Posts Tagged ‘servers’

No space left on device with free disk space / Why no space left on device while there is plenty of disk space on drive – Running out of Inodes

Tuesday, November 17th, 2015

no_space_left-on-device-while-there-is-disk-space-running-out-of-file-inodes-unix_linux_file_system_diagram.gif

 

On one of the servers, I'm administrating the websites started showing some Mysql database table corrup errors like:
 

 

Table './database_name/site_news_list_com' is marked as crashed and last (automatic?) repair failed

The server is using Oracle MySQL server community stable edition on Debian GNU / Linux 6.0, so I first thought during work the server crashed either due to some bug issue in MySQL or it crashed due to some PHP cron job that did something messy. Thus to solve the crashed tables, tried using mysqlcheck tool which helped pretty fine, at many times whether there were database / table corruptions. I've run the following set of mysqlcheck commands with root (superuser) in a bash shell after logging in through SSH:

:

server:~# /usr/bin/mysqlcheck –defaults-extra-file=/etc/mysql/debian.cnf \–check –all-databases -u root -p`grep -i password /root/.my.cnf |sed -e 's#password=##g'`>> /var/log/cronwork.log
server:~# /usr/bin/mysqlcheck –defaults-extra-file=/etc/mysql/debian.cnf –analyze –all-databases -u root -p`grep -i password /root/.my.cnf |sed -e 's#password=##g'`>> /var/log/cronwork.log
server:~# /usr/bin/mysqlcheck –defaults-extra-file=/etc/mysql/debian.cnf \–auto-repair –optimize –all-databases -u root -p`grep -i password /root/.my.cnf |sed -e 's#password=##g'`>> /var/log/cronwork.log
server:~# /usr/bin/mysqlcheck –defaults-extra-file=/etc/mysql/debian.cnf \–optimize –all-databases -u root -p`grep -i password /root/.my.cnf |sed -e 's#password=##g'`>> /var/log/cronwork.log


In order for above commands to work, I've created the /root/.my.cnf containing my root (mysql CLI) mysql username and password, e.g. file has content like below:

 

[client]
user=root
password=MySecretPassword8821238

 

Btw a good note here is its generally a good idea (if you want to have consistent mysql databases) to automatically execute via a cron job 2 times a month, I've in root cronjob the following:

 

crontab -u root -l |grep -i mysqlcheck
04 06 5,10,15,20,25,1 * * /usr/bin/mysqlcheck –defaults-extra-file=/etc/mysql/debian.cnf \–check –all-databases –silent -u root -p`grep -i password /root/.my.cnf |sed -e 's#password=##g'`>> /var/log/cronwork.log 07 06 5,10,15,20,25,1 * * /usr/bin/mysqlcheck –defaults-extra-file=/etc/mysql/debian.cnf –analyze –all-databases –silent -u root -p`grep -i password /root/.my.cnf |sed -e 's#password=##g'`>> /var/log/cronwork.log 12 06 5,10,15,20,25,1 * * /usr/bin/mysqlcheck –defaults-extra-file=/etc/mysql/debian.cnf \–auto-repair –optimize –all-databases –silent -u root -p`grep -i password /root/.my.cnf |sed -e 's#password=##g'`>> /var/log/cronwork.log 17 06 5,10,15,20,25,1 * * /usr/bin/mysqlcheck –defaults-extra-file=/etc/mysql/debian.cnf \–optimize –all-databases –silent -u root -p`grep -i password /root/.my.cnf |sed -e 's#password=##g'`>> /var/log/cronwork.log


Strangely I got a lot of errors that some .MYI / .MYD .frm temp files, necessery for the mysql tables recovery can't be written inside /home/mysql/database_name

That was pretty weird and I thought there might be some issues with permissions, causing the inability to write, due to some bug or something so I went straight and checked /home/mysql/database_name permissions, e.g.::

 

server:/home/mysql/database_name# ls -ld soccerfame
drwx—— 2 mysql mysql 36864 Nov 17 12:00 soccerfame
server:/home/mysql/database_name# ls -al1|head -n 10
total 1979012
drwx—— 2 mysql mysql 36864 Nov 17 12:00 .
drwx—— 36 mysql mysql 4096 Nov 17 11:12 ..
-rw-rw—- 1 mysql mysql 8712 Nov 17 10:26 1_campaigns_diez.frm
-rw-rw—- 1 mysql mysql 14672 Jul 8 18:57 1_campaigns_diez.MYD
-rw-rw—- 1 mysql mysql 1024 Nov 17 11:38 1_campaigns_diez.MYI
-rw-rw—- 1 mysql mysql 8938 Nov 17 10:26 1_campaigns.frm
-rw-rw—- 1 mysql mysql 8738 Nov 17 10:26 1_campaigns_logs.frm
-rw-rw—- 1 mysql mysql 883404 Nov 16 22:01 1_campaigns_logs.MYD
-rw-rw—- 1 mysql mysql 330752 Nov 17 11:38 1_campaigns_logs.MYI


As seen from above output, all was perfect with permissions, so it should have been something else, so I decided to try to create a random file with touch command inside /home/mysql/database_name directory:

 

touch /home/mysql/database_name/somefile-to-test-writtability.txt touch: cannot touch ‘/scr1/data/somefile-to-test-writtability.txt‘: No space left on device


Then logically I thought the /home/mysql/ mounted ext4 partition got filled, because of crashed SQL database or a bug thus, checked with disk free command df whether there is enough space on server:

server:~# df -h
Filesystem Size Used Avail Use% Mounted on
/dev/md1 20G 7.6G 11G 42% /
udev 10M 0 10M 0% /dev
tmpfs 13G 1.3G 12G 10% /run
tmpfs 32G 0 32G 0% /dev/shm
tmpfs 5.0M 0 5.0M 0% /run/lock
tmpfs 32G 0 32G 0% /sys/fs/cgroup
/dev/md2 256G 134G 110G 55% /home

Well that's weird? Obviously only 55% of available disk space is used and available 134G which was more than enough so I got totally puzzled why, files can't be written.

Then very logically, I thought it might be that /home directory has remounted as read only, because the SSD memory disk on server is failing and checked for errors in dmesg, i.e.:

 

server:~# dmesg|grep -i error


Also checked how exactly was partition mounted, to check whether it is (RO) read-only:

 

server:~# mount -l|grep -i /home
/dev/md2 on /home type ext4 (rw,relatime,discard,data=ordered)


Now everything become even more weirder, as obviously the disk continued to be claiming no space left on device, while in reality there was plenty of disk space.

Then after running a quick research on the internet for the no space left on device with free disk space, I've come across this great superuser.com thread which let me realize the partition run out of inodes and that's why no new file inodes could be assigned and therefore, the linux kernel is refusing to write the file on ext4 partition.

For those who haven't heard of Linux Partition Inodes here is link to Wikipedia and a quick quote:

 

In a Unix-style file system, the inode is a data structure used to represent a filesystem object, which can be one of various things including a file or a directory. Each inode stores the attributes and disk block location(s) of the filesystem object's data.[1] Filesystem object attributes may include manipulation metadata (e.g. change,[2] access, modify time), as well as owner and permission data (e.g. group-id, user-id, permissions).[3]
Directories are lists of names assigned to inodes. The directory contains an entry for itself, its parent, and each of its children.


Once I understood it is the inodes, I checked how many of them are occupied with cmd:

 

server:~# df -i /home
Filesystem Inodes IUsed IFree IUse% Mounted on
/dev/md2 17006592 17006592 0 100% /home


You see, there were 0 (zero) free file inodes on server and that was the reason for no space left on device while there was actually free disk space

To clean up (free) some inodes on partition, first thing I did is to delete all old logs which were inside /home and files I positively know not to be necessery, then to find which directories allocating most innodes used:

 

server:~# find . -xdev -type f | cut -d "/" -f 2 | sort | uniq -c | sort -n


If you're on a regular old fashined IDE Hard Drive and not SSD or you have too much files inside this command will take really long …:

Therefore a better solution might be to frist:

a) Try to find root folders with large inodes count:

for i in /home/*; do echo $i; find $i |wc -l; done
Try to find specific folders:


You should get output like:

 

/home/new_website
606692
/home/common
73
/home/pcfreak
5661
/home/hipo
33
/home/blog
13570
/home/log
123
/home/lost+found
1

b) Then once you know the directory allocating most inodes, run the command again to see the sub-directories with most files (eating) partition innodes:

 

for i in /home/webservice/*; do echo $i; find $i |wc -l; done

 

One usual large folder which could free you some nodes is the linux source headers, but in my case it was simply a lot of tiny old logs being logged on the system for few years in the past without cleaning:

After deleting the log dirs and cache folder in my case /home/new_website/{log,cache}:

server:~# rm -rf /home/new_website/log/*
server:~# rm -rf /home/new_website/cache/*

 

 

a) Then, stopping Apache webserver to check prevent Apache to use MySQl databases while running database repair and restaring MySQL:
 

server:~# /etc/init.d/apache2 stop Restarting MySQL server
..
server:~# /etc/init.d/mysql restart
..


b) And re-issuing MySQL Check / Repair / Optimize database commands:
 

 

mysqlcheck –defaults-extra-file=/etc/mysql/debian.cnf \–check –all-databases -u root -p`grep -i password /root/.my.cnf |sed -e 's#password=##g'`>> /var/log/cronwork.log

mysqlcheck –defaults-extra-file=/etc/mysql/debian.cnf –analyze –all-databases -u root -p`grep -i password /root/.my.cnf |sed -e 's#password=##g'`>> /var/log/cronwork.log

mysqlcheck –defaults-extra-file=/etc/mysql/debian.cnf \–auto-repair –optimize –all-databases -u root -p`grep -i password /root/.my.cnf |sed -e 's#password=##g'`>> /var/log/cronwork.log

mysqlcheck –defaults-extra-file=/etc/mysql/debian.cnf \–optimize –all-databases -u root -p`grep -i password /root/.my.cnf |sed -e 's#password=##g'`>> /var/log/cronwork.log

c) And finally starting the Apache Webserver again:
 

server:~# /etc/init.d/apache2 start


Some innodse got freed up:
 

server:~# df -i /home Filesystem Inodes IUsed IFree IUse% Mounted on
/dev/md2 17006592 16797196 209396 99% /home


And hooray by God's Grace and with help of prayers of The most Holy Theotokos (Virgin) Mary, websites started again !

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Adding another level of security to your shared Debian Linux webhosting server with SuPHP

Tuesday, April 7th, 2015

suphp_improve-apache-security-protect-against-virus-internal-server-infections-suphp-webserver-logo

There are plenty of security schemes and strategies you can implement if you're a Shared Web Hosting company sysadmin however probably the most vital one is to install on Apache + PHP Webserver SuPHP module.

# apt-cache show suphp-common|grep -i descrip -A 4

Description: Common files for mod suphp Suphp consists of an Apache module (mod_suphp for either Apache 1.3.x or Apache 2.x) and a setuid root binary (suphp) that is called by the Apache module to change the uid of the process executing the PHP interpreter to the owner of the php script.

So what SuPHP actuall  does is to run separate CPanel / Kloxo etc. Users with separate username and groupid permissions coinciding with the user present in /etc/passwd , /etc/shadow files existing users, thus in case if someone hacks some of the many customer sites he would be able to only write files and directories under the user with which the security breach occured.

On servers where SuPHP is not installed, all  systemusers are using the same UserID / GuID to run PHP executable scripts under separate domains Virtualhost which are coinciding with Apache (on Debian / Ubuntu  uid, gid – www-data) or on (CentOS / RHEL / Fedora etc. – user apache) so once one site is defaced  exploited by a worm all or most server websites might end up infected with a Web Virus / Worm which will be trying to exploit even more sites of a type running silently in the background.  This is very common scenarios as currently there are donezs of PHP / CSS / Javasripts / XSS vulnerability exploited on VPS and Shared hosting servers due to failure of a customer to update his own CMS  scripts / Website  (Joomla, Wordpress, Drupal etc.) and the lack of resource to regularly monitor all customer activities / websites.

Therefore installing SuPHP Apache module is essential one to install on new serverslarge hosting providers as it saves the admin a lot of headache from spreading malware across all hosted servers sites ..
Some VPS admins that are security freaks tend to also install SuPHP module together with many chrooted Apache / LiteSpeed / Nginx webservers each of which running in a separate Jailed environment.

Of course using SuPHP besides giving a improved security layer to the webserver has its downsides such as increased load for the server and making Apache PHP scripts being interpretted a little bit slower than with plain Apache + PHP but performance difference while running a site on top of SuPHP is often not so drastic so you can live it up ..

Installing SuPHP on a Debian / Ubuntu servers is a piece of cake, just run the as root superuser, usual:
 

# apt-get install libapache2-mod-suphp


Once installed only thing to make is to turn off default installed Apache PHP module (without SuPHP compiled support and restart Apache webserver):
 

# a2dismod php5 …

# /etc/init.d/apache2 restart


To test the SuPHP is properly working on the Apache Webserver go into some of many hosted server websites DocumentRoot

And create new file called test_suphp.php with below content:

# vim test_suphp.php
<?php
system('id');
?>

Then open in browser http://whatever-website/test_suphp.php assuming that system(); function is not disabled for security reasons in php.ini you should get an User ID, GroupID bigger than reserved system IDs on GNU / Linux e.g. ID > UID / GID 99

Its also a good idea to take a look into SuPHP configuration file /etc/suphp/suphp.conf and tailor options according to your liking 

If different hosted client users home directories are into /home directory, set in suphp.conf

;Path all scripts have to be in

docroot=/home/


Also usually it is a good idea to set 

umask=0022 

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Check your Server Download / Upload Internet Speed from Console on Linux / BSD / Unix howto

Tuesday, March 17th, 2015

tux-check-internet-network-download-upload-speed-on-linux-console-terminal-linux-bsd-unix
If you've been given a new dedicated server from a New Dedicated-Server-Provider or VPS with Linux and you were told that a certain download speed to the Server is guaranteed from the server provider, in order to be sure the server's connection to the Internet told by service provider is correct it is useful to run a simple measurement console test after logging in remotely to the server via SSH.

Testing connection from Terminal is useful because as you probably know most of Linux / UNIX servers doesn't have a GUI interface and thus it is not possible to test Internet Up / Down Bandwidth through speedtest.net.
 

1. Testing Download Internet Speed given by ISP / Dedi-Server Provider from Linux Console

For the download speed (internet) test the historical approach was to just try downloading the Linux kernel source code from www.kernel.org with some text browser such as lynx or links count the seconds for which the download is completed and then multiple the kernel source archive size on the seconds to get an approximate bandwidth per second, however as nowdays internet connection speeds are much higher, thus it is better to try to download some Linux distribution iso file, you can still use kernel tar archive but it completed too fast to give you some good (adequate) statistics on Download bandwidth.

If its a fresh installed Linux server probably you will probably not have links / elinks and lynx text internet browers  installed so install them depending on deb / rpm distro with:

If on Deb Linuz distro:

 

root@pcfreak:/root# apt-get install –yes links elinks lynx

 

On RPM Based Linuz distro:
 

 

[root@fedora ~]# yum install -y lynx elinks links

 

Conduct Internet  Download Speed with links
root@pcfreak:/root# links https://www.kernel.org/pub/linux/kernel/v3.x/linux-3.19.1.tar.xz

check_your_download_speed-from-console-linux-with-links-text-browser

(Note that the kernel link is current latest stable Kernel source code archive in future that might change, so try with latest archive.)

You can also use non-interactive tool such as wget curl or lftp to measure internet download speed

To test Download Internet Speed with wget without saving anything to disk set output to go to /dev/null 

 

root@pcfreak:~# wget -O /dev/null http://pc-freak.net/~hipo/hirens-bootcd/HirensBootCD15/Hirens.BootCD.15.0.zip

 

check_bandwidth_download-internet-speed-with-wget-from-console-non-interactively-on-linux

You see the Download speed is 104 Mbit/s this is so because I'm conducting the download from my local 100Mbit network.

For the test you can use my mirrored version of Hirens BootCD

2. Testing Uplink Internet speed provided by ISP / Server Provider from Linux (SSH) Console

To test your uplink speed you will need lftp or iperf command tool.

 

root@pcfreak:~# apt-cache show lftp|grep -i descr -A 12
Description: Sophisticated command-line FTP/HTTP client programs
 Lftp is a file retrieving tool that supports FTP, HTTP, FISH, SFTP, HTTPS
 and FTPS protocols under both IPv4 and IPv6. Lftp has an amazing set of
 features, while preserving its interface as simple and easy as possible.
 .
 The main two advantages over other ftp clients are reliability and ability
 to perform tasks in background. It will reconnect and reget the file being
 transferred if the connection broke. You can start a transfer in background
 and continue browsing on the ftp site. It does this all in one process. When
 you have started background jobs and feel you are done, you can just exit
 lftp and it automatically moves to nohup mode and completes the transfers.
 It has also such nice features as reput and mirror. It can also download a
 file as soon as possible by using several connections at the same time.

 

root@pcfreak:/root# apt-cache show iperf|grep -i desc -A 2
Description: Internet Protocol bandwidth measuring tool
 Iperf is a modern alternative for measuring TCP and UDP bandwidth performance,
 allowing the tuning of various parameters and characteristics.

 

To test Upload Speed to Internet connect remotely and upload any FTP file:

 

root@pcfreak:/root# lftp -u hipo pc-freak.net -e 'put Hirens.BootCD.15.0.zip; bye'

 

uploading-file-with-lftp-screenshot-test-upload-internet-speed-linux

On Debian Linux to install iperf:

 

root@pcfreak:/root# apt-get install –yes iperf

 

On latest CentOS 7 and Fedora (and other RPM based) Linux, you will need to add RPMForge repository and install with yum

 

[root@centos ~]# rpm -ivh  rpmforge-release-0.5.3-1.el7.rf.x86_64.rpm

[root@centos ~]# yum -y install iperf

 

Once having iperf on the server the easiest way currently to test it is to use
serverius.net speedtest server –  located at the Serverius datacenters, AS50673 and is running on a 10GE connection with 5GB cap.

 

root@pcfreak:/root# iperf -c speedtest.serverius.net -P 10
————————————————————
Client connecting to speedtest.serverius.net, TCP port 5001
TCP window size: 16.0 KByte (default)
————————————————————
[ 12] local 83.228.93.76 port 54258 connected with 178.21.16.76 port 5001
[  7] local 83.228.93.76 port 54252 connected with 178.21.16.76 port 5001
[  5] local 83.228.93.76 port 54253 connected with 178.21.16.76 port 5001
[  9] local 83.228.93.76 port 54251 connected with 178.21.16.76 port 5001
[  3] local 83.228.93.76 port 54249 connected with 178.21.16.76 port 5001
[  4] local 83.228.93.76 port 54250 connected with 178.21.16.76 port 5001
[ 10] local 83.228.93.76 port 54254 connected with 178.21.16.76 port 5001
[ 11] local 83.228.93.76 port 54255 connected with 178.21.16.76 port 5001
[  6] local 83.228.93.76 port 54256 connected with 178.21.16.76 port 5001
[  8] local 83.228.93.76 port 54257 connected with 178.21.16.76 port 5001
[ ID] Interval       Transfer     Bandwidth
[  9]  0.0-10.2 sec  4.05 MBytes  3.33 Mbits/sec
[ 10]  0.0-10.2 sec  3.39 MBytes  2.78 Mbits/sec
[ 11]  0.0-10.3 sec  3.75 MBytes  3.06 Mbits/sec
[  4]  0.0-10.3 sec  3.43 MBytes  2.78 Mbits/sec
[ 12]  0.0-10.3 sec  3.92 MBytes  3.18 Mbits/sec
[  3]  0.0-10.4 sec  4.45 MBytes  3.58 Mbits/sec
[  5]  0.0-10.5 sec  4.06 MBytes  3.24 Mbits/sec
[  6]  0.0-10.5 sec  4.30 MBytes  3.42 Mbits/sec
[  8]  0.0-10.8 sec  3.92 MBytes  3.03 Mbits/sec
[  7]  0.0-10.9 sec  4.03 MBytes  3.11 Mbits/sec
[SUM]  0.0-10.9 sec  39.3 MBytes  30.3 Mbits/sec

 

You see currently my home machine has an Uplink of 30.3 Mbit/s per second, that's pretty nice since I've ordered a 100Mbits from my ISP (Unguaranteed Bandwidth Connection Speed) and as you might know it is a standard practice for many Internet Proviers to give Uplink speed of 1/4 from the ISP provided overall bandwidth 1/4 would be 25Mbi/s, meaning my ISP (Bergon.NET) is doing pretty well providing me with even more than promised (ordered) bandwidth.

Iperf is probably the choice of most sysadmins who have to do regular bandwidth in local networks speed between 2 servers or test  Internet Bandwidth speed on heterogenous network with Linux / BSDs / AIX / HP-UX (UNIXes). On HP-UX and AIX and other UNIXes for which iperf doesn't have port you have to compile it yourself.

If you don't have root /admin permissions on server and there is python language enterpreter installed you can use speedtest_cli.py script to test internet throughput connectivity
speedtest_cli uses speedtest.net to test server up / down link just in case if script is lost in future I've made ownload mirror of speedtest_cli.py is here

Quickest way to test net speed with speedtest_cli.py:

 

$ lynx -dump https://raw.github.com/sivel/speedtest-cli/master/speedtest_cli.py > speedtest_cli.py
$ chmod +x speedtest_cli.py
python speedtest_cli.py

speedtest_cli_pyhon_script_screenshot-on-gnu-linux-test-internet-network-speed-on-unix

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WordPress Security: Fix WordPress wp-config.php improper permissions to protect your sites from Database password steal / Website deface

Thursday, March 12th, 2015

wordpress-security-Fix-wordpress-wp-config-improper-permissions-to-protect-your-sites-from-Database-pass-steal
Keeping WordPress Site / Blog and related installed plugins up-to-date
is essential to prevent an attacker to hack into your Site / Database and deface your site, however if you're a company providing shell access from Cpanel / Plesk / Kloxo Panel to customers often customers are messing up permissions leaving important security credential files such as wp-config.php (which is storing user / pass credentials about connection to MySQL / PostgreSQL to have improper permissions and be world readable e.g. have permissions such as 666 or 777 while in reality the WordPress recommended permissions for wp-config.php is 600. I will skip here to explain in details difference between file permissions on Linux as this is already well described in any Linux book, however I just will recommend for any Share hosting Admin where Wordperss is hosted on Lighttpd / Apache Webserver + Some kind of backend database to be extra cautious.

Hence it is very useful to list all your WordPress sites on server wp-config.php permissions with find like this:

 

find /  -iname 'wp-config.php' -print1;

 

I find it a generally good practice to also automatically set all wp-config.php permissions to 600 (6= Read / Write  permissions only for File Owner  user 0 = No permissions for All groups, 0 = No Permissions for all non-owner users)

If find command output gives you some file permissions such as:
 

ls -al /var/www/wordpress-bak/wp-config.php
-rw-rw-rw- 1 www-data www-data 2654 jul 28  2009 wp-config.php

 

E.g. file permission has 666 permissions (Readable for all users), then it is wise to fix this with:
 

chmod 600 /var/www/wordpress-bak/wp-config.php


It is generally a very good practice to run also a chmod 600 to each and every found wp-config.php file on server:
 

find /  -iname 'wp-config.php' -print1 -exec chmod 600 '{}' \;


Above command will also print each file to whcih permission is set to Read / Write for Owner (this si done with -print1 option).

It is a good practice for shared hosting server to always configure a root cronjob to run above find chmod command at least once daily (whenever server hosts 50 – 100 wordpress+ more sites).
 

crontab -u root -l | { cat; echo “05 03 * * * find /  -iname 'wp-config.php' -print1 -exec chmod 600 '{}' \; } | crontab – 


If you don't have the 600 permissions set for all wp-config.php files this security "backdoor" can be used by any existing non-root user to be read and to break up (crack)  in your database and even when there are Deface bot-nets involved to deface all your hosted server wordpress sites.

One of my servers with wordpress has just recently suffered with this little but very important security hole due to a WordPress site directory backup  with improper permissions which allowed anyone to enter MySQL database, so I guess there are plenty of servers with this hidden vulnerability silently living.

Many thanks to my dear friend (Dimitar PaskalevNomen for sharing with me about this vulnerability! Very important note to make here is admins who are using some security enhancement modules such as SuPHP (which makes Apache webserver to run Separate Website instances with different user), should be careful with his set all wp-config.php modules to Owner, as it is possible the wp-config.php owner change to make customer WP based websites inaccessible.

Another good security measure to  protect your server WordPress based sites from malicious theme template injections (for both personal own hosted wordpress based blog / sites or a WordPress hosting company) is to install and activate WordPress Antivirus plugin.

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Speed up WordPress / Joomla CMS and MySQL server on Linux with tmpfs ram file system / Decrease Website pageload times with RAM caching

Wednesday, March 4th, 2015

speed-up-accelerate-wordpress-joomla-drupal-cms-and-mysql-server-with-tmpfs_ramfs_decrease-pageload-times-with-ram-caching
As a WordPress blog owner and an sys admin that has to deal with servers running a lot of WordPress / Joomla / Droopal and other custom CMS installed on servers, performoing slow or big enough to put a significant load on servers
and I love efficiency and hardware cost saving is essential for my daily job, I'm constantly trying to find new ways to optimize Customer Website (WordPress) and rest of sites in order to utilize better our servers and improve our clients sites speed (and hence satisfaction). 

There is plenty of little things to do on servers but probably among the most crucial ones which we use nowadays that save us a lot of money is tmpfs, and earlier (ramfs) – previously known as shmfs).
TMPFS is a (Temporary File Storage Facility) Linux kernel technology based on ramfs (used by Linux kernel initrd / initramfs on boot time in order to load and store the Linux kernel in memory, before system hard disk partition file systems are mounted) which is heavily used by virtually all modern popular Linux distributions. 

Using ramfs (cramfs variation – Compressed ROM filesystem) has been used to store different system environment kernel and Desktop components of many Linux environment / applications and used by a lot of the Linux BootCD such as the most famous (Klaus Knopper's) KNOPPIX LiveCD and Trinity Rescue Kit Linux (TRK uses /dev/shm which btw can be seen on most modern Linux distros and is actually just another mounted tmpfs).
If you haven't tried Live Linux yet try it out as me and a lot of sysadmins out there use some kind of LiveLinux at least few times on yearly basis  to Recover Unbootable Linux servers after some applied remote Updates as well as for Rescuing (Save) Data from Linux server failing to properly boot because of hard disk (bad blocks) failures. As I said earlier TMPFS is also used on almost any distribution for the /dev/ filesystem which is kept in memory.

You can see which tmpfs partitions is used on your Linux server with:

 

debian-server:~# mount |grep -i tmpfs
tmpfs on /lib/init/rw type tmpfs (rw,nosuid,mode=0755)
udev on /dev type tmpfs (rw,mode=0755)
tmpfs on /dev/shm type tmpfs (rw,nosuid,nodev)

 

Above is an output from a standard Debian Linux server. On CentOS 7 standard mounted tmpfs are as follows:

 

[root@centos ~]# mount |grep -i tmpfs
devtmpfs on /dev type devtmpfs (rw,nosuid,seclabel,size=1016332k,nr_inodes=254083,mode=755)
tmpfs on /dev/shm type tmpfs (rw,nosuid,nodev,seclabel)
tmpfs on /run type tmpfs (rw,nosuid,nodev,seclabel,mode=755)
tmpfs on /sys/fs/cgroup type tmpfs (rw,nosuid,nodev,noexec,seclabel,mode=755)

 

[root@centos ~]# df -h|grep -i tmpfs
devtmpfs                 993M     0  993M   0% /dev
tmpfs                   1002M   92K 1002M   1% /dev/shm
tmpfs                   1002M  8.8M  993M   1% /run
tmpfs                   1002M     0 1002M   0% /sys/fs/cgroup

The /run tmpfs mounted directory is also to be seen also on latest Ubuntus and Fedoras and is actually the good old /var/run ( where applications keep there pids and some small app related files) stored in tmpfs filesystem stored in memory.

If you're wondering what is /dev/shm and why it appears mounted on every single Linux Server / Desktop you've ever used this is a special filesystem shared memory which various running programs (processes) can use to transfer data quick and efficient between each other to preven the slow disk swapping. People using Linux for the rest 15 years should remember /dev/shm has been a target of a lot of kernel exploits as historically it had a lot of security issues.

While writting this article I've just checked about KNOPPIX developed amd just for info as of time of writting this distro has already 1000+ programs on CD version and 2600+ packages / application on DVD version.
Nowadays Knoppix is mostly used mostly as USB Live Flash drive as a lot of people are dropping CD / DVD use (many servers doesn't have a CD / DVD Drive) and for USB Live Flash Linux distros tmpfs is also key technology used as this gives the end user an amazing fast experience (Desktop applications run much fasten on Live USBs when tmpfs is used than when the slow 7200 RPM HDDs are used).

Loading big parts of the distribution within RAM (with tmpfs from Linux Kernel 2.4+ onwards) is also heavily used by a lot of Cluster vendors in most of Clustered (Cloud) Linux based environemnts, cause TMPFS gives often speeds up improvements to x30 times and decreases greatly I/O HDD. FreeBSD users will be happy to know that TMPFS is already ported and could be used on from FreeBSD 7.0+ onward.

In this small article I will give you example use on how I use tmpfs to speed up our WordPress Websites which use WP Caching plugins such as W3 Total Cache and WP Super Cache
and Hyper Cache / WP Super Cache disk caching and MySQL server as a Database backend.
Below example is wordpress specific but since it can be easily applied to JoomlaDrupal or any other CMS out there that uses mySQL server to make a lot of CPU expensive memory hungry (LEFT JOIN) queries which end up using a slow 7200 RPM hard disk.


 

1. Preparing tmpfs partitions for WordPress File Cache directory
 

If you want to give tmpfs a test drive, I recommend you try to create / mount a 20 Megabyte partition. To create a tmpfs partition you don't need to use a tool like mkfs.ext3 / mkfs.ext4 as TMPFS is in reality a virtual filesystem that is mapped in the server system physical RAM (volatile memory). TMPFS is very nice because if you run out of free RAM system starts a combination of RAM use + some Hard disk SWAP 
The great thing about TMPFS is it never uses all of the available RAM and SWAP, which would not halt your server if TMPFS partition gets filled, but instead you will start getting the usual "Insufficient Disk Space", just like with a physical HDD parititon. RAMFS cares much less about server compared to TMPFS, because if RAMFS is historically older.

ramfs file systems cannot be limited in size like a disk base file system which is limited by it’s capacity, thus ramfs will continue using memory storage until the system runs out of RAM and likely crashes or becomes unresponsive. This is a problem if the application writing to the file system cannot be limited in total size, so in my opinion you better stay away from RAMFS except you have a good idea what you're doing. Another disadvantage of RAMFS compared to TMPFS is you cannot see the size of the file system in df and it can only be estimated by looking at the cached entry in free.

Note that before proceeding to use TMPFS or RAMFS you should know besides having advantages, there are certain serious disadvantage that if the server using tmpfs (in RAM) to store files crashes the customer might loose his data, therefore using RAM filesystems on Production servers is best to be used just for caching folders which are regularly synchronized with (rsync) to some folder to assure no data will be lost on server reboot or crash.

Memory of fast storage areas are ideally suited for applications which need repetitively small data areas for caching or using as temporary space such as Jira (Issue and Proejct Tracking Software) Indexing  As the data is lost when the machine reboots the tmpfs stored data must not be data of high importance as even scheduling backups cannot guarantee that all the data will be replicated in the even of a system crash.

To test mounting a tmpfs virtual (memory stored) filesystem issue:
 

mount -t tmpfs tmpfs -o size=256m /mnt/tmpfs


If you want to test mount a ramfs instead:

 

 mount -t ramfs -o size=256m ramfs /mnt/ramfs

 

debian-server:~#  mount |grep -i -E "ramfs|tmpfs"
tmpfs on /lib/init/rw type tmpfs (rw,nosuid,mode=0755)
udev on /dev type tmpfs (rw,mode=0755)
tmpfs on /dev/shm type tmpfs (rw,nosuid,nodev)
tmpfs on /mnt/tmpfs type tmpfs (rw,size=256m)
ramfs on /mnt/ramfs type tmpfs (rw,size=256m)

 

Once mounted tmpfs can be used in the same way as any ext4 / reiserfs filesystem. In the same way to make mounts permanent, its necessery to add a line to /etc/fstab

To illustrate better a tmpfs use case on my blog running WordPress with W3TotalCache (W3TC) plugin cache folder in /var/www/blog/wp-content/w3tc to get advantage of tmpfs to store w3tc files.

a) Stop Apache

On Debian
 

debian-server:~# /etc/init.d/apache stop


On CentOS 
 

[root@centos ~]# /etc/init.d/httpd stop


b) Move w3tc dir to w3tc-bak

 

debian-server:~# cd /var/www/blog/wp-content/
debian-server:~# mv w3tc w3tc-bak

 

c) Create w3tc directory
 

debian-server:/var/www/blog/wp-content# mkdir w3tc
debian-server:/var/www/blog/wp-content# chown -R www-data:www-data w3tc


d) Add tmpfs record to /etc/fstab

My W3TC Cache didn't grow bigger than 2Gigabytes so I create a 2Giga directory for it by adding following in /etc/fstab 
 

debian-server:~# vim /etc/fstab

 

tmpfs /var/www/blog/wp-content/w3tc tmpfs defaults,size=2g,noexec,nosuid,uid=33,gid=33,mode=1755 0 0


You might also want to add the nr_inodes (option) to tmpfs while mounting. nr_inodes is the maximum inode for instance. Default is half the number of your physical RAM pages, (on a machine with highmem) the number of lowmem RAM page, some common option that should work is nr_inodes=5k, if you're unsure what this option does you can safely skip it 🙂

e) Mount new added tmpfs folder

Then to mount the newly added filesystem issue:
 

mount -a


Or if you're on a CentOS / RHEL server use httpd Apache user instead and whenever you have docroot and wordpress installed.

 

[root@centos ~]# chown -R apache:apache: w3tc


If you're using Apache SuPHP use whatever the UID / GID is proper.

On CentOS you will need to set proper UID and GID (UserID / GroupID), to find out which ones to to use check in /etc/passwd:
 

[root@centos ~]# grep -i apache /etc/passwd
apache:x:48:48:Apache:/var/www:/sbin/nologin


f) Move old w3tc cache from w3tc-bak to w3tc

 

debian-server:/var/www/blog/wp-content# mv w3tc-bak/* w3tc/

 

g) Start again Apache

On Debian:

 

debian-server:~# /etc/init.d/apache2 start

 


On CentOS:
 

[root@centos~]# /etc/init.d/httpd start

h) Keeping w3tc cache site folder synced

As I said earlier the biggest problem with caching (the reason why many hosting providers) and site admins refuse to use it is they might loose some data, to prevent data loss or at least mitigate the data loss to few minutes intervals it is a good idea to synchronize tmpfs kept folders somewhere to disk with rsync.

To achieve that use a cronjob like this:
 

debian-server:~# crontab -u root -e
*/5 * * * * /usr/bin/ionice -c3 -n7 /usr/bin/nice -n 19 /usr/bin/rsync -ah –stats –delete /var/www/blog/wp-content/w3tc/ /backups/tmpfs/cache/ 1>/dev/null


Note that you will need to have the /backups/tmpfs/cache folder existing, create it with:

 

debian-server:~# mkdir -p /backups/tmpfs/cache


You will also need to add a rsync synchronization from backupped folder to tmpfs (in case if the server gets accidently rebooted because it hanged or power outage), place in

/etc/rc.local

 

ionice -c3 -n7 nice -n 19 rsync -ahv –stats –delete /backups/tmpfs/cache/ /var/www/blog/wp-content/w3tc/ 1>/dev/null


(somewhere before exit 0) line
 

0 05 * * * /usr/bin/ionice -c3 -n7 /bin/nice -n 19 /usr/bin/rsync -ah –stats –delete /var/www/blog/wp-content/w3tc/ /backups/tmpfs/cache/ 1>/dev/null

 

 

2. Preparing tmpfs partitions for MySQL server temp File Cache directory


Its common that MySQL servers had to serve a lot of long and heavy SQL JOIN Queries mostly by related posts WP plugins such as (Zemanta Related Posts) and Contextual Related posts though MySQLs are well optimized  to work as much as efficient using mysql tuner (tuning primer) still often SQL servers get a lot of temp tables created to disk (about 25% to 30%) of all SQL queries use somehow HDD to serve queries and as this is very slow and there is file lock created the overall MySQL performance becomes sluggish at times to fix (resolve) that without playing with SQL code to optimize the slow queries the best way I found is by using TMPFS as MySQL temp folder.

To do so I create a TMPFS usually the size of 256 MB because this is usually enough for us, but other hosting companies might want to add bigger virtual temp disk:

a) Add tmpfs new dir to /etc/fstab

In /etc/fstab add below record with vim editor:
 

debian-server:~# vim /etc/fstab

 

tmpfs /var/mysqltmp tmpfs rw,gid=111,uid=108,size=256M,nr_inodes=10k,mode=0700 0 0

 

Note that the uid / and gid 105 and 114 are taken again from /etc/passwd

On Debian

debian-server:~# grep -i mysql /etc/passwd
mysql:x:108:111:MySQL Server,,,:/var/lib/mysql:/bin/false


On CentOS
 

[root@centos ~]# grep -i mysql /etc/passwd
mysql:x:27:27:MySQL Server:/var/lib/mysql:/bin/bash


b) Create folder /var/mysqltmp or whenever you want to place the tmpfs memory kept SQL folder

 

debian-server:~# mkdir /var/mysqltmp
debian-server:~# chown mysql:mysql /var/mysqltmp

 

debian-server:~# mount|grep -i tmpfs
tmpfs on /lib/init/rw type tmpfs (rw,nosuid,mode=0755)
udev on /dev type tmpfs (rw,mode=0755)
tmpfs on /dev/shm type tmpfs (rw,nosuid,nodev)
tmpfs on /var/www/blog/wp-content/w3tc type tmpfs (rw,noexec,nosuid,size=2g,uid=33,gid=33,mode=1755)
tmpfs on /var/mysqltmp type tmpfs (rw,gid=108,uid=111,size=256M,nr_inodes=10k,mode=0700)


c) Add new path to tmpfs created folder in my.cnf 

Then  edit /etc/mysql/my.cnf

 

debian-server:~# vim /etc/mysql/my.cnf

[mysqld]
#
# * Basic Settings
#
user        = mysql
pid-file    = /var/run/mysqld/mysqld.pid
socket      = /var/run/mysqld/mysqld.sock
port        = 3306
basedir     = /usr
datadir     = /var/lib/mysql
tmpdir      = /var/mysqltmp

 

On CentOS edit and change tmpdir in same way within /etc/my.cnf


d) Finally Restart Apache and MySQL to make mysql start using new set tmpfs memory kept folder

On Debian:
 

debian-server:~# /etc/init.d/apache2 stop; /etc/init.d/mysql restart; /etc/init.d/apache2 start

On CentOS:
 

[root@centos ~]# /etc/init.d/httpd stop; /etc/init.d/mysqld restart; /etc/initd/httpd start


Now monitor your server and check your pagespeed increase for me such an optimization usually improves site performance so site becomes +50% faster, to see the difference you can test your website before applying tmpfs caching for site and after that by using Google PageInsight (PageSpeed) Online Test. Though this example is for MySQL and WordPress you can easily adopt the same for Joomla if you have Joomla Caching enabled to some folder, same goes for any other CMS such as Drupal that can take use of Disk Caching. Actually its a small secret of many Hosting providers that allow clients to create sites via CPanel and Kloxo this tmpfs optimizations are already used for sites and by this the provider is able to offer better website service on lower prices. VPS hosting providers also use heavy caching. A lot of people are using TMPFS also to accelerate Sites that have enabled Google Pagespeed as Cacher and accelerator, as PageSpeed module puts a heavy HDD I/O load that can easily stone the server. Many admins also choose to use TMPFS for  /tmp, /var/run, and /var/lock directories as this leads often to significant overall server services operations improvement.
Once you have tmpfs enabled, It is a good idea to periodically monitor your SWAP used space with (df -h), because if you allocate bigger tmpfs partitions than your physical memory and tmpfs's full size starts to be used your machine will start swapping heavily and this could have a very negative performance affect.
 

debian-server:~# df -h|grep -i tmpfs
tmpfs            3,9G     0   3,9G   0% /lib/init/rw
tmpfs            3,9G     0   3,9G   0% /dev/shm
tmpfs            2,0G  1,4G   712M  66% /var/www/blog/wp-content/w3tc
tmpfs            256M     0   256M   0% /mnt/tmpfs
tmpfs            256M  236K   256M   1% /var/mysqltmp

The applications of tmpfs to accelerate services is up to your imagination, so I will be glad to hear from other admins on any interesting other application or problems faced while using TMPFS.

 Enjoy! 🙂

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How much memory users uses in GNU / Linux and FreeBSD – Commands and Scripts to find user memory usage on Linux

Tuesday, February 17th, 2015

 

how-much-memory-users-use-in-gnu-linux-freebsd-command-to-find-and-show-ascending-descending-usage-of-system-memory-tux-memory-logo

 


If you have to administrate a heterogenous network with Linux and FreeBSD or other UNIX like OSes you should sooner or later need for scripting purposes to have a way to list how much memory separate users take up on your system. Listing memory usage per user is very helpful for admins who manager free-shells or for companies where you have developers, developing software directly on the server via ssh. Being able to check which process eats up most memory is essential for every UNIX / Linux sysadmin, because often we as admins setup (daemons) on servers and we forgot about their existence, just to remember they exist 2 years later and see the server is crashing because of memory exhaustion. Tracking server bottlenecks where RAM memory and Swapping is the bottleneck is among the main swiss amry knives of admins. Checking which user occupies all server memory is among the routine tasks we're forced to do as admins, but because nowdays servers have a lot of memory and we put on servers often much more memory than ever will be used many admins forget to routinely track users / daemons memory consumption or even many probably doesn't know how.  Probably all are aware of the easiest wy to get list of all users memory in console non interactively with free command, e.g.:
 

free -m
             total       used       free     shared    buffers     cached
Mem:         32236      26226       6010          0        983       8430
-/+ buffers/cache:      16812      15424
Swap:        62959        234      62725

 

but unfortunately free command only shows overall situation with memory and doesn't divide memory usage by user

Thus probably to track memory users the only known way for most pepole is to (interactively) use good old top command or if you like modern (colorful) visualization with htop:

debian:~# top

 

linux-check_memory_usage_by_logged-in-user-with-top-process-command-gnu-linux-freebsd-screenshot

Once top runs interactive press 'm' to get ordered list of processes which occupy most system memory on Linux server.Top process use status statistics will refresh by default every '3.0' seconds to change that behavior to '1' second press  s and type '1.0'. To get Sort by Memory Use in htop also press 'm'
 

[root@mail-server ~]# htop


htop_show_users_memory_usage_order_ascending-gnu-linux-screenshot

 

However if you need to be involved in scripting and setting as a cron job tasks to be performed in case if high memroy consumption by a service you will need to use few lines of code. Below are few examples on how Linux user memory usage can be shown with ps cmd.

Probably the most universal way to see memory usage by users on Debian / Ubuntu / CentOS / RHEL and BSDs (FreeBSD / NetBSD) is with below one liner:

 

server:~# ps hax -o rss,user | awk '{a[$2]+=$1;}END{for(i in a)print i” “int(a[i]/1024+0.5);}' | sort -rnk2
daemon 0
debian-tor 63
dnscache 1
dnslog 0
hipo 21
messagebus 1
mysql 268
ntp 2
privoxy 1
proftpd 1
qmaill 0
qmailq 0
qmailr 0
qmails 0
qscand 291
root 94
shellinabox 1
snmp 1
statd 1
vpopmail 80
www-data 6765

 

Output is in MBs

Below is output from machine where this blog is running, the system runs ( Apache + PHP + MySQL Webserver + Qmail Mail server and Tor) on Debian GNU / Linux.

 To get more human readable (but obscure to type – useful for scripting) output list of which user takes how much memory use on deb / rpm etc. based Linux :

 

server:~# echo "USER                 RSS      PROCS" ; echo "——————– ——– —–" ; \
ps hax -o rss,user | awk '{rss[$2]+=$1;procs[$2]+=1;}END{for(user in rss) printf “%-20s %8.0f %5.0f\n”, user, rss[user]/1024, procs[user];}' | sort -rnk2

 

USER                 RSS      PROCS
——————– ——– —–
www-data                 6918   100
qscand                    291     2
mysql                     273     1
root                       95   120
vpopmail                   81     4
debian-tor                 63     1
hipo                       21    15
ntp                         2     1
statd                       1     1
snmp                        1     1
shellinabox                 1     2
proftpd                     1     1
privoxy                     1     1
messagebus                  1     1
dnscache                    1     1
qmails                      0     2
qmailr                      0     1
qmailq                      0     2
qmaill                      0     4
dnslog                      0     1
daemon                      0     2

 

It is possible to get the list of memory usage listed in percentage proportion, with a tiny for bash loop and some awk + process list command
 

TOTAL=$(free | awk '/Mem:/ { print $2 }')
for USER in $(ps haux | awk '{print $1}' | sort -u)
do
    ps hux -U $USER | awk -v user=$USER -v total=$TOTAL '{ sum += $6 } END { printf "%s %.2f\n", user, sum / total * 100; }'
done

107 1.34
115 2.10
119 1.34
daemon 1.32
dnscache 1.34
dnslog 1.32
hipo 1.59
mysql 4.79
ntp 1.34
privoxy 1.33
proftpd 1.32
qmaill 1.33
qmailq 1.33
qmailr 1.32
qmails 1.33
qscand 4.98
root 1.33
snmp 1.33
statd 1.33
vpopmail 2.35
www-data 86.48

Also a raw script which can be easily extended to give you some custom information on memory use by user list_memory_use_by_user.sh is here.
You can also want to debug further how much memory a certain users (lets say user mysql and my username hipo) is allocating, this can easily be achieved ps like so:
 

root@pcfreak:~# ps -o size,pid,user,command -u mysql –sort -size
 SIZE   PID USER     COMMAND
796924 14857 mysql   /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@pcfreak~# ps -o size,pid,user,command -u hipo –sort -size|less
 SIZE   PID USER     COMMAND
13408 19063 hipo     irssi
 3168 19020 hipo     SCREEN
 2940  2490 hipo     -bash
 1844 19021 hipo     /bin/bash
 1844 19028 hipo     /bin/bash
 1844 19035 hipo     /bin/bash
 1844 19042 hipo     /bin/bash
 1844 19491 hipo     /bin/bash
 1844 22952 hipo     /bin/bash
  744  2487 hipo     sshd: hipo@pts/0
  744  2516 hipo     sshd: hipo@notty
  524  2519 hipo     screen -r
  412  2518 hipo     /usr/lib/openssh/sftp-server

You see from below output user running with www-data (this is Apache Webserver user in Debian) is eating 86.48% of overall system memory and MySQL server user is using only 4.79% of available memory

Output is shown in Megabytes per username memory usage, and user memory usage is ordered (stepping-down / descentive) from top to bottom

Getting more thoroughful and easier to read reporting without beeing a 31337 bash coder you can install and use on Linux smem – memory reporting tool .

SMEM can provide you with following memory info:

  • system overview listing
  • listings by process, mapping, user
  • filtering by process, mapping, or user
  • configurable columns from multiple data sources
  • configurable output units and percentages
  • configurable headers and totals
  • reading live data from /proc
  • reading data snapshots from directory mirrors or compressed tarballs
  • lightweight capture tool for embedded systems
  • built-in chart generation


Installing smem on Debian 6 / 7 / Ubuntu 14.04 / Turnkey Linux etc. servers is done with standard:

 

debian:~# apt-get install –yes smem
….

 

 

To install smem on CentOS 6 / 7:

 

[root@centos ~ ]# yum -y install smem
….


On Slackware and other Linux-es where smem is not available as a package you can install it easily from binary archive with:

 

cd /tmp/
wget http://www.selenic.com/smem/download/smem-1.3.tar.gz
tar xvf smem-1.3.tar.gz
sudo cp /tmp/smem-1.3/smem /usr/local/bin/
sudo chmod +x /usr/local/bin/smem

 


Two most common smem uses are:

 

root@mail:~# smem -u
User     Count     Swap      USS      PSS      RSS
dnslog       1       44       48       54      148
qmaill       4      232      124      145      464
hipo        11    13552     8596     9171    13160
qscand       2     4500   295336   295602   297508
root       188   217312  4521080  4568699  7712776

 

Below command shows (-u – Report memory usage by user, -t – show totals, -k – show unix suffixes)

root@mail:~# smem -u -t -k
User     Count     Swap      USS      PSS      RSS
dnslog       1    44.0K    48.0K    54.0K   148.0K
qmaill       4   232.0K   124.0K   145.0K   464.0K
hipo        11    13.2M     8.4M     9.0M    12.9M
qscand       2     4.4M   288.4M   288.7M   290.5M
root       188   212.2M     4.3G     4.4G     7.4G
—————————————————
           206   230.1M     4.6G     4.6G     7.7G


To get users memory use by percentage with smem:
 

root@mail:~# smem -u -p
User     Count     Swap      USS      PSS      RSS
dnslog       1    0.00%    0.00%    0.00%    0.00%
qmaill       4    0.00%    0.00%    0.00%    0.01%
hipo        11    0.17%    0.11%    0.11%    0.16%
qscand       2    0.05%    3.63%    3.63%    3.66%
root       194    2.64%   56.18%   56.77%   95.56%

It is also useful sometimes when you want to debug system overloads caused by external hardware drivers loaded into kernel causing issues to get list of system wide memory use sorted by user

 

 root@mail:~# smem -w -p
Area                           Used      Cache   Noncache
firmware/hardware             0.00%      0.00%      0.00%
kernel image                  0.00%      0.00%      0.00%
kernel dynamic memory        38.30%     36.01%      2.28%
userspace memory             60.50%      0.98%     59.53%
free memory                   1.20%      1.20%      0.00%


smem is very nice as if you're running it on a Desktop Linux system with Xserver installed you can see also graphical output of memory use by application:
 

root@desktop-pc:~# smem –bar pid -c "pss uss"


smem_graphical_representation-of-which-user-application-is-consuming-most-memory-gnu-linux-kde-screenshot-smem-command-line-tool

smem can even generate graphical pie charts to visualize better memory use
 

root@desktop-pc:~# smem -P '^k' –pie=name

 

generate-graphical-staticstics-linux-memory-use-by-pie-chart

If there is a high percentage shown in firmware/hardware this means some buggy module is loaded in kernel eating up memory, to fix it debug further and remove the problematic module.
userspace memory actually shows the percantage of memory out of all server available RAM that is being consumed by applications (non kernel and other system processes which make the system move). You see in above example the kernel itself is consuming about 40% of system overall available memory. 

We all know the SWAP field stands for hard disk drive used as a memory when system is out, but there are 3 fields which smem will report which will be probably unclear for most here is also explanation on what USS / PSS / RSS means?

RSS is the Resident Set Size and is used to show how much memory is allocated to that process and is in RAM. It does not include memory that is swapped out. It does include memory from shared libraries as long as the pages from those libraries are actually in memory. It does include all stack and heap memory too.

There is also PSS (proportional set size). This is a newer measure which tracks the shared memory as a proportion used by the current process. So if there were two processes using the same shared library from before.

USS stands for Unique set size, USS is just the unshared page count, i.e. memory returned when process is killed 

PSS = Proportional set size, (PSS),  is a more meaningful representation of the amount of memory used by libraries and applications in a virtual memory system.  
Because large portions of physical memory are typically shared among multiple applications, the standard measure of memory usage known as resident set size (RSS) will significantly overestimate memory usage. The parameter PSS instead measures each application’s “fair share” of each shared area to give a realistic measure. For most admins checking out the output from RSS (output) should be enough, it will indicate which user and therefore which daemon is eating up all your memory and will help you to catch problematic services which are cause your server to run out of RAM and start swapping to disk.

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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.

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How to stop / start services in boot time and install / remove / update SuSE SLES (Suse Enterprise Linux Server)?

Friday, February 6th, 2015

Suse-Logo-stop-start-services-on-linux-boot-time-howto-chkconfig
If you're long time Linux sysadmin but you haven't need to adminster SuSE Linux still and your company buys other business / company which already owns some SuSE servers and you need to deal with them, even though you're just starting up with SuSE Linux but you had already plenty of experience with other Linux distributions Fedora / RHEL / CentOS, don't worry set up / stop / start a service (daemon) to boot on Linux boot time is just the same as any other Redhat (RPM) Linux based distributions. it is done by multiple shell scripts located in /etc/init.d directory which can be manually stopped start by issuing the script with an argument e.g
 

suse:/etc/init.d# cd /etc/init.d/
suse:/etc/init.d# ./snmpd 
Usage: ./snmpd {start|stop|try-restart|restart|force-reload|reload|status}


To configure how each of the /etc/init.d/ existent service boots you can the use good old /sbin/chkconfig (a script written in perl) – which you already know from Fedora / CentOS and other RPM distros.

1. Get a list of all enabled on boot SuSE Linux services

To get a list of all set up to run on boot SuSE server services with chkconfig:

 

suse:/etc/init.d# /sbin/chkfong –list 

Makefile                  0:off  1:off  2:off  3:off  4:off  5:off  6:off
OVCtrl                    0:off  1:off  2:off  3:on   4:on   5:on   6:off
SuSEfirewall2_init        0:off  1:off  2:off  3:off  4:off  5:off  6:off
SuSEfirewall2_setup       0:off  1:off  2:off  3:off  4:off  5:off  6:off
Tivoli_lcfd1              0:off  1:off  2:on   3:on   4:off  5:on   6:off
Tivoli_lcfd1.bkp          0:off  1:off  2:off  3:off  4:off  5:off  6:off
aaeventd                  0:off  1:off  2:off  3:off  4:off  5:off  6:off
acpid                     0:off  1:off  2:on   3:on   4:off  5:on   6:off
alsasound                 0:off  1:off  2:on   3:on   4:off  5:on   6:off
apache2-eis               0:off  1:off  2:off  3:off  4:off  5:off  6:off
atd                       0:off  1:off  2:off  3:off  4:off  5:off  6:off
auditd                    0:off  1:off  2:off  3:on   4:off  5:on   6:off
autofs                    0:off  1:off  2:off  3:off  4:off  5:off  6:off
autoyast                  0:off  1:off  2:off  3:off  4:off  5:off  6:off
boot.apparmor             0:off  1:off  2:on   3:on   4:off  5:on   6:off  B:on
cron                      0:off  1:off  2:on   3:on   4:off  5:on   6:off
dbus                      0:off  1:off  2:off  3:on   4:off  5:on   6:off
earlykbd                  0:off  1:off  2:off  3:off  4:off  5:on   6:off
earlysyslog               0:off  1:off  2:off  3:off  4:off  5:on   6:off
esound                    0:off  1:off  2:off  3:off  4:off  5:off  6:off
evms                      0:off  1:off  2:off  3:off  4:off  5:off  6:off
fbset                     0:off  1:on   2:on   3:on   4:off  5:on   6:off
firstboot                 0:off  1:off  2:off  3:off  4:off  5:off  6:off
fixperms                  0:off  1:off  2:off  3:off  4:off  5:off  6:off
gpm                       0:off  1:off  2:off  3:off  4:off  5:off  6:off
gssd                      0:off  1:off  2:off  3:off  4:off  5:off  6:off
gwproxy                   0:off  1:off  2:on   3:on   4:off  5:on   6:off
haldaemon                 0:off  1:off  2:off  3:on   4:off  5:on   6:off
hp-health                 0:off  1:off  2:on   3:on   4:on   5:on   6:off
hp-ilo                    0:off  1:off  2:off  3:on   4:off  5:on   6:off
hp-snmp-agents            0:off  1:off  2:on   3:on   4:on   5:on   6:off
hpsmhd                    0:off  1:off  2:off  3:on   4:on   5:on   6:off
idmapd                    0:off  1:off  2:off  3:off  4:off  5:off  6:off
ipmi                      0:off  1:off  2:off  3:off  4:off  5:off  6:off
ipmi.hp                   0:off  1:off  2:off  3:off  4:off  5:off  6:off
irq_balancer              0:off  1:on   2:on   3:on   4:off  5:on   6:off
itcaIBMTivoliCommonAgent0  0:off  1:off  2:on   3:on   4:off  5:on   6:off
jboss                     0:off  1:off  2:off  3:off  4:off  5:off  6:off
joystick                  0:off  1:off  2:off  3:off  4:off  5:off  6:off
kadmind                   0:off  1:off  2:off  3:off  4:off  5:off  6:off
kbd                       0:off  1:on   2:on   3:on   4:off  5:on   6:off  S:on
kdump                     0:off  1:off  2:off  3:off  4:off  5:off  6:off
kpropd                    0:off  1:off  2:off  3:off  4:off  5:off  6:off
krb524d                   0:off  1:off  2:off  3:off  4:off  5:off  6:off
krb5kdc                   0:off  1:off  2:off  3:off  4:off  5:off  6:off
ldap                      0:off  1:off  2:off  3:on   4:off  5:on   6:off
lm_sensors                0:off  1:off  2:off  3:off  4:off  5:off  6:off
lw_agt                    0:off  1:off  2:off  3:off  4:off  5:off  6:off
mdadmd                    0:off  1:off  2:off  3:off  4:off  5:off  6:off
microcode                 0:off  1:on   2:on   3:on   4:off  5:on   6:off  S:on
multipathd                0:off  1:off  2:off  3:off  4:off  5:off  6:off
mysql                     0:off  1:off  2:off  3:off  4:off  5:off  6:off
network                   0:off  1:off  2:on   3:on   4:off  5:on   6:off
nfs                       0:off  1:off  2:off  3:on   4:off  5:on   6:off
nfsboot                   0:off  1:off  2:off  3:on   4:off  5:on   6:off
nfsserver                 0:off  1:off  2:off  3:off  4:off  5:off  6:off
nohup.out                 0:off  1:off  2:off  3:off  4:off  5:off  6:off
novell-zmd                0:off  1:off  2:off  3:off  4:off  5:off  6:off
nscd                      0:off  1:off  2:off  3:on   4:off  5:on   6:off
ntp                       0:off  1:off  2:on   3:on   4:off  5:on   6:off
openct                    0:off  1:off  2:off  3:off  4:off  5:off  6:off
opsware-agent             0:off  1:off  2:off  3:on   4:on   5:on   6:off
osddownt                  0:off  1:off  2:off  3:on   4:on   5:on   6:off
ovpa                      0:on   1:off  2:on   3:on   4:off  5:on   6:off
pcscd                     0:off  1:off  2:off  3:off  4:off  5:off  6:off
pctl                      0:off  1:off  2:on   3:on   4:off  5:on   6:off
portmap                   0:off  1:off  2:off  3:on   4:off  5:on   6:off
postfix                   0:off  1:off  2:off  3:on   4:off  5:on   6:off
powerd                    0:off  1:off  2:off  3:off  4:off  5:off  6:off
powersaved                0:off  1:off  2:off  3:off  4:off  5:off  6:off
random                    0:off  1:off  2:on   3:on   4:off  5:on   6:off
raw                       0:off  1:off  2:off  3:off  4:off  5:off  6:off
resmgr                    0:off  1:off  2:on   3:on   4:off  5:on   6:off
rpasswdd                  0:off  1:off  2:off  3:off  4:off  5:off  6:off
rpmconfigcheck            0:off  1:off  2:off  3:off  4:off  5:off  6:off
rrdtools                  0:off  1:off  2:off  3:on   4:off  5:on   6:off
rsyncd                    0:off  1:off  2:off  3:off  4:off  5:off  6:off
saslauthd                 0:off  1:off  2:off  3:off  4:off  5:off  6:off
skeleton.compat           0:off  1:off  2:off  3:off  4:off  5:off  6:off
slurpd                    0:off  1:off  2:off  3:off  4:off  5:off  6:off
smartd                    0:off  1:off  2:off  3:off  4:off  5:off  6:off
smpppd                    0:off  1:off  2:off  3:off  4:off  5:off  6:off
snmpd                     0:off  1:off  2:on   3:on   4:off  5:on   6:off
splash                    0:off  1:on   2:on   3:on   4:off  5:on   6:off  S:on
splash_early              0:off  1:off  2:on   3:on   4:off  5:on   6:off
sshd                      0:off  1:off  2:off  3:on   4:off  5:on   6:off
suseRegister              0:off  1:off  2:off  3:off  4:off  5:off  6:off
svcgssd                   0:off  1:off  2:off  3:off  4:off  5:off  6:off
syslog                    0:off  1:off  2:on   3:on   4:off  5:on   6:off
sysstat                   0:off  1:off  2:off  3:off  4:off  5:off  6:off
tecad_logfile             0:off  1:off  2:off  3:on   4:off  5:on   6:off
tomcat55                  0:off  1:off  2:off  3:off  4:off  5:off  6:off
tomcat_eis                0:off  1:off  2:off  3:off  4:off  5:off  6:off
tpmgwproxy.sh             0:off  1:off  2:on   3:on   4:off  5:on   6:off
uc4_smgrp                 0:off  1:off  2:off  3:on   4:off  5:on   6:off
uc4_smgrq1                0:off  1:off  2:off  3:on   4:off  5:on   6:off
xbis-ldap-tool            0:off  1:off  2:off  3:off  4:off  5:off  6:off
xdm                       0:off  1:off  2:off  3:off  4:off  5:on   6:off
xfs                       0:off  1:off  2:off  3:off  4:off  5:off  6:off
xinetd                    0:off  1:off  2:off  3:off  4:off  5:off  6:off
ypbind                    0:off  1:off  2:off  3:off  4:off  5:off  6:off
xinetd based services:
        chargen:            off
        chargen-udp:        off
        daytime:            off
        daytime-udp:        off
        echo:               off
        echo-udp:           off
        netstat:            off
        rsync:              off
        servers:            off
        services:           off
        systat:             off
        time:               off
        time-udp:           off

 

2. Stop / Disable a service in all Linux boot runlevels or in a concrete one

As you should know already in Linux there are multiple runlevels in which server can boot, under normal circumstances SuSE servers (as of time of writting) this article boots into runlevel 3, if you'r'e  unsure about the runlevel you can check it with runlevel command:
 

 suse:/etc/init.d# /sbin/runlevel
N 3

To stop a service on all possible boot runlevels – 1,2,3,4,5
 

suse:/etc/init.d# /sbin/chkconfig xinetd off


If you want to stop xinetd or any other service just for certain runlevels (lets say run-level 3,4,5):
 

suse:/etc/init.d# chkconfig –level 345 xinetd off

 

3. Start / Enable a service for a runlevel or all boot levels 1,2,3,4,5

To disable boot.apparmor on all boot runlevels –  kernel enhancement that enabled to set a limited set of resources for services (good for tightened security, but often creating issues with some external server configured services).
 

suse:/etc/init.d# chkconfig boot.apparmor off


Or for single boot modes again with –level option:
 

suse:/etc/init.d# chkconfig –level 345 boot.apparmor off

 

suse:/etc/init.d# chkconfig xfs off 


4. SuSE Linux Package management zypper console tool

If you need / wonder how to install /remove / update a service on a SuSE Linux server, take a look at zypper tool.
zypper is  a  command-line  interface to ZYPP system management library.

To install a package / service with zypper the syntax is very much like yum, for example:
 

suse: ~# zypper install vim -emacs

 


will remove emacs editor and install Vi Improved

The equivalent of yum -y  Fedora command in SuSE Enterprise Linux is –non-interactive option

 

suse:~# zypper –non-interactive install

 

In SuSE it is pretty annoying when you're asked for accepting licensing on some proprietary (external vendor) non-free software packages to get around this:
 

suse:~# zypper patch –auto-agree-with-licenses


To keep the SuSE server up2date – i.e. SLES equivalent of CentOS's yum update && yum upgrade

 

suse:~# zypper list-patches
Loading repository data…
Reading installed packages…
 
Repository                          | Name      | Version | Category | Status
————————————+———–+———+———-+——-
Updates for openSUSE 11.3 11.3-1.82 | lxsession | 2776    | security | needed

 

 

 

suse:~# zypper patch-check
Loading repository data…
Reading installed packages…
5 patches needed (1 security patch)


To look for a certain package with Zypper (equivalent of yum search packagename)

suse: ~# zypper search apache


To verify whether an RPM installed package dependecies are OK:
 

suse:~# zypper verify


The equivalent of Fedora yum update command in SuSE (SLES) are:

suse:~# zypper refresh


To force a complete refresh and rebuild of the database, including a forced download of raw metadata.
 

suse:~# zypper refresh -fdb

 


For people that are used to ncurses (midnight commander) like text interface you can also use yoast2 (text GUI) package manager:
 

suse:~# yoast2


update-linux-suse-server-with-yoast2-ncurses-package-text-gui-management-tool

If a package is messed you can always go back and use good old RPM (Redhat Package Manager) to solve it.

 

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