Posts Tagged ‘lib’

Reinstall all Debian packages with a copy of apt deb package list from another working Debian Linux installation

Wednesday, July 29th, 2020

Reinstall-all-Debian-packages-with-copy-of-apt-packages-list-from-another-working-Debian-Linux-installation

Few days ago, in the hurry in the small hours of the night, I've done something extremely stupid. Wanting to move out a .tar.gz binary copy of qmail installation to /var/lib/qmail with all the dependent qmail items instead of extracting to admin user /root directory (/root), I've extracted it to the main Operating system root / directrory.
Not noticing this, I've quickly executed rm -rf var with the idea to delete all directory tree under /root/var just 3 seconds later, I've realized I'm issuing the rm -rf var with the wrong location WITH a root user !!!! Being scared on what I've done, I've quickly pressed CTRL+C to immedately cancel the deletion operation of my /var.

wrong-system-var-rm-linux-dont-do-that-ever-or-your-system-will-end-up-irreversably-damaged

But as you can guess, since the machine has an Slid State Drive drive and SSD memory drive are much more faster in I/O operations than the classical ATA / SATA disks. I was not quick enough to cancel the operation and I've noticed already some part of my /var have been R.I.P-pped in the heaven of directories.

This was ofcourse upsetting so for a while I rethinked the situation to get some ideas on what I can do to recover my system ASAP!!! and I had the idea of course to try to reinstall All my installed .deb debian packages to restore system closest to the normal, before my stupid mistake.

Guess my unpleasent suprise when I have realized dpkg and respectively apt-get apt and aptitude package management tools cannot anymore handle packages as Debian Linux's package dependency database has been damaged due to missing dpkg directory 

/var/lib/dpkg 

Oh man that was unpleasent, especially since I've installed plenty of stuff that is custom on my Mate based desktop and, generally reinstalling it updating the sytem to the latest Debian security updates etc. will be time consuming and painful process I wanted to omit.

So of course the logical thing to do here was to try to somehow recover somehow a database copy of /var/lib/dpkg  if that was possible, that of course led me to the idea to lookup for a way to recover my /var/lib/dpkg from backup but since I did not maintained any backup copy of my OS anywhere that was not really possible, so anyways I wondered whether dpkg does not keep some kind of database backups somewhere in case if something goes wrong with its database.
This led me to this nice Ubuntu thred which has pointed me to the part of my root rm -rf dpkg db disaster recovery solution.
Luckily .deb package management creators has thought about situation similar to mine and to give the user a restore point for /var/lib/dpkg damaged database

/var/lib/dpkg is periodically backed up in /var/backups

A typical /var/lib/dpkg on Ubuntu and Debian Linux looks like so:
 

hipo@jeremiah:/var/backups$ ls -l /var/lib/dpkg
total 12572
drwxr-xr-x 2 root root    4096 Jul 26 03:22 alternatives
-rw-r–r– 1 root root      11 Oct 14  2017 arch
-rw-r–r– 1 root root 2199402 Jul 25 20:04 available
-rw-r–r– 1 root root 2199402 Oct 19  2017 available-old
-rw-r–r– 1 root root       8 Sep  6  2012 cmethopt
-rw-r–r– 1 root root    1337 Jul 26 01:39 diversions
-rw-r–r– 1 root root    1223 Jul 26 01:39 diversions-old
drwxr-xr-x 2 root root  679936 Jul 28 14:17 info
-rw-r—– 1 root root       0 Jul 28 14:17 lock
-rw-r—– 1 root root       0 Jul 26 03:00 lock-frontend
drwxr-xr-x 2 root root    4096 Sep 17  2012 parts
-rw-r–r– 1 root root    1011 Jul 25 23:59 statoverride
-rw-r–r– 1 root root     965 Jul 25 23:59 statoverride-old
-rw-r–r– 1 root root 3873710 Jul 28 14:17 status
-rw-r–r– 1 root root 3873712 Jul 28 14:17 status-old
drwxr-xr-x 2 root root    4096 Jul 26 03:22 triggers
drwxr-xr-x 2 root root    4096 Jul 28 14:17 updates

Before proceeding with this radical stuff to move out /var/lib/dpkg/info from another machine to /var mistakenyl removed oned. I have tried to recover with the well known:

  • extundelete
  • foremost
  • recover
  • ext4magic
  • ext3grep
  • gddrescue
  • ddrescue
  • myrescue
  • testdisk
  • photorec

Linux file deletion recovery tools from a USB stick loaded with a Number of LiveCD distributions, i.e. tested recovery with:

  • Debian LiveCD
  • Ubuntu LiveCD
  • KNOPPIX
  • SystemRescueCD
  • Trinity Rescue Kit
  • Ultimate Boot CD


but unfortunately none of them couldn't recover the deleted files … 

The reason why the standard file recovery tools could not recover ?

My assumptions is after I've done by rm -rf var; from sysroot,  issued the sync (- if you haven't used it check out man sync) command – that synchronizes cached writes to persistent storage and did a restart from the poweroff PC button, this should have worked, as I've recovered like that in the past) in a normal Sys V System with a normal old fashioned blocks filesystem as EXT2 . or any other of the filesystems without a journal, however as the machine run a EXT4 filesystem with a journald and journald, this did not work perhaps because something was not updated properly in /lib/systemd/systemd-journal, that led to the situation all recently deleted files were totally unrecoverable.

1. First step was to restore the directory skele of /var/lib/dpkg

# mkdir -p /var/lib/dpkg/{alternatives,info,parts,triggers,updates}

2. Recover missing /var/lib/dpkg/status  file

The main file that gives information to dpkg of the existing packages and their statuses on a Debian based systems is /var/lib/dpkg/status

# cp /var/backups/dpkg.status.0 /var/lib/dpkg/status

3. Reinstall dpkg package manager to make package management working again

Say a warm prayer to the Merciful God ! and do:

# apt-get download dpkg
# dpkg -i dpkg*.deb

4. Reinstall base-files .deb package which provides basis of a Debian system

Hopefully everything will be okay and your dpkg / apt pair will be in normal working state, next step is to:

# apt-get download base-files
# dpkg -i base-files*.deb

5. Do a package sanity and consistency check and try to update OS package list

Check whether packages have been installed only partially on your system or that have missing, wrong or obsolete control  data  or  files.  dpkg  should suggest what to do with them to get them fixed.

# dpkg –audit

Then resynchronize (fetch) the package index files from their sources described in /etc/apt/sources.list

# apt-get update


Do apt db constistency check:

#  apt-get check


check is a diagnostic tool; it updates the package cache and checks for broken dependencies.
 

Take a deep breath ! …

Do :

ls -l /var/lib/dpkg
and compare with the above list. If some -old file is not present don't worry it will be there tomorrow.

Next time don't forget to do a regular backup with simple rsync backup script or something like Bacula / Amanda / Time Vault or Clonezilla.
 

6. Copy dpkg database from another Linux system that has a working dpkg / apt Database

Well this was however not the end of the story … There were still many things missing from my /var/ and luckily I had another Debian 10 Buster install on another properly working machine with a similar set of .deb packages installed. Therefore to make most of my programs still working again I have copied over /var from the other similar set of package installed machine to my messed up machine with the missing deleted /var.

To do so …
On Functioning Debian 10 Machine (Working Host in a local network with IP 192.168.0.50), I've archived content of /var:

linux:~# tar -czvf var_backup_debian10.tar.gz /var

Then sftped from Working Host towards the /var deleted broken one in my case this machine's hostname is jericho and luckily still had SSHD and SFTP running processes loaded in memory:

jericho:~# sftp root@192.168.0.50
sftp> get var_backup_debian10.tar.gz

Now Before extracting the archive it is a good idea to make backup of old /var remains somewhere for example somewhere in /root 
just in case if we need to have a copy of the dpkg backup dir /var/backups

jericho:~# cp -rpfv /var /root/var_backup_damaged

 
jericho:~# tar -zxvf /root/var_backup_debian10.tar.gz 
jericho:/# mv /root/var/ /

Then to make my /var/lib/dpkg contain the list of packages from my my broken Linux install I have ovewritten /var/lib/dpkg with the files earlier backupped before  .tar.gz was extracted.

jericho:~# cp -rpfv /var /root/var_backup_damaged/lib/dpkg/ /var/lib/

7. Reinstall All Debian  Packages completely scripts

I then tried to reinstall each and every package first using aptitude with aptitude this is done with

# aptitude reinstall '~i'

However as this failed, tried using a simple shell loop like below:

for i in $(dpkg -l |awk '{ print $2 }'); do echo apt-get install –reinstall –yes $i; done

Alternatively, all .deb package reninstall is also possible with dpkg –get-selections and with awk with below cmds:

dpkg –get-selections | grep -v deinstall | awk '{print $1}' > list.log;
awk '$1=$1' ORS=' ' list.log > newlist.log
;
apt-get install –reinstall $(cat newlist.log)

It can also be run as one liner for simplicity:

dpkg –get-selections | grep -v deinstall | awk '{print $1}' > list.log; awk '$1=$1' ORS=' ' list.log > newlist.log; apt-get install –reinstall $(cat newlist.log)

This produced a lot of warning messages, reporting "package has no files currently installed" (virtually for all installed packages), indicating a severe packages problem below is sample output produced after each and every package reinstall … :

dpkg: warning: files list file for package 'iproute' missing; assuming package has no files currently installed
dpkg: warning: files list file for package 'brscan-skey' missing; assuming package has no files currently installed
dpkg: warning: files list file for package 'libapache2-mod-php7.4' missing; assuming package has no files currently installed
dpkg: warning: files list file for package 'libexpat1:amd64' missing; assuming package has no files currently installed
dpkg: warning: files list file for package 'libexpat1:i386' missing; assuming package has no files currently installed
dpkg: warning: files list file for package 'php5.6-readline' missing; assuming package has no files currently installed
dpkg: warning: files list file for package 'linux-headers-4.19.0-5-amd64' missing; assuming package has no files currently installed
dpkg: warning: files list file for package 'libgraphite2-3:amd64' missing; assuming package has no files currently installed
dpkg: warning: files list file for package 'libgraphite2-3:i386' missing; assuming package has no files currently installed
dpkg: warning: files list file for package 'libbonoboui2-0:amd64' missing; assuming package has no files currently installed
dpkg: warning: files list file for package 'libxcb-dri3-0:amd64' missing; assuming package has no files currently installed
dpkg: warning: files list file for package 'libxcb-dri3-0:i386' missing; assuming package has no files currently installed
dpkg: warning: files list file for package 'liblcms2-2:amd64' missing; assuming package has no files currently installed
dpkg: warning: files list file for package 'liblcms2-2:i386' missing; assuming package has no files currently installed
dpkg: warning: files list file for package 'libpixman-1-0:amd64' missing; assuming package has no files currently installed
dpkg: warning: files list file for package 'libpixman-1-0:i386' missing; assuming package has no files currently installed
dpkg: warning: files list file for package 'gksu' missing; assuming package has no files currently installed
dpkg: warning: files list file for package 'liblogging-stdlog0:amd64' missing; assuming package has no files currently installed
dpkg: warning: files list file for package 'mesa-vdpau-drivers:amd64' missing; assuming package has no files currently installed
dpkg: warning: files list file for package 'mesa-vdpau-drivers:i386' missing; assuming package has no files currently installed
dpkg: warning: files list file for package 'libzvbi0:amd64' missing; assuming package has no files currently installed
dpkg: warning: files list file for package 'libzvbi0:i386' missing; assuming package has no files currently installed
dpkg: warning: files list file for package 'libcdparanoia0:amd64' missing; assuming package has no files currently installed
dpkg: warning: files list file for package 'libcdparanoia0:i386' missing; assuming package has no files currently installed
dpkg: warning: files list file for package 'python-gconf' missing; assuming package has no files currently installed
dpkg: warning: files list file for package 'php5.6-cli' missing; assuming package has no files currently installed
dpkg: warning: files list file for package 'libpaper1:amd64' missing; assuming package has no files currently installed
dpkg: warning: files list file for package 'mixer.app' missing; assuming package has no files currently installed

After some attempts I found a way to be able to work around the warning message, for each package by simply reinstalling the package reporting the issue with

apt –reinstall $package_name


Though reinstallation started well and many packages got reinstalled, unfortunately some packages such as apache2-mod-php5.6 and other php related ones  started failing during reinstall ending up in unfixable states right after installation of binaries from packages was successfully placed in its expected locations on disk. The failures occured during the package setup stage ( dpkg –configure $packagename) …

The logical thing to do is a recovery attempt with something like the usual well known by any Debian admin:

apt-get install –fix-missing

As well as Manual requesting to reconfigure (issue re-setup) of all installed packages also did not produced a positive result

dpkg –configure -a

But many packages were still failing due to dpkg inability to execute some post installation scripts from respective .deb files.
To work around that and continue installing the rest of packages I had to manually delete all files related to the failing package located under directory 

/var/lib/dpkg/info#

For example to omit the post installation failure of libapache2-mod-php5.6 and have a succesful install of the package next time I tried reinstall, I had to delete all /var/lib/dpkg/info/libapache2-mod-php5.6.postrm, /var/lib/dpkg/info/libapache2-mod-php5.6.postinst scripts and even sometimes everything like libapache2-mod-php5.6* that were present in /var/lib/dpkg/info dir.

The problem with this solution, however was the package reporting to install properly, but the post install script hooks were still not in placed and important things as setting permissions of binaries after install or applying some configuration changes right after install was missing leading to programs failing to  fully behave properly or even breaking up even though showing as finely installed …

The final solution to this problem was radical.
I've used /var/lib/dpkg database (directory) from ther other working Linux machine with dpkg DB OK found in var_backup_debian10.tar.gz (linux:~# host with a working dpkg database) and then based on the dpkg package list correct database responding on jericho:~# to reinstall each and every package on the system using Debian System Reinstaller script taken from the internet.
Debian System Reinstaller works but to reinstall many packages, I've been prompted again and again whether to overwrite configuration or keep the present one of packages.
To Omit the annoying [Y / N ] text prompts I had made a slight modification to the script so it finally looked like this:
 

#!/bin/bash
# Debian System Reinstaller
# Copyright (C) 2015 Albert Huang
# Copyright (C) 2018 Andreas Fendt

# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.

# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.

# You should have received a copy of the GNU General Public License
# along with this program.  If not, see <http://www.gnu.org/licenses/>.

# —
# This script assumes you are using a Debian based system
# (Debian, Mint, Ubuntu, #!), and have sudo installed. If you don't
# have sudo installed, replace "sudo" with "su -c" instead.

pkgs=`dpkg –get-selections | grep -w 'install$' | cut -f 1 |  egrep -v '(dpkg|apt)'`

for pkg in $pkgs; do
    echo -e "\033[1m   * Reinstalling:\033[0m $pkg"    

    apt-get –reinstall -o Dpkg::Options::="–force-confdef" -o Dpkg::Options::="–force-confold" -y install $pkg || {
        echo "ERROR: Reinstallation failed. See reinstall.log for details."
        exit 1
    }
done

 

 debian-all-packages-reinstall.sh working modified version of Albert Huang and Andreas Fendt script  can be also downloaded here.

Note ! Omitting the text confirmation prompts to install newest config or keep maintainer configuration is handled by the argument:

-o Dpkg::Options::="–force-confold


I however still got few NCurses Console selection prompts during the reinstall of about 3200+ .deb packages, so even with this mod the reinstall was not completely automatic.

Note !  During the reinstall few of the packages from the list failed due to being some old unsupported packages this was ejabberd, ircd-hybrid and a 2 / 3 more.
This failure was easily solved by completely purging those packages with the usual

# dpkg –purge $packagename

and reruninng  debian-all-packages-reinstall.sh on each of the failing packages.

Note ! The failing packages were just old ones left over from Debian 8 and Debian 9 before the apt-get dist-upgrade towards 10 Duster.
Eventually I got a success by God's grance, after few hours of pains and trials, ending up in a working state package database and a complete set of freshly reinstalled packages.

The only thing I had to do finally is 2 hours of tampering why GNOME did not automatically booted after the system reboot due to failing gdm
until I fixed that I've temprary used ligthdm (x-display-manager), to do I've

dpkg –reconfigure gdm3

lightdm-x-display-manager-screenshot-gdm3-reconfige

 to work around this I had to also reinstall few libraries, reinstall the xorg-server, reinstall gdm and reinstall the meta package for GNOME, using below set of commands:
 

apt-get install –reinstall libglw1-mesa libglx-mesa0
apt-get install –reinstall libglu1-mesa-dev
apt install –reinstallgsettings-desktop-schemas
apt-get install –reinstall xserver-xorg-video-intel
apt-get install –reinstall xserver-xorg
apt-get install –reinstall xserver-xorg-core
apt-get install –reinstall task-desktop
apt-get install –reinstall task-gnome-desktop

As some packages did not ended re-instaled on system because on the original host from where /var/lib/dpkg db was copied did not have it I had to eventually manually trigger reinstall for those too:

apt-get install –reinstall –yes vlc
apt-get install –reinstall –yes thunderbird
apt-get install –reinstall –yes audacity
apt-get install –reinstall –yes gajim
apt-get install –reinstall –yes slack remmina
apt-get install –yes k3b
pt-get install –yes gbgoffice
pt-get install –reinstall –yes skypeforlinux
apt-get install –reinstall –yes vlc
apt-get install –reinstall –yes libcurl3-gnutls libcurl3-nss
apt-get install –yes virtualbox-5.2
apt-get install –reinstall –yes vlc
apt-get install –reinstall –yes alsa-tools-gui
apt-get install –reinstall –yes gftp
apt install ./teamviewer_15.3.2682_amd64.deb –yes

Note that some of above packages requires a properly configured third party repositories, other people might have other packages that are missing from the dpkg list and needs to be reinstalled so just decide according to your own case of left aside working system present binaries that doesn't belong to any dpkg installed package.

After a bit of struggle everything is back to normal Thanks God! 🙂 !
 

Why du and df reporting different on a filesystem / How to fix inconsistency between used space on FS and disk showing full strangeness

Wednesday, July 24th, 2019

linux-why-du-and-df-shows-different-result-inconsincy-explained-filesystem-full-oddity

If you're a sysadmin on a large server environment such as a couple of hundred of Virtual Machines running Linux OS on either physical host or OpenXen / VmWare hosted guest Virtual Machine, you might end up sometimes at an odd case where some mounted partition mount point reports its file use different when checked with
df
cmd than when checked with du command, like for example:
 

root@sqlserver:~# df -hT /var/lib/mysql
Filesystem   Type  Size Used Avail Use% Mounted On
/dev/sdb5      ext4    19G  3,4G    14G  20% /var/lib/mysql

Here the '-T' argument is used to show us the filesystem.

root@sqlserver:~# du -hsc /var/lib/mysql
0K    /var/lib/mysql/
0K    total

1. Simple debug on what might be the root cause for df / du inconsistency reporting

Of course the basic thing to do when in that weird situation is to be totally shocked how this is possible and to investigate a bit what is the biggest first level sub-directories that eat up the space on the mounted location, with du:

# du -hkx –max-depth=1 /var/lib/mysql/|uniq|sort -n
4       /var/lib/mysql/test
8       /var/lib/mysql/ezmlm
8       /var/lib/mysql/micropcfreak
8       /var/lib/mysql/performance_schema
12      /var/lib/mysql/mysqltmp
24      /var/lib/mysql/speedtest
64      /var/lib/mysql/yourls
144     /var/lib/mysql/narf
320     /var/lib/mysql/webchat_plus
424     /var/lib/mysql/goodfaithair
528     /var/lib/mysql/moonman
648     /var/lib/mysql/daniel
852     /var/lib/mysql/lessn
1292    /var/lib/mysql/gallery

The given output is in Kilobytes so it is a little bit hard to read, if you're used to Mbytes instead, do

 # du -hmx –max-depth=1 /var/lib/mysql/|uniq|sort -n|less

I've also investigated on the complete /var directory contents sorted by size with:

 # du -akx ./ | sort -n
5152564    ./cache/rsnapshot/hourly.2/localhost
5255788    ./cache/rsnapshot/hourly.2
5287912    ./cache/rsnapshot
7192152    ./cache


Even after finding out the bottleneck dirs and trying to clear up a bit, continued facing that inconsistently shown in two commands and if you're likely to be stunned like me and try … to move some files to a different filesystem to free up space or assigned inodes with a hope that shown inconsitency output will be fixed as it might be caused  due to some kernel / FS caching ?? and this will eventually make the mounted FS to refresh …

But unfortunately, if you try it you'll figure out clearing up a couple of Megas or Gigas will make no difference in cmd output.

In my exact case /var/lib/mysql is a separate mounted ext4 filesystem, however same issue was present also on a Network Filesystem (NFS) and thus, my first thought that this is caused by a network failure problem or NFS bug turned to be wrong.

After further short investigation on the inodes on the Filesystem, it was clear enough inodes are available:
 

# df -i /var/lib/mysql
Filesystem       Inodes  IUsed   IFree IUse% Mounted on
/dev/sdb5      1221600  2562 1219038   1% /var/lib/mysql

So the filled inodes count assumed issue also has been rejected.
P.S. (if you're not well familiar with them read manual, i.e. – man 7 inode).
 

– Remounting the mounted filesystem

To make sure the filesystem shown inconsistency between du and df is not due to some hanging network mount or bug, first logical thing I did is to remount the filesytem showing different in size, in my case this was done with:
 

# mount -o remount,rw -t ext4 /var/lib/mysql

For machines with NFS remote mounted storage locations, used:

# mount -o remount,rw -t nfs /var/www


FS remount did not solved it so I continued to ponder what oddity and of course I thought of a workaround (in case if this issues are caused by kernel bug or OS lib issue) reboot might be the solution, however unfortunately restarting the VMs was not a wanted easy to do solution, thus I continued investigating what is wrong …

Next check of course was to check, what kind of network connections are opened to the affected hosts with:
 

# netstat -tupanl


Did not found anything that might point me to the reported different Megabytes issue, so next step was to check what is the situation with currently opened files by running processes on the weird df / du reported systems with lsof, and boom there I observed oddity such as multiple files

# lsof -nP | grep '(deleted)'

COMMAND   PID   USER   FD   TYPE DEVICE    SIZE NLINK  NODE NAME
mysqld   2588  mysql    4u   REG 253,17      52     0  1495 /var/lib/mysql/tmp/ibY0cXCd (deleted)
mysqld   2588  mysql    5u   REG 253,17    1048     0  1496 /var/lib/mysql/tmp/ibOrELhG (deleted)
mysqld   2588  mysql    6u   REG 253,17       777884290     0  1497 /var/lib/mysql/tmp/ibmDFAW8 (deleted)
mysqld   2588  mysql    7u   REG 253,17       123667875     0 11387 /var/lib/mysql/tmp/ib2CSACB (deleted)
mysqld   2588  mysql   11u   REG 253,17       123852406     0 11388 /var/lib/mysql/tmp/ibQpoZ94 (deleted)

Notice that There were plenty of '(deleted)' STATE files shown in memory an overall of 438:

# lsof -nP | grep '(deleted)' |wc -l
438


As I've learned a bit online about the problem, I found it is also possible to find deleted unlinked files only without any greps (to list all deleted files in memory files with lsof args only):

# lsof +L1|less


The SIZE field (fourth column)  shows a number of files that are really hard in size and that are kept in open on filesystem and in memory, totally messing up with the filesystem. In my case this is temp files created by MYSQLD daemon but depending on the server provided service this might be apache's www-data, some custom perl / bash script executed via a cron job, stalled rsync jobs etc.
 

2. Check all the list open files with the mysql / root user as part of the the server filesystem inconsistency debugging with:

– Grep opened files on server by user

# lsof |grep mysql
mysqld    1312                       mysql  cwd       DIR               8,21       4096          2 /var/lib/mysql
mysqld    1312                       mysql  rtd       DIR                8,1       4096          2 /
mysqld    1312                       mysql  txt       REG                8,1   20336792   23805048 /usr/sbin/mysqld
mysqld    1312                       mysql  mem       REG               8,21      24576         20 /var/lib/mysql/tc.log
mysqld    1312                       mysql  DEL       REG               0,16                 29467 /[aio]
mysqld    1312                       mysql  mem       REG                8,1      55792   14886933 /lib/x86_64-linux-gnu/libnss_files-2.28.so

# lsof | grep root
COMMAND    PID   TID TASKCMD          USER   FD      TYPE             DEVICE   SIZE/OFF       NODE NAME
systemd      1                        root  cwd       DIR                8,1       4096          2 /
systemd      1                        root  rtd       DIR                8,1       4096          2 /
systemd      1                        root  txt       REG                8,1    1489208   14928891 /lib/systemd/systemd
systemd      1                        root  mem       REG                8,1    1579448   14886924 /lib/x86_64-linux-gnu/libm-2.28.so

Other command that helped to track the discrepancy between df and du different file usage on FS is:
 

# du -hxa  / | egrep '^[[:digit:]]{1,1}G[[:space:]]*'
 

3. Fixing large files kept in memory filesystem problem


What is the real reason for ending up with this file handlers opened by running backgrounded programs on the Linux OS?
It could be multiple  but most likely it is due to exceeded server / client interactions or breaking up RAM or HDD drive with writing plenty of logs on the FS without ending keeping space occupied or Programming library bugs used by hanged service leaving the FH opened on storage.

What is the solution to file system files left in memory problem?

The best solution is to first fix custom script or hanged service and then if possible to simply restart the server to make the kernel / services reload or if this is not possible just restart the problem creation processes.

Once the process is identified like in my case this was MySQL on systemd enabled newer OS distros, just do:

# systemctl restart mysqld.service


or on older init.d system V ones:

# /etc/init.d/service restart


For custom hanged scripts being listed in ps axuwef you can grep the pid and do a kill -HUP (if the script is written in a good way to recognize -HUP and restart the sub-running process properly – BE EXTRA CAREFUL IF YOU'RE RESTARTING BROKEN SCRIPTS as this might cause your running service disruptions …).

# pgrep -l script.sh
7977 script.sh


# kill -HUP PID

Now finally this should either mitigate or at best case completely solve the reported disagreement between df and du, after which the calculated / reported disk space should be back to normal and show up approximately the same (note that size changes a bit as mysql service is writting data) constantly extending the size between the two checks.

# df -hk /var/lib/mysql; du -hskc /var/lib/mysql
Filesystem       Inodes  IUsed   IFree IUse% Mounted on
/dev/sdb5        19097172 3472744 14631296  20% /var/lib/mysql
3427772    /var/lib/mysql
3427772    total

What we learned?

What I've explained in this article is why and how it comes that 'zoombie' files reside on a filesystem
appearing to be eating disk space on a mounted local or network partition, giving strange inconsistent
reports, leading to system service disruptions and impossibility to have correctly shown information on used
disk space on mounted drive.

I went through with some standard logic on debugging service / filesystem / inode issues up explainat, that led me to the finding about deleted files being kept in filesystem and producing the filesystem strange sized / showing not correct / filled even after it was extended with tune2fs and was supposed to have extra 50GBs.

Finally it was explained shortly how to HUP / restart hanging script / service to fix it.

Some few good readings that helped to fix the issue:

What to do when du and df report different usage is here
df in linux not showing correct free space after file removal is here
Why do “df” and “du” commands show different disk usage?
 

Fix MySQL ibdata file size – ibdata1 file growing too large, preventing ibdata1 from eating all your server disk space

Thursday, April 2nd, 2015

fix-solve-mysql-ibdata-file-size-ibdata1-file-growing-too-large-and-preventing-ibdata1-from-eating-all-your-disk-space-innodb-vs-myisam

If you're a webhosting company hosting dozens of various websites that use MySQL with InnoDB  engine as a backend you've probably already experienced the annoying problem of MySQL's ibdata1 growing too large / eating all server's disk space and triggering disk space low alerts. The ibdata1 file, taking up hundreds of gigabytes is likely to be encountered on virtually all Linux distributions which run default MySQL server <= MySQL 5.6 (with default distro shipped my.cnf). The excremental ibdata1 raise appears usually due to a application software bug on how it queries the database. In theory there are no limitation for ibdata1 except maximum file size limitation set for the filesystem (and there is no limitation option set in my.cnf) meaning it is quite possible that under certain conditions ibdata1 grow over time can happily fill up your server LVM (Storage) drive partitions.

Unfortunately there is no way to shrink the ibdata1 file and only known work around (I found) is to set innodb_file_per_table option in my.cnf to force the MySQL server create separate *.ibd files under datadir (my.cnf variable) for each freshly created InnoDB table.
 

1. Checking size of ibdata1 file

On Debian / Ubuntu and other deb based Linux servers datadir is /var/lib/mysql/ibdata1

server:~# du -hsc /var/lib/mysql/ibdata1
45G     /var/lib/mysql/ibdata1
45G     total


2. Checking info about Databases and Innodb storage Engine

server:~# mysql -u root -p
password:

mysql> SHOW DATABASES;
+——————–+
| Database           |
+——————–+
| information_schema |
| bible              |
| blog               |
| blog-sezoni        |
| blogmonastery      |
| daniel             |
| ezmlm              |
| flash-games        |


Next step is to get some understanding about how many existing InnoDB tables are present within Database server:

mysql> SELECT COUNT(1) EngineCount,engine FROM information_schema.tables WHERE table_schema NOT IN ('information_schema','performance_schema','mysql') GROUP BY engine;
+————-+——–+
| EngineCount | engine |
+————-+——–+
|         131 | InnoDB |
|           5 | MEMORY |
|         584 | MyISAM |
+————-+——–+
3 rows in set (0.02 sec)

To get some more statistics related to InnoDb variables set on the SQL server:
 

mysqladmin -u root -p'Your-Server-Password' var | grep innodb


Here is also how to find which tables use InnoDb Engine

mysql> SELECT table_schema, table_name
    -> FROM INFORMATION_SCHEMA.TABLES
    -> WHERE engine = 'innodb';

+————–+————————–+
| table_schema | table_name               |
+————–+————————–+
| blog         | wp_blc_filters           |
| blog         | wp_blc_instances         |
| blog         | wp_blc_links             |
| blog         | wp_blc_synch             |
| blog         | wp_likes                 |
| blog         | wp_wpx_logs              |
| blog-sezoni  | wp_likes                 |
| icanga_web   | cronk                    |
| icanga_web   | cronk_category           |
| icanga_web   | cronk_category_cronk     |
| icanga_web   | cronk_principal_category |
| icanga_web   | cronk_principal_cronk    |


3. Check and Stop any Web / Mail / DNS service using MySQL

server:~# ps -efl |grep -E 'apache|nginx|dovecot|bind|radius|postfix'

Below cmd should return empty output, (e.g. Apache / Nginx / Postfix / Radius / Dovecot / DNS etc. services are properly stopped on server).

4. Create Backup dump all MySQL tables with mysqldump

Next step is to create full backup dump of all current MySQL databases (with mysqladmin):

server:~# mysqldump –opt –allow-keywords –add-drop-table –all-databases –events -u root -p > dump.sql
server:~# du -hsc /root/dump.sql
940M    dump.sql
940M    total

If you have free space on an external backup server or remotely mounted attached (NFS or SAN Storage) it is a good idea to make a full binary copy of MySQL data (just in case something wents wrong with above binary dump), copy respective directory depending on the Linux distro and install location of SQL binary files set (in my.cnf).
To check where are MySQL binary stored database data (check in my.cnf):

server:~# grep -i datadir /etc/mysql/my.cnf
datadir         = /var/lib/mysql

If server is CentOS / RHEL Fedora RPM based substitute in above grep cmd line /etc/mysql/my.cnf with /etc/my.cnf

if you're on Debian / Ubuntu:

server:~# /etc/init.d/mysql stop
server:~# cp -rpfv /var/lib/mysql /root/mysql-data-backup

Once above copy completes, DROP all all databases except, mysql, information_schema (which store MySQL existing user / passwords and Access Grants and Host Permissions)

5. Drop All databases except mysql and information_schema

server:~# mysql -u root -p
password:

mysql> SHOW DATABASES;

DROP DATABASE blog;
DROP DATABASE sessions;
DROP DATABASE wordpress;
DROP DATABASE micropcfreak;
DROP DATABASE statusnet;

          etc. etc.

ACHTUNG !!! DON'T execute!DROP database mysql; DROP database information_schema; !!! – cause this might damage your User permissions to databases

6. Stop MySQL server and add innodb_file_per_table and few more settings to prevent ibdata1 to grow infinitely in future

server:~# /etc/init.d/mysql stop

server:~# vim /etc/mysql/my.cnf
[mysqld]
innodb_file_per_table
innodb_flush_method=O_DIRECT
innodb_log_file_size=1G
innodb_buffer_pool_size=4G

Delete files taking up too much space – ibdata1 ib_logfile0 and ib_logfile1

server:~# cd /var/lib/mysql/
server:~#  rm -f ibdata1 ib_logfile0 ib_logfile1
server:~# /etc/init.d/mysql start
server:~# /etc/init.d/mysql stop
server:~# /etc/init.d/mysql start
server:~# ps ax |grep -i mysql

You should get no running MySQL instance (processes), so above ps command should return blank.
 

7. Re-Import previously dumped SQL databases with mysql cli client

server:~# cd /root/
server:~# mysql -u root -p < dump.sql

Hopefully import should went fine, and if no errors experienced new data should be in.

Altearnatively if your database is too big and you want to import it in less time to mitigate SQL downtime, instead import the database with:

server:~# mysql -u root -p
password:
mysql>  SET FOREIGN_KEY_CHECKS=0;
mysql> SOURCE /root/dump.sql;
mysql> SET FOREIGN_KEY_CHECKS=1;

If something goes wrong with the import for some reason, you can always copy over sql binary files from /root/mysql-data-backup/ to /var/lib/mysql/
 

8. Connect to mysql and check whether databases are listable and re-check ibdata file size

Once imported login with mysql cli and check whther databases are there with:

server:~# mysql -u root -p
SHOW DATABASES;

Next lets see what is currently the size of ibdata1, ib_logfile0 and ib_logfile1
 

server:~# du -hsc /var/lib/mysql/{ibdata1,ib_logfile0,ib_logfile1}
19M     /var/lib/mysql/ibdata1
1,1G    /var/lib/mysql/ib_logfile0
1,1G    /var/lib/mysql/ib_logfile1
2,1G    total

Now ibdata1 will grow, but only contain table metadata. Each InnoDB table will exist outside of ibdata1.
To better understand what I mean, lets say you have InnoDB table named blogdb.mytable.
If you go into /var/lib/mysql/blogdb, you will see two files
representing the table:

  •     mytable.frm (Storage Engine Header)
  •     mytable.ibd (Home of Table Data and Table Indexes for blogdb.mytable)

Now construction will be like that for each of MySQL stored databases instead of everything to go to ibdata1.
MySQL 5.6+ admins could relax as innodb_file_per_table is enabled by default in newer SQL releases.


Now to make sure your websites are working take few of the hosted websites URLs that use any of the imported databases and just browse.
In my case ibdata1 was 45GB after clearing it up I managed to save 43 GB of disk space!!!

Enjoy the disk saving! 🙂

How to deb upgrade PHP 5.3.3-7 / MySQL Server 5.1 to PHP 5.4.37 MySQL 5.5 Server on Debian 6.0 / 7.0 Squeeze / Wheezy GNU / Linux

Thursday, February 12th, 2015

how-to-deb-upgrade-mysql-server-5.1-to-mysql-5.5-php-5.3-to-php-5.4-5.5-upgrade-howto-on-old-stable-debian-squeeze-wheezy

I've been still running Debian Squeeze 6.0 GNU / Linux on few of the Linux / Apache / MySQL servers I'm administrating and those servers are running few Wordperss / Joomla websites which lately face severe MySQL performance issues. I tried to optimize using various mysql performance optimization scripts such as mysql-tuner.pl, Tuning-primer.sh and Percona Toolkit – a collection of advanced command-line tools for system administrators and tech / support staff to perform a variety of MySQL and system tasks that are too difficult or complex to perform manually. Though with above tools and some my.cnf tunizations I managed to achieve positive performance improvement results with above optimizations, still I didn't like how MyQSL served queries and since the SQL server is already about 5 years old (running version 5.1) and the PHP on sever is still at 5.3 branch, I was advised by my dear colleague Anatoliy to try version update as a mean to improve SQLserver performance. I took seriously the suggestion to try upgrade as a mean to resolve performance issues in this article I will explain in short what I had to do to make MySQL upgrade a success

Of course to try keep deb installed software versions as fresh as possible possible deb packagse, I'm already using Debian Back Ports (for those who hear it a first time Debian Backports is a special repository for Stable versioned Debian Desktop and Servers  – supporting stable releases of Debian Linux) which allows you to keep install packages versions less outdated (than default installable software which usually are way behind latest stable package versions with 2-5 years).

If you happen to administer Stable Debian servers and you never used BackPorts I warmly recommend it as it often includes security patches of packages part of Debian stable releases that reached End Of Support (EOS) and already too old even for security updates to be issued by respective Debian Long Term Suport (LTS) repositories.

If you're like me and still in situation to manage remotely Debian 6.0 Squeeze and its the first time you hear about BackPorts and Debian LTShttps://wiki.debian.org/LTS/ to start using those two add to your /etc/apt/sources.list below 3 lines

Open with vim editor and press shift+G to go to last line of file and then press I to enter INSERT mode, once you're done to save, press (ESC) then press : and type x! in short key combination for exit and save setting in vim is 
 

Esc + :x! 

debian-server:~# vim /etc/apt/sources.list
deb http://http.debian.net/debian squeeze-lts main contrib non-free
deb-src http://http.debian.net/debian squeeze-lts main contrib non-free
deb http://http.debian.net/debian-backports squeeze-backports main

If you haven't been added a security updates line in /etc/apt/sources.list make sure you add also:

deb http://security.debian.org/ squeeze/updates main contrib non-free
deb-src http://security.debian.org/ squeeze/updates main contrib non-free


Then to apply latest security updates and packages from LTS / Backports repository run the usual:

debian-server:~# apt-get update && apt-get –yes upgrade
….

If you need to search a package or install something from just added backports repository use:

debian-server:~# apt-cache -t squeeze-backports search "mysql-server"
auth2db – Powerful and eye-candy IDS logger, log viewer and alert generator
torrentflux – web based, feature-rich BitTorrent download manager
cacti – Frontend to rrdtool for monitoring systems and services
mysql-server-5.1 – MySQL database server binaries and system database setup
mysql-server-core-5.1 – MySQL database server binaries
mysql-server – MySQL database server (metapackage depending on the latest version)

To install specific packages only with all their dependencies from Backports while keeping rest of packages from Debian Stable:

debian-server:~# apt-get install -t squeeze-backports "package_name"

In same way you can also search or install specific packages from LTS repo:

debian-server:~# apt-get search -t squeeze-lts "package_name"

debian-server:~# apt-get install -t squeeze-lts "package_name"

Latest mysql available from Debian BackPorts and LTS is still quite old 5.1.73-1+deb6u1 therefore I made an extensive research online on how can I easily update MySQL 5.1 to MySQL 5.5 / 5.6 on Debian Stable Linux.
 

Luckily there were already DotDeb deb repositories for Debian LAMP (Linux / Apache  / MySQL / PHP / Nginx ) running servers prepared in order to keep the essential Webserver services up2date even long after distro official support is over. I learned about existence of this repo thanks to a Ryan Tate's post who updates his LAMP stack on TurnKey Linux which by the way is based on slightly modified official stable Debian Linux releases packages

To start using DotDeb repos add in /etc/apt/sources.list (depending whereh you're on Squeeze or Wheeze Debian):

deb http://packages.dotdeb.org squeeze all
deb-src http://packages.dotdeb.org squeeze all

or for Debian Wheezy add repos:

deb http://packages.dotdeb.org wheezy all
deb-src http://packages.dotdeb.org wheezy all

I was updating my DebianLatest MySQL / PHP / Apache release to Latest ones on (6.0.4) Squeeze so added above squeeze repos:

Before refreshing list of package repositories, to authenticate repos issue:

debian-server:~# wget -q http://www.dotdeb.org/dotdeb.gpg
debian-server:~# apt-key add dotdeb.gpg

Once again to update my packages from newly added DodDeb repository

debian-server:~# apt-get update

Before running the SQL upgrade to insure myself, I dumped all databases with:

debian-server:~# mysqldump -u root -p -A > /root/dump.sql

Finally I was brave enough to run apt-get dist-upgrade to update with latest LAMP packages

debian-server:~# apt-get dist-upgrade
Reading package lists… Done
Building dependency tree
Reading state information… Done
Calculating upgrade… Done
The following packages will be REMOVED:
  mysql-client-5.1 mysql-server mysql-server-5.1
The following NEW packages will be installed:
  libaio1 libmysqlclient18 mysql-client-5.5 mysql-client-core-5.5 python-chardet python-debian
The following packages will be upgraded:
  curl krb5-multidev libapache2-mod-php5 libc-bin libc-dev-bin libc6 libc6-dev libc6-i386 libcurl3 libcurl3-gnutls libcurl4-openssl-dev libevent-1.4-2
  libgssapi-krb5-2 libgssrpc4 libjasper1 libk5crypto3 libkadm5clnt-mit7 libkadm5srv-mit7 libkdb5-4 libkrb5-3 libkrb5-dev libkrb53 libkrb5support0 libmysqlclient-dev
  libxml2 libxml2-dev locales mysql-client mysql-common ntp ntpdate php-pear php5 php5-cgi php5-cli php5-common php5-curl php5-dev php5-gd php5-imagick php5-mcrypt
  php5-mysql php5-odbc php5-recode php5-sybase php5-xmlrpc php5-xsl python-reportbug reportbug unzip

50 upgraded, 6 newly installed, 3 to remove and 0 not upgraded.
Need to get 51.7 MB of archives.
After this operation, 1,926 kB of additional disk space will be used.
Do you want to continue [Y/n]? Y

As you see from above output above command updates Apache webservers / PHP and PHP related modules, however it doesn't update MySQL installed version, to update also MySQL server 5.1 to MySQL server 5.5

debian-server:~#  apt-get install –yes mysql-server mysql-server-5.5

You will be prompted with the usual Debian ncurses text blue interface to set a root password to mysql server, just set it the same as it used to be on old upgraded MySQL 5.1 server.

Well now see whether mysql has properly restarted with ps auxwwf

debian-server:~#  ps axuwwf|grep -i sql
root     22971  0.0  0.0 112360   884 pts/11   S+   15:50   0:00  |                   \_ grep -i sql
root     19436  0.0  0.0 115464  1556 pts/1    S    12:53   0:00 /bin/sh /usr/bin/mysqld_safe
mysql    19837  4.0  2.3 728192 194552 pts/1   Sl   12:53   7:12  \_ /usr/sbin/mysqld –basedir=/usr –datadir=/var/lib/mysql –plugin-dir=/usr/lib/mysql/plugin –user=mysql –pid-file=/var/run/mysqld/mysqld.pid –socket=/var/run/mysqld/mysqld.sock –port=3306
root     19838  0.0  0.0 110112   700 pts/1    S    12:53   0:00  \_ logger -t mysqld -p daemon.error

In my case it was running, however if it fails to run try to debug what is going wrong on initialization by manually executing init script /etc/init.d/mysql stop; /etc/init.d/mysql start and look for errors. You can also manually try to run mysqld_safe from console if it is not running run:

debian-server:~# /usr/bin/mysqld_safe &

This should give you a good hint on why it is failing to run
 

One more thing left is to check whether php modules load correctly to do so issue:

debian-server:~# php -v
Failed loading /usr/lib/php5/20090626/xcache.so:  /usr/lib/php5/20090626/xcache.so: cannot open shared object file: No such file or directory

Failed loading /usr/lib/php5/20090626/xdebug.so:  /usr/lib/php5/20090626/xdebug.so: cannot open shared object file: No such file or directory


You will likely get an exception (error) like above.
To solve the error, reinstall xcache and xcache-debug debs

debian-server:~# apt-get purge php5-xcache php5-xdebug

Now PHP + MySQL + Apache environment should be running much smootly.

debian-squeeze-wheeze-update-install-mysql-sevver5.55-620x344-howto

Upgrading the MySQL server / PHP library to MySQL server 5.6 / PHP 5.5 on Wheeze Linux is done in very much analogous ways all you have to do is change the repositories with above wheeze 7.0 ones and to follow the process as described in this article. I haven't tested update on Wheezy yet, so if you happen to try my article with wheezy reports and got a positive upgrade result please drop a comment.

How to determine WordPress blogs with most spam on multiple blog hosting server

Thursday, November 27th, 2014

determine_find_blogs_with_most_spam-on-multiple-wordpress-blogs-hosting-server-stop-and-clea-large-amounts-ofrcomment-spam
If you're a hosting company that is hosts Joomla / WordPress / ModX websites (each) on separate servers and thus you end up with servers hosting multiple WordPress customer Blogs only, lets say (100+ WP blogs per host) soon your MySQL blogs databases will be full (overfilled) with spam comments. Blogs with multitude of spam comments reduces the WordPress site attractiveness, takes useless disk space, makes wp databases hard to backup and slowing drastically the SQL server.

As our duty as system administrators is to keep the servers optimized (improve performance) and prevent spam-bots to hammer your Linux servers, its is always a good idea to keep an eye on which hosted blogs attract more spammers and cause server overheads and bad hardware optimization.

WordPress blogs keeps logged comments under database_name.wp_comments  (table) thus the quickest way to find out blogs with largest comments tables is to use Linux's find command and print out only comments tables larger than set size.

Here is how:

find /var/lib/mysql/ -type f -size +1024k -name "*_comments.MYD" -exec ls -lh {} ; | awk '{ print $9 ": " $5 }'


/var/lib/mysql/funny-blog/wp_comments.MYD: 15,7M
/var/lib/mysql/wordblogger/wp_comments.MYD: 5,3M
/var/lib/mysql/loveblog/wp_comments.MYD: 50,5M

A comments database of 1MB means about at least 500+ comments, thus the blog loveblog's wp_comments.MYD = 50,5 Mbs contains probably about 10000! comments and should be definitely checked in a browser, if its overfilled with spam because of bad anti-spam policy or missing currently best wordpress spam catcher plugin Akismet. In cases of lack of client to protect his spam you can write quickly a script to auto mail him and ask him kindly to check / fix his blog spam.
In some cases it is useful to write a few liners bash script to automatically disable users with extraordinary blog spam comments databases (quickest way to do it is to move users blog data under quarantine directory and adding a Blog Suspended static html webpage with text like "Please contact support for more info".

1024k find arguments is 1MB, on a big hosted blogs this might be low and you might want to use (100Mb) = 102400kbytes.
You should note that *_comments.MYD in above find cmd is because though standardly wordpress sets wp_ as a prefix to its created skele table structures it is not always the case. 

In above command example find looks for spam comments in /var/lib/mysql (because this is a Debian Linux server), however on other MySQL custom installs, it might be in another dir i.e. /usr/local/mysql/data etc.

It is useful to set the wp_comments statistics output to execute at least once a day as a cronjob:

crontab -u root -e 00 24 * * * /usr/sbin/check_spammed_blogs.sh

vim /usr/check_soammed_blogs.sh

Set a script like:

#!/bin/sh
find /var/lib/mysql/ -type f -size +1024k -name "*_comments.MYD" -exec ls -lh {} ; | awk '{ print $9 ": " $5 }' | tee -a /var/log/blogs_with_most_spam_comments.log

Though above commands is to run on GNU / Linux, for Windows servers based hosting you can  install GNUWin tools and adapt above cmd using windows standard commands or PowerShell to do the same.
Finally you can might want to use some other SQL script to clear blogs with enormously large tables from spam or clear all unapproved spam comments

Run native Internet Explorer 6 on latest Debian / Ubuntu Linux with IEs4Linux

Thursday, July 24th, 2014

Install-internet-explorer-on-debian-linux-IEs4Linux_logo.svg
If you're a GNU / Linux Desktop user like me and you have to administrate hybrid server environments running mixture of MS Windows with Microsoft IIS webserver running active server pages (.ASP) developed application or UNIX / GNU Linux servers web applications using Mono as a server-side language, often you need to have browser which properly supports  Internet Explorer Trident web (layout) renderer (also famous as MSHTML).

Having Internet Explorer on your Linux is very useful for web developers who want to test how their website works under IE.

Of course you can always install Windows in Virtualbox VM and do your testing in the Virtual Machine but this takes time to install and also puts a useless load to a PC ….

IES4 Linux is a Linux free (open source) shell script that lets you run Internet Explorer on your Linux desktop.

ies4linux scripts collection uses emulation with WINE (Wine is Not Emulator) emulator to run the native  Windows Internet Explorer thus before use it you have to install Wine.

There are plenty of tutorials online about ies4Linux, problem is as it is not updated and developed most tutorials doesn't work on Debian Wheezy / Ubuntu and rest of deb based linux distros.
This is why I decided to write just another ies4linux tutorial that actually works!

On Debian / Ubuntu / Mint Linux install via apt-get:

apt-get –yes install wine

Then with a non-root user download ies4linux-latest.tar.gz. Just in case ies4linux-latest.tar.gz disappears in future I've created also a ies4linux-latest.tar.gz mirror for download here

and unarchive tar archive:

wget http://www.tatanka.com.br/ies4linux/downloads/ies4linux-latest.tar.gz
tar -zxvf ies4linux-latest.tar.gz
cd ies4linux-*
./ies4linux

You will get:
 

IEs4Linux 2 is developed to be used with recent Wine versions (0.9.x). It seems that you are using an old version. It's recommended that you update your wine to the latest version (Go to: winehq.com).

You need to install cabextract first!
Download it here: http://www.kyz.uklinux.net/cabextract.php

To fulfill this requirement you will need to also cabetract package which is luckily part of Debian:
 

apt-get install –yes cabextract

On wine version 1.0 and onwards winprefixcreate has been changed to winecfg binary.
To prevent missing wineprefixcreate, errors during ies4linux installer run  its necessery to symlink as a workaround:
 

ln -sv /usr/bin/winecfg /usr/bin/wineprefixcreate


To continue with Internet Explorer ies4Linux installater run again:

./ies4linux

images/internet-explorer-for-linux-debian-gnu-linux-screenshot

/images/internet-explorer-4-linux-installer-debian-gnu-linu-screenshot

You will get the installer GUI window with selection option which Internet Explorer version you want. Choose between IE 5.0, IE 5.5 and IE 6. It is also possible to install IE 7 which is still considered beta version and is less tested and unstable, will probably lead to crashes. If you want to install also IE 7 check it as an option from Advanced menu.

/images/ies4linux-internet-explorer-installer-debian-gnu-linux-screenshot

If you get permission errors after running ies4Linux gui installer to solve that chown recursively directory to the user with which you will be running it:
 

chown -R hipo:hipo ies4linux-2.99.0.1

Internet Explorer for Linux downloader, will connect Microsoft.com website and download DCOM, MCF and various IE required .CAB files.

If you get some ies4linux GUI installer unexpected crashes you can try to download all required IE binaries, surrounding files and flash player using no-gui installer with cmd:
 

./ies4linux –no-gui –install-corefonts

IEs4Linux 2 is developed to be used with recent Wine versions (0.9.x). It seems that you are using an old version. It's recommended that you update your wine to the latest version (Go to: winehq.com).

IEs4Linux will:
  – Install Internet Explorers: 6.0
  – Using IE locale: EN-US
  – Install Adobe Flash 9.0
  – Install MS Core Fonts
  – Install everything at: /home/hipo/.ies4linux
[ OK ]

Downloading everything we need
  Downloading from microsoft.com:
   DCOM98.EXE
   mfc42.cab
   249973USA8.exe
   ADVAUTH.CAB
   CRLUPD.CAB
   HHUPD.CAB
   IEDOM.CAB
   IE_EXTRA.CAB
   IE_S1.CAB
   IE_S2.CAB
   IE_S5.CAB
   IE_S4.CAB
   IE_S3.CAB
   IE_S6.CAB
   SETUPW95.CAB
   FONTCORE.CAB
   FONTSUP.CAB
   VGX.CAB
   SCR56EN.CAB

  Downloading from macromedia.com:
   100% swflash.cab

  Downloading from sourceforge.net
   0%   webdin32.exe[ OK ]bdin32.exe

Installing IE 6
  Initializing
  Creating Wine Prefix
Your wine does not have wineprefixcreate installed. Maybe you are running an old Wine version. Try to update it to the latest version.

To fix the error:

Your wine does not have wineprefixcreate installed. Maybe you are running an old Wine version. Try to update it to the latest version.

vim lib/functiions.sh

Go to line 36 (Type :36 in vim)

Line:

wine –version 2>&1 | grep -q "0.9." || warning $MSG_WARNING_OLDWINE

Has to be changed to:

wine –version 2>&1 | egrep -q "0.9.|-1." || warning $MSG_WARNING_OLDWINE


Also you need to substitute wineprefixcreate to wineboot (if you haven't already symlinked wineprefixcreate to winecfg – as pointed earlier in article.

To do so make following substitution in lib/install.sh and in lib/functions.sh

cp -rpf lib/install.sh lib/install.sh.bak; cat lib/install.sh |sed -e 's#wineprefixcreate#wineboot#g' > lib/install_new.sh; mv lib/install_new.sh lib/install.sh

cp -rpf lib/install.sh lib/functions.sh.bak; cat lib/functions.sh |sed -e 's#wineprefixcreate#wineboot#g' > lib/functions_new.sh; mv lib/functions_new.sh lib/functions.sh


Also it is necessery to change default corefonts download url which points to sourceforge but is failing. I've made mirror of corefonts files here
 

cp -rpf lib/install.sh lib/install.sh.bak; cat lib/install.sh |sed -e 's#http://internap.dl.sourceforge.net/sourceforge/corefonts/#pc-freak.net/files/corefonts/#g' > lib/install_new.sh; mv lib/install_new.sh lib/install.sh

Re-run the ies4linux console installer:
 

 ./ies4linux –no-gui –install-corefonts

….
Es4Linux installations finished!

On installation success you should get output like this
Hopefully you will see no errors like in my case, if you get the corefonts download error again re-run the installer and it should succesully download the files.

To then run ies4linux:

~/bin/ie6


internet-explorer-ies4linx-running-on-debian-gnu-linux-screenshot
Though Ies 4 Linux is good for basic testing it is not psosible to use the browser for normal browsing because its a bit buggy and slow.

By default Internet Explorer 6 behavior is to prompt security alert on various actions, though this might be useful for debugging it is really annoying so I personally disabled those by decreasing from:

Tools -> Internet Options -> Security -> (Security Level)
I've decreased it from Medium to Medium-Low

ies4Linux was not developed since 2008 and as of time of writting ies4linux official project website seems abandoned.

Allowing MySQL users access from all hosts – Fixing mysql ERROR 1045 (28000): Access denied for user ‘root’@’remote-admin.com’ (using password: YES)

Friday, June 20th, 2014

mysql_allow_access-from-remote-any-host-fix-access-error-after-sql-migration

I recently migrated MySQL database server from host A to host B (remotesystemadministration.com), because I wanted to have the mysql database server on a separate machine (have separation of server running services and have a dedicated mysql server).

MySQL server host (running on localhost previously was set from my mysql config my.cnf to listen and serve connections on localhost with

bind-address = 127.0.0.1

). MySQL is used by a Tomcat running Java application on localhost and my task was to set the Tomcat to use the MySQL database remotely to MySQL host B (new remote hostname where MySQL is moved is  remotesystemadminsitration.com and is running on IP 83.228.93.76).

Migration from MySQL Db server 1 (host A) to MySQL Db server 2 (host B) is done by binary copying the mysql database directory which in this case is (as it is a Debian server installed MySQL), the standard directory where mysql stores its database data is /var/lib/mysql ( datadir = /var/lib/mysql in /etc/mysql/my.cnf)

Binary copying of data from MySQL db (host A) to MySQL Db (host B) is done with rsync

After migrating and trying to login on migrated mysql  database on remotesystemadministration.net with mysql cli client:

remotesysadmin:~$ mysql -u root -p

I got following error:
 

ERROR 1045 (28000): Access denied for user 'root'@'remotesystemadministration.com' (using password: YES)


To fix the issue I had to login remotely from old migration server mysql (host A) cli:

mysql:~$ mysql -u root -p -h remotesystemadministration.com

and  run SQL commands:

GRANT ALL PRIVILEGES ON *.* TO 'root'@'remotesystemadministration.com' WITH GRANT OPTION;
GRANT USAGE ON *.* TO 'root'@'remotesystemadministration.com' IDENTIFIED BY 'secret-mysql-pass';
FLUSH PRIVILEGES;

Query OK, 0 rows affected (0.03 sec)
Query OK, 0 rows affected (0.00 sec)
Query OK, 0 rows affected (0.00 sec)


Another way to solve the problem is to add the root user to be able to connect from any host (Enable MySQL root access from all host), to do so issue:

GRANT ALL PRIVILEGES ON *.* TO 'root'@'%' IDENTIFIED BY 'password';
FLUSH PRIVILEGES;

Note: In newer version of MySQL, flush privileges could be omitted.

Another approach if you want to substitute access from localhost for all users and enable all users to be able to authenticate to mysql remotely is to execute SQL Query:

UPDATE USER SET host='%' WHERE host='localhost';

Allowing all users to be able to connect from anywhere on the internet is a very bad security practice anyways, if you already have a tight firewall setup and you can only access the server via specific remote IP addresses allowing MySQL access from all hosts / ips should be ok.

Linux: how to show all users crontab – List all cronjobs

Thursday, May 22nd, 2014

linux-unix-list-all-crontab-users-and-scripts
I'm doing another server services decomissioning and part of decomissioning plan is: Removing application and all related scripts from related machines (FTP, RSYNC, …). In project documentation I found a list with Cron enabled shell scripts:

#Cron tab excerpt:
1,11,21,31,41,51 * * * */webservices/tools/scripts/rsync_portal_sync.sh

that has to be deleted, however there was nowhere mentioned under what kind of credentials (with what kind of user) are the cron scripts running? Hence I had to look up all users that has cronjobs and find inside each user's cronjobs whether respective script is set to run. Herein I will explain shortly how I did that.

Cronjobs by default has few locations from where cronjobs are setupped depending on their run time schedule. First place I checked for the scripts is

/etc/crontabs # cat /etc/crontabs SHELL=/bin/sh
PATH=/usr/bin:/usr/sbin:/sbin:/bin:/usr/lib/news/bin
MAILTO=root
#
# check scripts in cron.hourly, cron.daily, cron.weekly, and cron.monthly
#
-*/15 * * * * root test -x /usr/lib/cron/run-crons && /usr/lib/cron/run-crons >/dev/null 2>&1
59 * * * * root rm -f /var/spool/cron/lastrun/cron.hourly
14 4 * * * root rm -f /var/spool/cron/lastrun/cron.daily
29 4 * * 6 root rm -f /var/spool/cron/lastrun/cron.weekly
44 4 1 * * root rm -f /var/spool/cron/lastrun/cron.monthly

I was not really user via what user is shell script run, therefore I looked first if someone doesn't set the script to run via crontab's standard locations for Daily, Hourly,Weekly and Monthly cronjobs:
 

a) Daily set cron jobs are in:

/etc/cron.daily/

b) Hourly set cron jobs:

/etc/cron.hourly

c) Weekly cron jobs are in:

/etc/cron.weekly/

d) Monthly cron jobs:

/etc/cron.monthly

There is also a location read by crontab for all Software (package distribution) specific cronjobs – all run under root user privileges.:

e) Software specific script cron jobs are in:

/etc/cron.d/  
As the system has about 327 users in /etc/passwd, checking each user's cronjob manually with:

# crontab -u UserName -l

was too much time consuming thus it is a good practice to list

/var/spool/cron/*

directory and to see which users has cron jobs defined

# ls -al /var/spool/cron/*
-rw——- 1 root root 11 2007-07-09 17:08 /var/spool/cron/deny

/var/spool/cron/lastrun:
total 0
drwxr-xr-x 2 root root 80 2014-05-22 11:15 .
drwx—— 4 root root 120 2008-02-25 15:45 ..
-rw-r–r– 1 root root 0 2014-05-22 04:15 cron.daily

/var/spool/cron/tabs:
total 8
drwx—— 2 root root 72 2014-04-03 03:43 .
drwx—— 4 root root 120 2008-02-25 15:45 ..
-rw——- 1 root root 4901 2014-04-03 03:43 root
 


/var/spool/cron – is crond (/usr/bin/cron/)'s spool directory.

# ls -al /var/spool/cron/tabs/ total 8
drwx------ 2 root root 72 2014-04-03 03:43 .
drwx------ 4 root root 120 2008-02-25 15:45 ..
-rw------- 1 root root 4901 2014-04-03 03:43 root

Above output shows only root superuser has defined crons.

Alternative way to check all user crontabs is via quick Linux one liner shell script show all user cron jobs

for i in $(cat /etc/passwd | sed -e "s#:# #g" | awk '{ print $1 }'); do
echo "user $i --- crontab ---";
crontab -u $i -l 2>&1 >/dev/null;
echo '----------';
done|less

Note that above short script has to run with root user. Enjoy 🙂

Mysql: How to disable single database without dropping or renaming it

Wednesday, January 22nd, 2014

mysql rename forbid disable database howto logo, how to disable single database without dropping it
A colleague of mine working on MySQL database asked me How it is possible to disable a MySQL database. He is in situation where the client has 2 databases and application and is not sure which of the two databases the application uses. Therefore the client asked one of the database is disabled and wait for few hours and see if something will break / stop working and in that way determine which of the two database is used by application.

My first guess was to backup both databases and drop one of them, then if it is the wrong one to restore from the SQL dump backup, however this wasn't acceptable solution. So second I though of RENAME of database to another one and then reverting the name, however as it is written in MySQL documentation RENAME database function was removed from MySQL (found to be dangerous) since version 5.1.23 onwards. Anyhow there is a quick hack to rename mysql database using a for loop shell script one below:

mysql -e "CREATE DATABASE \`new_database\`;"
for table in `mysql -B -N -e "SHOW TABLES;" old_database`
do
  mysql -e "RENAME TABLE \`old_database\`.\`$table\` to \`new_database\`.\`$table\`"
  done
  mysql -e "DROP DATABASE \`old_database\`;"

Other possible solution was to change permissions of Application used username, however this was also complicated from mysql cli, hence I thought of installing and using PHPMyAdmin to make modify of db user permissions easier but on this server there wasn't Apache installed and MySQL is behind a firewall and only accessible via java tomcat host.

Finally after some pondering what can be done I came with solution to request to disable mysql database using chmod in /var/lib/mysql/data/, i.e.:

sql-server:~# chmod 0 /var/lib/mysql/databasename

Where databasename is the same as the database is named listable via mysql cli.

After doing it that way with no need to restart MySQL server database stopped to appear in show databases; and client confirmed that disabled database is no longer needed so we proceeded dropping it.

Hope this little article will help someone out there. Cheers :

Windows Explorer (Open directory in command prompt preserving dir PATH) – Add Dos Prompt Here feature via tiny registry tweak

Friday, January 10th, 2014

Windows explorer dos prompt here open directory in windows command line

If you have to use Windows on system administration level, you had to use command prompt daily, thus its useful to be able to be able to open Command Line starting from desired directory with no need to copy directory Path by hand and CD to it manually.

By default Command Prompt, cmd.exe always opens itself setting a path to user home directory, reading what is defined by win system variable %USERPROFILE% or %HOMEPATH% – MS Windows equivalent of UNIX's $HOME shell variable.

To add open in  DOS Prompt Here Command Prompt option to Windows Explorer menus its necessary to apply few rules to Windows registry DB
Use above Download link and launch it and from there on clicking with right Mouse button to any directory will enable you to open directory in CMD.EXE.

Here is content of little registry tweak adding the new menu Dos Prompt Here button
Windows Registry Editor Version 5.00

[HKEY_CLASSES_ROOT\Directory\shell\DosHere]
@="Dos &Prompt Here"

[HKEY_CLASSES_ROOT\Directory\shell\DosHere\Command]
@="cmd.exe /k cd %1"

[HKEY_CLASSES_ROOT\Drive\shell\DosHere]
@="Dos &Prompt Here"

[HKEY_CLASSES_ROOT\Drive\shell\DosHere\Command]
@="cmd.exe /k cd %1"

Windows explorer open program files or any specific directory in windows command line

windows opening directory in command line program files screenshot win 7

This little registry code is originally for Windows 2000, anyways it is compatible with all NT technology based Windowses, Add DOS Prompt Here tweak works fine on Windows XP, Windows 7 and Windows 8 (Home, Pro and Business editions).

By Mentioning $HOME its interesting to say Windows equivalent of Linux's as it might be useful to know:

linux:~# echo $HOME
/home/hipo

is

C:\\> echo %USERPROFILE%
C:\\Users\\georgi

To list all Windows Command Prompt environment variable equivalent to Linux's bash shell env / setenv is SET command), here is example output from my Winblows;

C:\Users\georgi> SET
ALLUSERSPROFILE=C:\\ProgramData
APPDATA=C:\\Users\georgi\AppData\Roaming
CLASSPATH=.;C:\\Program Files (x86)\\Java\\jre6\\lib\\ext\\QTJava.zip
CommonProgramFiles=C:\\Program Files\Common Files
CommonProgramFiles(x86)=C:\\Program Files (x86)\\Common Files
CommonProgramW6432=C:\\Program Files\\Common Files
COMPUTERNAME=GEORGI
ComSpec=C:\\Windows\\system32\\cmd.exe
DEFLOGDIR=C:\\ProgramData\\McAfee\\DesktopProtection
FP_NO_HOST_CHECK=NO
HOMEDRIVE=C:
HOMEPATH=\\Users\\georgi
LOCALAPPDATA=C:\\Users\\georgi\\AppData\\Local
NUMBER_OF_PROCESSORS=4
OS=Windows_NT
Path=C:\\Program Files\\RA2HP\\;C:\\Windows\\system32;C:\\Windows;C:\\Windows\\S
Wbem;C:\\Windows\\System32\\WindowsPowerShell\v1.0\;C:\\Program Files\\WIDCOM
oth Software\\;C:\\Program Files\\WIDCOMM\\Bluetooth Software\\syswow64;C:\\Pr
les (x86)\\Hewlett-Packard\\HP ProtectTools Security Manager\\Bin\\;C:\\Progr
\\ActivIdentity\\ActivClient\\;C:\\Program Files (x86)\\ActivIdentity\\ActivCl
\\Program Files (x86)\\QuickTime\\QTSystem\\
PATHEXT=.COM;.EXE;.BAT;.CMD;.VBS;.VBE;.JS;.JSE;.WSF;.WSH;.MSC
PROCESSOR_ARCHITECTURE=AMD64
PROCESSOR_IDENTIFIER=Intel64 Family 6 Model 58 Stepping 9, GenuineIntel
PROCESSOR_LEVEL=6
PROCESSOR_REVISION=3a09
ProgramData=C:\\ProgramData
ProgramFiles=C:\\Program Files
ProgramFiles(x86)=C:\\Program Files (x86)
ProgramW6432=C:\\Program Files
PROMPT=$P$G
PSModulePath=C:\\Windows\\system32\\WindowsPowerShell\\v1.0\Modules\\
PTSMInstallPath_X86=C:\\Program Files (x86)\\Hewlett-Packard\\HP ProtectToo
ity Manager\\
PUBLIC=C:\\Users\\Public
QTJAVA=C:\\Program Files (x86)\\Java\\jre6\\lib\\ext\\QTJava.zip
SESSIONNAME=Console
SystemDrive=C:
SystemRoot=C:\\Windows
TEMP=C:\\Users\\georgi\\AppData\\Local\\Temp
TMP=C:\\Users\\georgi\\AppData\\Local\\Temp
USERDNSDOMAIN=EMEA.CPQCORP.NET
USERDOMAIN=EMEA
USERNAME=georgi
USERPROFILE=C:\\Users\\georgi
VSEDEFLOGDIR=C:\\ProgramData\\McAfee\\DesktopProtection
windir=C:\\Windows
windows_tracing_flags=3
windows_tracing_logfile=C:\\BVTBin\\Tests\\installpackage\\csilogfile.log

Hope this little trick hopes someone out there.
I will be glad to hear of other cool useful windows registry tweaks?