satisfy all dependencies if you try to remove package C. For central packages (like python), this can result in a large number of removed packages that are seemingly unrelated. – Sven♦ 19 hours ago
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@RussellBorogove: Yes, exactly, although coreutils doesn't depend on python directly in CentOS 5, but via one or more intermediate packages - the result is the same though: Removal. – Sven♦ 18 hours ago
up vote 11 down vote

I'm sincerely sorry: I can feel the pain to have a server unbootable/unserviceable.

However, I'm lost when reading that:

After that it asked me something about removing dependencies and it looked like nothing I could miss so I clicked [Y]

The list of to-be-removed packages surely was really huge, as python is an essential part of RHEL/CentOS. You should never confirm some warning message you don't really understand.

The best thing you can do, as already suggested, is to boot via a recovery media (ie: livecd), extract the required data files, and reinstall your machine with a newer CentOS release (and as CentOS 6 is quite old, I strongly suggest you to rebase on CentOS 7).

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up vote 6 down vote

How could this happen? Well, quite simple: By removing parts that were critical to your server.

Next steps for you: re-deploy a fresh OS and restore your data from backups.

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Uninstalling a package should never ever remove data. There really shouldn't be a need to restore anything, unless some package maintainer royally screwed up. – Jörg W Mittag 23 hours ago
    
If the OP restores a fresh OS like I recommended, restoration of data and configuration will most assuredly be required. – EEAA♦ 23 hours ago
up vote 4 down vote

You did something without fully understanding the consequences

That install is irrecoverable, would require a lot of work to reinstall centos5. And that is a bad plan because

  1. CentOS 5 is End of Life, and therefore has no updates. This is extra serious given it sounds like a webserver serving content on the public internet and that you use panel apps to control it.
  2. CentOS >5 would have stopped you from doing this update and killing the box. That's a nice airbag to have.
  3. CentOS 7 claims to support major version upgrades in place. I've never used it, but being able to jump from 7 to 8 when it releases will be very good. Debian's had this since forever, but Redhat always required a reinstall for major version jumps.

Solution

Your best bet is to create a new VPS, fresh install CentOS7, and then reattached the old centos5 disk volume and mount it read-only. Then work to copy (not move) your data from the old drive to the new.

Note this would be my method using AWS. If your VPS provider can't attach disks to different VMs then you'll have to tweak the plan.

No matter what you do, please consider setting up automated backups in the future. It wouldn't save you, but it would make recovery somewhat more flexible. Right now you need the data on that disk in a new working server. Don't loose the existing disk.

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up vote 0 down vote

You can typically boot from the install media and then chroot to run commands or enter into the current install and recover files or perform a reinstall of packages.

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3  
You won't be able to chroot into a root directory with no useful binaries in /usr/bin, etc. It would give the same result as booting into the dead system. Chroot also isn't necessary because once you have the filesystem mounted, you can copy out the files that you want to rescue from /var/www. – qris 23 hours ago
    
Definitely true, I'm recalling installing Gentoo/Arch where there are usually some useful binaries available. I've never uninstalled everything first. ;) – dragon788 21 hours ago
up vote 0 down vote

Upon reboot it will read your directories but without python and the other listed packages it will not read the full files. Most of what you see in the tree would be seen as blank files now. Since it has no way to process the info in said files. Good luck my friend.

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