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Tuesday, September 24, 2019  11:12 PM

Yum and "Thread died in Berkeley DB library" errors

I started getting intermittent sets of error messages like this:

error: rpmdb: BDB0113 Thread/process 26154/140393252489024 failed: BDB1507 Thread died in Berkeley DB library
error: db5 error(-30973) from dbenv->failchk: BDB0087 DB_RUNRECOVERY: Fatal error, run database recovery
error: cannot open Packages index using db5 -  (-30973)
error: cannot open Packages database in /var/lib/rpm

when deploying changes to a bunch of AWS EC2 instances.

The error messages are misleading as (in this case at least) the RPM database is not corrupted; the underlying issue was this:


[67897.740241] Out of memory: Kill process 28759 (yum) score 330 or sacrifice child
[67905.749492] yum invoked oom-killer: gfp_mask=0x201da, order=0, oom_score_adj=0

i.e. simply a lack of memory (the instances were just too small).


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The Prometheus PostgreSQL storage adapter does not seem amenable to being executed directly from a systemd service file.

As a workaround I created a wrapper script like this (adjust parameters as required):

#!/bin/bash

# Wrapper to launch prometheus-postgresql-adapter, as calling
# it directly from the systemd service file doesn't seem to work.
#
# Disclaimer: there is probably a better way of doing this.

nohup /usr/local/bin/prometheus-postgresql-adapter \
-pg-host=... \
-pg-port=... \
-pg-database="..." \
-pg-user="..." \
>> /var/log/prometheus-postgresql-storage-adapter/prometheus-pg-adapter.log 2>&1

and a service file like this:

[Unit]
Description=Prometheus PostgreSQL Storage Adapter
Documentation=https://github.com/timescale/prometheus-postgresql-adapter
Wants=network-online.target
After=network-online.target

[Service]
Type=simple
User=prometheus
Group=prometheus
ExecStart=/usr/local/bin/prometheus-postgresql-adapter-wrapper
Restart=on-failure

[Install]
WantedBy=multi-user.target

which works fine (YMMV of course).

There may of course be a more elegant way of solving this issue, if so feel free to share.


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Monday, May 30, 2016   9:54 PM

Forcing GPG passphrase input in the terminal

One annoyance when entering GPG passphrases in terminal applications on many systems is that a seperate GUI window pops up. To enable passphrase entry in the comfort of your own terminal, set the following line in .gnupg/gpg-agent.conf

pinentry-program /usr/bin/pinentry-curses


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Sunday, February 22, 2015   5:44 AM

openSUSE 13.2 - Notes


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Sunday, February 16, 2014   8:39 AM

OpenSUSE / Samba: "Invalid key 0 given to dptr_close" error

After upgrading to openSUSE 13.1, the Samba configuration - which I use mainly to share a directory on my workstation-cum-fileserver to a media player on the local network - mysteriously failed to work as expected. The client could mount, but not see, any directories or files. The only vaguely relevant clue appeared to be this entry in /var/log/samba/log.smbd:

Invalid key 0 given to dptr_close

After much head-scratching, it turns out AppArmor is enabled by default on openSUSE 13.1 and was the source of the error. Resolving the issue with AppArmor brought Samba back to life.


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Tuesday, February 11, 2014   1:53 AM

VirtualBox on openSUSE 13.1

I made the mistake of installing VirtualBox from the openSUSE repository, and after much pain trying to troubleshoot the error "This usually means that the vboxdrv module is not loaded. Try again after loading the module" (which pops up every time a virtual machine is launched), I remember the least painful way to install VirtualBox on openSUSE is to follow these instructions, adjusting the version numbers (both for openSUSE and for VirtualBox) accordingly.

As of the time of writing, download.virtualbox.org doesn't provide packages for openSUSE 13.1, however the packages for 12.3 installed just fine and seems to work so far using some pre-existing images, including different Windows versions.

Note: this issue appears to have gone away in OpenSUSE 13.2.


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