Document that Microsoft.Data.Sqlite shouldn't be used with Microsoft.EntityFrameworkCore.Sqlite.NetTopologySuite

Silent crash EF Core 9.0 with Net Topology Suite / Spatiallite on Linux

The following crashes silently on Linux (Ubuntu 20.04) or Docker image mcr.microsoft.com/dotnet/runtime:8.0.

Minimal reproducable code

Program.cs:

using Microsoft.EntityFrameworkCore;
using NetTopologySuite.Geometries;

// Create in memory sqlite context
var context = new TestContext(
    (new DbContextOptionsBuilder<TestContext>())
        .UseSqlite($"Data Source=test.db", 
        x => x.UseNetTopologySuite()).Options);

context.Database.EnsureCreated();

var neverReached = 0; // This line is never reached, crashes silently on Docker linux (mcr.microsoft.com/dotnet/runtime:8.0)

internal class TestContext(DbContextOptions<TestContext> options) : DbContext(options)
{
    public DbSet<TestEntity> TestEntities { get; set; }
}

internal class TestEntity
{
    public int Id { get; set; }

    public string Name { get; set; }

    public Point Geom { get; set; }
}

csproj:

<Project Sdk="Microsoft.NET.Sdk">

  <PropertyGroup>
    <OutputType>Exe</OutputType>
    <TargetFramework>net8.0</TargetFramework>
    <ImplicitUsings>enable</ImplicitUsings>
    <Nullable>enable</Nullable>
    <DockerDefaultTargetOS>Linux</DockerDefaultTargetOS>
    <DockerfileContext>.</DockerfileContext>
  </PropertyGroup>

  <ItemGroup>
    <PackageReference Include="Microsoft.EntityFrameworkCore" Version="9.0.0" />
    <PackageReference Include="Microsoft.EntityFrameworkCore.Sqlite" Version="9.0.0" />
    <PackageReference Include="Microsoft.EntityFrameworkCore.Sqlite.NetTopologySuite" Version="9.0.0" />
    <PackageReference Include="Microsoft.VisualStudio.Azure.Containers.Tools.Targets" Version="1.21.0" />
  </ItemGroup>

</Project>

Dockerfile (default generated Dockerfile with Spatiallite installed):

# See https://aka.ms/customizecontainer to learn how to customize your debug container and how Visual Studio uses this Dockerfile to build your images for faster debugging.

# This stage is used when running from VS in fast mode (Default for Debug configuration)
FROM mcr.microsoft.com/dotnet/runtime:8.0 AS base
RUN apt-get update && apt-get install -y libsqlite3-mod-spatialite # Install spatiallite
USER $APP_UID
WORKDIR /app


# This stage is used to build the service project
FROM mcr.microsoft.com/dotnet/sdk:8.0 AS build
ARG BUILD_CONFIGURATION=Release
WORKDIR /src
COPY ["EfCore9Test.csproj", "."]
RUN dotnet restore "./EfCore9Test.csproj"
COPY . .
WORKDIR "/src/."
RUN dotnet build "./EfCore9Test.csproj" -c $BUILD_CONFIGURATION -o /app/build

# This stage is used to publish the service project to be copied to the final stage
FROM build AS publish
ARG BUILD_CONFIGURATION=Release
RUN dotnet publish "./EfCore9Test.csproj" -c $BUILD_CONFIGURATION -o /app/publish /p:UseAppHost=false

# This stage is used in production or when running from VS in regular mode (Default when not using the Debug configuration)
FROM base AS final
WORKDIR /app
COPY --from=publish /app/publish .
ENTRYPOINT ["dotnet", "EfCore9Test.dll"]

Output

It crashes silently, but here is the output:

Loaded '/usr/share/dotnet/shared/Microsoft.NETCore.App/8.0.11/System.Private.CoreLib.dll'. Skipped loading symbols. Module is optimized and the debugger option 'Just My Code' is enabled.
Loaded '/app/bin/Debug/net8.0/EfCore9Test.dll'. Symbols loaded.
Loaded '/usr/share/dotnet/shared/Microsoft.NETCore.App/8.0.11/System.Runtime.dll'. Skipped loading symbols. Module is optimized and the debugger option 'Just My Code' is enabled.
Loaded '/HotReloadAgent/Microsoft.Extensions.DotNetDeltaApplier.dll'. Skipped loading symbols. Module is optimized and the debugger option 'Just My Code' is enabled.
Loaded '/usr/share/dotnet/shared/Microsoft.NETCore.App/8.0.11/System.IO.Pipes.dll'. Skipped loading symbols. Module is optimized and the debugger option 'Just My Code' is enabled.
Loaded '/usr/share/dotnet/shared/Microsoft.NETCore.App/8.0.11/System.Linq.dll'. Skipped loading symbols. Module is optimized and the debugger option 'Just My Code' is enabled.
Loaded '/usr/share/dotnet/shared/Microsoft.NETCore.App/8.0.11/System.Collections.dll'. Skipped loading symbols. Module is optimized and the debugger option 'Just My Code' is enabled.
Loaded '/usr/share/dotnet/shared/Microsoft.NETCore.App/8.0.11/System.Console.dll'. Skipped loading symbols. Module is optimized and the debugger option 'Just My Code' is enabled.
Loaded '/usr/share/dotnet/shared/Microsoft.NETCore.App/8.0.11/System.Memory.dll'. Skipped loading symbols. Module is optimized and the debugger option 'Just My Code' is enabled.
Loaded '/usr/share/dotnet/shared/Microsoft.NETCore.App/8.0.11/System.Threading.dll'. Skipped loading symbols. Module is optimized and the debugger option 'Just My Code' is enabled.
Loaded '/usr/share/dotnet/shared/Microsoft.NETCore.App/8.0.11/System.Net.Sockets.dll'. Skipped loading symbols. Module is optimized and the debugger option 'Just My Code' is enabled.
Loaded '/usr/share/dotnet/shared/Microsoft.NETCore.App/8.0.11/System.Net.Primitives.dll'. Skipped loading symbols. Module is optimized and the debugger option 'Just My Code' is enabled.
Loaded '/usr/share/dotnet/shared/Microsoft.NETCore.App/8.0.11/Microsoft.Win32.Primitives.dll'. Skipped loading symbols. Module is optimized and the debugger option 'Just My Code' is enabled.
Loaded '/usr/share/dotnet/shared/Microsoft.NETCore.App/8.0.11/System.Diagnostics.Tracing.dll'. Skipped loading symbols. Module is optimized and the debugger option 'Just My Code' is enabled.
Loaded '/usr/share/dotnet/shared/Microsoft.NETCore.App/8.0.11/System.Threading.ThreadPool.dll'. Skipped loading symbols. Module is optimized and the debugger option 'Just My Code' is enabled.
Loaded '/usr/share/dotnet/shared/Microsoft.NETCore.App/8.0.11/System.Threading.Thread.dll'. Skipped loading symbols. Module is optimized and the debugger option 'Just My Code' is enabled.
Loaded '/usr/share/dotnet/shared/Microsoft.NETCore.App/8.0.11/System.Collections.Concurrent.dll'. Skipped loading symbols. Module is optimized and the debugger option 'Just My Code' is enabled.
Loaded '/usr/share/dotnet/shared/Microsoft.NETCore.App/8.0.11/System.Runtime.InteropServices.dll'. Skipped loading symbols. Module is optimized and the debugger option 'Just My Code' is enabled.
Loaded '/usr/share/dotnet/shared/Microsoft.NETCore.App/8.0.11/System.Runtime.Loader.dll'. Skipped loading symbols. Module is optimized and the debugger option 'Just My Code' is enabled.
Loaded '/app/bin/Debug/net8.0/Microsoft.EntityFrameworkCore.dll'. Skipped loading symbols. Module is optimized and the debugger option 'Just My Code' is enabled.
Loaded '/usr/share/dotnet/shared/Microsoft.NETCore.App/8.0.11/System.ComponentModel.dll'. Skipped loading symbols. Module is optimized and the debugger option 'Just My Code' is enabled.
Loaded '/app/bin/Debug/net8.0/Microsoft.EntityFrameworkCore.Sqlite.dll'. Skipped loading symbols. Module is optimized and the debugger option 'Just My Code' is enabled.
Loaded '/app/bin/Debug/net8.0/Microsoft.EntityFrameworkCore.Relational.dll'. Skipped loading symbols. Module is optimized and the debugger option 'Just My Code' is enabled.
Loaded '/app/bin/Debug/net8.0/Microsoft.Extensions.DependencyInjection.Abstractions.dll'. Skipped loading symbols. Module is optimized and the debugger option 'Just My Code' is enabled.
Loaded '/usr/share/dotnet/shared/Microsoft.NETCore.App/8.0.11/System.Collections.Immutable.dll'. Skipped loading symbols. Module is optimized and the debugger option 'Just My Code' is enabled.
Loaded '/usr/share/dotnet/shared/Microsoft.NETCore.App/8.0.11/System.Data.Common.dll'. Skipped loading symbols. Module is optimized and the debugger option 'Just My Code' is enabled.
Loaded '/usr/share/dotnet/shared/Microsoft.NETCore.App/8.0.11/System.ComponentModel.Primitives.dll'. Skipped loading symbols. Module is optimized and the debugger option 'Just My Code' is enabled.
Loaded '/app/bin/Debug/net8.0/Microsoft.Extensions.Logging.Abstractions.dll'. Skipped loading symbols. Module is optimized and the debugger option 'Just My Code' is enabled.
Loaded '/app/bin/Debug/net8.0/Microsoft.Extensions.Caching.Abstractions.dll'. Skipped loading symbols. Module is optimized and the debugger option 'Just My Code' is enabled.
Loaded '/app/bin/Debug/net8.0/Microsoft.EntityFrameworkCore.Sqlite.NetTopologySuite.dll'. Skipped loading symbols. Module is optimized and the debugger option 'Just My Code' is enabled.
Loaded '/app/bin/Debug/net8.0/Microsoft.Extensions.DependencyInjection.dll'. Skipped loading symbols. Module is optimized and the debugger option 'Just My Code' is enabled.
Loaded '/app/bin/Debug/net8.0/System.Diagnostics.DiagnosticSource.dll'. Skipped loading symbols. Module is optimized and the debugger option 'Just My Code' is enabled.
Loaded '/usr/share/dotnet/shared/Microsoft.NETCore.App/8.0.11/System.Linq.Expressions.dll'. Skipped loading symbols. Module is optimized and the debugger option 'Just My Code' is enabled.
Loaded '/app/bin/Debug/net8.0/Microsoft.EntityFrameworkCore.Abstractions.dll'. Skipped loading symbols. Module is optimized and the debugger option 'Just My Code' is enabled.
Loaded '/usr/share/dotnet/shared/Microsoft.NETCore.App/8.0.11/System.Transactions.Local.dll'. Skipped loading symbols. Module is optimized and the debugger option 'Just My Code' is enabled.
Loaded '/app/bin/Debug/net8.0/NetTopologySuite.dll'. Skipped loading symbols. Module is optimized and the debugger option 'Just My Code' is enabled.
Loaded '/usr/share/dotnet/shared/Microsoft.NETCore.App/8.0.11/netstandard.dll'. Skipped loading symbols. Module is optimized and the debugger option 'Just My Code' is enabled.
Loaded '/app/bin/Debug/net8.0/Microsoft.Extensions.Logging.dll'. Skipped loading symbols. Module is optimized and the debugger option 'Just My Code' is enabled.
Loaded '/app/bin/Debug/net8.0/Microsoft.Extensions.Options.dll'. Skipped loading symbols. Module is optimized and the debugger option 'Just My Code' is enabled.
Loaded '/usr/share/dotnet/shared/Microsoft.NETCore.App/8.0.11/System.ComponentModel.TypeConverter.dll'. Skipped loading symbols. Module is optimized and the debugger option 'Just My Code' is enabled.
Loaded '/usr/share/dotnet/shared/Microsoft.NETCore.App/8.0.11/System.Reflection.Emit.ILGeneration.dll'. Skipped loading symbols. Module is optimized and the debugger option 'Just My Code' is enabled.
Loaded '/usr/share/dotnet/shared/Microsoft.NETCore.App/8.0.11/System.Reflection.Emit.Lightweight.dll'. Skipped loading symbols. Module is optimized and the debugger option 'Just My Code' is enabled.
Loaded '/usr/share/dotnet/shared/Microsoft.NETCore.App/8.0.11/System.Reflection.Primitives.dll'. Skipped loading symbols. Module is optimized and the debugger option 'Just My Code' is enabled.
Loaded 'Anonymously Hosted DynamicMethods Assembly'. 
Loaded '/app/bin/Debug/net8.0/System.Text.Json.dll'. Skipped loading symbols. Module is optimized and the debugger option 'Just My Code' is enabled.
Loaded '/app/bin/Debug/net8.0/Microsoft.Extensions.Configuration.Abstractions.dll'. Skipped loading symbols. Module is optimized and the debugger option 'Just My Code' is enabled.
Loaded '/app/bin/Debug/net8.0/Microsoft.Extensions.Caching.Memory.dll'. Skipped loading symbols. Module is optimized and the debugger option 'Just My Code' is enabled.
Loaded '/app/bin/Debug/net8.0/Microsoft.Extensions.Primitives.dll'. Skipped loading symbols. Module is optimized and the debugger option 'Just My Code' is enabled.
Loaded '/app/bin/Debug/net8.0/Microsoft.Data.Sqlite.dll'. Skipped loading symbols. Module is optimized and the debugger option 'Just My Code' is enabled.
Loaded '/app/bin/Debug/net8.0/SQLitePCLRaw.core.dll'. Skipped loading symbols. Module is optimized and the debugger option 'Just My Code' is enabled.
Loaded '/app/bin/Debug/net8.0/SQLitePCLRaw.batteries_v2.dll'. Skipped loading symbols. Module is optimized and the debugger option 'Just My Code' is enabled.
Loaded '/app/bin/Debug/net8.0/SQLitePCLRaw.provider.e_sqlite3.dll'. Skipped loading symbols. Module is optimized and the debugger option 'Just My Code' is enabled.
Loaded '/usr/share/dotnet/shared/Microsoft.NETCore.App/8.0.11/System.ComponentModel.Annotations.dll'. Skipped loading symbols. Module is optimized and the debugger option 'Just My Code' is enabled.
Loaded '/app/bin/Debug/net8.0/NetTopologySuite.IO.SpatiaLite.dll'. Skipped loading symbols. Module is optimized and the debugger option 'Just My Code' is enabled.
Loaded '/usr/share/dotnet/shared/Microsoft.NETCore.App/8.0.11/System.ObjectModel.dll'. Skipped loading symbols. Module is optimized and the debugger option 'Just My Code' is enabled.
Loaded '/usr/share/dotnet/shared/Microsoft.NETCore.App/8.0.11/System.Text.RegularExpressions.dll'. Skipped loading symbols. Module is optimized and the debugger option 'Just My Code' is enabled.
Loaded '/app/bin/Debug/net8.0/Microsoft.Extensions.DependencyModel.dll'. Skipped loading symbols. Module is optimized and the debugger option 'Just My Code' is enabled.
Loaded '/usr/share/dotnet/shared/Microsoft.NETCore.App/8.0.11/System.Runtime.InteropServices.RuntimeInformation.dll'. Skipped loading symbols. Module is optimized and the debugger option 'Just My Code' is enabled.
The program 'dotnet' has exited with code 0 (0x0).

Include provider and version information

EF Core version: 9.0.0
Database provider: Microsoft.EntityFrameworkCore.Sqlite 9.0.0
Target framework: .NET 8.0
Operating system: Linux (Ubuntu 20.04) or Docker image (mcr.microsoft.com/dotnet/runtime:8.0)

This behavior/crash still happens with ef core 9.0.9 and runtime:8.0-noble

There are two things to fix the crash:

the SQLitePCLRaw.bundle_e_sqlite3 included package in Microsoft.EntityFrameworkCore.Sqlite need to be added explicitly in the project. I didn't discover exactly why it does not work with the nested package.
The LD_LIBRARY_PATH need to be set. The default dotnet env does not look into the linux lib directories by default.
example: ENV LD_LIBRARY_PATH="/usr/lib/x86_64-linux-gnu:/usr/lib"

The result versions of the sqlite inside the container would currently be
SQLite version: 3.50.4
spatialite version: 5.1.0

To use the native linux dist sqlite lib it need it need to be installed with libsqlite3-0
and because the file name libsqlite3.so.0 is not searched for it need to be linked
with RUN ln -s /usr/lib/x86_64-linux-gnu/libsqlite3.so.0 /usr/lib/libsqlite3.so
and the package SQLitePCLRaw.bundle_sqlite3 need to be used (without e in the name)

This will produce a version in runtime:8.0-noble
SQLite version: 3.45.1 (lower then nuget package)
spatialite version: 5.1.0

If the project need to be run also on windows then a conditional package can to be included with:

    <ItemGroup Condition="'$(OS)' == 'Windows_NT'">
	    <PackageReference Include="SQLitePCLRaw.bundle_e_sqlite3" Version="3.0.2" />
    </ItemGroup>

Windows Host:
SQLite version: 3.50.4
spatialite version: 4.3.0a

I narrowed down the issue.

The bundled sqlite lib "e_sqlite3" does not work well with mod_spatialite under linux/docker

if both packages SQLitePCLRaw.bundle_e_sqlite3 and SQLitePCLRaw.bundle_sqlite3 are added,
then the trick is to explicitly use the SQLitePCLRaw.bundle_sqlite3 to load the native libsqlite3.so.0

The DbContext will call SQLitePCL.Batteries.Init() and LoadExtension('mod_spatialite') for all connections
even if the native lib was loaded and used before and working fine.

The SQLitePCL.Batteries.Init() will reset the SQLitePCL.raw.SetProvider provider back to the wrong SQLite3Provider_e_sqlite3 provider and this will make 1/3 malock/module not found and other sudden term issues.

To prevent this behavior the SQLitePCL.raw.SetProvider need to be frozen.

Working code snipped:

if (OperatingSystem.IsLinux())
{
    NativeLibrary.SetDllImportResolver(typeof(SQLite3Provider_sqlite3).Assembly, DllImportResolver);

    //prevent loading of bundled libe_sqlite3.so
    NativeLibrary.SetDllImportResolver(typeof(SQLite3Provider_e_sqlite3).Assembly, DllImportResolver);
    
    static IntPtr DllImportResolver(string libraryName, Assembly assembly, DllImportSearchPath? searchPath)
    {
        if (libraryName == "sqlite3")
            return NativeLibrary.Load("libsqlite3.so.0", assembly, searchPath);
    
        if (libraryName == "e_sqlite3")
            throw new DllNotFoundException("e_sqlite3 not usable with mod_spatialite");
        
        return IntPtr.Zero;
    }
    
    SQLitePCL.raw.SetProvider(new SQLitePCL.SQLite3Provider_sqlite3());
    SQLitePCL.raw.FreezeProvider(true); //important
}

In the base plane of the dockerfile only the native libs need to be installed:

FROM mcr.microsoft.com/dotnet/runtime:8.0-noble AS base

# Add system dependencies
RUN apt-get update && apt-get install -y \
    libsqlite3-0 \
    libsqlite3-mod-spatialite \
    && apt-get clean \
    && rm -rf /var/lib/apt/lists/*

USER $APP_UID
WORKDIR /app

@ericsink

@ericsink any pointers on how this experience can be improved?

Well that's a mess, isn't it?

No suggestions right now, but I've been thinking about trying to set up an easy path for using spatialite. It's good to see this case.

Actually, one tip:

SQLitePCLRaw's bundles are designed to make very common cases easy, but for anything even a little bit complicated, they mostly make things harder.

It's usually better to switch to the package variant that references SQLitePCLRaw.core only, and not the bundle. It's called Microsoft.Data.Sqlite.Core, I think.

Then do the initialization yourself with SetProvider().

But there are a number of details in this thread that I haven't investigated right now specifically, so consider this a high-level remark.

Document SpatiaLite incompatibility with Microsoft.Data.Sqlite on mac…

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Document that Microsoft.Data.Sqlite shouldn't be used with Microsoft.EntityFrameworkCore.Sqlite.NetTopologySuite #5308

Silent crash EF Core 9.0 with Net Topology Suite / Spatiallite on Linux

Minimal reproducable code

Output

Include provider and version information

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Assignees

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Document that Microsoft.Data.Sqlite shouldn't be used with Microsoft.EntityFrameworkCore.Sqlite.NetTopologySuite #5308

Description

Silent crash EF Core 9.0 with Net Topology Suite / Spatiallite on Linux

Minimal reproducable code

Output

Include provider and version information

Activity

Zetanova commented on Oct 14, 2025

Zetanova commented on Oct 19, 2025

AndriySvyryd commented on Oct 24, 2025

ericsink commented on Oct 24, 2025

ericsink commented on Oct 24, 2025

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