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I run a number of CentOS servers. I was recently doing the occasional yum update but this failed on a handful of the servers. On most I have been able to move forward by doing:

# yum clean all
# rm -f /var/lib/rpm/__db*
# rpm --rebuilddb
# yum update

However on one server, the yum clean command hangs. I have tried running:

# yum -v --noplugins clean all

but I get no output at all. Yum just hangs, and will sit there for hours if I let it, not using any cpu, just stopped. Doing

# strace -f yum -v --noplugins clean all

produces quite a lot of output, but then stops with:

...
stat64("/var/lib/rpm/__db.003", {st_mode=S_IFREG|0644, st_size=450560, ...}) = 0
open("/var/lib/rpm/__db.003", O_RDWR|O_LARGEFILE) = 4
fcntl64(4, F_SETFD, FD_CLOEXEC)         = 0
mmap2(NULL, 450560, PROT_READ|PROT_WRITE, MAP_SHARED, 4, 0) = 0xb6b34000
close(4)                                = 0
stat64("/var/lib/rpm/Packages", {st_mode=S_IFREG|0644, st_size=14938112, ...}) = 0
open("/var/lib/rpm/Packages", O_RDONLY|O_LARGEFILE) = 4
fcntl64(4, F_SETFD, FD_CLOEXEC)         = 0
read(4, "\0\0\0\0\1\0\0\0\0\0\0\0a\25\6\0\10\0\0\0\0\20\0\0\0\10\0\0k\t\0\0"..., 512) = 5
12
close(4)                                = 0
open("/var/lib/rpm/Packages", O_RDONLY|O_LARGEFILE) = 4
fcntl64(4, F_SETFD, FD_CLOEXEC)         = 0
fstat64(4, {st_mode=S_IFREG|0644, st_size=14938112, ...}) = 0
futex(0xb6b7bd1c, FUTEX_WAIT, 1, NULL

At this point I'm feeling stuck. This is a production server, so I don't want to just blow it away, or even blow away all the yum information. Apart from the yum stuff, the server is working fine.

Itai Ganot
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Hamish Downer
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  • What does `lsof` reveal, if anything? – Janne Pikkarainen May 25 '12 at 11:21
  • @JannePikkarainen - `lsof /var/lib/rpm/Packages` originally showed an old rpm process. I've killed that, and my yum, checked that `lsof` didn't show anything else accessing the file, and tried again, but I stop at the same place. I've also scanned through the full `lsof` output and not seen anything that looks likely. – Hamish Downer May 25 '12 at 12:56
  • Also, I can open the file `/var/lib/rpm/Packages` for reading in another application. – Hamish Downer May 25 '12 at 12:59
  • Does the server have access to outside world? Yes, I know, yum is not supposed to contact the net that soon, but ... – Janne Pikkarainen May 25 '12 at 13:06
  • @JannePikkarainen - yes there is network access. I can ssh into and out of it, and ping other servers. I can load web pages in lynx. – Hamish Downer May 25 '12 at 13:29
  • need output: rpm -qa|grep yum – GioMac Jul 31 '12 at 14:18
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    Try doing the `yum clean all` along with `yum update` after rebuilding the databases (`rm -f /var/lib/rpm/__db*` and `rpm --rebuilddb`) instead of before. – Brian Jul 12 '15 at 21:33
  • do you have any nfs mounted filesystems that are currently hung? – Tom May 25 '12 at 11:15
  • There is a single root fs (with plenty of space) and then just proc, sysfs and tmpfs (and tmpfs has plenty of space). – Hamish Downer May 25 '12 at 12:46

5 Answers5

13

I had the same problem, all my yum commands were hanging.

I ran the following commands

rm /var/lib/rpm/__db*
rm /var/lib/rpm/.rpm.lock
rm /var/lib/rpm/.dbenv.lock

So a combination of some of the above comments and answers.

Community
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Mz A
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  • Brilliant! This worked like a charm for me! I saw the other superuser thread regarding a similar issue, but it turns out the locks were what were freezing it for me. Appreciate this greatly! https://superuser.com/questions/384963/yum-hangs-and-wont-respond – David Morton Jul 18 '19 at 13:10
  • second command helped me in centos – Lkbhai Lr Mar 30 '21 at 04:05
4

On my Redhat 7.2 this helps to let run the yum commands. 

 rm /var/lib/rpm/.dbenv.lock
Sven Kirsten
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    This corrupted my `yum` installation, but then running `sudo rpm --rebuilddb && yum clean all` did the trick. – dimiguel Mar 23 '19 at 03:51
1

In my case, I had all but one server with

[main]
enabled=1

in

/etc/yum/pluginconf.d/subscription-manager.conf

Setting this to enabled=0 fixed my issue.

mforsetti
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Mike D
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1

This is not a direct answer, but if none of the commands from the other answers helped then I'd check the command package-cleanup.

All the proposed commands are for handling the RPM database, but it could be that there's something broken in the relation of some installed packages.

From man package-cleanup:

DESCRIPTION
       package-cleanup is a program for cleaning up the locally-installed RPMs.
EXAMPLES
       List all dependency problems:
              package-cleanup --problems

       List all packages that are not in any Yum repository:
              package-cleanup --orphans

I'd start with the command in the second example, I've used it before and it solved some weird issues I had in one of my CentOS machines which was related to yum clean.

Itai Ganot
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0

All of the above but also:

ps -ef | grep yum # kill off all yum processes
ps -ef | grep rpm # kill off rpm processes

I couldn't get any of the above to work until I did this.

Credit to: https://cloudlinux.zendesk.com/hc/en-us/articles/115004580385-If-RPM-or-yum-processes-hangs

Gerald Schneider
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Mr Tony Payne
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