SIGSEGV crash in embedded Dolt driver on Linux (Ubuntu 25.04)

[wortmanb]

Description

beads crashes with SIGSEGV when attempting any database operation on Linux. The crash occurs in the embedded Dolt driver before any beads logic executes.

Environment

• OS: Ubuntu 25.04 (Plucky), Linux 6.14.0-37-generic x86_64
• beads: 0.55.1 (Homebrew/Linuxbrew)
• gastown: 0.7.0 (Homebrew/Linuxbrew)
• dolt (standalone): 1.82.3 (installed separately, but shouldn't affect embedded driver)

Steps to Reproduce

1. Install beads via Homebrew on Linux: brew install beads
2. Initialize a new database: bd init --prefix test
3. Run any bd command: bd list

Expected Behavior

Commands should execute normally.

Actual Behavior

Immediate SIGSEGV crash:

panic: runtime error: invalid memory address or nil pointer dereference
[signal SIGSEGV: segmentation violation code=0x1 addr=0x0 pc=0x27a1b3a]

goroutine 1 [running]:
github.com/dolthub/dolt/go/libraries/doltcore/doltdb.(*DoltDB).SetCrashOnFatalError(0x0?)
	github.com/dolthub/dolt/go@v0.40.5-0.20260217214010-5634e120aae3/libraries/doltcore/doltdb/doltdb.go:2041 +0x1a
github.com/dolthub/dolt/go/cmd/dolt/commands/engine.newDatabase(...)
	github.com/dolthub/dolt/go@v0.40.5-0.20260217214010-5634e120aae3/cmd/dolt/commands/engine/utils.go:65 +0xeb
...
github.com/steveyegge/beads/internal/storage/dolt.newEmbeddedMode(...)
	github.com/steveyegge/beads/internal/storage/dolt/store_embedded.go:124 +0x7a8

Notes

• Crash occurs consistently on every database access
• bd init partially succeeds (creates .beads directory) but crashes during diagnostics
• Server mode (--server) also fails because init still tries embedded mode first
• Setting no-db: true in config.yaml doesn't prevent the crash
• The crash is in the Dolt library code, not beads code directly
• gastown commands that don't use beads (gt status, gt rig list) work fine

Workaround Attempted

• Reinstalling beads: No change
• Using server mode: Fails because init uses embedded mode
• Using BEADS_DIR env var: Same crash
• Removing lock files: Temporary success, then crashes again

Possible Cause

The embedded Dolt driver (compiled into beads at v0.40.5) may have a Linux-specific issue or incompatibility with this kernel/glibc version.

[jeffpoulton]

Happening on macOS, too.

Environment

• OS: macOS 26.2
• Beads: 0.55.1 (Homebrew)
• Dolt: 1.82.3

panic: runtime error: invalid memory address or nil pointer dereference
[signal SIGSEGV: segmentation violation code=0x2 addr=0x0 pc=0x103f2467c]

goroutine 1 [running]:
github.com/dolthub/dolt/go/libraries/doltcore/doltdb.(*DoltDB).SetCrashOnFatalError(0x7bf1de223040?)
	github.com/dolthub/dolt/go@v0.40.5-0.20260217214010-5634e120aae3/libraries/doltcore/doltdb/doltdb.go:2041 +0x1c
github.com/dolthub/dolt/go/cmd/dolt/commands/engine.newDatabase({0x108163968, 0x7bf1de215e90}, {0x7bf1de41c2f7, 0x5}, 0x7bf1de422680?)
	github.com/dolthub/dolt/go@v0.40.5-0.20260217214010-5634e120aae3/cmd/dolt/commands/engine/utils.go:65 +0x98
github.com/dolthub/dolt/go/cmd/dolt/commands/engine.CollectDBs.func1(...)
	github.com/dolthub/dolt/go@v0.40.5-0.20260217214010-5634e120aae3/cmd/dolt/commands/engine/utils.go:35
github.com/dolthub/dolt/go/libraries/doltcore/env.(*MultiRepoEnv).Iter(...)
	github.com/dolthub/dolt/go@v0.40.5-0.20260217214010-5634e120aae3/libraries/doltcore/env/multi_repo_env.go:338
github.com/dolthub/dolt/go/cmd/dolt/commands/engine.CollectDBs({0x108163968, 0x7bf1de215e90}, 0x7bf1ddfcd470?)
	github.com/dolthub/dolt/go@v0.40.5-0.20260217214010-5634e120aae3/cmd/dolt/commands/engine/utils.go:34 +0xf4
github.com/dolthub/dolt/go/cmd/dolt/commands/engine.NewSqlEngine({0x108163680, 0x109ae23a0}, 0x7bf1de378410, 0x7bf1de322780)
	github.com/dolthub/dolt/go@v0.40.5-0.20260217214010-5634e120aae3/cmd/dolt/commands/engine/sqlengine.go:146 +0x1b4
github.com/dolthub/driver.openSqlEngine({0x108163680, 0x109ae23a0}, {0x108179af8?, 0x7bf1dd702878?}, {0x108215c38?, 0x7bf1ddfcd2e0?}, {0x7bf1dd6a8687?, 0x13a2ae650?}, {0x104984960?, 0x69986eb4?}, ...)
	github.com/dolthub/driver@v0.2.1-0.20260217223228-000d23ad5f19/driver.go:70 +0xc4
github.com/dolthub/driver.(*Connector).openEngineWithRetry.func1({0x108163680?, 0x109ae23a0?})
	github.com/dolthub/driver@v0.2.1-0.20260217223228-000d23ad5f19/connector.go:249 +0x40
github.com/dolthub/driver.(*Connector).openEngineWithRetry.func2()
	github.com/dolthub/driver@v0.2.1-0.20260217223228-000d23ad5f19/connector.go:263 +0x38
github.com/cenkalti/backoff/v4.RetryNotifyWithTimer.Operation.withEmptyData.func1()
	github.com/cenkalti/backoff/v4@v4.3.0/retry.go:18 +0x24
github.com/cenkalti/backoff/v4.doRetryNotify[...](0x7bf1de0bef08?, {0x108143f20, 0x7bf1dd6af020}, 0x0, {0x0, 0x0?})
	github.com/cenkalti/backoff/v4@v4.3.0/retry.go:88 +0xcc
github.com/cenkalti/backoff/v4.RetryNotifyWithTimer(0x109959f60?, {0x108143f20?, 0x7bf1dd6af020?}, 0x36?, {0x0?, 0x0?})
	github.com/cenkalti/backoff/v4@v4.3.0/retry.go:61 +0x58
github.com/cenkalti/backoff/v4.RetryNotify(...)
	github.com/cenkalti/backoff/v4@v4.3.0/retry.go:49
github.com/cenkalti/backoff/v4.Retry(...)
	github.com/cenkalti/backoff/v4@v4.3.0/retry.go:38
github.com/dolthub/driver.(*Connector).openEngineWithRetry(0x7bf1de310c60, {0x108163680, 0x109ae23a0})
	github.com/dolthub/driver@v0.2.1-0.20260217223228-000d23ad5f19/connector.go:275 +0x434
github.com/dolthub/driver.(*Connector).getOrOpenEngine(0x7bf1de310c60, {0x108163680, 0x109ae23a0})
	github.com/dolthub/driver@v0.2.1-0.20260217223228-000d23ad5f19/connector.go:199 +0x168
github.com/dolthub/driver.(*Connector).Connect(0x7bf1de310c60, {0x108163680, 0x109ae23a0})
	github.com/dolthub/driver@v0.2.1-0.20260217223228-000d23ad5f19/connector.go:113 +0x2c
database/sql.(*DB).conn(0x7bf1de22edd0, {0x108163680, 0x109ae23a0}, 0x1)
	database/sql/sql.go:1431 +0x910
database/sql.(*DB).PingContext.func1(0xf8?)
	database/sql/sql.go:900 +0x38
database/sql.(*DB).retry(0x7bf1dd6a8680?, 0x7bf1de0bf408)
	database/sql/sql.go:1576 +0x4c
database/sql.(*DB).PingContext(0x7bf1de22edd0, {0x108163680, 0x109ae23a0})
	database/sql/sql.go:899 +0x54
github.com/steveyegge/beads/internal/storage/dolt.newEmbeddedMode({0x108163b98, 0x7bf1dd6983c0}, 0x7bf1de22e5b0)
	github.com/steveyegge/beads/internal/storage/dolt/store_embedded.go:124 +0x5dc
github.com/steveyegge/beads/internal/storage/dolt.New({0x108163b98, 0x7bf1dd6983c0}, 0x7bf1de22e5b0)
	github.com/steveyegge/beads/internal/storage/dolt/store.go:302 +0xd0
main.init.func135(0x109a4aaa0, {0x109ae23a0, 0x0, 0x104979f4b?})
	github.com/steveyegge/beads/cmd/bd/main.go:562 +0x16c4
github.com/spf13/cobra.(*Command).execute(0x109a4aaa0, {0x109ae23a0, 0x0, 0x0})
	github.com/spf13/cobra@v1.10.2/command.go:993 +0x6c0
github.com/spf13/cobra.(*Command).ExecuteC(0x109a4b620)
	github.com/spf13/cobra@v1.10.2/command.go:1148 +0x350
github.com/spf13/cobra.(*Command).Execute(...)
	github.com/spf13/cobra@v1.10.2/command.go:1071
main.main()
	github.com/steveyegge/beads/cmd/bd/main.go:710 +0x70

[nerzhulart]

Same to me on MacOS

[aperepel]

Additional reproduction: bd doctor in bare git worktree + server mode (macOS)

beads version: 0.55.1 (Homebrew)
OS: macOS (Darwin, arm64)
Dolt mode: server

Reproduction steps

1. Set up a project using bare git repo + worktrees
2. Configure dolt in server mode (bd dolt set mode server, server running)
3. Run bd doctor

Crash context

The crash occurs specifically in the CheckFederationRemotesAPI diagnostic check. The call path is:

runDiagnostics (doctor.go:460)
  → CheckFederationRemotesAPI (federation.go:51)
    → dolt.New()
      → newEmbeddedMode (store_embedded.go:124)
        → (*DoltDB).SetCrashOnFatalError on nil pointer

This is the same nil *DoltDB root cause as the original report, but triggered via bd doctor's federation checks rather than normal database operations. Notably, bd doctor attempts to open an embedded Dolt connection via dolt.New() even when the project is configured for server mode — the federation check code path bypasses the server mode configuration.

Stack trace (truncated)

panic: runtime error: invalid memory address or nil pointer dereference
[signal SIGSEGV: segmentation violation code=0x2 addr=0x0 pc=0x106e1867c]

goroutine 1 [running]:
github.com/dolthub/dolt/go/libraries/doltcore/doltdb.(*DoltDB).SetCrashOnFatalError(0x7c170c332c0?)
    doltdb.go:2041 +0x1c
github.com/dolthub/dolt/go/cmd/dolt/commands/engine.newDatabase(...)
    engine/utils.go:65 +0x98
...
github.com/steveyegge/beads/cmd/bd/doctor.CheckFederationRemotesAPI(...)
    doctor/federation.go:51 +0x1d0

Related: #1904 (federation checks use wrong dolt.New() path), #1907 (upstream nil guard fix).

[steveyegge]

Closing: embedded Dolt mode has been fully removed from beads (server-only operation now). The SIGSEGV/deadlock conditions in this issue cannot occur in server mode. See commits: 53e9f8cc (remove embedded mode), 1ade634a (drop dolthub/driver dependency), 9abb7dd5 (remove vestigial artifacts).