How we reduced memory usage by 90%

Written by

Miroslav Bajtoš

Date published

January 11, 2024

TL;DR

Four easy changes reduced the total memory usage of Spark’s Node.js backend from 4+ GB to ~360 MB:

Convert plain data objects to class instances.
De-duplicate immutable string values.
Carefully choose how you calculate percentiles.
Represent timestamps as numbers.

Introduction

After I finished optimizing our database usage, another problem came to our attention: the spark-evaluate service was consuming too much memory. This service periodically processes a large batch of records (measurements).

Here comes the issue: as the Station node network grows, so does the number of measurements submitted each round. In early December 2023, we were evaluating more than 1.5 million measurements every round. Each measurement had around 600 bytes; we had to process 900MB of raw data at once.

We implemented spark-evaluate to keep all data in memory because itwas the fastest way to ship a working version. As we watched the network grow, every now and then, we would receive an email from Fly.io that spark-evaluate crashed on an “out of memory” error. In the current stage, cloud resources are cheaper than engineering efforts, so we fixed these incidents by doubling the memory size of the virtual machine running the service. When we reached the point of 8 GB of RAM not being enough, we decided the situation was no longer sustainable, and the time came to do some engineering work.

Fortunately, we found a small number of easy changes that significantly reduced our memory usage without any major changes in the implementation, such as offloading the data from memory to the filesystem.

Plain data objects

Spoiler: this change reduced our memory usage by 50%! 😳

My colleague Julian Gruber discovered the first low-hanging fruit: apparently, plain data objects take more memory than class instances. Adding a step to map objects parsed from JSON to instances of a newly introduced Measurement class reduced our memory usage by 50%.

The original version parsed measurements from JSON and then stored these objects for future evaluations.

const measurements = /* fetch and parse JSON */
const validMeasurements = measurements.map(measurement => {
  try {
    return {
      ...measurement,      
      // additional fields parsed from data      
    }
  } catch (err) {
    logger.error('Invalid measurement:', err.message, measurement)
    return null  
  }
})

The new version converts each plain data object into a class instance. The class constructor performs preprocessing, e.g., parsing additional fields.

const measurements = /* fetch and parse JSON */
const validMeasurements = measurements.map(measurement => {
  try {
    return new Measurement(measurement)
  } catch (err) {
    logger.error('Invalid measurement:', err.message, measurement)
    return null  
  }
})

Take a look at the pull request filecoin-station/spark-evaluate#84 if you are interested in more details.

Duplicate string values

Spoiler: this change reduced heap usage from 570 MB to 167 MB.

This first improvement sparked my interest. What other easy optimizations can we make?

Let’s take a look at an example measurement:

{  
  "id": 280847321,  
  "spark_version": "1.6.0",  
  "zinnia_version": "0.15.0",  
  "participant_address": "0x000000000000000000000000000000000000dEaD",
  "finished_at": "2023-12-11T08:31:00.157Z",
  "timeout": false,
  "start_at": "2023-12-11T08:30:29.947Z",
  "status_code": 502,
  "first_byte_at": null,
  "end_at": "2023-12-11T08:30:59.954Z",
  "byte_length": 0,
  "attestation": null,
  "inet_group": "uWJAEcUyzouo",
  "car_too_large": false,
  "cid": "QmU4P3dfgDHUJ8GUREND2p3hH6T7hsQiPL9NrHs5T86NAp",
  "provider_address": "/ip4/127.0.0.1/tcp/8080/http",
  "protocol": "http"
}

Setting aside timestamps, most of the string properties can contain only a small number of possible values; each value is repeated many times in different measurements. For example, we pick 4000 different CIDs to test every round. With 100k measurements submitted per round, there are, on average, 10,000 measurements for the same CID.

Here comes the question: how does V8 (the JavaScript runtime in Node.js) represent strings? If two object properties hold the same string value, how many copies of the string’s bytes are stored in the memory? The answer seems to be two copies.

Measurements and CID strings with duplicated bytes

Aside: I guess this makes sense - most applications don’t have that many duplicate string values. The cost of maintaining a lookup table would outweigh the benefits of memory savings.

Using the knowledge about the specific usage patterns of our application, we can trade additional CPU load for less memory usage and implement a lookup table ourselves. The idea is simple: whenever we encounter a new string coming from the parsed JSON data, check if we have seen it before. If yes, replace the new string value with a pointer to the same string we have seen before.

Measurements and CID strings reusing the same bytes

This solution has one fantastic property: we don’t need to change any code reading the measurement objects; only the ingestion part needs changing. But, there is also an essential requirement: we must never mutate these string values.

Here is a code snippet illustrating the algorithm:

const knownStrings = new Map();
function pointerize(str) {
  if (str === undefined || str === null) return str;
  const found = knownStrings.get(str);
  if (found !== undefined) return found;
  knownStrings.set(str, str);
  return str;
}

// usage in Measurement constructor
this.cid = pointerize(m.cid);
this.provider_address = pointerize(m.provider_address);
this.protocol = pointerize(m.protocol);
// etc.

This change reduced our memory usage from 70% - the heapTotal metric went down from 570 MB to 167 MB. You can find more details in the pull request filecoin-station/spark-evaluate#86.

External memory and `hdr-histogram-js`

Spoiler: this change reduced our total memory usage (rss) from 3,526 MB to 375 MB.

I stumbled across this opportunity by a lucky coincidence. After evaluating all measurements, we calculate various statistics about the round and submit them to InfluxDB for visualization. For some data, we are interested in values at different percentiles. For example, what’s the time-to-first-byte (TTFB) at the 5th, 50th, and 95th percentile? (What’s TTFB for the fast, typical, and slow retrieval?)

When I was implementing these calculations, I didn’t want to implement percentiles myself and looked for an existing npm module to use. The module hdr-histogram-js offers the features I needed; it has more than two million weekly downloads and is also used by Matteo Collina in his tools like autocannon. I highly respect Matteo for his knowledge of Node.js & V8 performance tuning. If hdr-histogram-js is good for him, then it surely should be good for us, too. Right?

Well, our data set is different from what autocannon produces. I think the major difference is that we have a much wider range of possible values. For example, “CAR size in bytes” can be anywhere between zero to hundreds of million.

Anyway, this is what I saw in our logs:

For many rounds, the histogram module threw an error while adding more data points.
Often, the values at percentiles were inaccurate. For example, “CAR size in bytes” at p5 and p10 was zero.

Instead of debugging the library, I decided to calculate the histogram ourselves. If we can fit all measurements in memory, we can surely keep in memory an array of all values for an individual measurement field like “CAR size in bytes” or “TTFB,” too.

Calculating values at a given percentile is easy when we have all data points in memory:

Sort the array by values.

Remember to provide a custom comparator function because JavaScript sorts lexicographically by default: the word 10 comes before the word 2!

Calculate the value at the percentile p as the array item at position Math.ceil(p * count / 100).

This formula produces the so-called discrete percentile. As I quickly discovered during testing, discrete percentiles are not very useful if you have a small number of data points. For example, if you record values [1, 50, 100], the discrete percentile 5% (p5) is the same as the median value (p50): 50.

Fortunately, there are also continuous percentiles that use interpolation to get finer-grained values. In my previous example, p5 is calculated as 5.9.

Here is the final implementation we use:

export const getValueAtPercentile = (values, p) => {
  // See https://www.calculatorsoup.com/calculators/statistics/percentile-calculator.php
  // 1. Arrange n number of data points in ascending order: x1, x2, x3, ... xn
  const n = values.length;
  // 2. Calculate the rank r for the percentile p you want to find: r = (p/100) * (n - 1) + 1
  const r = ((n - 1) * p) / 100 + 1;
  // 3. If r is an integer then the data value at location r, xr, is the percentile p: p = xr
  if (Number.isInteger(r)) {
    // Remember that we are indexing from 0, i.e. x1 is stored in values[0]
    return values[r - 1];
  }
  const ri = Math.floor(r);
  const rf = r - ri;
  // 4. If r is not an integer, p is interpolated using ri, the integer part of r,
  // and rf, the fractional part of r:
  // p = xri + rf * (xri+1 - xri)
  return values[ri - 1] + rf * (values[ri] - values[ri - 1]);};

Replacing hdr-histogram-js with my in-house implementation reduced our total memory usage (rss) from 3,526 MB to 375 MB — trading 3 GB of external memory used by hdr-histogram-js for a 90 MB increase in heap usage. You can learn more in the following pull requests: filecoin-station/spark-evaluate#88 and filecoin-station/spark-evaluate#89.

Note: While revisiting this blog post, I performed another search on npmjs.com and found a package that provides the same functionality: just-percentile. I’ll use it the next time I need to calculate percentiles.

Timestamps

Storing timestamps as Date instances is more expensive than storing them as the number of milliseconds has elapsed since the Unix epoch.

In filecoin-station/spark-evaluate#85, Julian modified our code parsing timestamps from ISO-8601-formatted strings (e.g. 2023-12-11T08:31:00.157Z) to convert the parsed date object to the numeric representation.

   const value = new Date(str)
   if (Number.isNaN(value.getTime())) return undefined
-  return value
+  return value.getTime()

This improvement shaved off only 5% but was still worthwhile.

Conclusions

These four relatively easy changes dramatically reduced the memory used by our spark-evaluate service. It deferred the need to undertake the major rewrite from all-in-memory to stream-from-filesystem design by several months, if not more.