Jul
10
2018
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When Database Warm Up is Not Really UP

first few minutes MySQL Warm Up graph from PMM

The common wisdom with database performance management is that a “cold” database server has poor performance. Then, as it “warms up”, performance improves until finally you reach a completely warmed up state with peak database performance. In other words, that to get peak performance from MySQL you need to wait for database warm up.

This thinking comes from the point of view of database cache warmup. Indeed from the cache standpoint, you start with an empty cache and over time the cache is filled with data. Moreover the longer the database runs, the more statistics about data access patterns it has, and the better it can manage database cache contents.

Over recent years with the rise of SSDs, cache warmup has become less of an issue. High Performance NVMe Storage can do more than 1GB/sec read, meaning you can warm up a 100GB database cache in less than 2 minutes. Also, SSD IO latency tends to be quite good so you’re not paying as high a penalty for a higher miss rate during the warm up stage.

It is not all so rosy with database performance over time. Databases tend to delay work when possible, but there is only so much delaying you can do. When the database can’t delay work any longer performance tends to be negatively impacted. Here are some examples of delaying work:

  • Checkpointing: depending on the database technology and configuration, checkpointing may be delayed for 30 minutes or more after database start
  • Change Buffer (Innodb) can delay index maintenance work
  • Pushing Messages from Buffers to Leaves (TokuDB) can be delayed until space in the buffers is exhausted
  • Compaction for RocksDB and other LSM-Tree based system can take quite a while to reach steady state

In all these cases database performance can be a lot better almost immediately after start compared to when it is completely “warmed up”.

An experiment with database warm up

Let’s illustrate this with a little experiment running Sysbench with MySQL and Innodb storage engine for 15 minutes:

sysbench --db-driver=mysql --threads=200 --rand-type=uniform --report-interval=10 --percentile=99 --time=900 --mysql-user=root --mysql-password= /usr/share/sysbench/oltp_update_index.lua --table_size=100000000 run

Let’s look in detail at what happens during the run using graphs from Percona Monitoring and Management

PMM graph of first three minutes db warm up

As you can see the number of updates/sec we’re doing actually gets worse (and more uneven) after the first 3 minutes, while a jump to peak performance is almost immediate

InnoDB Checkpoint Age graph from PMM

The log space usage explains some of this—in the first few minutes, we did not need to do as aggressive flushing as we had to do later.

first few minutes MySQL Warm Up graph from PMM

On the InnoDB I/O graph we can see a couple of interesting things. First, you can see how quickly warm up happens—in 2 minutes the IO is already at half of its peak. You can also see the explanation for the little performance dip after its initial high performance (around 19:13)—this is where we got close to using all log space, so active flushing was required while, at the same time, a lot of IO was still needed for cache warmup.

Reaching Steady State is another term commonly used to describe the stage after warm up completes. Note though that such steady state is not guaranteed to be steady at all. In fact, the most typical steady state is unsteady. For example, you can see in this blog post both InnoDB and MyRocks have quite a variance.

Summary

While the term database warm up may imply performance after warm up will be better, it is often not the case. “Reaching Steady State” is a better term as long as you understand that “steady” does not mean uniform performance.

 

The post When Database Warm Up is Not Really UP appeared first on Percona Database Performance Blog.

Jul
03
2018
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Linux OS Tuning for MySQL Database Performance

Linux OS tuning for MySQL database performance

Linux OS tuning for MySQL database performanceIn this post we will review the most important Linux settings to adjust for performance tuning and optimization of a MySQL database server. We’ll note how some of the Linux parameter settings used OS tuning may vary according to different system types: physical, virtual or cloud. Other posts have addressed MySQL parameters, like Alexander’s blog MySQL 5.7 Performance Tuning Immediately After Installation. That post remains highly relevant for the latest versions of MySQL, 5.7 and 8.0. Here we will focus more on the Linux operating system parameters that can affect database performance.

Server and Operating System

Here are some Linux parameters that you should check and consider modifying if you need to improve database performance.

Kernel – vm.swappiness

The value represents the tendency of the kernel  to swap out memory pages. On a database server with ample amounts of RAM, we should keep this value as low as possible. The extra I/O can slow down or even render the service unresponsive. A value of 0 disables swapping completely while 1 causes the kernel to perform the minimum amount of swapping. In most cases the latter setting should be OK:

# Set the swappiness value as root
echo 1 > /proc/sys/vm/swappiness
# Alternatively, using sysctl
sysctl -w vm.swappiness=1
# Verify the change
cat /proc/sys/vm/swappiness
1
# Alternatively, using sysctl
sysctl vm.swappiness
vm.swappiness = 1

The change should be also persisted in /etc/sysctl.conf:

vm.swappiness = 1

Filesystems – XFS/ext4/ZFS
XFS

XFS is a high-performance, journaling file system designed for high scalability. It provides near native I/O performance even when the file system spans multiple storage devices.  XFS has features that make it suitable for very large file systems, supporting files up to 8EiB in size. Fast recovery, fast transactions, delayed allocation for reduced fragmentation and near raw I/O performance with DIRECT I/O.

The default options for mkfs.xfs are good for optimal speed, so the simple command:

# Use default mkfs options
mkfs.xfs /dev/target_volume

will provide best performance while ensuring data safety. Regarding mount options, the defaults should fit most cases. On some filesystems you can see a performance increase by adding the noatime mount option to the /etc/fstab.  For XFS filesystems the default atime behaviour is relatime, which has almost no overhead compared to noatime and still maintains sane atime values.  If you create an XFS file system on a LUN that has a battery backed, non-volatile cache, you can further increase the performance of the filesystem by disabling the write barrier with the mount option nobarrier. This helps you to avoid flushing data more often than necessary. If a BBU (backup battery unit) is not present, however, or you are unsure about it, leave barriers on, otherwise you may jeopardize data consistency. With this options on, an /etc/fstab file should look like the one below:

/dev/sda2              /datastore              xfs     defaults,nobarrier
/dev/sdb2              /binlog                 xfs     defaults,nobarrier

ext4

ext4 has been developed as the successor to ext3 with added performance improvements. It is a solid option that will fit most workloads. We should note here that it supports files up to 16TB in size, a smaller limit than xfs. This is something you should consider if extreme table space size/growth is a requirement. Regarding mount options, the same considerations apply. We recommend the defaults for a robust filesystem without risks to data consistency. However, if an enterprise storage controller with a BBU cache is present, the following mount options will provide the best performance:

/dev/sda2              /datastore              ext4     noatime,data=writeback,barrier=0,nobh,errors=remount-ro
/dev/sdb2              /binlog                 ext4     noatime,data=writeback,barrier=0,nobh,errors=remount-ro

Note: The data=writeback option results in only metadata being journaled, not actual file data. This has the risk of corrupting recently modified files in the event of a sudden power loss, a risk which is minimised with a presence of a BBU enabled controller. nobh only works with the data=writeback option enabled.

ZFS

ZFS is a filesystem and LVM combined enterprise storage solution with extended protection vs data corruption. There are certainly cases where the rich feature set of ZFS makes it an essential option to consider, most notably when advance volume management is a requirement. ZFS tuning for MySQL can be a complex topic and falls outside the scope of this blog. For further reference, there is a dedicated blog post on the subject by Yves Trudeau:

Disk Subsystem – I/O scheduler 

Most modern Linux distributions come with noop or deadline I/O schedulers by default, both providing better performance than the cfq and anticipatory ones. However it is always a good practice to check the scheduler for each device and if the value shown is different than noop or deadline the policy can change without rebooting the server:

# View the I/O scheduler setting. The value in square brackets shows the running scheduler
cat /sys/block/sdb/queue/scheduler
noop deadline [cfq]
# Change the setting
sudo echo noop > /sys/block/sdb/queue/scheduler

To make the change persistent, you must modify the GRUB configuration file:

# Change the line:
GRUB_CMDLINE_LINUX_DEFAULT="quiet splash"
# to:
GRUB_CMDLINE_LINUX_DEFAULT="quiet splash elevator=noop"

AWS Note: There are cases where the I/O scheduler has a value of none, most notably in AWS VM instance types where EBS volumes are exposed as NVMe block devices. This is because the setting has no use in modern PCIe/NVMe devices. The reason is that they have a very large internal queue and they bypass the IO scheduler altogether. The setting in this case is none and it is the optimal in such disks.

Disk Subsystem – Volume optimization

Ideally different disk volumes should be used for the OS installation, binlog, data and the redo log, if this is possible. The separation of OS and data partitions, not just logically but physically, will improve database performance. The RAID level can also have an impact: RAID-5 should be avoided as the checksum needed to ensure integrity is costly. The best performance without making compromises to redundancy is achieved by the use of an advanced controller with a battery-backed cache unit and preferably RAID-10 volumes spanned across multiple disks.

AWS Note: For further information about EBS volumes and AWS storage optimisation, Amazon has documentation at the following links:

https://docs.aws.amazon.com/AWSEC2/latest/UserGuide/nvme-ebs-volumes.html

https://docs.aws.amazon.com/AWSEC2/latest/UserGuide/storage-optimized-instances.html

Database settings

System Architecture – NUMA settings

Non-uniform memory access (NUMA) is a memory design where an SMP’s system processor can access its own local memory faster than non-local memory (the one assigned local to other CPUs). This may result in suboptimal database performance and potentially swapping. When the buffer pool memory allocation is larger than size of the RAM available local to the node, and the default memory allocation policy is selected, swapping occurs. A NUMA enabled server will report different node distances between CPU nodes. A uniformed one will report a single distance:

# NUMA system
numactl --hardware
available: 4 nodes (0-3)
node 0 cpus: 0 1 2 3 4 5 6 7
node 0 size: 65525 MB
node 0 free: 296 MB
node 1 cpus: 8 9 10 11 12 13 14 15
node 1 size: 65536 MB
node 1 free: 9538 MB
node 2 cpus: 16 17 18 19 20 21 22 23
node 2 size: 65536 MB
node 2 free: 12701 MB
node 3 cpus: 24 25 26 27 28 29 30 31
node 3 size: 65535 MB
node 3 free: 7166 MB
node distances:
node   0   1   2   3
  0:  10  20  20  20
  1:  20  10  20  20
  2:  20  20  10  20
  3:  20  20  20  10
# Uniformed system
numactl --hardware
available: 1 nodes (0)
node 0 cpus: 0 1 2 3 4 5 6 7
node 0 size: 64509 MB
node 0 free: 4870 MB
node distances:
node   0
  0:  10

In the case of a NUMA system, where numactl shows different distances across nodes, the MySQL variable innodb_numa_interleave should be enabled to ensure memory interleaving. Percona Server provides improved NUMA support by introducing the flush_caches variable. When enabled, it will help with allocation fairness across nodes. To determine whether or not allocation is equal across nodes, you can examine numa_maps for the mysqld process with this script:

# The perl script numa_maps.pl will report memory allocation per CPU node:
# 3595 is the pid of the mysqld process
perl numa_maps.pl < /proc/3595/numa_maps
N0        :     16010293 ( 61.07 GB)
N1        :     10465257 ( 39.92 GB)
N2        :     13036896 ( 49.73 GB)
N3        :     14508505 ( 55.35 GB)
active    :          438 (  0.00 GB)
anon      :     54018275 (206.06 GB)
dirty     :     54018275 (206.06 GB)
kernelpagesize_kB:         4680 (  0.02 GB)
mapmax    :          787 (  0.00 GB)
mapped    :         2731 (  0.01 GB)

Conclusion

In this blog post we examined a few important OS related settings and explained how they can be tuned for better database performance.

While you are here …

You might also find value in this recorded webinar Troubleshooting Best Practices: Monitoring the Production Database Without Killing Performance

 

The post Linux OS Tuning for MySQL Database Performance appeared first on Percona Database Performance Blog.

Jul
24
2010
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Caching could be the last thing you want to do

I recently had a run-in with a very popular PHP ecommerce package which makes me want to voice a recurring mistake I see in how many web applications are architected.

What is that mistake?

The ecommerce package I was working with depended on caching.  Out of the box it couldn’t serve 10 pages/second unless I enabled some features which were designed to be “optional” (but clearly they weren’t).

I think with great tools like memcached it is easy to get carried away and use it as the mallet for every performance problem, but in many cases it should not be your first choice.  Here is why:

  • Caching might not work for all visitors – You look at a page, it loads fast.  But is this the same for every user?  Caching can sometimes be an optimization that makes the average user have a faster experience, but in reality you should be caring more that all users get a good experience (Peter explains why here, talking about six sigma).  In practice it can often be the same user that has all the cache misses, which can make this problem even worse.
  • Caching can reduce visibility – You look at the performance profile of what takes the most time for a page to load and start trying to apply optimization.  The problem is that the profile you are looking at may skew what you should really be optimizing.  The real need (thinking six sigma again) is to know what the miss path costs, but it is somewhat hidden.
  • Cache management is really hard – have you planned for cache stampeding, or many cache items being invalidated at the same time?

What alternative approach should be taken?

Caching should be seen more as a burden that many applications just can’t live without.  You don’t want that burden until you have exhausted all other easily reachable optimizations.

What other optimizations are possible?

Before implementing caching, here is a non-exhaustive checklist to run through:

  • Do you understand every execution plan of every query? If you don’t, set long_query_time=0 and use mk-query-digest to capture queries.  Run them through MySQL’s EXPLAIN command.
  • Do your queries SELECT *, only to use subset of columns?  Or do you extract many rows, only to use a subset? If so, you are extracting too much data, and (potentially) limiting further optimizations like covering indexes.
  • Do you have information about how many queries were required to generate each page? Or more specifically do you know that each one of those queries is required, and that none of those queries could potentially be eliminated or merged?

I believe this post can be summed up as “Optimization rarely decreases complexity. Avoid adding complexity by only optimizing what is necessary to meet your goals.”  – a quote from Justin’s slides on instrumentation-for-php.  In terms of future-proofing design, many applications are better off keeping it simple and (at least initially) refusing the temptation to try and solve some problems “like the big guys do”.


Entry posted by Morgan Tocker |
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