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Saturday, August 28 2010

Solving Linux system lock up when intensive disk I/O are performed

When a system lock up occurs, we often blame applications but when you look carefully you may see that despite your multi-core CPU, your applications are sleeping! No cpu activity! So what happens then? Check the I/Os, it could be the root cause!

With Ubuntu 10.04, my desktop computer was freezing when the ReadyNAS Bacula backup was running. Indeed, the Bacula daemon was performing intensive disk operations (on a fast SATA hard disk). The situation was such that it was impossible to use the system, the interface was freezing for a several seconds then working for a few seconds and freezing again.

Linux I/O Scheduler

The I/O scheduler is responsible for organizing the order in which disk operations are performed. Some algorithms allow to minimize the disk head moves, other algorithms tend to anticipate read operations,

When I/O operations are not scheduled correctly, an interactive application such as a desktop or a browser can be blocked until its I/O operations are scheduled and executed (the situation can be even worse for those applications that use the O_SYNC writing mode).

By default, the Linux kernel is configured to use the Completely Fair Queuing scheduler. This I/O scheduler does not provide any time guarantee but it gives in general good performances. Linux provides other I/O schedulers such as the Noop scheduler, the Anticipatory scheduler and the Deadline scheduler.

The deadline scheduler puts an execution time limit to requests to make sure the I/O operation is executed before an expiration time. Typically, a read operation will wait at most 500 ms. This is the I/O scheduler we need to avoid the system lock up.

Checking the I/O Scheduler

To check which I/O scheduler you are using, you can use the following command:

$ cat /sys/block/sda/queue/scheduler
noop anticipatory deadline [cfq]

where sda is the device name of your hard disk (or try hda).

The result indicates the list of supported I/O scheduler as well as the current scheduler used (here the Completely Fair Queuing ).

Changing the I/O Scheduler

To change the scheduler, you can echo the desired scheduler name to activate it (you must be root):

# echo deadline >  /sys/block/sda/queue/scheduler

To make sure the I/O scheduler is configured after each system startup, you can add the following lines to your /etc/rc.local startup script:

test -f /sys/block/sda/queue/scheduler &&
  echo deadline > /sys/block/sda/queue/scheduler

test -f /sys/block/sdb/queue/scheduler &&
   echo deadline > /sys/block/sdb/queue/scheduler

test -f /sys/block/hda/queue/scheduler &&
   echo deadline > /sys/block/hda/queue/scheduler

You may have to change the sda and sdb into hda and hdb if you have an IDE hard disk.

Conclusion

After changing the I/O scheduler to use the Deadline scheduler, the desktop was not freezing any more when backups are running.

Friday, April 9 2010

One year of data backup with Bacula on a ReadyNAS duo

After one year of daily and weekly backup using Bacula on a ReadyNAS duo, I wanted to share information about this success story. Bacula is a network backup solution that I installed on a ReadyNAS duo. Bacula allows to make full as well as incremental backups of remote machines. It uses a MySQL database that also runs on the ReadyNAS (see Installing Mysql server on a ReadyNAS duo) and it stores backups on media such as tapes, CDs, DVDs or files.

Backup Architecture

The Bacula software is running directly on the ReadyNAS duo. The backup is configured to backup my desktop which is accessed locally, and it also backups a server running on the Internet (vacs.fr). Since the ReadyNAS is behind my Livebox, it connects to the Internet server by using a secure tunnel with OpenVPN.

Network Backup with Bacula on a ReadyNAS

The ReadyNAS duo has two 1To hard disks configured as RAID 1 mirrors.

  • Bacula director and bacular storage daemons are running on the ReadyNAS duo
  • Bacula client is running on each machine that must be backed up (Desktop and Remote Server).

Backup Pools and Strategy

Bacula is configured to create backups on file tapes. Each tape is a flat file stored on the ReadyNAS duo in some directory. I've configured file tapes so that they do not extend 4.3G (so that copying and burning DVDs could be possible).

File tapes are grouped in several pools. Each pool represent a class of backup. My primary backup strategy is split in 3 backup grades:

A-Grade backups represent critical files that must not be lost at all. They represent the files that I really care and for which I want to have one year of backup. The retention policy is set to one year with one full backup per month. In short, it means I can restore the data I had anytime during the last year. Basically it contains my full desktop home directory as well as specific directories (private photos and so on).

B-Grade backups represent less critical files for which I may not need to restore an old version. The retention policy is 180 days. This backup grade is used for software or files that I download from Internet.

C-Grade backups have a 65-days retention policy and they are used for the system. Basically, re-installation of a server or desktop from scratch is always possible but keeping the configuration files in the backup is very helpful.

A Pool is defined for each of these grades:

# A-Grade pool: 1 year retention, 12 full backups (1 full bkp/month)
Pool {
  Name = A-Full-Pool
  Pool Type = Backup
  # Bacula can automatically recycle Volumes
  Recycle = yes 
  AutoPrune = yes # Prune expired volumes
  Volume Retention = 360 days
  Label Format=A-Full-
  # 100 volumes of 4G (expecting 8 volumes/full backup)
  Maximum Volumes=100
}

# B-Grade pool: 6 months retention, 3 full backups (1 full bkp/2 months)
Pool {
  Name = B-Full-Pool
  Pool Type = Backup
  Recycle = yes
  AutoPrune = yes # Prune expired volumes
  Volume Retention = 180 days
  Label Format=B-Full-
  Maximum Volumes=40
}

# C-Grade pool: 2 months retention, 2 full backups (1 full bkp/45 day)
Pool {
  Name = C-Full-Pool
  Pool Type = Backup
  Recycle = yes
  AutoPrune = yes
  Volume Retention = 65 days # 2 months
  Label Format=C-Full-
  # 5 volumes of 4G (expecting 2 volumes/full backup)
  Maximum Volumes=5
}

In addition to these pools, an incremental and a differential pool must be defined.

Bacula FileSet

The Bacula FileSet represent the file patterns that have to be backed up. I have defined one FileSet for each machine and backup grade combination. The filesets are compressed. Files matching some patterns are excluded (*.o, *.log, *.bak, *~). The FileSet below is for my desktop and for the A-Grade backup. Directories /home, /data and /photos will be taken into account in the backup.

# List of files to be backed up
FileSet {
  Name = "Zebulon A-Grade"     
  Include {                    
  Options {                  
      signature=SHA1           
      compression=GZIP         
      verify = pins1           
      onefs = yes              
      WildFile = "*~"          
      WildFile = "*.bak"       
      WildFile = "*.log"       
      WildFile = "*.o"         
      Exclude = yes            
    }
    File = /home
    File = /data
    File = /photos
  }
}

Other FileSets are defined for the same machine but for different files. They will be used for other backup grades.

Backup Schedule

The schedule defines when the backup has to be executed. Each backup grade has its own schedule. This allows to run B-Grade and C-Grade backups less frequently than A-Grade.

The A-Grade backups have a full backup schedule the first Saturday of each month. A full backup of the desktop takes arround 5 hours and uses 57Go (compressed). A differential backup takes arround 2 hours and uses 10Go (compressed). The incremental backup uses 2-4Go (compressed) and 5 to 15 minutes. (these numbers depend on what is being backed up). The schedule hours are defined according to this.

Schedule {
  Name = "Weekly-A-Grade"
  Run = Full 1st sat at 23:05
  Run = Differential 2nd-5th sun at 22:10
  Run = Incremental sun-fri at 22:10
}
Schedule {
  Name = "Weekly-B-Grade"
  Run = Full jan 1st sat at 23:05
  Run = Full mar 1st sat at 23:05
  Run = Full may 1st sat at 23:05
  Run = Full jul 1st sat at 23:05
  Run = Full sep 1st sat at 23:05
  Run = Full nov 1st sat at 23:05
  Run = Differential 2nd-5th sun at 22:10
  Run = Incremental wed at 22:10
}
Schedule {
  Name = "Weekly-C-Grade"
  Run = Full jan 1st sat at 2:05
  Run = Full mar 1st sat at 2:05
  Run = Full may 1st sat at 2:05
  Run = Full jul 1st sat at 2:05
  Run = Full sep 1st sat at 2:05
  Run = Full nov 1st sat at 2:05
  Run = Differential 2nd-5th sat at 2:10
  Run = Incremental sat at 2:10
}

Bacula Job

The Bacula Job describes what must be backed up (FileSets), when (Schedule) and where (Pools). There is one job definition for each fileset.

Job {
  Name = "Zebulon-A"
  Type = Backup
  Client = zebulon-fd
  FileSet = "Zebulon A-Grade"
  Schedule = "Weekly-A-Grade"
  Storage = File
  Messages = Standard
  Pool = Default
  Full Backup Pool = A-Full-Pool
  Incremental Backup Pool = Incr-Pool
  Differential Backup Pool = Diff-Pool
  Priority = 8
}

Some Statistics

After more than one year of backups, the total storage space used is now 599G, each tape is 4.3G. The storage space used by file pools is as follows:

A Grade Full Tapes  73  313Go
B Grade Full Tapes  28  120Go
C Grade Full Tapes   4   17Go
Differential tapes  22   94Go
Incremental tapes   13   55Go

The MySQL database has grown a lot and is quite large. The InnoDB database file only contains the bacula database and it has grown up to 2Go now. The filename table references 885527 records and the path table references 546784 rows.

Conclusion

Bacula is not easy to configure but when you do it right it provides a performant backup solution. To learn more about the configuration, have a look at Bacula Documentation. Installed on a ReadyNAS duo, it proved to be a robust solution for a backup of a small set of machines. You cannot expect big performances during backup or restore. The performance bottleneck is the MySQL database which runs on the ReadyNAS.

Restoring files from the backup is quite easy but this is another story...

Saturday, January 9 2010

Simple mysql database backup for ReadyNAS duo

With a mysql database running on the ReadyNAS duo, it becomes necessary to put in place a backup of the database. This article describes a simple method to automatically backup the mysql database.

All actions described here require that you are connected to your ReadyNAS duo using SSH (See Connecting to a ReadyNAS duo using SSH)

ssh -l root pollux
root@pollux's password:
Last login: Sat Jan  9 12:59:54 2010 from zebulon
Last login: Sat Jan  9 15:34:19 2010 from zebulon on pts/0
Linux nas-D2-24-F2 2.6.17.8ReadyNAS #1 Fri Mar 20 04:41:57 PDT 2009 padre unknown
nas-D2-24-F2:~#

Backup Directory Preparation

First, we have to create a protected directory which will contain the backups:

nas-D2-24-F2:# mkdir /c/backup-mysql
nas-D2-24-F2:# chmod 700 /c/backup-mysql

Mysql Backup User

To make the backup, a special user should be used to restrict the rights to the minimum. Basically, the user only needs the SELECT and LOCK TABLES privileges. The database access should be protected with a password.

nas-D2-24-F2:# mysql -u root -p
Enter password:
Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 7
Server version: 5.0.32-Debian_7etch5~bpo31+1-log Debian etch distribution

Type 'help;' or '\h' for help. Type '\c' to clear the buffer.

mysql> GRANT SELECT, LOCK TABLES ON *.* 
    TO 'dump'@'localhost' identified by 'XXXX';
Query OK, 0 rows affected (0.04 sec)

mysql> flush privileges;
Query OK, 0 rows affected (0.02 sec)

mysql> quit
Bye

Backup Script

To make the backup, you have to write a simple script which uses mysqldump and compresses the backup file. This script is written in /etc/cron.daily directory. This way it will be run automatically by the cron daemon each day at 6:25am (Look at the /etc/crontab file).

Create the file /etc/cron.daily/backup-mysql and put the content below.

#!/bin/sh
D=`date --iso-8601`
BKP_DIR=/c/backup-mysql
DB_LIST="bacula mysql"
for i in $DB_LIST; do
  mysqldump --user=dump \
    --password=XXXX \
    --opt $i | gzip -c > $BKP_DIR/$i-$D.sql.gz &&
  chmod 400 $BKP_DIR/$i-$D.sql.gz
done

You have to update the DB_LIST variable to put the name of the databases you want to backup.

You have to protect the script because it contains the password of our backup user. The script must be executable.

nas-D2-24-F2:# cd /etc/cron.daily
nas-D2-24-F2:# chmod 700 backup-mysql

Test the script

It's necessary to execute the script at least once to make sure it backups what you need.

nas-D2-24-F2:# ./backup-mysql

Then, check that a backup file was created correctly.

Test the database backup or restore

You may also test that the backup SQL file is correct by creating a fake database and importing the file. You can do this with the following command:

nas-D2-24-F2:# mysql -u root -p 
create database test-backup;

Then decompress the backup file and import it with the mysql command into new test (or the real database if you want to restore it).

nas-D2-24-F2:# gzip -c \
-d /c/backup-mysql/xxx.sql.gz | \
mysql --force --force -u root -p test-backup

Conclusion

This process remains simple and is very easy to put in place. However, it has some limitations because it is best to make sure no applications are writing to the database when the backup is running. Otherwise you may backup data which are not consistent.

Sunday, October 4 2009

Tuning mysql configuration for the ReadyNAS duo

After installing mysql server on a Ready NAS duo, it is necessary to tune the configuration to make the server run well on this small hardware. This article describes a possible configuration for tuning the Mysql server.

Mysql Temporary directory

Mysql uses files in the temporary directory to store temporary tables. Depending on your database and your queries, temporary tables could be quite large. To avoid problems in the /tmp partition becomming full, the best thing is to use a directory in the /c partition

tmpdir          = /c/backup/tmp

Make sure the directory exist before starting mysql:

# mkdir -p /c/backup/tmp

Mysql storage engine

After playing with a reasonably big database and the MyISAM storage engine, it turns out that the mysql server was sometimes crashing and barking at some corrupted myisam tables. I switched to the InnoDB storage engine, which is better for transactions anyway. Since the readynas does not have a lot of memory I've used the following configuration:

default_storage_engine = InnoDB
thread_cache_size = 0

innodb_buffer_pool_size = 6M
innodb_thread_concurrency = 1

Other mysql settings

To reduce the resources used by the mysql server to the minimum, I changed the max number of connections to a small number.

key_buffer_size = 16k
sort_buffer_size = 100k
max_connection = 10

I'm using these settings for almost 6 months now; my bacula database now contains a table with 5 milions of rows. Of course you can't expect big performance but the mysql server is stable.

Saturday, May 9 2009

Install Epson Stylus PX700W printer with CUPS on Ubuntu 8.10

Printing with an Epson PX700W printer from Ubuntu is a real challenge. No driver really work out of the box. After looking at many places, digging in dozen of forums and other answers sites, no real solution emerged. The article describes some steps to make the printer work for Ubuntu.

Continue reading...

Sunday, March 22 2009

Installing Mysql server on a ReadyNAS duo

Being able to connect to my ReadyNAS duo using SSH (See Connecting to a ReadyNAS duo using SSH ), the next step for setting up a Bacula backup solution was to setup a MySQL server. The Mysql server is used by Bacula for the backup catalog (jobs, files ...).

Continue reading...

Saturday, March 21 2009

Connecting to a ReadyNAS duo using SSH

Having acquired a ReadyNAS duo for my new backup system, I wanted to explore the system that runs on it and see if I could run more services on it. There is nothing terrific in this article as many people have already done this before. Anyway it describes step by step what must be done to connect to the ReadyNAS.

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Saturday, February 7 2009

Server configuration management: track changes with subversion and be notified

Tracking changes in a server configuration can be critical to understand problems, identify security breaches and repair a server. When several people are in charge of administering one or several servers, sharing the configuration changes is helpful to inform each other about these modifications. The article describes a simple organization that uses subversion and daily mail notifications in case of change.

Continue reading...

Sunday, December 21 2008

Audit errors reported by linux kernel - why you must care

On Ubuntu 8.04 running a Linux 2.6.24 kernel, you may see some strange error logs reported by dmesg. First you will look at them, you'll wonder where they come from and you will soon ignore them. You should better fix the problem, in most cases they point out a need to update AppArmor configuration files.

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Saturday, July 5 2008

Restoring a complete system after a hard disk failure: bacula to the rescue!!!

Last day the main disk of by computer stopped to work. My Western Digital 150Gb raptor hard disk was no longer recognized by the system: it was simply dead after one year of work. The 10000 rpm disk contained the Ubuntu 8 system, my home directory with all my files and other important critical and important data. When this kind of problem happens, you don't care about the 3 year warranty of your disk, but you are very thankful to the backup system that you put in place. Indeed at the end of the day, you will only have lost some time but not your critical data. Here is how.

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Sunday, February 11 2007

Ubuntu Server and Ubuntu Desktop

After having used a RedHat distribution (1998-2002), a Mandrake distribution (2002-2005) and then a Debian distribution (2005-2006), I have switch my systems to an Ubuntu Server and Ubuntu Desktop distribution. Is it worth to switch, well may be. But, still there are issues and none of the Linux distributions I have used so far have reach a complete satisfactory point for me as a end user.

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