Problems compiling MySQL 5.4

Seem’s the year Sun had for improving MySQL, and with an entire new 5.4 branch the development team could not fix the autoconf and compile dependencies that has been in MySQL for all the years I’ve been compiling MySQL. Drizzle has got it right, thanks to the great work of Monty Taylor.

I’m working on the Wafflegrid AWS EC2 AMI’s for Matt Yonkovit and while compiling 5.1 was straight forward under Ubuntu 8.10 Intrepid, compiling 5.4 was more complicated.

For MySQL 5.1 I needed only to do the following:

apt-get install -y build-essential
apt-get install libncurses5-dev
./configure
make
make install

For MySQL 5.4, I elected to use the BUILD scripts (based on Wafflegrid recommendations). That didn’t go far before I needed.

apt-get install -y automake libtool

You then have to go compiling MySQL 5.4 for 10+ minutes to get an abstract error, then you need to consider what dependencies may be missing.
I don’t like to do a blanket apt-get of a long list of proposed packages unless I know they are actually needed.

The error was:

make[1]: Entering directory `/src/mysql-5.4.0-beta/sql'
make[1]: warning: -jN forced in submake: disabling jobserver mode.
/bin/bash ../ylwrap sql_yacc.yy y.tab.c sql_yacc.cc y.tab.h sql_yacc.h y.output sql_yacc.output -- -d --verbose
make -j 6 gen_lex_hash
make[2]: Entering directory `/src/mysql-5.4.0-beta/sql'
rm -f mini_client_errors.c
/bin/ln -s ../libmysql/errmsg.c mini_client_errors.c
make[2]: warning: -jN forced in submake: disabling jobserver mode.
rm -f pack.c
../ylwrap: line 111: -d: command not found
/bin/ln -s ../sql-common/pack.c pack.c
....
make[1]: Leaving directory `/src/mysql-5.4.0-beta/sql'
make: *** [all-recursive] Error 1

What a lovely error ../ylwrap: line 111: -d: command not found

ylwrap is part of yacc, and by default in this instance it’s not even an installed package. I’ve compiled MySQL long enough that it requires yacc, and actually bison but to you think it would hurt if the configure told the user this.

It’s also been some time since I’ve compiled MySQL source, rather focusing on Drizzle. I had forgotten just how many compile warnings MySQL throws. Granted a warning is not an error, but you should not just ignore them in building a quality product.

Understanding your RAID Configuration

For any production MySQL Database system, running RAID is a given these days. Do you know what RAID your database is? Are you sure?. Ask for quantifiable reproducible output from your systems provider or your System Administrator.

As a consultant I don’t always know the specific tools for the clients deployed H/W, but I ask the question. On more the one occasion the actual result differed from the clients’ perspective or what they were told, and twice I’ve discovered that clients when asked if their RAID was running in a degraded mode, it actually was and they didn’t know.

You can read about various benchmarks at MySQL blogs such as BigDBAHead and MySQL Performance Blog however getting first hand experience of your actually RAID configuration, the H/W and S/W variables is critical to knowing how your technology works. You can then build on this to run your own benchmarks.

Over 50% of my clients run on DELL equipment, most using local storage or shared storage options such as Dell MD1000, Dell MD3000, NetApps or EMC. I’ve had the opportunity to spend a few days looking into the more details of RAID, specifically the DELL PERC 5/i Raid Controllers, and I’ve started a few MySQL Cheatsheets for my own reference that others may also benefit from.

Understanding PERC RAID Controllers gives an overview of using the MegaCLI tools to retrieve valuable information on the Adapter, Physical Drives, Logical Drives and the all important Battery Backed Cache.

There are several Google search results out there about finding the MegaCLI tools, I found them to be all outdated. There is of course other tools including Dell OpenManage Server Administrator (GUI and CLI) and an Open Source project called megactl.

Here is just a summary of a few lines of each that yields valuable information:

Adapter Details

$ /opt/MegaRAID/MegaCli/MegaCli64 -AdpAllInfo -aALL

RAID Level Supported             : RAID0, RAID1, RAID5, RAID10, RAID50
Max Stripe Size         : 128kB
Stripe Size                    : 64kB

Physical Details

$ /opt/MegaRAID/MegaCli/MegaCli64 -LDPDInfo -aall

Adapter #0
Number of Virtual Disks: 1

RAID Level: Primary-5, Secondary-0, RAID Level Qualifier-3
Size:208128MB
Stripe Size: 64kB
Number Of Drives:4
Default Cache Policy: WriteBack, ReadAheadNone, Direct, No Write Cache if Bad BBU
Current Cache Policy: WriteBack, ReadAheadNone, Direct, No Write Cache if Bad BBU

Raw Size: 70007MB [0x88bb93a Sectors]
Inquiry Data: FUJITSU MAY2073RC       D108B363P7305KAU
Inquiry Data: FUJITSU MAY2073RC       D108B363P7305KAJ
Inquiry Data: FUJITSU MAY2073RC       D108B363P7305JSW
Inquiry Data: FUJITSU MAY2073RC       D108B363P7305KB1

Battery

$ MegaCli -AdpBbuCmd -aALL
  Fully Charged           : Yes
  Discharging             : Yes

BBU Capacity Info for Adapter: 0
Relative State of Charge: 100 %
Absolute State of charge: 88 %
Run time to empty: 65535 Min

BBU Properties for Adapter: 0

Auto Learn Period: 7776000 Sec
Next Learn time: 304978518 Sec

The big detail that was missing was the details in this ouput of the drive speed, such as 7.2K, 10K, 15K. What is the impact? Well that’s the purpose of the next step.

Following this investigation, testing of the RAID configuration with Bonnie++ was performed to determine the likely performance of various configurations, and to test RAID0, RAID1, RAID5 and RAID10.

Further testing that would be nice would include for example RAID 5 with 3 drives verses 4 drives. The speed of the drives, the performance in a degraded situation, and the performance during a disk rebuild.

This still leaves the question about how to test the performance with and without the Battery Backed Cache. You can easily disable this via CLI tools, but testing an actually database test, and pulling the power plug for example with and without would yield some interesting results. More concerning is when Dell specifically discharges the batters, and it takes like 8 hours to recharge. In your production environment you are then running in degraded mode. Disaster always happens at the worse time.

(Mis)Understanding RAID configuration

Update 8 June 2009
Be sure you to check out some of my research including Understanding your RAID Configuration and Understanding PERC RAID Controllers.

Last week I got caught thinking a MySQL production system wasn’t configured with RAID when it actually was. The following is the Linux dmesg output of 3 different client MySQL servers, where the H/W is all the same, a Dell 2950.

In the first two cases you will see individual references to the internal disks, however in the third you do not. This threw me, but as Matt Yonkovit correctly pointed out to me, the sizes are not standard drive sizes.

A deeper level of understanding via CLI tools, or actually console output would appear necessary to understand the disk configuration in the future.


Nov 2007 – Dell 2950 Running RHEL 4. Note the individual SEAGATE drive details and single sda (70G) and sdb(300G)

scsi0 : LSI Logic SAS based MegaRAID driver
  Vendor: SEAGATE   Model: ST973451SS        Rev: SM04
  Type:   Direct-Access                      ANSI SCSI revision: 05
  Vendor: SEAGATE   Model: ST973451SS        Rev: SM04
  Type:   Direct-Access                      ANSI SCSI revision: 05
  Vendor: SEAGATE   Model: ST973451SS        Rev: SM04
  Type:   Direct-Access                      ANSI SCSI revision: 05
  Vendor: SEAGATE   Model: ST973451SS        Rev: SM04
  Type:   Direct-Access                      ANSI SCSI revision: 05
usb 4-1: new high speed USB device using ehci_hcd and address 2
usb 4-1: configuration #1 chosen from 1 choice
hub 4-1:1.0: USB hub found
hub 4-1:1.0: 2 ports detected
  Vendor: SEAGATE   Model: ST973451SS        Rev: SM04
  Type:   Direct-Access                      ANSI SCSI revision: 05
  Vendor: SEAGATE   Model: ST973451SS        Rev: SM04
  Type:   Direct-Access                      ANSI SCSI revision: 05
  Vendor: SEAGATE   Model: ST973451SS        Rev: SM04
  Type:   Direct-Access                      ANSI SCSI revision: 05
  Vendor: DP        Model: BACKPLANE         Rev: 1.05
  Type:   Enclosure                          ANSI SCSI revision: 05
  Vendor: DELL      Model: PERC 5/i          Rev: 1.03
  Type:   Direct-Access                      ANSI SCSI revision: 05
SCSI device sda: 142082048 512-byte hdwr sectors (72746 MB)
sda: Write Protect is off
sda: Mode Sense: 1f 00 10 08
SCSI device sda: drive cache: write through w/ FUA
SCSI device sda: 142082048 512-byte hdwr sectors (72746 MB)
sda: Write Protect is off
sda: Mode Sense: 1f 00 10 08
SCSI device sda: drive cache: write through w/ FUA
 sda: sda1 sda2 sda3 sda4 < sda5 >
sd 0:2:0:0: Attached scsi disk sda
  Vendor: DELL      Model: PERC 5/i          Rev: 1.03
  Type:   Direct-Access                      ANSI SCSI revision: 05
SCSI device sdb: 568328192 512-byte hdwr sectors (290984 MB)
sdb: Write Protect is off
sdb: Mode Sense: 1f 00 10 08
SCSI device sdb: drive cache: write through w/ FUA
SCSI device sdb: 568328192 512-byte hdwr sectors (290984 MB)
sdb: Write Protect is off
sdb: Mode Sense: 1f 00 10 08
SCSI device sdb: drive cache: write through w/ FUA

Oct 2008 – Dell 2950 running Ubuntu 8.04. Note the individual SEAGATE drive details and single sda (600GB)

[   88.069326] scsi0 : LSI Logic SAS based MegaRAID driver
[   88.087755] scsi 0:0:0:0: Direct-Access     SEAGATE  ST3300656SS      HS09 PQ: 0 ANSI: 5
[   88.104931] scsi 0:0:1:0: Direct-Access     SEAGATE  ST3300656SS      HS09 PQ: 0 ANSI: 5
[   88.122079] scsi 0:0:2:0: Direct-Access     SEAGATE  ST3300656SS      HS09 PQ: 0 ANSI: 5
[   88.139064] scsi 0:0:3:0: Direct-Access     SEAGATE  ST3300656SS      HS09 PQ: 0 ANSI: 5
[   88.205346] scsi1 : ata_piix
[   88.205387] scsi2 : ata_piix
[   88.205409] ata1: PATA max UDMA/100 cmd 0x1f0 ctl 0x3f6 bmdma 0xfc00 irq 14
[   88.205411] ata2: PATA max UDMA/100 cmd 0x170 ctl 0x376 bmdma 0xfc08 irq 15
[   88.240207] scsi 0:0:32:0: Enclosure         DP       BACKPLANE        1.05 PQ: 0 ANSI: 5
[   88.252370] scsi 0:2:0:0: Direct-Access     DELL     PERC 6/i         1.21 PQ: 0 ANSI: 5
[   88.263532] scsi 0:0:32:0: Attached scsi generic sg0 type 13
[   88.263547] scsi 0:2:0:0: Attached scsi generic sg1 type 0
[   88.265390] Driver 'sd' needs updating - please use bus_type methods
[   88.265671] sd 0:2:0:0: [sda] 1169686528 512-byte hardware sectors (598880 MB)
[   88.265700] sd 0:2:0:0: [sda] Write Protect is off
[   88.265702] sd 0:2:0:0: [sda] Mode Sense: 1f 00 10 08
[   88.265771] sd 0:2:0:0: [sda] Write cache: disabled, read cache: enabled, supports DPO and FUA
[   88.266135] sd 0:2:0:0: [sda] 1169686528 512-byte hardware sectors (598880 MB)
[   88.266173] sd 0:2:0:0: [sda] Write Protect is off
[   88.266175] sd 0:2:0:0: [sda] Mode Sense: 1f 00 10 08
[   88.266232] sd 0:2:0:0: [sda] Write cache: disabled, read cache: enabled, supports DPO and FUA
[   88.266240]  sda: sda1 sda2 sda3
[   88.270085] sd 0:2:0:0: [sda] Attached SCSI disk

May 2009 – Dell 2950 running RHEL 5. Note no individual drive details, only partition sizes for sda (300G) and sdb (600G).

scsi0 : LSI Logic SAS based MegaRAID driver
  Vendor: DP        Model: BACKPLANE         Rev: 1.05
  Type:   Enclosure                          ANSI SCSI revision: 05
  Vendor: DELL      Model: PERC 5/i          Rev: 1.03
  Type:   Direct-Access                      ANSI SCSI revision: 05
SCSI device sda: 584843264 512-byte hdwr sectors (299440 MB)
SCSI device sda: drive cache: write through
SCSI device sda: 584843264 512-byte hdwr sectors (299440 MB)
SCSI device sda: drive cache: write through
 sda: sda1 sda2 sda3 sda4 < sda5 sda6 sda7 sda8 sda9 sda10 sda11 >
Attached scsi disk sda at scsi0, channel 2, id 0, lun 0
  Vendor: DELL      Model: PERC 5/i          Rev: 1.03
  Type:   Direct-Access                      ANSI SCSI revision: 05
SCSI device sdb: 1169686528 512-byte hdwr sectors (598880 MB)
SCSI device sdb: drive cache: write through
SCSI device sdb: 1169686528 512-byte hdwr sectors (598880 MB)
SCSI device sdb: drive cache: write through
 sdb: sdb1 sdb2 sdb3

Leveraging the power of Twitter

Last week I posted the following twitter request“Can somebody loan me (or buy me) a Dell 2950 decked out so I can run and publish some benchmarks. Please!”

In a same day response I was offered access to use 2 x Dell 1950’s, and today I’m now actually using these machines for my own testing. I would like to thank cafemom (Barry, Anthony & Dan) for the loan of hardware.

And now the chance to better understand the RAID configuration of the DELL PERC Controllers, trying out some different RAID types, LVM configurations and disk tests. When I’m done with my System Administrator refresher, I’m then be trying some different MySQL Benchmarks to test various MySQL configuration settings including using the new Juice benchmark.

For MySQL DBA fame and glory. Prize included.

I came across the following configuration today on a Production MySQL system (5.0.67) running 30+ blogs using WordPress MU.

$ cat /etc/my.cnf
[mysqld]
set-variable = max_connections=500
safe-show-database

No I did not truncate the output. I could say I’ve seen worse, but that’s a stretch.


So the quiz and a prize for the best response, for the next 48 hours I’ll accept your comments as responses to this post for the top 5 settings you would add, and additionally what information you may need to add these settings. Bonus points for giving a reason why you would add the settings as well.

For example, I’ll give you the most obvious.

key_buffer_size = ????

To determine a key_buffer_size to start with I would look at the size of all Indexes via I_S, and combine with some estimate of growth, say 2x-5x.

For the best answer with the top 5 settings, I’ll send you a copy of Sheeri Cabral’s book MySQL Administrators Bible which even I as a resident MySQL Expert has enjoyed scanning and learning something new.

Basic OS/MySQL Security

If you can do either of these on your MySQL production server, you need to correct immediately.

1. Login directly to your MySQL server as the ‘root’ Linux Operating System user. For example:

$ ssh [email protected]
Password:  ************

2. Connect to MySQL database as the ‘root’ MySQL user without a password.

$ mysql -uroot

Here are the 60 second fixes to address these major security flaws.
To disable direct root access to your server, first ensure you can login as a normal user, then su – or sudo su – appropriately. Then, disable ssh root access with the following configuration change.

$   vi /etc/ssh/sshd_config
    # ensure this is commented out and set to no
    PermitRootLogin no

$   /etc/init.d/sshd restart

This will stop any brute force attack on your server by automated bots and password generators.

Second, the default installation of MySQL *DOES NOT SET A PASSWORD*. Apart from being crazy, I’ve seen production systems without a MySQL ‘root’ user password. To set a password run:

$ mysqladmin -uroot password SOMEPASSWORD
$ mysqladmin -uroot -pSOMEPASSWORD -hlocalhost password SOMEPASSWORD

Announcing Drizzle on EC2

I have published the very first sharable Drizzle Amazon Machine Image (AMI) for AWS EC2, based on the good feedback from my discussion at the Drizzle Developer Day on what options we should try.

This first version is a 32bit Developer instance, showcasing Drizzle and all necessary developer tools to build Drizzle from source.

What you will find on drizzle-ami/intrepid-dev32 – ami-b858bfd1

Ubuntu 8.10 Intrepid 32 bit base server installation:

  • build tools
  • drizzle dependencies
  • bzr 1.31.1

From the respective source trees the following software is available:

  • drizzle 2009.04.997
  • libdrizzle 0.0.2
  • gearman 0.0.4
  • memcached 1.2.8
  • libmemcached 0.28

Drizzle has been configured with necessary dependencies for PAM authentication, http_auth, libgearman and MD5 but these don’t seem to be available in the binary distribution.

I will be creating additional AMI’s including 64bit and LAMP ready binary only images.

The following example shows using drizzle on this AMI. Some further work is necessary for full automation, parameters and logging. I’ve raised a number of issues the Drizzle Developers are now hard at work on.

1. Starting Drizzle

ssh [email protected]
sudo /etc/init.d/drizzle-server.init start &

2. Testing Drizzle (the sakila database has been installed)

$ drizzle
Welcome to the Drizzle client..  Commands end with ; or g.
Your Drizzle connection id is 4
Server version: 2009.04.997 Source distribution

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

drizzle> select version();
+-------------+
| version()   |
+-------------+
| 2009.04.997 |
+-------------+
1 row in set (0 sec)

drizzle> select count(*) from sakila.film;
+----------+
| count(*) |
+----------+
|     1000 |
+----------+
1 row in set (0 sec)

3. Compiling Drizzle

sudo su - drizzle
ls
deploy  drizzle  libdrizzle  sakila-drizzle
cd drizzle
./configure --help
Description of plugins:

   === HTTP Authentication Plugin ===
  Plugin Name:      auth_http
  Description:      HTTP based authentications
  Supports build:   static and dynamic

   === PAM Authenication Plugin ===
  Plugin Name:      auth_pam
  Description:      PAM based authenication.
  Supports build:   dynamic

   === compression UDFs ===
  Plugin Name:      compression
  Description:      UDF Plugin for compression
  Supports build:   static and dynamic
  Status:           mandatory

   === crc32 UDF ===
  Plugin Name:      crc32
  Description:      UDF Plugin for crc32
  Supports build:   static and dynamic
  Status:           mandatory

   === Error Message Plugin ===
  Plugin Name:      errmsg_stderr
  Description:      Errmsg Plugin that sends messages to stderr.
  Supports build:   dynamic

   === Daemon Example Plugin ===
  Plugin Name:      hello_world
  Description:      UDF Plugin for Hello World.
  Supports build:   dynamic

   === Gearman Logging Plugin ===
  Plugin Name:      logging_gearman
  Description:      Logging Plugin that logs to Gearman.
  Supports build:   dynamic

   === Query Logging Plugin ===
  Plugin Name:      logging_query
  Description:      Logging Plugin that logs all queries.
  Supports build:   static and dynamic
  Status:           mandatory

   === Syslog Logging Plugin ===
  Plugin Name:      logging_syslog
  Description:      Logging Plugin that writes to syslog.
  Supports build:   static and dynamic
  Status:           mandatory

   === MD5 UDF ===
  Plugin Name:      md5
  Description:      UDF Plugin for MD5
  Supports build:   static and dynamic

   === One Thread Per Connection Scheduler ===
  Plugin Name:      multi_thread
  Description:      plugin for multi_thread
  Supports build:   static
  Status:           mandatory

   === Old libdrizzle Protocol ===
  Plugin Name:      oldlibdrizzle
  Description:      plugin for oldlibdrizzle
  Supports build:   static
  Status:           mandatory

   === Pool of Threads Scheduler ===
  Plugin Name:      pool_of_threads
  Description:      plugin for pool_of_threads
  Supports build:   static
  Status:           mandatory

   === Default Signal Handler ===
  Plugin Name:      signal_handler
  Description:      plugin for signal_handler
  Supports build:   static
  Status:           mandatory

   === Single Thread Scheduler ===
  Plugin Name:      single_thread
  Description:      plugin for single_thread
  Supports build:   static
  Status:           mandatory

   === Archive Storage Engine ===
  Plugin Name:      archive
  Description:      Archive Storage Engine
  Supports build:   static
  Status:           mandatory

   === Blackhole Storage Engine ===
  Plugin Name:      blackhole
  Description:      Basic Write-only Read-never tables
  Supports build:   static and dynamic
  Configurations:   max, max-no-ndb

   === CSV Storage Engine ===
  Plugin Name:      csv
  Description:      Stores tables in text CSV format
  Supports build:   static
  Status:           mandatory

   === Memory Storage Engine ===
  Plugin Name:      heap
  Description:      Volatile memory based tables
  Supports build:   static
  Status:           mandatory

   === InnoDB Storage Engine ===
  Plugin Name:      innobase
  Description:      Transactional Tables using InnoDB
  Supports build:   static and dynamic
  Configurations:   max, max-no-ndb
  Status:           mandatory

   === MyISAM Storage Engine ===
  Plugin Name:      myisam
  Description:      Traditional non-transactional MySQL tables
  Supports build:   static
  Status:           mandatory


Report bugs to <http://bugs.launchpad.net/drizzle>.

Compiling libdrizzle

Compiling libdrizzle is a rather trivial task. The following are the steps I undertook on Ubuntu 8.10 Intrepid 32 bit.

There was one pre-requisite from the most basic installed developer tools.

sudo apt-get install -y  automake
bzr clone lp:libdrizzle
cd libdrizzle
./config/autorun.sh
./configure
make
make install

And there they are:

$ ls -l /usr/local/lib/libdrizzle*
-rw-r--r-- 1 root root 1122710 2009-04-26 18:10 /usr/local/lib/libdrizzle.a
-rwxr-xr-x 1 root root     940 2009-04-26 18:10 /usr/local/lib/libdrizzle.la
lrwxrwxrwx 1 root root      19 2009-04-26 18:10 /usr/local/lib/libdrizzle.so -> libdrizzle.so.0.0.2
lrwxrwxrwx 1 root root      19 2009-04-26 18:10 /usr/local/lib/libdrizzle.so.0 -> libdrizzle.so.0.0.2
-rwxr-xr-x 1 root root 1003734 2009-04-26 18:10 /usr/local/lib/libdrizzle.so.0.0.2

I added the following to enable other programs using libdrizzle to find the libraries in the system path.

echo "/usr/local/lib" > /etc/ld.so.conf.d/drizzle.conf
ldconfig

Setting up MySQL on Amazon Web Services (AWS) Presentation

On Tuesday at the MySQL Camp 2009 in Santa Clara I presented Setting up MySQL on Amazon Web Services (AWS).

This presentation assumed you know nothing about AWS, and have no account. With Internet access via a Browser and a valid Credit Card, you can have your own running Web Server on the Internet in under 10 minutes, just point and click.

We also step into some more detail online click and point and supplied command line tools to demonstrate some more advanced usage.

Identifying resource bottlenecks – Memory

Continuing on from CPU, we turn our attention to Memory. One of the first steps when addressing a MySQL performance tuning problem is to perform a system audit of the physical hardware resources, then identify any obvious bottlenecks in these resources.

In auditing, I start with the ‘free’ command, the already used ‘vmstat’ command, the /proc/meminfo and /proc/sys/vm/swappiness files to get an indication of memory and swap resources. While we are looking at the Memory, the configuration of Swap is also very important. I will discuss this in more detail later.

$ free -m
             total       used       free     shared    buffers     cached
Mem:          3955       3838        117          0        402       2366
-/+ buffers/cache:       1069       2886
Swap:         1027          0       1027
$ vmstat 1
procs -----------memory---------- ---swap-- -----io---- --system-- -----cpu------
 r  b   swpd   free   buff  cache   si   so    bi    bo   in   cs us sy id wa st
 0  0    128 234088 409632 2474372    0    0     0     0 1081  198  0  0 100  0  0
 0  0    128 234088 409632 2474396    0    0     0     0 1003   59  0  0 100  0  0
 0  0    128 234088 409636 2474392    0    0     0   100 1085  209  0  0 100  0  0
 0  0    128 233836 409636 2474396    0    0     0     0 1014  184  3  0 97  0  0
 0  0    128 233284 409636 2474396    0    0     0     0 1182  435  2  0 98  0  0
 0  0    128 233176 409636 2474396    0    0     0     0 1024  104  1  0 99  0  0
 0  0    128 233176 409636 2474396    0    0     0     0 1079  195  0  0 100  0  0
 1  0    128 233168 409644 2474396    0    0     0   232 1021  188  3  0 97  0  0
 0  0    128 233176 409644 2474396    0    0     0     0 1111  213  2  0 98  0  0
 0  0    128 233176 409644 2474396    0    0     0     0 1005   60  0  0 100  0  0

Memory

  • swpd: the amount of virtual memory used.
  • free: the amount of idle memory.
  • buff: the amount of memory used as buffers.
  • cache: the amount of memory used as cache.
  • inact: the amount of inactive memory. (-a option)
  • active: the amount of active memory. (-a option)

Swap

  • si: Amount of memory swapped in from disk (/s).
  • so: Amount of memory swapped to disk (/s).
$ cat /proc/meminfo
MemTotal:      4050776 kB
MemFree:        120984 kB
Buffers:        411928 kB
Cached:        2423468 kB
SwapCached:          0 kB
Active:        1861536 kB
Inactive:      1492152 kB
HighTotal:           0 kB
HighFree:            0 kB
LowTotal:      4050776 kB
LowFree:        120984 kB
SwapTotal:     1052248 kB
SwapFree:      1052120 kB
Dirty:             172 kB
Writeback:           0 kB
AnonPages:      518112 kB
Mapped:          23140 kB
Slab:           544448 kB
PageTables:       9528 kB
NFS_Unstable:        0 kB
Bounce:              0 kB
CommitLimit:   3077636 kB
Committed_AS:   859208 kB
VmallocTotal: 34359738367 kB
VmallocUsed:    263132 kB
VmallocChunk: 34359474803 kB
HugePages_Total:     0
HugePages_Free:      0
HugePages_Rsvd:      0
Hugepagesize:     2048 kB
$ cat /proc/sys/vm/swappiness
60

What’s important is not to believe that ‘free’ or ‘MemFree’ values are the total free memory. Linux/Unix distributions use available memory as a File System Cache, dumping this data if additional memory is needed. It’s important to add Cached to get a better indication of the true memory available.

Your initial audit should also look at the processes that are using the memory. Options include ‘top’ and ‘ps’.

$ top
M

op - 15:33:56 up 36 days, 17:08,  2 users,  load average: 0.01, 0.11, 0.08
Tasks: 133 total,   1 running, 132 sleeping,   0 stopped,   0 zombie
Cpu(s):  0.0%us,  0.1%sy,  0.0%ni, 99.9%id,  0.0%wa,  0.0%hi,  0.0%si,  0.0%st
Mem:   4050776k total,  3792952k used,   257824k free,   368140k buffers
Swap:  1052248k total,      128k used,  1052120k free,  2329212k cached

  PID USER      PR  NI  VIRT  RES  SHR S %CPU %MEM    TIME+  COMMAND
 2159 mysql     15   0  411m 204m 5624 S    0  5.2  33:26.43 mysqld
 2965 buildbot  15   0  280m 105m 1932 S    0  2.7 393:15.54 buildbot
 8533 nobody    15   0  168m  25m 4092 S    0  0.7   0:03.49 httpd
 9121 nobody    15   0  166m  24m 3432 S    0  0.6   0:01.61 httpd
...
$ ps -eopid,fname,rss,vsz,user,command | more
  PID COMMAND    RSS    VSZ USER     COMMAND
    1 init       700  10324 root     init [3]
   346 httpd    25252 170484 nobody   /opt/httpd-2.2.9/bin/httpd -k start
  364 httpd    25184 170344 nobody   /opt/httpd-2.2.9/bin/httpd -k start
  425 kpsmouse     0      0 root     [kpsmoused]
  452 httpd    21000 165684 nobody   /opt/httpd-2.2.9/bin/httpd -k start
...
 2095 mysqld_s  1204  63800 root     /bin/sh bin/mysqld_safe
 2159 mysqld   209448 421248 mysql   /opt/mysql51/bin/mysqld --basedir=/opt/mysql51 --datadir=/opt/mysql51/data --user=mysql --log-error=/opt/mysql51/data/dc1.onegreendog.com.err --pid-file=/opt/mysql51/data/dc
1.onegreendog.com.pid
 ...
  • rss RSS resident set size, the non-swapped physical memory that a task has used (in kiloBytes). (alias rssize, rsz).
  • vsz VSZ virtual memory size of the process in KiB (1024-byte units). Device mappings are currently excluded; this is subject to change.
    (alias vsize).

As I have written about previously, Are you monitoring RSS & VSZ?, these columns are important and should be monitored appropriately.

Regarding Swap. This is pre assigned disk space that is used to swap out (dump) memory processes when you have run out of memory for all the running processes. You never want to run out of memory on your database server. Swapping is both extremely slow, and if your database server swaps out the mysqld process, this will effectively kill your database. If you have insufficient swap space for the process, again in the case of database server this can cause your system to crash.

Historically in Unix world, swap was always defined as 2x Memory. This also doubled as a place to dump all memory in a kernel panic. I spent time in a past life doing core dump analysis.
Today, most Linux systems are ill-configured for swap. If you use a dedicated server for example, you may be limited to what is configured by a third party. The above example shows a configuration I would not recommend where swap is less then 1x the memory.
There is also a consideration to have no Swap. By setting swapiness to 0, you are effectively saying never swap. I would also not recommend this.

Monitoring memory usage closely is important. Taking appropriate action regarding the mysql process because you can’t control how much total memory it uses is critical. Correctly configuring mysql to use memory optimally is key to a well and long running database server.

Next, we will be looking at Disk and Network resource bottlenecks.

A beginners look at Drizzle – Getting around with SHOW

Assuming you have successfully compiled Drizzle, and you are ready to start for the first time, here are some beginner differences with those familiar with the current MySQL 5.1 GA version. Note: drizzle is actually an original fork of the 6.0.x codebase however the code looks very little like mysql anymore.

Getting started differences

The first default MySQL installation step scripts/install_mysql_db is gone, and there is no replacement. The ‘mysql’ schema no longer exists. Talking about schemas, ‘test’ is also gone by default.

While a bin/drizzled_safe exists to start drizzle, this presently doesn’t operate as expected. You should start drizzle with sbin/drizzled &

They still have an empty password for ‘root’. Would be nice if it was at least a default like an Oracle installation, and a password became a mandatory requirement. Speaking of passwords, trying ‘drizzle -uroot -pxxxx’ will result in an unexpected error.

$ bin/drizzle -uroot -pxxx

ERROR:
Non-integer value supplied for port.  If you are trying to enter a password please use --password instead.

Taking a look around at some common mysql commands you may be familiar with.

Information Schema

drizzle> show schemas;
+--------------------+
| Database           |
+--------------------+
| information_schema |
+--------------------+
1 row in set (0.00 sec)
drizzle> use information_schema;
drizzle> show tables;
+---------------------------------------+
| Tables_in_information_schema          |
+---------------------------------------+
| CHARACTER_SETS                        |
| COLLATIONS                            |
| COLLATION_CHARACTER_SET_APPLICABILITY |
| COLUMNS                               |
| GLOBAL_STATUS                         |
| GLOBAL_VARIABLES                      |
| KEY_COLUMN_USAGE                      |
| PLUGINS                               |
| PROCESSLIST                           |
| REFERENTIAL_CONSTRAINTS               |
| SCHEMATA                              |
| SESSION_STATUS                        |
| SESSION_VARIABLES                     |
| STATISTICS                            |
| TABLES                                |
| TABLE_CONSTRAINTS                     |
| INNODB_CMP                            |
| INNODB_CMP_RESET                      |
| INNODB_CMPMEM                         |
| INNODB_CMPMEM_RESET                   |
| INNODB_LOCK_WAITS                     |
| INNODB_LOCKS                          |
| INNODB_TRX                            |
+---------------------------------------+
23 rows in set (0.00 sec)

Gone are COLUMN_PRIVILEGES ENGINES EVENTS FILES KEY_COLUMN_USAGE PARTITIONS PROFILING ROUTINES SCHEMA_PRIVILEGES TABLE_PRIVILEGES TRIGGERS USER_PRIVILEGES VIEWS. With MySQL privileges and a number of 5.x features removed, that’s expected. I was surprised to see ENGINES gone. More on that later.

SIDE NOTE: Disappointed to see (0.00 sec) still around. I would have expected the client interface could have had an overhaul for timing output, and report say 0.00 milliseconds.

Variables

drizzle> show variables
+----------------------------------------+---------------------------------------------+
| Variable_name                          | Value                                       |
+----------------------------------------+---------------------------------------------+
| archive_aio                            | OFF                                         |
..
| innodb_change_buffering                | inserts                                     |
| innodb_file_format                     | Antelope                                    |
| innodb_file_format_check               | Antelope                                    |
| innodb_replication_delay               | 0                                           |
| innodb_stats_on_metadata               | ON                                          |
| innodb_stats_sample_pages              | 8                                           |
| innodb_strict_mode                     | OFF                                         |
| innodb_use_sys_malloc                  | ON                                          |
| innodb_version                         | 1.0.3                                       |
...
| logging_query_enable                   | OFF                                         |
| logging_query_filename                 |                                             |
| logging_query_threshold_big_examined   | 0                                           |
| logging_query_threshold_big_resultset  | 0                                           |
| logging_query_threshold_slow           | 0                                           |
| logging_syslog_enable                  | OFF                                         |
| logging_syslog_facility                | local0                                      |
| logging_syslog_ident                   | drizzled                                    |
| logging_syslog_priority                | info                                        |
| logging_syslog_threshold_big_examined  | 0                                           |
| logging_syslog_threshold_big_resultset | 0                                           |
| logging_syslog_threshold_slow          | 0                                           |
...
| multi_thread_max_threads               | 2048                                        |
| myisam_block_size                      | 1024                                        |
| optimizer_switch                       |                                             |
| optimizer_use_mrr                      | force                                       |
| pool_of_threads_size                   | 8                                           |
| replicator_directory                   |                                             |
| replicator_enabled                     | OFF                                         |

161 rows in set (0.01 sec)

MySQL 5.1 has some 265 variables values, so huge changes here. The big sections gone are around CHARACTER SETS, SSL, REPLICATION, QUERY_CACHE, LOG, FULL TEXT. The above list shows new variables, some of these are Innodb plugin related.

Status

drizzle> show status
...
112 rows in set (0.01 sec)

MySQL 5.1 has some 290 status and Drizzle currently 112. Same suspects, REPLICATION, SSL, QUERY_CACHE, a lot of COM_ commands, all INNODB related status and THREADS_CREATED and THREADS_RUNNING. Nothing new from Drizzle.

Engines

drizzle> show engines;
ERROR 1064 (42000): You have an error in your SQL syntax; check the manual that corresponds to your Drizzle server version for the right syntax to use near 'engines' at line 1
drizzle> show plugins;
ERROR 1064 (42000): You have an error in your SQL syntax; check the manual that corresponds to your Drizzle server version for the right syntax to use near 'plugins' at line 1

An initial surprise here, but knowing that all work is converting to plugins, you found this all in INFORMATION_SCHEMA.PLUGINS

drizzle> select * from plugins;
+---------------------+----------------+---------------+--------------------+----------------+--------------------------------------+--------------------------------------------------------------------------+----------------+
| PLUGIN_NAME         | PLUGIN_VERSION | PLUGIN_STATUS | PLUGIN_TYPE        | PLUGIN_LIBRARY | PLUGIN_AUTHOR                        | PLUGIN_DESCRIPTION                                                       | PLUGIN_LICENSE |
+---------------------+----------------+---------------+--------------------+----------------+--------------------------------------+--------------------------------------------------------------------------+----------------+
| binlog              | 1.0            | ACTIVE        | STORAGE ENGINE     | NULL           | MySQL AB                             | This is a pseudo storage engine to represent the binlog in a transaction | GPL            |
| compress            | 1.0            | ACTIVE        | UDF                | NULL           | Stewart Smith                        | UDF for compress()                                                       | GPL            |
| crc32               | 1.0            | ACTIVE        | UDF                | NULL           | Stewart Smith                        | UDF for computing CRC32                                                  | GPL            |
| logging_query       | 0.2            | ACTIVE        | LOGGER             | NULL           | Mark Atwood  mark @fallenpegasus.com  | Log queries to a CSV file                                                | GPL            |
| logging_syslog      | 0.2            | ACTIVE        | LOGGER             | NULL           | Mark Atwood  mark @fallenpegasus.com  | Log to syslog                                                            | GPL            |
| multi_thread        | 0.1            | ACTIVE        | SCHEDULING         | NULL           | Brian Aker                           | One Thread Per Session Scheduler                                         | GPL            |
| pool_of_threads     | 0.1            | ACTIVE        | SCHEDULING         | NULL           | Brian Aker                           | Pool of Threads Scheduler                                                | GPL            |
| replicator          | 0.1            | ACTIVE        | REPLICATOR         | NULL           | Brian Aker                           | Basic replication module                                                 | GPL            |
| signal_handler      | 0.1            | ACTIVE        | DAEMON             | NULL           | Brian Aker                           | Default Signal Handler                                                   | GPL            |
| single_thread       | 0.1            | ACTIVE        | SCHEDULING         | NULL           | Brian Aker                           | Single Thread Scheduler                                                  | GPL            |
| uncompressed_length | 1.0            | ACTIVE        | UDF                | NULL           | Stewart Smith                        | UDF for compress()                                                       | GPL            |
| uncompress          | 1.0            | ACTIVE        | UDF                | NULL           | Stewart Smith                        | UDF for compress()                                                       | GPL            |
| ARCHIVE             | 3.5            | ACTIVE        | STORAGE ENGINE     | NULL           | Brian Aker, MySQL AB                 | Archive storage engine                                                   | GPL            |
| CSV                 | 1.0            | ACTIVE        | STORAGE ENGINE     | NULL           | Brian Aker, MySQL AB                 | CSV storage engine                                                       | GPL            |
| MEMORY              | 1.0            | ACTIVE        | STORAGE ENGINE     | NULL           | MySQL AB                             | Hash based, stored in memory, useful for temporary tables                | GPL            |
| InnoDB              | 1.0.1          | ACTIVE        | STORAGE ENGINE     | NULL           | Innobase Oy                          | Supports transactions, row-level locking, and foreign keys               | GPL            |
| INNODB_TRX          | 1.0.2          | ACTIVE        | INFORMATION SCHEMA | NULL           | Innobase Oy                          | InnoDB transactions                                                      | GPL            |
| INNODB_LOCKS        | 1.0.2          | ACTIVE        | INFORMATION SCHEMA | NULL           | Innobase Oy                          | InnoDB conflicting locks                                                 | GPL            |
| INNODB_LOCK_WAITS   | 1.0.2          | ACTIVE        | INFORMATION SCHEMA | NULL           | Innobase Oy                          | InnoDB which lock is blocking which                                      | GPL            |
| INNODB_CMP          | 1.0.2          | ACTIVE        | INFORMATION SCHEMA | NULL           | Innobase Oy                          | Statistics for the InnoDB compression                                    | GPL            |
| INNODB_CMP_RESET    | 1.0.2          | ACTIVE        | INFORMATION SCHEMA | NULL           | Innobase Oy                          | Statistics for the InnoDB compression; reset cumulated counts            | GPL            |
| INNODB_CMPMEM       | 1.0.2          | ACTIVE        | INFORMATION SCHEMA | NULL           | Innobase Oy                          | Statistics for the InnoDB compressed buffer pool                         | GPL            |
| INNODB_CMPMEM_RESET | 1.0.2          | ACTIVE        | INFORMATION SCHEMA | NULL           | Innobase Oy                          | Statistics for the InnoDB compressed buffer pool; reset cumulated counts | GPL            |
| MyISAM              | 1.0            | ACTIVE        | STORAGE ENGINE     | NULL           | MySQL AB                             | Default engine as of MySQL 3.23 with great performance                   | GPL            |
+---------------------+----------------+---------------+--------------------+----------------+--------------------------------------+--------------------------------------------------------------------------+----------------+
24 rows in set (0.00 sec)

This is where we start to see some significant differences. Storage engines are now all plugins. We see some entire new features for SCHEDULING, LOGGING and REPLICATOR.

drizzle> select plugin_type,count(*) from information_schema.plugins group by plugin_type order by 2 desc;
+--------------------+----------+
| plugin_type        | count(*) |
+--------------------+----------+
| INFORMATION SCHEMA |        7 |
| STORAGE ENGINE     |        6 |
| UDF                |        4 |
| SCHEDULING         |        3 |
| LOGGER             |        2 |
| REPLICATOR         |        1 |
| DAEMON             |        1 |
+--------------------+----------+
7 rows in set (0.00 sec)

SHOW Commands

Drizzle supports the following SHOW Commands.

SHOW COLUMNS FROM information_schema.tables;
SHOW CREATE DATABASE information_schema;
SHOW DATABASES;
SHOW ENGINE INNODB STATUS;
SHOW ERRORS;
SHOW INDEX FROM information_schema.tables;
SHOW OPEN TABLES;
SHOW PROCESSLIST;
SHOW STATUS;
SHOW TABLE STATUS;
SHOW TABLES;
SHOW VARIABLES;
SHOW WARNINGS;
SHOW CREATE SCHEMA;
SHOW SCHEMAS;

The following are no longer valid.

AUTHORS, CHARACTER SET, COLLATION, CONTRIBUTORS, EVENT event_name, FUNCTION func_name, PROCEDURE proc_name, TRIGGER trigger_name, VIEW view_name, ENGINES, EVENTS, FUNCTION CODE func_name, FUNCTION STATUS, GRANTS FOR , INNODB STATUS, PLUGINS, PROCEDURE CODE proc_name, PROCEDURE STATUS, PRIVILEGES, PROFILE, PROFILES, SCHEDULER STATUS, TRIGGERS, BINARY LOGS, MASTER LOGS, BINLOG EVENTS, MASTER STATUS, SLAVE HOSTS, SLAVE STATUS,

Extending vmplot

Taking the work already done with vmplot.sh, a useful tool for MySQL performance tuning by Yves and Matt at BigDBAHead, and in true Open Source fashion I’ve enhanced and modified for my own purposes.

These changes include:

  • Error checking for ‘gnuplot’ command on the system
  • Eliminate the first row of sample data, as this is often not a complete sample for the vmstat duration.
  • Created a HTML output file for easy browser viewing
  • Changed Memory scale values from Kilobytes to Megabytes
  • Resizing png’s for optimal 1024×768 display output (2 per row)

Download vmplot

And I get:

So more specifics of what I did.

Install gnuplot.

$ yum install gnuplot

Create vmstat sample file.

vmstat 1 100 > vmstat.out

Generate output graphs (need to work out those warnings)

 ./vmplot -i vmstat.out -o tmp
Warning: empty y range [0:0], adjusting to [-1:1]
Warning: empty y range [0:0], adjusting to [0:1]

And then I can view via a browser, in this case http://localhost/tmp/vmplot.htm

Some worthwhile references include Gnuplot Reference Manual, Gnuplot Examples and Gnuplot in Action

Your Code, Your Community, Your Cloud… Project Kenai

Following the opening keynote announcement about Kenai I ventured into a talk on Project Kenai.

With today’s economy, the drive is towards efficiency is certainly a key consideration, it was quoted that dedicated hosting servers only run at 30% efficiency.

An overview again of Cloud Computing

  • Economics – Pay as you go,
  • Developer Centric – rapid self provisioning, api-driven, faster deployment
  • Flexibility – standard services, elastic, on demand, multi-tenant

Types of Clouds

  • Public – pay as you go, multi-tenant application and services
  • Private – Cloud computing model run within a company’s own data center
  • Mixed – Mixed user of public and private clouds according to applications

SmugMug was referenced as a Mixed Cloud example.

Cloud Layers

  • Infrastructure as a Services – Basic storage and computer capabilities offer as a service (eg. AWS)
  • Platform as a Service – Developer platform with build-in services. e.g. Google App Engine
  • Software as Service – applications offered on demand over the network e.g salesforce.com

Some issues raised about this layers included.

  • IaaS issues include Service Level, Privacy, Security, Cost of Exit
  • PaaS interesting point, one that is the bane of MySQL performance tuning, that is instrumentation
  • SaaS nothing you need to download, you take the pieces you need, interact with the cloud. More services simply like doing your Tax online.

Sun offers Project Kenai as well as Zembly.

Project Kenai

  • A platform and ecosystem for developers.
  • Freely host open source projects and code.
  • Connect, community, collaborate and Code with peers
  • Eventually easily deploy application/services to “clouds”

Kenai Features

  • Code Repository with SVN, Mercurial, or an external repository
  • Issue tracking with bugzilla, jira
  • collaboration tools such as wiki, forums, mailing lists
  • document hosting
  • your profile
  • administrative role

Within Kenai you can open up to 5 open source projects and various metrics of the respositories, issue trackers, wiki etc.

The benefits were given as the features are integrated into your project, not distributed across different sites. Agile development within the project sees a release every 2 weeks. Integration with NetBeans and Eclipse is underway.

Kenai is targeted as being the core of the next generation of Sun’s collaboration tools. However when I asked for more details about uptake in Sun, it’s only a request, not a requirement for internal teams.

The API’s for the Sun Cloud are at http://kenai.com/projects/suncloudapis.

Event: CommunityOne East in New York, NY.
Presenter: Tori Wieldt, Sun Microsystems
Article Author: Ronald Bradford

Beginner CSV Engine issues

I’ve just started using the CSV engine for a practical application and I’ve come across a few subtle and unexpected issues/limitations.

First, you can’t create any columns in your CSV table nullable.

mysql> create table t1(i INT) ENGINE=CSV;
ERROR 1178 (42000): The storage engine for the table doesn't support nullable columns

RTFM shows this was introduced in 5.1.23. See CSV Limitations

The second and more annoying was creating a CSV table, inserting a sample row (just to check the syntax), then replacing the file ([datadir]/[schema]/[table].CSV) with the same format, but with additional generated rows. This was to no avail when attempting to SELECT from the table.

The solution was to do a REPAIR TABLE [table] in order to see the newly refreshed data.
Futhermore, some more RTFM shows in Repairing and Checking CSV Tables an important caveat to using the CSV engine and loading data directly by file copy.

Warning: Note that during repair, only the rows from the CSV file up to the first damaged row are copied to the new table. All other rows from the first damaged row to the end of the table are removed, even valid rows.

Buyer beware.

Identifying Bad Memory

I was having problems recently with a dedicated production server, that runs my MySQL Server and a number of websites. It’s most annoying when your system crashes without any reporting in /var/log/messages

The tool of choice from the host provider SoftLayer was PassMark BurnInTest Linux which is installed with every dedicated server.

I will need to investigate open source alternatives, as this is a commercial product, but for the purposes of my pain, this included tool was well worth the investment.

**************
RESULT SUMMARY
**************
Test Start time: Sun Feb 22 16:02:48 2009
Test Stop time: Sun Feb 22 16:07:49 2009
Test Duration: 000h 05m 01s

Test Name Cycles Operations Result Errors Last Error
CPU - Maths 261 488 Billion PASS 0 No errors
Memory (RAM) 2 3.081 Billion FAIL 1 Error verifying data in RAM
Network: 127.0.0.1 412995 4.295 Billion PASS 0 No errors
TEST RUN FAILED

*********************
SERIOUS ERROR SUMMARY
*********************
SERIOUS : 2009-02-22 16:07:31, RAM, SERIOUS: Error verifying data in RAM (x 1)

It was great to get a simple resolution to the problem, bad memory?
With a scheduled maintenance replacement I was operational again.

 **************
RESULT SUMMARY
**************
Test Start time: Sun Feb 22 20:34:37 2009
Test Stop time: Sun Feb 22 20:39:38 2009
Test Duration: 000h 05m 01s

Test Name Cycles Operations Result Errors Last Error
CPU - Maths 267 406 Billion PASS 0 No errors
Memory (RAM) 1 3.664 Billion PASS 0 No errors
Network: 127.0.0.1 334578 3.480 Billion PASS 0 No errors
TEST RUN PASSED

*********************
SERIOUS ERROR SUMMARY
*********************

Are you monitoring RSS & VSZ?

Monitoring MySQL Memory is a rather critical task because you can’t limit MySQL’s usage of physical memory resources. Improperly configured servers running MySQL can crash because you don’t understand memory usage.

MySQL uses memory in a number of different ways. Using the Oracle analogy, you can divide the mysqld memory usage into main areas of:

  • SGA – System Global Area
  • PGA – Process Global Area

The SGA is the footprint that MySQL uses for startup. This is attributed to the base footprint of the mysqld process and a number of buffers including:

NOTE: This is for a default MySQL 5.1 install. Other storage engines and/or other versions of MySQL may have additional buffers. Falcon for example in MySQL 6.x has additional buffers.

The PGA is more complex, and the cause of problems for the possible occurrence of your server running out of memory and needing to swap. The goal of monitoring memory usage is to of course avoid this.
This additional memory is a combination of a few areas including:

  • MEMORY tables
  • Connection management (such as thread_cache and table_cache)
  • Per Connection memory usage

The later is the cause of greatest concern, especially for environments that have persistent connections. Per Connection memory usage is a combination of many buffers including the thread_stack, 2 x net_buffer_length (to max_allowed_packet), read_buffer_size, read_rnd_buffer_size, join_buffer_size, sort_buffer_size, and up to min(max_heap_table_size,tmp_table_size). In fact, for example with temporary tables, a query may use multiple temporary tables.

Memory on a per connection basis is kept until the connection is closed. In some instances such as next_buffer_size, this is apparently reduced aftter each SQL Statement result. With a persistent connection model (e.g. Java), ensuring idle connections drop to a low watermark is a valuable task. The confusing part is MySQL instrumentation does not tell you exactly how much is used, and it’s impossible to calculate with available provided data.

As part of monitoring your server, you should monitor the size of the mysqld memory usage, because this will cause you to be proactive rather then reactive to scarce memory resources. You can easily get this using the ps command. For example:

$ps -eopid,fname,rss,vsz,user,command | grep -e "RSS" -e "mysql"
  PID COMMAND    RSS    VSZ USER     COMMAND
 5463 grep       764   5204 ronald   grep -e RSS -e mysql
13894 mysqld_s   596   3936 root     /bin/sh /usr/bin/mysqld_safe
13933 mysqld   4787812 5127208 mysql /usr/sbin/mysqld --basedir=/usr --datadir=/vol/mysql/mysqldata --user=mysql --pid-file=/var/run/mysqld/mysqld.pid --skip-external-locking --port=3306 --socket=/var/run/mysqld/mysqld.sock
13934 logger     608   3840 root     logger -p daemon.err -t mysqld_safe -i -t mysqld
$ ps -eopid,fname,rss,vsz,user,command | grep " mysqld " | grep -v grep | awk '{print $3,$4}'
4787820 5127208


From man ps
rss RSS resident set size, the non-swapped physical memory that a task has used (in kiloBytes). (alias rssize, rsz).
vsz VSZ virtual memory size of the process in KiB (1024-byte units). Device mappings are currently excluded; this is subject to change.
(alias vsize).

The motto of the story, don’t just monitor the free memory of your system, for a database server, you need to closely monitor the primary process on the server, that is mysqld.

References

How MySQL Uses Memory

More Information

Join me for my MySQL User Conference talk on “Monitoring 101 – Simple stuff to save your bacon”.

I also cover monitoring MySQL in my “MySQL Essentials” training course. For more information visit MySQL Education.

Watching a slave catchup

This neat one line command can be of interest when you are rebuilding a MySQL slave and replication is currently catching up.

$ watch --interval=1 --differences 'mysql -uuser -ppassword -e "SHOW SLAVE STATUS\G"'

You will see the standard SHOW SLAVE STATUS output, but the watch command presents an updated view every second, and highlights differences. This can be useful in a background window to keep an eye on those ‘Seconds Behind Master’.

*************************** 1. row ***************************
             Slave_IO_State: Waiting for master to send event
                Master_Host: 10.10.10.10
                Master_User: slave
                Master_Port: 3306
              Connect_Retry: 60
            Master_Log_File: mysql-bin.000626
        Read_Master_Log_Pos: 88159239
             Relay_Log_File: slave-relay.000005
              Relay_Log_Pos: 426677632
      Relay_Master_Log_File: mysql-bin.000621
           Slave_IO_Running: Yes
          Slave_SQL_Running: Yes
            Replicate_Do_DB:
        Replicate_Ignore_DB:
         Replicate_Do_Table:
     Replicate_Ignore_Table:
    Replicate_Wild_Do_Table:
Replicate_Wild_Ignore_Table:
                 Last_Errno: 0
                 Last_Error:
               Skip_Counter: 0
        Exec_Master_Log_Pos: 426677495
            Relay_Log_Space: 2714497549
            Until_Condition: None
             Until_Log_File:
              Until_Log_Pos: 0
         Master_SSL_Allowed: No
         Master_SSL_CA_File:
         Master_SSL_CA_Path:
            Master_SSL_Cert:
          Master_SSL_Cipher:
             Master_SSL_Key:
      Seconds_Behind_Master: 24131

Reducing the MySQL 5.1.30 disk footprint

The current size of a MySQL 5.1.30 installation is around 420M.

$ du -sh .
426M	.

A further breakdown.

$ du -sh *
213M	bin
20K	COPYING
9.8M	docs
8.0K	EXCEPTIONS-CLIENT
436K	include
12K	INSTALL-BINARY
121M	lib
504K	man
4.0K	my.cnf
77M	mysql-test
4.0K	README
20K	scripts
2.3M	share
2.9M	sql-bench
100K	support-files

A means to reduce the footprint by 25% is to delete some unused stuff.

$ rm -rf docs/ mysql-test/ sql-bench/
$ du -sh .
337M	.

It’s no big deal, however it certainly does cut down on verbose output in the backup logs removing the mysql-test directory and files.

Dependency error installing mylvmbackup on Ubuntu 8.04

I’ve started an investigation of MySQL Backups using LVM. I’m working with Lenz’s mylvmbackup but I found it both used Perl and needed a number of dependencies installed.

Installing dependencies failed on my test system, yet I found it actually worked when I went back to my dev system (but it is not configured with LVM for full testing).

$ sudo cpan Config::IniFiles Sys::Syslog Date::Format Getopt::Long  DBI

Details of error:

....
 CPAN.pm: Going to build S/SA/SAPER/Sys-Syslog-0.27.tar.gz

WARNING: LICENSE is not a known parameter.
Checking if your kit is complete...
Looks good
'LICENSE' is not a known MakeMaker parameter name.
Writing Makefile for Sys::Syslog
cp Syslog.pm blib/lib/Sys/Syslog.pm
/usr/bin/perl /usr/share/perl/5.8/ExtUtils/xsubpp -noprototypes -typemap /usr/share/perl/5.8/ExtUtils/typemap  Syslog.xs > Syslog.xsc && mv Syslog.xsc Syslog.c
cc -c   -D_REENTRANT -D_GNU_SOURCE -DTHREADS_HAVE_PIDS -DDEBIAN -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2   -DVERSION="0.27" -DXS_VERSION="0.27" -fPIC "-I/usr/lib/perl/5.8/CORE"  -DUSE_PPPORT_H Syslog.c
In file included from Syslog.xs:6:
/usr/lib/perl/5.8/CORE/perl.h:420:24: error: sys/types.h: No such file or directory
/usr/lib/perl/5.8/CORE/perl.h:451:19: error: ctype.h: No such file or directory
/usr/lib/perl/5.8/CORE/perl.h:463:23: error: locale.h: No such file or directory
/usr/lib/perl/5.8/CORE/perl.h:480:20: error: setjmp.h: No such file or directory

Some searching was necessary to find this thread and confirm that my prod server did not have a correct dev package.

apt-get install libc6-dev

NOTE: While the doc refers to the module File::Basename, trying to install this throws an error which when you investigate further is a false positive. The README does refer to this being normally part of the default perl installation.

Some MySQL pairs terminology

In response to a number of comments, I thought I would clarify the scope of my discussion regarding Options using MySQL pairs before I begin. As mentioned their is no one way or type of configuration for MySQL in a HA solution, however the simplest progression from a single Master/Slave environment is the concept of a pair of servers, configured to support a fail over and fail back via MySQL Replication.

The concept of a MySQL Pair in this context is to have a “hot” MySQL standby ready for controlled and hopefully! automated fail over. I say hopefully because with MySQL Replication as an asynchronous solution there is no guarantee for no loss of data.

I consider DRBD/Heatbeat for example a “cold” standby, as MySQL on the slave server is not actually running. DRBD does provide a guarantee of consistency in data (a synchronous solution) that is written at a disk level, which is a significant advantage over asynchronous replication. I consider Red Hat Cluster suite, simply a management process, and definitely “cold”.

A Shared disk solution, for example a SAN, and a failover server that uses the shared storage, is also a “cold” standby.

There are advantages and disadvantages to each option. These relative merits of the strengths and weaknesses should be considered carefully when you are making a design decision.

VirtualBox, compiling Part 2

So I managed to find all dependencies after some trial and error for compiling VirtualBox 1.6.4 under Ubuntu 8.0.4, then finding the Linux build instructions to confirm.

It was not successful however in building, throwing the following error:

kBuild: Compiling dyngen - dyngen.c
kBuild: Linking dyngen
kmk[2]: Leaving directory `/usr/local/VirtualBox-1.6.4/src/recompiler'
kmk[2]: Entering directory `/usr/local/VirtualBox-1.6.4/src/apps'
kmk[2]: pass_bldprogs: No such file or directory
kmk[2]: *** No rule to make target `pass_bldprogs'. Stop.
kmk[2]: Leaving directory `/usr/local/VirtualBox-1.6.4/src/apps'
kmk[1]: *** [pass_bldprogs_before] Error 2
kmk[1]: Leaving directory `/usr/local/Virtu

More searching, I needed to add two more files manually. Read More Here.

A long wait, compiling for 20+ minutes, and a necessary reboot as upgraded images threw another error, I got 1.6.4 running, and able to boot Fedora Core 9 image created under 1.5.6

But the real test, and the need for this version was to install Intrepid.

This also failed with a Kernel panic during boot. More info to see this reported as a Ubuntu Bug and Virtual Box Bug.

More work still needed.

Installing Skype

A fresh install of my laptop with Ubuntu 7.10 after stuff just didn’t work causes pains sometimes of the installed programs. Skype being one of them.

Goto Skype for Linux and get the Ubuntu installer.

I needed some dependencies.

$ su -
$ apt-get install libqt4-gui libqt4-core
$ dpkg -i skype-debian_1.4.0.118-1_i386.deb
$ exit
$ skype

Voila, all my old preferences (from ~) work just nicely. I see it’s also a newer version.

Ubuntu Tricks today

ctrl-alt-l – Lock Screen
ctrl-alt-d – Desktop

# Multi Cut-Paste History
apt-get install glipper

Add to System|Preferences|Sessions|Startup Programs

Thanks Yves

Perl Tricks

perl_modules.pl

#!/usr/bin/perl

use ExtUtils::Installed;
my $instmod = ExtUtils::Installed->new();
foreach my $module ($instmod->modules()) {
my $version = $instmod->version($module) || "???";
       print "$module -- $versionn";
}

remove_perl_module.pl

#!/usr/bin/perl -w
use ExtUtils::Packlist;
use ExtUtils::Installed;

$ARGV[0] or die "Usage: $0 Module::Namen";

my $mod = $ARGV[0];

my $inst = ExtUtils::Installed->new();

    foreach my $item (sort($inst->files($mod))) {
             print "removing $itemn";
             unlink $item;
          }

     my $packfile = $inst->packlist($mod)->packlist_file();
          print "removing $packfilen";
          unlink $packfile;

http://www.cpan.org/misc/cpan-faq.html

Ubuntu 7.04 Fiesty

I upgraded my work laptop to Ubuntu 7.04 Fiesty. The process was not as smooth as I expected. First it complained about not enough space on /var, so I cleaned up sufficient space. It continued to complain about 3 times.

The install itself I was hoping would have been automated, so when starting at night I wake up, and it’s done, however there were a number of installation errors, and prompts to keep or override configuration files, which I had to do manually at least 10 times. This of course made my laptop unavailable for a number of hours.

Today I’ve found the first real problem. My Open Office has lost all it’s fonts that I’ve loaded on in the past. Arial for example is no longer available. Of course searching on the web for installing fonts gives you several links, do you think any of these worked?

I found in reviewing my backup that the directory /usr/share/fonts/truetype/msttcorefonts/ had been removed. Re-instating this gave me back my fonts.

Things that irk me!

As part of my job, I spend a lot of time assisting people when they are driving. But sometimes is can be trying.

  • People that type commands, make a mistake, then backspace over typed text (like 10-20 characters), only to have to retype the text again. Using bash for example, you can just arrow back, change then goto end of line, saving all that re-typing. And it’s so painful when they are slow typer’s.
  • People that have to use copy/paste (ie, mouse). But when they scroll up several pages to find a command, copy, then scroll down to paste when up arrow a few times in command history gives you the command you want. Even, simply removing the scrolling down (it’s not needed to paste) would save 1 of 4 operations.
  • Using copy/paste in vi, where your not in insert mode(so it doesn’t work properly, so they have to exit insert mode, copy, enter insert mode, paste, just to do it again)! People need to learn the power of Yank (Y or yy)

Linux One Liner – dirtree alternative

Linux has a cool command called dirtree that gives a more visual representation of your directory structure. If you have the misfortune of working on a Unix variant that doesn’t have it, checkout this cool one liner.

ls -R . | grep ":$" | sed -e 's/:$//' -e 's/[^-][^/]*\//--/g' -e 's/^/   /' -e 's/-/|/'

Thanks for the command Tom.

Determining Linux Video Driver Refresh Rates

I found this cool command called glxgears that you can run under X.

$ glxgears
10524 frames in 5.0 seconds = 2104.650 FPS
10003 frames in 5.0 seconds = 2000.501 FPS
8417 frames in 5.0 seconds = 1683.340 FPS    * Moved the window from left to right
10538 frames in 5.0 seconds = 2107.443 FPS
5639 frames in 5.0 seconds = 1120.850 FPS   * Moved the window around constantly
X connection to :0.0 broken (explicit kill or server shutdown).
$ glxgears --help
Warrning: unknown parameter: --help

Note the spelling error in “Warrning”.