PHP trait extraction consumes 64 GB memory and continues after MCP request timeout

[yemao688]

Version

codebase-memory-mcp 0.9.0

Platform

macOS (Apple Silicon)

Install channel

GitHub release archive / install.sh / install.ps1

Binary variant

ui

What happened, and what did you expect?

Summary

Indexing a small PHP/TypeScript source tree causes codebase-memory-mcp to consume over 64 GB of physical memory.

Sampling the process shows the PHP extractor repeatedly working inside:

process_class_for_fields -> flatten_trait_into_class -> memmove

The indexing process also continues running after the MCP request has timed out.

Environment

• macOS 26.5.1 (25F80)
• Apple Silicon / ARM64
• codebase-memory-mcp binary reports version 0
• Source project: BuildAdmin v2.3.7
• Source size:
  • Full tree: approximately 16 MB
  • Reduced tree used for the final reproduction: approximately 3.5 MB
• No vendor, node_modules, Git history, public assets, or runtime data were included in the reduced tree

The same timeout behavior was also observed with full and moderate modes.

Actual behavior
The MCP request times out after approximately 120 seconds.
The indexing process continues running after the client request has timed out.
Memory continues increasing.
After approximately 10 minutes, the process reaches:
Physical footprint: 64.3G
Physical footprint (peak): 64.3G
No indexed project is produced.
The process has to be terminated manually.

Sample stack
main
handle_index_repository
cbm_pipeline_run
cbm_parallel_extract_ex
cbm_parallel_for
cbm_thread_join
The active extraction worker is:
pthread_worker
extract_worker
cbm_extract_file
cbm_run_php_lsp
php_lsp_collect_class_fields
process_class_for_fields
flatten_trait_into_class
_platform_memmove

The main thread is waiting for the extraction worker to finish.

Expected behavior
Trait expansion should have bounded memory usage.
Recursive or repeated trait expansion should detect cycles and deduplicate already-expanded traits.
fast mode should not consume tens of gigabytes for a source tree of only a few megabytes.
When the MCP request is cancelled or times out, the indexing pipeline and worker threads should terminate.
A failed index should clean up partial state and return a useful error.
Suspected cause
The stack suggests algorithmic or recursive growth in:

BuildAdmin/ThinkPHP uses PHP traits extensively. Class-field collection may be repeatedly flattening the same trait members, missing cycle detection, or copying an exponentially growing field collection.

There may be two separate issues:

Unbounded memory growth during PHP trait flattening.
Missing cancellation propagation after the MCP request timeout.
Suggested safeguards
Track visited traits while flattening each class.
Detect direct and indirect trait cycles.
Deduplicate inherited/flattened fields.
Add limits for trait recursion depth and expanded field count.
Propagate request cancellation to extraction workers.
Abort indexing when memory or expansion limits are exceeded.
Include the current file/class/trait name in diagnostic errors.
Additional information
After the runaway process exited, the remaining MCP processes returned to approximately 11 MB and 17 MB RSS, confirming that the 64 GB footprint belonged to the indexing task.

I can provide the complete macOS sample report if needed.

Reproduction

Create a standalone copy containing only:

git clone https://github.com/build-admin/buildadmin

Then call:

{
  "repo_path": "/tmp/buildadmin-php-v2.3.7-index-lite",
  "name": "buildadmin-php-v2.3.7",
  "mode": "fast",
  "persistence": false
}

### Logs

```text

Diagnostics trajectory (memory / performance / leak issues)

Analysis of sampling codebase-memory-mcp (pid 9654) every 1 millisecond
Process: codebase-memory-mcp [9654]
Path: /Users/USER/*/codebase-memory-mcp
Load Address: 0x100488000
Identifier: codebase-memory-mcp
Version: 0
Code Type: ARM64
Platform: macOS
Parent Process: codebase-memory-mcp [99275]
Target Type: live task

Date/Time: 2026-07-25 19:48:31.386 +0800
Launch Time: 2026-07-25 19:37:49.125 +0800
OS Version: macOS 26.5.1 (25F80)
Report Version: 7
Analysis Tool: /usr/bin/sample

Physical footprint: 64.3G
Physical footprint (peak): 64.3G
Idle exit: untracked
Call graph:
2591 Thread_51647992 DispatchQueue_1: com.apple.main-thread (serial)
+ 2591 start (in dyld) + 6992 [0x18507be00]
+ 2591 main (in codebase-memory-mcp) + 3552 [0x10048b800]
+ 2591 handle_index_repository (in codebase-memory-mcp) + 1308 [0x1004c11b0]
+ 2591 cbm_pipeline_run (in codebase-memory-mcp) + 3664 [0x1004dbd90]
+ 2591 cbm_parallel_extract_ex (in codebase-memory-mcp) + 1520 [0x1004e0994]
+ 2591 cbm_parallel_for (in codebase-memory-mcp) + 312 [0x1004e0314]
+ 2591 cbm_thread_join (in codebase-memory-mcp) + 28 [0x100491028]
+ 2591 _pthread_join (in libsystem_pthread.dylib) + 616 [0x18543c114]
+ 2591 __ulock_wait (in libsystem_kernel.dylib) + 8 [0x1853f7af8]
2591 Thread_51647993
+ 2591 thread_start (in libsystem_pthread.dylib) + 8 [0x185434c1c]
+ 2591 _pthread_start (in libsystem_pthread.dylib) + 136 [0x185439c58]
+ 2591 parent_watchdog_thread (in codebase-memory-mcp) + 44 [0x10048bd04]
+ 2591 usleep (in libsystem_c.dylib) + 68 [0x1852d5bd8]
+ 2591 nanosleep (in libsystem_c.dylib) + 220 [0x1852d5cc0]
+ 2591 __semwait_signal (in libsystem_kernel.dylib) + 8 [0x1853f9308]
2591 Thread_51648075
2591 thread_start (in libsystem_pthread.dylib) + 8 [0x185434c1c]
2591 _pthread_start (in libsystem_pthread.dylib) + 136 [0x185439c58]
2591 pthread_worker (in codebase-memory-mcp) + 48 [0x1004e0374]
2591 extract_worker (in codebase-memory-mcp) + 1224 [0x1004e1248]
2591 cbm_extract_file (in codebase-memory-mcp) + 1172 [0x10055bd84]
2591 cbm_run_php_lsp (in codebase-memory-mcp) + 2420 [0x1013ad8c4]
2591 php_lsp_collect_class_fields (in codebase-memory-mcp) + 436 [0x1013d6394]
2591 process_class_for_fields (in codebase-memory-mcp) + 6800 [0x101620ac4]
2591 flatten_trait_into_class (in codebase-memory-mcp) + 576 [0x101621ed8]
2591 _platform_memmove (in libsystem_platform.dylib) + 96,88 [0x1854433c0,0x1854433b8]

Total number in stack (recursive counted multiple, when >=5):

Sort by top of stack, same collapsed (when >= 5):
__semwait_signal (in libsystem_kernel.dylib) 2591
__ulock_wait (in libsystem_kernel.dylib) 2591
_platform_memmove (in libsystem_platform.dylib) 2591

Binary Images:
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0x18522c000 - 0x18527c1d7 libsystem_malloc.dylib (812.100.31) <5FAE4807-4D2B-3A95-A63A-DD96D3DA11B4> /usr/lib/system/libsystem_malloc.dylib
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0x191a47000 - 0x191a7f257 libsystem_containermanager.dylib (725.120.2) <518BE44D-AA31-31E6-B44B-A37AD5E47040> /usr/lib/system/libsystem_containermanager.dylib
0x192e58000 - 0x192e5c5d7 libsystem_configuration.dylib (1405.120.5) <0F7BBC1C-3D50-3E59-A31F-E4672A80BCEB> /usr/lib/system/libsystem_configuration.dylib
0x192e5d000 - 0x192e638cf libsystem_sandbox.dylib (2680.120.12) <EC3A75EA-44C0-3A0B-9BF7-71C117B0A9C6> /usr/lib/system/libsystem_sandbox.dylib
0x1944b7000 - 0x1944ba1fb libquarantine.dylib (196.120.2) <5849009B-ACA3-3796-94C4-BBDF8D300EBA> /usr/lib/system/libquarantine.dylib
0x194c56000 - 0x194c5cd03 libsystem_coreservices.dylib (191.4.5) <9576143B-C303-35A3-BA63-1FD06EDA2BB1> /usr/lib/system/libsystem_coreservices.dylib
0x1951d2000 - 0x1951e0d97 libz.1.dylib (100.120.1) <863BB312-F115-32B0-889F-D3B42857A7A6> /usr/lib/libz.1.dylib
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0x19523d000 - 0x19524a3a7 libcommonCrypto.dylib (600035) <CE357BB1-2D49-37CC-9FFE-D093936B1475> /usr/lib/system/libcommonCrypto.dylib
0x19524b000 - 0x195254ca3 libunwind.dylib (2100.2) <FC8F0C4E-6FB0-3E27-ABEF-B0FA720CD5E4> /usr/lib/system/libunwind.dylib
0x19525d000 - 0x1952677ff libcopyfile.dylib (240) <8ACFAC7A-88E9-3EF4-853F-A9140FF110E5> /usr/lib/system/libcopyfile.dylib
0x195268000 - 0x19526b987 libcompiler_rt.dylib (103.3) <AA79151F-C19D-3C7C-92F8-B10F04D82C1C> /usr/lib/system/libcompiler_rt.dylib
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0x195271000 - 0x1952744cf libsystem_secinit.dylib (168.100.7) <E525C566-CDA4-3D99-B12B-1615FD54A1F3> /usr/lib/system/libsystem_secinit.dylib
0x195275000 - 0x195277bf7 libremovefile.dylib (85.100.6) <635E661D-80A7-340D-A165-3F7D318FDFC9> /usr/lib/system/libremovefile.dylib
0x195278000 - 0x195278f27 libkeymgr.dylib (31) <8C08891A-DF1C-3DCC-AB64-4742FD6BE9BA> /usr/lib/system/libkeymgr.dylib
0x195279000 - 0x195281e37 libsystem_dnssd.dylib (2881.120.11) <6F45DF3F-233B-3BC3-BA8C-B43E7DA884BF> /usr/lib/system/libsystem_dnssd.dylib
0x195282000 - 0x19528709b libcache.dylib (95) <189B576E-6176-3F82-8FA4-5914B0BEAEE7> /usr/lib/system/libcache.dylib
0x195288000 - 0x195289ce3 libSystem.B.dylib (1356) <D65E4112-C151-3FF8-BEB7-4841436012D6> /usr/lib/libSystem.B.dylib
0x2884bf000 - 0x2884c6349 libRosetta.dylib (367.9) <8651ED4F-6506-3788-B56B-32EE414A85CA> /usr/lib/libRosetta.dylib
0x28a0dc000 - 0x28a0dfa4b libsystem_darwindirectory.dylib (122) <CF277A2C-C818-3F16-8B3F-3C7B39FCD164> /usr/lib/system/libsystem_darwindirectory.dylib
0x28a0e0000 - 0x28a0e95d3 libsystem_eligibility.dylib (319.121.1) <DDAC0531-0262-3DDC-8EC8-80EB9438847A> /usr/lib/system/libsystem_eligibility.dylib
0x28a0ea000 - 0x28a0f188b libsystem_sanitizers.dylib (26.1) <44C4234F-8B2D-38D3-A774-B4B3C75AF3A7> /usr/lib/system/libsystem_sanitizers.dylib
0x28a0f2000 - 0x28a0f2bb7 libsystem_trial.dylib (474.2.18.2) <68C583BA-AFF5-3916-86AE-6E38BFEF98D6> /usr/lib/system/libsystem_trial.dylib

Project scale (if relevant)

No response

Confirmations

• I searched existing issues and this is not a duplicate.
• My reproduction uses shareable code (a dummy snippet or a public OSS repository), not proprietary code.

[DeusData]

Thanks for the public reproducer and the process sample; the stack makes this much more actionable than a generic OOM report.

Current main's PHP field pass still calls flatten_trait_into_class from process_class_for_fields, and there is no visited-trait/cycle set around that expansion path (internal/cbm/lsp/php_lsp.c:3451, 3550, 3610-3624). The main thread waiting in the worker join is consistent with the extractor continuing after the client-side timeout.

This is routed to 0.9.1-rc at priority/high under stability. The trait-expansion bound and request-cancellation behavior should be treated as two binding acceptance criteria, even if one fix addresses both. Thank you for reducing the source tree and sharing the exact stack.