High iowait on Amazon EC2 MySQL instance with EBS volume

Question

We have a MySQL server running on an Amazon EC2 c1.medium instance relying on a single EBS volume using the ext3 filesystem for storage.

This MySQL server is queried ~500/ps by several applications running on some web servers, which are also at the Amazon EC2.

As you can see below, server's load avg and processor idle time seems fine, but there's something disturbing and worrying me right now, which is the high iowait it's been experiencing.

Another number that worried me a lot is the number of iostat's transfers per second (tps), which stays above 450 most of the time. After doing some research on this topic, I saw some people saying that this is ask too much of a EBS volume: https://forums.aws.amazon.com/thread.jspa?threadID=30769

By the way, the command outputs you'll see below were not captured in a peak time. That's the way the server behaves/performs most of the time.

Well, all said, here go my questions:

1- Is it time to consider moving for a RAID architecture (I'd say RAID 0)?

2- Should I spent time on a clustering solution such as MySQL Cluster?

3- Do you believe such scenario is heavily impacting our apps? Would they perform much better in case we move to a RAID 0 and/or cluster solution? (Seems that the apps are happy so far, but would they be happier?)

Please let me know if you need any further information.

~ # uptime 
 12:34:14 up 2 days,  4:06,  1 user,  load average: 2.24, 1.90, **1.84**

########################################################

~ # vmstat 5

procs -----------memory---------- ---swap-- -----io---- --system-- -----cpu------

 r  b   swpd   free   buff  cache   si   so    bi    bo   in   cs us sy id **wa** st

 0  1     52  11168  16420 1498728    0    0  4586   231   11   81  6  3 52 39  0

 2  1     52  10460  16320 1499588    0    0 11631   397 3194 4319 10  4 47 39  0

 4  1     52  11448  16064 1499156    0    0 12231   592 2301 3331  9  5 50 36  0

 4  0     52  10328  16068 1500176    0    0  8578   392 2131 2745  8  6 49 37  0

 0  1     52  11164  15732 1499928    0    0  9604   578 2609 3510  7  4 49 40  0

 0  1     52  10824  15768 1499836    0    0  5038   634 1912 2509  8  3 47 42  0

 3  1     52  12040  15888 1498096    0    0  5068   204 1927 2531 10  8 45 37  0

 8  2     52  11252  15784 1499272    0    0  8521   390 2437 3100 14 15 39 31  0

 1  2     52  11436  15724 1499748    0    0  8287   401 2159 3113 11 10 42 36  1

 0  1     52  12016  15704 1498752    0    0 11576   499 3324 3984 16 17 31 36  0

 1  1     52  10536  15664 1500508    0    0  8430   718 2686 3265 15 14 37 34  0

 1  1     52  10300  15676 1500744    0    0 10186   720 2488 3488 16  5 45 34  0

########################################################

~ # iostat -dm 5 /dev/sdf 
Linux 2.6.21.7-2.fc8xen (database-new)  01/20/12

Device:            tps    MB_read/s    MB_wrtn/s    MB_read    MB_wrtn

sdf             464.81         8.84         0.33    1658860      61390

Device:            tps    MB_read/s    MB_wrtn/s    MB_read    MB_wrtn

sdf             402.20         7.39         0.43         36          2

Device:            tps    MB_read/s    MB_wrtn/s    MB_read    MB_wrtn

sdf             431.40         7.74         0.32         38          1

Device:            tps    MB_read/s    MB_wrtn/s    MB_read    MB_wrtn

sdf             461.40         8.26         0.39         41          1

Device:            tps    MB_read/s    MB_wrtn/s    MB_read    MB_wrtn

sdf             475.65         9.20         0.29         46          1

Device:            tps    MB_read/s    MB_wrtn/s    MB_read    MB_wrtn

sdf             534.80         9.82         0.52         49          2

Device:            tps    MB_read/s    MB_wrtn/s    MB_read    MB_wrtn

sdf             526.60         9.97         0.52         49          2

########################################################

~ # iostat -mdx 5 /dev/sdf 

Device:         rrqm/s   wrqm/s   r/s   w/s    rMB/s    wMB/s avgrq-sz avgqu-sz   await  svctm  %util

sdf              22.21    46.28 427.47 37.54     8.84     0.33    40.38     1.78    3.82   1.72  79.87

Device:         rrqm/s   wrqm/s   r/s   w/s    rMB/s    wMB/s avgrq-sz avgqu-sz   await  svctm  %util

sdf              22.36    80.04 450.30 60.48     9.29     0.55    39.44     1.45    2.85   1.58  80.48

Device:         rrqm/s   wrqm/s   r/s   w/s    rMB/s    wMB/s avgrq-sz avgqu-sz   await  svctm  %util

sdf              23.40    43.60 370.60 47.00     7.75     0.35    39.76     1.45    3.47   1.97  82.08

Device:         rrqm/s   wrqm/s   r/s   w/s    rMB/s    wMB/s avgrq-sz avgqu-sz   await  svctm  %util

sdf              20.20    33.20 382.60 29.60     8.02     0.25    41.05     1.31    3.17   2.11  87.12

Device:         rrqm/s   wrqm/s   r/s   w/s    rMB/s    wMB/s avgrq-sz avgqu-sz   await  svctm  %util

sdf              28.80    35.20 422.40 33.40     9.04     0.27    41.80     1.45    3.19   1.95  88.96

Device:         rrqm/s   wrqm/s   r/s   w/s    rMB/s    wMB/s avgrq-sz avgqu-sz   await  svctm  %util

sdf              14.20    45.00 291.80 51.40     5.97     0.38    37.86     1.45    4.22   2.50  85.68

Device:         rrqm/s   wrqm/s   r/s   w/s    rMB/s    wMB/s avgrq-sz avgqu-sz   await  svctm  %util

sdf              19.16    56.89 535.33 41.32    11.44     0.38    42.00     1.49    2.59   1.53  88.46

Device:         rrqm/s   wrqm/s   r/s   w/s    rMB/s    wMB/s avgrq-sz avgqu-sz   await  svctm  %util

sdf              20.40    81.40 233.00 64.40     4.86     0.57    37.39     1.74    5.84   3.18  94.72

################################################## my.cnf

[mysqld]
datadir=/var/lib/mysql
socket=/var/lib/mysql/mysql.sock
user=mysql
long_query_time=1
key_buffer = 64M
thread_cache_size = 30
table_cache = 1024
table_definition_cache = 512
query_cache_type = 1
query_cache_size = 64M
tmp_table_size = 64M
max_heap_table_size = 64M
innodb_buffer_pool_size = 512M
old_passwords=1
max_connections=400
wait_timeout=30

[mysqld_safe]
log-error=/var/log/mysqld.log
pid-file=/var/run/mysqld/mysqld.pid

[ndbd]
connect-string="nodeid=2;host=localhost:1186"

[ndb_mgm]
connect-string="host=localhost:1186"

################################################## sundry's tuning script output

~ # ./tuning-primer.sh 

    -- MYSQL PERFORMANCE TUNING PRIMER --
         - By: Matthew Montgomery -

MySQL Version 5.1.52 i686

Uptime = 0 days 1 hrs 1 min 1 sec
Avg. qps = 517
Total Questions = 1894942
Threads Connected = 94

Warning: Server has not been running for at least 48hrs.
It may not be safe to use these recommendations

To find out more information on how each of these
runtime variables effects performance visit:
http://dev.mysql.com/doc/refman/5.1/en/server-system-variables.html
Visit http://www.mysql.com/products/enterprise/advisors.html
for info about MySQL's Enterprise Monitoring and Advisory Service

SLOW QUERIES
The slow query log is NOT enabled.
Current long_query_time = 1.000000 sec.
You have 207 out of 1894981 that take longer than 1.000000 sec. to complete
Your long_query_time seems to be fine

BINARY UPDATE LOG
The binary update log is NOT enabled.
You will not be able to do point in time recovery
See http://dev.mysql.com/doc/refman/5.1/en/point-in-time-recovery.html

WORKER THREADS
Current thread_cache_size = 30
Current threads_cached = 8
Current threads_per_sec = 0
Historic threads_per_sec = 0
Your thread_cache_size is fine

MAX CONNECTIONS
Current max_connections = 400
Current threads_connected = 93
Historic max_used_connections = 195
The number of used connections is 48% of the configured maximum.
Your max_connections variable seems to be fine.

INNODB STATUS
Current InnoDB index space = 1.33 G
Current InnoDB data space = 5.04 G
Current InnoDB buffer pool free = 0 %
Current innodb_buffer_pool_size = 512 M
Depending on how much space your innodb indexes take up it may be safe
to increase this value to up to 2 / 3 of total system memory

MEMORY USAGE
Max Memory Ever Allocated : 1.13 G
Configured Max Per-thread Buffers : 1.04 G
Configured Max Global Buffers : 642 M
Configured Max Memory Limit : 1.67 G
Physical Memory : 1.70 G

Max memory limit exceeds 90% of physical memory

KEY BUFFER
Current MyISAM index space = 379 M
Current key_buffer_size = 64 M
Key cache miss rate is 1 : 162
Key buffer free ratio = 80 %
Your key_buffer_size seems to be fine

QUERY CACHE
Query cache is enabled
Current query_cache_size = 64 M
Current query_cache_used = 43 M
Current query_cache_limit = 1 M
Current Query cache Memory fill ratio = 67.44 %
Current query_cache_min_res_unit = 4 K
MySQL won't cache query results that are larger than query_cache_limit in size

SORT OPERATIONS
Current sort_buffer_size = 2 M
Current read_rnd_buffer_size = 256 K
Sort buffer seems to be fine

JOINS
Current join_buffer_size = 132.00 K
You have had 4013 queries where a join could not use an index properly
You should enable "log-queries-not-using-indexes"
Then look for non indexed joins in the slow query log.
If you are unable to optimize your queries you may want to increase your
join_buffer_size to accommodate larger joins in one pass.

Note! This script will still suggest raising the join_buffer_size when
ANY joins not using indexes are found.

OPEN FILES LIMIT
Current open_files_limit = 2458 files
The open_files_limit should typically be set to at least 2x-3x
that of table_cache if you have heavy MyISAM usage.
Your open_files_limit value seems to be fine

TABLE CACHE
Current table_open_cache = 1024 tables
Current table_definition_cache = 512 tables
You have a total of 45237 tables
You have 1024 open tables.
Current table_cache hit rate is 0%
, while 100% of your table cache is in use
You should probably increase your table_cache
You should probably increase your table_definition_cache value.

TEMP TABLES
Current max_heap_table_size = 64 M
Current tmp_table_size = 64 M
Of 38723 temp tables, 44% were created on disk
Perhaps you should increase your tmp_table_size and/or max_heap_table_size
to reduce the number of disk-based temporary tables
Note! BLOB and TEXT columns are not allow in memory tables.
If you are using these columns raising these values might not impact your 
ratio of on disk temp tables.

TABLE SCANS
Current read_buffer_size = 128 K
Current table scan ratio = 537 : 1
read_buffer_size seems to be fine

TABLE LOCKING
Current Lock Wait ratio = 1 : 954
You may benefit from selective use of InnoDB.
If you have long running SELECT's against MyISAM tables and perform
frequent updates consider setting 'low_priority_updates=1'
If you have a high concurrency of inserts on Dynamic row-length tables
consider setting 'concurrent_insert=2'.

Solution 1

It would help if you posted your my.cnf and whether you are using InnoDB or MyISAM tables and whether you are a read-heavy or write-heavy workload. Otherwise, we are just making guesses. Here are mine:

First, I would look and make sure that your queries are properly indexed. High I/O on MySQL databases is either caused by extremely high concurrency, a poorly tuned server, or by poorly performing queries that have to do full table or index scans. Some hints on how to find the poorly performing queries can be found in my post on Ideeli's technical blog.

Check your my.cnf. If you are using InnoDB, make sure innodb_buffer_pool_size and innodb_log_file_size are sufficiently large. Because EBS has such variable latency, maxing out innodb_log_file_size can have substantial performance benefits. If you are using MyISAM (and you shouldn't), make sure your key_buffer size is large enough.

If you are confident that your queries are well optimized, and your server is well-tuned, we can move on to the next item. ext3 is less than ideal for databases. One of the main reasons for this is that ext3 only allows a single thread to update an inode at a time (trying to find documentation for this). If you aren't running with innodb-file-per-table, this means that there is a ton of filesystem contention on the ibdata file. xfs does not have this limitation and has been shown to perform much better (need source) for database workloads.

If you can't change to xfs, make sure that you are using innodb-file-per-table and at a minimum, make sure that you have noatime,nodiratime on the mount.

Next, on to your instance size. A c1.medium is not an ideal instance size for most databases unless the data set is tiny. MySQL ordinarily will benefit from memory over compute power. c1.medium only has 1.7GB of RAM! How big is your data set? In general, a m1.large (with 7.5GB of RAM) will outperform a c1.medium except in very rare cases. It is also twice as expensive, at $0.34/hr.

Now on to RAID of EBS volumes. Yes, RAID will greatly increase your IOPS. (As will increasing your instance size). Do not RAID0...If you care about your data, at least. I have explained this in many places, including on my blog, as a speaker at Percona Live NYC in 2011, and here on serverfault. The short version is that EBS volumes fail in atypical ways and being able to remove a volume from the set has proven to be valuable on serveral occasions, most notably during the great EBS outage of 2011 where some sites were offline for several days...We were offline for 45 minutes at 4AM despite having dozens of instances affected by the EBS issue.

Here are some benchmarks for RAIDed EBS volumes using MySQL.

Finally, Percona Server has a huge number of scalability optimizations. Here is a white paper about my company's experience when switching from MySQL to Percona Server. We were experiencing database stalls and outages every day. Simply switching to Percona Server from MySQL resolved that issue literally overnight due to a number of scalability improvements.

So, in summary...

• Tune your queries
• Tune your server
• Get yourself better "hardware"
• Use xfs, not ext3
• RAID10, not RAID0
• Switch from MySQL to Percona Server

As for MySQL Cluster, it's a completely different animal than MySQL and generally not suitable for most OLTP applications. Galera/Percona XtraDB Cluster are new and interesting clustering products, as well. You have a lot of options before you get to any of this, however. We served 24k qps at peak from a single m2.4xlarge with RAID10 in EC2.

Good luck!

Solution 2

Since 500gps is a fairly mild load on the sql server i suggest looking at the percentage of temp tables created on disk and start optimizing your queries and MySQL Server Settings.

1, Do not do the Raid0 approach, it will eventually fail and you will regret it.

2, No, at this low number of queries per second you do not need MySQL Cluster.

3, Yes, it surely does affect App Performance, to measure how much you could enable the slow log and see for yourself.

How much memory is mysql using currently, is there any headroom left?
If not you should consider switching to a bigger instance and start optimizing settings with sundry's mysql tuning script:
http://www.day32.com/MySQL/tuning-primer.sh

Solution 3

This is a problem many, many companies have run into, and solutions to it are fairly well-discussed on various online forums.

Typically to increase the potential iops, two or more EBS volumes are joined together in a RAID0 array. This doesn't come without risk, though. As you know, with RAID0, all it takes is for one of the member EBS volumes to have an issue and your data is toast. As such, you may consider using a more resilient RAID level, say RAID 10 perhaps.

Solution 4

3- Do you believe such scenario is heavily impacting our apps? Would they perform much better in case we move to a RAID 0 and/or cluster solution?

Since you are running an SQL server, it would make more sense to take a look at the SQL server metrics instead to know if queries are served quickly. Looking at your single-digit average request wait times (await), I do not think I/O would be much of a concern yet.

Also, as what you mostly see is read load, you could reduce it by having a larger cache / increasing the amount of RAM and tuning the cache parameters of your MySQL instance. I would expect this to have a significantly larger performance impact than having your storage changed to handle more I/Os.

View more solutions

Comments

[Luis Fernando Alen]

Thanks for you reply, ErikA. I know that many companies run into this problem and RAID0 is by no means a safe approach, although it's quite simple to configure and performs very well. I also know that in order to solve this issue a more sophisticated solution such as RAID and clustering is required. However, what I'm really asking here is: Is it time to put my efforts on that? Should I be worrying that much? I ask that because I see the processor idle half of the time and the server's load is also fine. Such scenario is somehow different from the ones I see all over the web.

[EEAA]

If it's causing performance problems with your application, then yes, it's probably good to start thinking about it. If not, well then don't worry about it.

[Luis Fernando Alen]

Hello, syneticon-dj. We already have some parameters set on MySQL for caching such as query_cache_size and table_cache but I'll dig deeper into MySQL tuning options in order to make better use of the available RAM and unburden the EBS volume. Thanks for the tip.

[the-wabbit]

@LuisFernandoAlen table_cache is not doing what you think it is. If you are using MyISAM tables, there is no explicit data cache beyond the OS filesystem cache. An index cache is maintained and controlled by the key_buffer_size global variable. But with your instance having just 1.7 GB of RAM, migrating to a "Large" EC2 instance would probably have the best visible effect without an awful lot of tuning.

[Admin]

Write performance under Percona XtraDB Cluster / Galera actually doesn't degrade as you might expect; it can actually improve, especially on slow I/O like EBS, because writing to a remote server's RAM is faster than writing to local "disk". Henrik Ingo has some benchmarks on this. We should benchmark and write it up more, too. This might be off-topic for this discussion, though.

[Admin]

The more EBS volumes you have, the more likely you are to have performance problems. You run into the weakest-link problem where the slowest one hurts the whole system. And the more volumes you have, the more likely that one of them will misbehave.

[Admin]

The tuning script referenced is dangerous and I don't recommend it. I've seen more DE-optimized servers with such tuning scripts than optimized ones.

[Luis Fernando Alen]

First of all I'd like to thank you for such a complete answer. Second, making things clearer, most of our tables use the InnoDB engine and the server has a read-heavy workload. I also edited my question and added our my.cnf and the output of sundry's mysql tuning script. I tried some tuning parameters you suggested, specially the innodb_buffer_pool_size but the server is still experiencing a high iowait. Nevertheless, since I'm not a DBA I'm sure I'm missing several things here and will need to work harder :) Regarding the filesystem, I'll follow your advice and move to xfs as soon as I can.

[Luis Fernando Alen]

Niko, thanks for the script. Dangerous or not, I can say it provided some important information and some points I need to work on :)