Very slow performance for Deserialization of a large Bundle

[KLazarov]

Describe the bug
When I deserialize a large (1-4MB) Bundle resource the performance goes down 10-20x times. A 4MB Bundle can take up to 400ms to deserialize.

If I instead used dynamic object instead of Bundle, the performance is closer to 11ms for the same 4MB Bundle.

To Reproduce
Steps to reproduce the behavior:

1. Load a 1+ MB json file, for example the json definitions as they are pretty big Fhir R4 definitions. I used the valuesets.json which is around 9.3 million characters.
2. Deserialize it multiple times using Bundle -> get 400ms or more per object
3. Deserialize it multiple times using object -> get around 11ms per object

Expected behavior
The deserializer should not lose 95%+ of it's performance just because I have set the type.

Code

The code also prewarms the Bundle deserialization as otherwise it can go up to 1.5 seconds. All tests were done on a AMD 5900x CPU, 64GB 3600MHz RAM, and Windows 11. The file is loaded only once in memory.

using System.Text.Json;
using Hl7.Fhir.Model;
using Hl7.Fhir.Serialization;

class Program
{
    public static void FhirR4SerializerTest(int runs, string filename)
    {
        Console.WriteLine("Running C# FHIR SDK benchmark!");

        string source = File.ReadAllText(filename);
        var parser = new FhirJsonParser();
        for (int i = 0; i < 20; i++)
        {
            Bundle bundle = parser.Parse<Bundle>(source);
        }

        DateTime dateTimeStart = DateTime.Now;

        for (int i = 0; i < runs; i++)
        {
            Bundle bundle = parser.Parse<Bundle>(source);
        }
        DateTime dateTimeFinish = DateTime.Now;
        var totalTimeTake = dateTimeFinish - dateTimeStart;
        Console.WriteLine($"Fhir SDK miliseconds taken: {totalTimeTake.TotalMilliseconds}");
    }

    public static void FhirR4SerializerTestv2(int runs, string filename)
    {
        Console.WriteLine("Running C# FHIR SDK system.text benchmark!");

        string source = File.ReadAllText(filename);
        var parser = new FhirJsonParser();
        var options = new JsonSerializerOptions().ForFhir(ModelInfo.ModelInspector);
        for (int i = 0; i < 20; i++)
        {
            Bundle bundle = JsonSerializer.Deserialize<Bundle>(source, options);
        }

        DateTime dateTimeStart = DateTime.Now;

        for (int i = 0; i < runs; i++)
        {
            Bundle bundle = JsonSerializer.Deserialize<Bundle>(source, options);
        }
        DateTime dateTimeFinish = DateTime.Now;
        var totalTimeTake = dateTimeFinish - dateTimeStart;
        Console.WriteLine($"Fhir SDK system.text miliseconds taken: {totalTimeTake.TotalMilliseconds}");
    }

    public static void FhirObjectSerializerTest(int runs, string filename)
    {
        Console.WriteLine("Running C# FHIR object benchmark!");

        string source = File.ReadAllText(filename);
        for (int i = 0; i < 20; i++)
        {
            object bundle = JsonSerializer.Deserialize<object>(source);
        }

        DateTime dateTimeStart = DateTime.Now;

        for (int i = 0; i < runs; i++)
        {
            object bundle = JsonSerializer.Deserialize<object>(source);
        }
        DateTime dateTimeFinish = DateTime.Now;
        var totalTimeTake = dateTimeFinish - dateTimeStart;
        Console.WriteLine($"Fhir object miliseconds taken: {totalTimeTake.TotalMilliseconds}");
    }
    static void Main(string[] args)
    {
        Console.WriteLine("Running C# benchmark!");

        int runs = 100;
        string filename = "bundle_file.json"; // Replace with the name of your file

        FhirR4SerializerTest(runs, filename);
        FhirObjectSerializerTest(runs, filename);
        FhirR4SerializerTestv2(runs, filename);
    }
}

Results

With custom Bundle that we use at work:

PS C:\Users\user\net-test> dotnet run -c Release
Running C# benchmark!
Running C# FHIR SDK benchmark!
Fhir SDK miliseconds taken: 45401,7309
Running C# FHIR object benchmark!
Fhir object miliseconds taken: 1280,7618
Running C# FHIR SDK system.text benchmark!
Fhir SDK system.text miliseconds taken: 28314,5444

With valuesets.json:

PS C:\Users\user\net-test> dotnet run -c Release
Running C# benchmark!
Running C# FHIR SDK benchmark!
Fhir SDK miliseconds taken: 38795,9362
Running C# FHIR object benchmark!
Fhir object miliseconds taken: 2475,0446
Running C# FHIR SDK system.text benchmark!
Fhir SDK system.text miliseconds taken: 29868,7799

Version used:

• FHIR Version: only R4 tested
• Version: Hl7.Fhir.R4 5.8.1