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Database engine

The Database Engine works like a traditional time series database. Unlike other database modes, the amount of historical metrics stored is based on the amount of disk space you allocate and the effective compression ratio, not a fixed number of metrics collected.

Tiering

Tiering is a mechanism of providing multiple tiers of data with different granularity on metrics.

For Netdata Agents with version netdata-1.35.0.138.nightly and greater, dbengine supports Tiering, allowing almost unlimited retention of data.

Metric size

Every Tier down samples the exact lower tier (lower tiers have greater resolution). You can have up to 5 Tiers [0. . 4] of data (including the Tier 0, which has the highest resolution)

Tier 0 is the default that was always available in dbengine mode. Tier 1 is the first level of aggregation, Tier 2 is the second, and so on.

Metrics on all tiers except of the Tier 0 also store the following five additional values for every point for accurate representation:

  1. The sum of the points aggregated
  2. The min of the points aggregated
  3. The max of the points aggregated
  4. The count of the points aggregated (could be constant, but it may not be due to gaps in data collection)
  5. The anomaly_count of the points aggregated (how many of the aggregated points found anomalous)

Among min, max and sum, the correct value is chosen based on the user query. average is calculated on the fly at query time.

Tiering in a nutshell

The dbengine is capable of retaining metrics for years. To further understand the dbengine tiering mechanism let's explore the following configuration.

[db]
mode = dbengine

# per second data collection
update every = 1

# enables Tier 1 and Tier 2, Tier 0 is always enabled in dbengine mode
storage tiers = 3

# Tier 0, per second data for a week
dbengine multihost disk space MB = 1100

# Tier 1, per minute data for a month
dbengine tier 1 multihost disk space MB = 330

# Tier 2, per hour data for a year
dbengine tier 2 multihost disk space MB = 67

For 2000 metrics, collected every second and retained for a week, Tier 0 needs: 1 byte x 2000 metrics x 3600 secs per hour x 24 hours per day x 7 days per week = 1100MB.

By setting dbengine multihost disk space MB to 1100, this node will start maintaining about a week of data. But pay attention to the number of metrics. If you have more than 2000 metrics on a node, or you need more that a week of high resolution metrics, you may need to adjust this setting accordingly.

Tier 1 is by default sampling the data every 60 points of Tier 0. In our case, Tier 0 is per second, if we want to transform this information in terms of time then the Tier 1 "resolution" is per minute.

Tier 1 needs four times more storage per point compared to Tier 0. So, for 2000 metrics, with per minute resolution, retained for a month, Tier 1 needs: 4 bytes x 2000 metrics x 60 minutes per hour x 24 hours per day x 30 days per month = 330MB.

Tier 2 is by default sampling data every 3600 points of Tier 0 (60 of Tier 1, which is the previous exact Tier). Again in term of "time" (Tier 0 is per second), then Tier 2 is per hour.

The storage requirements are the same to Tier 1.

For 2000 metrics, with per hour resolution, retained for a year, Tier 2 needs: 4 bytes x 2000 metrics x 24 hours per day x 365 days per year = 67MB.

Legacy configuration

v1.35.1 and prior

These versions of the Agent do not support Tiering. You could change the metric retention for the parent and all of its children only with the dbengine multihost disk space MB setting. This setting accounts the space allocation for the parent node and all of its children.

To configure the database engine, look for the page cache size MB and dbengine multihost disk space MB settings in the [db] section of your netdata.conf.

[db]
dbengine page cache size MB = 32
dbengine multihost disk space MB = 256

v1.23.2 and prior

For Netdata Agents earlier than v1.23.2, the Agent on the parent node uses one dbengine instance for itself, and another instance for every child node it receives metrics from. If you had four streaming nodes, you would have five instances in total (1 parent + 4 child nodes = 5 instances).

The Agent allocates resources for each instance separately using the dbengine disk space MB (deprecated) setting. If dbengine disk space MB(deprecated) is set to the default 256, each instance is given 256 MiB in disk space, which means the total disk space required to store all instances is, roughly, 256 MiB * 1 parent * 4 child nodes = 1280 MiB.

Backward compatibility

All existing metrics belonging to child nodes are automatically converted to legacy dbengine instances and the localhost metrics are transferred to the multihost dbengine instance.

All new child nodes are automatically transferred to the multihost dbengine instance and share its page cache and disk space. If you want to migrate a child node from its legacy dbengine instance to the multihost dbengine instance, you must delete the instance's directory, which is located in /var/cache/netdata/MACHINE_GUID/dbengine, after stopping the Agent.

Information

For more information about setting [db].mode on your nodes, in addition to other streaming configurations, see streaming.

Requirements & limitations

Memory

Using database mode dbengine we can overcome most memory restrictions and store a dataset that is much larger than the available memory.

There are explicit memory requirements per DB engine instance:

  • The total page cache memory footprint will be an additional #dimensions-being-collected x 4096 x 2 bytes over what the user configured with dbengine page cache size MB.
  • an additional #pages-on-disk x 4096 x 0.03 bytes of RAM are allocated for metadata.

    • roughly speaking this is 3% of the uncompressed disk space taken by the DB files.

    • for very highly compressible data (compression ratio > 90%) this RAM overhead is comparable to the disk space footprint.

An important observation is that RAM usage depends on both the page cache size and the dbengine multihost disk space options.

You can use our database engine calculator to validate the memory requirements for your particular system(s) and configuration (out-of-date).

Disk space

There are explicit disk space requirements per DB engine instance:

  • The total disk space footprint will be the maximum between #dimensions-being-collected x 4096 x 2 bytes or what the user configured with dbengine multihost disk space or dbengine disk space.

File descriptor

The Database Engine may keep a significant amount of files open per instance (e.g. per streaming child or parent server). When configuring your system you should make sure there are at least 50 file descriptors available per dbengine instance.

Netdata allocates 25% of the available file descriptors to its Database Engine instances. This means that only 25% of the file descriptors that are available to the Netdata service are accessible by dbengine instances. You should take that into account when configuring your service or system-wide file descriptor limits. You can roughly estimate that the Netdata service needs 2048 file descriptors for every 10 streaming child hosts when streaming is configured to use [db].mode = dbengine.

If for example one wants to allocate 65536 file descriptors to the Netdata service on a systemd system one needs to override the Netdata service by running sudo systemctl edit netdata and creating a file with contents:

[Service]
LimitNOFILE=65536

For other types of services one can add the line:

ulimit -n 65536

at the beginning of the service file. Alternatively you can change the system-wide limits of the kernel by changing /etc/sysctl.conf. For linux that would be:

fs.file-max = 65536

In FreeBSD and OS X you change the lines like this:

kern.maxfilesperproc=65536
kern.maxfiles=65536

You can apply the settings by running sysctl -p or by rebooting.

Files

With the DB engine mode the metric data are stored in database files. These files are organized in pairs, the datafiles and their corresponding journalfiles, e.g.:

datafile-1-0000000001.ndf
journalfile-1-0000000001.njf
datafile-1-0000000002.ndf
journalfile-1-0000000002.njf
datafile-1-0000000003.ndf
journalfile-1-0000000003.njf
...

They are located under their host's cache directory in the directory ./dbengine (e.g. for localhost the default location is /var/cache/netdata/dbengine/*). The higher numbered filenames contain more recent metric data. The user can safely delete some pairs of files when Netdata is stopped to manually free up some space.

Users should back up their ./dbengine folders if they consider this data to be important. You can also set up one or more exporting connectors to send your Netdata metrics to other databases for long-term storage at lower granularity.

Operation

The DB engine stores chart metric values in 4096-byte pages in memory. Each chart dimension gets its own page to store consecutive values generated from the data collectors. Those pages comprise the Page Cache.

When those pages fill up, they are slowly compressed and flushed to disk. It can take 4096 / 4 = 1024 seconds = 17 minutes, for a chart dimension that is being collected every 1 second, to fill a page. Pages can be cut short when we stop Netdata or the DB engine instance so as to not lose the data. When we query the DB engine for data we trigger disk read I/O requests that fill the Page Cache with the requested pages and potentially evict cold (not recently used) pages.

When the disk quota is exceeded the oldest values are removed from the DB engine at real time, by automatically deleting the oldest datafile and journalfile pair. Any corresponding pages residing in the Page Cache will also be invalidated and removed. The DB engine logic will try to maintain between 10 and 20 file pairs at any point in time.

The Database Engine uses direct I/O to avoid polluting the OS filesystem caches and does not generate excessive I/O traffic so as to create the minimum possible interference with other applications.

Evaluation

We have evaluated the performance of the dbengine API that the netdata daemon uses internally. This is not the web API of netdata. Our benchmarks ran on a single dbengine instance, multiple of which can be running in a Netdata parent node. We used a server with an AMD Ryzen Threadripper 2950X 16-Core Processor and 2 disk drives, a Seagate Constellation ES.3 2TB magnetic HDD and a SAMSUNG MZQLB960HAJR-00007 960GB NAND Flash SSD.

For our workload, we defined 32 charts with 128 metrics each, giving us a total of 4096 metrics. We defined 1 worker thread per chart (32 threads) that generates new data points with a data generation interval of 1 second. The time axis of the time-series is emulated and accelerated so that the worker threads can generate as many data points as possible without delays.

We also defined 32 worker threads that perform queries on random metrics with semi-random time ranges. The starting time of the query is randomly selected between the beginning of the time-series and the time of the latest data point. The ending time is randomly selected between 1 second and 1 hour after the starting time. The pseudo-random numbers are generated with a uniform distribution.

The data are written to the database at the same time as they are read from it. This is a concurrent read/write mixed workload with a duration of 60 seconds. The faster dbengine runs, the bigger the dataset size becomes since more data points will be generated. We set a page cache size of 64MiB for the two disk-bound scenarios. This way, the dataset size of the metric data is much bigger than the RAM that is being used for caching so as to trigger I/O requests most of the time. In our final scenario, we set the page cache size to 16 GiB. That way, the dataset fits in the page cache so as to avoid all disk bottlenecks.

The reported numbers are the following:

devicepage cachedatasetreads/secwrites/sec
HDD64 MiB4.1 GiB813K18.0M
SSD64 MiB9.8 GiB1.7M43.0M
N/A16 GiB6.8 GiB118.2M30.2M

where "reads/sec" is the number of metric data points being read from the database via its API per second and "writes/sec" is the number of metric data points being written to the database per second.

Notice that the HDD numbers are pretty high and not much slower than the SSD numbers. This is thanks to the database engine design being optimized for rotating media. In the database engine disk I/O requests are:

  • asynchronous to mask the high I/O latency of HDDs.
  • mostly large to reduce the amount of HDD seeking time.
  • mostly sequential to reduce the amount of HDD seeking time.
  • compressed to reduce the amount of required throughput.

As a result, the HDD is not thousands of times slower than the SSD, which is typical for other workloads.

An interesting observation to make is that the CPU-bound run (16 GiB page cache) generates fewer data than the SSD run (6.8 GiB vs 9.8 GiB). The reason is that the 32 reader threads in the SSD scenario are more frequently blocked by I/O, and generate a read load of 1.7M/sec, whereas in the CPU-bound scenario the read load is 70 times higher at 118M/sec. Consequently, there is a significant degree of interference by the reader threads, that slow down the writer threads. This is also possible because the interference effects are greater than the SSD impact on data generation throughput.

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