How to measure database scaling & density on Nutanix HCI platform.

How can database density be measured?

  • How does database performance behave as more DBs are consolidated?
  • What impact does running the CVM have on available host resources?

tl;dr

  • The cluster was able to achieve ~90% of the theoretical maximum.
  • CVM overhead was 5% for this workload.

Experiment setup

The goal was to establish how database performance is affected as additional database workloads are added into the cluster. As a secondary metric, measure the overhead from running the virtual storage controller on the same host as the database servers themselves. We use the Postgres database with pgbench workload and measure the total transactions per second.

Cluster configuration

  • 4 Node Nutanix cluster, with 2x Xeon CPU’s per host with 20 cores per socket.

Database configuration

Each database is identically configured with

  • Postgres 9.3
  • Ubuntu Linux
  • 4 vCPU
  • 8GB of memory
  • pgbench benchmark, running the “simple” query set.

The database is sized so that it fits entirely in memory. This is a test of CPU/Memory not IO.

Experiment steps.

The experiment starts with a single Database on a single host. We add more databases into the cluster until we reach 40 databases in total. At 40 databases with 4 vCPU each and a CPU bound workload we use all 160 CPU cores on the cluster.

The database is configured to fit into the host DRAM memory, and the benchmark runs as fast as it can – the benchmark is CPU bound.

Results

Below are the measured results from running 1-40 databases on the 4 node cluster.

Performance scales almost linearly from 4 to 160 CPU with no obvious bottlenecks before all of the CPU cores are saturated in the host at 40 databases.

Scaling from 1 Databases to 40 on a 4 node cluster.
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How to run vertica vioperf tool

The vertica vioperf tool is used to determine whether the storage you are planning on using is fast enough to feed the vertica database. When I initially ran the tool, the IO performance reported by the tool and confirmed by iostat was much lower than I expected for the storage device (a 6Gbit SATA device capable of around 500MB/s read and write).

The vioperf tool runs on a linux host or VM and can be pointed at any filesystem just like fio or vdbench

Simple execution of vioperf writing to the location /vertica

vioperf --thread-count=8 --duration=120s  /vertica

Working Set Size

Unlike traditional IO generators vioperf does not allow you to specify the working-set size. The amount of data written is simply 1MB* Achieved IO rate * runtime. So, fast storage with long run-times will need a lot of capacity otherwise the tool simply fills the partition and crashes!

Measurement and goodness

The primary metric is MB/s Per-Core. The idea is that you give 1 Thread per core in the system, though there is nothing stopping you from using whatever –thread-count value you like.

Although the measure is throughput, the primary metric of (Throughput/Core) does not improve just by giving lots of concurrency. Concurrency is generated purely by the number of threads and since the measure of goodness is Throughput/Core (or per thread) it’s not possible to simply create throughput from concurrency alone.

Throughput compared to FIo

Compared to fio the reported throughput is lower for the same device and same degree of concurrency. Vertica continually writes, and extends the files so there is some filesystem work going on whereas fio is typically overwriting an existing file. If you observe iostat during the vioperf run you will see that the IO size to disk is different than what an fio run will generate. Again this is due to the fact that vioperf is continually extending the file(s) being written and so it needs to update filesystem metadata quite frequently. These small metadata updates skew the average IO size lower.

fio with 1MB IO and 1 thread

Notice the avgrq size is 1024 blocks (512KB) which is the maximum transfer size that this drive supports.

 fio --filename=/samsung/vertica/file --size=5g --bs=1m --ioengine=libaio --iodepth=1 --rw=write --direct=1 --name=samsung --create_on_open=0


avg-cpu:  %user   %nice %system %iowait  %steal   %idle
           4.16    0.00    3.40    0.00    0.00   92.43

Device:         rrqm/s   wrqm/s     r/s     w/s    rkB/s    wkB/s avgrq-sz avgqu-sz   await r_await w_await  svctm  %util
sdb               0.00     0.00    0.00  920.00     0.00 471040.00  1024.00     1.40    1.53    0.00    1.53   1.02  93.80

Vertica IOstat 1 thread

Firstly we see that iostat reports much lower disk throughput than what we achieved with fio for the same offered workload (1MB IO size with 1 outstanding IO (1 thread).

Also notice that that although vioperf issues 1MB IO sizes (which we can see from strace) iostat does not report the same 1024 block transfers as we see when we run iostat during an fio run (as above).

In the vioperf case the small metadata writes that are needed to continually extend the file cause a average IO size than than overwriting an existing file. Perhaps that is the cause of the lower performance?

./vioperf --duration=300s --thread-count=1 /samsung/vertica

avg-cpu:  %user   %nice %system %iowait  %steal   %idle
           8.77    0.13    2.38    5.26    0.00   83.46

Device:         rrqm/s   wrqm/s     r/s     w/s    rkB/s    wkB/s avgrq-sz avgqu-sz   await r_await w_await  svctm  %util
sdb               0.00     0.00    0.00  627.00     0.00 223232.00   712.06     1.02    1.63    0.00    1.63   0.69  43.20
strace -f ./vioperf --duration=300s --thread-count=1 --disable-crc /samsung/vertica
...
[pid  1350] write(6, "v\230\242Q\357\250|\212\256+}\224\270\256\273\\\366k\210\320\\\330z[\26[\6&\351W%D"..., 1048576) = 1048576
[pid  1350] write(6, "B\2\224\36\250\"\346\241\0\241\361\220\242,\207\231.\244\330\3453\206'\320$Y7\327|5\204b"..., 1048576) = 1048576
[pid  1350] write(6, "\346r\341{u\37N\254.\325M'\255?\302Q?T_X\230Q\301\311\5\236\242\33\1)4'"..., 1048576) = 1048576
[pid  1350] write(6, "\5\314\335\264\364L\254x\27\346\3251\236\312\2075d\16\300\245>\256mU\343\346\373\17'\232\250n"..., 1048576) = 1048576
[pid  1350] write(6, "\272NKs\360\243\332@/\333\276\2648\255\v\243\332\235\275&\261\37\371\302<\275\266\331\357\203|\6"..., 1048576) = 1048576
[pid  1350] write(6, "v\230\242Q\357\250|\212\256+}\224\270\256\273\\\366k\210\320\\\330z[\26[\6&\351W%D"..., 1048576) = 1048576
...

However, look closely and you will notice that the %user is higher than fio for a lower IO rate AND the disk is not 100% busy. That seems odd.

./vioperf --duration=300s --thread-count=1 /samsung/vertica

avg-cpu:  %user   %nice %system %iowait  %steal   %idle
           8.77    0.13    2.38    5.26    0.00   83.46

Device:         rrqm/s   wrqm/s     r/s     w/s    rkB/s    wkB/s avgrq-sz avgqu-sz   await r_await w_await  svctm  %util
sdb               0.00     0.00    0.00  627.00     0.00 223232.00   712.06     1.02    1.63    0.00    1.63   0.69  43.20

vioperf with –disable-crc

Finally we disable the crc checking (which vioperf does by default) to get a higher throughput more similar to what we see with fio.

It turns out that the lower performance was not due to the smaller IO sizes (and additonal filesystem work) but was caused the CRC checking that the tool does to simulate the vertica application.

 ./vioperf --duration=300s --thread-count=1 --disable-crc /samsung/vertica

avg-cpu:  %user   %nice %system %iowait  %steal   %idle
           8.77    0.13    2.38    5.26    0.00   83.46

Device:         rrqm/s   wrqm/s     r/s     w/s    rkB/s    wkB/s avgrq-sz avgqu-sz   await r_await w_await  svctm  %util
sdb               0.00     0.00    0.00  627.00     0.00 223232.00   712.06     1.02    1.63    0.00    1.63   0.69  43.20

View from Nutanix storage during Postgres DB benchmark

Following on from the previous [1] [2] experiments with Postgres & pgbench. A quick look at how the workload is seen from the Nutanix CVM.

The Linux VM running postgres has two virtual disks:

  • One is taking transaction log writes.
  • The other is doing reads and writes from the main datafiles.

Since the database size is small (50% the size of the Linux RAM) – the data is mostly cached inside the guest, and so most reads do not hit storage. As a result we only see writes going to the DB files.

Additionally, we see that database datafile writes the arrive in a bursty fashion, and that these write bursts are more intense (~10x) than the log file writes.

Charts from Prometheus/Grafana showing IO rates seen from the perspective of the Linux guest VM

Despite the database flushes ocurring in bursts with a decent amount of concurrency the Nutanix CVM provides an average of 1.5ms write response time.

From the Nutanix CVM port 2009 handler, we can access the individual vdisk statistics. In this particular case vDisk 45269 is the data file disk, and 40043 is the database transaction log disk.

Datafile writes completed in 1.5millisecond average – despite deep queues during burst

The vdisk categorizer correctly identifies the database datafile write pattern as highly random.

Writes to the datbase datafiles are almost entirely random

As a result, the writes are passed into the replicated oplog

The burst of writes hits the oplog as expected

Meanwhile the log writes are categorized as mostly sequential, which is expected for a database log file workload.

Meanwhile, log file writes are mostly categorized as sequential.

Even though the log writes are sequential, they are low-concurrency and small size (looks like mostly 16K-32K). This write pattern is also a good candidate for oplog.

These low-concurrency log writes also hit oplog

Benchmarking with Postgres PT2

In this example we run pgbench with a scale factor of 1000 which equates to a database size of around 15GB. The linux VM has 32G RAM, so we don’t expect to see many reads.

Using prometheus with the Linux node exporter we can see the disk IO pattern from pgbench. As expected the write pattern to the log disk (sda) is quite constant, while the write pattern to the database files (sdb) is bursty.

pgbench with DB size 50% of Linux buffer cache.

I had to tune the parameter checkpoint_completion_target from 0.5 to 0.9 otherwise the SCSI stack became overwhelmed during checkpoints, and caused log-writes to stall.

default pgbench – notice the sharp drop in log-writes before tuning.


Benchmarking with Postgres PT1

Image By Daniel Lundin

In this example, we use Postgres and the pgbench workload generator to drive some load in a virtual machine.  Assume a Linux virtual machine that has Postgres installed. Specifically using a Bitnami virtual appliance.

  • Once the VM has been started, connect to the console
  • Allow access to postgres port 5432 – which is the postgres DB port or allow ssh
$ sudo ufw allow 5432
  • Note the postgres user password (cat ./bitnami_credentials)
  •  Login to psql from the console or ssh
psql -U postgres
  • Optionally change password (the password prompted is the one from bitnami_credentials for the postgres database user).
psql -U postgres
postgres=# alter user postgres with password 'NEW_PASSWORD';
postgresl=# \q
  • Create a DB to run the pgbench workload.  In this case I name the db pgbench-sf10 for “Scale Factor 10”.  Scale Factors are how the size of the database is determined.
$ sudo -u postgres createdb pgbench-sf10
  • Initialise the DB with data ready to run the benchmark.  The “createdb” step just creates an empty schema.
    • -i means “initialize”
    • -s means “scale factor” e.g. 10
    • pgbench-sf10 is the database schema to use.  We use the one just created pgbench-sf10
$ sudo -u postgres pgbench -i -s 10 pgbench-sf10
  • Noe run a workload against the DB schema called pgbench-sf10
$ sudo -u postgres pgbench pgbench-sf10

The workload pattern, and load on the system will vary greatly depending on the scale factor.  

Scale-Factor        Working Set Size


1                                   23M
10                                157M
100                             1.7GB
1000                          15GB
2500                          37GB
5000                         74GB
10000                       147GB

 

 

Install a bitnami image to Nutanix AHV cluster.

One of the nice things about using public cloud is the ability to use pre-canned application virtual appliances created by companies like Bitnami.

We can use these same appliance images on Nutanix AHV to easily do a Postgres database benchmark

Step 1. Get the bitnami image

wget  https://bitnami.com/redirect/to/587231/bitnami-postgresql-11.3-0-r56-linux-debian-9-x86_64.zip

Step 2. Unzip the file and convert the bitnami vmdk images to a single qcow2[1] file.

qemu-img convert *vmdk bitnami.qcow2

Put the bitnami.qcow2 image somewhere accessible to a browser, connected to the Prism service, then upload using the “Image Configuration”

Once the image is uploaded, it’s time to create a new VM based on that image

Once booted, you’ll see the bitnami logo and you can configure the bitnami passwords, enable ssh etc. using the console.

Enable/disable ssh in bitnami images
Connecting to Postgres in bitnami images
Note – when you “sudo -c postgres <some-psql-tool> the password it is asking for is the Postgres DB password (stored in ./bitnami-credentials) not any unix user password.

Once connected to the appliance we can use postgres and pgbench to generate simplistic database workload.

[1] Do this on a Linux box somewhere. For some reason the conversion failed using my qemu utilities installed via brew. Importing OVAs direct into AHV should be available in the future.

HCI Performance testing made easy (Part 3)

Creating a HCI benchmark to simulate multi-tennent workloads

 

 

HCI deployments are typically multi-tennant and often different nodes will support different types of workloads. It is very common to have large resource-hungry databases separated across nodes using anti-affinity rules.  As with traditional storage, applications are writing to a shared storage environment which is necessary to support VM movement.  It is the shared storage that often causes performance issues for data bases which are otherwise separated across nodes.  We call this the noisy neighbor problem.  A particular problem occurs when a reporting / analytical workload shares storage with a transactional workload.

In such a case we have a Bandwidth heavy workload profile (reporting) sharing with a Latency Sensitive workload (transactional)

In the past it has been difficult to measure the noisy neighbor impact without going to the trouble of configuring the entire DB stack, and finding some way to drive it.  However in X-Ray we can do exactly this sort of workload.  We supply a pre-configured scenario which we call the  DB Colocation test.

The DB Colocation test utilizes two properties of X-Ray not found in other benchmarking tools

  • Time based benchmark actions
  • Distinct per-VM workload patterns
  • Ability to provision particular workloads, to particular hosts

In our example scenario X-Ray begins by starting a workload modeled after a transactional DB (we call this the OLTP workload) on one of the nodes.  This workload runs for 60 minutes.  Then after 30 minutes X-Ray starts workloads modeled after reporting/analytical workloads on two other nodes (we call this the DSS workload).

After 30 minutes we have three independent workloads running on three independent nodes, but sharing the same storage.  The key thing to observe is the impact on the latency sensitive (OLTP) workload.  In this experiment it is the DSS workloads which are the noisy neighbor, since they will tend to utilize a lot of the storage bandwidth.  An ideal result is one where there is very little interference with the running OLTP workload, even though we expect latency to increase.  We can compare the impact on the OLTP workload by comparing the IOPS/response time during the first 30 minutes (no interference) with the remaining 60 minutes (after the DSS workloads are started).  We should expect to see some increase in response time from the OLTP application because the other nodes in the cluster have gone from idle to under-load.  The key thing to observe is whether the OLTP IOP target rate (4,000 IOPS) is achieved when the reporting workload is applied.

 

X-Ray Scenario configuration

We specify the timing rules and workloads in the test.yml file.  You can modify this to contain whichever values suit your model.  I covered editing an existing workload in Part 1.

The overall scenario begins with the OLTP workload, which will run for 3600 seconds (1 hour).  The stagger_secs value is used if there are multiple OLTP sub-workloads.  In the simple case we do use a single OLTP workload.

The scenario pauses for 1800 seconds using the test.wait specification then immediately starts the DSS workload

Finally the scenario uses the workload.Wait specification to wait for the OLTP workload to finish (approx 1 hour) before the test is deemed completed.

X-Ray Workload specification

The DB Co-Location test uses two workload profiles that aim to simulate transactional (OLTP) and reporting/analytical (DSS) workloads.  The specifications for those workloads are contained in the two .fio files (oltp.fio and dss.fio)

OLTP


The OLTP workload (oltp.fio) that we ship as  has the following characteristcs based on typical configurations that we see in the field (of course you can change these to whatever you like).

  • Target IOP rate of 4,000 IOPS
  • 4 “Data” Disks
    • 50/50 read/write ratio.
    • 90% 8KB, 10% 32KB bloc-ksize
    • 8 outstanding IO per disk
  • 2 “Log” Disks
    • 100% write
    • 90% sequential
    • 32k block-size
    • 1 outstanding IO per disk

The idea here is to simulate the two main storage workloads of a DB.  The “data” portion and the “log” portion.  Log writes are just used to commit transactions and so are 100% write.  The only time the logs are read is during DB recovery, which is not part of this scenario.  The “Data” disks are doing both reads (from DB cache misses) and writes committed transactions.  A 50/50 read/write mix might be considered too write intensive – but we wanted to stress the storage in this scenario.

DSS


The DSS workload is configured to have the following characteristics

  • Target IOP rate of 1400 IOPS
  • 4 “Data” Disks
    • 100% Read workload with 1MB blocksize
    • 10 Outstanding IOs
  • 2 “Log” Disk
    • 100% Write workload
    • 90% sequential
    •  32K block-size
    • 1 outstanding IO per disk

The idea here is to simulate a large database doing a lot of reads across a large workingset size.  The IO to the data disks is entirely read, and uses large blocks to simulate a database scanning a lot of records.  The “Log” disks have a very light workload, purely to simulate an active database which is probably updating a few tables used for housekeeping.