[Bug]: Chroma fails to load persisted DB: Rust panic range start index XX out of range for slice length YY (metadata/segment mismatch)

[king-66jack]

What happened?

Has Chroma undergone a major version update? The library I built back in July still works, but the one I'm trying to create now is throwing errors instead.

Versions

chromadb1.0.15
Python 3.9.12
windows 11

Relevant log output

(base) PS C:\Users\18390\Desktop\debug> python .\serve.py
D:\miniconda3\lib\site-packages\jieba\_compat.py:18: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
  import pkg_resources
C:\Users\18390\Desktop\debug\serve.py:68: LangChainDeprecationWarning: The class `Chroma` was deprecated in LangChain 0.2.9 and will be removed in 1.0. An updated version of the class exists in the :class:`~langchain-chroma package and should be used instead. To use it run `pip install -U :class:`~langchain-chroma` and import as `from :class:`~langchain_chroma import Chroma``.
  vectordb = Chroma(persist_directory=persist_directory, embedding_function=get_embedding())
2025-11-25 10:55:46,236 - INFO - Anonymized telemetry enabled. See                     https://docs.trychroma.com/telemetry for more information.
thread '<unnamed>' panicked at rust\sqlite\src\db.rs:157:42:
range start index 10 out of range for slice of length 9
note: run with `RUST_BACKTRACE=1` environment variable to display a backtrace
Traceback (most recent call last):
  File "C:\Users\18390\Desktop\debug\serve.py", line 323, in <module>
    get_retriever(DOMAIN)
  File "C:\Users\18390\Desktop\debug\serve.py", line 104, in get_retriever
    retriever = get_ensemble_retriever(domain, k=3)
  File "C:\Users\18390\Desktop\debug\serve.py", line 86, in get_ensemble_retriever
    bm25_retriever, vectordb_retriever = get_bm25_retriever(domain, k)
  File "C:\Users\18390\Desktop\debug\serve.py", line 68, in get_bm25_retriever
    vectordb = Chroma(persist_directory=persist_directory, embedding_function=get_embedding())
  File "D:\miniconda3\lib\site-packages\langchain_core\_api\deprecation.py", line 222, in warn_if_direct_instance
    return wrapped(self, *args, **kwargs)
  File "D:\miniconda3\lib\site-packages\langchain_community\vectorstores\chroma.py", line 122, in __init__
    self._client = chromadb.Client(_client_settings)
  File "D:\miniconda3\lib\site-packages\chromadb\__init__.py", line 379, in Client
    return ClientCreator(tenant=tenant, database=database, settings=settings)
  File "D:\miniconda3\lib\site-packages\chromadb\api\client.py", line 65, in __init__
    super().__init__(settings=settings)
  File "D:\miniconda3\lib\site-packages\chromadb\api\shared_system_client.py", line 19, in __init__
    SharedSystemClient._create_system_if_not_exists(self._identifier, settings)
  File "D:\miniconda3\lib\site-packages\chromadb\api\shared_system_client.py", line 32, in _create_system_if_not_exists
    new_system.start()
  File "D:\miniconda3\lib\site-packages\chromadb\config.py", line 471, in start
    component.start()
  File "D:\miniconda3\lib\site-packages\chromadb\api\rust.py", line 112, in start
    self.bindings = chromadb_rust_bindings.Bindings(
pyo3_runtime.PanicException: range start index 10 out of range for slice of length 9
(base) PS C:\Users\18390\Desktop\debug>

[vgezer]

Same here,

Enabled backtrace=full maybe it can help further:

thread '<unnamed>' panicked at rust\sqlite\src\db.rs:157:42:
range start index 10 out of range for slice of length 9
stack backtrace:
   0:     0x7ff9f4e2abaa - PyInit_chromadb_rust_bindings
   1:     0x7ff9f45e1bda - PyInit_chromadb_rust_bindings
   2:     0x7ff9f4e25128 - PyInit_chromadb_rust_bindings
   3:     0x7ff9f4e2a9d5 - PyInit_chromadb_rust_bindings
   4:     0x7ff9f4e2d7e6 - PyInit_chromadb_rust_bindings
   5:     0x7ff9f4e2d550 - PyInit_chromadb_rust_bindings
   6:     0x7ff9f4e2e04f - PyInit_chromadb_rust_bindings
   7:     0x7ff9f4e2ddea - PyInit_chromadb_rust_bindings
   8:     0x7ff9f4e2b6ff - PyInit_chromadb_rust_bindings
   9:     0x7ff9f4e2d9ce - PyInit_chromadb_rust_bindings
  10:     0x7ff9f5154ef1 - PyInit_chromadb_rust_bindings
  11:     0x7ff9f45e833e - PyInit_chromadb_rust_bindings
  12:     0x7ff9f515537f - PyInit_chromadb_rust_bindings
  13:     0x7ff9f3e27a8b - bz_internal_error
  14:     0x7ff9f3e2aa4a - bz_internal_error
  15:     0x7ff9f399b845 - bz_internal_error
  16:     0x7ff9f421023e - bz_internal_error
  17:     0x7ff9f43c2d01 - bz_internal_error
  18:     0x7ff9f44ca717 - PyInit_chromadb_rust_bindings
  19:     0x7ff9f443056d - bz_internal_error
  20:     0x7ff9f4418e46 - bz_internal_error
  21:     0x7ff9f442fb72 - bz_internal_error
  22:     0x7ffa21d0c5e3 - type_call
                               at D:\a\1\s\Objects\typeobject.c:1985
  23:     0x7ffa21d0c5e3 - _PyObject_MakeTpCall       
                               at D:\a\1\s\Objects\call.c:242
  24:     0x7ffa21d0c5e3 - _PyObject_VectorcallTstate 
                               at D:\a\1\s\Include\internal\pycore_call.h:166
  25:     0x7ffa21d0c229 - PyObject_Vectorcall        
                               at D:\a\1\s\Objects\call.c:327
  26:     0x7ffa21d14557 - _PyEval_EvalFrameDefault   
                               at D:\a\1\s\Python\generated_cases.c.h:1502
  27:     0x7ffa21d0cf87 - _PyEval_EvalFrame
                               at D:\a\1\s\Include\internal\pycore_ceval.h:119
  28:     0x7ffa21d0cf87 - _PyEval_Vector
                               at D:\a\1\s\Python\ceval.c:1816
  29:     0x7ffa21d0cf87 - _PyFunction_Vectorcall     
                               at D:\a\1\s\Objects\call.c:413
  30:     0x7ffa21da1c30 - _PyObject_VectorcallDictTstate
                               at D:\a\1\s\Objects\call.c:146
  31:     0x7ffa21da1c30 - _PyObject_Call_Prepend     
                               at D:\a\1\s\Objects\call.c:504
  32:     0x7ffa21da1c30 - slot_tp_init
                               at D:\a\1\s\Objects\typeobject.c:9816
  33:     0x7ffa21d0c635 - type_call
                               at D:\a\1\s\Objects\typeobject.c:1997
  34:     0x7ffa21d0c635 - _PyObject_MakeTpCall       
                               at D:\a\1\s\Objects\call.c:242
  35:     0x7ffa21d0c635 - _PyObject_VectorcallTstate 
                               at D:\a\1\s\Include\internal\pycore_call.h:166
  36:     0x7ffa21d0c229 - PyObject_Vectorcall        
                               at D:\a\1\s\Objects\call.c:327
  37:     0x7ffa21d14557 - _PyEval_EvalFrameDefault   
                               at D:\a\1\s\Python\generated_cases.c.h:1502
  38:     0x7ffa21d70d3d - _PyEval_EvalFrame
                               at D:\a\1\s\Include\internal\pycore_ceval.h:119
  39:     0x7ffa21d70d3d - _PyEval_Vector
                               at D:\a\1\s\Python\ceval.c:1816
  40:     0x7ffa21d70d3d - _PyFunction_Vectorcall     
                               at D:\a\1\s\Objects\call.c:413
  41:     0x7ffa21d70d3d - _PyObject_VectorcallTstate 
                               at D:\a\1\s\Include\internal\pycore_call.h:168
  42:     0x7ffa21d70d3d - method_vectorcall
                               at D:\a\1\s\Objects\classobject.c:93
  43:     0x7ffa21d70571 - _PyVectorcall_Call
                               at D:\a\1\s\Objects\call.c:273
  44:     0x7ffa21d704bb - _PyObject_Call
                               at D:\a\1\s\Objects\call.c:348
  45:     0x7ffa21d704bb - PyObject_Call
                               at D:\a\1\s\Objects\call.c:373
  46:     0x7ffa21d13edc - _PyEval_EvalFrameDefault   
                               at D:\a\1\s\Python\generated_cases.c.h:1355
  47:     0x7ffa21d0cf87 - _PyEval_EvalFrame
                               at D:\a\1\s\Include\internal\pycore_ceval.h:119
  48:     0x7ffa21d0cf87 - _PyEval_Vector
                               at D:\a\1\s\Python\ceval.c:1816
  49:     0x7ffa21d0cf87 - _PyFunction_Vectorcall     
                               at D:\a\1\s\Objects\call.c:413
  50:     0x7ffa21d70e25 - _PyObject_VectorcallTstate 
                               at D:\a\1\s\Include\internal\pycore_call.h:168
  51:     0x7ffa21d70e25 - method_vectorcall
                               at D:\a\1\s\Objects\classobject.c:71
  52:     0x7ffa21d70571 - _PyVectorcall_Call
                               at D:\a\1\s\Objects\call.c:273
  53:     0x7ffa21d704bb - _PyObject_Call
                               at D:\a\1\s\Objects\call.c:348
  54:     0x7ffa21d704bb - PyObject_Call
                               at D:\a\1\s\Objects\call.c:373
  55:     0x7ffa21e12338 - thread_run
                               at D:\a\1\s\Modules\_threadmodule.c:343
  56:     0x7ffa21e1215e - bootstrap
                               at D:\a\1\s\Python\thread_nt.h:183
  57:     0x7ffafb4237b0 - wcsrchr
  58:     0x7ffafcf0e8d7 - BaseThreadInitThunk
  59:     0x7ffafe1ec53c - RtlUserThreadStart
Exception in thread Thread-1 (_run_index):
Traceback (most recent call last):
  File "C:\Users\MDL\AppData\Local\Programs\Python\Python313\Lib\threading.py", line 1043, in _bootstrap_inner
    self.run()
    ~~~~~~~~^^
  File "C:\Users\MDL\AppData\Local\Programs\Python\Python313\Lib\threading.py", line 994, in run
    self._target(*self._args, **self._kwargs)
    ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\Users\MDL\Documents\_MDL\p\b\a\job_runner.py", line 48, in _run_index
    id.start_indexing()
    ~~~~~~~~~~~~~~~~~~~~~~^^
  File "C:\Users\MDL\Documents\_MDL\p\b\id.py", line 1743, in start_indexing
    _work_doc()
    ~~~~~~~~~^^
  File "C:\Users\MDL\Documents\_MDL\p\b\id.py", line 1465, in _work_doc
    client = chromadb.PersistentClient(path=self.index_folder)
  File "C:\Users\MDL\Documents\_MDL\p\fe\venv\Lib\site-packages\chromadb\__init__.py", line 213, in PersistentClient  
    return ClientCreator(tenant=tenant, database=database, settings=settings)
  File "C:\Users\MDL\Documents\_MDL\p\fe\venv\Lib\site-packages\chromadb\api\client.py", line 66, in __init__
    super().__init__(settings=settings)
    ~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^
  File "C:\Users\MDL\Documents\_MDL\p\fe\venv\Lib\site-packages\chromadb\api\shared_system_client.py", line 19, in __init__
    SharedSystemClient._create_system_if_not_exists(self._identifier, settings)
    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\Users\MDL\Documents\_MDL\p\fe\venv\Lib\site-packages\chromadb\api\shared_system_client.py", line 32, in _create_system_if_not_exists
    new_system.start()
    ~~~~~~~~~~~~~~~~^^
  File "C:\Users\MDL\Documents\_MDL\p\fe\venv\Lib\site-packages\chromadb\config.py", line 471, in start
    component.start()
    ~~~~~~~~~~~~~~~^^
chromadb\api\rust.py", line 115, in start
    self.bindings = chromadb_rust_bindings.Bindings(
chromadb\api\rust.py", line 115, in start
    self.bindings = chromadb_rust_bindings.Bindings(
                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
        allow_reset=self._system.settings.require("allow_reset"),      
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^      
    ...<2 lines>...
        hnsw_cache_size=self.hnsw_cache_size,
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    )
    ^
pyo3_runtime.PanicException: range start index 10 out of range for slice of length 9

[MortalWombat-repo]

Is it close to fixing this?

Both production builds broke for me currently. Everything was working smoothly before.