Description of problem: During textbased installation of Fedora Core 6, there's an error: rpmdb: PANIC: fatal region error detected; run recovery - further details at the attached screenshot. Version-Release number of selected component (if applicable): anaconda-11.1.1.3-1 rpm-4.4.2-32 How reproducible: Everytime without doing something special, but I'm absolutely not able to figger out why... Actual results: rpmdb: PANIC: fatal region error detected; run recovery Expected results: Simply a working installation, not more and not less :)
Created attachment 139161 [details] Screenshot
Are there any messages on tty3 and tty4 can you go into tty2 and grab the logs under /tmp and /mnt/sysimage.
If I could reproduce it now again, I would be happy. Looks like system gets out of memory (192 MB RAM), but I'm not sure.
Running out of resources would explain a lot.
I had the same problem upgrading FC5 to FC6 on an HP Pavilion n5430 notebook (AMD Duron 850MHz, 128MB RAM). The "free" command showed plenty of swap unused, so I think memory was not the issue. I don't have the logs any more, but the upgrade log was 50MB at one point.
Created attachment 140057 [details] anaconda install.log this is the log file from my last install attempt. I could boot this system if I added selinux=0 to the boot prompt using grub to edit the boot line.
I've had possibly this problem upgrading from fed5 and installing fresh, text mode and gui, local cd and http, dhcp and static ip, autopartion LVM and manual partition and every time it failed. Tried nolapic etc and selinux=0. The failure varies but the most common way is for it to halt while installing a package. Sometimes tty0 shows "db4 error..." sometimes not but I think it could be grinding too hard to update tty0 in these cases. The system sometimes seems to lock up and needs a hard reset (no mouse of kbrd response) but most often will respond to ctrl+alt+bksp (in X) or ctl+alt+del. Top shows anaconda using 98 to 100% cpu. I left this overnight once and it was the same in the morning. Intel(R) Pentium(R) 4 CPU 2.00GHz 256meg Mem. I re-installed fedora 5 to check the box and it still installs fine.
I have the some on an "IBM ThinkPad T23". However, I am not affected by this issue at install time but rather -afterwards- when I try to install additional packages. This happens even in single user mode by a mere "rpm -i ..." command but not necessarily immediately but after an a priori number of packages. When this happens, the system freezes completely during the transaction. It has to be powered off by hand. If the packages were additional ones, the last package may be corrupted, may be not. If packages were scheduled to be updated, both packages versions are then displayed when one queries for the name of the package. After a certain number of incidents of this kind, one finally reads: rpmdb: PANIC: fatal region error detected; run recovery error: db4 error(-30977) from dbenv->open: DB_RUNRECOVERY: Fatal error, run database recovery error: cannot open Packages index using db3 - (-30977) error: cannot open Packages database in /var/lib/rpm It is impossible to carry out any "rpm" action from now on. The system thus needs a complete reinstall. This bug is really nasty. The issue occurred with "FC6" and current "rawhide". After reverting the system to "FC5" [plus updates or not] nothing similar ever happens. The priority should be set to "high" or even "urgent" as this issue makes "FC6/rawhide" essentially unusable.
Joachim, how many RAM do you have?
(In reply to comment #9) The amount of system memory is 512 MB. "SELinux" is enabled but set to "permissive" mode.
Instead of reinstalling, you might try to fix the existing database as suggested in the error message. 0) Save a copy of existing database. cd /var/lib tar czvf rpmdb.tar.gz ./rpm 1) Verify the contents of Packages. cd /var/lib/rpm /usr/lib/rpm/rpmdb_verify Packages 2) If there are problems, then dump and load to recover what can be salvaged. cd /var/lib/rpm mv Packages Packages-ORIG /usr/lib/rpm/rpmdb_dump Packages-ORIG | \ /usr/lib/rpm/rpmdb_laod Packages 3) Rebuild the indices. rpm --rebuilddb -vv
(In reply to comment #11) As matter of fact, I'm using current "rawhide" again, and 2 hours ago, I had the same trouble again [rpmdb: PANIC: ...] when installing today's and yesterday's updates. Interestingly, after rebooting the system, "rpm" commands were available again. To be on the safe side, I ran an "rpm --rebuilddb" [before reading your post], and step by step, I installed all packages again [using the "--force" option to remove remaining old packages]. I have experienced no problems during this 200 MB install. There was an "rpm" update, but it remains to be seen, if this has had some impact.
The rawhide rpm update fixes a segfault and is unrelated to your problem. Be careful with --rebuilddb, make sure you do rm -f /var/lib/rpm/__db* first, or a corrupted cache can do more damage than good. Reinstalling all packages with --force is unnecessary imho. Will neither hurt nor help. Try running rpm -Va instead. What version of glibc and kernel are installed? My guess is that there's something different with your machines, as a rpmdb PANIC is a very loud signal, and is clearly not happening everywhere. The underlying common mechanism is NPTL, used by rpmdb for locking, supplied by kernel/glibc.
(In reply to comment #13) Hm, I actually did not remove the '__db*' files, but this doesn't seem to have done any harm. I haven't had any problems since then. Reinstalling packages with "--force" had been used to remove the obsolete duplicates from the data base ['rpm -e name-old.rpm' would have probably done the job, too] after the system had got frozen in midst of an "RPM" transaction, and to reinstall corrupted packages as indicated by "rpm -V new.rpm' [usually the last one]. My system is a current "rawhide" system: kernel-2.6.18-1.2798.fc6, glibc-2.5.90-3. I recall: the issue also appeared immediately after a fresh "FC6" install.
I'm curious wether the problem is related to the RPM delivered with Fedora Core 6, because I'm running Fedora Core 6 equivalent systems with RPM 4.4.7/ 4.4.8-devel on different machines and I'm not able to reproduce the problem independent of what I'm trying to do. Somebody of the people here willing or interested to try a patched (and thus Fedora compatible) RPM 4.4.7/4.4.8-devel at a installed "broken" Fedora Core 6 system? Feel free to contact me via e-mail...
I'm seeing the rpm PANIC problem too on a laptop upgraded from FC5 to FC6. No problems during the upgrade itself, only after when installing updates. I did a --rebuilddb and it seemed OK for a while, then yum started to hang again and rpm --rebuilddb PANICed. A reboot seems to have cleared the problem, at least temporarily. I had been monitoring the CPU temperature and it was well within safe range before the PANIC. Smartctl testing shows no errors with the drive. Memtest86 is clean. glibc-2.5-3 kernel-2.6.18-1.2786.fc6 (the i686 version, forceably replacing i586) 256M RAM, 458744k swap, GBs free on /
I seem to be having this problem on my newly installed FC6 box also. I had no problems running rpm on my FC5 install. I have a generically built AMD box that has been running some version of Linux (both FC and Ubuntu) without complaint since we got it three years ago. I can provide additional details if you tell me the commands, since it has been a while since I had to check out hardware details. I am willing to run a patched version of rpm if it would help solve the problem. I am getting awfully tired of running "rm -rf __*; rpm --rebuilddb".
I have been able to trigger system freezes also by unpacking a bzip2 compressed tar file of about 35 MB [in single user mode]. It took me a couple of trials to extract the file completely. I am thus wondering if the issue is not related to a generic file I/O issue. There have been issues with the 2.6.18 kernel, e.g. bug 209005. According to comment #13, it might be related to a thread issue with the C library or the kernel.
Today, I have reinstalled my "rawhide" system from scratch. After booting into single user mode, I tried to install "kernel-2.6.18-1.2835.fc6" from "updates/testing/6". The system froze three times consecutively. Only after *disabling* hard disk "DMA", the installation completed successfully. This observation may point to the root of the issue. After rebooting the system, "kernel-2.6.18-1.2835.fc6" turned out to be a huge improvement. I have been able to install a huge number of additional "RPM" packages without any problem. I strongly recommend all affected users to retrieve and to install this new "FC6" testing kernel "RPM"!
After 3 days of usage without any glitch, "kernel-2.6.18-1.2835.fc6" can be considered to settle the issue for me completely.
Annoying: random freezes again with "kernel-2.6.18-1.2849.fc6".
Freezes? Panics? What was running? rpm runs with signals masked, so the annoyance is usually from having to get your terminal back. Try ^Z suspend and then kill -9 whatever process. Remember that you need to do "rm -f /var/lib/rpm/__db*" after *every* exceptional even, like "kill -9", segfaults, reboots, ENOSPC, EIO, etc, etc.
The whole system freezes including "X". In text mode, no reaction to keyboard input anymore. The issue can be triggered by increasing disk I/O e.g. installing packages, creating "tar" files, but this can of course happen at any time given the regular disk I/O traffic by the OS.
*** This bug has been marked as a duplicate of 181363 ***
Tell the kernel debutantes, not me, please.