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Troubleshooting Unix / Linux Servers

Troubleshooting tips about Linux, *BSD, UNIX, Apple OS X, programming and MS-Windows servers and desktop systems ( rss feed ).

I am using a CentOS Linux v6.5 on my home server and I am getting the following error when I execute yum command:

rpmdb: PANIC: fatal region error detected; run recovery
error: db3 error(-30974) from dbenv->open: DB_RUNRECOVERY: Fatal error, run database recovery
error: cannot open Packages index using db3 - (-30974)
error: cannot open Packages database in /var/lib/rpm
CRITICAL:yum.main:

Error: rpmdb open failed

How do I fix this problem on a CentOS / RHEL based system?
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I mount /tmp with nodev, nosuid, and noexec options to increase the security of my Linux based web server. And, whenever I ran apt-get install or apt-get upgrade command, I am getting the following error:

apt-get install linux-generic linux-headers-generic linux-image-generic
.....
....
..
Generating grub.cfg ...
Found linux image: /boot/vmlinuz-3.2.0-43-generic
Found initrd image: /boot/initrd.img-3.2.0-43-generic
....
ldconfig deferred processing now taking place
Processing triggers for initramfs-tools ...
update-initramfs: Generating /boot/initrd.img-3.2.0-43-generic
W: TMPDIR is mounted noexec, will not cache run scripts.
....
...

How do I fix this problem without compromising security of the data or web-server?
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I recently added SSD to my home server and reloaded the operating system. However, when I try to access my dm-crypt based old disk, I am getting the following error:

Reading all physical volumes. This may take a while...
WARNING: Duplicate VG name server01: Existing bc7YA8-eEXt-1aA1-OHTr-zJkA-ucd0-DsbRTc (created here) takes precedence over RIKiar-w3MG-Gzh5-VFWq-bkRT-9IFc-ia8k87
WARNING: Duplicate VG name server01: Existing bc7YA8-eEXt-1aA1-OHTr-zJkA-ucd0-DsbRTc (created here) takes precedence over RIKiar-w3MG-Gzh5-VFWq-bkRT-9IFc-ia8k87
Found volume group "server01" using metadata type lvm2
Found volume group "server01" using metadata type lvm2

Tutorial details
DifficultyAdvanced (rss)
Root privilegesYes
RequirementsLVM2+dm-crypt
Estimated completion timeN/A

The problem is my volume group. I set to to server01 on both old and new hard disk. How can I rename old LVM2? How do I access my old hard disk?
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How do I match dot files under Unix / Linux using bash shell? Why .* considered as harmful when matching dot files under bash shell?
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I have the following message whenever I use the apt-get command under Debian or Ubuntu Linux:

The following packages were automatically installed and are no longer required:
libaccess-bridge-java libjs-mochikit python-cheetah libjs-excanvas
libaccess-bridge-java-jni sabnzbdplus-theme-smpl tzdata-java
ca-certificates-java
Use 'apt-get autoremove' to remove them.
0 upgraded, 0 newly installed, 0 to remove and 4 not upgraded.

Tutorial details
DifficultyEasy (rss)
Root privilegesYes
Requirementsapt-get
Estimated completion timeN/A
How do I fix this issue? Is it safe to remove all unwanted packages?
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I run a BT client and few other server program on Linux. Sometime these programs get overloaded with too many connections and crashes. If I restart my apps, I see lots of old IPs in a TIME_WAIT state. How do I force and and close everything in a TIME_WAIT state under Linux operating systems?
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I'm setting up server on an Amazon EC2 compute instance powered by Suse Enterprise Linux server. I am using the following command to login into the my EC2 compute from OS X/Ubuntu desktop:

ssh -i suse-ec2-server-jp.pem root@ec2-xx-yy-zzz-yyy.compute-1.amazonaws.com

I am getting the following error:
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
@ WARNING: UNPROTECTED PRIVATE KEY FILE! @
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
Permissions 0440 for 'suse-ec2-server-jp.pem' are too open.
It is recommended that your private key files are NOT accessible by others.
This private key will be ignored.
bad permissions: ignore key: suse-ec2-server-jp.pem
Password:

How do I fix this problem and login using ssh command?
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